bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Elements in the 5′-Untranslated Region of Giardiavirus Transcript Essential for Internal Ribosome Entry Site-Mediated Translation Initiation
Authors: Garlapati Srinivas , Wang Ching C. 
Published: April 2005

ABSTRACT

Translation of uncapped giardiavirus (GLV) mRNA in
Giardia lamblia
requires the presence of a 5′-untranslated region (5′-UTR) and a viral capsid coding region. We used dicistronic viral constructs to show that the downstream 253 nucleotides (nt) of the 5′-UTR plus the initial 264-nt capsid coding region constitute an internal ribosome entry site (IRES). Predicted secondary structures in the 253-nt 5′-UTR include stem-loops U3, U4a, U4b, U4c, and U5. Chemical and enzymatic probing analysis confirmed the presence of all predicted stem-loops except U4a. Disruption of stem-loop structures U3 and U5 by site-directed mutagenesis resulted in a drastic reduction in translation of a monocistronic viral transcript, which could be restored by compensatory sequence changes. Mutations disrupting stem-loops U4b and U4c do not exert an appreciable effect on translation, but certain sequences in the U4a region and in U4b do appear to play important roles in the IRES. Structural analysis also suggests that an 8-nt U3 loop sequence (nt 147 to 154) pairs with an 8-nt downstream sequence (nt 168 to 175) to form a pseudoknot. Disruption of this pseudoknot by mutagenesis resulted in a drastic reduction in translation, which could be restored by compensatory sequence changes. This study has defined the secondary structure in the 5′-UTR of the IRES. Together with the previous results, we have now completed analysis of the entire structure of GLV IRES and fully defined the functionally essential structural elements in it.
Mitochondrial DNA Ligases of
Trypanosoma brucei
Authors: Downey Nick , Hines Jane C. , Sinha Krishna M. , Ray Dan S. 
Published: April 2005

ABSTRACT

The mitochondrial DNA of
Trypanosoma brucei
, termed kinetoplast DNA or kDNA, consists of thousands of minicircles and a small number of maxicircles catenated into a single network organized as a nucleoprotein disk at the base of the flagellum. Minicircles are replicated free of the network but still contain nicks and gaps after rejoining to the network. Covalent closure of remaining discontinuities in newly replicated minicircles after their rejoining to the network is delayed until all minicircles have been replicated. The DNA ligase involved in this terminal step in minicircle replication has not been identified. A search of kinetoplastid genome databases has identified two putative DNA ligase genes in tandem. These genes (
LIG k
α and
LIG k
β) are highly diverged from mitochondrial and nuclear DNA ligase genes of higher eukaryotes. Expression of epitope-tagged versions of these genes shows that both LIG kα and LIG kβ are mitochondrial DNA ligases. Epitope-tagged LIG kα localizes throughout the kDNA, whereas LIG kβ shows an antipodal localization close to, but not overlapping, that of topoisomerase II, suggesting that these proteins may be contained in distinct structures or protein complexes. Knockdown of the
LIG k
α mRNA by RNA interference led to a cessation of the release of minicircles from the network and resulted in a reduction in size of the kDNA networks and rapid loss of the kDNA from the cell. Closely related pairs of mitochondrial DNA ligase genes were also identified in
Leishmania major
and
Crithidia fasciculata
.
S
t
, a Truncated Envelope Protein Derived from the S Protein of Duck Hepatitis B Virus, Acts as a Chaperone for the Folding of the Large Envelope Protein
Authors: Grgacic Elizabeth V. L. , Anderson David A. 
Published: April 2005

ABSTRACT

Envelope proteins of hepadnaviruses undergo a unique folding mechanism which results in the posttranslational translocation of 50% of the large envelope protein (L) chains across the endoplasmic reticulum. This mechanism is essential for the eventual positioning of the receptor-binding domain on the surface of the virus particle and in duck hepatitis B virus (DHBV) is dependent on the small (S) envelope protein as part of the assembly process. In this study, we report the identification of a third envelope protein, S
t
, derived from the S protein and carrying functions previously attributed to S. Antibody mapping and mutagenesis studies indicated S
t
to be C terminally truncated, spanning the N-terminal transmembrane domain (TM1) plus the adjacent cysteine loop. We have previously shown that the mutation of two conserved polar residues in TM1 of S (S
AA
) eliminates L translocation and assembly. A plasmid expressing a functional equivalent of S
t
was able to rescue assembly, demonstrating that this assembly defect is due to mutations of the corresponding residues in S
t
and not in S per se. Immunofluorescence analysis showed that S
t
directly affects L protein cellular localization. These results indicate that S
t
acts as a viral chaperone for L folding, remaining associated with the DHBV envelope upon secretion. The presence of S
t
at a molar ratio of half that of L suggests that it is S
t
which regulates L translocation to 50%.
Effects of Nonstructural Proteins NS1 and NS2 of Human Respiratory Syncytial Virus on Interferon Regulatory Factor 3, NF-κB, and Proinflammatory Cytokines
Authors: Spann Kirsten M. , Tran Kim C. , Collins Peter L. 
Published: April 2005

