bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stem tilting in the inter‐tropical cactus Echinocactus platyacanthus: an adaptive solution to the trade‐off between radiation acquisition and temperature control
Authors: Herce M. F. , Martorell C. , Alonso‐Fernandez C. , Boullosa L. F. V. V. , Meave J. A. 
Published: August 2013

AbstractWhile plants require radiation for photosynthesis, radiation in warm deserts can have detrimental effects from high temperatures. This dilemma may be solved through plant morphological attributes. In cold deserts, stem tilting keeps reproductive organs warm by increasing radiation interception at the cost of decreased annual light interception. Conversely, little is known about stem tilting in warm deserts. We hypothesised that stem tilting in Echinocactus platyacanthus prevents high temperatures near the apex, where reproduction occurs. The study was conducted in the warm, inter‐tropical portion of the Chihuahuan Desert, Mexico. We found that cacti preferentially tilted towards the south, which reduced temperatures of reproductive organs during the hot season, but increased total annual near‐apex PAR interception. Tilting also maximised reproduction, a likely consequence of temperature control but perhaps also of the difficulty in translocating photosynthates in cacti; therefore, annual energy acquisition near floral meristems may be largely allocated to reproduction. Unlike plants of higher latitudes, in inter‐tropical deserts sunlight at noon comes either from the north or the south, depending on the season, and thus stem tilting may more strongly affect total annual radiation received in different portions of the stem. Inter‐tropical cacti can synchronise reproduction with irradiance peaks if flowering occurs in a specific (north or south) portion of the stem; also, they effectively solve the conflict between maximising annual PAR interception and minimising temperature at the hottest time of day. Notably, the two inter‐tropical cacti in which stem tilting has been studied successfully solve this conflict.
Combining mechanical rhizome removal and cover crops for Elytrigia repens control in organic barley systems
Authors: Melander B , Nørremark M , Kristensen E F 
Published: August 2013

SummaryMechanical weed control of perennial weeds in organic crop production over long post‐harvest periods is incompatible with the establishment of cover crops for improving soil quality and preventing nutrient leaching. We suggest a new concept that comprises uprooting and immediate removal of vegetative propagules located within the plough layer to allow for quick re‐establishment of a plant cover. A field experiment comparing the effects of conventional practices (stubble cultivation) with different combinations of rotary cultivation (One, Two or four passes) and cover crops (none vs. rye‐vetch‐mustard mixture) on Elytrigia repens rhizome removal, shoot growth and suppression of a subsequent barley crop was examined in two growing seasons. Four passes with a modified rotary cultivator, where each pass was followed by rhizome removal, reduced E. repens shoot growth in barley by 84% and 97%. In general, the cover crop developed poorly and did not affect barley or E. repens. Barley yield was only affected by treatments in the first season, where yield was negatively correlated with E. repens shoot biomass. The concept has potential for the control of severe E. repens infestations, but future research aimed at identifying more effective smother crops and less intensive methods of rhizome removal is needed.
Investigating the Use of Protein Saver Cards for Storage and Subsequent Detection of Bovine Anti-Brucella abortus Smooth Lipopolysaccharide Antibodies and Gamma Interferon
Authors: Duncombe Lucy , Commander Nicola J. , Erdenlig Sevil , McGiven John A. , Stack Judy 
Published: August 2013

ABSTRACTBrucella abortus, a smooth strain of the genusBrucella, is the causative agent of bovine brucellosis. To support the ongoing development of diagnostic tests for bovine brucellosis, the use of Protein Saver cards (Whatman) for bovine blood serum and plasma sample collection has been evaluated. These cards offer significant logistical and safety alternatives to transporting and storing liquid samples and may aid in diagnostic programs and validation studies. To evaluate the utility of these cards, 204 bovine blood serum samples fromBrucella-infected and noninfected animals were stored on and eluted from the Protein Saver cards. Anti-Brucellasmooth lipopolysaccharide (sLPS) antibody titers for the serum eluates were compared to those of the unprocessed original serum samples by indirect enzyme-linked immunosorbent assay (ELISA). The results showed a highly significant correlation between titers from the serum eluates and the unprocessed sera. Therefore, under these circumstances, serum eluates and unprocessed serum samples may be used interchangeably. Blood plasma from 113 mitogen-stimulated whole-blood samples was added to and eluted from the Protein Saver cards. The gamma interferon (IFN-γ) titers in the plasma eluates were compared to those of the unprocessed plasma samples obtained by IFN-γ ELISA. The results showed a significant correlation between the plasma eluates and the unprocessed plasma samples. To derive a signal in the plasma eluate, it was necessary to develop a novel and highly sensitive ELISA for the detection of IFN-γ. The serum samples stored on cards at room temperature over a 10-day period showed little variation in antibody titers. However, the plasma eluates showed a progressive loss of IFN-γ recovery over 10 days when stored at room temperature.
Development of an Unbiased Antigen-Mining Approach To Identify Novel Vaccine Antigens and Diagnostic Reagents for Bovine Tuberculosis
Authors: Jones Gareth J. , Khatri Bhagwati L. , Garcia-Pelayo M. Carmen , Kaveh Daryan A. , Bachy Véronique S. , Hogarth Philip J. , Wooff Esen , Golby Paul , Vordermeier H. Martin 
Published: August 2013

