bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitation of Human Immunodeficiency Virus Type 1 DNA Forms with the Second Template Switch in Peripheral Blood Cells Predicts Disease Progression Independently of Plasma RNA Load
Authors: Kostrikis Leondios G. , Touloumi Giota , Karanicolas Rose , Pantazis Nikos , Anastassopoulou Cleo , Karafoulidou Anastasia , Goedert James J. , Hatzakis Angelos 
Published: September 2002

ABSTRACT

There are several forms of human immunodeficiency virus type 1 (HIV-1) DNA in peripheral blood T cells and lymph nodes in untreated HIV-1-infected individuals and in patients whose plasma HIV-1 RNA levels are suppressed by long-term combination antiretroviral therapy. However, it remains to be established whether the concentration of HIV-1 DNA in cells predicts the clinical outcome of HIV-1 infection. In this report, we measured the concentration of HIV-1 DNA forms which has undergone the second template switch (STS DNA) and 2-long-terminal-repeat DNA circles in peripheral blood mononuclear cell (PBMC) samples. To do this, we used molecular-beacon-based real-time PCR assays and studied 130 patients with hemophilia in the Multicenter Hemophilia Cohort Study. We assessed the influence of baseline HIV-1 STS DNA levels on the progression of HIV-1 disease in the absence of combination antiretroviral therapy by Kaplan-Meier and Cox regression analysis. Among the patients who progressed to AIDS, the median levels (interquartile ranges) of STS HIV-1 DNA in PBMC were significantly higher than those of patients who remained AIDS free during the 16 years of follow-up (1,017 [235 to 6,059] and 286 [31 to 732] copies per 10
6
PBMC, respectively;
P
< 0.0001). Rates of progression to death and development of AIDS varied significantly (log rank
P
< 0.001) by quartile distribution of HIV-1 STS DNA levels. After adjustment for age at seroconversion, baseline CD4
+
T-cell counts, plasma viral load, and T-cell-receptor excision circles, the relative hazards (RH) of death and AIDS were significantly increased with higher HIV-1 STS DNA levels (adjusted RH, 1.84 [95% confidence interval {CI}, 1.30 to 2.59] and 2.62 [95% CI, 1.75 to 3.93] per 10-fold increase per 10
6
PBMC, respectively). HIV-1 STS DNA levels in each individual remained steady in longitudinal PBMC samples during 16 years of follow-up. Our findings show that the concentration of HIV-1 STS DNA in PBMC complements the HIV-1 RNA load in plasma in predicting the clinical outcome of HIV-1 disease. This parameter may have important implications for understanding the virological response to combination antiretroviral therapy.
Signal Transduction and Transcription Factor Modification during Reactivation of Epstein-Barr Virus from Latency
Authors: Bryant Helen , Farrell Paul J. 
Published: September 2002

ABSTRACTReactivation of Epstein-Barr virus (EBV) from latency involves activation of the Zp promoter of the EBV BZLF1 gene. This occurs rapidly and efficiently in response to cross-linking the B-cell receptor on Akata Burkitt's lymphoma cells. After optimizing conditions for induction, signal transduction responses to B-cell receptor cross-linking were observed within 10 min, well before any autoactivation effects of BZLF1 protein. The primary events in reactivation were shown to involve dephosphorylation of the myocyte enhancer factor 2D (MEF-2D) transcription factor via the cyclosporin A-sensitive, calcium-mediated signaling pathway. This and other signal transduction events were correlated with the quantitative promoter analysis reported in the accompanying paper (U. K. Binné, W. Amon, and P. J. Farrell, this issue). Dephosphorylation of MEF-2D is known to be associated with histone acetylase recruitment, correlating with the histone acetylation at Zp during reactivation that we reported previously (Jenkins et al., J. Virol.74:710-720, 2000). Histone deacetylation in response to phosphorylated MEF-2D can be mediated by class I or class II histone deacetylases (HDACs); HDAC 7 was the most readily detected class II HDAC in Akata and Raji cells, suggesting that it may be involved in Zp repression during latency.
Role for Human Immunodeficiency Virus Type 1 Membrane Cholesterol in Viral Internalization
Authors: Guyader Mireille , Kiyokawa Etsuko , Abrami Laurence , Turelli Priscilla , Trono Didier 
Published: September 2002

