bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Composition of Human Immunodeficiency Virus Type 1 in Cerebrospinal Fluid and Blood without Treatment and during Failing Antiretroviral Therapy
Authors: Strain M. C. , Letendre S. , Pillai S. K. , Russell T. , Ignacio C. C. , Günthard H. F. , Good B. , Smith D. M. , Wolinsky S. M. , Furtado M. , Marquie-Beck J. , Durelle J. , Grant I. , Richman D. D. , Marcotte T. , McCutchan J. A. , Ellis R. J. , Wong J. K. 
Published: January 2005

ABSTRACTHuman immunodeficiency virus (HIV) infection of the central nervous system (CNS) is a significant cause of morbidity. The requirements for HIV adaptation to the CNS for neuropathogenesis and the value of CSF virus as a surrogate for virus activity in brain parenchyma are not well established. We studied 18 HIV-infected subjects, most with advanced immunodeficiency and some neurocognitive impairment but none with evidence of opportunistic infection or malignancy of the CNS. Clonal sequences of C2-V3 env and population sequences of pol from HIV RNA in cerebrospinal fluid (CSF) and plasma were correlated with clinical and virologic variables. Most (14 of 18) subjects had partitioning of C2-V3 sequences according to compartment, and 9 of 13 subjects with drug resistance exhibited discordant resistance patterns between the two compartments. Regression analyses identified three to seven positions in C2-V3 that discriminated CSF from plasma HIV. The presence of compartmental differences at one or more of the identified positions in C2-V3 was highly associated with the presence of discordant resistance (P= 0.007), reflecting the autonomous replication of HIV and the independent evolution of drug resistance in the CNS. Discordance of resistance was associated with severity of neurocognitive deficits (P= 0.07), while low nadir CD4 counts were linked both to the severity of neurocognitive deficits and to discordant resistance patterns (P= 0.05 and 0.09, respectively). These observations support the study of CSF HIV as an accessible surrogate for HIV virions in the brain, confirm the high frequency of discordant resistance in subjects with advanced disease in the absence of opportunistic infection or malignancy of the CNS, and begin to identify genetic patterns in HIVenvassociated with adaptation to the CNS.
Characterization of Snakehead Rhabdovirus Infection in Zebrafish (
Danio rerio
)
Authors: Phelan Peter E. , Pressley Meagan E. , Witten P. Eckhard , Mellon Mark T. , Blake Sharon , Kim Carol H. 
Published: January 2005

ABSTRACT

The zebrafish,
Danio rerio
, has become recognized as a valuable model for the study of development, genetics, and toxicology. Recently, the zebrafish has been recognized as a useful model for infectious disease and immunity. In this study, the pathogenesis and antiviral immune response of zebrafish to experimental snakehead rhabdovirus (SHRV) infection was characterized. Zebrafish 24 h postfertilization to 30 days postfertilization were susceptible to infection by immersion in 10
6
50% tissue culture infective doses (TCID
50
) of SHRV/ml, and adult zebrafish were susceptible to infection by intraperitoneal (i.p.) injection of 10
5
TCID
50
of SHRV/ml. Mortalities exceeded 40% in infected fish, and clinical presentation of infection included petechial hemorrhaging, redness of the abdomen, and erratic swim behavior. Virus reisolation and reverse transcription-PCR analysis of the viral nucleocapsid gene confirmed the presence of SHRV. Histological sections of moribund embryonic and juvenile fish revealed necrosis of the pharyngeal epithelium and liver, in addition to congestion of the swim bladder by cell debris. Histopathology in adult fish injected i.p. was confined to the site of injection. The antiviral response in zebrafish was monitored by quantitative real-time PCR analysis of zebrafish interferon (IFN) and Mx expression. IFN and Mx levels were elevated in zebrafish exposed to SHRV, although expression and intensity differed with age and route of infection. This study is the first to examine the pathogenesis of SHRV infection in zebrafish. Furthermore, this study is the first to describe experimental infection of zebrafish embryos with a viral pathogen, which will be important for future experiments involving targeted gene disruption and forward genetic screens.
Nitric Oxide Inhibits the Replication Cycle of Severe Acute Respiratory Syndrome Coronavirus
Authors: Åkerström Sara , Mousavi-Jazi Mehrdad , Klingström Jonas , Leijon Mikael , Lundkvist Åke , Mirazimi Ali 
Published: January 2005