ABSTRACT

Previous experiments for the identification of novel diagnostic or vaccine candidates for bovine tuberculosis have followed a targeted approach, wherein specific groups of proteins suspected to contain likely candidates are prioritized for immunological assessment (for example, with
in silico
approaches). However, a disadvantage of this approach is that the sets of proteins analyzed are restricted by the initial selection criteria. In this paper, we describe a series of experiments to evaluate a nonbiased approach to antigen mining by utilizing a Gateway clone set for
Mycobacterium tuberculosis
, which constitutes a library of clones expressing 3,294
M. tuberculosis
proteins. Although whole-blood culture experiments using
Mycobacterium bovis
-infected animals and
M. bovis
BCG-vaccinated controls did not reveal proteins capable of differential diagnosis, several novel immunogenic proteins were identified and prioritized for efficacy studies in a murine vaccination/challenge model. These results demonstrate that Rv3329-immunized mice had lower bacterial cell counts in their spleens following challenge with
M. bovis
. In conclusion, we demonstrate that this nonbiased approach to antigen mining is a useful tool for identifying and prioritizing novel proteins for further assessment as vaccine antigens.
Molecular Typing of “Candidatus Bartonella ancashi,” a New Human Pathogen Causing Verruga Peruana
Authors: Mullins Kristin E. , Hang Jun , Jiang Ju , Leguia Mariana , Kasper Matthew R. , Maguiña Ciro , Jarman Richard G. , Blazes David L. , Richards Allen L. 
Published: August 2013

ABSTRACT

A recently described clinical isolate, “
Candidatus
Bartonella ancashi,” was obtained from a blood sample of a patient presenting with verruga peruana in the Ancash region of Peru. This sample and a second isolate obtained 60 days later from the same patient were molecularly typed using multilocus sequence typing (MLST) and multispacer sequence typing (MST). The isolates were 100% indistinguishable from each other but phylogenetically distant from
Bartonella bacilliformis
and considerably divergent from other known
Bartonella
species, confirming their novelty.
Evaluation of Bactec Mycosis IC/F and Plus Aerobic/F Blood Culture Bottles for Detection of Candida in the Presence of Antifungal Agents
Authors: Köck Robin , Eißing Lea C. , Boschin Matthias G. , Ellger Björn , Horn Dagmar , Idelevich Evgeny A. , Becker Karsten 
Published: August 2013

