bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Umbraviral Protein, Involved in Long-Distance RNA Movement, Binds Viral RNA and Forms Unique, Protective Ribonucleoprotein Complexes
Authors: Taliansky Michael , Roberts Ian M. , Kalinina Natalia , Ryabov Eugene V. , Raj Shri Krishna , Robinson David J. , Oparka Karl J. 
Published: February 2003

ABSTRACT

Umbraviruses are different from most other viruses in that they do not encode a conventional capsid protein (CP); therefore, no recognizable virus particles are formed in infected plants. Their lack of a CP is compensated for by the ORF3 protein, which fulfils functions that are provided by the CPs of other viruses, such as protection and long-distance movement of viral RNA. When the
Groundnut rosette virus
(GRV) ORF3 protein was expressed from
Tobacco mosaic virus
(TMV) in place of the TMV CP [ΤMV(ORF3)], in infected cells it interacted with the TMV RNA to form filamentous ribonucleoprotein (RNP) particles that had elements of helical structure but were not as uniform as classical virions. These RNP particles were observed in amorphous inclusions in the cytoplasm, where they were embedded within an electron-dense matrix material. The inclusions were detected in all types of cells and were abundant in phloem-associated cells, in particular companion cells and immature sieve elements. RNP-containing complexes similar in appearance to the inclusions were isolated from plants infected with ΤMV(ORF3) or with GRV itself. In vitro, the ORF3 protein formed oligomers and bound RNA in a manner consistent with its role in the formation of RNP complexes. It is suggested that the cytoplasmic RNP complexes formed by the ORF3 protein serve to protect viral RNA and may be the form in which it moves through the phloem. Thus, the RNP particles detected here represent a novel structure which may be used by umbraviruses as an alternative to classical virions.
Role of Quail in the Interspecies Transmission of H9 Influenza A Viruses: Molecular Changes on HA That Correspond to Adaptation from Ducks to Chickens
Authors: Perez Daniel R. , Lim Wilina , Seiler Jon P. , Yi Guan , Peiris Malik , Shortridge Kennedy F. , Webster Robert G. 
Published: February 2003

ABSTRACT
H9 influenza viruses have become endemic in land-based domestic poultry in Asia and have sporadically crossed to pigs and humans. To understand the molecular determinants of their adaptation to land-based birds, we tested the replication and transmission of several 1970s duck H9 viruses in chickens and quail. Quail were more susceptible than chickens to these viruses, and generation of recombinant H9 viruses by reverse genetics showed that changes in the HA gene are sufficient to initiate efficient replication and transmission in quail. Seven amino acid positions on the HA molecule corresponded to adaptation to land-based birds. In quail H9 viruses, the pattern of amino acids at these seven positions is intermediate between those of duck and chicken viruses; this fact may explain the susceptibility of quail to duck H9 viruses. Our findings suggest that quail provide an environment in which the adaptation of influenza viruses from ducks generates novel variants that can cross the species barrier.
T-cell epitopes within the complementarity-determining and framework regions of the tumor-derived immunoglobulin heavy chain in multiple myeloma
Authors: Hansson Lotta , Rabbani Hodjattallah , Fagerberg Jan , Österborg Anders , Mellstedt Håkan 
Published: February 2003

AbstractThe idiotypic structure of the monoclonal immunoglobulin (Ig) in multiple myeloma (MM) might be regarded as a tumor-specific antigen. The present study was designed to identify T-cell epitopes of the variable region of the Ig heavy chain (VH) in MM (n = 5) using bioinformatics and analyze the presence of naturally occurring T cells against idiotype-derived peptides. A large number of human-leukocyte-antigen (HLA)–binding (class I and II) peptides were identified. The frequency of predicted epitopes depended on the database used: 245 in bioinformatics and molecular analysis section (BIMAS) and 601 in SYFPEITHI. Most of the peptides displayed a binding half-life or score in the low or intermediate affinity range. The majority of the predicted peptides were complementarity-determining region (CDR)–rather than framework region (FR)–derived (52%-60% vs 40%-48%, respectively). Most of the predicted peptides were confined to the CDR2-FR3-CDR3 “geographic” region of the Ig-VH region (70%), and significantly fewer peptides were found within the flanking (FR1-CDR1-FR2 and FR4) regions (P &lt; .01). There were 8– to 10–amino acid (aa) long peptides corresponding to the CDRs and fitting to the actual HLA-A/B haplotypes that spontaneously recognized, albeit with a low magnitude, type I T cells (interferon γ), indicating an ongoing major histocompatibility complex (MHC) class I–restricted T-cell response. Most of those peptides had a low binding half-life (BIMAS) and a low/intermediate score (SYFPEITHI). Furthermore, 15- to 20-aa long CDR1-3–derived peptides also spontaneously recognized type I T cells, indicating the presence of MHC class II–restricted T cells as well. This study demonstrates that a large number of HLA-binding idiotypic peptides can be identified in patients with MM. Such peptides may spontaneously induce a type I MHC class I– as well as class II–restricted memory T-cell response.
Complement receptor 1 inhibitors for prevention of immune-mediated red cell destruction: potential use in transfusion therapy
Authors: Yazdanbakhsh Karina , Kang Stanley , Tamasauskas Daniel , Sung Dorothy , Scaradavou Andromachi 
Published: February 2003

