bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virus-Host Cell Interactions during Hepatitis C Virus RNA Replication: Impact of Polyprotein Expression on the Cellular Transcriptome and Cell Cycle Association with Viral RNA Synthesis
Authors: Scholle Frank , Li Kui , Bodola Francis , Ikeda Masanori , Luxon Bruce A. , Lemon Stanley M. 
Published: January 2004

ABSTRACTConsiderable controversy surrounds the impact of hepatitis C virus (HCV) protein expression on viability of host cells and regulation of the cell cycle. Both promotion of cellular proliferation and apoptosis have been observed in different experimental systems. To determine whether expression of the entire complement of HCV proteins in the context of ongoing viral RNA replication significantly alters the host cell transcriptome and cell cycle regulatory processes, we carried out high-density oligonucleotide microarray studies and analyzed cell cycle distributions and S-phase entry in Huh7 cell clones harboring selectable, full-length, replicating HCV RNAs that express the entire genotype 1b, HCV-N polyprotein, and clonally related cells in which all viral RNA was eliminated by prior treatment with alpha interferon. Oligonucleotide microarray analyses revealed only subtle, coordinated differences in the mRNA profiles of cells containing replicating viral RNA and their interferon-cured progeny, with variation between different cell clones having a greater influence on the cellular transcriptome than the presence or absence of replicating HCV RNA. Flow cytometric analysis demonstrated no significant differences in cell cycle distribution among populations of asynchronously growing cells of both types. Cell lines containing replicating viral RNA and their interferon-cured progeny were able to reenter the cell cycle similarly after transient G1arrest. In contrast, although viral protein expression and genome replication did not alter cell cycle control in these cells, HCV genome replication was highly dependent on cellular proliferation, with viral RNA synthesis strongly decreased in poorly proliferating, confluent, or serum-starved cells and substantially enhanced in the S phase of the cell cycle.
Effects of Mutations in the Cytoplasmic Domain of Herpes Simplex Virus Type 1 Glycoprotein B on Intracellular Transport and Infectivity
Authors: Beitia Ortiz de Zarate Igor , Kaelin Karin , Rozenberg Flore 
Published: January 2004

ABSTRACTHerpes simplex virus type 1 (HSV-1) is a human pathogen of the alphaherpesvirus family which infects and spreads in the nervous system. Glycoproteins play a key role in the process of assembly and maturation of herpesviruses, which is essential for neuroinvasion and transneuronal spread. Glycoprotein B (gB) is a main component of the HSV-1 envelope and is necessary for the production of infectious particles. The cytoplasmic domain of gB, the longest one among HSV-1 glycoproteins, contains several highly conserved peptide sequences homologous to motifs involved in intracellular sorting. To determine the specific roles of these motifs in processing, subcellular localization, and the capacity of HSV-1 gB to complement a gB-null virus, we generated truncated or point mutated forms of a green fluorescent protein (GFP)-tagged gB. GFP-gB with a deletion in the acidic cluster DGDADEDDL (amino acids [aa] 896 to 904) behaved the same as the parental form. Deletion or disruption of the YTQV motif (aa 889 to 892) abolished internalization and reduced complementation by 60%. Disruption of the LL motif (aa 871 to 872) impaired the return of the protein to thetrans-Golgi network (TGN) while enhancing its recycling to the plasma membrane. Truncations from residue E 857 abolished transport and processing of the truncated proteins, which had null complementation activity, through the Golgi complex. Altogether, our results favor a model in which HSV-1 gets its final envelope in the TGN, and they suggest that endocytosis, albeit not necessary, might play a role in infectivity.
Cell-Type-Dependent Targeting of Human Immunodeficiency Virus Type 1 Assembly to the Plasma Membrane and the Multivesicular Body
Authors: Ono Akira , Freed Eric O. 
Published: January 2004

