bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of single cross hybrids to measure heterosis for yield in diverse lucerne genotypes growing in a subtropical environment
Authors: Irwin J. A. G. , Pepper P. M. , Armour D. , Mackie J. M. , Lowe K. F.
Published: October 2008

Yield stagnation is a worldwide issue for lucerne breeding, and reasons for the yield plateau include emphasis on disease and pest resistance and not yield per se, and the broad-based synthetic approach to lucerne breeding which is generally used. In this study, an incomplete diallel was made between 50 lucerne clones with representatives from the 3 hypothetical heterotic groups, Medicago sativa subsp. falcata, dormant subsp. sativa, and non-dormant subsp. sativa. Male sterile clones were also included among the dormant group. The single crosses were compared in a subtropical environment at Gatton, Queensland, for yield and other relevant agronomic traits against the adapted synthetics Sequel (dormancy group 9), UQL-1 (group 7), and a highly non-dormant experimental synthetic (line B) derived by introgression of highly non-dormant Arabian germplasm into Sequel. The trial was conducted in a known low-disease-pressure site for Phytophthora root rot, and anthracnose was managed by regular application of prophylactic treatments. The best single cross outyielded Sequel and line B by 13% and 8%, respectively. In this environment, yield was very much influenced by the dormancy group of the test material, with group 9 material significantly outyielding more dormant material. General combining ability (GCA) effects were more important determinants of cumulative yields than specific combining ability (SCA) effects, with these effects being significantly greater than zero for only 4 of the 236 crosses tested over the 15-month period. Similarly, GCA effects were more important for determining autumn height and persistence. The research did identify a small number of clones with good GCA for yield per se, and it would appear that future work should focus on developing more narrow-based synthetics with 4–8 parents which have been selected on the basis of their GCA for yield per se. DNA markers would appear to have a role in selecting clones carrying multiple resistances, and in establishing marker pedigrees for high-yielding parental clones such as we have identified, which can be traced through subsequent generations of recurrent selection in cultivar improvement.
Taxonomy, ecology, genetics and conservation status of the pale imperial hairstreak (Jalmenus eubulus) (Lepidoptera:Lycaenidae): a threatened butterfly from the Brigalow Belt, Australia
Authors: Eastwood Rod , Braby Michael F. , Schmidt Daniel J. , Hughes Jane M.
Published: October 2008

The taxonomic status of Jalmenus eubulus Miskin stat. rev. is revised and considered to be specifically distinct from J. evagoras (Donovan) based on fundamental differences in morphology, ecology and genetics. Miskin’s holotype is fixed by monotypy and illustrated, with type locality Rockhampton, Queensland. Fixed differences in the mitochondrial genomes of J. eubulus and J. evagoras in which the mean pairwise divergence is only 0.85% indicate absence of matrilineal gene flow, whereas allozyme data show significant structure within and between populations of both species consistent with recent diversification. Underlying causes for the observed genetic patterns are investigated. The two species are parapatric, with a narrow range of overlap along the Great Escarpment in south-eastern Queensland. Jalmenus eubulus is restricted to vegetation communities comprising brigalow-dominated old-growth open-forests and woodlands in the Brigalow Belt (with larvae monophagous on Acacia harpophylla F. Muell. Ex Benth), whereas J. evagoras occurs in a range of disturbed eucalypt woodlands/open-forests predominantly in montane and coastal areas east of this bioregion (with larvae polyphagous on Acacia species other than A. harpophylla). The conservation status of J. eubulus is considered to be vulnerable nationally and critically endangered in New South Wales according to International Union for Conservation of Nature (IUCN) criteria. Nationally, the geographic range has an estimated area of occupancy of less than 2000 km2, is severely fragmented, and the extent or quality of its habitat, which is poorly conserved, continues to decline. It is recommended that the taxon be used as an indicator for identification of remnant old-growth forest for conservation planning, as well as a flagship for the conservation of invertebrate biodiversity associated with this threatened ecological community.
Tasmanitachoides belongs to Trechini (Coleoptera:Carabidae): discovery of the larva, its phylogenetic implications and revised key to Trechitae genera
Authors: Grebennikov Vasily V.
Published: October 2008

This study is aimed at solving the long-standing ambiguity about the phylogenetic placement of the Australian ground-beetle genus Tasmanitachoides. A recently published phylogeny of the supertribe Trechitae using morphological characters of larvae is re-examined in light of new discoveries. The results of the phylogenetic analysis of 65 informative characters for 36 taxa reject the previously maintained opinion of affinities between Tasmanitachoides and Tachyini. Instead it is hypothesised that the genus is a member of the monophyletic tribe Trechini and most likely belongs to the Trechodina radiation, represented in the analysis by the genera Perileptus and Thalassophilus. Older-instar larvae of Tasmanitachoides, Kenodactylus and Mioptachys, as well as the first-instar larva of Pachydesus, are described. An updated identification key to all analysed Trechitae genera is provided.
Conserved role for the
Drosophila
Pax6 homolog Eyeless in differentiation and function of insulin-producing neurons
Authors: Clements Jason , Hens Korneel , Francis Carmen , Schellens Ann , Callaerts Patrick
Published: October 2008

