bluuebunny/crossref_metadata_2025_split huggingface dataset:
A gene for a dioxygenase‐like protein determines the production of the DF signal in Xanthomonas campestris pv. campestris
Authors: POPLAWSKY ALAN R. , WALTERS DANA M. , ROUVIERE PIERRE E. , CHUN WESLEY 
Published: November 2005

SUMMARYThe DF signal molecule regulates the production of both yellow pigments (xanthomonadins) and extracellular polysaccharide (EPS) in Xanthomonas campestris pv. campestris. These two bacterial products are crucial to the epiphytic survival and pathogenicity of this pathogen on its plant hosts. Previous work suggested that DF is a butyrolactone, which the Streptomyces bacteria are known to utilize as signals. pigB is one of seven transcriptional units in the X. c. pv. campestris xanthomonadin gene cluster, and its inactivation results in the loss of DF signal, xanthomonadin and EPS production. Here, determination and analysis of the pigB DNA sequence reveals the presence of two open reading frames, the first (xanB1) encoding a putative reductase/halogenase, and the second (xanB2) showing the highest level of identity to Streptomyces genes encoding putative pteridine‐dependent dioxygenase‐like proteins. We show that xanB2 (but not xanB1) is needed for production of the DF signal, and that some Streptomyces strains produce functional analogues of DF. A role for xanB2 in the biosynthesis of DF is proposed.
Pyrichalasin H production and pathogenicity of Digitaria‐specific isolates of Pyricularia grisea
Authors: TSURUSHIMA TETSU , DON LE DINH , KAWASHIMA KENJI , MURAKAMI JIRO , NAKAYASHIKI HITOSHI , TOSA YUKIO , MAYAMA SHIGEYUKI 
Published: November 2005

SUMMARYCulture filtrates from 72 isolates of Pyricularia, grouped into 13 rDNA types, were analysed via HPLC. Of these isolates, 31 (r9 DNA type) from crabgrass (Digitaria sanguinalis), one (r9 DNA type) from pangolagrass (Digitaria smutsii) and six (r8 DNA type) from Digitaria horizontalis produced 20–280 µg pyrichalasin H per millilitre of culture. These same isolates were pathogenic on five Digitaria species. Interestingly, two isolates, KM‐1 and Br 29, which were originally isolated from Digitaria plants, did not produce pyrichalasin H, nor caused blast lesion on Digitaria plants. Because these two isolates were identified as Digitaria pathogens by PCR analysis using Digitaria‐specific primers, they are likely to be mutants lacking pyrichalasin H production. Isolates that belonged to the remaining 11 rDNA types did not produce pyrichalasin H and were avirulent to Digitaria plants. Therefore, the virulence of Pyricularia on Digitaria plants correlates with pyrichalasin H production. Pyrichalasin H was also present in spore germination fluid of a crabgrass isolate (IBDS 5‐1‐1), but not in that of isolates from rice, foxtail millet, finger millet, common millet and wheat. In addition, pyrichalasin H was detected in host leaves infected with IBDS 5‐1‐1, but not in leaves from other plants infected with compatible Pyricularia isolates. Pretreatment of leaf sheaths of crabgrass with 3 µg/mL pyrichalasin H led to the penetration and colonization by non‐host isolates. Overall, these results indicate that production of pyrichalasin H is responsible for the genus‐specific pathogenicity of Digitaria isolates.
Review article: putting immediate‐release proton‐pump inhibitors into clinical practice – improving nocturnal acid control and avoiding the possible complications of excessive acid exposure
Authors: KATZ P. O. 
Published: November 2005

SummaryNocturnal gastro‐oesphageal reflux is an under‐appreciated clinical challenge. This condition may cause symptoms such as nocturnal heartburn, or it may be asymptomatic. In addition, patients may experience sleep disturbances that can potentially lead to complications such as erosive oesophagitis and Barrett's oesophagus, and may be a risk factor for development of oesophageal adenocarcinoma. Delayed‐release proton‐pump inhibitors (PPIs) have traditionally been effective in treating both daytime and night‐time reflux symptoms, but are limited in control of nocturnal acidity by their pharmacodynamic characteristics.This narrative review addresses the prevalence, impact and pharmacologic approaches used to control nocturnal acidity. Methods to optimize nocturnal acid control include careful attention to dosing schedule, using higher doses of PPIs, adding an histamine H2‐receptor antagonist at bedtime to once or twice daily delayed‐release PPI, or using immediate‐relase omeprazole (Zegerid powder for oral suspension; Santarus, Inc., San Diego, CA, USA).This new formulation appears to provide sustained control of intragastric pH at steady state, and when dosed at bedtime, and may be effective in improving control of nocturnal pH and treating night‐time GERD.
Atlantic bluefin tuna: population dynamics, ecology, fisheries and management
Authors: Fromentin Jean‐Marc , Powers Joseph E 
Published: November 2005

