bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution and migratory destinations of humpback whales off the Pacific coast of Central America during the boreal winters of 1996–2003
Authors: Rasmussen Kristin , Calambokidis John , Steiger Gretchen H. 
Published: September 2011

AbstractHere, we examine the distribution, habitat use, and migratory destinations of North Pacific humpback whales wintering off Central America. Coastal boat surveys were conducted off Costa Rica and Panama between 1996 and 2003. In 1999, a broader survey was conducted along most of Central America. Over 23,000 km were surveyed, with the greatest effort off southern Costa Rica. We made 191 sightings of 320 individual humpback whales. Whales were seen between 14°N and 8°N, making this the most southerly of the North Pacific wintering areas. Encounters included singles, adult pairs, singers, and mother/calf pairs. Mother/calf pairs accounted for 27% of all groups sighted, which is one of the highest sighting rates reported among North Pacific wintering areas. Sixty percent of sightings occurred in depths <50 m. Average sea surface temperature was 28.6°C (±1.0 SD). Ninety percent of the 77 unique whales photo‐identified were also seen in the California–Oregon–Washington feeding aggregation. The 1999 survey showed that humpback whales were widely distributed along the Central American coast at relatively low densities. The extensive distribution of animals, the higher proportion of calves, and the almost exclusive migration to a single feeding area contrast with observations in other regions.
Slow Solvent Relaxation Dynamics of Nanometer Sized Reverse Micellar Systems Through Tryptophan Metabolite, Kynurenine
Authors: Rakshit Surajit , Goswami Nirmal , Pal Samir Kumar 
Published: September 2011

AbstractExploration of environmental dynamics using intrinsic biological probe tryptophan is very important; however, it suffers from various difficulties. An alternative probe, kynurenine (KN), has been found to be an efficient probe for the ultrafast dynamics in the biological environment (Goswami et al., [2010] J. Phys. Chem. B., 114, 15236–15243). In the present study, we have investigated the efficacy of KN for the exploration of relatively slower dynamics of biologically relevant environments. A detailed investigation involving UV–Vis, steady‐state/time‐resolved fluorescence spectroscopy and Förster resonance energy transfer (FRET) studies on KN compared to a well‐known solvation probe, H33258, a DNA‐minor groove binder in a model nonionic reverse micelle reveals that ultrafast internal conversion associated with the hydrogen‐bonding dynamics masks KN to become a dynamical reporter of the immediate environments of the probe.
Caffeic acid phenethyl ester (CAPE) prevents methotrexate-induced hepatorenal oxidative injury in rats
Authors: Çakır Tuğrul , Özkan Erkan , Dulundu Ender , Topaloğlu Ümit , Şehirli Ahmet Özer , Ercan Feriha , Şener Emre , Şener Göksel 
Published: September 2011

Abstract

Objectives
This study aimed to investigate the antioxidant and anti-inflammatory effects of caffeic acid phenethyl ester (CAPE) on the methotrexate (MTX)-induced hepatorenal oxidative damage in rats.

Methods
Following a single dose of methotrexate (20 mg/kg), either vehicle (MTX group) or CAPE (10 µmol/kg, MTX + CAPE group) was administered for five days. In other rats, vehicle (control group) or CAPE was injected for five days, following a single dose of saline injection. After decapitation of the rats, trunk blood was obtained, and the liver and kidney tissues were removed for histological examination and for the measurement of malondialdehyde (MDA) and glutathione (GSH) levels and myeloperoxidase (MPO) and sodium potassium-adenosine triphosphatase (Na+/K+-ATPase) activity. TNF-α and IL-1β levels were measured in the blood.

Key findings
Methotrexate administration increased the tissue MDA levels, MPO activity and decreased GSH levels and Na+/K+-ATPase activity, while these alterations were reversed in the CAPE-treated MTX group. Elevated TNF-α and IL-1β levels were also reduced with CAPE treatment.

