bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased Multinucleoside Drug Resistance and Decreased Replicative Capacity of a Human Immunodeficiency Virus Type 1 Variant with an 8-Amino-Acid Insert in the Reverse Transcriptase
Authors: van der Hoek Lia , Back Nicole , Jebbink Maarten F. , de Ronde Anthony , Bakker Margreet , Jurriaans Suzanne , Reiss Peter , Parkin Neil , Berkhout Ben 
Published: February 2005

ABSTRACT
Resistance to antiretroviral drugs is generally conferred by specific amino acid substitutions, rather than insertions or deletions, in reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1). The exception to these findings is the amino acid insertions found in the β3-β4 loop of the RT enzyme in response to treatment with nucleoside reverse transcriptase inhibitors. This insert consists most commonly of two amino acids, but we describe in detail the evolution of a variant with an 8-amino-acid (aa) insert in a patient treated with zidovudine (ZDV) and 2′-3′-dideoxycytidine (ddC). The 24-nucleotide insert is a partial duplication of local sequences but also contains a sequence segment of unknown origin. Extensive sequence analysis of longitudinal patient samples indicated that the HIV-1 population prior to the start of therapy contained not the wild-type amino acid 215T in RT but a mixture with 215D and 215C. Treatment with ZDV and subsequent ZDV-ddC combination therapy resulted in the evolution of an HIV-1 variant with a typical ZDV resistance genotype (41L, 44D, 67N, 69D, 210W, 215Y), which was slowly replaced by the insert-containing variant (41L, 44D, insert at position 69, 70R, 210W, 215Y). The latter variant demonstrated increased resistance to a wide range of drugs, indicating that the 8-aa insert augments nucleoside analogue resistance. The gain in drug resistance of the insert variant came at the expense of a reduction in replication capacity when assayed in the absence of drugs. We compared these data with the resistance and replication properties of 133 insert-containing sequences of different individuals present in the ViroLogic database and found that the size and actual sequence of the insert at position 69 influence the level of resistance to nucleoside analogues.
Stable Secondary Structure near the Nicking Site for Adeno-Associated Virus Type 2 Rep Proteins on Human Chromosome 19
Authors: Jang Ming Y. , Yarborough OrLando H. , Conyers Gary B. , McPhie Peter , Owens Roland A. 
Published: February 2005

ABSTRACT

Adeno-associated virus serotype 2 (AAV-2) can preferentially integrate its DNA into a 4-kb region of human chromosome 19, designated
AAVS1
. The nicking activity of AAV-2's Rep68 or Rep78 proteins is essential for preferential integration. These proteins nick at the viral origin of DNA replication and at a similar site within
AAVS1
. The current nicking model suggests that the strand containing the nicking site is separated from its complementary strand prior to nicking. In AAV serotypes 1 through 6, the nicking site is flanked by a sequence that is predicted to form a stem-loop with standard Watson-Crick base pairing. The region flanking the nicking site in
AAVS1
(5′-GGCGGCGGT/TGGGGCTCG-3′ [the slash indicates the nicking site]) lacks extensive potential for Watson-Crick base pairing. We therefore performed an empirical search for a stable secondary structure. By comparing the migration of radiolabeled oligonucleotides containing wild-type or mutated sequences from the
AAVS1
nicking site to appropriate standards, on native and denaturing polyacrylamide gels, we have found evidence that this region forms a stable secondary structure. Further confirmation was provided by circular dichroism analyses. We identified six bases that appear to be important in forming this putative secondary structure. Mutation of five of these bases, within the context of a double-stranded nicking substrate, reduces the ability of the substrate to be nicked by Rep78 in vitro. Four of these five bases are outside the previously recognized GTTGG nicking site motif and include parts of the CTC motif that has been demonstrated to be important for integration targeting.
Analysis of Human Cytomegalovirus
ori
Lyt Sequence Requirements in the Context of the Viral Genome
Authors: Borst Eva-Maria , Messerle Martin 
Published: February 2005