AbstractActivation of complement cascade via the antibody-mediated classical pathway can initiate red blood cell (RBC) destruction, causing transfusion reactions and hemolytic anemia. In the present study, we have assessed the ability of a human recombinant soluble form of complement receptor 1 (sCR1) to inhibit complement-mediated RBC destruction in vitro and in vivo. Using an in vitro alloimmune incompatibility model, sCR1 inhibited complement activation and prevented hemolysis. Following transfusion of human group O RBCs into mice lacking detectable pre-existing antibodies against the transfused RBCs, systemic coadministration of 10 mg/kg sCR1, a dose well tolerated in human subjects for prevention of tissue injury, completely inhibited the in vivo clearance of the transfused RBCs and surface C3 deposition in the first hour after transfusion, correlating with the half-life of sCR1 in the circulation. Treatment with sCR1 increased the survival of transfused human group A RBCs in the circulation of mice with pre-existing anti-A for 2 hours after transfusion by 50%, reduced intravascular hemolysis, and lowered the levels of complement deposition (C3 and C4), but not immunoglobulin G (IgG) or IgM, on the transfused cells by 100-fold. We further identified potential functional domains in CR1 that can act to limit complement-mediated RBC destruction in vitro and in vivo. Collectively, our data highlight a potential use of CR1-based inhibitors for prevention of complement-dependent immune hemolysis.
Stabilities and Isomeric Equilibria in Aqueous Solution of Monomeric Metal Ion Complexes of Adenosine 5′‐Diphosphate (ADP3−) in Comparison with Those of Adenosine 5′‐Monophosphate (AMP2−)
Authors: Bianchi Emanuela M. , Sajadi S. Ali A. , Song Bin , Sigel Helmut 
Published: February 2003

AbstractUnder experimental conditions in which the self‐association of the adenine phosphates (AP), that is, of adenosine 5′‐monophosphate (AMP2−) and adenosine 5′‐diphosphate (ADP3−), is negligible, potentiometric pH titrations were carried out to determine the stabilities of the M(H;AP) and M(AP) complexes where M2+=Mg2+, Ca2+, Sr2+, Ba2+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, or Cd2+ (25 °C; I=0.1 M, NaNO3). It is concluded that in the M(H;AMP)+ species M2+ is bound at the adenine moiety and in the M(H;ADP) complexes at the diphosphate unit; however, the proton resides in both types of monoprotonated complexes at the phosphate residue. The stabilities of nearly all the M(AMP) and M(ADP)− complexes are significantly larger than what is expected for a sole coordination of M2+ to the phosphate residue. This increased complex stability is attributed, in agreement with previous 1H NMR shift studies and further information existing in the literature, to the formation of macrochelates of the phosphate‐coordinated metal ions with N7 of the adenine residues. On the basis of recent measurements with simple phosphate monoesters and phosphonate ligands (R‐MP2−) as well as with diphosphate monoesters (R‐DP3−), where R is a noncoordinating and noninhibiting residue, the increased stabilities of the M(AMP) and M(ADP)− complexes due to the M2+–N7 interaction could be evaluated and the extent of macrochelate formation calculated. The results show that the formation degrees of the macrochelates for the complexes of the alkaline earth ions are small (about 15 % at the most), whereas for the 3d metal ions as well as for Zn2+ and Cd2+ the formation degrees vary between about 15 % (Mn2+) and 75 % (Ni2+) with values of about 40 and 50 % for Zn2+ and Cu2+, respectively. It is interesting to note, taking earlier results for M(ATP)2− complexes also into account (ATP4−=adenosine 5′‐triphosphate), that for a given metal ion in nearly all instances the formation degrees of the macrochelates are within the error limits the same for M(AMP), M(ADP)− and M(ATP)2− complexes; except for Co2+ and Ni2+ it holds M(AMP) > M(ADP)− ∼ M(ATP)2−. This result is astonishing if one considers that the absolute stability constants of these complexes, which are determined largely by the affinity of the phosphate residues, can differ by more than two orders of magnitude. The impact and conclusions of these observations for biological systems are shortly lined out.
An Unprecedented [2+3] Cycloadditive Dimerization of a Transient Thiocarbonyl S‐Ylide
Authors: El‐Sayed Ibrahim , Grønbæk Hazell Rita , Øgaard Madsen Jørgen , Norrby Per‐Ola , Senning Alexander 
Published: February 2003