ABSTRACT
Human respiratory syncytial virus (HRSV) is the leading cause of serious pediatric acute respiratory tract infections, and a better understanding is needed of the host response to HRSV and its attenuated vaccine derivatives. It has been shown previously that HRSV nonstructural proteins 1 and 2 (NS1 and NS2) inhibit the induction of alpha/beta interferon (IFN-α/β) in A549 cells and human macrophages. Two principal transcription factors for the early IFN-β and -α1 response are interferon regulatory factor 3 (IRF-3) and nuclear factor κB (NF-κB). At early times postinfection, wild-type HRSV and the NS1/NS2 deletion mutants were very similar in the ability to activate IRF-3. However, once NS1 and NS2 were expressed significantly, they acted cooperatively to suppress activation and nuclear translocation of IRF-3. Since these viruses differed greatly in the induction of IFN-α/β, NF-κB activation was evaluated in Vero cells, which lack the structural genes for IFN-α/β and would preclude confounding effects of IFN-α/β. This showed that deletion of the NS2 gene sharply reduced the ability of HRSV to induce activation of NF-κB. Since recombinant HRSVs from which the NS1 or NS2 genes have been deleted are being developed as vaccine candidates, we investigated whether the changes in activation of host transcription factors and increased IFN-α/β production had an effect on the epithelial production of proinflammatory factors. Viruses lacking NS1 and/or NS2 stimulated modestly lower production of RANTES (Regulated on Activation Normal T-cell Expressed and Secreted), interleukin 8, and tumor necrosis factor alpha compared to wild-type recombinant RSV, supporting their use as attenuated vaccine candidates.
Highly Protective In Vivo Function of Cytomegalovirus IE1 Epitope-Specific Memory CD8 T Cells Purified by T-Cell Receptor-Based Cell Sorting
Authors: Pahl-Seibert Marcus-Folker , Juelch Markus , Podlech Jürgen , Thomas Doris , Deegen Petra , Reddehase Matthias J. , Holtappels Rafaela 
Published: April 2005

ABSTRACTReconstitution of antiviral CD8 T cells is essential for controlling cytomegalovirus (CMV) infection after bone marrow transplantation. Accordingly, polyclonal CD8 T cells derived from BALB/c mice infected with murine CMV protect immunocompromised adoptive transfer recipients against CMV disease. The protective population comprises CD8 T cells with T-cell receptors (TCRs) specific for defined and for as-yet-unknown viral epitopes, as well as a majority of nonprotective cells with unrelated specificities. Defined epitopes include IE1/m123 and m164, which are immunodominant in terms of the magnitude of the CD8 T-cell response, and a panel of subordinate epitopes (m04, m18, M45, M83, and M84). While cytolytic T-lymphocyte lines (CTLLs) were shown to be protective regardless of the immunodominance of the respective epitope, the individual contributions of in vivo resident epitope-specific CD8 T cells to the antiviral control awaited investigation. The IE1 peptide 168-YPHFMPTNL-176 is generated from the immediate-early protein 1 (IE1) (pp89/76) of murine CMV and is presented by the major histocompatibility complex class I (MHC-I) molecule Ld. To quantitate its contribution to the protective potential of a CD8-T memory (CD8-TM) cell population, IE1-TCR+and IE1-TCR−CD8-TMcells were purified by epitope-specific cell sorting with IE1 peptide-loaded MHC-immunoglobulin G1 dimers as ligands of cognate TCRs. Of relevance for clinical approaches to an adoptive cellular immunotherapy, sorted IE1 epitope-specific CD8-TMcells were found to be exceedingly protective upon adoptive transfer. Compared with CTLLs specific for the same epitope and of comparable avidity and TCR β-chain variable region (Vβ)-defined polyclonality, sorted CD8-TMcells proved to be superior by more than 2 orders of magnitude.
Cross-Reactive Cytotoxic T Lymphocytes against Human Immunodeficiency Virus Type 1 Protease and Gamma Interferon-Inducible Protein 30
Authors: Mason R. D. , Bowmer M. I. , Howley C. M. , Grant M. D. 
Published: April 2005