ABSTRACT

During the lytic phase of infection, replication of herpesvirus genomes initiates at the lytic origin of replication,
ori
Lyt. Many herpesviruses harbor more than one lytic origin, but so far, only one
ori
Lyt has been identified for human cytomegalovirus (HCMV). Evidence for the existence of additional lytic origins of HCMV has remained elusive. On the basis of transient replication assays with cloned viral fragments, HCMV
ori
Lyt was described as a core region of 1.5 kbp (minimal
ori
Lyt) flanked by auxiliary sequences required for maximal replication activity (complete
ori
Lyt). It remained unclear whether minimal
ori
Lyt alone can drive the replication of HCMV in the absence of its accessory regions. To investigate the sequence requirements of
ori
Lyt in the context of the viral genome, mutant genomes were constructed lacking either minimal or complete
ori
Lyt. These genomes were not infectious, suggesting that HCMV contains only one lytic origin of replication. Either minimal or complete
ori
Lyt was then ectopically reinserted into the
ori
Lyt-depleted genomes. Only the mutant genomes carrying complete
ori
Lyt led to infectious progeny. Remarkably, inversion of the 1.5-kbp core origin relative to its flanking regions resulted in a replication-defective genome. Mutant genomes carrying minimal
ori
Lyt plus the left flanking region gave rise to minifoci, but genomes harboring minimal
ori
Lyt together with the right flanking region were noninfectious. We conclude that the previously defined minimal lytic origin is not sufficient to drive replication of the HCMV genome. Rather, our results underline the importance of the accessory regions and their correct arrangement for the function of HCMV
ori
Lyt.
Long-Term Cytomegalovirus Infection Leads to Significant Changes in the Composition of the CD8+T-Cell Repertoire, Which May Be the Basis for an Imbalance in the Cytokine Production Profile in Elderly Persons
Authors: Almanzar Giovanni , Schwaiger Susanne , Jenewein Brigitte , Keller Michael , Herndler-Brandstetter Dietmar , Würzner Reinhard , Schönitzer Diether , Grubeck-Loebenstein Beatrix 
Published: February 2005

ABSTRACTIn spite of the present belief that latent cytomegalovirus (CMV) infection drives CD8+T-cell differentiation and induces premature immune senescence, no systematic studies have so far been performed to compare phenotypical and functional changes in the CD8+T-cell repertoire in CMV-infected and noninfected persons of different age groups. In the present study, number, cytokine production, and growth potential of naïve (CD45RA+CD28+), memory (CD45RA−CD28+), and effector (CD45RA+CD28−or CD45RA−CD28−) CD8+T cells were analyzed in young, middle-aged, and elderly clinically healthy persons with a positive or negative CMV antibody serology. Numbers and functional properties of CMVpp65495-503-specific CD8+T cells were also studied. We demonstrate that aging as well as CMV infection lead to a decrease in the size of the naïve CD8+T-cell pool but to an increase in the number of CD8+effector T cells, which produce gamma interferon but lack substantial growth potential. The size of the CD8+memory T-cell population, which grows well and produces interleukin-2 (IL-2) and IL-4, also increases with aging, but this increase is missing in CMV carriers. Life-long latent CMV infection seems thus to diminish the size of the naïve and the early memory T-cell pool and to drive a Th1 polarization within the immune system. This can lead to a reduced diversity of CD8 responses and to chronic inflammatory processes which may be the basis of severe health problems in elderly persons.
Importance of both the Coding and the Segment-Specific Noncoding Regions of the Influenza A Virus NS Segment for Its Efficient Incorporation into Virions
Authors: Fujii Ken , Fujii Yutaka , Noda Takeshi , Muramoto Yukiko , Watanabe Tokiko , Takada Ayato , Goto Hideo , Horimoto Taisuke , Kawaoka Yoshihiro 
Published: February 2005