ABSTRACT

Clinical practice guidelines recommend performing follow-up cultures for patients with candidemia in order to determine the time when
Candida
is cleared from the bloodstream. Since this requires culturing blood samples from patients undergoing antifungal treatment, we evaluated two blood culture bottles (the Bactec Mycosis IC/F [MICF], specifically adapted to the growth of fungi, and the Bactec Plus Aerobic/F [PAF], containing resins to inactivate anti-infective agents) for their effectiveness in detecting
Candida albicans
and
Candida glabrata
when seeded in concentrations of 1 CFU/ml and 10 CFU/ml, respectively, together with human whole blood and various antifungal agents in therapeutic peak serum concentrations (
C
max
). Significant differences between the MICF and PAF vials for the detection of
Candida
spp. were found when inoculated with caspofungin (0/12 versus 8/12) (
P
< 0.001) or amphotericin B (3/12 versus 12/12) (
P
< 0.001). Inoculation of fluconazole or voriconazole did not influence the effectiveness of detection in the MICF and PAF bottles (
P
= 1.0). Neither the MICF nor the PAF bottles detected
Candida
spp. reliably when seeded together with anidulafungin (1/12 versus 1/12) (
P
= 1.0) or micafungin (0/12 versus 1/12) (
P
= 1.0). The times to positivity of both bottles were significantly prolonged when antifungal agents were added compared to those of controls without antimycotic drugs (
P
< 0.001). Overall, the results of this
in vitro
study indicate that the PAF bottles detected
Candida
spp. more reliably than the MICF bottles when supplemented with certain antifungal agents. Consequently, clinical studies should evaluate whether this holds true when blood cultures from patients undergoing antifungal treatment are performed.
Preservation of Dendritic Cell Function during Vesicular Stomatitis Virus Infection Reflects both Intrinsic and Acquired Mechanisms of Resistance to Suppression of Host Gene Expression by Viral M Protein
Authors: Westcott Marlena M. , Ahmed Maryam , Smedberg Jason R. , Rajani Karishma R. , Hiltbold Elizabeth M. , Lyles Douglas S. 
Published: August 2013

ABSTRACT

Inhibition of host-directed gene expression by the matrix (M) protein of vesicular stomatitis virus (VSV) effectively blocks host antiviral responses, promotes virus replication, and disables the host cell. However, dendritic cells (DC) have the capacity to resist these effects and remain functional during VSV infection. Here, the mechanisms of DC resistance to M protein and their subsequent maturation were addressed. Flt3L-derived murine bone marrow dendritic cells (FDC), which phenotypically resemble resident splenic DC, continued to synthesize cellular proteins and matured during single-cycle (high-multiplicity) and multicycle (low-multiplicity) infection with VSV. Granulocyte-macrophage colony-stimulating factor (GM-CSF)-derived myeloid DC (GDC), which are susceptible to M protein effects, were nevertheless capable of maturing, but the response was delayed and occurred only during multicycle infection. FDC resistance was manifested early and was type I interferon (IFN) receptor (IFNAR) and MyD88 independent, but sustained resistance required IFNAR. MyD88-dependent signaling contributed to FDC maturation during single-cycle infection but was dispensable during multicycle infection. Similar to FDC, splenic DC were capable of maturing
in vivo
during the first 24 h of infection with VSV, and neither Toll-like receptor 7 (TLR7) nor MyD88 was required. We conclude that FDC resistance to M protein is controlled by an intrinsic, MyD88-independent mechanism that operates early in infection and is augmented later in infection by type I IFN. In contrast, while GDC are not intrinsically resistant, they can acquire resistance during multicycle infection.
In vivo
, splenic DC resist the inhibitory effects of VSV, and as in multicycle FDC infection, MyD88-independent signaling events control their maturation.
Foot-and-Mouth Disease Virus 3C Protease Induces Fragmentation of the Golgi Compartment and Blocks Intra-Golgi Transport
Authors: Zhou Zhigang , Mogensen Mette M. , Powell Penny P. , Curry Stephen , Wileman Thomas 
Published: August 2013

ABSTRACT

Picornavirus infection can cause Golgi fragmentation and impose a block in the secretory pathway which reduces expression of major histocompatibility antigens at the plasma membrane and slows secretion of proinflammatory cytokines. In this study, we show that Golgi fragmentation and a block in secretion are induced by expression of foot-and-mouth disease virus (FMDV) 3C
pro
and that this requires the protease activity of 3C
pro
. 3C
pro
caused fragmentation of early, medial, and late Golgi compartments, but the most marked effect was on early Golgi compartments, indicated by redistribution of ERGIC53 and membrin. Golgi fragments were dispersed in the cytoplasm and were able to receive a model membrane protein exported from the endoplasmic reticulum (ER). Golgi fragments were, however, unable to transfer the protein to the plasma membrane, indicating a block in intra-Golgi transport. Golgi fragmentation was coincident with a loss of microtubule organization resulting from an inhibition of microtubule regrowth from the centrosome. Inhibition of microtubule regrowth also required 3C
pro
protease activity. The loss of microtubule organization induced by 3C
pro
caused Golgi fragmentation, but loss of microtubule organization does not block intra-Golgi transport. It is likely that the block of intra-Golgi transport is imposed by separate actions of 3C
pro
, possibly through degradation of proteins required for intra-Golgi transport.
A Cholesterol Recognition Amino Acid Consensus Domain in GP64 Fusion Protein Facilitates Anchoring of Baculovirus to Mammalian Cells
Authors: Luz-Madrigal Agustin , Asanov Alexander , Camacho-Zarco Aldo R. , Sampieri Alicia , Vaca Luis 
Published: August 2013