AbstractBoth old and new information on the biology and ecology of Atlantic bluefin tuna have confronted scientists with research challenges: research needs to be connected to current stock‐assessment and management issues. We review recent studies on habitat, migrations and population structure, stressing the importance of electronic tagging results in the modification of our perception of bluefin tuna population dynamics and behaviour. Additionally, we question, from both scientific and management perspectives, the usefulness of the classical stock concept and suggest other approaches, such as Clark's contingent and metapopulation theories. Current biological information confirms that a substantial amount of uncertainty still exists in the understanding of reproduction and growth. In particular, we focus on intriguing issues such as the difference in age‐at‐maturity between West Atlantic and Mediterranean bluefin tuna. Our description of Atlantic bluefin tuna fisheries places today's fishing patterns within the two millennium history of exploitation of this species: we discuss trap fisheries that existed between the 17th and the early 20th centuries; Atlantic fisheries during the 1950s and 1960s; and the consequences of the recent development of the sushi–sashimi market. Finally, we evaluate stock status and management issues since the early 1970s. While important uncertainties remain, when the fisheries history is confronted with evidence from biological and stock‐assessment studies, results indicate that Atlantic bluefin tuna has been undergoing heavy overfishing for a decade. We conclude that the current exploitation of bluefin tuna has many biological and economic traits that have led several fish stocks to extreme depletion in the past.
Amyloid precursor protein‐mediated free radicals and oxidative damage: Implications for the development and progression of Alzheimer's disease
Authors: Reddy P. Hemachandra 
Published: November 2005

AbstractAlzheimer's disease (AD) is a late‐onset dementia that is characterized by the loss of memory and an impairment of multiple cognitive functions. Advancements in molecular, cellular, and animal model studies have revealed that the formation of amyloid beta (Aβ) and other derivatives of the amyloid precursor protein (APP) are key factors in cellular changes in the AD brain, including the generation of free radicals, oxidative damage, and inflammation. Recent molecular, cellular, and gene expression studies have revealed that Aβ enters mitochondria, induces the generation of free radicals, and leads to oxidative damage in post‐mortem brain neurons from AD patients and in brain neurons from cell models and transgenic mouse models of AD. In the last three decades, tremendous progress has been made in mitochondrial research and has provided significant findings to link mitochondrial oxidative damage and neurodegenerative diseases such as AD. Researchers in the AD field are beginning to recognize the possible involvement of a mutant APP and its derivatives in causing mitochondrial oxidative damage in AD. This article summarizes the latest research findings on the generation of free radicals in mitochondria and provides a possible model that links Aβ proteins, the generation of free radicals, and oxidative damage in AD development and progression.
Use of Fast Fourier Transform Analysis of Atrial Electrograms for Rapid Characterization of Atrial Activation—Implications for Delineating Possible Mechanisms of Atrial Tachyarrhythmias
Authors: RYU KYUNGMOO , SAHADEVAN JAYAKUMAR , KHRESTIAN CELEEN M. , STAMBLER BRUCE S. , WALDO ALBERT L. 
Published: November 2005

