bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biodiversity of periphyton (diatoms) and echinoderms around a refinery effluent, and possible associations with stability
Authors: Izsak C. , Price A. R. G. , Hardy J. T. , Basson P. W. 
Published: September 2002

We examine biodiversity in Tarut Bay, Saudi Arabia, around the effluent of a refinery that has operated since 1945. The spatial study involved quarterly assessment of diatom biodiversity in 1976/77 at 24 sites. Taxonomic distinctness decreased significantly towards the refinery outfall, in contrast to the pattern for number of species, Simpson'sindex and Margalef'sspecies richness index. Ammonia-nitrogen concentrations and primary productivity (mg chlorophyll-a cm−1 d−1) also increased significantly towards the effluent, probably due to nearby sewage/nutrient enrichment.
The spatio-temporal assessment involved comparison of echinoderm biodiversity at eight sites in 1945 through 1947 and 1977. No significant temporal differences were observed in number of species, taxonomic distinctness or beta-diversity, nor was significant correlation detected between biodiversity and proximity to the refinery outfall. The absence of obvious impact is confirmed by statistical comparison of taxonomic distinctness for echinoderms in Tarut Bay with values for the whole Gulf.
Periphyton in Tarut Bay may be perturbed towards the refinery outfall, ‘positively’ when measured by Simpson's and other ‘absolute’ biodiversity measures, but ‘negatively’ according to taxonomic distinctness, a measure of ‘average’ properties. Hence, diatom persistence stability appears moderate to low. In contrast, the echinoderm fauna may exhibit high stability, explained by either high persistence (withstanding perturbation), or high resilience (perturbation experienced, but system reverted or acclimated to ‘normal’ Gulf state) over a time scale of 30 y.
A structure for the yeast prohibitin complex: Structure prediction and evidence from chemical crosslinking and mass spectrometry
Authors: Back Jaap W. , Sanz Marta Artal , de Jong Luitzen , de Koning Leo J. , Nijtmans Leo G.J. , de Koster Chris G. , Grivell Les A. , van der Spek Hans , Muijsers Anton O. 
Published: September 2002

AbstractThe mitochondrial prohibitin complex consists of two subunits (PHB1 of 32 kD and PHB2 of 34 kD), assembled into a membrane‐associated supercomplex of approximately 1 MD. A chaperone‐like function in holding and assembling newly synthesized mitochondrial polypeptide chains has been proposed. To further elucidate the function of this complex, structural information is necessary. In this study we use chemical crosslinking, connecting lysine side chains, which are well scattered along the sequence. Crosslinked peptides from protease digested prohibitin complexes were identified with mass spectrometry. From these results, spatial restraints for possible protein conformation were obtained. Many interaction sites between PHB1 and PHB2 were found, whereas no homodimeric interactions were observed. Secondary and tertiary structural predictions were made using several algorithms and the models best fitting the spatial restraints were selected for further evaluation. From the structure predictions and the crosslink data we derived a structural building block of one PHB1 and one PHB2 subunit, strongly intertwined along most of their length. The size of the complex implies that approximately 14 of these building blocks are present. Each unit contains a putative transmembrane helix in PHB2. Taken together with the unit building block we postulate a circular palisade‐like arrangement of the building blocks projecting into the intermembrane space.
Molecular modeling‐based analysis of interactions in the RFC‐dependent clamp‐loading process
Authors: Venclovas Česlovas , Colvin Michael E. , Thelen Michael P. 
Published: September 2002