Insulin/insulin-like growth factor (IGF) signaling constitutes an evolutionarily conserved pathway that controls growth, energy homeostasis, and longevity. In
Drosophila melanogaster
, key components of this pathway are the insulin-like peptides (Dilps). The major source of Dilps is a cluster of large neurons in the brain, the insulin-producing cells (IPCs). The genetic control of IPC development and function is poorly understood. Here, we demonstrate that the Pax6 homolog Eyeless is required in the IPCs to control their differentiation and function. Loss of
eyeless
results in phenotypes associated with loss of insulin signaling, including decreased animal size and increased carbohydrate levels in larval hemolymph. We show that mutations in
eyeless
lead to defective differentiation and morphologically abnormal IPCs. We also demonstrate that Eyeless controls IPC function by the direct transcriptional control of one of the major Dilps,
dilp5
. We propose that Eyeless has an evolutionarily conserved role in IPCs with remarkable similarities to the role of vertebrate Pax6 in β cells of the pancreas.
Intestinal signaling to GABAergic neurons regulates a rhythmic behavior in
Caenorhabditis elegans
Authors: Mahoney Timothy R. , Luo Shuo , Round Elaine K. , Brauner Martin , Gottschalk Alexander , Thomas James H. , Nonet Michael L.
Published: October 2008

The
Caenorhabditis elegans
defecation motor program (DMP) is a highly coordinated rhythmic behavior that requires two GABAergic neurons that synapse onto the enteric muscles. One class of DMP mutants, called anterior body wall muscle contraction and expulsion defective (
aex
) mutants, exhibits similar defects to those caused by the loss of these two neurons. Here, we demonstrate that
aex-2
encodes a G-protein–coupled receptor (GPCR) and
aex-4
encodes an exocytic SNAP25 homologue. We found that
aex-2
functions in the nervous system and activates a G
s
α signaling pathway to regulate defecation.
aex-4
, on the other hand, functions in the intestinal epithelial cells. Furthermore, we show that
aex-5
, which encodes a pro-protein convertase, functions in the intestine to regulate the DMP and that its secretion from the intestine is impaired in
aex-4
mutants. Activation of the G
s
α GPCR pathway in GABAergic neurons can suppress the defecation defect of the intestinal mutants
aex-4
and
aex-5
. Lastly, we demonstrate that activation of GABAergic neurons using the light-gated cation channel channelrhodopsin-2 is sufficient to suppress the behavioral defects of
aex-2
,
aex-4
, and
aex-5
. These results genetically place intestinal genes
aex-4
and
aex-5
upstream of GABAergic GPCR signaling. We propose a model whereby the intestinal genes
aex-4
and
aex-5
control the DMP by regulating the secretion of a signal, which activates the neuronal receptor
aex-2
.
Structural determinants of MIF functions in CXCR2-mediated inflammatory and atherogenic leukocyte recruitment
Authors: Weber Christian , Kraemer Sandra , Drechsler Maik , Lue Hongqi , Koenen Rory R. , Kapurniotu Aphrodite , Zernecke Alma , Bernhagen Jürgen
Published: October 2008

We have recently identified the archaic cytokine macrophage migration inhibitory factor (MIF) as a non-canonical ligand of the CXC chemokine receptors CXCR2 and CXCR4 in inflammatory and atherogenic cell recruitment. Because its affinity for CXCR2 was particularly high, we hypothesized that MIF may feature structural motives shared by canonical CXCR2 ligands, namely the conserved N-terminal Glu-Leu-Arg (ELR) motif. Sequence alignment and structural modeling indeed revealed apseudo-(E)LRmotif (Asp-44-X-Arg-11) constituted by non-adjacent residues in neighboring loops but with identical parallel spacing as in the authentic ELR motif. Structure–function analysis demonstrated that mutation of residues R11, D44, or both preserve proper folding and the intrinsic catalytic property of MIF but severely compromises its binding to CXCR2 and abrogates MIF/CXCR2-mediated functions in chemotaxis and arrest of monocytes on endothelium under flow conditions. R11A-MIF and the R11A/D44A-MIF double-mutant exhibited a pronounced defect in triggering leukocyte recruitment to early atherosclerotic endothelium in carotid arteries perfusedex vivoand upon application in a peritonitis model. The function of D44A-MIF in peritoneal leukocyte recruitment was preserved as a result of compensatory use of CXCR4. In conjunction, our data identify apseudo-(E)LRmotif as the structural determinant for MIF's activity as a non-canonical CXCR2 ligand, epitomizing the structural resemblance of chemokine-like ligands with chemokines and enabling selective targeting of pro-inflammatory MIF/CXCR2 interactions.
Global gene expression profiles for life stages of the deadly amphibian pathogenBatrachochytrium dendrobatidis
Authors: Rosenblum Erica Bree , Stajich Jason E. , Maddox Nicole , Eisen Michael B.
Published: October 2008

Amphibians around the world are being threatened by an emerging pathogen, the chytrid fungusBatrachochytrium dendrobatidis(Bd). Despite intensive ecological study in the decade sinceBdwas discovered, little is known about the mechanism by whichBdkills frogs. Here, we compare patterns of global gene expression in controlled laboratory conditions for the two phases of the life cycle ofBd: the free-living zoospore and the substrate-embedded sporangia. We find zoospores to be transcriptionally less complex than sporangia. Several transcripts more abundant in zoospores provide clues about how this motile life stage interacts with its environment. Genes with higher levels of expression in sporangia provide new hypotheses about the molecular pathways involved in metabolic activity, flagellar function, and pathogenicity inBd. We highlight expression patterns for a group of fungalysin metallopeptidase genes, a gene family thought to be involved in pathogenicity in another group of fungal pathogens that similarly cause cutaneous infection of vertebrates. Finally we discuss the challenges inherent in developing a molecular toolkit for chytrids, a basal fungal lineage separated by vast phylogenetic distance from other well characterized fungi.
A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication
Authors: Ratia Kiira , Pegan Scott , Takayama Jun , Sleeman Katrina , Coughlin Melissa , Baliji Surendranath , Chaudhuri Rima , Fu Wentao , Prabhakar Bellur S. , Johnson Michael E. , Baker Susan C. , Ghosh Arun K. , Mesecar Andrew D.
Published: October 2008