ABSTRACT
The membrane of human immunodeficiency virus type 1 (HIV-1) virions contains high levels of cholesterol and sphingomyelin, an enrichment that is explained by the preferential budding of the virus through raft microdomains of the plasma membrane. Upon depletion of cholesterol from HIV-1 virions with methyl-β-cyclodextrin, infectivity was almost completely abolished. In contrast, this treatment had only a mild effect on the infectiousness of particles pseudotyped with the G envelope of vesicular stomatitis virus. The cholesterol-chelating compound nystatin had a similar effect. Cholesterol-depleted HIV-1 virions exhibited wild-type patterns of viral proteins and contained normal levels of cyclophilin A and glycosylphosphatidylinositol-anchored proteins. Nevertheless, and although they could still bind target cells, these virions were markedly defective for internalization. These results indicate that the cholesterol present in the HIV-1 membrane plays a prominent role in the fusion process that is key to viral entry and suggest that drugs capable of disturbing the lipid composition of virions could serve as a basis for the development of microbicides.
A Structural Model of Pestivirus E
rns
Based on Disulfide Bond Connectivity and Homology Modeling Reveals an Extremely Rare Vicinal Disulfide
Authors: Langedijk J. P. M. , van Veelen P. A. , Schaaper W. M. M. , de Ru A. H. , Meloen R. H. , Hulst M. M. 
Published: September 2002

ABSTRACT

E
rns
is a pestivirus envelope glycoprotein and is the only known viral surface protein with RNase activity. E
rns
is a disulfide-linked homodimer of 100 kDa; it is found on the surface of pestivirus-infected cells and is secreted into the medium. In this study, the disulfide arrangement of the nine cysteines present in the mature dimer was established by analysis of the proteolytically cleaved protein. Fragments were obtained after digestion with multiple proteolytic enzymes and subsequently analyzed by liquid chromatography-electrospray ionization mass spectrometry. The analysis demonstrates which cysteine is involved in dimerization and reveals an extremely rare vicinal disulfide bridge of unknown function. With the assistance of the disulfide arrangement, a three-dimensional model was built by homology modeling based on the alignment with members of the Rh/T2/S RNase family. Compared to these other RNase family members, E
rns
shows an N-terminal truncation, a large insertion of a cystine-rich region, and a C-terminal extension responsible for membrane translocation. The homology to mammalian RNase 6 supports a possible role of E
rns
in B-cell depletion.
Evolutionary Dynamics of Viral Attenuation
Authors: Badgett Marty R. , Auer Alexandra , Carmichael Leland E. , Parrish Colin R. , Bull James J. 
Published: September 2002

ABSTRACT
The genetic trajectory leading to viral attenuation was studied in a canine parvovirus (CPV) strain grown on dog kidney cells for 115 transfers. Consensus sequences of viral populations at passages 0, 3, 30, 50, 80, and 115 were obtained from PCR products covering 86% of the genome; clones from each of the 80th and 115th passages were also sequenced, covering 69% of the genome. Sixteen changes were fixed in the 115th-passage virus sample. Levels of polymorphism were strikingly different over time, in part because of a plaque-cloning step at passage 112 that reduced variation: passage 80 had 19 variants common among the clones, but passage 115 had only a single common variant. Several mutations increased in the culture at the same time, with most reaching fixation only after the 80th passage. The pattern of evolution was consistent with recombination and not with separate selective sweeps of individual mutations. Thirteen of the changes observed were identical to or at the same positions as changes observed in other isolates of CPV or feline panleukopenia virus.
NONCOMMUTATIVE FIELD THEORY AND THE DYNAMICS OF QUANTUM HALL FLUIDS
Authors: BARBÓN J. L. F. , PAREDES A. 
Published: September 2002

