bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Secondary Structure That Contains the 5′ and 3′ Splice Sites Suppresses Splicing of Duck Hepatitis B Virus Pregenomic RNA
Authors: Loeb Daniel D. , Mack Amanda A. , Tian Ru 
Published: September 2002

ABSTRACT
Pregenomic RNA (pgRNA) plays two major roles in the hepadnavirus life cycle. It is the mRNA for two proteins required for DNA replication, C and P, and it is the template for reverse transcription. pgRNA is a terminally redundant transcript whose synthesis does not involve RNA splicing. For duck hepatitis B virus (DHBV), a spliced RNA is derived from pgRNA by removal of a single intron. The mechanism for the simultaneous cytoplasmic accumulation of unspliced (pgRNA) and spliced RNA was not known. We found that mutations within two regions of the DHBV genome reduced the level of pgRNA while increasing the level of spliced RNA. One region is near the 5′ end of pgRNA (region A), while the second is near the middle of pgRNA (region B). Inspection of the DHBV nucleotide sequence indicated that region A could base pair with region B. The 5′ and 3′ splice sites of the intron of the spliced RNA are within regions A and B, respectively. Substitutions that disrupted the predicted base pairing reduced the accumulation of pgRNA and increased the accumulation of spliced RNA. Restoration of base pairing, albeit mutant in sequence, resulted in restoration of pgRNA accumulation with a decrease in the level of spliced RNA. Our data are consistent with a model in which splicing of the pgRNA is suppressed by a secondary structure between regions A and B that occludes the splicing machinery from modifying pgRNA.
Characterization of the Putative Replisome Organizer of the Lactococcal Bacteriophage r1t
Authors: Zúñiga Manuel , Franke-Fayard Blandine , Venema Gerard , Kok Jan , Nauta Arjen 
Published: September 2002

ABSTRACT

Analysis of the nucleotide sequence of the genome of the lactococcal bacteriophage r1t showed that it may encode at least two proteins involved in DNA replication. On the basis of its similarity with the G38P protein encoded by the
Bacillus subtilis
phage SPP1, the product of
orf11
(Pro11) is thought to be involved in the initiation of phage DNA replication. This protein was overexpressed in
Lactococcus lactis
and partially purified. Gel retardation analysis using various r1t DNA fragments indicates that Pro11 specifically binds to a sequence located within its cognate gene. DNase I footprinting showed that Pro11 protects a stretch of DNA of 47 bp. This region spans four 6-bp short direct repeats, which suggests that the region contains four binding sites for Pro11. 1,10-Phenanthroline-copper footprinting confirmed the protection of the hexamers. An asymmetric protection pattern of each strand was observed, suggesting that Pro11 contacts each DNA strand separately at contiguous hexamers. We propose a model for the binding of Pro11 to its target sites that may account for the torsion strain required for strand opening at the origin of replication.
Mice Deficient in Perforin, CD4+T Cells, or CD28-Mediated Signaling Maintain the Typical Immunodominance Hierarchies of CD8+T-Cell Responses to Influenza Virus
Authors: Chen Weisan , Bennink Jack R. , Morton Phillip A. , Yewdell Jonathan W. 
Published: September 2002

ABSTRACTCD8 T-cell (TCD8+) responses elicited by viral infection demonstrate the phenomenon of immunodominance: the numbers of TCD8+responding to different viral peptides vary over a wide range in a reproducible manner for individuals with the same major histocompatibility complex class I alleles. To better understand immunodominance, we examined TCD8+responses to multiple defined viral peptides following infection of mice with influenza virus. The immunodominance hierarchy of influenza virus-specific TCD8+was not greatly perturbed by the absence of either perforin or T-helper cells or by interference with B7 (CD80)-mediated signaling. These findings indicate that costimulation by antigen-presenting cells (APCs) or killing of APCs by TCD8+plays only a minor role in establishing the immunodominance hierarchy of antiviral TCD8+in this system. This points to intrinsic features of the TCD8+repertoire as major contributors to immunodominance.
Rev Inhibition Strongly Affects Intracellular Distribution of Human Immunodeficiency Virus Type 1 RNAs
Authors: Cmarko Dusan , Bøe Stig-Ove , Scassellati Catia , Szilvay Anne Marie , Davanger Svend , Fu Xiang-Dong , Haukenes Gunnar , Kalland Karl-Henning , Fakan Stanislav 
Published: September 2002