We report the discovery and optimization of a potent inhibitor against the papain-like protease (PLpro) from the coronavirus that causes severe acute respiratory syndrome (SARS-CoV). This unique protease is not only responsible for processing the viral polyprotein into its functional units but is also capable of cleaving ubiquitin and ISG15 conjugates and plays a significant role in helping SARS-CoV evade the human immune system. We screened a structurally diverse library of 50,080 compounds for inhibitors of PLpro and discovered a noncovalent lead inhibitor with an IC
50
value of 20 μM, which was improved to 600 nM via synthetic optimization. The resulting compound, GRL0617, inhibited SARS-CoV viral replication in Vero E6 cells with an EC
50
of 15 μM and had no associated cytotoxicity. The X-ray structure of PLpro in complex with GRL0617 indicates that the compound has a unique mode of inhibition whereby it binds within the S4-S3 subsites of the enzyme and induces a loop closure that shuts down catalysis at the active site. These findings provide proof-of-principle that PLpro is a viable target for development of antivirals directed against SARS-CoV, and that potent noncovalent cysteine protease inhibitors can be developed with specificity directed toward pathogenic deubiquitinating enzymes without inhibiting host DUBs.
An amino acid polymorphism in the
couch potato
gene forms the basis for climatic adaptation in
Drosophila melanogaster
Authors: Schmidt Paul S. , Zhu Chen-Tseh , Das Jayatri , Batavia Mariska , Yang Li , Eanes Walter F.
Published: October 2008

Diapause is the classic adaptation to seasonality in arthropods, and its expression can result in extreme lifespan extension as well as enhanced resistance to environmental challenges. Little is known about the underlying evolutionary genetic architecture of diapause in any organism.
Drosophila melanogaster
exhibits a reproductive diapause that is variable within and among populations; the incidence of diapause increases with more temperate climates and has significant pleiotropic effects on a number of life history traits. Using quantitative trait mapping, we identified the RNA-binding protein encoding gene
couch potato
(
cpo
) as a major genetic locus determining diapause phenotype in
D. melanogaster
and independently confirmed this ability to impact diapause expression through genetic complementation mapping. By sequencing this gene in samples from natural populations we demonstrated through linkage association that variation for the diapause phenotype is caused by a single Lys/Ile substitution in one of the six
cpo
transcripts. Complementation analyses confirmed that the identified amino acid variants are functionally distinct with respect to diapause expression, and the polymorphism also shows geographic variation that closely mirrors the known latitudinal cline in diapause incidence. Our results suggest that a naturally occurring amino acid polymorphism results in the variable expression of a diapause syndrome that is associated with the seasonal persistence of this model organism in temperate habitats.
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism
Authors: Zhou Chun , Huang Raven H.
Published: October 2008

Hypermodifications near the anticodon of tRNA are fundamental for the efficiency and fidelity of protein synthesis. Dimethylallyltransferase (DMATase) catalyzes transfer of a dimethylallyl moiety from dimethylallyl pyrophosphate to N6 of A37 in certain tRNAs. Here we present the crystal structures of
Saccharomyces cerevisiae
DMATase–tRNA
Cys
complex in four distinct forms, which provide snapshots of the RNA modification reaction catalyzed by DMATase. The structures reveal that the enzyme recognizes the tRNA substrate through indirect sequence readout. The targeted nucleotide A37 flips out from the anticodon loop of tRNA and flips into a channel in DMATase, where it meets its reaction partner di methylallyl pyrophosphate, which enters the channel from the opposite end. Structural changes accompanying the transfer reaction taking place in the crystal result in disengagement of DMATase–tRNA interaction near the reaction center. In addition, structural comparison of DMATase in the complex with unliganded bacterial DMATase provides a molecular basis of ordered substrate binding by DMATase.
Theory, analysis, and interpretation of single-molecule force spectroscopy experiments
Authors: Dudko Olga K. , Hummer Gerhard , Szabo Attila
Published: October 2008

Dynamic force spectroscopy probes the kinetic and thermodynamic properties of single molecules and molecular assemblies. Here, we propose a simple procedure to extract kinetic information from such experiments. The cornerstone of our method is a transformation of the rupture-force histograms obtained at different force-loading rates into the force-dependent lifetimes measurable in constant-force experiments. To interpret the force-dependent lifetimes, we derive a generalization of Bell's formula that is formally exact within the framework of Kramers theory. This result complements the analytical expression for the lifetime that we derived previously for a class of model potentials. We illustrate our procedure by analyzing the nanopore unzipping of DNA hairpins and the unfolding of a protein attached by flexible linkers to an atomic force microscope. Our procedure to transform rupture-force histograms into the force-dependent lifetimes remains valid even when the molecular extension is a poor reaction coordinate and higher-dimensional free-energy surfaces must be considered. In this case the microscopic interpretation of the lifetimes becomes more challenging because the lifetimes can reveal richer, and even nonmonotonic, dependence on the force.
The transcriptome of
Plasmodium vivax
reveals divergence and diversity of transcriptional regulation in malaria parasites
Authors: Bozdech Zbynek , Mok Sachel , Hu Guangan , Imwong Mallika , Jaidee Anchalee , Russell Bruce , Ginsburg Hagai , Nosten Francois , Day Nicholas P. J. , White Nicholas J. , Carlton Jane M. , Preiser Peter R.
Published: October 2008