We study the spectrum of density fluctuations of fractional Hall fluids in the context of the noncommutative hydrodynamical model of Susskind. We show that, within the weak-field expansion, the leading correction to the noncommutative Chern–Simons Lagrangian (a Maxwell term in the effective action), destroys the incompressibility of the Hall fluid due to strong UV/IR effects at one loop. We speculate on possible relations of this instability with the transition to the Wigner crystal, and conclude that calculations within the weak-field expansion must be carried out with an explicit ultraviolet cutoff at the noncommutativity scale. We point out that the noncommutative dipoles exactly match the spatial structure of the Halperin–Kallin quasiexcitons. Therefore, we propose that the noncommutative formalism must describe accurately the spectrum at very large momenta, provided no weak-field approximations are made. We further conjecture that the noncommutative open Wilson lines are "vertex operators" for the quasiexcitons.
UV Absorbance By Thallus Extracts of Umbilicate Lichens
Authors: Fahselt Dianne 
Published: September 2002

AbstractEleven stands of umbilicate lichens exhibiting a range of variabilities in enzyme banding patterns were compared on the basis of the ultraviolet (UV)absorbing properties of thallus extracts. Stands of Umbilicaria veilea, which were some of the most variable enzymatically, had the lowest UV absorbancy in extracts, and stands of Lasallia papulosa, which were among the least variable enzymatically, showed more UV absorbance than others. Umbilicaria deusta, U. muhlenbergii and U. mammulata had intermediate levels of absorbance. Negative correlations (P = 005–007) were found between enzyme polymorphism and UV absorbance in the ranges 215–220, 269–271 and 304–305 nm. There was also a significant negative correlation at P = 003 between enzyme variability and thallus dry weight extractable with either ethanol or acetone.
Decomposition studies on New Zealand and antarctic lichens
Authors: Greenfield L. G. 
Published: September 2002

AbstractThe decomposition of ground, dead (oven-dried) lichens has been studied in laboratory experiments that aimed to simulate decomposition in nature. Enzymes, common in soil animal guts and soil microbes, solubilized 29% of the lichen weight and 25% of lichen nitrogen. Approximately 9% of lichen nitrogen was mobilized to mineral forms during 97 days' incubation in soil or sand. Low moisture levels reduced the amount of nitrogen mobilized. In short-term (30 days) incubation studies, lichens at optimum moisture but low temperature lost 9% of their initial dry weight due to microbial metabolism. In contrast, lichens incubated for 30 and 135 days at similar moisture levels but higher temperatures lost 19% and 30% respectively of their initial dry weight due to microbial metabolism.
Phaeographina Buxi, A New Genus And Species For The European Lichen Flora
Authors: Etayo J. 
Published: September 2002

AbstractPhaeographina buxi is described from Buxus sempervirens to the south of the Pyrenees. It lives in canyons and geomorphologically similar habitats with a rich assemblage of epiphyllous lichens. The tropical genus Phaeographina is reported for the first time on the European continent.
The Lichen Genus Bactrospora
Authors: Egea J. M. , Torrente P. 
Published: September 2002

AbstractTwenty species and one variety of the genus Bactrospora Massal. are revised. The following new species are described: B. arthonioides sp. nov., B. brodoi sp. nov., B. carneopallida sp. nov., B. incana sp. nov., B. intermedia sp. nov., and B. spiralis sp. nov. Six species of Lecanactis and one of Bacidia are transferred to Bactrospora. A key is given.
Biatora Meiocarpa (NYL.) Arnold, a Misunderstood Species
Authors: Ekman Stefan 
Published: September 2002

