bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence against a Simple Tethering Model for Enhancement of Herpes Simplex Virus DNA Polymerase Processivity by Accessory Protein UL42
Authors: Chaudhuri Murari , Parris Deborah S. 
Published: September 2002

ABSTRACT
The DNA polymerase holoenzyme of herpes simplex virus type 1 (HSV-1) is a stable heterodimer consisting of a catalytic subunit (Pol) and a processivity factor (UL42). HSV-1 UL42 differs from most DNA polymerase processivity factors in possessing an inherent ability to bind to double-stranded DNA. It has been proposed that UL42 increases the processivity of Pol by directly tethering it to the primer and template (P/T). To test this hypothesis, we took advantage of the different sensitivities of Pol and Pol/UL42 activities to ionic strength. Although the activity of Pol is inhibited by salt concentrations in excess of 50 mM KCl, the activity of the holoenzyme is relatively refractory to changes in ionic strength from 50 to 125 mM KCl. We used nitrocellulose filter-binding assays and real-time biosensor technology to measure binding affinities and dissociation rate constants of the individual subunits and holoenzyme for a short model P/T as a function of the ionic strength of the buffer. We found that as observed for activity, the binding affinity and dissociation rate constant of the Pol/UL42 holoenzyme for P/T were not altered substantially in high- versus low-ionic-strength buffer. In 50 mM KCl, the apparent affinity with which UL42 bound the P/T did not differ by more than twofold compared to that observed for Pol or Pol/UL42 in the same low-ionic-strength buffer. However, increasing the ionic strength dramatically decreased the affinity of UL42 for P/T, such that it was reduced more than 3 orders of magnitude from that of Pol/UL42 in 125 mM KCl. Real-time binding kinetics revealed that much of the reduced affinity could be attributable to an extremely rapid dissociation of UL42 from the P/T in high-ionic-strength buffer. The resistance of the activity, binding affinity, and stability of the holoenzyme for the model P/T to increases in ionic strength, despite the low apparent affinity and poor stability with which UL42 binds the model P/T in high concentrations of salt, suggests that UL42 does not simply tether the Pol to DNA. Instead, it is likely that conformational alterations induced by interaction of UL42 with Pol allow for high-affinity and high-stability binding of the holoenzyme to the P/T even under high-ionic-strength conditions.
Addition of a Single gp120 Glycan Confers Increased Binding to Dendritic Cell-Specific ICAM-3-Grabbing Nonintegrin and Neutralization Escape to Human Immunodeficiency Virus Type 1
Authors: Lue James , Hsu Mayla , Yang David , Marx Preston , Chen Zhiwei , Cheng-Mayer Cecilia 
Published: September 2002

ABSTRACTThe potential role of dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN) binding in human immunodeficiency virus transmission across the mucosal barrier was investigated by assessing the ability of simian-human immunodeficiency chimeric viruses (SHIVs) showing varying degrees of mucosal transmissibility to bind the DC-SIGN expressed on the surface of transfected cells. We found that gp120 of the highly transmissible, pathogenic CCR5-tropic SHIVSF162P3bound human and rhesus DC-SIGN with an efficiency threefold or greater than that of gp120 of the nonpathogenic, poorly transmissible parental SHIVSF162, and this increase in binding to the DC-SIGN of the SHIVSF162P3envelope gp120 translated into an enhancement of T-cell infection intrans. The presence of an additional glycan at the N-terminal base of the V2 loop of SHIVSF162P3gp120 compared to that of the parental virus was shown to be responsible for the increase in binding to DC-SIGN. Interestingly, this glycan also conferred escape from autologous neutralization, raising the possibility that the modification occurred as a result of immune selection. Our data suggest that more-efficient binding of envelope gp120 to DC-SIGN could be relevant to the enhanced mucosal transmissibility of SHIVSF162P3compared to that of parental SHIVSF162.
Bronchoalveolar Fluid Is Not a Major Hindrance to Virus-Mediated Gene Therapy in Cystic Fibrosis
Authors: Rooney C. P. , Denning G. M. , Davis B. P. , Flaherty D. M. , Chiorini J. A. , Zabner J. 
Published: September 2002