ABSTRACT
The genome of influenza A virus consists of eight single-strand negative-sense RNA segments, each comprised of a coding region and a noncoding region. The noncoding region of the NS segment is thought to provide the signal for packaging; however, we recently showed that the coding regions located at both ends of the hemagglutinin and neuraminidase segments were important for their incorporation into virions. In an effort to improve our understanding of the mechanism of influenza virus genome packaging, we sought to identify the regions of NS viral RNA (vRNA) that are required for its efficient incorporation into virions. Deletion analysis showed that the first 30 nucleotides of the 3′ coding region are critical for efficient NS vRNA incorporation and that deletion of the 3′ segment-specific noncoding region drastically reduces NS vRNA incorporation into virions. Furthermore, silent mutations in the first 30 nucleotides of the 3′ NS coding region reduced the incorporation efficiency of the NS segment and affected virus replication. These results suggested that segment-specific noncoding regions together with adjacent coding regions (especially at the 3′ end) form a structure that is required for efficient influenza A virus vRNA packaging.
Identification of an Essential Domain in the Herpes Simplex Virus 1 U
L
34 Protein That Is Necessary and Sufficient To Interact with U
L
31 Protein
Authors: Liang Li , Baines Joel D. 
Published: February 2005

ABSTRACT

Previous results have indicated that the herpes simplex virus 1 U
L
31 and U
L
34 proteins interact and form a complex at the inner nuclear membranes of infected cells, where both play important roles in the envelopment of nucleocapsids at the inner nuclear membrane. In the work described here, mapping studies using glutathione
S
-transferase pull-down assays indicated that amino acids 137 to 181 of the U
L
34 protein are sufficient to mediate an interaction with the U
L
31 protein. A recombinant virus (v3480) lacking U
L
34 codons 138 to 181 was constructed. Similar to a U
L
34 null virus, v3480 failed to replicate on Vero cells and grew to a limited extent on rabbit skin cells. A U
L
34-expressing cell line restored v3480 growth and plaque formation. Similar to the localization of U
L
31 protein in cells infected with a U
L
34 null virus, the U
L
31 protein was present in the nuclei of Hep2 cells infected with v3480. Hep2 cells infected with v3480 contained the U
L
34 protein in the cytoplasm, the nucleus, and the nuclear membrane, and this was noted to be similar to the appearance of cells infected with a U
L
31 null virus. In transient expression assays, the interaction between U
L
34 amino acids 137 to 181 and the U
L
31 protein was sufficiently robust to target green fluorescent protein and emerin to intranuclear sites that contained the U
L
31 protein. These data indicate that amino acids 137 to 181 of the U
L
34 protein are (i) sufficient to mediate interactions with the U
L
31 protein in vitro and in vivo, (ii) necessary for the colocalization of U
L
31 and U
L
34 in infected cells, and (iii) essential for normal viral replication.
Complementarity in the Supramolecular Design of Arenaviruses and Retroviruses Revealed by Electron Cryomicroscopy and Image Analysis
Authors: Neuman Benjamin W. , Adair Brian D. , Burns John W. , Milligan Ronald A. , Buchmeier Michael J. , Yeager Mark 
Published: February 2005

ABSTRACT
Arenaviruses are rodent-borne agents of diseases, including potentially lethal human hemorrhagic fevers. These enveloped viruses encapsidate a bisegmented ambisense single-stranded RNA genome that can be packaged in variable copy number. Electron cryomicroscopy and image analysis of New World Pichinde and Tacaribe arenaviruses and Old World lymphocytic choriomeningitis virus revealed pleomorphic enveloped particles ranging in diameter from ∼400 to ∼2,000 Å. The surface spikes were spaced ∼100 Å apart and extended ∼90 Å from the maximum phospholipid headgroup density of the outer bilayer leaflet. Distinctive stalk and head regions extended radially ∼30 and ∼60 Å from the outer bilayer leaflet, respectively. Two interior layers of density apposed to the inner leaflet of the viral lipid bilayer were assigned as protein Z and nucleoprotein (NP) molecules on the basis of their appearance, spacing, and projected volume. Analysis of en face views of virions lacking the GP-C spikes showed reflections consistent with paracrystalline packing of the NP molecules in a lattice with edges of ∼57 and ∼74 Å. The structural proteins of retroviruses and arenaviruses assemble with similar radial density distributions, using common cellular components.
Deletion of the Second Immunoglobulin-Like Domain of Nectin-1 Alters Its Intracellular Processing and Localization and Ability To Mediate Entry of Herpes Simplex Virus
Authors: Struyf Frank , Plate Aileen E. , Spear Patricia G. 
Published: February 2005

