bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains
Authors: Cytryn Eddie J , Jitacksorn Siriluck , Giraud Eric , Sadowsky Michael J 
Published: January 2008

Abstract
In silico, physiological and in planta analyses were used to characterize pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1, and assess its potential ecological function under free-living and symbiotic growth conditions. Sequence analysis revealed the presence of an uptake hydrogenase system, a repABC family plasmid replication module and open reading frames encoding type IV secretion system, TraI and TraR autoinducer proteins and several copper resistance-related proteins. Bradyrhizobium sp. BTAi1 was capable of growing in 200 mg l−1 CuCl2. In contrast, the closely related, plasmid-free Bradyrhizobium sp. strain ORS278 could not grow at copper concentrations exceeding 100 mg l−1. The plasmid-localized hydrogenase genes were phylogenetically distinct from those typically found in other rhizobial species, and were most related to hup genes from Thiobacillus denitrificans. The induction of the plasmid-borne hydrogenase genes during symbiosis was significantly lower than the two chromosomal-borne hydrogenase clusters. CHEF-pulsed-field gel electrophoresis was used for a comprehensive analysis of the diversity, abundance and genetic composition of accessory plasmids in other Bradyrhizobium strains. Plasmids were detected in 11 of 46 (23.9%) geographically diverse Bradyrhizobium japonicum and Bradyrhizobium elkanii strains, isolated from the United States, China and Thailand. Plasmid size was heterogeneous, ranging from 75 to 330 kb, with only two strains (DASA01244 and DASA01265) harboring plasmids with identical (240 kb) size. None of the plasmids harbored nodulation or hydrogenase genes. Taken together, our results indicate that while plasmids having ecologically significant functions may be detected in Bradyrhizobium sp. strains, they lack genes necessary for symbioses with legumes.
Arsenite-dependent photoautotrophy by an Ectothiorhodospira-dominated consortium
Authors: Budinoff Charles R , Hollibaugh James T 
Published: January 2008

Abstract
Over the past decade numerous lineages of bacteria have been shown to obtain energy for growth through redox transformations of arsenic. However, phototrophic growth using reduced arsenic as an electron donor has not been described. Here we report the light-dependent oxidation of arsenite to arsenate, coupled with autotrophic growth, by an Ectothiorhodospira-dominated consortium of bacteria from alkaline, hypersaline Mono Lake, California. Pure cultures of the Mono Lake Ectothiorhodospira were not capable of phototrophic arsenite oxidation under the culture conditions tested. Electron micrographs of the culture showed a close association between consortia members, although the specific contribution of the individual bacteria is currently unknown. This report extends the list of compounds known to support anoxygenic photosynthesis and documents a previously unknown pathway in arsenic geochemistry.
3D FISH for the quantification of methane- and sulphur-oxidizing endosymbionts in bacteriocytes of the hydrothermal vent musselBathymodiolus azoricus
Authors: Halary Sébastien , Riou Virginie , Gaill Françoise , Boudier Thomas , Duperron Sébastien 
Published: January 2008

AbstractDual endosymbioses involving methane- and sulphur-oxidizing bacteria occur in the gills of several species of mussels from deep-sea hydrothermal vents and cold seeps. Variations of total and relative abundances of symbionts depending on local environmental parameters are not yet understood, due to a lack of reliable quantification of bacteria in the host tissue. Here, we report the first attempt to quantify volumes occupied by each type of symbiont in bacteriocyte sections from a vent mussel, Bathymodiolus azoricus, using fluorescence in situ hybridization (FISH) coupled to three dimentional microscopy and image analysis carried out by a dedicated software, which we developped. Bacteriocytes from mussels recovered at different vent sites displayed significantly different abundances of bacteria. Specimens kept in aquaria at atmospheric pressure and exposed to an artificial pulse of sulphur displayed an increase in absolute and relative abundance of sulphur oxidizers within their bacteriocytes. Distributions of all measured parameters fitted normal distributions, indicating that bacteriocytes from a specimen tend to display similar behaviours. This study shows that symbiont volume quantification is tractable using 3D FISH, and confirms the impact of local environmental parameters on symbiont abundances.
Stochasticity in fusion plasmas
Authors: Finken K.H. 
Published: January 2008