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) assembly-and-release pathway begins with the targeting of the Gag precursor to the site of virus assembly. The molecular mechanism by which Gag is targeted to the appropriate subcellular location remains poorly understood. Based on the analysis of mutant Gag proteins, we and others have previously demonstrated that a highly basic patch in the matrix (MA) domain of Gag is a major determinant of Gag transport to the plasma membrane. In this study, we determined that in HeLa and T cells, the MA mutant Gag proteins that are defective in plasma membrane targeting form virus particles in a CD63-positive compartment, defined as the late endosome or multivesicular body (MVB). Interestingly, we find that in primary human macrophages, both wild-type (WT) and MA mutant Gag proteins are targeted specifically to the MVB. Despite the fact that particle assembly in macrophages occurs at an intracellular site rather than at the plasma membrane, we observe that WT Gag expressed in this cell type is released as extracellular virions with high efficiency. These results demonstrate that Gag targeting to and assembly in the MVB are physiologically important steps in HIV-1 virus particle production in macrophages and that particle release in this cell type may follow an exosomal pathway. To determine whether Gag targeting to the MVB is the result of an interaction between the late domain in p6
Gag
and the MVB sorting machinery (e.g., TSG101), we examined the targeting and assembly of Gag mutants lacking p6. Significantly, the MVB localization of Gag was still observed in the absence of p6, suggesting that an interaction between Gag and TSG101 is not required for Gag targeting to the MVB. These data are consistent with a model for Gag targeting that postulates two different cellular binding partners for Gag, one on the plasma membrane and the other in the MVB.
Astrovirus-Induced Synthesis of Nitric Oxide Contributes to Virus Control during Infection
Authors: Koci Matthew D. , Kelley Laura A. , Larsen Diane , Schultz-Cherry Stacey 
Published: January 2004

ABSTRACTAstrovirus is one of the major causes of infant and childhood diarrhea worldwide. Our understanding of astrovirus pathogenesis trails behind our knowledge of its molecular and epidemiologic properties. Using a recently developed small-animal model, we investigated the mechanisms by which astrovirus induces diarrhea and the role of both the adaptive and innate immune responses to turkey astrovirus type-2 (TAstV-2) infection. Astrovirus-infected animals were analyzed for changes in total lymphocyte populations, alterations in CD4+/CD8+ratios, production of virus-specific antibodies (Abs), and macrophage activation. There were no changes in the numbers of circulating or splenic lymphocytes or in CD4+/CD8+ratios compared to controls. Additionally, there was only a modest production of virus-specific Abs. However, adherent spleen cells from infected animals produced more nitric oxide (NO) in response to ex vivo stimulation with lipopolysaccharide. In vitro analysis demonstrated that TAstV-2 induced macrophage production of inducible nitric oxide synthase. Studies using NO donors and inhibitors in vivo demonstrated, for the first time, that NO inhibited astrovirus replication. These studies suggest that NO is important in limiting astrovirus replication and are the first, to our knowledge, to describe the potential role of innate immunity in astrovirus infection.
Influence of the Route of Infection on Development of T-Cell Receptor β-Chain Repertoires of Reovirus-Specific Cytotoxic T Lymphocytes
Authors: Fulton Jonathan R. , Smith Jeremy , Cunningham Cynthia , Cuff Christopher F. 
Published: January 2004

ABSTRACTIt is well established that the route of infection affects the nature of the adaptive immune response. However, little is known about the effects of the route of exposure on development of cytotoxic T-lymphocyte (CTL) responses. Alternative antigen-presenting cell populations, tissue-restricted expression of class I major histocompatibility complex-encoded molecules, and unique T-cell receptor (TCR)-bearing cells in mucosal tissues could influence the selection and expansion of responder T cells. This study addresses the question of whether the route of virus infection affects the selection and expansion of subpopulations of virus-specific CTLs. Mice were infected orally or in the hind footpads with reovirus, and the repertoires of TCR β-chains expressed on virus-specific CD8+T cells in Peyer's patches or lymph nodes and spleens were examined. CD8+cells expressing the variable gene segment of the TCR β-chain 6 (Vβ6) expanded in the spleens of mice infected by either route and in CTL lines established from the spleens and draining lymphoid tissues. Adoptively transferred Vβ6+CD8+T cells from orally or parenterally infected donors expanded in reovirus-infected severe combined immunodeficient recipient mice and mediated cytotoxicity ex vivo. Furthermore, recovered Vβ6+cells were enriched for clones utilizing uniform complementarity-determining region 3 (CDR3) lengths. However, sequencing of CDR3β regions from Vβ6+CD8+cells indicated that Jβ gene segment usage is significantly more restricted in CTLs from orally infected mice, suggesting that the route of infection affects selection and/or subsequent expansion of virus-specific CTLs.
PROBABILISTIC ASPECTS OF SCORE SYSTEMS
Authors: SCHRAMM MANFRED , FRONHÖFER BERTRAM 
Published: January 2004