ABSTRACT
Nectin-1 is an immunoglobulin (Ig)-like entry receptor for herpes simplex virus (HSV). Like other nectins, nectin-1 forms dimers and mediates cell adhesion through interactions with other nectins. We constructed a second-domain deletion mutant of nectin-1 (nectin-1-Δ2) to examine the role of the second Ig-like domain in HSV entry. Nectin-1-Δ2 exhibited a severely reduced ability to mediate HSV entry and accumulated in the endoplasmic reticulum but retained the ability to interact with its HSV ligand, gD. The failure of nectin-1-Δ2 to mediate HSV entry probably resulted from its failure to be transported to a membrane targeted by HSV for viral entry.
Lambda Interferon Inhibits Hepatitis B and C Virus Replication
Authors: Robek Michael D. , Boyd Bryan S. , Chisari Francis V. 
Published: February 2005

ABSTRACT
Lambda interferon (IFN-λ) induces an intracellular IFN-α/β-like antiviral response through a receptor complex distinct from the IFN-α/β receptor. We therefore determined the ability of IFN-λ to inhibit hepatitis B virus (HBV) and hepatitis C virus (HCV) replication. IFN-λ inhibits HBV replication in a differentiated murine hepatocyte cell line with kinetics and efficiency similar to IFN-α/β and does not require the expression of IFN-α/β or IFN-γ. Furthermore, IFN-λ blocked the replication of a subgenomic and a full-length genomic HCV replicon in human hepatocyte Huh7 cells. These results suggest the possibility that IFN-λ may be therapeutically useful in the treatment of chronic HBV or HCV infection.
Transient Role for CD1d-Restricted Natural Killer T Cells in the Formation of Atherosclerotic Lesions
Authors: Aslanian Ara M. , Chapman Harold A. , Charo Israel F. 
Published: February 2005

Objective—CD1d-restricted natural killer T (NKT) cells are reported to play a proatherogenic role in the development of atherosclerosis. However, the contribution of NKT cells to mature lesion formation and the effector mechanisms through which they act are unknown.Methods and Results—We measured lesion size in CD1d-null (CD1d−/−) mice on the low-density lipoprotein (LDL) receptor–deficient (LDLR−/−) genetic background after 4, 8, and 12 weeks of feeding on a Western diet. Lesions inCD1d−/−LDLR−/−mice were 47% smaller at 4 weeks thanCD1d+/+LDLR−/−controls; however, there were no differences in lesion size betweenCD1d−/−LDLR−/−andCD1d+/+LDLR−/−mice at 8 or 12 weeks. We found that although NKT cells were present in the aortic arch ofCD1d+/+LDLR−/−mice on the Western diet, no differences in mRNA abundance for Th1 or Th2 cytokines were observed betweenCD1d−/−LDLR−/−andCD1d+/+LDLR−/−mice.Conclusions—CD1d-restricted NKT cells contribute to the formation of fatty streaks; however, their influence on lesion progression is transient, and they do not significantly affect the inflammatory cytokine milieu of mature lesions.
Intracellular interaction of von Willebrand factor and factor VIII depends on cellular context: lessons from platelet-expressed factor VIII
Authors: Yarovoi Helen , Nurden Alan T. , Montgomery Robert R. , Nurden Paquita , Poncz Mortimer 
Published: February 2005