ABSTRACT

To define the human immunodeficiency virus type 1 (HIV-1) RNA maturation pathways, we analyzed the intracellular distribution of HIV-1 RNA and the viral regulatory proteins Rev and Tat in transfected COS cells and HIV-1-infected lymphoid C8166 cells by means of ultrastructural in situ hybridization using antisense RNA probes and immunoelectron microscopy. The intranuclear viral RNA occurs in ribonucleoprotein fibrils in the perichromatin and interchromatin regions. The simultaneous demonstration of Rev, Tat, Br-labeled RNA, and cellular proteins SC35 and CRM1 in such fibrils reveals the potential of Rev to associate with nascent HIV pre-mRNA and its splicing complex and transport machinery. In a
rev
-minus system, the
env
intron-containing, incompletely spliced viral RNAs are revealed only in the nucleus, indicating that Rev is required to initiate the transport to the cytoplasm. Moreover,
env
intron sequences frequently occur in the periphery of interchromatin granule clusters, while the probe containing the
rev
exon sequence does not associate with this nucleoplasmic domain. When cells were treated with the CRM1 inhibitor leptomycin B in the presence of Rev protein, the
env
intron containing HIV RNAs formed clusters throughout the nucleoplasm and accumulated at the nuclear pores. This suggests that Rev is necessary and probably also sufficient for the accumulation of incompletely spliced HIV RNAs at the nuclear pores while CRM1 is needed for translocation across the nuclear pore complex.
Elevated Chemokine Responses Are Maintained in Lungs after Clearance of Viral Infection
Authors: Weinberg Jason B. , Lutzke Mary L. , Efstathiou Stacey , Kunkel Steven L. , Rochford Rosemary 
Published: September 2002

ABSTRACT
We observed two patterns of chemokine expression in the lungs of mice infected with murine gammaherpesvirus 68: peaks of chemokine expression correlated with or occurred after the peak of viral gene expression. Chemokine expression remained elevated through 29 days postinfection.
Human Herpesvirus 8 Gene Encodes a Functional Thymidylate Synthase
Authors: Gáspár Gábor , De Clercq Erik , Neyts Johan 
Published: September 2002

ABSTRACT
We demonstrate that human herpesvirus 8, obtained from the lymphoma cell line BC-3 as well as from Kaposi's sarcoma lesions, carries a gene that encodes a functional thymidylate synthase (TS). The particular characteristics of this enzyme are studied and compared to the characteristics of TSs encoded by other organisms.
ON THE INDEX AND DILATIONS OF COMPLETELY POSITIVE SEMIGROUPS
Authors: ARVESON WILLIAM 
Published: September 2002

It is known that every semigroup of normal completely positive maps P = {Pt:t≥ 0} of ℬ(H), satisfying Pt(1) = 1 for every t ≥ 0, has a minimal dilation to an E0 acting on ℬ(K) for some Hilbert space K⊇H. The minimal dilation of P is unique up to conjugacy. In a previous paper a numerical index was introduced for semigroups of completely positive maps and it was shown that the index of P agrees with the index of its minimal dilation to an E0-semigroup. However, no examples were discussed, and no computations were made. In this paper we calculate the index of a unital completely positive semigroup whose generator is a bounded operator [Formula: see text] in terms of natural structures associated with the generator. This includes all unital CP semigroups acting on matrix algebras. We also show that the minimal dilation of the semigroup P={ exp tL:t≥ 0} to an E0-semigroup is is cocycle conjugate to a CAR/CCR flow.
Transgenic Mice Harboring Murine Luteinizing Hormone Receptor Promoter/β-Galactosidase Fusion Genes: Different Structural and Hormonal Requirements of Expression in the Testis, Ovary, and Adrenal Gland
Authors: Hämäläinen Tuula , Kero Jukka , Poutanen Matti , Huhtaniemi Ilpo 
Published: September 2002