In recent years the importance of externally imposed resonant magnetic fields on plasmas
has become more and more recognized. These fields act either at well defined plasma layers, e.g. by
ergodization or more globally by exciting large-size modes in the plasma. A major
achievement of research in recent years is the possibility to suppress large type 1 ELMS by
resonant perturbation fields which modify the transport at the plasma edge. This option has
been studied extensively at DIII-D and recently progress has also been made at JET and
TEXTOR. Several devices are preparing further experiments to study the important aim of avoiding
transient heat pulses and thus to substantially increase the lifetime of ITER. Other topics of
interest for fusion reactors are the option of distributing the heat to a large area, optimizing
methods for heat and particle exhaust, and understanding the transport around tearing
mode instabilities.
Since October 2003, three SFP workshops have taken place. Important papers from the first two
workshops have been published in previous special issues of Nuclear Fusion (stacks.iop.org/NF/44/i=6 and stacks.iop.org/NF/46/i=4)
and the contents of this issue are based on presentations to the Third Workshop on
Stochasticity in Fusion Plasmas (SFP) held in Jülich, Germany, 5–7 March 2007.
The SFP workshops have been stimulated by the installation of the Dynamic Ergodic Divertor
(DED) in the TEXTOR tokamak. It has attracted colleagues working on various plasma
configurations such as tokamaks, stellarators or reversed field pinches. The workshop is
devoted to phenomena on the plasma edge and to transport questions over the whole plasma
cross section. It is a meeting place for experimental and theoretical working groups. The
next workshop is planned for February/March 2009 in Jülich. For details see www.fzjuelich.de/sfp/.
We hope that the article series in Nuclear Fusion will stimulate interest in the fascinating
subject of plasma physics.
Evaluation of Feline Monocyte-Derived Dendritic Cells Loaded with Internally Inactivated Virus as a Vaccine against Feline Immunodeficiency Virus
Authors: Freer Giulia , Matteucci Donatella , Mazzetti Paola , Tarabella Francesca , Catalucci Valentina , Ricci Enrica , Merico Antonio , Bozzacco Leonia , Pistello Mauro , Bendinelli Mauro 
Published: January 2008

ABSTRACT

Dendritic cells are the only antigen-presenting cells that can present exogenous antigens to both helper and cytolytic T cells and prime Th1-type or Th2-type cellular immune responses. Given their unique immune functions, dendritic cells are considered attractive “live adjuvants” for vaccination and immunotherapy against cancer and infectious diseases. The present study was carried out to assess whether the reinjection of autologous monocyte-derived dendritic cells loaded with an aldithriol-2-inactivated primary isolate of feline immune deficiency virus (FIV) was able to elicit protective immune responses against the homologous virus in naive cats. Vaccine efficacy was assessed by monitoring immune responses and, finally, by challenge with the homologous virus of vaccinated, mock-vaccinated, and healthy cats. The outcome of challenge was followed by measuring cellular and antibody responses and viral and proviral loads and quantitating FIV by isolation and a count of CD4
+
/CD8
+
T cells in blood. Vaccinated animals exhibited clearly evident FIV-specific peripheral blood mononuclear cell proliferation and antibody titers in response to immunization; however, they became infected with the challenge virus at rates comparable to those of control animals.
Characterization of Genetic Diversity of Carbapenem-ResistantAcinetobacter baumanniiClinical Strains Collected from 2004 to 2007
Authors: Qi Chao , Malczynski Michael , Parker Michelle , Scheetz Marc H. 
Published: January 2008

ABSTRACTGenotypes of carbapenem-resistantAcinetobacter baumanniicollected by the clinical microbiology laboratory of a university hospital in Chicago, IL, between 2004 and 2007 were analyzed by pulsed-field gel electrophoresis. A single genotype established predominance after being introduced in 2005. Analysis of carbapenemases by PCR revealed that imipenem resistance but not meropenem resistance was associated with the presence ofblaOXA-23andblaOXA-40genes.
Transmission Events within Outbreaks of Gastroenteritis Determined through Analysis of Nucleotide Sequences of the P2 Domain of Genogroup II Noroviruses
Authors: Xerry Jacqueline , Gallimore Chris I. , Iturriza-Gómara Miren , Allen David J. , Gray Jim J. 
Published: January 2008