Abstract
We have previously reported that ectopically expressed factor VIII (FVIII) is stored within platelets and is released upon platelet activation. Studies by others in various cell lines have suggested that having von Willebrand factor (VWF) coexpression is necessary for FVIII granular storage and for its secretion. We tested the importance of VWF coexpression for ectopic storage of FVIII in platelets and for its bioavailability. Transgenic mice expressing platelet-specific FVIII were crossed onto a VWF-/- background. Antigenic levels of platelet FVIII in these mice were nearly unchanged whether VWF was present or not. Whole-blood clotting times and FeCl3 carotid artery injury correction demonstrated that platelet FVIII demonstrably improved the bleeding diathesis in FVIIInull mice independent of the platelets' VWF status. Immunogold electron microscopy demonstrated that platelet FVIII is stored in platelet α-granules independent of the presence of VWF. It appears that FVIII's interaction with VWF and its intracellular transportation, storage, and secretion differ greatly depending on the cell type. The molecular basis for these differences now needs to be elucidated. (Blood. 2005;105:4674-4676)
Abdominal fat and hip fracture risk in the elderly: The Dubbo Osteoporosis Epidemiology Study
Authors: Nguyen Nguyen D , Pongchaiyakul Chatlert , Center Jacqueline R , Eisman John A , Nguyen Tuan V 
Published: February 2005

AbstractBackgroundFat mass, which is a major component of body weight, is directly related to bone mineral density and reduced fracture risk. It is not known whether abdominal fat is associated with hip fracture. The present study was designed to examine the association between abdominal fat and hip fracture in women and men aged 60+ years.MethodsThis was a nested case-control study with one fracture case being matched with two controls of the same age. In women 63 cases were matched with 126 controls, and in men 26 cases were matched with 52 controls. Hip fracture was confirmed by X-ray and personal interview. Other measurements included weight, height, body mass index (BMI), abdominal fat, and femoral neck bone density (FNBMD). Conditional logistic regression model was used to analyse data.ResultsThe odds ratio of hip fracture risk associated with each 10% lower abdominal fat was 1.5 (95% CI, 1.1 to 2.1) in women and 1.2 (95% CI, 0.7 to 2.0) in men. However after adjusting for FNBMD or body weight, the abdominal fat-fracture association was no longer statistically significant. Similarly, body weight and BMI was each significantly associated with hip fracture risk (in women), but after taking with account the effect of FNBMD, the association become statistically non-significant.ConclusionLower abdominal fat was associated with an increased risk of hip fracture in elderly women, but the association was not independent of FNBMD or weight. The contribution of abdominal fat to hip fracture risk is likely to be modest.
Synergistic inhibition of human cytomegalovirus replication by interferon-alpha/beta and interferon-gamma
Authors: Sainz Bruno , LaMarca Heather L , Garry Robert F , Morris Cindy A 
Published: February 2005