ABSTRACT

Nitric oxide (NO) is an important signaling molecule between cells which has been shown to have an inhibitory effect on some virus infections. The purpose of this study was to examine whether NO inhibits the replication cycle of the severe acute respiratory syndrome coronavirus (SARS CoV) in vitro. We found that an organic NO donor,
S
-nitroso-
N
-acetylpenicillamine, significantly inhibited the replication cycle of SARS CoV in a concentration-dependent manner. We also show here that NO inhibits viral protein and RNA synthesis. Furthermore, we demonstrate that NO generated by inducible nitric oxide synthase, an enzyme that produces NO, inhibits the SARS CoV replication cycle.
G→A Hypermutation in Protease and Reverse Transcriptase Regions of Human Immunodeficiency Virus Type 1 Residing in Resting CD4
+
T Cells In Vivo
Authors: Kieffer Tara L. , Kwon Patty , Nettles Richard E. , Han Yefei , Ray Stuart C. , Siliciano Robert F. 
Published: January 2005

ABSTRACT

In vitro studies have shown that the host cytidine deaminase APOBEC3G causes lethal hypermutation in human immunodeficiency virus type 1 reverse transcripts unless its incorporation into virions is blocked by Vif. By examining stably archived sequences in resting CD4
+
T cells, we show that hypermutation occurs in most if not all infected individuals. Hypermutated sequences comprised >9% of archived species in resting CD4
+
T cells but were not found in plasma virus. Mutations occurred in predicted contexts, with notable hotspots. Thus, defects in Vif function in vivo give rise to hypermutated viral genomes that can be integrated but do not produce progeny viruses.
Thermal Effects of Urban Canyon Structure on the Nocturnal Heat Island: Numerical Experiment Using a Mesoscale Model Coupled with an Urban Canopy Model
Authors: Kusaka Hiroyuki , Kimura Fujio 
Published: January 2005

Abstract
A single-layer urban canopy model is incorporated into a simple two-dimensional atmospheric model in order to examine the individual impacts of anthropogenic heating, a large heat capacity, and a small sky-view factor on mesoscale heat island formation. It is confirmed that a nocturnal heat island on a clear, calm summer day results from the difference in atmospheric stability between a city and its surroundings. The difference is caused by anthropogenic heating and the following two effects of urban canyon structure: (i) a larger heat capacity due to the walls and (ii) a smaller sky-view factor. Sensitivity experiments show that the anthropogenic heating increases the surface air temperature though the day. (This factor strongly affects the nocturnal temperature, and the maximum increase of 0.67°C occurs at 0500 LST.) The larger heat capacity due to the walls decreases the daytime temperature and increases the nocturnal temperature. (The maximum increase of 0.39°C occurs at 0600 LST.) The smaller sky-view factor increases the temperature though the day, particularly during the first several hours after sunset. (The maximum increase of 0.52°C occurs at midnight.) In urban areas, this factor results in uniform cooling that occurs at a constant rate. The impact of the canyon structure is shown to be as significant as anthropogenic heating.
An Organizing Center for Thermohaline Excitability
Authors: Abshagen Jan , Timmermann Axel 
Published: January 2005

Abstract
The bifurcation behavior of a conceptual heat–salt oscillator model is analyzed by means of numerical continuation methods. A global (homoclinic) bifurcation acts as an organizing center for the dynamics of the simplified convective model. It originates from a codimension-2 bifurcation in an extended parameter space. Comparison with earlier work by Cessi shows that the intriguing stochastic thermohaline excitability can be understood from the bifurcation structure of the model. It is argued that global bifurcations may play a crucial role in determining long-term variability of the thermohaline circulation.
Dynamic Potential Vorticity Initialization and the Diagnosis of Mesoscale Motion
Authors: Viúdez Álvaro , Dritschel David G. 
Published: January 2005