Abstract4‐Chlorophenyl C‐(phenylsulfonyl)dithioformate reacts with diazo(trimethylsilyl)methane to form 2‐(4‐chlorophenylthio)‐2‐phenylsulfonyl‐4,5‐bis(trimethylsilyl)‐1,3‐dithiolan‐1‐ium (4‐chlorophenylthio)(phenylsulfonyl)methylide. It is assumed that this product is formed by [2+3] cycloadditive dimerization of the transient (trimethylsilyl)methanethial S‐[(4‐chlorophenylthio)(phenylsulfonyl)methylide]. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Asymmetric Total Synthesis of the Gastroprotective Microbial Agent AI‐77‐B
Authors: Ghosh Arun K. , Bischoff Alexander , Cappiello John 
Published: February 2003

AbstractAn enantioselective total synthesis of the pseudopeptide microbial agent AI‐77‐B, which has shown potent antiulcerogenic properties, is described. The synthesis is convergent and involves the assembly of a dihydroisocoumarin fragment and a hydroxy amino acid. The dihydroisocoumarin derivative was synthesised by means of a Diels−Alder reaction between 1‐methoxy‐1,3‐cyclohexadiene and an alkynyl ester derivative as the dienophile. The alkynyl ester was obtained stereoselectively by two different synthetic routes: (1) A stereoselective allylation of leucinal, and (2) a titanium enolate‐mediated anti‐aldol reaction with trichlorobutyraldehyde, a novel homopropargylaldehyde equivalent. The stereocentres of the hydroxy amino acid moiety were generated through a titanium enolate‐mediated syn‐aldol reaction, Curtius rearrangement, and application of Dondoni's aldehyde homologation. Condensation of the dihydroisocoumarin and hydroxy amino acid moieties and subsequent removal of the protecting groups furnished optically active AI‐77‐B. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Nitrogen isotopes in mammalian herbivores: hair δ15N values from a controlled feeding study
Authors: Sponheimer M. , Robinson T. , Ayliffe L. , Roeder B. , Hammer J. , Passey B. , West A. , Cerling T. , Dearing D. , Ehleringer J. 
Published: February 2003

AbstractNitrogen isotope analysis is a common technique for investigating dietary behaviour in modern and archaeological populations. One of its primary uses is to provide trophic level information. This application is possible because of a ∼3‰ enrichment in15N along each step in the food chain, resulting in carnivores having higher δ15N values than herbivores, which in turn have higher δ15N values than plants. Much variation has also been observed within a trophic level, although the reasons for this are poorly understood. Here we present the results of a controlled feeding study designed to test the effects of gut anatomy and dietary protein levels on hair δ15N values within a trophic level. The data reveal that mammalian herbivores eating identical diets can have hair δ15N values that differ by as much as 3.6‰. This is particularly striking as it suggests that interspecific physiological differences can lead to larger shifts in δ15N values than a shift in trophic level. We also found that diet‐hair fractionation was 2.3‰ greater when herbivores were fed high‐protein (19%) diets than when they were fed low‐protein (9%) diets. The primary nitrogen losses in mammalian herbivores are15N‐depleted urine and15N‐enriched faeces. We reason that an increase in the ratio of urinary to faecal nitrogen efflux leads to greater diet‐hair fractionation on the high‐protein diet. Copyright © 2003 John Wiley & Sons, Ltd.
The Database of Quantitative Cellular Signaling:
management and analysis of chemical kinetic models of signaling
networks
Authors: Sivakumaran Sudhir , Hariharaputran Sridhar , Mishra Jyoti , Bhalla Upinder S. 
Published: February 2003