Due to their simple applicability score systems are in widespread use as a tool for decision making. Unfortunately, as we all feel, they are somehow not apt to take into account interdependencies among the values which are input to them when trying to decide an actual application case; a drawback which is overcome by the more powerful probabilistic systems. In order to analyze which assumptions are inherent in score systems, we translate them as faithfully as possible into probabilistic systems thus making available the technical machinery of the latter for this analysis task. Such a translation (as also given in1) reveals indeed some properties of score systems, but leads to an exponential number of probabilistic rules, which rules it out for practical use. For this reason we also developed further translations into probabilistic systems, which keep the simplicity of a score system (i.e. they use the same amount of rules as the score system). Moreover, the resulting probabilistic systems show their structure more explicitly than score systems, and they are also open to the addition of further knowledge.
Effect of a nitrification inhibitor on nematicidal activity of organic and inorganic ammonia-releasing compounds against the root-knot nematode Meloidogyne javanica
Authors: Oka Yuji , Pivonia Shimon 
Published: January 2004

AbstractThe nematicidal activities of ammonium hydroxide, chitin and cottonseed meal applied to soil were enhanced by nitrapyrin, a nitrification inhibitor, in pot experiments. In a field trial, root galling index of tomato plants grown in the soil treated with 250 kg NH4OH-N/ha in combination with nitrapyrin was lower than that of tomato plants grown without nitrapyrin 40 days after planting; however, there was no difference between these treatments in tomato yields and root galling indices at the end of the experiment (128 days). Nitrapyrin inhibited the nitrification of the ammonium added to the soil or released from cottonseed meal for up to 28 days, and kept ammonium concentrations and soil pH values higher for longer periods compared with those in soils treated without nitrapyrin. It is suggested that higher ammonia (NH3) concentrations due to high soil pH and ammonium concentrations in the soil for longer periods caused the enhancement of nematicidal activities by nitrapyrin. The use of ammonia-releasing compounds in combination with a nitrification inhibitor may make nematode control more feasible by reducing the amount of amendments applied.
Molecular and morphological characterisation of the Heterodera avenae species complex (Tylenchida: Heteroderidae)
Authors: Subbotin Sergei , Sturhan Dieter , Rumpenhorst Hans Jürgen , Moens Maurice 
Published: January 2004

Abstract
Species of the Heterodera avenae complex, including populations of H.
arenaria, H. aucklandica, H. australis, H. avenae, H. filipjevi, H. mani, H.
pratensis and H. ustinovi, obtained from different regions of the world were
analysed with PCR-RFLP and sequencing of the ITS-rDNA, RAPD and light
microscopy. Phylogenetic relationships between species and populations of
the H. avenae complex as inferred from analyses of 70 sequences of the ITS
region and of 237 RAPD markers revealed that the cereal cyst nematode H.
avenae is a paraphyletic taxon. The taxonomic status of the Australian
cereal cyst nematode H. australis based on sequences of the ITS-rDNA and
RAPD data is confirmed. Morphometrical and ITS-rDNA sequence analyses
revealed that the Chinese cereal cyst nematode is different from other H.
avenae populations infecting cereals and is related to H. pratensis. Bidera
riparia Kazachenko, 1993 is transferred to the genus Heterodera as H.
riparia (Kazachenko, 1993) comb. n. As a consequence, H. riparia Subbotin,
Sturhan, Waeyenberge & Moens, 1997 becomes a junior secondary homonym
and is renamed as H. ripae nom. nov. Morphological, morphometrical
characters and RFLP profiles for identification of the nine species
presently placed in the H. avenae species complex are given.
Laboratory bioassays of virulence of entomopathogenic nematodes against soil-inhabiting stages of Frankliniella occidentalis Pergande (Thysanoptera: Thripidae)
Authors: Premachandra Dammini , Borgemeister Christian , Berndt Oliver , Ehlers Ralf-Udo , Poehling Hans-Michael 
Published: January 2004

