bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Rgd1p Rho GTPase-Activating Protein and the Mid2p Cell Wall Sensor Are Required at Low pH for Protein Kinase C Pathway Activation and Cell Survival in
Saccharomyces cerevisiae
Authors: Claret Sandra , Gatti Xavier , Doignon François , Thoraval Didier , Crouzet Marc 
Published: August 2005

ABSTRACT

The protein kinase C (PKC) pathway is involved in the maintenance of cell shape and cell integrity in
Saccharomyces cerevisiae
. Here, we show that this pathway mediates tolerance to low pH and that the Bck1 and Slt2 proteins belonging to the mitogen-activated protein kinase cascade are essential for cell survival at low pH. The PKC pathway is activated during acidification of the extracellular environment, and this activation depends mainly on the Mid2p cell wall sensor. Rgd1p, which encodes a Rho GTPase-activating protein for the small G proteins Rho3p and Rho4p, also plays a role in low-pH response. The
rgd1
Δ strain is sensitive to low pH, and Rgd1p activates the PKC pathway in an acidic environment. Inactivation of both genes in the double mutant
rgd1
Δ
mid2
Δ strain renders yeast cells unable to survive at low pH as in
bck1
Δ and
slt2
Δ strains. Our data provide evidence for the existence of two distinct ways, one involving Mid2p and the other involving Rgd1p, with both converging to the cell integrity pathway to mediate low-pH tolerance in
Saccharomyces cerevisiae
. Nevertheless, even if Rgd1p acts on the PKC pathway, it seems that its mediating action on low-pH tolerance is not limited to this pathway. As the Mid2p amount plays a role in
rgd1
Δ sensitivity to low pH, Mid2p seems to act more like a molecular rheostat, controlling the level of PKC pathway activity and thus allowing phenotypical expression of
RGD1
inactivation.
Disruption of Histone Deacetylase Gene
RPD3
Accelerates
PHO5
Activation Kinetics through Inappropriate Pho84p Recycling
Authors: Wongwisansri Sriwan , Laybourn Paul J. 
Published: August 2005

ABSTRACT

The histone deacetylase Rpd3p functions as a transcriptional repressor of a diverse set of genes, including
PHO5
. Here we describe a novel role for
RPD3
in the regulation of phosphate transporter Pho84p retention in the cytoplasmic membrane. We show that under repressing conditions (with P
i
),
PHO5
expression is increased in a
pho4Δ rpd3Δ
strain, demonstrating
PHO
regulatory pathway independence. However, the effect of
RPD3
disruption on
PHO5
activation kinetics is dependent on the
PHO
regulatory pathway. Upon switching to activating conditions (without P
i
),
PHO5
transcripts accumulated more rapidly in
rpd3Δ
cells. This more rapid response correlates with a defect in phosphate uptake due to premature recycling of Pho84p, the high-affinity H
+
/PO
4
3−
symporter. Thus,
RPD3
also participates in
PHO5
regulation through a previously unidentified effect on maintenance of high-affinity phosphate uptake during phosphate starvation. We propose that Rpd3p has a negative role in the regulation of Pho84p endocytosis.
Clonality and Recombination in Genetically Differentiated Subgroups of
Cryptococcus gattii
Authors: Campbell Leona T. , Currie Bart J. , Krockenberger Mark , Malik Richard , Meyer Wieland , Heitman Joseph , Carter Dee 
Published: August 2005

ABSTRACT

Cryptococcus gattii
is a pathogenic yeast that together with
Cryptococcus neoformans
causes cryptococcosis in humans and animals. High numbers of viable
C. gattii
propagules can be obtained from certain species of Australian
Eucalyptus camaldulensis
trees, and an epidemiological link between
Eucalyptus
colonization and human exposure has been proposed. However, the highest prevalence of
C. gattii
cryptococcosis occurs in Papua New Guinea and in regions of Australia where the eucalypt species implicated to date are not endemic. This study investigated the population structure of three geographically distinct clinical and veterinary populations of
C. gattii
from Australia and Papua New Guinea. All populations that consisted of a genotype found frequently in Australia (VGI) were strongly clonal and were highly differentiated from one another. Two populations of the less common VGII genotype from Sydney and the Northern Territory had population structures inferring recombination. In addition, there was some evidence of reduced genetic differentiation between these geographically remote regions. In a companion study presented in this issue, VGII isolates were overwhelmingly more fertile than those of the VGI genotype, giving biological support to the indirect assessment of sexual exchange. It appears that the VGI genotype propagates clonally on eucalypts in Australia and on an unknown substrate in Papua New Guinea, with infection initiated by an unidentified infectious propagule. VGII isolates are completing their life cycles and may be dispersed via sexually produced basidiospores, which are also likely to initiate respiratory infection.
Clinical and Environmental Isolates of
Cryptococcus gattii
from Australia That Retain Sexual Fecundity
Authors: Campbell Leona T. , Fraser James A. , Nichols Connie B. , Dietrich Fred S. , Carter Dee , Heitman Joseph 
Published: August 2005