Abstract
Motivation: Analysis of cellular signaling interactions is expected to pose an enormous informatics challenge, perhaps even larger than analyzing the genome. The complex networks arising from signaling processes are traditionally represented as block diagrams. A key step in the evolution toward a more quantitative understanding of signaling is to explicitly specify the kinetics of all chemical reaction steps in a pathway. Technical advances in proteomics and high-throughput protein interaction assays promise a flood of such quantitative data. While annotations, molecular information and pathway connectivity have been compiled in several databases, and there are several proposals for general cell model description languages, there is currently little experience with databases of chemical kinetics and reaction level models of signaling networks.
Results: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It is intended both to serve the growing field of chemical-reaction level simulation of signaling networks, and to anticipate issues in large-scale data management for signaling chemistry.
Availability: The Database of Quantitative Cellular Signaling is available at http://doqcs.ncbs.res.in. Links to the signaling model simulator, GENESIS/Kinetikit are at http://www.ncbs.res.in/~bhalla/kkit/index.html
Contact: bhalla@ncbs.res.in
* To whom correspondence should be addressed.
Quantitative Role of the Human Papillomavirus Type 16 E5 Gene during the Productive Stage of the Viral Life Cycle
Authors: Genther Sybil M. , Sterling Stephanie , Duensing Stefan , Münger Karl , Sattler Carol , Lambert Paul F. 
Published: February 2003

ABSTRACT
Human papillomaviruses (HPVs) are small circular DNA viruses that cause warts. Infection with high-risk anogenital HPVs, such as HPV type 16 (HPV16), is associated with human cancers, specifically cervical cancer. The life cycle of HPVs is intimately tied to the differentiation status of the host epithelium and has two distinct stages: the nonproductive stage and the productive stage. In the nonproductive stage, which arises in the poorly differentiated basal epithelial compartment of a wart, the virus maintains itself as a low-copy-number nuclear plasmid. In the productive stage, which arises as the host cell undergoes terminal differentiation, viral DNA is amplified; the capsid genes, L1 and L2, are expressed; and progeny virions are produced. This stage of the viral life cycle relies on the ability of the virus to reprogram the differentiated cells to support DNA synthesis. Papillomaviruses encode multiple oncoproteins, E5, E6, and E7. In the present study, we analyze the role of one of these viral oncogenes, E5, in the viral life cycle. To assess the role of E5 in the HPV16 life cycle, we introduced wild-type (WT) or E5 mutant HPV16 genomes into NIKS, a keratinocyte cell line that supports the papillomavirus life cycle. By culturing these cells under conditions that allow them to remain undifferentiated, a state similar to that of basal epithelial cells, we determined that E5 does not play an essential role in the nonproductive stage of the HPV16 life cycle. To determine if E5 plays a role in the productive stage of the viral life cycle, we cultured keratinocyte populations in organotypic raft cultures, which promote the differentiation and stratification of epithelial cells. We found that cells harboring E5 mutant genomes displayed a quantitative reduction in the percentage of suprabasal cells undergoing DNA synthesis, compared to cells containing WT HPV16 DNA. This reduction in DNA synthesis, however, did not prevent amplification of viral DNA in the differentiated cellular compartment. Likewise, late viral gene expression and the perturbation of normal keratinocyte differentiation were retained in cells harboring E5 mutant genomes. These data demonstrate that E5 plays a subtle role during the productive stage of the HPV16 life cycle.
Dimerization and Template Switching in the 5′ Untranslated Region between Various Subtypes of Human Immunodeficiency Virus Type 1
Authors: Andersen Ebbe Sloth , Jeeninga Rienk E. , Damgaard Christian Kroun , Berkhout Ben , Kjems Jørgen 
Published: February 2003