Introduction:Different analysis techniques have been developed to help understand and characterize the mechanisms responsible for atrial arrhythmias. We tested the hypothesis that Fast Fourier Transform (FFT) analysis of recorded atrial electrograms (AEGs) will rapidly and accurately identify regular and irregular patterns of atrial activation, and, thereby, may provide evidence suggestive of underlying mechanisms of atrial tachyarrhythmias.Methods and Results:During induced atrial tachyarrhythmias in both the canine sterile pericarditis model and canine rapid ventricular pacing‐induced congestive heart failure model; 380–404 AEGs were recorded simultaneously from epicardial electrodes on both atria. From AEGs, atrial activation sequences were determined during atrial flutter (AFL), focal atrial tachycardia (AT), and atrial fibrillation (AF). Four‐second recording segments of each AEG were subjected to FFT analysis. Frequencies found during FFT analyses in all studies precisely corresponded to the cycle lengths of the AEGs. In AFL and AT, one dominant frequency peak was found throughout both atria. In AF due to multiple unstable reentry circuits, multiple and broad frequency peaks were found in both atria. In AF due to a stable rapid rhythm (driver) in the left atrium with fibrillatory conduction to the rest of the atria, one dominant frequency peak in areas with 1:1 conduction from the driver, and multiple and/or broad frequency peaks in areas with fibrillatory conduction produced by the driver were found. Computation time for all FFT analyses took <5 minutes.Conclusion:FFT analysis accurately and rapidly identifies global atrial activation patterns during AFL, AT, and AF, thereby assisting in determining arrhythmia mechanisms.
Time allocation ofOrius sauteriin attackingThrips palmion an eggplant leaf
Authors: Yano Eizi , Jiang Nanqing , Hemerik Lia , Mochizuki Masatoshi , Mitsunaga Takayuki , Shimoda Takeshi 
Published: November 2005

AbstractOrius sauteri(Poppius) (Heteroptera: Anthocoridae) is a polyphagous predator used as a biological control agent of palm thrips,Thrips palmi(Karny) (Thysanoptera: Thripidae). We studiedO. sauteri'ssearching efficiency, time allocation on a leaf, leaving tendency, and attacking of prey. Approximately 78% of the encountered prey was eaten. Searching for prey was concentrated for 86% of the time on the lower leaf side, where palm thrips are usually found. Patch residence times on empty leaves were different from those on leaves withT. palmilarvae. Walking activity was not affected by the thrips density, and walking took place during 64% of the total search time. The leaving tendency ofO. sauteriwas affected by the time from patch entry and the presence or absence of palm thrips, but not by the thrips density. If prey were present, the leaving tendency decreased (multiplication factor 0.327), resulting in longer giving‐up times than when no prey was present. The fact that the leaving tendency increases when patch exploitation lasts longer suggests that not much time is wasted on patches where encounters with prey are scarce.
Occurrence of three genotypic clusters of Bemisia tabaci and the rapid spread of the B biotype in south India
Authors: Rekha A.R. , Maruthi M.N. , Muniyappa V. , Colvin J. 
Published: November 2005

AbstractThe whitefly, Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae), is generally considered to have originated from the Indian subcontinent, although little information has so far been collected on the molecular diversity of populations present in this region. The genetic diversity of B. tabaci populations from Karnataka State, south India was analysed using the random amplified polymorphic DNA‐polymerase chain reaction (RAPD‐PCR) technique and partial mitochondrial cytochrome oxidase I (mtCOI) gene sequences (689 bases) of 22 selected samples. A total of 108 whitefly samples analysed by RAPD‐PCR produced 89 polymorphic bands, and cluster analyses grouped them according to their geographic origin into ‘north’ and ‘south’ Karnataka. Phylogenetic analysis of mtCOI gene sequences with reference B. tabaci sequences from other Asian countries divided them into three genotypic clusters. Each cluster was supported with high bootstrap values (82–100%) and the individuals belonging to each cluster shared high nucleotide identities (up to 100%). This indicated at least three distinct genotypes, apparently indigenous to India, which are also present in China, Malaysia, Nepal, Pakistan, and Thailand. These coexist with the B biotype, which was first reported in India in 1999, and has since spread rapidly to other states in south India. The B biotype was more common than the indigenous B. tabaci, in locations where it had been present for more than 2 years. This is reminiscent of the situation in the Americas during the early 1990s, where the B biotype replaced existing biotypes and caused unprecedented losses to agriculture.
Induction of Innate Immune Response Genes by Sin Nombre Hantavirus Does Not Require Viral Replication
Authors: Prescott Joseph , Ye Chunyan , Sen Ganes , Hjelle Brian 
Published: November 2005