ABSTRACT

Cryptococcus gattii
is a primary pathogenic yeast that causes disease in both animals and humans. It is closely related to
Cryptococcus neoformans
and diverged from a common ancestor ∼40 million years ago. While
C. gattii
has a characterized sexual cycle dependent upon a dimorphic region of the genome known as the MAT locus, mating has rarely been observed in this species. In this study, we identify for the first time clinical (both human and veterinary) and environmental isolates from Australia that retain sexual fecundity. A collection of 120 isolates from a variety of geographic locations was analyzed for molecular type, mating type, and the ability to develop mating structures when cocultured with fertile tester strains. Nine isolates produced dikaryotic filaments with paired nuclei, fused clamp connections, and basidiospores. DNA sequence analysis of three genes (
URA5
, the MATα-specific
SXI1
α gene, and the MAT
a
-specific

SXI2
a

gene) revealed little or no variability in
URA5
and

SXI2
a

, respectively. However across the 108 MATα strains sequenced, the
SXI1
α gene was found to exist as 11 different alleles. Phylogenetic analysis found most variation to occur in the more fertile genotypes. Although some lineages of Australian
C. gattii
have retained the ability to mate, the majority of isolates were sterile, suggesting that asexuality is the dominant mode of propagation in these populations.
Cryptococcus neoformansGene Expression during Murine Macrophage Infection
Authors: Fan Weihua , Kraus Peter R. , Boily Marie-Josee , Heitman Joseph 
Published: August 2005

ABSTRACTThe fungal pathogenCryptococcus neoformanssurvives phagocytosis by macrophages and proliferates within, ultimately establishing latent infection as a facultative intracellular pathogen that can escape macrophage control to cause disseminated disease. This process is hypothesized to be important forC. neoformanspathogenesis; however, it is poorly understood howC. neoformansadapts to and overcomes the hostile intracellular environment of the macrophage. Using DNA microarray technology, we have investigated the transcriptional response ofC. neoformansto phagocytosis by murine macrophages. The expression profiles of several genes were verified using quantitative reverse transcription-PCR and a green fluorescent protein reporter strain. Multiple membrane transporters for hexoses, amino acids, and iron were up-regulated, as well as genes involved in responses to oxidative stress. Genes involved in autophagy, peroxisome function, and lipid metabolism were also induced. Interestingly, almost the entire mating type locus displayed increased expression 24 h after internalization, suggesting an intrinsic connection between infection and theMATlocus. Genes in the Gpa1-cyclic AMP-protein kinase A pathway were also up-regulated. Bothgpa1andpka1mutants were found to be compromised in macrophage infection, confirming the important role of this virulence pathway. A large proportion of the repressed genes are involved in ribosome-related functions, rRNA processing, and translation initiation/elongation, implicating a reduction in translation as a central response to phagocytosis. In summary, this gene expression profile allows us to interpret the adaptation ofC. neoformansto the intracellular infection process and informs the search for genes encoding novel virulence attributes.
Histone H3 K36 Methylation Is Associated with Transcription Elongation in
Schizosaccharomyces pombe
Authors: Morris Stephanie A. , Shibata Yoichiro , Noma Ken-ichi , Tsukamoto Yuko , Warren Erin , Temple Brenda , Grewal Shiv I. S. , Strahl Brian D. 
Published: August 2005