ABSTRACTThe gamma interferon (IFN-γ)-inducible protein 30 (IP-30) signal peptide −11 to −3 (LLDVPTAAV) is a prominent self peptide expressed with the class I human histocompatibility leukocyte antigen A2 (HLA-A2). Stimulation of peripheral blood mononuclear cells (PBMC) from HLA-A2 human immunodeficiency virus type 1 (HIV-1)-infected individuals with an HLA-A2-restricted HIV protease (PR) peptide 76-84 (LVGPTPVNI) activated cytotoxic T lymphocytes (CTL) against the IP-30 signal peptide. Since HIV-1 PR 76-84 stimulated CD8+T cells from these individuals to secrete IFN-γ, we tested whether the activation of IP-30-specific CTL in vitro resulted from T-cell cross-reactivity or from up-regulation of IP-30 by IFN-γ. Neither high levels of exogenous IFN-γ nor incubation of PBMC with other HIV peptides triggering substantial IFN-γ release activated IP-30-specific CTL. Although the IP-30 signal peptide did not stimulate IFN-γ release from freshly isolated PBMC, it activated CTL in vitro against itself and HIV PR 76-84. Peptide-stimulated IFN-γ release, cold target inhibition, and HLA-A2/immunoglobulin dimer-mediated binding and depletion of effector cells all indicated that in vitro stimulation with HIV PR 76-84 or the IP-30 signal peptide activated a comparable population of cross-reactive effector cells. Neither IP-30 nor HIV PR 76-84 activated CTL against themselves following in vitro stimulation of PBMC from non-HIV-infected HLA-A2 individuals. Peptide titrations indicated higher-avidity T-cell interactions with HIV PR 76-84 than with the IP-30 signal peptide. These data indicate that HIV PR 76-84 is a heteroclitic variant of the IP-30 signal peptide −11 to −3, which has implications for immune memory and autoimmunity.
Rift Valley Fever Virus Nonstructural Protein NSs Promotes Viral RNA Replication and Transcription in a Minigenome System
Authors: Ikegami Tetsuro , Peters C. J. , Makino Shinji 
Published: April 2005

ABSTRACT

Rift Valley fever virus
(RVFV), which belongs to the genus
Phlebovirus
, family
Bunyaviridae
, has a tripartite negative-strand genome (S, M, and L segments) and is an important mosquito-borne pathogen for domestic animals and humans. We established an RVFV T7 RNA polymerase-driven minigenome system in which T7 RNA polymerase from an expression plasmid drove expression of RNA transcripts for viral proteins and minigenome RNA transcripts carrying a reporter gene between both termini of the M RNA segment in 293T cells. Like other viruses of the
Bunyaviridae
family, replication and transcription of the RVFV minigenome required expression of viral N and L proteins. Unexpectedly, the coexpression of an RVFV nonstructural protein, NSs, with N and L proteins resulted in a significant enhancement of minigenome RNA replication. Coexpression of NSs protein with N and L proteins also enhanced minigenome mRNA transcription in the cells expressing viral-sense minigenome RNA transcripts. NSs protein expression increased the RNA replication of minigenomes that originated from S and L RNA segments. Enhancement of minigenome RNA synthesis by NSs protein occurred in cells lacking alpha/beta interferon (IFN-α/β) genes, indicating that the effect of NSs protein on minigenome RNA replication was unrelated to a putative NSs protein-induced inhibition of IFN-α/β production. Our finding that RVFV NSs protein augmented minigenome RNA synthesis was in sharp contrast to reports that Bunyamwera virus (genus
Bunyavirus
) NSs protein inhibits viral minigenome RNA synthesis, suggesting that RVFV NSs protein and Bunyamwera virus NSs protein have distinctly different biological roles in viral RNA synthesis.
Peptide Mimetics of Gamma Interferon Possess Antiviral Properties against Vaccinia Virus and Other Viruses in the Presence of Poxvirus B8R Protein
Authors: Ahmed Chulbul M. I. , Burkhart Marjorie A. , Subramaniam Prem S. , Mujtaba Mustafa G. , Johnson Howard M. 
Published: April 2005