AbstractReplication and related processes in eukaryotic cells require replication factor C (RFC) to load a molecular clamp for DNA polymerase in an ATP‐driven process, involving multiple molecular interactions. The detailed understanding of this mechanism is hindered by the lack of data regarding structure, mutual arrangement, and dynamics of the players involved. In this study, we analyzed interactions that take place during loading onto DNA of either the PCNA clamp or the Rad9‐Rad1‐Hus1 checkpoint complex, using computationally derived molecular models. Combining the modeled structures for each RFC subunit with known structural, biochemical, and genetic data, we propose detailed models of how two of the RFC subunits, RFC1 and RFC3, interact with the C‐terminal regions of PCNA. RFC1 is predicted to bind PCNA similarly to the p21‐PCNA interaction, while the RFC3‐PCNA binding is proposed to be similar to theE. coliδ‐β interaction. Additional sequence and structure analysis, supported by experimental data, suggests that RFC5 might be the third clamp loader subunit to bind the equivalent PCNA region. We discuss functional implications stemming from the proposed model of the RFC1‐PCNA interaction and compare putative clamp‐interacting regions in RFC1 and its paralogs, Rad17 and Ctf18. Based on the individual intermolecular interactions, we propose RFC and PCNA arrangement that places three RFC subunits in association with each of the three C‐terminal regions in PCNA. The two other RFC subunits are positioned at the two PCNA interfaces, with the third PCNA interface left unobstructed. In addition, we map interactions at the level of individual subunits between the alternative clamp loader/clamp system, Rad17‐RFC2–5/Rad9‐Rad1‐Hus1. The proposed models of interaction between two clamp/clamp loader pairs provide both structural framework for interpretation of existing experimental data and a number of specific findings that can be subjected to direct experimental testing.
Mapping and characterization of the functional epitopes of tissue inhibitor of metalloproteinases (TIMP)‐3 using TIMP‐1 as the scaffold: A new frontier in TIMP engineering
Authors: Lee Meng‐Huee , Maskos Klaus , Knäuper Vera , Dodds Philippa , Murphy Gillian 
Published: September 2002

AbstractTumor necrosis factor‐α (TNF‐α) converting enzyme (TACE/ADAM‐17) is responsible for the release of TNF‐α, a potent proinflammatory cytokine associated with many chronic debilitating diseases such as rheumatoid arthritis. Among the four variants of mammalian tissue inhibitor of metalloproteinases (TIMP‐1 to ‐4), TACE is specifically inhibited by TIMP‐3. We set out to delineate the basis for this specificity by examining the solvent accessibility of every epitope on the surface of a model of the truncated N‐terminal domain form of TIMP‐3 (N‐TIMP‐3) in a hypothetical complex with the crystal structure of TACE. The epitopes suspected of interacting with TACE were systematically transplanted onto N‐TIMP‐1. We succeeded in transforming N‐TIMP‐1 into an active inhibitor for TACE (Kiapp 15 nM) with the incorporation of Ser4, Leu67, Arg84, and the TIMP‐3 AB‐loop. The combined effects of these epitopes are additive. Unexpectedly, introduction of “super‐N‐TIMP‐3” epitopes, defined in our previous work, only impaired the affinity of N‐TIMP‐1 for TACE. Our mutagenesis results indicate that TIMP‐3‐TACE interaction is a delicate process that requires highly refined surface topography and flexibility from both parties. Most importantly, our findings confirm that the individual characteristics of TIMP could be transplanted from one variant to another.
CxxS: Fold‐independent redox motif revealed by genome‐wide searches for thiol/disulfide oxidoreductase function
Authors: Fomenko Dmitri E. , Gladyshev Vadim N. 
Published: September 2002

AbstractRedox reactions involving thiol groups in proteins are major participants in cellular redox regulation and antioxidant defense. Although mechanistically similar, thiol‐dependent redox processes are catalyzed by structurally distinct families of enzymes, which are difficult to identify by available protein function prediction programs. Herein, we identified a functional motif, CxxS (cysteine separated from serine by two other residues), that was often conserved in redox enzymes, but rarely in other proteins. Analyses of complete Escherichia coli, Campylobacter jejuni, Methanococcus jannaschii, and Saccharomyces cerevisiae genomes revealed a high proportion of proteins known to use the CxxS motif for redox function. This allowed us to make predictions in regard to redox function and identity of redox groups for several proteins whose function previously was not known. Many proteins containing the CxxS motif had a thioredoxin fold, but other structural folds were also present, and CxxS was often located in these proteins upstream of an α‐helix. Thus, a conserved CxxS sequence followed by an α‐helix is typically indicative of a redox function and corresponds to thiol‐dependent redox sites in proteins. The data also indicate a general approach of genome‐wide identification of redox proteins by searching for simple conserved motifs within secondary structure patterns.
Newcastle Disease Virus (NDV) Marker Vaccine: an Immunodominant Epitope on the Nucleoprotein Gene of NDV Can Be Deleted or Replaced by a Foreign Epitope
Authors: Mebatsion Teshome , Koolen Marck J. M. , de Vaan Leonie T. C. , de Haas Niels , Braber Marian , Römer-Oberdörfer Angela , van den Elzen Paul , van der Marel Pieter 
Published: September 2002