Plasmodium vivax
causes over 100 million clinical infections each year. Primarily because of the lack of a suitable culture system, our understanding of the biology of this parasite lags significantly behind that of the more deadly species
P. falciparum
. Here, we present the complete transcriptional profile throughout the 48-h intraerythrocytic cycle of three distinct
P. vivax
isolates. This approach identifies strain specific patterns of expression for subsets of genes predicted to encode proteins associated with virulence and host pathogen interactions. Comparison to
P. falciparum
revealed significant differences in the expression of genes involved in crucial cellular functions that underpin the biological differences between the two parasite species. These data provide insights into the biology of
P. vivax
and constitute an important resource for the development of therapeutic approaches.
MicroRNA-directed transcriptional gene silencing in mammalian cells
Authors: Kim Daniel H. , Sætrom Pål , Snøve Ola , Rossi John J.
Published: October 2008

MicroRNAs (miRNAs) regulate gene expression at the posttranscriptional level in the cytoplasm, but recent findings suggest additional roles for miRNAs in the nucleus. To address whether miRNAs might transcriptionally silence gene expression, we searched for miRNA target sites proximal to known gene transcription start sites in the human genome. One conserved miRNA, miR-320, is encoded within the promoter region of the cell cycle gene POLR3D in the antisense orientation. We provide evidence of a
cis
-regulatory role for miR-320 in transcriptional silencing of POLR3D expression. miR-320 directs the association of RNA interference (RNAi) protein Argonaute-1 (AGO1), Polycomb group (PcG) component EZH2, and tri-methyl histone H3 lysine 27 (H3K27me3) with the POLR3D promoter. Our results suggest the existence of an epigenetic mechanism of miRNA-directed transcriptional gene silencing (TGS) in mammalian cells.
Adaptive and Probabilistic Power Control Algorithms for RFID Reader Networks
Authors: Cha Kainan , Ramachandran Anil , Jagannathan Sarangapani
Published: October 2008

In radio frequency identification (RFID) systems, the detection range and read rates will suffer from interference among high power reading devices. This problem grows severely and degrades system performance in dense RFID networks. Consequently, medium access protocols (MAC) protocols are needed for such networks to assess and provide access to the channel so that tags can be read accurately. In this paper, we investigate a suite of feasible power control schemes to ensure overall coverage area of the system while maintaining a desired read rate. The power control scheme and MAC protocol dynamically adjusts the RFID reader power output in response to the interference level seen during tag reading and acceptable signal-to-noise ratio (SNR). We present novel distributed adaptive power control (DAPC) and probabilistic power control (PPC) as two possible solutions. A suitable back off scheme is also added with DAPC to improve coverage. Both the methodology and implementation of the schemes are presented, simulated, compared, and discussed for further work.
The HINT1 tumor suppressor regulates both γ-H2AX and ATM in response to DNA damage
Authors: Li Haiyang , Balajee Adayabalam S. , Su Tao , Cen Bo , Hei Tom K. , Weinstein I. Bernard
Published: October 2008

Hint1 is a haploinsufficient tumor suppressor gene and the underlying molecular mechanisms for its tumor suppressor function are unknown. In this study we demonstrate that HINT1 participates in ionizing radiation (IR)–induced DNA damage responses. In response to IR, HINT1 is recruited to IR-induced foci (IRIF) and associates with γ-H2AX and ATM. HINT1 deficiency does not affect the formation of γ-H2AX foci; however, it impairs the removal of γ-H2AX foci after DNA damage and this is associated with impaired acetylation of γ-H2AX. HINT1 deficiency also impairs acetylation of ATM and activation of ATM and its downstream effectors, and retards DNA repair, in response to IR. HINT1-deficient cells exhibit resistance to IR-induced apoptosis and several types of chromosomal abnormalities. Our findings suggest that the tumor suppressor function of HINT1 is caused by, at least in part, its normal role in enhancing cellular responses to DNA damage by regulating the functions of both γ-H2AX and ATM.
Mitochondrial protein import: precursor oxidation in a ternary complex with disulfide carrier and sulfhydryl oxidase
Authors: Stojanovski Diana , Milenkovic Dusanka , Müller Judith M. , Gabriel Kipros , Schulze-Specking Agnes , Baker Michael J. , Ryan Michael T. , Guiard Bernard , Pfanner Nikolaus , Chacinska Agnieszka
Published: October 2008

The biogenesis of mitochondrial intermembrane space proteins depends on specific machinery that transfers disulfide bonds to precursor proteins. The machinery shares features with protein relays for disulfide bond formation in the bacterial periplasm and endoplasmic reticulum. A disulfide-generating enzyme/sulfhydryl oxidase oxidizes a disulfide carrier protein, which in turn transfers a disulfide to the substrate protein. Current views suggest that the disulfide carrier alternates between binding to the oxidase and the substrate. We have analyzed the cooperation of the disulfide relay components during import of precursors into mitochondria and identified a ternary complex of all three components. The ternary complex represents a transient and intermediate step in the oxidation of intermembrane space precursors, where the oxidase Erv1 promotes disulfide transfer to the precursor while both oxidase and precursor are associated with the disulfide carrier Mia40.
Tuning sensitivity to IL-4 and IL-13: differential expression of IL-4Rα, IL-13Rα1, and γc regulates relative cytokine sensitivity
Authors: Junttila Ilkka S. , Mizukami Kiyoshi , Dickensheets Harold , Meier-Schellersheim Martin , Yamane Hidehiro , Donnelly Raymond P. , Paul William E.
Published: October 2008