ABSTRACT

Set2 methylation of histone H3 at lysine 36 (K36) has recently been shown to be associated with RNA polymerase II (Pol II) elongation in
Saccharomyces cerevisiae
. However, whether this modification is conserved and associated with transcription elongation in other organisms is not known. Here we report the identification and characterization of the Set2 ortholog responsible for K36 methylation in the fission yeast
Schizosaccharomyces pombe
. We find that similar to the budding yeast enzyme,
S. pombe
Set2 is also a robust nucleosome-selective H3 methyltransferase that is specific for K36. Deletion of the
S. pombe set2

+

gene results in complete abolishment of K36 methylation as well as a slow-growth phenotype on plates containing synthetic medium. These results indicate that Set2 is the sole enzyme responsible for this modification in fission yeast and is important for cell growth under stressed conditions. Using the chromatin immunoprecipitation assay, we demonstrate that K36 methylation in
S. pombe
is associated with the transcribed regions of Pol II-regulated genes and is devoid in regions that are not transcribed by Pol II. Consistent with a role for Set2 in transcription elongation, we find that
S. pombe
Set2 associates with the hyperphosphorylated form of Pol II and can fully rescue K36 methylation and Pol II interaction in budding yeast cells deleted for Set2. These results, along with our finding that K36 methylation is highly conserved among eukaryotes, imply a conserved role for this modification in the transcription elongation process.
Methylation of Histone H3 Lysine 36 Is Required for Normal Development in
Neurospora crassa
Authors: Adhvaryu Keyur K. , Morris Stephanie A. , Strahl Brian D. , Selker Eric U. 
Published: August 2005

ABSTRACT

The SET domain is an evolutionarily conserved domain found predominantly in histone methyltransferases (HMTs). The
Neurospora crassa
genome includes nine SET domain genes (
set-1
through
set-9
) in addition to
dim-5
, which encodes a histone H3 lysine 9 HMT required for DNA methylation. We demonstrate that
Neurospora set-2
encodes a histone H3 lysine 36 (K36) methyltransferase and that it is essential for normal growth and development. We used repeat induced point mutation to make a
set-2
mutant (
set-2

RIP1

) with multiple nonsense mutations. Western analyses revealed that the mutant lacks SET-2 protein and K36 methylation. An amino-terminal fragment that includes the AWS, SET, and post-SET domains of SET-2 proved sufficient for K36 HMT activity in vitro. Nucleosomes were better substrates than free histones. The
set-2

RIP1

mutant grows slowly, conidiates poorly, and is female sterile. Introducing the wild-type gene into the mutant complemented the defects, confirming that they resulted from loss of
set-2
function. We replaced the wild-type histone H3 gene (
hH3
) with an allele producing a Lys to Leu substitution at position 36 and found that this
hH3

K36L

mutant phenocopied the
set-2

RIP1

mutant, confirming that the observed defects in growth and development result from inability to methylate K36 of H3. Finally, we used chromatin immunoprecipitation to demonstrate that actively transcribed genes in
Neurospora crassa
are enriched for H3 methylated at lysines 4 and 36. Taken together, our results suggest that methylation of K36 in
Neurospora crassa
is essential for normal growth and development.
The
pkaB
Gene Encoding the Secondary Protein Kinase A Catalytic Subunit Has a Synthetic Lethal Interaction with
pkaA
and Plays Overlapping and Opposite Roles in
Aspergillus nidulans
Authors: Ni Min , Rierson Sara , Seo Jeong-Ah , Yu Jae-Hyuk 
Published: August 2005

ABSTRACT

Filamentous fungal genomes contain two distantly related cyclic AMP-dependent protein kinase A catalytic subunits (PKAs), but only one PKA is found to play a principal role. In
Aspergillus nidulans
, PkaA is the primary PKA that positively functions in vegetative growth and spore germination but negatively controls asexual sporulation and production of the mycotoxin sterigmatocystin. In this report, we present the identification and characterization of
pkaB
, encoding the secondary PKA in
A. nidulans
. Although deletion of
pkaB
alone does not cause any apparent phenotypic changes, the absence of both
pkaB
and
pkaA
is lethal, indicating that PkaB and PkaA are essential for viability of
A. nidulans
. Overexpression of
pkaB
enhances hyphal proliferation and rescues the growth defects caused by Δ
pkaA
, indicating that PkaB plays a role in vegetative growth signaling. However, unlike Δ
pkaA
, deletion of
pkaB
does not suppress the fluffy-autolytic phenotype resulting from Δ
flbA
. While upregulation of
pkaB
rescues the defects of spore germination resulting from Δ
pkaA
in the presence of glucose, overexpression of
pkaB
delays spore germination. Furthermore, upregulation of
pkaB
completely abolishes spore germination on medium lacking a carbon source. In addition, upregulation of
pkaB
enhances the level of submerged sporulation caused by Δ
pkaA
and reduces hyphal tolerance to oxidative stress. In conclusion, PkaB is the secondary PKA that has a synthetic lethal interaction with PkaA, and it plays an overlapping role in vegetative growth and spore germination in the presence of glucose but an opposite role in regulating asexual sporulation, germination in the absence of a carbon source, and oxidative stress responses in
A. nidulans
.
Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors
Authors: Metpally Raghu Prasad Rao , Sowdhamini Ramanathan 
Published: August 2005