ABSTRACTWe have developed peptide mimetics of gamma interferon (IFN-γ) that play a direct role in the activation and nuclear translocation of STAT1α transcription factor. These mimetics do not act through recognition by the extracellular domain of IFN-γ receptor but rather bind to the cytoplasmic domain of the receptor chain 1, IFNGR-1, and thereby initiate the cellular signaling. Thus, we hypothesized that these mimetics would bypass the poxvirus virulence factor B8R protein that binds to intact IFN-γ and prevents its interaction with the receptor. Human and murine IFN-γ mimetic peptides were introduced into an adenoviral vector for intracellular expression. Murine IFN-γ mimetic peptide was also expressed via chemical synthesis with an attached lipophilic group for penetration of cell plasma membrane. In contrast to intact human IFN-γ, the mimetics did not bind poxvirus B8R protein, a homolog of the IFN-γ receptor extracellular domain. Expression of B8R protein in WISH cells did not block the antiviral effect of the mimetics against encephalomyocarditis or vesicular stomatitis virus, while the antiviral activity of human IFN-γ was neutralized. Consistent with the antiviral activity, the upregulation of MHC class I molecules on WISH cells by the IFN-γ mimetics was not affected by B8R protein, while IFN-γ-induced upregulation was blocked. Finally, the mimetics, but not IFN-γ, inhibited vaccinia virus replication in African green monkey kidney BSC-40 cells. The data presented demonstrate that small peptide mimetics of IFN-γ can avoid the B8R virulence factor for poxviruses and, thus, are potential candidates for antivirals against smallpox virus.
A 7-Yr Climatological Study of Land Breezes over the Florida Spaceport
Authors: Case Jonathan L. , Wheeler Mark M. , Manobianco John , Weems Johnny W. , Roeder William P. 
Published: April 2005

Abstract
Seven years of wind and temperature data from a high-resolution network of 44 towers at the Kennedy Space Center and Cape Canaveral Air Force Station were used to develop an objective method for identifying land breezes, which are defined as seaward-moving wind shift lines in this study. The favored meteorological conditions for land breezes consisted of surface high pressure in the vicinity of the Florida peninsula, mainly clear skies, and light synoptic onshore flow and/or the occurrence of a sea breeze during the afternoon preceding a land breeze. The land breeze characteristics are examined for two events occurring under different weather regimes—one with light synoptic onshore flow and no daytime sea breeze, and another following a daytime sea breeze under a prevailing offshore flow. Land breezes were found to occur over east-central Florida in all months of the year and had varied onset times and circulation depths. Land breezes were most common in the spring and summer months and least common in the winter. The average onset times were ∼4–5 h after sunset from May to July and ∼6.5–8 h after sunset from October to January. Land breezes typically moved from the west or southwest during the spring and summer, from the northwest in the autumn, and nearly equally from all directions in the winter. Shallow land breezes (&lt;150-m depth) were typically not associated with the afternoon sea breeze and behaved like density currents, exhibiting the largest temperature decreases and latest onset times. Deep land breezes (&gt;150-m depth) were most often preceded by an afternoon sea breeze, had the smallest horizontal temperature gradients, and experienced a mean onset time that is 4 h earlier than that of shallow land breezes.
A Very Large, Spontaneous Stratospheric Sudden Warming in a Simple AGCM: A Prototype for the Southern Hemisphere Warming of 2002?
Authors: Kushner Paul J. , Polvani Lorenzo M. 
Published: April 2005

Abstract
An exceptionally strong stratospheric sudden warming (SSW) that spontaneously occurs in a very simple stratosphere–troposphere AGCM is discussed. The model is a dry, hydrostatic, primitive equation model without planetary stationary waves. Transient baroclinic wave–wave interaction in the troposphere thus provides the only source of upward-propagating wave activity into the stratosphere. The model’s SSW is grossly similar to the Southern Hemisphere major SSW of 2002: it occurs after weaker warmings “precondition” the polar vortex for breaking, it involves a split of the polar vortex, and it has a downward-propagating signature. These similarities suggest that the Southern Hemisphere SSW of 2002 might itself have been caused by transient baroclinic wave–wave interaction. The simple model used for this study also provides some insight into how often such extreme events might occur. The frequency distribution of SSWs in the model has exponential, as opposed to Gaussian, tails. This suggests that very large amplitude SSWs, though rare, might occur with higher frequency than might be naively expected.
Ground-Based DOAS Measurements of Stratospheric Trace Gases at Two Antarctic Stations during the 2002 Ozone Hole Period
Authors: Frieß U. , Kreher K. , Johnston P. V. , Platt U. 
Published: April 2005