ABSTRACT
The nucleoprotein (NP) of Newcastle disease virus (NDV) functions primarily to encapsidate the virus genome for the purpose of RNA transcription, replication, and packaging. This conserved multifunctional protein is also efficient in inducing NDV-specific antibody in chickens. Here, we localized a conserved B-cell immunodominant epitope (IDE) spanning residues 447 to 455 and successfully generated a recombinant NDV lacking the IDE by reverse genetics. Despite deletion of NP residues 443 to 460 encompassing the NP-IDE, the mutant NDV propagated in embryonated specific-pathogen-free chicken eggs to a level comparable to that of the parent virus. In addition, a B-cell epitope of the S2 glycoprotein of murine hepatitis virus (MHV) was inserted in-frame to replace the NP-IDE. Recombinant viruses properly expressing the introduced MHV epitope were successfully generated, demonstrating that the NP-IDE not only is dispensable for virus replication but also can be replaced by foreign sequences. Chickens immunized with the hybrid recombinants produced specific antibodies against the S2 glycoprotein of MHV and completely lacked antibodies directed against the NP-IDE. These marked-NDV recombinants, in conjunction with a diagnostic test, enable serological differentiation of vaccinated animals from infected animals and may be useful tools in ND eradication programs. The identification of a mutation-permissive region on the NP gene allows a rational approach to the insertion of protective epitopes and may be relevant for the design of NDV-based cross-protective marker vaccines.
Slowly Declining Levels of Viral RNA and DNA in DNA/Recombinant Modified Vaccinia Virus Ankara-Vaccinated Macaques with Controlled Simian-Human Immunodeficiency Virus SHIV-89.6P Challenges
Authors: Tang Yuyang , Villinger Francois , Staprans Silvija I. , Amara Rama Rao , Smith James M. , Herndon James G. , Robinson Harriet L. 
Published: September 2002

ABSTRACT
In a recent vaccine trial, we showed efficient control of a virulent simian-human immunodeficiency virus SHIV-89.6P challenge by priming with a Gag-Pol-Env-expressing DNA and boosting with a Gag-Pol-Env- expressing recombinant-modified vaccinia virus Ankara. Here we show that long-term control has been associated with slowly declining levels of viral RNA and DNA. In the vaccinated animals both viral DNA and RNA underwent an initial rapid decay, which was followed by a lower decay rate. Between 12 and 70 weeks postchallenge, the low decay rates have had half-lives of about 20 weeks for viral RNA in plasma and viral DNA in peripheral blood mononuclear cells and lymph nodes. In vaccinated animals the viral DNA has been mostly unintegrated and has appeared to be largely nonfunctional as evidenced by a poor ability to recover infectious virus in cocultivation assays, even after CD8 depletion. In contrast, in control animals, which have died, viral DNA was mostly integrated and a larger proportion appeared to be functional as evidenced by the recovery of infectious virus. Thus, to date, control of the challenge infection has appeared to improve with time, with the decay rates for viral DNA being at the lower end of values reported for patients on highly active antiretroviral therapy.
Phenotypic and Functional Alterations of Dendritic Cells Induced by Human Herpesvirus 6 Infection
Authors: Kakimoto Miki , Hasegawa Atsuhiko , Fujita Shigeru , Yasukawa Masaki 
Published: September 2002

ABSTRACTHuman herpesvirus 6 (HHV-6) has a tropism for T lymphocytes and monocytes/macrophages, suggesting that HHV-6 infection affects the immunosurveillance system. In the present study, we investigated the HHV-6-induced phenotypic and functional alterations of dendritic cells (DCs), which are professional antigen-presenting cells. HHV-6 infection of monocyte-derived immature DCs appeared to induce the up-regulation of CD80, CD83, CD86, and HLA class I and class II molecules, suggesting that HHV-6 infection induces the maturation of DCs. In addition, the antigen capture capacity of DCs was found to decrease following infection with HHV-6. In contrast to up-regulation of mature-DC-associated surface molecules on HHV-6-infected DCs, their capacity for presentation of alloantigens and exogenous virus antigens to T lymphocytes decreased significantly from that of uninfected DCs. In contrast, there appeared to be no reduction in the capacity for presentation of an HLA class II-binding peptide to the peptide-specific CD4+T lymphocytes. These data indicate that HHV-6 infection induces phenotypic alterations and impairs the antigen presentation capacity of DCs. The present data also suggest that the dysfunction of HHV-6-infected DCs is attributable mainly to impairment of the antigen capture and intracellular antigen-processing pathways.
Improved Hepatic Gene Transfer by Using an Adeno-Associated Virus Serotype 5 Vector
Authors: Mingozzi Federico , Schüttrumpf Jörg , Arruda Valder R. , Liu Yuhong , Liu Yi-Lin , High Katherine A. , Xiao Weidong , Herzog Roland W. 
Published: September 2002