ABSTRACTSuccessfully targeting the airway epithelium is essential for gene therapy of some pulmonary diseases. However, the airway epithelium is resistant to virus-mediated gene transfer with commonly used vectors. Vectors that interact with endogenously expressed receptors on the apical surface significantly increase gene transfer efficiency. However, other endogenous components involved in host immunity may hinder virus-mediated gene transfer. We tested the effect of bronchoalveolar lavage liquid (BAL) from patients with cystic fibrosis (CF), BAL from subjects without CF (non-CF BAL),Pseudomonas aeruginosa-derived proteins, and an array of inflammatory proteins on gene transfer mediated by adeno-associated virus type 5 (AAV5) and adenovirus targeted to an apically expressed glycosylphosphatidylinositol-modified coxsackie-adenovirus receptor. We found that neither CF BAL nor its components had a significant effect on gene transfer to human airway epithelium by these vectors. Non-CF BAL significantly impaired adenovirus-mediated gene transfer. Removal of immunoglobulins in non-CF BAL restored gene transfer efficiency. As virus vectors are improved and mechanisms of humoral immunity are elucidated, barriers to successful gene therapy found in the complex environment of the human lung can be circumvented.
Identification and Expression of Immunogenic Proteins of a Disease-Associated Marine Turtle Herpesvirus
Authors: Coberley Sadie S. , Condit Richard C. , Herbst Lawrence H. , Klein Paul A. 
Published: September 2002

ABSTRACT

Herpesviruses are associated with several diseases of marine turtles, including lung-eye-trachea disease (LETD) and fibropapillomatosis. Two approaches were used to identify immunodominant antigens of LETV, the LETD-associated herpesvirus. The first approach targeted glycoprotein B, which is known to be immunogenic and neutralizing in other species. The second strategy identified LETV proteins recognized on Western blots by antibodies in immune green turtle plasma. A 38-kDa protein was resolved by two-dimensional gel electrophoresis, sequenced, and identified as a scaffolding protein encoded by the overlapping open reading frames of UL26 and UL26.5. Glycoprotein B and the scaffolding protein were cloned and expressed in
Escherichia coli
. The expressed proteins were recognized on Western blots by antibodies in immune green turtle plasma. Phylogenetic studies based on UL26, DNA polymerase, and glycoprotein B revealed that LETV clusters with the alphaherpesviruses.
COMPUTING CONTINGENCIES FOR STABLE RELATIONS
Authors: EILERS SØREN , LORING TERRY A. 
Published: September 2002

Close ties between approximation properties for relations on C*-algebra elements and lifting results for the universal C*-algebras the relations generate is a very widespread and useful phenomenon in C*-algebra theory. In this paper, we explore how to achieve results of this kind when the approximation properties and the lifting results are true only in special cases determined by K-theoretical contingencies. To interpolate between properties of these two basic types, we must investigate C*-algebras given by softened relations, in particular with emphasis on their K-theory. A surprisingly weak correlation between the K-theory of the C*-algebras given by exact and softened relations leads to delicate problems which must be treated with care. As an example of a set of relations which are prone to an analysis of this kind we study the pairs of unitaries commuting up to rational rotation.
Cladonia Azorica in the British Isles
Authors: Orange Alan 
Published: September 2002

AbstractCladonia azorica is widespread in western Great Britain, mainly as the grey colour-form lacking usnic acid. Cladonia azorica is distinguished from the related species C. portentosa and C. mediterranea by the presence of fumarprotocetraric acid, and from C. ciliata by a number of characters including the presence of perlatolic acid. The structure of the pycnidial wall may have some taxonomic significance in Cladonia subgenus Cladin
New and Interesting Species of Porina, Mainly from Tasmanian Rainforest
Authors: McCarthy P. M. , Kantvilas G. 
Published: September 2002

AbstractPorina constrictospora sp. nov., P. decrescens sp. nov., P. hyperleptalea sp. nov. and P. sylvatica sp. nov. are described from western Tasmania. All appear to be especially common m cool-tempertate tamforest. A Key is provided to xhe six corticolous species of Porina known from Tasmania.
Four New Species of Caloplaca from Antarctica
Authors: Olech Maria , Søchting Ulrik 
Published: September 2002

AbstractFour new species of Caloplaca are described from Antarctica: C. buelliae is parasitic on Buellia, C. iomma has a characteristic deep reddish orange colour on the apothecia, C. psoromatis is parasitic on Psoroma and Pannaria, and C. siphonospora is a parasitic species of mosses, very similar to C. nivalis, but with much shorter spores.
The Lobarion, an Epiphytic Community of Ancient Forests Threatened by Acid Rain
Authors: Gauslaa Y. 
Published: September 2002