ABSTRACTMaladaptive immune responses are considered to be important factors in the pathogenesis of the two diseases caused by hantaviruses, hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome (HCPS). While the intensity of adaptive antiviral T-cell responses seems to correlate with the severity of HCPS, there is increasing evidence that innate antiviral responses by endothelial cells, the native targets for hantavirus infection in vivo, are induced within hours of exposure to infectious hantaviruses. To investigate early events in the innate response to Sin Nombre virus (SNV), the principal etiologic agent of HCPS in North America, we treated human endothelial cells with live virus, or virus subjected to inactivation by UV irradiation at minimal doses required to inhibit replication, and assayed host expression of interferon-stimulated genes (ISG) by microarray and reverse transcription-PCR. We show herein that a variety of ISG are induced between 4 and 24 h after exposure to both live and killed virus. The levels of such induction at early time points (before 24 h) were generally higher in cells treated with SNV particles that had been killed by exposure to UV irradiation. Additionally, SNV exposed to increasing doses of UV irradiation induced ISG better than live virus despite increased disruption of viral RNA integrity. However, SNV replication was required for continued ISG overexpression by 3 days posttreatment. These results suggest that hantavirus particles may themselves be capable of early induction of ISG and that ongoing production of viral particles during infection could contribute to the pathogenic process.
Luxury at a Cost? Recombinant Mouse Hepatitis Viruses Expressing the Accessory Hemagglutinin Esterase Protein Display Reduced Fitness In Vitro
Authors: Lissenberg A. , Vrolijk M. M. , van Vliet A. L. W. , Langereis M. A. , de Groot-Mijnes J. D. F. , Rottier P. J. M. , de Groot R. J. 
Published: November 2005

ABSTRACT

Group 2 coronaviruses encode an accessory envelope glycoprotein species, the hemagglutinin esterase (HE), which possesses sialate-
O
-acetylesterase activity and which, presumably, promotes virus spread and entry in vivo by facilitating reversible virion attachment to O-acetylated sialic acids. While HE may provide a strong selective advantage during natural infection, many laboratory strains of mouse hepatitis virus (MHV) fail to produce the protein. Apparently, their HE genes were inactivated during cell culture adaptation. For this report, we have studied the molecular basis of this phenomenon. By using targeted RNA recombination, we generated isogenic recombinant MHVs which differ exclusively in their expression of HE and produce either the wild-type protein (HE
+
), an enzymatically inactive HE protein (HE
0
), or no HE at all. HE expression or the lack thereof did not lead to gross differences in in vitro growth properties. Yet the expression of HE was rapidly lost during serial cell culture passaging. Competition experiments with mixed infections revealed that this was not due to the enzymatic activity: MHVs expressing HE
+
or HE
0
propagated with equal efficiencies. During the propagation of recombinant MHV-HE
+
, two types of spontaneous mutants accumulated. One produced an anchorless HE, while the other had a Gly-to-Trp substitution at the predicted C-terminal residue of the HE signal peptide. Neither mutant incorporated HE into virion particles, suggesting that wild-type HE reduces the in vitro propagation efficiency, either at the assembly stage or at a postassembly level. Our findings demonstrate that the expression of “luxury” proteins may come at a fitness penalty. Apparently, under natural conditions the costs of maintaining HE are outweighed by the benefits.
Expression of Hemagglutinin Esterase Protein from Recombinant Mouse Hepatitis Virus Enhances Neurovirulence
Authors: Kazi Lubna , Lissenberg Arjen , Watson Richard , de Groot Raoul J. , Weiss Susan R. 
Published: November 2005