Abstract
Compared to recent years, the development of the Antarctic ozone hole in 2002 showed very unusual dynamical features. The midwinter polar vortex was one of the smallest observed during the past decade. Driven by planetary waves, the vortex showed a strong asymmetry in early spring. A large air mass separated in late September, leaving what was previously a small vortex even smaller. Furthermore, stratospheric temperatures exceeded the polar stratospheric cloud (PSC) threshold earlier than in previous years, leading to a decrease in halogen activation by heterogeneous surface reactions.
Ground-based observation of stratospheric trace gases in austral spring of 2001 and 2002 using passive Differential Optical Absorption Spectroscopy (DOAS) observations of zenith-scattered sunlight in the UV and visible wavelength region (320–650 nm) are presented. Using DOAS measurements of ozone, NO2, BrO, and OClO at two different Antarctic sites, Neumayer Station (70°S, 8°W) and Arrival Heights (78°S, 167°E), the chemical composition of the stratosphere is investigated under the unusual conditions of the 2002 ozone hole period and compared to the more typical observations of the previous year (2001).
Antarctic Ozone Transport and Depletion in Austral Spring 2002
Authors: Siegmund Peter , Eskes Henk , van Velthoven Peter 
Published: April 2005

Abstract
The ozone budget in the Antarctic region during the stratospheric warming in 2002 is studied, using ozone analyses from the Royal Netherlands Meteorological Institute (KNMI) ozone-transport and assimilation model called TM3DAM. The results show a strong poleward ozone mass flux during this event south of 45°S between about 20 and 40 hPa, which is about 5 times as large as the ozone flux in 2001 and 2000, and is dominated by eddy transport. Above 10 hPa, there exists a partially compensating equatorward ozone flux, which is dominated by the mean meridional circulation. During this event, not only the ozone column but also the ozone depletion rate in the Antarctic region, computed as a residual from the total ozone tendency and the ozone mass flux into this region, is large. The September–October integrated ozone depletion in 2002 is similar to that in 2000 and larger than that in 2001. Simulations for September 2002 with and without ozone assimilation and parameterized ozone chemistry indicate that the parameterized ozone chemistry alone is able to produce the evolution of the ozone layer in the Antarctic region in agreement with observations. A comparison of the ozone loss directly computed from the model’s chemistry parameterization with the residual ozone loss in a simulation with parameterized chemistry but without ozone assimilation shows that the numerical error in the residual ozone loss is small.
Interannual Variations of the Seasonal March in the Southern Hemisphere Stratosphere for 1979–2002 and Characterization of the Unprecedented Year 2002
Authors: Hio Yasuko , Yoden Shigeo 
Published: April 2005

Abstract
Dynamical features of the interannual variations of the seasonal march in the Southern Hemisphere stratosphere are investigated with the NCEP–NCAR reanalysis dataset from 1979 to 2002, and the unprecedented year 2002, in which a major stratosphere sudden warming occurred, is characterized by comparing it with the other 23 yr.
A multiple empirical orthogonal function analysis of the stratospheric mean zonal wind and a composite analysis based on the principal component of the leading mode show that the interannual variations are characterized by early or late deceleration of the polar-night jet, which is well correlated with the variation of a time-averaged upward Eliassen–Palm (EP) flux in the lower stratosphere. The stronger wave activity in the lower stratosphere is associated with the earlier “shift down” of the jet. The composite difference of the stratospheric mean zonal wind can be traced down to the lower troposphere in September and October. These features are consistent with the variations of the Southern Hemisphere annular mode, although the main disturbance to maintain the variations is different between the stratosphere and troposphere.
Some scatter diagrams show the extreme situation of the year 2002. It is far from the cluster of the other 23 yr, but the large deviation in 2002 is consistent with the tendency of the fluctuations in the other years except for its extreme nature.