Conclusions
The results of this study revealed that CAPE, through its anti-inflammatory and antioxidant actions, alleviates methotrexate-induced oxidative damage, which suggests that CAPE may be of therapeutic benefit when used with methotrexate.
Evaluation of Chlamydia trachomatis and Neisseria gonorrhoeae Detection in Urine, Endocervical, and Vaginal Specimens by a Multiplexed Isothermal Thermophilic Helicase-Dependent Amplification (tHDA) Assay
Authors: O'Neil Dominic , Doseeva Victoria , Rothmann Thomas , Wolff John , Nazarenko Irina 
Published: September 2011

ABSTRACT

We have developed a new research assay that combines sequence-specific sample preparation and isothermal amplification for the detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
infections. The assay targets both the
omp
gene and the cryptic plasmid of
C. trachomatis
and the multicopy
opa
gene of
N. gonorrhoeae
, which are amplified and detected in a single reaction. We evaluated the ability of the assay to detect
C. trachomatis
and
N. gonorrhoeae
infections in first-catch urine, swab, and liquid-based cytology samples. Total agreement between the new assay and APTIMA Combo 2 varied between 95.3% and 100%, depending on the sample type and target detected. Total agreement between the new assay and BD ProbeTec varied between 96.7% and 100%, depending on the sample type and target detected. The assay has a simple work flow, and endpoint results can be achieved in 3 h, including sample preparation. The assay described here was evaluated for research use and was compared to commercially available assays.
Systematic Survey of Clonal Complexity in Tuberculosis at a Populational Level and Detailed Characterization of the Isolates Involved
Authors: Navarro Yurena , Herranz Marta , Pérez-Lago Laura , Martínez Lirola Miguel , Ruiz-Serrano Maria Jesús , Bouza Emilio , García de Viedma Darío 
Published: September 2011

ABSTRACT

Clonally complex infections by
Mycobacterium tuberculosis
are progressively more accepted. Studies of their dimension in epidemiological scenarios where the infective pressure is not high are scarce. Our study systematically searched for clonally complex infections (mixed infections by more than one strain and simultaneous presence of clonal variants) by applying mycobacterial interspersed repetitive-unit (MIRU)–variable-number tandem-repeat (VNTR) analysis to
M. tuberculosis
isolates from two population-based samples of respiratory (703 cases) and respiratory-extrapulmonary (R+E) tuberculosis (TB) cases (71 cases) in a context of moderate TB incidence. Clonally complex infections were found in 11 (1.6%) of the respiratory TB cases and in 10 (14.1%) of those with R+E TB. Among the 21 cases with clonally complex TB, 9 were infected by 2 independent strains and the remaining 12 showed the simultaneous presence of 2 to 3 clonal variants. For the 10 R+E TB cases with clonally complex infections, compartmentalization (different compositions of strains/clonal variants in independent infected sites) was found in 9 of them. All the strains/clonal variants were also genotyped by IS
6110
-based restriction fragment length polymorphism analysis, which split two MIRU-defined clonal variants, although in general, it showed a lower discriminatory power to identify the clonal heterogeneity revealed by MIRU-VNTR analysis. The comparative analysis of IS
6110
insertion sites between coinfecting clonal variants showed differences in the genes coding for a cutinase, a PPE family protein, and two conserved hypothetical proteins. Diagnostic delay, existence of previous TB, risk for overexposure, and clustered/orphan status of the involved strains were analyzed to propose possible explanations for the cases with clonally complex infections. Our study characterizes in detail all the clonally complex infections by
M. tuberculosis
found in a systematic survey and contributes to the characterization that these phenomena can be found to an extent higher than expected, even in an unselected population-based sample lacking high infective pressure.
Differing Neisseria gonorrhoeae Bacterial Loads in the Pharynx and Rectum in Men Who Have Sex with Men: Implications for Gonococcal Detection, Transmission, and Control
Authors: Bissessor M. , Tabrizi S. N. , Fairley C. K. , Danielewski J. , Whitton B. , Bird S. , Garland S. , Chen M. Y. 
Published: September 2011

ABSTRACT

The bacterial loads for gonococcal infections of the pharynx and rectum were determined among men with male sexual partners. The median bacterial load for rectal infections (18,960 copies/swab) was significantly higher than the load for pharyngeal infections (2,100 copies/swab;
P
= 0.001). Bacterial loads among men with symptomatic proctitis were strikingly high (median, 278,000 copies/swab).
Target Cell-Mediated Editing of HIV-1 cDNA by APOBEC3 Proteins in Human Macrophages
Authors: Koning Fransje A. , Goujon Caroline , Bauby Hélène , Malim Michael H. 
Published: September 2011

ABSTRACTApolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins are encapsidated by assembling HIV-1 virions and edit viral cDNA in the next round of infection. Using alpha interferon (IFN-α)-treated monocyte-derived macrophages, we show that infrequent editing of HIV-1 reverse transcripts can also be mediated by APOBEC3 proteins supplied by the targets of infection. Based on the local sequence contexts of these mutations and the established characteristics of APOBEC3 protein expression in myeloid cells, we speculate that APOBEC3A may be responsible for a substantial proportion of this activity.
Hypoxia Induces the Gene Expression and Extracellular Transmission of Persistent Lymphocytic Choriomeningitis Virus
Authors: Tomaskova Jana , Oveckova Ingrid , Labudova Martina , Lukacikova Lubomira , Laposova Katarina , Kopacek Juraj , Pastorekova Silvia , Pastorek Jaromir 
Published: September 2011