Abstract
A new method for diagnosing the balanced three-dimensional velocity from a given density field in mesoscale oceanic flows is described. The method is referred to as dynamic potential vorticity initialization (PVI) and is based on the idea of letting the inertia–gravity waves produced by the initially imbalanced mass density and velocity fields develop and evolve in time while the balanced components of these fields adjust during the diagnostic period to a prescribed initial potential vorticity (PV) field. Technically this is achieved first by calculating the prescribed PV field from given density and geostrophic velocity fields; then the PV anomaly is multiplied by a simple time-dependent ramp function, initially zero but tending to unity over the diagnostic period. In this way, the PV anomaly builds up to the prescribed anomaly. During this time, the full three-dimensional primitive equations—except for the PV equation—are integrated for several inertial periods. At the end of the diagnostic period the density and velocity fields are found to adjust to the prescribed PV field and the approximate balanced vortical motion is obtained. This adjustment involves the generation and propagation of fast, small-amplitude inertia–gravity waves, which appear to have negligible impact on the final near-balanced motion. Several practical applications of this method are illustrated. The highly nonlinear, complex breakup of baroclinically unstable currents into eddies, fronts, and filamentary structures is examined. The capability of the method to generate the balanced three-dimensional motion is measured by analyzing the ageostrophic horizontal and vertical velocity—the latter is the velocity component most sensitive to initialization, and one for which a quasigeostrophic diagnostic solution is available for comparison purposes. The authors find that the diagnosed fields are closer to the actual fields than are either the geostrophic or the quasigeostrophic approximations. Dynamic PV initialization thus appears to be a promising way of improving the diagnosis of balanced mesoscale motions.
Superantigen recognition by HLA class II on monocytes up-regulates toll-like receptor 4 and enhances proinflammatory responses to endotoxin
Authors: Hopkins Philip A. , Fraser John D. , Pridmore Alison C. , Russell Hugh H. , Read Robert C. , Sriskandan Shiranee 
Published: January 2005

AbstractThe devastating systemic effects of bacterial superantigens may be explained by powerful proinflammatory synergy with lipopolysaccharide (LPS). However, the mechanism underlying this phenomenon remains unclear and has never been investigated in humans. Specifically, there is no known link between superantigen-induced immune effects and the pattern recognition of LPS at toll-like receptor 4 (TLR4). Here we show that bacterial superantigens induce rapid transcription and increased membrane expression of TLR4 in primary human monocytes by ligation of major histocompatibility complex (MHC) class II. We also demonstrate that superantigens are solely responsible for monocyte TLR4 up-regulation induced by products from Gram-positive bacteria. In parallel with enhanced TLR4 expression, priming of purified monocytes or mixed peripheral blood mononuclear cells with superantigens significantly enhanced the induction of proinflammatory cytokines by known TLR4 ligands. Staphylococcal enterotoxin A constructs containing targeted mutations were used to demonstrate a requirement for MHC class II ligation in both TLR4 up-regulation and enhanced responses to endotoxin. In contrast to results from animal models, superantigen-endotoxin interaction was not dependent on T-cell receptor ligation by superantigen or interferon gamma production. Pattern recognition of bacterial superantigens by MHC class II receptors may exacerbate the proinflammatory response of monocytes to Gram-negative infection or endotoxin by up-regulation of TLR4.
A systematic scan of interactions with tyrosine motifs in the erythropoietin receptor using a mammalian 2-hybrid approach
Authors: Montoye Tony , Lemmens Irma , Catteeuw Dominiek , Eyckerman Sven , Tavernier Jan 
Published: January 2005