Abstract

Background
The cell-membrane G-protein coupled receptors (GPCRs) are one of the largest known superfamilies and are the main focus of intense pharmaceutical research due to their key role in cell physiology and disease. A large number of putative GPCRs are 'orphans' with no identified natural ligands. The first step in understanding the function of orphan GPCRs is to identify their ligands. Phylogenetic clustering methods were used to elucidate the chemical nature of receptor ligands, which led to the identification of natural ligands for many orphan receptors. We have clustered human and Drosophila receptors with known ligands and orphans through cross genome phylogenetic analysis and hypothesized higher relationship of co-clustered members that would ease ligand identification, as related receptors share ligands with similar structure or class.

Results
Cross-genome phylogenetic analyses were performed to identify eight major groups of GPCRs dividing them into 32 clusters of 371 human and 113 Drosophila proteins (excluding olfactory, taste and gustatory receptors) and reveal unexpected levels of evolutionary conservation across human and Drosophila GPCRs. We also observe that members of human chemokine receptors, involved in immune response, and most of nucleotide-lipid receptors (except opsins) do not have counterparts in Drosophila. Similarly, a group of Drosophila GPCRs (methuselah receptors), associated in aging, is not present in humans.

Conclusion
Our analysis suggests ligand class association to 52 unknown Drosophila receptors and 95 unknown human GPCRs. A higher level of phylogenetic organization was revealed in which clusters with common domain architecture or cellular localization or ligand structure or chemistry or a shared function are evident across human and Drosophila genomes. Such analyses will prove valuable for identifying the natural ligands of Drosophila and human orphan receptors that can lead to a better understanding of physiological and pathological roles of these receptors.
β-adrenergic receptor activation in immortalized human urothelial cells stimulates inflammatory responses by PKA-independent mechanisms
Authors: Harmon Erin B , Porter Jill M , Porter James E 
Published: August 2005

Abstract

Background
Interstitial cystitis (IC) is a debilitating disease characterized by chronic inflammation of the urinary bladder, yet specific cellular mechanisms of inflammation in IC are largely unknown. Multiple lines of evidence suggest that β-adrenergic receptor (AR) signaling is increased in the inflamed urothelium, however the precise effects of these urothelial cell signals have not been studied. In order to better elucidate the AR signaling mechanisms of inflammation associated with IC, we have examined the effects of β-AR stimulation in an immortalized human urothelial cell line (UROtsa). For these studies, UROtsa cells were treated with effective concentrations of the selective β-AR agonist isoproterenol, in the absence or presence of selective inhibitors of protein kinase A (PKA). Cell lysates were analyzed by radioimmunoassay for generation of cAMP or by Western blotting for induction of protein products associated with inflammatory responses.

Results
Radioligand binding demonstrated the presence of β-ARs on human urothelial UROtsa cell membranes. Stimulating UROtsa cells with isoproterenol led to concentration-dependent increases of cAMP production that could be inhibited by pretreatment with a blocking concentration of the selective β-AR antagonist propranolol. In addition, isoproterenol activation of these same cells led to significant increases in the amount of phosphorylated extracellular signal-regulated kinase (pERK), inducible nitric oxide synthase (iNOS) and the induced form of cyclooxygenase (COX-2) when compared to control. Moreover, preincubation of UROtsa cells with the selective PKA inhibitors H-89 or Rp-cAMPs did not diminish this isoproterenol mediated phosphorylation of ERK or production of iNOS and COX-2.