ABSTRACT
The physiological context of virus-infected cells can markedly affect multiplication and spread of the virus progeny. During persistent infection, the virus exploits the host cell without disturbing its vital functions. However, microenvironmental hypoxia can uncouple this intimate relationship and escalate virus pathogenesis. Accumulating evidence suggests that hypoxia-inducible factor (HIF) modulates gene expression of the viruses that pass through a DNA stage, contain hypoxia-responsive promoter elements, and replicate in the nucleus. Here we show that hypoxia can influence the gene expression and transmission of the cytoplasmic RNA virus lymphocytic choriomeningitis virus (LCMV), which is a neglected human pathogen and teratogen. The MX strain of LCMV, which we used as a model, replicates in a persistent mode in human HeLa cells, fails to produce mature envelope glycoproteins, and spreads through cell-cell contacts in the absence of extracellular infectious virions. Both exposure of MX-infected HeLa cells to chronic hypoxia and gene transfer approaches led to increased virus RNA transcription and higher levels of the viral proteins via a HIF-dependent mechanism. Moreover, hypoxia enhanced the formation of infectious virions capable of transmitting LCMV by cell-free medium. This LCMV “reactivation” might have health-compromising consequences in hypoxia-associated situations, such as fetal development and ischemia-related pathologies.
Retrofitting the Genome: L1 Extinction Follows Endogenous Retroviral Expansion in a Group of Muroid Rodents
Authors: Erickson Issac K. , Cantrell Michael A. , Scott LuAnn , Wichman Holly A. 
Published: September 2011

ABSTRACT
Long interspersed nuclear element 1 (LINE-1; L1) retrotransposons are the most common retroelements in mammalian genomes. Unlike individual families of endogenous retroviruses (ERVs), they have remained active throughout the mammalian radiation and are responsible for most of the retroelement movement and much genome rearrangement within mammals. They can be viewed as occupying a substantial niche within mammalian genomes. Our previous demonstration that L1s and B1 short interspersed nuclear elements (SINEs) are inactive in a group of South American rodents led us to ask if other elements have amplified to fill the empty niche. We identified a novel and highly active family of ERVs (mysTR). To determine whether loss of L1 activity was correlated with expansion of mysTR, we examined mysTR activity in four South American rodent species that have lost L1 and B1 activity and four sister species with active L1s. The copy number of recent mysTR insertions was extremely high, with an average of 4,200 copies per genome. High copy numbers exist in both L1-active and L1-extinct species, so the mysTR expansion appears to have preceded the loss of both SINE and L1 activity rather than to have filled an empty niche created by their loss. It may be coincidental that two unusual genomic events—loss of L1 activity and massive expansion of an ERV family—occur in the same group of mammals. Alternatively, it is possible that this large ERV expansion set the stage for L1 extinction.
A Genetic Interaction between the Core and NS3 Proteins of Hepatitis C Virus Is Essential for Production of Infectious Virus
Authors: Jones Daniel M. , Atoom Ali M. , Zhang Xiaozhen , Kottilil Shyamasundaran , Russell Rodney S. 
Published: September 2011

ABSTRACT

By analogy to other members of the
Flaviviridae
family, the hepatitis C virus (HCV) core protein is presumed to oligomerize to form the viral nucleocapsid, which encloses the single-stranded RNA genome. Core protein is directed to lipid droplets (LDs) by domain 2 (D2) of the protein, and this process is critical for virus production. Domain 1 (D1) of core is also important for infectious particle morphogenesis, although its precise contribution to this process is poorly understood. In this study, we mutated amino acids 64 to 75 within D1 of core and examined the ability of these mutants to produce infectious virus. We found that residues 64 to 66 are critical for generation of infectious progeny, whereas 67 to 75 were dispensable for this process. Further investigation of the defective 64 to 66 mutant (termed JFH1
T
-64–66) revealed it to be incapable of producing infectious intracellular virions, suggesting a fault during HCV assembly. Furthermore, isopycnic gradient analyses revealed that JFH1
T
-64–66 assembled dense intracellular species of core, presumably representing nucleocapsids. Thus, amino acids 64 to 66 are seemingly not involved in core oligomerization/nucleocapsid assembly. Passaging of JFH1
T
-64–66 led to the emergence of a single compensatory mutation (K1302R) within the helicase domain of NS3 that completely rescued its ability to produce infectious virus. Importantly, the same NS3 mutation abrogated virus production in the context of wild-type core protein. Together, our results suggest that residues 64 to 66 of core D1 form a highly specific interaction with the NS3 helicase that is essential for the generation of infectious HCV particles at a stage downstream of nucleocapsid assembly.
Fusion of Epstein-Barr Virus with Epithelial Cells Can Be Triggered by αvβ5 in Addition to αvβ6 and αvβ8, and Integrin Binding Triggers a Conformational Change in Glycoproteins gHgL
Authors: Chesnokova Liudmila S. , Hutt-Fletcher Lindsey M. 
Published: September 2011