ABSTRACT
Tracking the spread of noroviruses during outbreaks of gastroenteritis is hampered by the lack of sequence diversity in those regions of the genome chosen for virus detection and characterization. Sequence analysis of regions of the genes encoding the RNA-dependent RNA polymerase and the S domain of the capsid does not provide sufficient discrimination between genotypically related strains of different outbreaks. However, analysis of sequences derived from the region encoding the P2 domain showed 100% similarity among strains from the same outbreak and <100% similarity among strains of different outbreaks. The prolonged nature of some hospital outbreaks, links between hospitals, and the introduction of multiple strains of a single genotype associated with an outbreak aboard a cruise ship were determined using this method. This provides a powerful tool for tracking outbreak strains and the subsequent analysis and validation of interventions in a background of multiple introductions of virus strains of the same genotype or genetic cluster.
IRF-1 Is Required for Full NF-κB Transcriptional Activity at the Human Immunodeficiency Virus Type 1 Long Terminal Repeat Enhancer
Authors: Sgarbanti Marco , Remoli Anna L. , Marsili Giulia , Ridolfi Barbara , Borsetti Alessandra , Perrotti Edvige , Orsatti Roberto , Ilari Ramona , Sernicola Leonardo , Stellacci Emilia , Ensoli Barbara , Battistini Angela 
Published: January 2008

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) gene expression is controlled by a complex interplay between viral and host factors. We have previously shown that interferon-regulatory factor 1 (IRF-1) is stimulated early after HIV-1 infection and regulates promoter transcriptional activity even in the absence of the viral transactivator Tat. In this work we demonstrate that IRF-1 is also required for full NF-κB transcriptional activity. We provide evidence that IRF-1 and NF-κB form a functional complex at the long terminal repeat (LTR) κB sites, which is abolished by specific mutations in the two adjacent κB sites in the enhancer region. Silencing IRF-1 with small interfering RNA resulted in impaired NF-κB-mediated transcriptional activity and in repressed HIV-1 transcription early in de novo-infected T cells. These data indicate that in early phases of HIV-1 infection or during virus reactivation from latency, when the viral transactivator is absent or present at very low levels, IRF-1 is an additional component of the p50/p65 heterodimer binding the LTR enhancer, absolutely required for efficient HIV-1 replication.
Rearrangements of Rotavirus Genomic Segment 11 Are Generated during Acute Infection of Immunocompetent Children and Do Not Occur at Random
Authors: Schnepf Nathalie , Deback Claire , Dehee Axelle , Gault Elyanne , Parez Nathalie , Garbarg-Chenon Antoine 
Published: January 2008

ABSTRACT
Group A rotaviruses are the main cause of viral gastroenteritis in infants. The viral genome consists of 11 double-stranded RNA (dsRNA) segments. Dysfunction of the viral RNA polymerase can lead to gene rearrangements, which most often consist of partial sequence duplication of a dsRNA segment. Gene rearrangements have been detected in vivo during chronic infection in immunodeficient children or in vitro during passages at a high multiplicity of infection in cell culture, suggesting that these replication conditions lead to selective advantages favoring the recovery of viruses with rearranged genes. During acute rotavirus infection, the replication level is high, but the occurrence of rearrangement events has never been reported. By the use of a reverse transcription-PCR assay specifically designed to detect small numbers of copies of rearranged forms of segment 11 in a high background of its standard counterpart, we detected 12 rearrangement events among 161 cases (7.5%) of acute rotavirus infection in immunocompetent children. Strikingly, in all but one case, rearrangement took place at the same location within the short direct repeat AUGU sequence. For the unique case with a different rearrangement pattern, the rearrangement occurred within the direct repeat ACAAGUC that was specific for this isolate. In conclusion, we report the occurrence of segment 11 rearrangements during acute rotavirus infection in immunocompetent children. We show that under such conditions of infection, the viral RNA polymerase generates rearrangements which occur not at random but within direct repeats which might constitute hot spots for RNA recombination.
Antiviral RNA Silencing Is Restricted to the Marginal Region of the Dark Green Tissue in the Mosaic Leaves of
Tomato Mosaic Virus
-Infected Tobacco Plants
Authors: Hirai Katsuyuki , Kubota Kenji , Mochizuki Tomofumi , Tsuda Shinya , Meshi Tetsuo 
Published: January 2008