ABSTRACTBaculoviridaeis a large family of double-stranded DNA viruses that selectively infect insects.Autographa californicamultiple nucleopolyhedrovirus (AcMNPV) is the best-studied baculovirus from the family. Many studies over the last several years have shown that AcMNPV can enter a wide variety of mammalian cells and deliver genetic material for foreign gene expression. While most animal viruses studied so far have developed sophisticated mechanisms to selectively infect specific cells and tissues in an organism, AcMNPV can penetrate and deliver foreign genes into most cells studied to this date. The details about the mechanisms of internalization have been partially described. In the present study, we have identified a cholesterol recognition amino acid consensus (CRAC) domain present in the AcMNPV envelope fusion protein GP64. We demonstrated the association of a CRAC domain with cholesterol, which is important to facilitate the anchoring of the virus at the mammalian cell membrane. Furthermore, this initial anchoring favors AcMNPV endocytosis via a dynamin- and clathrin-dependent mechanism. Under these conditions, efficient baculovirus-driven gene expression is obtained. In contrast, when cholesterol is reduced from the plasma membrane, AcMNPV enters the cell via a dynamin- and clathrin-independent mechanism. The result of using this alternative internalization pathway is a reduced level of baculovirus-driven gene expression. This study is the first to document the importance of a novel CRAC domain in GP64 and its role in modulating gene delivery in AcMNPV.
Genome-Wide Analysis of T Cell Responses during Acute and Latent Simian Varicella Virus Infections in Rhesus Macaques
Authors: Haberthur Kristen , Kraft Aubrey , Arnold Nicole , Park Byung , Meyer Christine , Asquith Mark , Dewane Jesse , Messaoudi Ilhem 
Published: August 2013

ABSTRACTVaricella zoster virus (VZV) is the etiological agent of varicella (chickenpox) and herpes zoster (HZ [shingles]). Clinical observations suggest that VZV-specific T cell immunity plays a more critical role than humoral immunity in the prevention of VZV reactivation and development of herpes zoster. Although numerous studies have characterized T cell responses directed against select VZV open reading frames (ORFs), a comprehensive analysis of the T cell response to the entire VZV genome has not yet been conducted. We have recently shown that intrabronchial inoculation of young rhesus macaques with simian varicella virus (SVV), a homolog of VZV, recapitulates the hallmarks of acute and latent VZV infection in humans. In this study, we characterized the specificity of T cell responses during acute and latent SVV infection. Animals generated a robust and broad T cell response directed against both structural and nonstructural viral proteins during acute infection in bronchoalveolar lavage (BAL) fluid and peripheral blood. During latency, T cell responses were detected only in the BAL fluid and were lower and more restricted than those observed during acute infection. Interestingly, we identified a small set of ORFs that were immunogenic during both acute and latent infection in the BAL fluid. Given the close genome relatedness of SVV and VZV, our studies highlight immunogenic ORFs that may be further investigated as potential components of novel VZV vaccines that specifically boost T cell immunity.
Systemic Toll-Like Receptor Ligation and Selective Killing of Dendritic Cell Subsets Fail To Dissect Priming Pathways for Anti-Vaccinia Virus CD8+T Cells
Authors: Wong Yik Chun , Smith Stewart A. , Tscharke David C. 
Published: August 2013

ABSTRACTCD8+T cell responses can be generated by direct or cross-priming mechanisms, and several mouse models have been used to reveal which of these is the most important pathway for various viruses. Among these models is systemic treatment of mice with a CpG-containing oligodeoxynucleotide (CpG) to mature all dendritic cells (DCs), rendering them incapable of cross-presentation. A second is the use of cytochromec(cytc) as a selective poison of the subsets of DCs able to cross-present antigen. In this study, using two vaccinia virus (VACV) strains, namely, WR and MVA, we found that the CpG and cytc methods gave conflicting data. Moreover, we show for both strains of VACV that treatment of mice with CpG and cytc inhibited CD8+T cell responses to antigens designed to prime exclusively by direct presentation. Further investigation of the CpG method found that the extent to which priming is inhibited depends on the antigen examined, immunization route, replication ability of the virus, and, crucially, immunization dose. We suggest that greater caution is required when interpreting data using these methods and that priming pathways for antiviral CD8+T cells are not simply separated according to DC subsets or their maturation state.
Comparative Analysis of the Complete Genome Sequence of the California MSW Strain of Myxoma Virus Reveals Potential Host Adaptations
Authors: Kerr Peter J. , Rogers Matthew B. , Fitch Adam , DePasse Jay V. , Cattadori Isabella M. , Hudson Peter J. , Tscharke David C. , Holmes Edward C. , Ghedin Elodie 
Published: August 2013