AbstractSignaling via the erythropoietin receptor (EpoR) depends on the interaction of several proteins with phosphorylated tyrosine-containing motifs in its cytosolic domain. Detailed mapping of these interactions is required for an accurate insight into Epo signaling. We recently developed a mammalian protein-protein interaction trap (MAPPIT), a cytokine receptor-based 2-hybrid method that operates in intact Hek293-T mammalian cells. As baits, we used intracellular segments of the EpoR containing 1 or 2 tyrosines. Several known signaling molecules, including cytokine-inducible SH2-containing protein (CIS), suppressor of cytokine signaling-2 (SOCS2), phosphatidylinositol 3′-kinase (PI3-K), phospholipase C-γ (PLC-γ), and signal transducer and activator of transcription 5 (STAT5) were used as prey. We also extended the MAPPIT method to enable interaction analysis with wild-type EpoR. In this relay MAPPIT approach, instead of using isolated EpoR fragments as bait, we used the full-length EpoR itself as a “receptor bait.” Finally, we introduced MAPPIT in the erythroleukemic TF-1 cell line, which is a more natural setting of the EpoR. With these strategies several known interactions with the EpoR were analyzed and evidence for new interactions was obtained.
Gene expression profiling reveals novel TGFβ targets in adult lung fibroblasts
Authors: Renzoni Elisabetta A , Abraham David J , Howat Sarah , Shi-Wen Xu , Sestini Piersante , Bou-Gharios George , Wells Athol U , Veeraraghavan Srihari , Nicholson Andrew G , Denton Christopher P , Leask Andrew , Pearson Jeremy D , Black Carol M , Welsh Kenneth I , du Bois Roland M 
Published: January 2005

Abstract
Background
Transforming growth factor beta (TGFβ), a multifunctional cytokine, plays a crucial role in the accumulation of extracellular matrix components in lung fibrosis, where lung fibroblasts are considered to play a major role. Even though the effects of TGFβ on the gene expression of several proteins have been investigated in several lung fibroblast cell lines, the global pattern of response to this cytokine in adult lung fibroblasts is still unknown.

Methods
We used Affymetrix oligonucleotide microarrays U95v2, containing approximately 12,000 human genes, to study the transcriptional profile in response to a four hour treatment with TGFβ in control lung fibroblasts and in fibroblasts from patients with idiopathic and scleroderma-associated pulmonary fibrosis. A combination of the Affymetrix change algorithm (Microarray Suite 5) and of analysis of variance models was used to identify TGFβ-regulated genes. Additional criteria were an average up- or down- regulation of at least two fold.

Results
Exposure of fibroblasts to TGFβ had a profound impact on gene expression, resulting in regulation of 129 transcripts. We focused on genes not previously found to be regulated by TGFβ in lung fibroblasts or other cell types, including nuclear co-repressor 2, SMAD specific E3 ubiquitin protein ligase 2 (SMURF2), bone morphogenetic protein 4, and angiotensin II receptor type 1 (AGTR1), and confirmed the microarray results by real time-PCR. Western Blotting confirmed induction at the protein level of AGTR1, the most highly induced gene in both control and fibrotic lung fibroblasts among genes encoding for signal transduction molecules.
Upregulation of AGTR1 occurred through the MKK1/MKK2 signalling pathway. Immunohistochemical staining showed AGTR1 expression by lung fibroblasts in fibroblastic foci within biopsies of idiopathic pulmonary fibrosis.

Conclusions
This study identifies several novel TGFβ targets in lung fibroblasts, and confirms with independent methods the induction of angiotensin II receptor type 1, underlining a potential role for angiotensin II receptor 1 antagonism in the treatment of lung fibrosis.
Coccidioides posadasii infection alters the expression of pulmonary surfactant proteins (SP)-A and SP-D
Authors: Awasthi Shanjana , Magee D Mitchell , Coalson Jacqueline J 
Published: January 2005

Abstract
Background
Coccidioidomycosis or Valley Fever is caused by Coccidioides in Southwest US and Central America. Primary pulmonary infection is initiated by inhalation of air-borne arthroconidia. Since, lung is the first organ that encounters arthroconidia, different components of the pulmonary innate immune system may be involved in the regulation of host defense. Pulmonary surfactant proteins (SP)-A and SP-D have been recognized to play an important role in binding and phagocytosis of various microorganisms, but their roles in Coccidioides infection are not known.

Methods
In this study, we studied the changes in amounts of pulmonary SP-A, SP-D and phospholipid in murine model of Coccidioides posadasii infection, and binding of SP-A and SP-D to Coccidioidal antigens. Mice were challenged intranasally with a lethal dose of C. posadasii (n = 30 arthroconidia) and bronchoalveolar lavage fluid (BALF) samples were collected on day 10, post infection. In another group of animals, mice were immunized with protective formalin killed spherule (FKS) vaccine prior to infection. The concentrations of BALF SP-A, SP-D, total phospholipid were measured using enzyme linked immunosorbent assay and biochemical assays.