Interleukin (IL)-4 and -13 are related cytokines sharing functional receptors. IL-4 signals through the type I (IL-4Rα/common γ-chain [γc]) and the type II (IL-4Rα/-13Rα1) IL-4 receptors, whereas IL-13 utilizes only the type II receptor. In this study, we show that mouse bone marrow–derived macrophages and human and mouse monocytes showed a much greater sensitivity to IL-4 than to IL-13. Lack of functional γc made these cells poorly responsive to IL-4, while retaining full responsiveness to IL-13. In mouse peritoneal macrophages, IL-4 potency exceeds that of IL-13, but lack of γc had only a modest effect on IL-4 signaling. In contrast, IL-13 stimulated greater responses than IL-4 in fibroblasts. Using levels of receptor chain expression and known binding affinities, we modeled the assemblage of functional type I and II receptor complexes. The differential expression of IL-4Rα, IL-13Rα1, and γc accounted for the distinct IL-4–IL-13 sensitivities of the various cell types. These findings provide an explanation for IL-13's principal function as an “effector” cytokine and IL-4's principal role as an “immunoregulatory” cytokine.
ENaC Proteolytic Regulation by Channel-activating Protease 2
Authors: García-Caballero Agustín , Dang Yan , He Hong , Stutts M. Jackson
Published: October 2008

Epithelial sodium channels (ENaCs) perform diverse physiological roles by mediating Na+ absorption across epithelial surfaces throughout the body. Excessive Na+ absorption in kidney and colon elevates blood pressure and in the airways disrupts mucociliary clearance. Potential therapies for disorders of Na+ absorption require better understanding of ENaC regulation. Recent work has established partial and selective proteolysis of ENaCs as an important means of channel activation. In particular, channel-activating transmembrane serine proteases (CAPs) and cognate inhibitors may be important in tissue-specific regulation of ENaCs. Although CAP2 (TMPRSS4) requires catalytic activity to activate ENaCs, there is not yet evidence of ENaC fragments produced by this serine protease and/or identification of the site(s) where CAP2 cleaves ENaCs. Here, we report that CAP2 cleaves at multiple sites in all three ENaC subunits, including cleavage at a conserved basic residue located in the vicinity of the degenerin site (α-K561, β-R503, and γ-R515). Sites in α-ENaC at K149/R164/K169/R177 and furin-consensus sites in α-ENaC (R205/R231) and γ-ENaC (R138) are responsible for ENaC fragments observed in oocytes coexpressing CAP2. However, the only one of these demonstrated cleavage events that is relevant for the channel activation by CAP2 takes place in γ-ENaC at position R138, the previously identified furin-consensus cleavage site. Replacement of arginine by alanine or glutamine (α,β,γR138A/Q) completely abolished both the Na+ current (INa) and a 75-kD γ-ENaC fragment at the cell surface stimulated by CAP2. Replacement of γ-ENaC R138 with a conserved basic residue, lysine, preserved both the CAP2-induced INa and the 75-kD γ-ENaC fragment. These data strongly support a model where CAP2 activates ENaCs by cleaving at R138 in γ-ENaC.
Return times of polynomials as meta-Fibonacci numbers
Authors: Emerson Nathaniel
Published: October 2008

We consider generalized closest return times of a complex polynomial of degree at least two. Most previous studies on this subject have focused on the properties of polynomials with particular return times, especially the Fibonacci numbers. We study the general form of these closest return times. The main result of this paper is that these closest return times are meta-Fibonacci numbers. In particular, this result applies to the return times of a principal nest of a polynomial. Furthermore, we show that an analogous result holds in a tree with dynamics that is associated with a polynomial.
Efficacy of Muscodor albus for the Control of Phytophthora Blight of Sweet Pepper and Butternut Squash
Authors: Camp A. R. , Dillard H. R. , Smart C. D.
Published: October 2008

The efficacy of Muscodor albus, a potential soil biofumigant, to control root and stem rot by Phytophthora capsici, was examined in a greenhouse study. P. capsici-infested potting mix was treated with three rates of M. albus, mefenoxam (Ridomil Gold EC, Syngenta Crop Protection, Inc.), or nothing. Seedlings of five sweet pepper cultivars and one butternut squash cultivar were transplanted into the treated potting mix. After 7 days, the plants were rated on a scale of 0 (healthy) to 5 (dead). The experiment was conducted three times and there was a significant interaction between pepper cultivar and soil treatment. Treatment with the highest rate of M. albus resulted in a slight but significant reduction in disease severity on Alliance, Aristotle, Paladin, and Revolution pepper compared with the pathogen-only control, while no significant decreases in disease severity were observed with butternut squash or the highly susceptible pepper cv. Red Knight. Of the four less-susceptible pepper cultivars, Paladin (the most tolerant cultivar) was the only one on which M. albus, as applied in this study, reduced disease severity to commercially acceptable levels.
Reaction of Exotic Soybean Germplasm to Phakopsora pachyrhizi in Uganda
Authors: Oloka H. K. , Tukamuhabwa P. , Sengooba T. , Shanmugasundram S.
Published: October 2008