ABSTRACT
Fusion of herpesviruses with their target cells requires a minimum of three glycoproteins, namely, gB and a complex of gH and gL. Epstein-Barr virus (EBV) fusion with an epithelial cell requires no additional virus glycoproteins, and we have shown previously that it can be initiated by an interaction between integrin αvβ6 or αvβ8 and gHgL. We now report that integrin αvβ5 can also bind to gHgL and trigger fusion. Binding of gHgL to integrins is a two-step reaction. The first step, analyzed by surface plasmon resonance, was fast, with high association and low dissociation rate constants. The second step, detected by fluorescence spectroscopy of gHgL labeled at cysteine 153 at the domain I-domain II interface with the environmentally sensitive probes acrylodan and IANBD, involved a slower conformational change. Interaction of gHgL with neutralizing monoclonal antibodies or Fab′ fragments was also consistent with a two-step reaction involving fast high-affinity binding and a subsequent slower conformational change. None of the antibodies bound to the same epitope, and none completely inhibited integrin binding. However, binding of each decreased the rate of conformational change induced by integrin binding, suggesting that neutralization might involve a conformational change that precludes fusion. Overall, the data are consistent with the interaction of gHgL with an integrin inducing a functionally important rearrangement at the domain I-domain II interface.
Regulation of Vaccinia Virus E3 Protein by Small Ubiquitin-Like Modifier Proteins
Authors: González-Santamaría José , Campagna Michela , García María Angel , Marcos-Villar Laura , González Dolores , Gallego Pedro , Lopitz-Otsoa Fernando , Guerra Susana , Rodríguez Manuel S. , Esteban Mariano , Rivas Carmen 
Published: September 2011

ABSTRACT
The vaccinia virus (VACV) E3 protein is essential for virulence and has antiapoptotic activity and the ability to impair the host innate immune response. Here we demonstrate that E3 interacts with SUMO1 through a small ubiquitin-like modifier (SUMO)-interacting motif (SIM). SIM integrity is required for maintaining the stability of the viral protein and for the covalent conjugation of E3 to SUMO1 or SUMO2, a modification that has a negative effect on the E3 transcriptional transactivation of the p53-upregulated modulator of apoptosis (PUMA) and APAF-1 genes. We also demonstrate that E3 is ubiquitinated, a modification that does not destabilize the wild-type protein but triggers the degradation of an E3-ΔSIM mutant. This report constitutes the first demonstration of the important roles that both SUMO and ubiquitin play in the regulation of the VACV protein E3.
Immunovirological Analyses of Chronically Simian Immunodeficiency Virus SIVmnd-1- and SIVmnd-2-Infected Mandrills (Mandrillus sphinx)
Authors: Apetrei Cristian , Sumpter Beth , Souquiere Sandrine , Chahroudi Ann , Makuwa Maria , Reed Patricia , Ribeiro Ruy M. , Pandrea Ivona , Roques Pierre , Silvestri Guido 
Published: September 2011