Conclusion
Functional β-ARs expressed on human urothelial UROtsa cell membranes increase the generation of cAMP and production of protein products associated with inflammation when activated by the selective β-AR agonist isoproterenol. However, the increased production of iNOS and COX-2 by isoproterenol is not blocked when UROtsa cells are preincubated with inhibitors of PKA. Therefore, UROtsa cell β-AR activation significantly increases the amount of iNOS and COX-2 produced by a PKA-independent mechanism. Consequently, this immortalized human urothelial cell line can be useful in characterizing potential AR signaling mechanisms associated with chronic inflammatory diseases of the bladder.
Discharge and follow-up for people with stroke: what happens and why
Authors: Tyson Sarah , Turner Gill 
Published: August 2005

Objective: To assess the quality of the process of discharge from hospital and follow-up services for people with stroke. Design: A criterion-based process audit and basic outcome measures, combined with surveys of patients' satisfaction and staff opinion of the service. Setting: All units treating stroke patients in a health care district including an acute and a community NHS trust, and 23 participating GP practices. Subjects: Process audit: documented notes of 98 stroke patients admitted and discharged over a four-month period. Patient satisfaction survey: 93 surviving stroke patients. Staff opinion survey: general practitioners, hospital doctors, therapists and nurses treating stroke patients throughout the district. Results: A poor level of service was found. The main shortcomings were poor communication and liaison and a narrow focus of rehabilitation which concentrated on the assessment and provision of basic home care and activities of daily living (ADL) required to obtain discharge. There was a paucity of provision beyond this most basic level and little follow-up after discharge. Pass rates against agreed criteria were: communication between staff and patients/carers 47%, liaison between staff 44%, assessment of home-based needs 48%, assessment of domestic skills 15.5%. Fifty-one per cent of patients were referred for follow-up therapy and of these 72% started follow-up therapy within six weeks of discharge, only 27% had any follow-up assessment of activity levels and well-being. Patients were dissatisfied with the information, support services and therapy they received. The main reasons for the shortcomings were lack of awareness of the services provided, professionals' low expectations of patients' abilities, and limitations of community-based therapy services. Conclusions: Evidence from other publications suggests that these results do not indicate a service that is any worse than other districts, rather it represents the poor deal offered to stroke patients. By comprehensively assessing several aspects of the service together this methodology has been able to reveal these inadequacies and the reasons for them.
2,3,7,8-Tetrachlorodibenzo-p-Dioxin Increases Glycodelin Gene and Protein Expression in Human Endometrium
Authors: Mueller Michael D. , Vigne Jean-Louis , Streich Matthias , Tee Meng Kian , Raio Luigi , Dreher Ekkehard , Bersinger Nick A. , Taylor Robert N. 
Published: August 2005

Context: Glycodelin (GdA) is an immunosuppressive endometrial glycoprotein critical for embryonic implantation and pregnancy establishment.
Objective: The aim of the present study was to examine the effect of dioxin [2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)] on GdA production in human endometrial cells.
Design: Controlled endometrial explant (EE) and cell cultures were used in this study.
Setting: Work was conducted at university hospital research laboratories in Bern, Switzerland, and in San Francisco, California.
Patients: Ovulatory women provided endometrial biopsies in the proliferative or secretory phase.
Intervention(s): EEs and cells were cultured without and with TCDD.
Main Outcome Measure(s): GdA protein and gene expression were quantified.
Results: A 2.5-fold increase in GdA production was demonstrated in EEs treated with 10 nm TCDD for 9 d. Fluorography revealed a 3- to 4-fold increase in new GdA biosynthesis and secretion in TCDD-treated endometrial epithelial cells. Because the action of dioxin is mediated by the aryl hydrocarbon receptor (AhR), we ascertained that primary epithelial and Ishikawa cells express AhR. Dose responses to TCDD and expressed AhR were established in transiently transfected Ishikawa cells using luciferase fusion vectors containing 1.0 kb of 5′ flanking DNA relative to the GdA transcriptional start site but not when shorter promoter constructs were used. A dioxin response element was mapped to nucleotides −539 to −533 of the gene promoter and verified by site-directed mutagenesis.
Conclusions: We demonstrated a direct AhR-mediated effect of dioxin on GdA gene transcription and protein secretion that might influence human female fertility.