ABSTRACT

Mosaic is a common disease symptom caused by virus infection in plants. Mosaic leaves of
Tomato mosaic virus
(ToMV)-infected tobacco plants consist of yellow-green and dark green tissues that contain large and small numbers of virions, respectively. Although the involvement of RNA silencing in mosaic development has been suggested, its role in the process that results in an uneven distribution of the virus is unknown. Here, we investigated whether and where ToMV-directed RNA silencing was established in tobacco mosaic leaves. When transgenic tobaccos defective in RNA silencing were infected with ToMV, little or no dark green tissue appeared, implying the involvement of RNA silencing in mosaic development. ToMV-related small interfering RNAs were rarely detected in the dark green areas of the first mosaic leaves, and their interior portions were susceptible to infection. Thus, ToMV-directed RNA silencing was not effective there. By visualizing the cells where ToMV-directed RNA silencing was active, it was found that the effective silencing occurs only in the marginal regions of the dark green tissue (∼0.5 mm in width) and along the major veins. Further, the cells in the margins were resistant against recombinant potato virus X carrying a ToMV-derived sequence. These findings demonstrate that RNA silencing against ToMV is established in the cells located at the margins of the dark green areas, restricting the expansion of yellow-green areas, and consequently defines the mosaic pattern. The mechanism of mosaic symptom development is discussed in relation to the systemic spread of the virus and RNA silencing.
Immunomodulatory Properties of a Viral Homolog of Human Interleukin-10 Expressed by Human Cytomegalovirus during the Latent Phase of Infection
Authors: Jenkins C. , Garcia W. , Godwin M. J. , Spencer J. V. , Stern J. Lewis , Abendroth A. , Slobedman B. 
Published: January 2008

ABSTRACTHuman cytomegalovirus (HCMV) establishes a latent infection in hematopoietic cells, from which it can reactivate to cause significant disease in immunocompromised individuals. HCMV expresses a functional homolog of the immunosuppressive cytokine interleukin-10 (termed cmvIL-10), and alternate splicing of the cmvIL-10 transcript results in expression of a latency-associated cmvIL-10 transcript (LAcmvIL-10). To determine whether LAcmvIL-10 encodes immunosuppressive functions, recombinant LAcmvIL-10 protein was generated, and its impact on major histocompatibility complex class II (MHC-II) expression was examined on granulocyte macrophage progenitor cells (GM-Ps) and monocytes. LAcmvIL-10 (and cmvIL-10) downregulated MHC-II on the surfaces of both cell types. This downregulation was associated with a decrease in total MHC-II protein and transcription of components of the MHC-II biosynthesis pathway. Unlike cmvIL-10, LAcmvIL-10 did not trigger phosphorylation of Stat3, and its ability to downregulate MHC-II was not blocked by neutralizing antibodies to the human IL-10 receptor, suggesting that LAcmvIL-10 either does not engage the cellular IL-10 receptor or utilizes it in a different manner from cmvIL-10. The impact of LAcmvIL-10 on dendritic cell (DC) maturation was also assessed. In contrast to cmvIL-10, LAcmvIL-10 did not inhibit the expression of costimulatory molecules CD40, CD80, and CD86 and the maturation marker CD83 on DCs, nor did it inhibit proinflammatory cytokines (IL-1α, IL-1β, IL-6 and tumor necrosis factor alpha). Thus, LAcmvIL-10 retains some, but not all, of the immunosuppressive functions of cmvIL-10. As GM-Ps and monocytes support latent infection, expression of LAcmvIL-10 may enable HCMV to avoid immune recognition and clearance during latency.
Kaposi's Sarcoma-Associated Herpesvirus Transactivator RTA Promotes Degradation of the Repressors To Regulate Viral Lytic Replication
Authors: Yang Zhilong , Yan Zhangcai , Wood Charles 
Published: January 2008