ABSTRACT

Murine hepatitis virus (MHV) infection provides a model system for the study of hepatitis, acute encephalitis, and chronic demyelinating disease. The spike glycoprotein, S, which mediates receptor binding and membrane fusion, plays a critical role in MHV pathogenesis. However, viral proteins other than S also contribute to pathogenicity. The JHM strain of MHV is highly neurovirulent and expresses a second spike glycoprotein, the hemagglutinin esterase (HE), which is not produced by MHV-A59, a hepatotropic but only mildly neurovirulent strain. To investigate a possible role for HE in MHV-induced neurovirulence, isogenic recombinant MHV-A59 viruses were generated that produced either (i) the wild-type protein, (ii) an enzymatically inactive HE protein, or (iii) no HE at all (A. Lissenberg, M. M. Vrolijk, A. L. W. van Vliet, M. A. Langereis, J. D. F. de Groot-Mijnes, P. J. M. Rottier, and R. J. de Groot, J. Virol.
79:
15054-15063, 2005 [accompanying paper]). A second, mirror set of recombinant viruses was constructed in which, in addition, the MHV-A59 S gene had been replaced with that from MHV-JHM. The expression of HE in combination with A59 S did not affect the tropism, pathogenicity, or spread of the virus in vivo. However, in combination with JHM S, the expression of HE, regardless of whether it retained esterase activity or not, resulted in increased viral spread within the central nervous system and in increased neurovirulence. Our findings suggest that the properties of S receptor utilization and/or fusogenicity mainly determine organ and host cell tropism but that HE enhances the efficiency of infection and promotes viral dissemination, at least in some tissues, presumably by serving as a second receptor-binding protein.
Ubiquitination of the Prototype Foamy Virus Envelope Glycoprotein Leader Peptide Regulates Subviral Particle Release
Authors: Stanke Nicole , Stange Annett , Lüftenegger Daniel , Zentgraf Hanswalter , Lindemann Dirk 
Published: November 2005

ABSTRACT

Foamy virus (FV) particle egress is unique among retroviruses because of its essential requirement for Gag and Env coexpression for budding and particle release. The FV glycoprotein undergoes a highly unusual biosynthesis resulting in the generation of three particle-associated, mature subunits, leader peptide (LP), surface (SU), and transmembrane (TM), derived from a precursor protein by posttranslational proteolysis mediated by furin or furinlike proteases. Previously at least three LP products of different molecular weights were detected in purified FV particles. Here we demonstrate that the higher-molecular-weight forms gp28
LP
and gp38
LP
are ubiquitinated variants of the major gp18
LP
cleavage product, which has a type II membrane topology. Furthermore, we show that all five lysine residues located within the N-terminal 60-amino-acid cytoplasmic domain of gp18
LP
can potentially be ubiquitinated, however, there seems to be a preference for using the first three. Inactivation of ubiquitination sites individually resulted in no obvious phenotype. However, simultaneous inactivation of the first three or all five ubiquitination sites in gp18
LP
led to a massive increase in subviral particles released by these mutant glycoproteins that were readily detectable by electron microscopy analysis upon expression of the ubiquitination-deficient glycoprotein by itself or in a proviral context. Surprisingly, only the quintuple ubiquitination mutant showed a two- to threefold increase in single-cycle infectivity assays, whereas all other mutants displayed infectivities similar to that of the wild type. Taken together, these data suggest that the balance between viral and subviral particle release of FVs is regulated by ubiquitination of the glycoprotein LP.
Transcriptional Analysis of Latent and Inducible Kaposi's Sarcoma-Associated Herpesvirus Transcripts in the K4 to K7 Region
Authors: Taylor Jennifer L. , Bennett Heather N. , Snyder Beth A. , Moore Patrick S. , Chang Yuan 
Published: November 2005

ABSTRACT

Kaposi's sarcoma-associated herpesvirus (KSHV) is a gamma-2 herpesvirus with a genome containing a long unique coding region (LUR) flanked by GC-rich terminal repeat sequences. The LUR encodes approximately 90 annotated open reading frames (ORFs) with complex patterns of gene expression during viral latency, reactivation, and de novo infection. To identify unannotated KSHV genes, we examined the region between 21,500 and 30,000 bp of the KSHV LUR, representing approximately 8.5 kb of sequence. This region encodes seven known single-exon ORFs (
K4
,
K4.1
,
K4.2
,
K5
,
K6
,
K7
, and
PAN
), but previous computer analyses have failed to identify additional likely genes in the remaining 5.2 kb. We identified four novel transcripts using Northern blotting, phage library screening, and 5′ rapid amplification of cDNA ends analysis in the region between ORFs
K4.2
and
K7
. In vitro analysis of KSHV-infected primary effusion lymphoma cell lines in the presence of 12-
O
-tetradecanoylphorbol-13-acetate and phosphonoformic acid suggests that one latent transcript is coterminal with the previously annotated
K3
gene encoding an ubiquitin-ligase known to downregulate major histocompatibility complex class I expression. This alternatively spliced transcript may contribute to KSHV adaptive immune evasion during latent infection. Other transcripts are inducible, including a 6.1-kb transcript that is the largest transcript found in the KSHV genome to date.