Host plant resistance is the best long-term strategy for managing soybean rust (Phakopsora pachyrhizi) in endemic areas. Resistance breeding efforts are hampered by the presence of several races of the pathogen that often overcome single resistance genes deployed against them. In Uganda, only two soybean cultivars show moderate resistance to Phakopsora pachyrhizi, but this is likely to break down given the aggressive nature of the pathogen. A total of 25 rust tolerant or resistant accessions were imported from the Asian Vegetable Research and Development Centre and screened at Namulonge, in central Uganda. Only 10 accessions, G 33, G 8527, G8586, G 8587, GC 60020-8-7-7-18, GC 87016-11-B-2, GC 87021-26-B-1, SRE-D-14A, SRE-D-14B, and SS 86045-23-2, showed no rust symptoms at growth stage R6 during the three seasons of testing. Soybean rust resistance genes Rpp1, Rpp3, and Rpp4 did not confer resistance at Namulonge; gene Rpp2 was effective.
The Importance of an Invasive Aphid Species in Vectoring a Persistently Transmitted Potato Virus: Aphis glycines Is a Vector of Potato leafroll virus
Authors: Davis J. A. , Radcliffe E. B.
Published: October 2008

Experiments were undertaken to determine soybean aphid (i) landing rates in potato fields, (ii) population dynamics on potato, (iii) feeding behavior compared with green peach aphid on potato using the electrical penetration graph technique (EPG), (iv) acquisition, retention, and transmission of Potato leafroll virus (PLRV), and (v) if soybean aphid–infested crop borders could increase PLRV spread in seed potato. Soybean aphid (Aphis glycines) landed on potato but failed to establish colonies. EPG showed no significant differences between the aphid species in preprobe, xylem phase, sieve element salivation, and phloem sap ingestion durations on potato. Soybean aphid acquired PLRV 78% of the time, and 75 and 70% of individual aphids retained infectivity after 72 and 144 h, respectively. Soybean aphid transmitted PLRV to susceptible potato with 6 to 9% efficiency. Prior to the invasion of this exotic pest, soybean borders were commonly used in Minnesota and North Dakota to protect seed potato against spread of Potato virus Y. In 2002 and 2004, PLRV incidence was not different in potatoes with soybean borders whether treated with insecticide or not. In 2005, with extreme soybean aphid pressure, potatoes with untreated (no insecticide) borders had significantly greater PLRV spread. This is the first report of soybean aphid transmitting PLRV.
Disease on Nursery Stock as Affected by Environmental Factors and Seasonal Inoculum Levels of Phytophthora ramorum in Stream Water Used for Irrigation
Authors: Tjosvold S. A. , Chambers D. L. , Koike S. T. , Mori S. R.
Published: October 2008

A pear bait monitoring system was used to detect and quantify Phytophthora ramorum propagules in streams that flow through woodland areas with sudden oak death in Santa Cruz County, CA from 2001 to 2007. Stream propagules were detected most frequently or occurred in highest concentrations in winter and spring. The stream propagule concentration was characterized with statistical models using temperature and rainfall variables from 2004 to 2007. The highest concentrations of propagules occurred when stream sampling was preceded by about 2 months with low maximum daily temperatures and by 4 days with high rainfall. The occurrence of propagules in streams in the summer was mostly associated with infected leaves from the native host Umbellaria californica that prematurely abscised and fell into the water. When the stream water was used for irrigating rhododendron nursery stock from 2004 to 2007, disease occurred only three times in the two wettest springs (2005 and 2006) on plants sprinkler irrigated with stream water with relatively high concentrations of propagules. Disease incidence was described with a statistical model using the concentration of infective propagules as measured by pear baiting and consecutive hours of leaf wetness measured by electronic sensors at rhododendron height. The concentration of infective propagules was significantly reduced after water was pumped from the stream and applied through sprinklers.
First Report of Ranunculus mild mosaic virus on Ranunculus asiaticus in Yunnan Province, China
Authors: Wang J. H. , Zhao S. , Yang X. M.
Published: October 2008

In June 2007, a new viral disease occurred in commercial fields of Ranunculus asiaticus in the Yunnan Province of China. Infected plants exhibited mosaic symptoms and growth abnormalities. Viral disease incidence for this ornamental crop host in the Yunnan Province was estimated to range from 10 to 20%. Electron microscopic examination of negatively stained leaf-dip preparations from symptomatic plants identified long, flexuous linear particles (approximately 800 nm). The samples were tested using indirect antigen-coated plate (ACP)-ELISA. ACP-ELISA results showed that the leaf samples from symptomatic plants reacted positively to the potyvirus group antibody (Agdia Inc., Eklhart, IN). Total nucleic acid extracted from symptomatic plants was tested using reverse transcription (RT)-PCR with primers (S 5′-GGNAAAAYAGYGGNCARCC-3′; M4: 5′-GTTTTCCCAGTCACGAC-3′ [N = A, G, C, or T; Y = C or T; and R = A or G]) designed to amplify the 3′ terminal region of genomic RNA of the genus Potyvirus (1). RT-PCR produced a 1,650-bp amplification product that was cloned and sequenced (GenBank Accession No. EU684747). The sequenced portion showed 90 and 99% identity with the Ranunculus mild mosaic virus (RMMV) isolates (GenBank Accession Nos. DQ152191 and EF445546) from Italy and Israel, respectively (2). To our knowledge, this is the first report of RMMV in China. Infection from this virus may cause losses for cut-flower production of Ranunculus asiaticu and it is also a potential threat for international trade of Ranunculus germplasm.