AbstractIn vivo regulation of the LH receptor (LHR) promoter was studied using transgenic (TG) mice harboring fusion genes containing three different lengths of the LHR promoter (7.4 kb, 2.1 kb, and 173 bp), fused with coding sequence of the Escherichia coli β-galactosidase (β-GAL) reporter gene. The length of the LHR promoter significantly affected the pattern of β-GAL expression. In the testis the shortest promoter directed expression primarily of the full-length β-GAL mRNA, but mainly truncated messages were transcribed from the longer LHR promoter/β-GAL constructs. The case was reversed in the ovary and adrenal gland. Furthermore, we have recently detected strong LHR expression in the adrenal gland of female mice with chronically elevated serum LH. Therefore, the regulation of the adrenal LHR expression was addressed in the present study using the LHR/β-GAL TG mice. Elevated LH levels were achieved in the LHR/β-GAL mice either by gonadectomy or cross-breeding them with TG mice overexpressing a chimeric protein of bovine LH β-subunit and the C-terminal fragment of human chorionic gonadotropin-β. In both models, β-GAL mRNA was found in the adrenal cortex when the 7.4-kb LHR promoter was applied but not in mice carrying the 173-bp LHR promoter. The 7.4-kb construct was activated also in the ovaries in the double TG LHR(β-GAL)/bovine LH β-subunit/C-terminal fragment of human chorionic gonadotropin-βmice in some theca-interstitial cells surrounding the follicles. Hence, the LHR promoter elements essential for directing β-GAL expression to the adrenal gland and ovary (7.4 kb) are different from those recently shown to be essential for the testicular expression (173 bp). In conclusion, elevated serum LH concentrations were found seminal for the LHR promoter activation in the ovaries and adrenals, and different lengths of the promoter are responsible for reporter gene expression in the testis, ovary, and adrenal gland.
Ovarian Stanniocalcin Is Structurally Unique in Mammals and Its Production and Release Are Regulated through the Luteinizing Hormone Receptor
Authors: Paciga Mark , Watson Andrew J. , DiMattia Gabriel E. , Wagner Graham F. 
Published: September 2002

AbstractStanniocalcin (STC) is a recently discovered mammalian hormone that is widely distributed in many tissues. In rodents the STC gene is most highly expressed in ovary, specifically in androgen-producing thecal and interstitial cells. In addition, ovarian levels of expression rise 15-fold over pregnancy. The objective of this study was to develop a primary culture system for ovarian thecal-interstitial cells (TICs) to identify factors governing STC production and release. We used highly purified primary cultures of rat and bovine TICs, the purity of which was routinely assessed with antigenic and enzymatic markers. The functionality of cells was assured by their responsiveness to LH in the form of progesterone release. We found that forskolin significantly increased STC gene expression and secretion by both rat and bovine TICs, an effect that was only replicated by human (h) chorionic gonadotropin (CG). Coincubation of TICs with hCG and phosphodiesterase inhibitors further increased STC secretion, whereas coincubation of TICs with hCG and protein kinase A inhibitors attenuated hCG-stimulated release. Intriguingly, ovarian STC proved to be substantially larger than the 50-kDa homodimer produced in most other tissues. These results indicate that ovarian STC is physically distinct, a feature that could explain its presence in serum during pregnancy and lactation.
Phylogeny of the Parmeliaceae–DNA Data Versus Morphological Data
Authors: Mattsson Jan-Eric , Wedin Mats 
Published: September 2002

AbstractIn order to identify monophyletic groups within the family Parmeliaceae, eleven taxa (Bryoria capillaris, Cetraria islandica, Evernia pruniastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usneaflorida, Vulpicida juniperina, V. pinastri, and Xanthoparmelia conspersa) were studied using newly produced nuclear rDNA sequence data from the ITS and 5·8S regions. The resulting evolutionary hypothesis was compared with results from previous phylogenetic analyses based on anatomy, morphology, and chemistry. The outcome of this comparison does not support the earlier proposed phylogenies but is not stable enough for identifying monophyletic groups, with one exception. The results indicate a close relationship between Cetraria and Vulpicida, which is contradictory to previous published analyses. The variation in ascus structures in the Parmeliaceae is discussed and it is questioned whether the earlier distinguished ‘ forms ’ of ascus types represent synapomorphies, if they are based on poorly supported analyses, or if they are exaggerations of relatively slight variation in shape. Further interpretations of the results are discussed and areas of future studies based on DNA-data are suggested.
Notes on Polysporina Vězda, with a Description of a New Species from Tasmania
Authors: Kantvilas Gintaras 
Published: September 2002

AbstractThe new species, Polysponna terricola Kantvilas from south-eastern Tasmania, is described and compared to other species in the genus. It is well characterized by a range of morphological, anatomical and ecological characters, especially by the presence of oil paraphyses and oil droplets in the hymenium, features unknown in other members of the genus. Species of Polysporina are best separated by the following characters: size and morphology of the apothecia, size of ascospores, thickness of paraphyses and height of the hymenium. The combinations P. ferniginea (Lettau) M. Steiner and P. pusilla (Anzi) M. Steiner are validated. A key to the taxa studied is provided.
Process and Pattern in Cladonia Subcervicornis
Authors: Hammer Samuel 
Published: September 2002