AbstractBiatora meiocarpa (Nyl.) Arnold (Lecanorales, lichenized Ascomycotina) is described and compared with some of its relatives, particularly B. helvola Körber ex Hellbom (syn. Lecideahelvola), a species with which it has often been confused. Biatora meiocarpa and B. helvola differ in (1) width of the paraphysis tops, (2) hymenium height, (3) apothecium width, (4) gelatinization of the paraphyses, (5) composition of the excipulum (hyphae with ellipsoid or shortly rectangular lumina in B. meiocarpa, narrowly linear lumina in B. helvola), (6) chemistry (1-2 triterpenoids or no substances in B. meiocarpa, gyrophoric acid plus 1-2 triterpenoids in B. helvola), and (7) length and shape of conidia. The variation in the first three characters overlaps but one–way analysis of variance (ANOVA) shows that B. meiocarpa and B. helvola differ significantly in each of these characters. Three further characters were subjected to ANOVA: spore length, spore width and length/width ratio of the spores. No statistically significant differences were observed in these characters.Biatora meiocarpa generally occurs on smooth bark of broad–leaved trees and shrubs. It is known from northern Sweden, Finland, and northwestern Russia
Notes on Amandinea Petermannii Comb.nov. (Physciaceae) from Antarctica
Authors: Matzer M. , Mayrhofer H. , Scheidegger Ch. 
Published: September 2002

AbstractThe new combination Amandinea petermannii (Hue) Matzer, Mayrh. & Scheidegger; is proposed. The taxonomy, morphology, anatomy, chemistry, ecology and distribution of this lichen are discussed. Rinodina convoluta D. C. Lindsay is synonym of A. petermannii.
Deux Associations Lichéniques Corticoles Nouvelles, Mésoméditerranéennes, Sciaphiles: Le Ramonio-Striguletum Mediterraneae Et Le Striguletum Affinis
Authors: Bricaud Olivier , Roux et Claude 
Published: September 2002

AbstractA description is given of the corticolous, sciaphilous lichen associations Ramonio-Stiguletum mediterraneae Bricaud & Roux ass. nov. and Striguletum affinis Bricaud & Roux ass. nov. These associations occur mainly in mesomediterranean Quercus ilex forests and less usually in mesomediterranean or supramediterranean Quercus pubescens forests. The former usually grow on the more or less decayed rhytidome of Quercus ilex, the latter exclusively on Hedera helix trunks.
New and Noteworthy Lichenicolous Fungi From Southernmost South America
Authors: Wedin Mats 
Published: September 2002

AbstractAbrothallus secedens Wedin & R. Sant. sp. nov., commensalistic on species of Pseudocyphellaria, from Argentina and Kenya and Abrothallus granulatae Wedin sp. nov., parasitic on Pseudocyphellariagranulata, from Argentina (Tierra del Fuego) are described. Vouauxiomycesgranulatae Wedin sp. nov., is regarded as the anamorph of A. granulatae. Sphaerellothecium minutum Hafellner is recorded for the first time from Antarctica and South America, Phaeosporobolus alpinus R. Sant., Alstrup & D. Hawksw. from Antarctica and Argentina, Arthonia epiphyscia Nyl., Dacampia rufescentis (Vouaux) D. Hawksw., Polycoccum pulvinatum (Eitner) R. Sant. And Stigmidium pumilum (Lettau) Matzer & Hafellner from South America and Nesolechia oxyspora (Tul.) Massal. and Pyrenidium actinellum Nyl. from Chile.
Bacidia Caesiovirens, A New Lichen Species from Western Europe
Authors: Ekman Stefan , Holien Håkon 
Published: September 2002