AbstractBackgroundRecent studies have shown that gamma interferon (IFN-γ) synergizes with the innate IFNs (IFN-α and IFN-β) to inhibit herpes simplex virus type 1 (HSV-1) replicationin vitro. To determine whether this phenomenon is shared by other herpesviruses, we investigated the effects of IFNs on human cytomegalovirus (HCMV) replication.ResultsWe have found that as with HSV-1, IFN-γ synergizes with the innate IFNs (IFN-α/β) to potently inhibit HCMV replicationin vitro. While pre-treatment of human foreskin fibroblasts (HFFs) with IFN-α, IFN-β or IFN-γ alone inhibited HCMV plaque formation by ~30 to 40-fold, treatment with IFN-α and IFN-γ or IFN-β and IFN-γ inhibited HCMV plaque formation by 163- and 662-fold, respectively. The generation of isobole plots verified that the observed inhibition of HCMV plaque formation and replication in HFFs by IFN-α/β and IFN-γ was a synergistic interaction. Additionally, real-time PCR analyses of the HCMV immediate early (IE) genes (IE1 and IE2) revealed that IE mRNA expression was profoundly decreased in cells stimulated with IFN-α/β and IFN-γ (~5-11-fold) as compared to vehicle-treated cells. Furthermore, decreased IE mRNA expression was accompanied by a decrease in IE protein expression, as demonstrated by western blotting and immunofluorescence.ConclusionThese findings suggest that IFN-α/β and IFN-γ synergistically inhibit HCMV replication through a mechanism that may involve the regulation of IE gene expression. We hypothesize that IFN-γ produced by activated cells of the adaptive immune response may potentially synergize with endogenous type I IFNs to inhibit HCMV disseminationin vivo.
Stimulation of P2X receptors enhances lipooligosaccharide-mediated apoptosis of endothelial cells
Authors: Sylte Matt J , Kuckleburg Chris J , Inzana Thomas J , Bertics Paul J , Czuprynski Charles J 
Published: February 2005

AbstractExposure of endothelial cells to lipid A-containing molecules, such as lipopolysaccharide (LPS) or lipooligosaccharide (LOS), causes the release of purinergic compounds [e.g., adenosine 5′-triphosphate (ATP)] and can lead to apoptosis. The P2X family of purinergic receptors (e.g., P2X7) has been reported to modulate LPS signaling events and to participate in apoptosis. We investigated the role that P2X receptors play in the apoptosis that follows exposure of bovine endothelial cells to Haemophilus somnus LOS. Addition of P2X inhibitors, such as periodate-oxidized ATP (oATP) or pyridoxal-phosphate-6-azophenyl-2′,4′-disulfonic acid tetrasodium, significantly reduced LOS-induced apoptosis. Incubation of endothelial cells with apyrase, which degrades ATP, diminished LOS-induced apoptosis of endothelial cells. Concomitant addition of P2X agonists [e.g., 2′,3′-(4-benzoyl)-benzoyl ATP or ATP] to LOS-treated endothelial cells significantly enhanced caspase-3 activation. The P2X antagonist oATP significantly blocked caspase-8 but not caspase-9 activation in LOS-treated endothelial cells. Together, these data indicate that stimulation of P2X receptors enhances LOS-induced apoptosis of endothelial cells, possibly as a result of endogenous release of ATP, which results in caspase-8 activation.
Leaf-fiber lignins of Phormium varieties compared bysolid-state 13C NMR spectroscopy
Authors: Newman Roger H. , Tauwhare Stephen E.K. , Scheele Sue , Te Kanawa Rangi 
Published: February 2005

Abstract
Solid-state NMR spectroscopy was used to determine total lignin and to distinguish between the syringyl and guaiacyl components of Phormium leaves. Fibers obtained from the upper (shiny) and lower (dull) surfaces of a P. tenax leaf showed guaiacyl lignin contents of 1.5% and 5.4% by weight, respectively. Guaiacyl lignin is known to have poor photostability, so the analyses supported a traditional view of the upper-surface fibers as the more suitable for textiles. All other analyses involved mixtures of fibers from both upper and lower surfaces. They showed no detectable differences in guaiacyl content between leaves within a ramet, or between ramets in a P. tenax bush, with a mean value of 2.2% for 20 leaves. There were no detectable differences in guaiacyl content between bushes of the variety Taeore grown at different sites, with a mean value of 2.7% for 6 sites. There were detectable differences in guaiacyl content between 15 named varieties grown at a single site, with values as low as 2.3% and as high as 4.5%. Lowest guaiacyl contents were found in varieties traditionally used for textiles. The highest guaiacyl lignin contents, 6.0% and 5.8%, were found in P. cookianum and in a plant grown from stock obtained at Norfolk Island. Syringyl lignin contents were relatively uniform between varieties, with a mean value of 6.7%.