ABSTRACT

Myxomatosis is a rapidly lethal disease of European rabbits that is caused by myxoma virus (MYXV). The introduction of a South American strain of MYXV into the European rabbit population of Australia is the classic case of host-pathogen coevolution following cross-species transmission. The most virulent strains of MYXV for European rabbits are the Californian viruses, found in the Pacific states of the United States and the Baja Peninsula, Mexico. The natural host of Californian MYXV is the brush rabbit,
Sylvilagus bachmani
. We determined the complete sequence of the MSW strain of Californian MYXV and performed a comparative analysis with other MYXV genomes. The MSW genome is larger than that of the South American Lausanne (type) strain of MYXV due to an expansion of the terminal inverted repeats (TIRs) of the genome, with duplication of the
M156R
,
M154L
,
M153R
,
M152R
, and
M151R
genes and part of the
M150R
gene from the right-hand (RH) end of the genome at the left-hand (LH) TIR. Despite the extreme virulence of MSW, no novel genes were identified; five genes were disrupted by multiple indels or mutations to the ATG start codon, including two genes,
M008.1L/R
and
M152R
, with major virulence functions in European rabbits, and a sixth gene,
M000.5L/R
, was absent. The loss of these gene functions suggests that
S. bachmani
is a relatively recent host for MYXV and that duplication of virulence genes in the TIRs, gene loss, or sequence variation in other genes can compensate for the loss of
M008.1L/R
and
M152R
in infections of European rabbits.
The Kissing-Loop T-Shaped Structure Translational Enhancer of Pea Enation Mosaic Virus Can Bind Simultaneously to Ribosomes and a 5′ Proximal Hairpin
Authors: Gao Feng , Gulay Suna P. , Kasprzak Wojciech , Dinman Jonathan D. , Shapiro Bruce A. , Simon Anne E. 
Published: August 2013

ABSTRACT

The
Pea Enation Mosaic Virus
(PEMV) 3′ translational enhancer, known as the kissing-loop T-shaped structure (kl-TSS), binds to 40S subunits, 60S subunits, and 80S ribosomes, whereas the
Turnip crinkle virus
(TCV) TSS binds only to 60S subunits and 80S ribosomes. Using electrophoretic mobility gel shift assay (EMSA)-based competition assays, the kl-TSS was found to occupy a different site in the ribosome than the P-site-binding TCV TSS, suggesting that these two TSS employ different mechanisms for enhancing translation. The kl-TSS also engages in a stable, long-distance RNA-RNA kissing-loop interaction with a 12-bp 5′-coding-region hairpin that does not alter the structure of the kl-TSS as revealed by molecular dynamics simulations. Addition of the kl-TSS in
trans
to a luciferase reporter construct containing either wild-type or mutant 5′ and 3′ PEMV sequences suppressed translation, suggesting that the kl-TSS is required in
cis
to function, and both ribosome-binding and RNA interaction activities of the kl-TSS contributed to translational inhibition. Addition of the kl-TSS was more detrimental for translation than an adjacent eIF4E-binding 3′ translational enhancer known as the PTE, suggesting that the PTE may support the ribosome-binding function of the kl-TSS. Results of in-line RNA structure probing, ribosome filter binding, and high-throughput selective 2′-hydroxyl acylation analyzed by primer extension (hSHAPE) of rRNAs within bound ribosomes suggest that kl-TSS binding to ribosomes and binding to the 5′ hairpin are compatible activities. These results suggest a model whereby posttermination ribosomes/ribosomal subunits bind to the kl-TSS and are delivered to the 5′ end of the genome via the associated RNA-RNA interaction, which enhances the rate of translation reinitiation.