AbstractLobaria pulmonaria and other members of the Lobarion were found to inhabit drainage channels below old and large wounds on the trunks of various deciduous trees in stands of long ecological continuity in a forest reserve dominated by Picea abies in southeastern Norway. Such channels were richer in minerals and had a higher pH than normal bark, which was covered with more acidophytic epiphytic communities, mainly the Pseudevernion. Chemical microhabitat differentiation was most clear in edaphically poor sites. The restriction of a previously ubiquitous Lobarion to mineral-rich microsites on stems is probably an effect of acid rain. Since acidification seems to make the Lobarion more dependent upon old and damaged stems, modern forestry probably aggravates the damage caused by acid rain.
Labyrintha Implexa (Porpidiaceae), a New Genus and Species from New Zealand
Authors: Malcolm W. M. , Elix J. A. , Owe-Larsson B. 
Published: September 2002

AbstractLabyrintha Malcolm, Elix & Owe-Larsson, a new genus in the Porpidiaceae, is described. It is based on the crustose taxon L. implexa Malcolm, Elix & Owe-Larsson, a saxicolous species from acidic rocks in alpine and subalpine areas in New Zealand. Labyrintha is distinguished from closely related genera by a combination of characters: cephalodia, immersed apothecia, large, simple ascospores (60–70 × 30–35 μm), halonate when young and dark-pigmented when mature, fusiform conidia, no cortex, no thallus chemistry, densely packed anticlinal hyphae, and a previously undescribed thallus anatomy in which the photobiont is arranged in anastomosing vertical sheets.
Thelopsis Foveolata, A New Lichen from Northern Spain
Authors: Renobales G. , Barreno E. , Atienza V. 
Published: September 2002

AbstractThelopsis foveolata Renob. & Barreno sp. nov., is described from Northern Spain. It appears to be very rare and easily overlooked, but has a well-defined ecology. It grows on limestone within sciaphilous and humidity-loving communities, such as Gyalectetum leucaspidis and Petractinetum hypoleucae. The pycnidia and conidiogenous cells are described and illustrated, this being the first detailed account of these structures in the genus Thelopsis.
Comparative Studies on Xanthoria Parietina, a Pollution Resistant Lichen, and Ramalina Duriaei, a Sensitive Species. II. Evaluation of Possible Air Pollution-Protection Mechanisms
Authors: Silberstein L. , Siegel B. Z. , Siegel S. M. , Mukhtar A. , Galun M. 
Published: September 2002

AbstractSurveys of the distribution of the lichens Xanthoria panetina and Ramalina duriaei in Israel showed that environments with air pollution had no damaging effectson X. panetina, whereas R. duriaei had disappeared from polluted environments: physiological studies supported this relative sensitivity. Investigations of possible defence mechanisms protecting X. parietina from the damaging effects of air pollution showed a multitude of possible protective systems. These included constitutive avoidance such as: efficient buffering capacity; a relatively high potassium content; and antioxidation by parietin, and induced tolerance such as: SO2 oxidation to non-toxic sulphate; increased glutathione content; induced praline and arginine synthesis; and increased detoxification of active oxygen forms.
Lecania Poeltii, A New Lichen Species From Portugal And Northern Africa
Authors: van den Boom P. P. G. , Alonso F. L. , Egea J. M. 
Published: September 2002

AbstractLecania poeltii v.d. Boom, Alonso & Egea sp. nov. is described from Portugal and northern Africa. The species is characterized by its inconspicuous hairs on thallus and apothecia, in which it differs from the other known species of the genus.
The Distinction of Punctelia Perreticulata and P. Subrudecta (Parmeliaceae, Lecanorales)
Authors: Adler M. T. , Ahti T. 
Published: September 2002

AbstractPunctelia perreticulata (Räsäanen) G. Wilh. & Ladd is recognized as a distinct species. The only consistent differences between P. perreticulata and P. subrudecta (Nyl.) Krog are the shape and length of conidia. Both species are widespread in the world. In P. perreticulata, there are differences in conidial length among the European, American and Australasian samples studied, but they neither correlate with differences observed in other morphological traits nor with the substratum. An epitype is selected to support the holotype of P. perreticulata, because its identity is uncertain due to the absence of conidia.
Notes on the Genus Usnea Dill. Ex Adanson
Authors: Clerc Philippe 
Published: September 2002