References: (1) J. Chen and J. P. Chen. Chin. J. Virol. 18:371, 2002. (2) M. Turina et al. Phytopathology 96:560, 2006.
First Report of Cucumber mosaic virus Infecting Solanum jasminoides in Italy
Authors: Davino S. , Di Serio F. , Polizzi G. , Tessitori M.
Published: October 2008

Solanum jasminoides Paxton (potato vine or jasmine nightshade) is a vegetatively propagated ornamental species within the Solanaceae family. Recently, symptomless plants of this species were reported as natural hosts of the quarantine pest, Potato spindle tuber viroid (PSTVd) in Italy (1). In January 2008, approximately 1,000 potted, 2-year-old plants of S. jasminoides growing in an ornamental nursery in Sicily showed virus-like mosaic and malformation of leaves. Symptoms were observed on approximately 60% of the plants. Leaf tissue, collected from 30 symptomatic and 10 symptomless plants, was analyzed by double-antibody sandwich-ELISA with polyclonal antisera specific to Cucumber mosaic virus (CMV), Tomato spotted wilt virus, and Impatiens necrotic spot virus (Loewe Biochemica, Sauerlach, Germany). The same samples were also analyzed by tissue-printing hybridization with a PSTVd-specific digoxigenin-labelled riboprobe. All the symptomatic samples tested positive only with antisera against CMV, but negative in all other tests. The symptomless samples were negative in all the performed tests. To confirm the association of CMV with the diseased plants, total RNA was extracted from the same samples (RNeasy Plant Mini Kit; Qiagen, Hilden, Germany) and analyzed by reverse transcription (RT)-PCR using CMV-specific primers MP+5′-CATGGCTTTCCAAGGTACCAG-3′ and MP-5′-CTAAAGACCGTTAACCACCTGC-3′ that amplify a 844-bp fragment from the MP gene (2). The expected fragment was amplified only from samples of symptomatic tissue. CMV was also detected in mother plants grown in the same nursery and showing same mosaic symptoms. Definitive identification of the pathogen was obtained by cloning and sequencing the RT-PCR product. The obtained sequence (GenBank Accession No. EU828783) had 99 and 98% similarity with the subgroup I-A isolates CMV-LUN (GenBank Accession No. EU432183) and CMV-Fny (GenBank Accession No. DI0538), respectively. To our knowledge, this is the first report of CMV infecting S. jasminoides and it adds a new host to the more than 1,000 species (85 plant families) infected by this virus. The high incidence of the disease in the nursery could be due to propagation of cuttings from an infected source.

References: (1) F. Di Serio. J. Plant Pathol. 89:297, 2007. (2) H. X. Lin et al. J. Virol. 78:6666, 2004.
First Report of Leaf Rust of Blueberry Caused by Pucciniastrum vaccinii in Hawaii
Authors: Keith L. , Sugiyama L. , Strauss A. , Kai R. , Zee F. , Hamasaki R. , Yamasaki M. , Nakamoto S.
Published: October 2008

Blueberries (Vaccinium corymbosum L.) are a potential high-value, niche market crop for Hawaii. In May of 2007, rust-like symptoms were observed on multiple blueberry plants in a private nursery in Waimea, HI. In September of 2007, a similar leaf rust was observed on one bush of V. corymbosum cv. Sharpblue in the corner of a 36.6 × 9.1-m experimental plot at Mealani Research Station in Waimea. Within a month, rust was observed throughout the plot on ‘Biloxi’, ‘Emerald’, ‘Jewel’, ‘Misty’, ‘Sapphire’, and ‘Sharpblue’. Preliminary field observations suggest that ‘Sharpblue’ and ‘Sapphire’ are highly susceptible to the rust and ‘Biloxi’ shows some tolerance. Leaf lesions began as approximately 1-mm2 chlorotic flecks that expanded and developed into reddish brown, necrotic spots with a chlorotic halo. New lesions and uredinia kept appearing over the course of 4 months. Defoliation occurred on plants where infection was severe. Yellowish orange pustules containing urediniospores first appeared on the abaxial side of older leaves and later appeared on new leaves. Urediniospores were elliptical to obovate (19.4 to 24.8 × 15.2 to 19.8 μm) with a thick, slightly roughened wall and a well-developed pore. Urediniospore morphology and dimensions were consistent with the description of Pucciniastrum vaccinii (G. Wint.) (1). A pathogenicity test was conducted with two 18-month-old ‘Sharpblue’ plants. Fully expanded leaves were sprayed with freshly collected urediniospores (3.8 × 105 spores per ml) suspended in a 0.05% solution of Tween 20 in water. The control plant was sprayed with sterile distilled water (SDW). Plants were covered with plastic bags for 48 h and held in a growth chamber at 20 to 22°C under continuous fluorescent lighting. The plastic bags were then removed and the plants were maintained in the growth chamber. Yellowish orange pustules that were identical to the original symptoms developed on 100% of inoculated leaves after 10 days. The plant inoculated with SDW remained symptomless. While leaf rust caused by P. vaccinii has been reported on Ohelo berry (V. reticulatum) (2), it has not been reported on V. corymbosum in Hawaii. To our knowledge, this is the first report of P. vaccinii on blueberry plants in Hawaii. This rust disease may pose a threat to the potential blueberry industry in Hawaii.