ABSTRACT
The human immunodeficiency virus type 1 (HIV-1) particle contains two identical RNA strands, each corresponding to the entire genome. The 5′ untranslated region (UTR) of each RNA strand contains extensive secondary and tertiary structures that are instrumental in different steps of the viral replication cycle. We have characterized the 5′ UTRs of nine different HIV-1 isolates representing subtypes A through G and, by comparing their homodimerization and heterodimerization potentials, found that complementarity between the palindromic sequences in the dimerization initiation site (DIS) hairpins is necessary and sufficient for in vitro dimerization of two subtype RNAs. The 5′ UTR sequences were used to design donor and acceptor templates for a coupled in vitro dimerization-reverse transcription assay. We showed that template switching during reverse transcription is increased with a matching DIS palindrome and further stimulated proportional to the level of homology between the templates. The presence of the HIV-1 nucleocapsid protein NCp7 increased the template-switching efficiency for matching DIS palindromes twofold, whereas the recombination efficiency was increased sevenfold with a nonmatching palindrome. Since NCp7 did not effect the dimerization of nonmatching palindromes, we concluded that the protein most likely stimulates the strand transfer reaction. An analysis of the distribution of template-switching events revealed that it occurs throughout the 5′ UTR. Together, these results demonstrate that the template switching of HIV-1 reverse transcriptase occurs frequently in vitro and that this process is facilitated mainly by template proximity and the level of homology.
Evaluation of Genetically Engineered Derivatives of a Chinese Strain of Foot-and-Mouth Disease Virus Reveals a Novel Cell-Binding Site Which Functions in Cell Culture and in Animals
Authors: Zhao Qizu , Pacheco Juan M. , Mason Peter W. 
Published: February 2003

ABSTRACT

Adaptation of field isolates of foot-and-mouth disease virus (FMDV) to grow in cells in culture can result in changes in viral properties that include acquisition of the ability to bind to cell surface heparan sulfate (HS). After 13 passages on BHK cells to produce a vaccine, a Cathay topotype isolate of FMDV serotype O from China (O/CHA/90) extended its cell culture host range and bound to heparin-Sepharose, although it did not require cell surface HS as a receptor molecule. To understand these phenomena, we constructed chimeric viruses by using a type A
12
infectious cDNA and the capsid protein-coding regions of O/CHA/90 and its cell culture-adapted derivative (vac-O/CHA/90). Using a set of viruses derived from these chimeras by exchanging portions of the capsid-coding regions, we discovered that a group of amino acid residues that surround the fivefold axis of the icosahedral virion determine host range in cell culture and influence pathogenicity in pigs. These residues included aromatic amino acids at positions 108 and 174 and positively charged residues at positions 83 and 172 in protein 1D. To test if these residues participated in non-integrin-dependent cell binding, the integrin-binding RGD sequence in protein 1D was changed to KGE in two different chimeras. Evaluation of these KGE viruses indicated that growth in cell culture was not dependent on HS. One of these viruses was tested in pigs, where it produced a mild disease and maintained its KGE sequence. These results are discussed in terms of receptor utilization and pathogenesis of this important pathogen.
Structures of Rotavirus Reassortants Demonstrate Correlation of Altered Conformation of the VP4 Spike and Expression of Unexpected VP4-Associated Phenotypes
Authors: Pesavento Joseph B. , Billingsley Angela M. , Roberts Ed J. , Ramig Robert F. , Prasad B. V. Venkataram 
Published: February 2003

ABSTRACT
Numerous prior studies have indicated that viable rotavirus reassortants containing structural proteins of heterologous parental origin may express unexpected phenotypes, such as changes in infectivity and immunogenicity. To provide a structural basis for alterations in phenotypic expression, a three-dimensional structural analysis of these reassortants was conducted. The structures of the reassortants show that while VP4 generally maintains the parental structure when moved to a heterologous protein background, in certain reassortants, there are subtle alterations in the conformation of VP4. The alterations in VP4 conformation correlated with expression of unexpected VP4-associated phenotypes. Interactions between heterologous VP4 and VP7 in reassortants expressing unexpected phenotypes appeared to induce the conformational alterations seen in VP4.
Ebola Virus Transcription Activator VP30 Is a Zinc-Binding Protein
Authors: Modrof Jens , Becker Stephan , Mühlberger Elke 
Published: February 2003

ABSTRACT

Ebola virus VP30 is an essential activator of viral transcription. In viral particles, VP30 is closely associated with the nucleocapsid complex. A conspicuous structural feature of VP30 is an unconventional zinc-binding Cys
3
-His motif comprising amino acids 68 to 95. By using a colorimetric zinc-binding assay we found that the VP30-specific Cys
3
-His motif stoichiometrically binds zinc ions in a one-to-one relationship. Substitution of the conserved cysteines and the histidine within the motif led to a complete loss of the capacity for zinc binding. Functional analyses revealed that none of the tested mutations of the proposed zinc-coordinating residues influenced binding of VP30 to nucleocapsid-like particles but, concerning its role in activating viral transcription, all resulted in a protein that was inactive.