AbstractBacidia caesiovirens S. Ekman & Holien sp. nov. is described from Norway, and the British Isles. It occurs on trunks of deciduous trees in coastal forests. This species is usually sterile and is characterized by its conspicuously blue-green, granular thallus, which contains a bluish, N+ purple pigment. It is closely related to B. biatorina (Körb.) Vain., but differs from this species in a number of features apart from thallus pigmentation: the thallus granules are smaller, the amount of hyphal projections from the surface of the thallus granules is larger, and the internal pigmentation of the apothecia is different. Bacidia auerswaldii (Hepp ex Stizenb.) Mig. has a similarly granular thallus but differs from B. biatorina and B. caesiovirens in having wide, fusiform spores and smaller thallus granules. Bacidia absistens (Nyl.) Arnold has an internal apothecium pigmentation similar to B. caesiovirens, but differs in having a smooth thallus, and an abundance of minute crystals in the excipulum.
Aquatic Species of Verrucaria in Eastern Australia
Authors: McCarthy P. M. 
Published: September 2002

AbstractTen species and one variety of Verrucaria Schrader are known from creeks and rivers in eastern Australia. Verrucaria austroalpina sp. nov., V. inconstans sp. nov., V. mundula sp. nov., V. mundula var. deminuta var. nov., V. phaeoderma sp. nov., V. tasmanica sp. nov. and V. tholocarpa sp. nov. are described. The combination V. puncticulata (P. M. McCarthy) P. M. McCarthy is made for V. hydrela var. puncticulata P. M. McCarthy. Verrucaria margacea (Wahlenb.)Wahlenb. and V. praetermissa (Trevisan) Anzi are reported from the Southern Hemisphere for the first time.
Aphanopsidaceae—A New Family of Lichenized Ascomycetes
Authors: Printzen C. , Rambold G. 
Published: September 2002

AbstractThe monotypic lichen genera Aphanopsis and Steinia have various ecological and anatomical features in common. Both genera exhibit a particular ascus type and are recognized as representing a family of their own, the Aphanopsidaceae. This family is preliminarily placed in the order Lecanorales.
Chlorophyll A Fluorescence and Chlorophyll Content in Parmelia Quercina Thalli from a Polluted Region of Northern Castellon (Spain)
Authors: Calatayud A. , Sanz M. J. , Calvo E. , Barreno E. , del Valle-Tascon S. 
Published: September 2002

AbstractMeasurements of modulated chlorophyll a fluorescence emission and chlorophyll content were made in thalli of Parmelia quercina collected from northern Castellon(Spain). Althoug high air pollution concentrations have been measured in this area, the ratio of variable to maximal fluorescence is unaffected. Following dark-adaptation, the response to irradiance of chlorophyll fluorescence was examined. With respect to control samples, thalli collected in northern Castellon consistently showed differences in fluorescence quenching, the efficiency of excitation energy capture and quenching of basal fluorescence. However, the quantum ield of photochemistry and non-cyclic electron flow were not affected. The changes in chlorophyll fluorescence parameters were observed in the absence of both visual injuries and decrease in chlorophyll content. The results are discussed with regard to the possible role of environmental stress in chlorophyll fluorescence yield.
Distribution and Succession of Lichens Associated with Prunus Spinosa at Dungeness, England
Authors: Ferry B. W. , Lodge E. 
Published: September 2002

AbstractThe distribution and succession of epiphytic and other associated lichens on blackthorn (Prunus spinosa) growing on the shingle at Dungeness is described. Some 33 epiphytic species, which exhibited a range of ecological strategies from pioneer to late colonizers, were recorded. Both the rate of change of status (age) of blackthorns and the progress of lichen colonization seemed to depend on whether the bushes were growing directly on shingle or on adjacent alluvial soil; both processes seeming to be more rapid on the former substratum. Terricolous lichens, of which 18 were recorded, generally appeared late in the succession and mostly amongst bushes growing on shingle. Rabbits often invaded the blackthorns, especially those on alluvium, and probably contributed to the lack of terrestrial lichens under these bushes. Blackthorns growing on shingle tended to be more prostrate in form than those on alluvium.
New Foliicolous Species of Strigula from Lord Howe Island, Australia
Authors: McCarthy P. M. , Streimann H. , Elix J. A. 
Published: September 2002