References: (1) P. R. Bristow and A. W. Stretch. Page 20 in: Compendium of Blueberry and Cranberry Diseases. F. L. Caruso and D. C. Ramsdell, eds. The American Phytopathological Society, St. Paul, MN, 1995. (2) D. F. Farr et al. Fungal Databases. Systematic Botany and Mycology Laboratory. Online publication. ARS, USDA, 2008.
Quantifying sources and sinks of trace gases using space-borne measurements: current and future science
Authors: Palmer Paul I
Published: October 2008

We have been observing the Earth's upper atmosphere from space for several decades, but only over the past decade has the necessary technology begun to match our desire to observe surface air pollutants and climate-relevant trace gases in the lower troposphere, where we live and breathe. A new generation of Earth-observing satellites, capable of probing the lower troposphere, are already orbiting hundreds of kilometres above the Earth's surface with several more ready for launch or in the planning stages. Consequently, this is one of the most exciting times for the Earth system scientists who study the countless current-day physical, chemical and biological interactions between the Earth's land, ocean and atmosphere. First, I briefly review the theory behind measuring the atmosphere from space, and how these data can be used to infer surface sources and sinks of trace gases. I then present some of the science highlights associated with these data and how they can be used to improve fundamental understanding of the Earth's climate system. I conclude the paper by discussing the future role of satellite measurements of tropospheric trace gases in mitigating surface air pollution and carbon trading.
Pliocene climate and seasonality in North Atlantic shelf seas
Authors: Williams Mark , Haywood Alan M , Harper Elizabeth M , Johnson Andrew L.A , Knowles Tanya , Leng Melanie J , Lunt Daniel J , Okamura Beth , Taylor Paul D , Zalasiewicz Jan
Published: October 2008

This paper reviews North Atlantic shelf seas palaeoclimate during the interval 4–3 Ma, prior to and incorporating the ‘Mid-Pliocene warm period’ (ca3.29–2.97 Ma). Fossil assemblages and stable isotope data demonstrate northwards extension of subtropical faunas along the coast of the Carolinas–Virginia (Yorktown and Duplin Formations) relative to the present day, suggesting a more vigorous Florida Current, with reduced seasonality and warm water extending north of Cape Hatteras (reconstructed annual range for Virginia 12–30°C). This interpretation supports conceptual models of increased meridional heat transport for the Pliocene. Sea temperatures for Florida (Lower Pinecrest Beds) were similar to or slightly cooler than (summers 25–27°C) today, and were probably influenced by seasonal upwelling of cold deep water. Reduced seasonality is also apparent in the Coralline Crag Formation of the southern North Sea, with ostracods suggesting winter sea temperatures of 10°C (modern 4°C). However, estimates from Pliocene bivalves (3.6–16.6°C) are similar to or cooler than the present day. This ‘mixed’ signal is problematic given warmer seas in the Carolinas–Virginia, and climate model and oceanographic data that show warmer seas in the ‘Mid-Pliocene’ eastern North Atlantic. This may be because the Coralline Crag Formation was deposited prior to peak Mid-Pliocene warmth.
A clinical study of kuru patients with long incubation periods at the end of the epidemic in Papua New Guinea
Authors: Collinge John , Whitfield Jerome , McKintosh Edward , Frosh Adam , Mead Simon , Hill Andrew F , Brandner Sebastian , Thomas Dafydd , Alpers Michael P
Published: October 2008

Kuru is so far the principal human epidemic prion disease. While its incidence has steadily declined since the cessation of its route of transmission, endocannibalism, in Papua New Guinea in the 1950s, the arrival of variant Creutzfeldt–Jakob disease (vCJD), also thought to be transmitted by dietary prion exposure, has given kuru a new global relevance. We investigated all suspected cases of kuru from July 1996 to June 2004 and identified 11 kuru patients. There were four females and seven males, with an age range of 46–63 years at the onset of disease, in marked contrast to the age and sex distribution when kuru was first investigated 50 years ago. We obtained detailed histories of residence and exposure to mortuary feasts and performed serial neurological examination and genetic studies where possible. All patients were born a significant period before the mortuary practice of transumption ceased and their estimated incubation periods in some cases exceeded 50 years. The principal clinical features of kuru in the studied patients showed the same progressive cerebellar syndrome that had been previously described. Two patients showed marked cognitive impairment well before preterminal stages, in contrast to earlier clinical descriptions. In these patients, the mean clinical duration of 17 months was longer than the overall average in kuru but similar to that previously reported for the same age group, and this may relate to the effects of both patient age and
PRNP
codon 129 genotype. Importantly, no evidence for lymphoreticular colonization with prions, seen uniformly in vCJD, was observed in a patient with kuru at tonsil biopsy.
Kuru and its contribution to medicine
Authors: Gajdusek D. Carleton
Published: October 2008

The solution of kuru led us to the solution of Creutzfeldt–Jakob disease and to the elucidation, in humans and other species, of previously unknown mechanisms of infection. These require very close three-dimensional matching, which determines infectious nucleant or prion activity. Evidence for nucleation processes is found widely in the organic and inorganic worlds and in the interactions between them: in the formation of amyloid fibrils; in the biochemistry of silicon; in cave formations deep in the Earth; and in outer space. Kuru in its location in Papua New Guinea has also led to an understanding of the cultural achievements of the Palaeo-Melanesians, with deep roots in human history.
Mortuary rites of the South Fore and kuru
Authors: Whitfield Jerome T , Pako Wandagi H , Collinge John , Alpers Michael P
Published: October 2008

This paper is part of a wider study to explain the historical spread and changing epidemiological patterns of kuru by analysing factors that affect the transmission of kuru. Part of the study has been to look at the mortuary feasts that were the means of transmission of the kuru agent. This paper shows the complexity of Fore eschatology, and the variations and contradictions of human behaviour in relation to mortuary rites and the transmission of kuru. It also confirms that oral ingestion was the primary route of inoculation though some cases of parenteral inoculation may have occurred. The exclusion of alternative routes of transmission is of importance owing to the dietary exposure of the UK and other populations to bovine spongiform encephalopathy prions.