Abstract
The efficacy of entomopathogenic nematodes (EPN) was evaluated in a
laboratory trial against soil-dwelling stages, late second instar larvae and
pupal stages of western flower thrips (WFT), Frankliniella occidentalis
Pergande. Among the six EPN strains assessed for the first time, Steinernema
feltiae (Nemaplus®) and Heterorhabditis bacteriophora (HD01) caused 65 and
59% mortality, respectively. Steinernema carpocapsae (Agriotos) and S.
arenarium (Anomali) caused moderate mortality (40-45%) while Steinernema
spp. (Morocco) and H. bacteriophora (Nematop®) had little effect. In a dose
response study with concentrations of 100, 400 and 800 infective juveniles
(IJ) per cm2 soil of H. bacteriophora (HK3), S. feltiae (Nemaplus®) and H.
bacteriophora (HD01), mortality increased only up to 400 IJ cm-2. The rate
of infectivity of H. bacteriophora (HK3) and S. feltiae (Nemaplus®)
indicated that both strains could survive at least 6 days in the soil and
infect WFT immature stages.
Between-isolate difference in dispersal ability of Bursaphelenchus xylophilus and vulnerability to inhibition by Pinus densiflora
Authors: Togashi Katsumi , Matsunaga Koji 
Published: January 2004

Abstract
Differences among four isolates of Bursaphelenchus xylophilus and one of B.
mucronatus in vulnerability to the inhibitory effect of Pinus densiflora on
nematode dispersal were investigated by inoculating boiled and living branch
sections 5 cm long. The intrinsic dispersal ability and vulnerability to the
inhibitory effect of living branches differed among isolates. Additionally,
the degree of branch inhibition of nematode dispersal was examined by
inoculating the five isolates on 2.5 and 5.0 cm long, P. densiflora living
branch sections. An increase in section length induced an 80% decrease in
the number of nematodes of all isolates passing through the branch. The
extent to which passing nematode number decreased as branch section length
increased can be used to express susceptibility of pine species to pine wilt
disease. Virulence had no relation to intrinsic and realised dispersal rates
in B. xylophilus.
The genus Oigolaimella Paramonov, 1952 (Nematoda: Diplogastridae) and description of O. kruegeri n. sp. and O. ninae n. sp.
Authors: Fürst von Lieven Alexander 
Published: January 2004

AbstractOigolaimella kruegeri n. sp. and Oigolaimella ninae n. sp. are described. Oigolaimella kruegeri n. sp. males can be recognised by the lack of the gubernacular keel characteristic of other Oigolaimella species and by the modified distribution pattern of the genital sensillae. Oigolaimella ninae n. sp. can be recognised and distinguished from the other members of the genus by the refractive cuticularised ring formed by the anterior edge of the cheilostomatal collar. Oigolaimella longicauda (Claus, 1862) n. comb. is accepted as a valid species, regarded as a senior synonym of O. agilis (Skwarra, 1921) and redescribed. Oigolaimella diplogaster (von Linstow, 1890) n. comb. is proposed. The phylogenetic relationship of Oigolaimella is discussed and an ecological characterisation of the taxon given on the basis of observations on feeding behaviour and locomotion in the habitat.
Host-finding ability of three entomopathogenic nematode isolates in the presence of plant roots
Authors: Cutler G. Christopher , Webster John 
Published: January 2004

Abstract
The effect of plant roots on the host-finding ability of three isolates of
entomopathogenic nematodes (EPN), Heterorhabditis bacteriophora D-H-Da1,
Steinernema sp. Dongrae and Steinernema sp. BJ was studied. In Petri dish
experiments the overall response of the infective juveniles (IJ) of these
isolates differed from one another, but all were attracted to a Galleria
mellonella larva and to a tomato seedling when either of these targets was
presented with a blank control. The BJ and D-H-Da1 IJ aggregated more around
a tomato root than a G. mellonella larva when these targets were presented
separately, but showed no preference for a G. mellonella-tomato seedling
combination over a blank control. Dongrae IJ showed no preference for a G.
mellonella larva or tomato seedling when each was presented simultaneously
in the same Petri dish. In experiments in pots of soil, plant roots did not
affect the host-finding ability of Dongrae IJ. In contrast, compared to
control pots with no roots, roots of bean plants hindered the ability of BJ
IJ to infect a G. mellonella larva, but tomato roots increased host-finding
by D-H-Da1 IJ. Roots of certain plant species modify the host-finding
ability of EPN, but the extent and direction of the response varied with the
EPN applied.
Nematode communities of anthropogenous birch stands in central Finland
Authors: Räty Mika , Huhta Veikko 
Published: January 2004