AbstractStrigula fossulicola sp. nov. and S. oceanica sp. nov. are described from Lord Howe Island, New South Wales, Australia. They inhabit the leaves of endemic shrubs and trees and are distinguished by ascospores that fracture at the septum prior to maturity.
Some Aspects of the Water Relations of the Lichen Parmotrema Tinctorum Measured Using Thermocouple Psychrometry
Authors: Beckett R. P. 
Published: September 2002

AbstractThe thermocouple psychrometer was used to determine water potential, Ψ and its components in the lichen Parmotrema tinctorum. Data suggested that using conventional pressure-volume curves to study the water relations of lichens may give anomalous results, possibly because lichens may contain appreciable amounts of intercellular water. A way of correcting pressure-volume curves to remove the effect of intercellular water is discussed. Parmotrema tinctorum had a very low osmotic potential at full turgor (c. −2.5 MPa), and a low bulk modulus of elasticit (c. 2.1 MPa). As a result, P. tinctorum lost turgor only when the relative water content dropped below 0.47. Likely benefits of this for the lichen are discussed.
Two New Freshwater Species of Verrucariaceae From Yunnan, China
Authors: Harada H. , Wang L.-S. 
Published: September 2002

AbstractTwo species of Verrucariaceae, Endocarpon globosum Harada & L.-S. Wangsp. nov., and Staurothele yunnana Harada & L.-S. Wang sp. nov., are described. Both grow on stones submerged in a stream on Meili Snow Mountain in NW Yunnan, China.
Spirographa Vinosa, a New Odontotremoid Fungus on Ochrolechia and Pertusaria
Authors: Holien Håkon , Triebel Dagmar 
Published: September 2002

AbstractSpirographa vinosa Holien & Triebel is described from boreal spruce forest of Norway. It is lichenicolous on different species of Ochrolechia and Pertusaria. Within the genus S. vinosa is characterized by its 8-spored asci, up to 5-septate ascospores with obtuse ends and its apothecial pigments causing aeruginose and purplish reactions with KOH.
Hyalpyrenia Japonica, a Peculiar New Pyrenocarpous Lichen Genus from Japan
Authors: Harada H. 
Published: September 2002

AbstractHyalopyrenia japonica Harada (lichenized Ascomycotina) is described as new genus on the basis of a specimen from friable rock in forests in Chiba-ken, central Japan. It is characterized by a poorly developed crustose thallus, a Trentepohlia phycobiont, immersed perithecia with hyaline walls, simple paraphyses and periphyses, non-amyloid bitunicate asci with an ocular chamber, and transversely septate hyaline spores. Hyalopyrenia is monotypic, and its taxonomic position is uncertain.
Vagnia, a Remarkable Coelomycete Producing a Black Columnar Cirrus on Peltigera in Poland
Authors: Hawksworth David L. , Miadlikowska Jolanta 
Published: September 2002

AbstractThe new genus Vagnia is introduced for the single species V. cirriformia discovered on thalli of Peltigera in Poland; it appears to be a pathogen as the cortex is destroyed in a rounded patch within which the conidiomata occur. The fungus is characterized by cupulate to doliiform conidiomata clothed in white hairs and from which a black columnar cirrus of conidia arises. The simple ellipsoid conidia are hyaline when viewed individually and are formed enteroblastically from elongate conidiogenous cells supported by branched conidiophores.
Amplification of Fungal rDNA-Its Regions from Non-Fertile Specimens of the Lichen-Forming Genus Parmelia
Authors: Crespo Ana , Bridge Paul D. , Hawksworth David L. 
Published: September 2002

AbstractA method is described for the selective amplification of single mycobiont rDNA sequences from vegetative, non-ascomatal material of the lichenized thalli of Parmelia sulcata and P. saxatilis. The method includes a simple DNA extraction procedure employing rhizines, which avoids the use of liquid nitrogen disruption methods and phenol based extractions. The resulting amplified DNA is suitable for restriction enzyme analysis, and can be used to provide material for investigating population distribution and species concepts.