ABSTRACT
Adeno-associated viral (AAV) vectors have been shown to direct stable gene transfer and expression in hepatocytes, which makes them attractive tools for treatment of inherited disorders such as hemophilia B. While substantial levels of coagulation factor IX (F.IX) have been achieved using AAV serotype 2 vectors, use of a serotype 5 vector further improves transduction efficiency and levels of F.IX transgene expression by 3- to 10-fold. In addition, the AAV-5 vector transduces a higher proportion of hepatocytes (∼15%). The subpopulations of hepatocytes transduced with either vector widely overlap, with the AAV-5 vector transducing additional hepatocytes and showing a wider area of transgene expression throughout the liver parenchyma.
Specificity and Affinity of Sialic Acid Binding by the Rhesus Rotavirus VP8* Core
Authors: Dormitzer Philip R. , Sun Zhen-Yu J. , Blixt Ola , Paulson James C. , Wagner Gerhard , Harrison Stephen C. 
Published: September 2002

ABSTRACT

Nuclear magnetic resonance spectroscopy demonstrates that the rhesus rotavirus hemagglutinin specifically binds α-anomeric
N
-acetylneuraminic acid with a

K
d

of 1.2 mM. The hemagglutinin requires no additional carbohydrate moieties for binding, does not distinguish 3′ from 6′ sialyllactose, and has approximately tenfold lower affinity for
N
-glycolylneuraminic than for
N
-acetylneuraminic acid. The broad specificity and low affinity of sialic acid binding by the rotavirus hemagglutinin are consistent with this interaction mediating initial cell attachment prior to the interactions that determine host range and cell type specificity.
Protective Antiviral Immune Responses to Pseudorabies Virus Induced by DNA Vaccination Using Dimethyldioctadecylammonium Bromide as an Adjuvant
Authors: van Rooij Eugene M. A. , Glansbeek Harrie L. , Hilgers Luuk A. T. , te Lintelo Eddie G. , de Visser Yolanda E. , Boersma Wim J. A. , Haagmans Bart L. , Bianchi Andre T. J. 
Published: September 2002

ABSTRACTTo enhance the efficacy of a DNA vaccine against pseudorabies virus (PRV), we evaluated the adjuvant properties of plasmids coding for gamma interferon or interleukin-12, of CpG immunostimulatory motifs, and of the conventional adjuvants dimethyldioctadecylammonium bromide in water (DDA) and sulfolipo-cyclodextrin in squalene in water. We demonstrate that a DNA vaccine combined with DDA, but not with the other adjuvants, induced significantly stronger immune responses than plasmid vaccination alone. Moreover, pigs vaccinated in the presence of DDA were protected against clinical disease and shed significantly less PRV after challenge infection. This is the first study to demonstrate that DDA, a conventional adjuvant, enhances DNA vaccine-induced antiviral immunity.
Activation of Phosphatidylinositol 3-Kinase Contributes to Insulin-Like Growth Factor I-Mediated Inhibition of Pancreatic β-Cell Death
Authors: Liu Wenli , Chin-Chance Catherine , Lee Eun-Jig , Lowe William L. 
Published: September 2002

Abstract
To begin to determine whether IGF-I treatment represents a potential means of enhancing the survival of islet cell grafts after transplantation, the present studies established a model of β-cell death secondary to loss of trophic support and examined the ability of IGF-I to prevent cell death. The studies were performed using the rat pancreatic β-cell line, INS-1. Incubating INS-1 cells in RPMI 1640 and 0.25% BSA for 48 h increased cell death, as determined by lactate dehydrogenase release, compared with that of cells maintained in RPMI and 10% fetal calf serum. Addition of 100 ng/ml IGF-I to the serum-free medium decreased lactate dehydrogenase release to a level comparable to that found in cells maintained in fetal calf serum. Similar results were seen using a mouse β-cell line, MIN6, infected with an adenovirus expressing IGF-I. Examination of IGF-I-stimulated signaling demonstrated that IGF-I increased the phosphorylation of protein kinase B in both cell lines, whereas IGF-I-induced phosphorylation of the MAPKs, ERK1 and -2, was observed only in INS-1 cells. The effect of IGF-I on phosphorylation of substrates of phosphatidylinositol 3-kinase (PI 3-kinase) or protein kinase B was also examined in INS-1 cells. IGF-I increased the phosphorylation of glycogen synthase kinase 3β, BAD, FKHR, and p70S6 kinase. Another pathway that has been shown to mediate the protective of IGF-I in some cell types is activation of cAMP response element-binding protein (CREB). IGF-I increased CREB phosphorylation at a concentration as low as 10 ng/ml, and this effect was inhibited by H89, a PKA inhibitor, and PD98059, a MAPK kinase inhibitor. Consistent with the effect of IGF-I on CREB phosphorylation, IGF-I increased the transcriptional activity of CREB, although it had no effect on CREB binding to DNA. Use of inhibitors of the PI 3-kinase (LY 294002) or ERK (PD98059) pathways or CREB phosphorylation (H89) in the cell death assay demonstrated partial abrogation of the protective effect of IGF-I with LY 294002. These data demonstrate that IGF-I protects pancreatic β-cells from cell death secondary to loss of trophic support and that, although IGF-I activates several signaling pathways that contribute to its protective effect in other cell types, only activation of PI 3-kinase contributes to this effect in β-cells.
Two New Species of the Lichen Genus Immersaria (Porpidiaceae)
Authors: Calatayud V. , Rambold G. 
Published: September 2002