AbstractUsnea quercina Bystrek & Gòrzynska, based on heterogeneous type material, is lectotypified and becomes a synonym of U. wirthii P. Clerc. Usnea wirthii is new for South America. A distribution map of U. madeirensis Motyka (Syn. U. silesiaca Motyka) in Europe is given. Usnea hesperina Motyka (Syn. U. elongate Motyka, U. schadenbergiana Göpp & Stein, U. subgracilis Vain., U. subplicata (Vain.) Motyka) is new for Africa, Asia and South America. Usnea hirta (L.) F. H. Wigg. (Syn. U. corrugate Motyka, U. foveata Vain., U. leprosa Motyka) is new for Africa. Usnea subscabrosa Nyl. ex Motyka (Syn. U. santae-annae Motyka) is new for South America. The holotype of U. marocana Motyka (=U. mutabilis Stirt.) was found in LBL.
Structural Studies on the Galactomannans of Lichens of the Genus Cladonia
Authors: Woranovicz S. M. , Gorin P. A. J. , Marcelli M. P. , Torri G. , Iacomini* M. 
Published: September 2002

AbstractGalactomannans were isolated from Cladonia signata, C. furcata, C. imperialis, and C. clathrata via successive alkaline extraction and precipitation with Fehling solution and Cetavlon. They were investigated using ⊃13C-NMR spectroscopy, methylation analysis, and Smith degradation, and their specific rotations and monosaccharide compositions determined. As with galactomannans of other Cladonia species, they contained (l →6)-linked main chains of α-mannopyranose, which were non-substituted (structure 4 in Fig. 2), monosubstituted at O-2 with α-mannopyranose (structure 6) or α-galactopyranose (structure 1), O-4 with β-galactopyranose (structure 2), and disubstituted at O-2 and O-4 with α-mannopyranosyl and β-galactopyranosyl units, respectively (structure 5). Disubstitution was present to a greater extent in the galactomannans of C. clathrata and C. imperialis than in those of C. signata and C. furcata. In the case of the galactomannans of C. furcata, C. clathrata, and C. imperialis, substitution also occurred at O-2 with O-β-galactofuranosyl-(l→6)-O-α-mannopyranosyl units (structure 7). As observed in previous investigations, the C-l portion of the ⊃13C-NMR of mannose-containing polysaccharides is typical of the lichen species. However, those of galactomannans of C. imperialis and C. clathrata are almost identical and, although other chemical data showed many structures in common, some differences were evident.
The ‘Mediterranean’ Ramalina Panizzei North of the alps: Morphological, Chemical and rDNA Sequence Data
Authors: Groner Urs , LaGreca Scott 
Published: September 2002

AbstractRamalina panizzei De Not. is reported from Switzerland and north of the Alps for the first time. Recent collections and thalli found amongst specimens of R. fastigiata (Pers.) Ach. are described; the species is obviously not restricted to the Mediterranean. The confusion in several herbaria around this and related corticolous species, particularly R. subgeniculata Nyl. and R. fastigiata, can be traced back to imprecise original and subsequent diagnoses, all of which lack a clear species delimitation. Similarities and differences of these species are discussed. In addition, sequences from the rDNA ITS regions were determined for two individuals of R. panizzei and two of R. fastigiata, including one of each from a site where both species grow intermixed. Kimura 2-parameter genetic-distance estimates indicate that R. panizzei and R. fastigiata are as different from each other as either is from the reference species R. siliquosa (Hudson) A. L. Sm. s.l. A broad-based taxonomic revision of involved species is not possible due to the limited number of analyses, but the results demonstrate the potential for using DNA sequence data to investigate species-level questions in lichens. Based on morphology, chemistry, and DNA sequence data, R. panizzei is retained as a distinct species.
A New Technique for Photobiont Culturing and Manipulation
Authors: Goldsmith S.J. , Thomas M.A. , Gries C. 
Published: September 2002

AbstractComparisons of whole-lichen physiology to the respective photobionts have often been unclear due to inherent differences in isolated photobiont culturing techniques. The use of 13-mm-diameter cellulose-acetate discs allows photobiont cultures access to nutrient agar medium, while improving ease of manipulation and distinct separation from the agar. Adequate culture growth for experimentation is reached in approximately three weeks, a time comparable to standard nutrient agar and liquid cultures. These discs are then available for use in a variety of manipulative techniques. Chlorophyll determination of an entire algal disc culture is obtainable because the discs readily dissolve in dimethylsulphoxide (DMSO), with no interference in the 400–700 nm range. Photosynthesis and respiration may be measured with standard gas exchange equipment. Photobiont discs allow for fumigation in the gas phase with no increase in external ⊂pH reported to occur during gaseous fumigations in liquid media. The disc system is also useful for fluorescence studies. Trebouxia erici cultures exhibited a CO⊂2 gas exchange on a gram dry weight basis similar to whole lichen systems. The ease with which photobionts can be cultured and manipulated using this system allows for expanded experimentation and comparisons.
The Lichenicolous Fungi on Species of the Genera Baeomyces, Dibaeis, and Icmadophila in Norway
Authors: Ihlen P. G. 
Published: September 2002