ABSTRACTKaposi's sarcoma-associated herpesvirus/human herpesvirus 8 (KSHV/HHV-8) RTA is an important protein involved in the induction of KSHV lytic replication from latency through activation of the lytic cascade. A number of cellular and viral proteins, including K-RBP, have been found to repress RTA-mediated transactivation and KSHV lytic replication. However, it is unclear as to how RTA overcomes the suppression during lytic reactivation. In this study, we found that RTA can induce K-RBP degradation through the ubiquitin-proteasome pathway and that two regions in RTA are responsible. Moreover, we found that RTA can promote the degradation of several other RTA repressors. RTA mutants that are defective in inducing K-RBP degradation cannot activate RTA responsive promoter as efficiently as wild-type RTA. Interference of the ubiquitin-proteasome pathway affected RTA-mediated transactivation and KSHV reactivation from latency. Our results suggest that KSHV RTA can stimulate the turnover of repressors to modulate viral reactivation. Since herpes simplex virus type 1 transactivator ICP0 and human cytomegalovirus transactivator pp71 also stimulate the degradation of cellular silencers, it is possible that the promotion of silencer degradation by viral transactivators may be a common mechanism for regulating the lytic replication of herpesviruses.
Full Genome-Based Classification of Rotaviruses Reveals a Common Origin between Human Wa-Like and Porcine Rotavirus Strains and Human DS-1-Like and Bovine Rotavirus Strains
Authors: Matthijnssens Jelle , Ciarlet Max , Heiman Erica , Arijs Ingrid , Delbeke Thomas , McDonald Sarah M. , Palombo Enzo A. , Iturriza-Gómara Miren , Maes Piet , Patton John T. , Rahman Mustafizur , Van Ranst Marc 
Published: January 2008

ABSTRACT
Group A rotavirus classification is currently based on the molecular properties of the two outer layer proteins, VP7 and VP4, and the middle layer protein, VP6. As reassortment of all the 11 rotavirus gene segments plays a key role in generating rotavirus diversity in nature, a classification system that is based on all the rotavirus gene segments is desirable for determining which genes influence rotavirus host range restriction, replication, and virulence, as well as for studying rotavirus epidemiology and evolution. Toward establishing such a classification system, gene sequences encoding VP1 to VP3, VP6, and NSP1 to NSP5 were determined for human and animal rotavirus strains belonging to different G and P genotypes in addition to those available in databases, and they were used to define phylogenetic relationships among all rotavirus genes. Based on these phylogenetic analyses, appropriate identity cutoff values were determined for each gene. For the VP4 gene, a nucleotide identity cutoff value of 80% completely correlated with the 27 established P genotypes. For the VP7 gene, a nucleotide identity cutoff value of 80% largely coincided with the established G genotypes but identified four additional distinct genotypes comprised of murine or avian rotavirus strains. Phylogenetic analyses of the VP1 to VP3, VP6, and NSP1 to NSP5 genes showed the existence of 4, 5, 6, 11, 14, 5, 7, 11, and 6 genotypes, respectively, based on nucleotide identity cutoff values of 83%, 84%, 81%, 85%, 79%, 85%, 85%, 85%, and 91%, respectively. In accordance with these data, a revised nomenclature of rotavirus strains is proposed. The novel classification system allows the identification of (i) distinct genotypes, which probably followed separate evolutionary paths; (ii) interspecies transmissions and a plethora of reassortment events; and (iii) certain gene constellations that revealed (a) a common origin between human Wa-like rotavirus strains and porcine rotavirus strains and (b) a common origin between human DS-1-like rotavirus strains and bovine rotaviruses. These close evolutionary links between human and animal rotaviruses emphasize the need for close simultaneous monitoring of rotaviruses in animals and humans.
Three-Dimensional Structure of Canine Adenovirus Serotype 2 Capsid
Authors: Schoehn Guy , El Bakkouri Majida , Fabry Céline M. S. , Billet Oliver , Estrozi Leandro F. , Le Long , Curiel David T. , Kajava Andrey V. , Ruigrok Rob W. H. , Kremer Eric J. 
Published: January 2008

ABSTRACT
There are more than 100 known adenovirus (AdV) serotypes, including 50 human serotypes. Because AdV-induced disease is relatively species specific, vectors derived from nonhuman serotypes may have wider clinical potential based, in part, on the lack of ubiquitous memory immunity. Whereas a few of the human serotype capsids have been studied at the structural level, none of the nonhuman serotypes has been analyzed. The basis laid by the analysis of human AdV (hAdV) has allowed us to determine and compare the three-dimensional structure of the capsid of canine serotype 2 (CAV-2) to that of hAdV serotype 5 (hAdV-5). We show that CAV-2 capsid has a smoother structure than the human serotypes. Many of the external loops found in the hAdV-5 penton base and the hexon, against which the antibody response is directed, are shorter or absent in CAV-2. On the other hand, the CAV-2 fiber appears to be more complex, with two bends in the shaft. An interesting difference between the human and canine viruses is that the C-terminal part of protein IX is in a different position, making an antenna sticking out of the CAV-2 capsid. The comparison between the two viruses allows the identification of sites that should be easy to modify on the CAV-2 capsid for altering tissue tropism or other biological activities.