Abstract
This study compared the nematode communities in anthropogenous birch (Betula
pendula) stands of different origin with each other and with natural forests
and arable soils at the same latitude in Finland and Scandinavia. Nine
forest sites were investigated in central Finland: three birch stands
planted ca 30 years prior to the study after the clear-cutting of spruce
stands (BS), three birch stands planted ca 30 years earlier on arable soil
(BF) and three natural deciduous forests (D). There were clear differences
between the birch stands established after spruce forest and after arable
cropping, and between these and deciduous forests, but even more between
replicates of similarly managed forests. Total numbers, species diversity,
and populations of most taxa and feeding groups were the lowest in BF sites.
The relative proportion of bacterial feeders and omnivores was higher and
that of plant feeders lower in BS than in D sites. The BS sites were
relatively similar in community structure to natural deciduous forests, and
BF were dissimilar to both, although one deciduous site was similar to one
BF site. Non-metric multidimensional scaling ordination placed the three BS
sites in one cluster, while the BF sites were clearly separated from these
and from each other. Several environmental variables related to soil
moisture and acidity contributed to explain the variation in community
structure. A hypothesis is suggested that the presence of burrowing
earthworms plays a role in regulating populations of nematodes.
Why Caenorhabditis elegans adults sacrifice their bodies to progeny
Authors: Chen Jianjun , Caswell-Chen Edward 
Published: January 2004

Abstract
We present a novel interpretation regarding the ecology and evolution of
matricidal hatching ('bagging') in Caenorhabditis elegans. Subjecting young
and mature adult C. elegans to stress induced matricidal hatching. The
process of egg retention followed by internal hatching under starvation was
reversible, depending on whether adults were returned to food before
internal juveniles caused irreversible harm to the adult. We surface
sterilised adult C. elegans and then starved them to test the hypothesis
that matricidal hatching promotes progeny survival by enhancing to some
degree the transition to the dauer stage. When the surface sterilisation
stress time was short, the parent C. elegans enclosed many progeny that
competed for resources so that apparently only a few progeny obtained
sufficient nutrition to support transition to the dauer stage. Longer
sterilisation stress and starvation resulted in fewer, larger progeny with a
higher proportion reaching the dauer stage, suggesting a direct correlation
between the phenomena. In stressful environments, the production of even a
single, stress-resistant, long-lived dauer, in lieu of progeny that cannot
achieve the dauer, is a fitness advantage. The results are consistent with
the hypothesis. We infer that intra-uterine hatch is a part of the C.
elegans life cycle, and complements androdioecy and the dauer stage to
enhance progeny survival and dispersal under stress. This is a possible
explanation of why a seemingly detrimental behaviour, matricidal hatching,
has been perpetuated in C. elegans through evolutionary time.
Judaic Social Teaching in Christian and Pagan Context
Authors: Neusner Jacob 
Published: January 2004

AbstractThe social teaching of Rabbinic Judaism takes up the narrative of the Torah and recasts it into an account of the norms of Israel's social order. Its recapitulation of the Torah's story regulates relationships between Israelites and corporate Israel, among Israelites in their units of propagation and production, and between corporate Israel and the ever-present, always-sentient God. The details coalesce to yield a clear picture of an entire social order, its relationships and its points of stability and order. To treat any detail apart from its larger context is to miss its point. That point is, Rabbinic Judaism undertakes to realize in the everyday and here and now of the Jews' communal existence the imperatives set forth in the Torah for the formation of God's abode on earth.
Is it Possible to Write a History of Jewish Thought?
Authors: Schwartz Dov 
Published: January 2004

AbstractIn the past few years, traditional scholars and would-be innovators have been locked in controversy over the scholarly study of Qabbalah. The field of Jewish philosophical thought, however, has witnessed no such upheavals. This is not to say that no progress has been made: Texts are being rescued from oblivion; philosophical systems are constantly under review. However, little work has been done in the direction of a new scholarly awareness of the history of Jewish thought wholly outside the area of mysticism. This situation is clearly mirrored in various attempts to write and document the history of Jewish philosophy. In what follows I describe various aspects of current efforts to write the history of ideas in the area of medieval and modern Jewish thought and speculate on what might have been. Without intending to exhaust the topic of the historiography of Jewish ideas, I would like to propose some new goals for future research into Jewish rationalism.