AbstractLichenicolous fungi on species of the genera Baeomyces, Dibaeis, and Icrnadophila in Norway include Acarosporium lichenicola Ihien & Tonsberg sp. nov., Cercidospora parva Hafellner & Ihlen sp. nov., Phoma macuhformans Ihien sp. nov., Micarea inquinans (reported new to Scandinavia), Arthrorhaphzs vacillans, Pyrenzdzum actinellurn s. lat., Sphaerellotheciurn coniodes (all new to Norway), Arthrorhaphzs alpina, A. citrinella, A. grisea, A. rnuddii, Dactylospora athallina, D. attendenda, Epilichen glauconigellus, E. scabrosus, Stigmidium icmadophilae, Thelocarpon epibolum, and T. lichenicola. Their anatomy and morphology are described, and a key to the taxa provided. Host preferences are discussed, and distribution maps are provided for the obligately lichenicolous fungi and those that also occur autonomously.
Cultural and molecular characterization of photobionts of Peltigera Membranacea
Authors: Mioa V.P.W. , Rabenau A. , Lee A. 
Published: September 2002

AbstractA molecular study was undertaken to clarify the identity of the photobiont in colourmorphs of the lichen, Peltigera membranacea. Two strains of cyanobacteria, identified as Nosroc sp. by morphology, were cultivated from each of two lichen specimens. Prokaryotic (16S) ribosomal RNA gene fragments were amplified by the polymerase chain reaction (PCR) from DNA extracted from the isolated strains and the lichens, and sequenced directly. Sequences were 98 1% identical between lichen specimens, TDI#AR94 and TDI#AR95, and highly similar to sequences published, or generated in this study from a type culture, for Nostoc. The 16S ribosomal RNA gene sequences (‘ 16S rDNA’) of all four lichen-derived cyanobacteria appeared the same, even though the lichen specimens from which they originated had different sequences. The 16S rDXA from strains 9A and 9B were different from that of specimen TDI#AR94, the thallus from which they were isolated, and instead were the same as that of strains 10A and 10B, and their source, specimen TDI#AR95. When primers selective for the strain 9A sequence were used, however, a small amount of PCR product corresponding to the 16S rDNA of strain 9A was obtained from lichen TDI#AR94. The results confirm that the photobionts of P. membranacea belong to Nostoc, and suggest that genetic differences in the photobiont may be a factor in the occurrence of colourmorphs among cyanolichens.
Fellhanera Viridisorediata, a New Sorediate Species From Sheltered Trees and Shrubs in Western Europe
Authors: Aptroot André , Brand Maarten , Spier Leo 
Published: September 2002

AbstractFelihanera viridisorediata Aptroot, Brand & Spier, a corticolous sorediate species commonly found sterile, is described from fertile material on Juglans glabra in the Netherlands. It was also found with apothecia on, for example, twigs of Vaccinium myrtillus, Lonicera, and other trees. It seems to be common and rapidly spreading in sheltered habitats in Belgium, Germany and the Netherlands, also occasionally on wood, roofs, granite and brick. It is close to other Felihanera species, especially F. seroexpectata and F. viridis, but it differs in the paler soredia, smaller, 1-septate and constricted ascospores and the presence of roccellic acid.
Practice and Prejudice in Lichen Classification
Authors: Tibell Leif 
Published: September 2002

AbstractOrganismal species exist as historical entities, and essentialistic thinking about ‘ defining ’ species and higher taxa should be avoided. Lichens are biological phenomena that are best understood as processes, and they behave very differently from the model organisms of most systematic theories. Classification and phylogenetic reconstructions are seen as different endeavours, having different aims and languages. A hierarchical classification is supported, and recognition of superspecific taxa is seen as a matter of convenience. Superspecific taxa may be recognized as groups having correlated features, whereas the common recognition of such taxa by a priori cardinal characters should be abandoned. Superspecific taxa having correlated features are distinctive and are likely to be monophyletic. Distinctive and phylogenetically coherent grades may need naming to avoid nomenclatural instability. In classifications, the hypothesized monophyletic status of taxa may be indicated by some convention. Phylogenetic reconstruction by cladistic parsimony analyses includes assumptions that need scrutinizing and modifying to improve the methodology. Analyses should be examined with respect to robustness for changes in the frequently applied equal weighting assumption. For some types of data an a priori weight assignment might be possible, or equal weighting may be justified.