AbstractMorphogenesis of podetia in Cladonia subcervicornis is a non-linear, repeating process based upon a pattern of meristem enlargement and division. Variability in mature podetia of C. subcervicornis, which may appear branched or scyphoid, is the result of variation early in ontogeny. The growth pattern of C. subcervicornis represents a continuum of developmental stages. It is impossible to predict the form of the mature thallus of C. subcervicornis because growth in this species is fluid. The morphology of the mature thallus of C. subcervicornis is difficult to circumscribe using conventional Cladonia terminology, because the processes that form the thallus are dynamic and heterogeneous. The meristem shapes that are produced during early ontogeny in C. subcervicornis are relatively simple, and the processes by which they are formed are uncomplicated. Yet podetial form in C.subcercicornis is difficult to interpret.
Natural Levels of Saline Elements in Lichens: Determination of Cellular Fractions and Their Importance as Saline Tracers
Authors: Figueira Rui , Sousa António J. , Brown Dennis H. , Catarino Fernando , Pacheco Adriano M. G. 
Published: September 2002

AbstractUsing a sequential elution procedure, the cellular location of Cl−, Na+, Mg2+, K+ and Ca2+ was determined in the lichen Ramalina canariensis from the southwest coast of Portugal. After a dry deposition period, a logarithmic decrease in the extracellular (surface and wall-bound) concentration of Cl−, Na+ and Mg2+ was observed with increasing distance from the coast. The importance of each cellular fraction as an indication of the airborne salts was identified using factorial analysis methods, as was the relationship between the extracellular and intracellular concentration of the saline elements. The factorial analysis showed that the most important elements for the biomonitoring of airborne salinity were Cl−, Na+ and Mg2+. However, for the cations, only the surface and wall-bound (for Na+) fractions seem to be related to sea-salt deposition on the lichens. The intracellular fractions of these elements are relatively independent of the surface and wall-bound concentrations, or reflect some non-linear processes induced by extreme extracellular concentrations. Although they may represent a significant proportion of the total element concentration, intracellular element concentrations are of little value in monitoring salt deposition, due to physiological control by the organism. The use of total analyses, without any fractional differentiation, can be a biased method for biomonitoring the accumulation of salt spray by lichens, because it includes the intracellular fraction, which may be independent of the deposition taking place. The use of the different cellular fractions provides a more informative indication of the deposition of atmospheric elements, while also giving information on any physiological alterations induced by the specific environmental chemical factors, including membrane damage.
Anisomeridium Musaesporoides, a new Foliicolous Lichen from Tropical America
Authors: Etayo Javier , Lücking Robert 
Published: September 2002

AbstractA fourth foliicolous species of Anisomeridium is described. Anisomeridium musaesporoides has so far only been found in Guyana and Panama. It is characterized by applanate perithecia with a white marginal zone, large spores with a submedian septum and apical ostiole. A key to all known foliicolous Anisomeridium species is provided.
Caloplaca Cancarixiticola, A New Species from South-East Spain Growing on Ultrapotassic Rocks
Authors: Navarro-Rosinés P. , Egea J.M. , Llimona X. 
Published: September 2002

AbstractCaloplaca cancarixiticola Nav. -Ros., Egea & Llimona (Teloschistales, Lichenes) is described as new. It is characterized by a lobate thallus weakly attached to the substratum, and narrowly ellipsoid or ellipsoid-fusiform ascospores, (14.5–) 16–22(–25) × (4–)4–5–6um3 with a narrow equatorial wall-thickening, only (1–) 2.5–3.5(–4) um wide. This new species, related to the Caloplaca aurea-group of the subgenus Gasparrinia, was found on cancarixite, an ultrapotassic rock, in a volcanic region of Albacete (SE Spain).
Kantvilasia (Lecanorales, Ectolechiaceae), A New Foliicolous Lichen Genus From Tasmania
Authors: McCarthy P. M. , Elix J. A. , Sérusiaux E. 
Published: September 2002

AbstractThe new genus and species Kantvilasia hians (Lecanorales, Ectolechiaceae) is described from leaves of Atherosperma moschatum at the margin of cool-temperate rainforest in western Tasmania. Notes are provided on characterization, distribution, habitat, associated species, the opening mechanism of campylidia and likely dispersal processes of conidia.
On Rhizocarpon Obscuratum (ACH.) Massal., with notes on some Related Species in the British Isles
Authors: Fryday Alan 
Published: September 2002