Results
We found that in lavage fluid samples of C. posadasii infected mice, the concentrations of total phospholipid, SP-A and SP-D were 17 % (SEM 3.5, p < 0.001), 38 % (SEM 5.8, p < 0.001) and 4 % (SEM 1.3, p < 0.001) of those in lavage fluid samples of non-infected control mice, respectively. However, the concentrations of SP-A and SP-D remained unchanged in BALF samples of C. posadasii protected mice after immunization with FKS vaccine. Also, we found that both SP-A and SP-D bind to Coccidiodal antigens.

Conclusion
Our results suggest that the C. posadasii infection perturbs the pulmonary SP-A, SP-D, and phospholipids, potentially enabling the disease progression and promoting fungal dissemination.
Modulation of epithelial sodium channel (ENaC) expression in mouse lung infected with Pseudomonas aeruginosa
Authors: Dagenais André , Gosselin Diane , Guilbault Claudine , Radzioch Danuta , Berthiaume Yves 
Published: January 2005

Abstract
Background
The intratracheal instillation of Pseudomonas aeruginosa entrapped in agar beads in the mouse lung leads to chronic lung infection in susceptible mouse strains. As the infection generates a strong inflammatory response with some lung edema, we tested if it could modulate the expression of genes involved in lung liquid clearance, such as the α, β and γ subunits of the epithelial sodium channel (ENaC) and the catalytic subunit of Na+-K+-ATPase.

Methods
Pseudomonas aeruginosa entrapped in agar beads were instilled in the lung of resistant (BalB/c) and susceptible (DBA/2, C57BL/6 and A/J) mouse strains. The mRNA expression of ENaC and Na+-K+-ATPase subunits was tested in the lung by Northern blot following a 3 hours to 14 days infection.

Results
The infection of the different mouse strains evoked regulation of α and β ENaC mRNA. Following Pseudomonas instillation, the expression of αENaC mRNA decreased to a median of 43% on days 3 and 7 after infection and was still decreased to a median of 45% 14 days after infection (p < 0.05). The relative expression of βENaC mRNA was transiently increased to a median of 241%, 24 h post-infection before decreasing to a median of 43% and 54% of control on days 3 and 7 post-infection (p < 0.05). No significant modulation of γENaC mRNA was detected although the general pattern of expression of the subunit was similar to α and β subunits. No modulation of α1Na+-K+-ATPase mRNA, the catalytic subunit of the sodium pump, was recorded. The distinctive expression profiles of the three subunits were not different, between the susceptible and resistant mouse strains.

Conclusions
These results show that Pseudomonas infection, by modulating ENaC subunit expression, could influence edema formation and clearance in infected lungs.
Identification of α-type subunits of the Xenopus 20S proteasome and analysis of their changes during the meiotic cell cycle
Authors: Wakata Yuka , Tokumoto Mika , Horiguchi Ryo , Ishikawa Katsutoshi , Nagahama Yoshitaka , Tokumoto Toshinobu 
Published: January 2005

Abstract
Background
The 26S proteasome is the proteolytic machinery of the ubiquitin-dependent proteolytic system responsible for most of the regulated intracellular protein degradation in eukaryotic cells. Previously, we demonstrated meiotic cell cycle dependent phosphorylation of α4 subunit of the 26S proteasome. In this study, we analyzed the changes in the spotting pattern separated by 2-D gel electrophoresis of α subunits during Xenopus oocyte maturation.

Results
We identified cDNA for three α-type subunits (α1, α5 and α6) of Xenopus, then prepared antibodies specific for five subunits (α1, α3, α5, α6, and α7). With these antibodies and previously described monoclonal antibodies for subunits α2 and α4, modifications to all α-type subunits of the 26S proteasome during Xenopus meiotic maturation were examined by 2D-PAGE. More than one spot for all subunits except α7 was identified. Immunoblot analysis of 26S proteasomes purified from immature and mature oocytes showed a difference in the blots of α2 and α4, with an additional spot detected in the 26S proteasome from immature oocytes (in G2-phase).

Conclusions
Six of α-type subunits of the Xenopus 26S proteasome are modified in Xenopus immature oocytes and two subunits (α2 and α4) are modified meiotic cell cycle-dependently.