ABSTRACT

Simian immunodeficiency virus (SIV) infection in African nonhuman primate (NHP) natural hosts is usually nonpathogenic, despite high levels of virus replication. We have previously shown that chronic SIV infection in sooty mangabeys (SMs) and African green monkeys (AGMs) is associated with low levels of immune activation and bystander T cell apoptosis. To compare these features with those observed in another natural host, the mandrill (MND), we conducted a cross-sectional survey of the 23 SIV-infected and 25 uninfected MNDs from the only semifree colony of mandrills available worldwide. Viral loads (VLs) were determined and phenotypic and functional analysis of peripheral blood- and lymph node-derived lymphocytes was performed. We found that mandrills chronically infected with SIVmnd-1 or SIVmnd-2 have similar levels of viral replication, and we observed a trend toward lower CD4
+
T cell counts in chronically SIVmnd-2-infected MNDs than SIVmnd-1-infected MNDs. No correlation between CD4
+
T cell counts and VLs in SIV-infected MNDs could be established. Of note, the levels of T cell activation, proliferation, and apoptosis were comparable between SIVmnd-1- and SIVmnd-2-infected MNDs and to those observed in uninfected animals, with the only exception being an increase in tumor necrosis factor alpha-producing CD8
+
T cells in SIVmnd-2-infected MNDs. Overall, these findings recapitulate previous observations in SIV-infected SMs and AGMs and lend further evidence to the hypothesis that low levels of immune activation protect natural SIV hosts from disease progression.
CD8+T Cell Escape Mutations in Simian Immunodeficiency Virus SIVmac239 Cause Fitness DefectsIn Vivo, and Many Revert after Transmission
Authors: Mudd Philip A. , Ericsen Adam J. , Walsh Andrew D. , León Enrique J. , Wilson Nancy A. , Maness Nicholas J. , Friedrich Thomas C. , Watkins David I. 
Published: September 2011

ABSTRACTVirus-specific CD8+T lymphocytes select for escape mutations in human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). To assess the effects of these mutations on viral fitness, we introduced escape mutations into 30 epitopes (bound by five major histocompatibility complex class I [MHC-I] molecules) in three different viruses. Two of these MHC-I alleles are associated with elite control. Two of the three viruses demonstrated reduced fitnessin vivo, and 27% of the introduced mutations reverted. These findings suggest that T cell epitope diversity may not be such a daunting problem for the development of an HIV vaccine.
Poliovirus Unlinks TIA1 Aggregation and mRNA Stress Granule Formation
Authors: White James P. , Lloyd Richard E. 
Published: September 2011

ABSTRACT
In response to environmental stress and viral infection, mammalian cells form foci containing translationally silenced mRNPs termed stress granules (SGs). As aggregates of stalled initiation complexes, SGs are defined by the presence of translation initiation machinery in addition to mRNA binding proteins. Here, we report that cells infected with poliovirus (PV) can form SGs early that contain T-cell-restricted intracellular antigen 1 (TIA1), translation initiation factors, RNA binding proteins, and mRNA. However, this response is blocked as infection progresses, and a type of pseudo-stress granule remains at late times postinfection and contains TIA but lacks translation initiation factors, mRNA binding proteins, and most polyadenylated mRNA. This result was observed using multiple stressors, including viral infection, oxidative stress, heat shock, and endoplasmic reticulum stress. Multiple proteins required for efficient viral internal ribosome entry site-dependent translation are localized to SGs under stress conditions, providing a potential rationale for the evolution and maintenance of the SG inhibition phenotype. Further, the expression of a noncleavable form of the RasGAP-SH3 domain binding protein in PV-infected cells enables SGs whose constituents are consistent with the presence of stalled 48S translation preinitiation complexes to persist throughout infection. These results indicate that in poliovirus-infected cells, the functions of TIA self-aggregation and aggregation of stalled translation initiation complexes into stress granules are severed, leading to novel foci that contain TIA1 but lack other stress granule-defining components.
CD8
+
T Cell Immunodominance in Lymphocytic Choriomeningitis Virus Infection Is Modified in the Presence of Toll-Like Receptor Agonists
Authors: Siddiqui Sarah , Basta Sameh 
Published: September 2011

ABSTRACT

Currently, we have limited understanding of how Toll-like receptor (TLR) engagement by microbial products influences the immune response during a concurrent virus infection. In this study, we established that dual TLR2 plus TLR3 (designated TLR2+3) stimulation alters the immunodominance hierarchies of lymphocytic choriomeningitis virus (LCMV) epitopes by reducing NP396-specific CD8
+
T cell responses and shifting it to a subdominant position. The shift in immunodominance occurred due to a reduction in antigen uptake and the reduced cross-presentation of NP396, a major LCMV immunodominant epitope that is efficiently cross-presented. Moreover, the altered immunodominance was dependent on TLR stimulation occurring at the site of infection. Finally, as lipopolysaccharide failed to induce the same phenomenon, the data suggest that these findings are dependent not only on the dual engagement of the TRIF/MyD88 pathways but also on how TLR agonists activate antigen-presenting cells. Taken together, our data demonstrate a novel role for TLR ligands in regulating antiviral CD8
+
T cell responses due to the regulation of the cross-presentation of cell-associated antigens.