AbstractThe specimens upon which Lecidea petraea var. obscurata Ach., the basionym of Rhizocarpon obscuratum (Ach.) Massal., is based are shown to be mostly referable to the species currently known as R. lavatum (Fr.) Hazslin. Rhizocarpon reductum Th. Fr. is resurrected to accommodate specimens with small ascospores previously referred there. The related species R. sublavatum is described from the Scottish Highlands and descriptions provided for R. anaperum (Vain.) Vain, and R. amphibium (Fr.) Th. Fr. These species are compared with R. reductum, R. lavatum and R. petraeum. Rhizocarpon rubescens Th. Fr. is shown to be a distinct species recorded from Europe and N. America.
Caloplaca Erecta, A New Subfruticose Species From New Zealand
Authors: Arup Ulf , Mayrhofer Helmut 
Published: September 2002

AbstractCaloplaca erecta Arup & H. Mayrhofer is described here as new to science. It belongs to a group of dwarf-fruticose species, but cannot be accommodated within any of the known species of that group. It forms dense cushions of erect lobes on siliceous rocks, and is known only from Mt. Maungatua. This is the second dwarf-fruticose species of Caloplaca in the Australasian area, in addition to C. cribosa.
Amandinea Crassiuscula, a New Corticolous Species from the Iberian Peninsula
Authors: Giralt Mireia , Etayoj Javier , Góomez–Bolea Antonio 
Published: September 2002

AbstractAmandinea crassiuscula Giralt & Etayo, a new corticolous lichen species is described from the Iberian Peninsula. It is characterized by a thickly crustose to subsquamulose thallus that lacks secondary lichen compounds, lecideine apothecia, Buellia–type ascospores with rugulate ornamentation and filiform spermatia. The new species is compared with other corticolous Amandinea and Buellia species, such as A. punctata and B. chloroleuca. Habit photographs of the new species and illustrations of its thallus, spermatia and ascospores are also provided.
Structural indicators of Richness and rarity of epiphytic lichens on Corylus avellana in two different forest types within a nature reserve in south-western Norway
Authors: Ihlen Per G. , Gjerde Ivar , Sætersdal Magne 
Published: September 2002

AbstractEpiphytic lichens (and some non-lichenizedfungi) on 34 coppices (204 stems) of Corylus avellana were investigated in a 140 ha study area in south-western Norway. A total of 65 species were recorded on a total bark area of 63 m⊃2. Corylus in broad-leaved deciduous forest supported more species of macrolichens, and fewer species of microlichens, than Corylus in pine forest. The macrolichen flora of the deciduous forest differed from that of the pine forest by having a rich flora of species belonging to the Lobarion alliance. Old Corylus coppices with tall stems (>8 m), large girth (>8cm diameter at breast height) and a noticeable cover of macrolichens (>10% of bark area) supported the highest number of rare species, and overall, species of macrolichens. More than 50% cover of microlichens indicated richness and rarity of microlichens on Corylus. 11 2001 The British Lichen Society
Biatora Britannica sp. Nov. and the Occurrence of Biatora Efflorescens in the British Isles
Authors: Printzen Christian , Lumbsch H. Thorsten , Orange Alan 
Published: September 2002

AbstractBiatora Britannica sp. nov is described from Wales. The species is the sorediate sister taxon of the Madeiran Biatora hertelii. The close relationship is supported by the presence of the hymenial pigment Hertelii-green, which is hitherto known only from these two species. Molecular data from the nuclear ITS-region of 14 Bratora¯ species renders further support for the close relationship of both species. Sterile, sorediate material from the British Isles earlier referred to B. efflorescens may in fact belong to B. britannica.
A new method to isolate lichen algae by using percoll® gradient centrifugation
Authors: Calatayud Angeles , Guera Alfredo , Fos Simón , Barreno Eva 
Published: September 2002

AbstractA rapid method to isolate intact functional algae from the lichens Evemia prunastri and Ramalina farinacea has been developed. This method is based on the use of Percoll® gradients after mechanical disruption of lichen thalli. Results obtained show that the algal preparations were virtually free of contamination by fungal hyphae. The purified algal cells were photosynthetically active and without symptoms of photoinhibition, which indicates their functional integrity. This method may be used for the isolation of intact algae from a broad range of lichen species.