AbstractImmersaria olivacea, its lichenicolous fungus Polycoccum decolorans, and Immersaria mehadiana are described as new species from Spain and Romania, respectively. A new combination, Immersaria cupreoatra is proposed, and a revised concept of the genera Bellemerea and Immersaria is supplied.
Ascoma Ontogeny: is this Character Set of any Use in the Systematics of Lichenized Ascomycetes?
Authors: Döring Heidi , Lumbsch H. Thorsten 
Published: September 2002

AbstractThe use of ascoma ontogeny in the systematics of lichenized ascomycetes is reviewed briefly. Two recently studied examples are discussed to illustrate the use of ontogenetic studies to discover phylogenetic relationships. As one example, the Agyriaceae was mainly circumscribed by the ascus type and included diverse genera. Xylographa is characterized by lirelliform apothecia. However, the ascoma development shares the ontogenetic pattern observed in Trapelia and its placement in the family was confirmed. In contrast, Anamylopsora exhibited a substantially different apothecial development and was separated as a family of its own. As a second example, the Candelariaceae is based on chemical characters. With the detection of pulvinic acid derivatives also in the genus Lecanora, the distinction of the Candelariaceae and Lecanoraceae became doubtful. Therefore, the ascoma ontogeny was employed to evaluate this classification and is illustrated here in detail for Candelaria fibrosa. The substantial similarity of the ascoma development found in both families suggests that both might be better united. Finally, a general discussion of the significance of ontogenetic characters in lichen taxonomy is included.
What Molecular Biology has to Tell us at the Species Level in Lichenized Fungi
Authors: Bridge Paul D. , Hawksworth David L. 
Published: September 2002

AbstractMolecular biological techniques now provide many opportunities for determining relationships between organisms. In lichen-forming fungi, polymerase chain reaction (PCR) amplification can be undertaken with primers that have enhanced specificity for fungi, allowing the recovery of precise regions of the genome of the fungal partner. Such PCR techniques are suitable for the analysis of both fresh and dried specimens of great age, and as the techniques require only minimal amounts of starting material, they are suitable for the analysis of large numbers of specimens. PCR can be used to examine both conserved and variable regions of the fungal genome that may be taxonomically significant, and variability in these sequences can be used to describe species boundaries. The ease of analysis of large numbers of specimens without the need to purify or culture the fungal partner makes analysis and comparison of infra- and inter-specific relationships possible, and provides valuable information into their genetic background. Most molecular analyses undertaken with lichen-forming fungi have considered variation within ribosomal RNA clusters, and in this paper we consider the application and interpretation of such PCR-based analysis in the circumscription of species and in determining concepts for individuality and infra-specific groupings.
The Use of Metabolic Data in Lichenology at the Species and Subspecific Levels
Authors: Lumbsch H. Thorsten 
Published: September 2002

AbstractThe different views on the taxonomic use of chemical characters in lichenology are reviewed using the opposing opinions of W. L. Culberson and Rogers and the somewhat intermediate position of Hawksworth as examples. The differing significance of secondary metabolites is illustrated with two examples in the genus Lecanora. In L. campestris and similar species, the chemistry has been useful to differentiate morphologically similar species, which subsequently were found to differ in minute anatomical differences as well. However, in L. caesiorubella, a remarkable chemical variation can be observed that is not correlated with other differences and is thus interpreted as intraspecific variation. An a posteriori valuation of the taxonomic significance of metabolic data is preferred.