bluuebunny/crossref_metadata_2025 huggingface dataset:
Atypical neuroleptic malignant syndrome caused by olanzapine
Authors: Nielsen J. , Bruhn A. M.
Published: August 2005

Objective:  Neuroleptic malignant syndrome (NMS) is a rare syndrome with four main symptoms: rigidity, hyperthermia, altered mental status and autonomic instability. We report a patient with an atypical manifestation of NMS.

Method:  A single case was reported.

Results:  A patient with pneumonia developed delirium and was treated with olanzapine and developed a NMS with fluctuating hyperthermia and autonomic instability during a month. Only slight rigidity was present. Creatine kinase was not elevated. The patient was severely agitated and manic. After discontinuation of olanzapine the patient showed no psychopathology or hyperthermia.

Conclusion:  NMS should be considered when patients treated with antipsychotics develop one or more symptoms of NMS.
The pigtail macaque MHC class I allele Mane‐A*10 presents an immundominant SIV Gag epitope: identification, tetramer development and implications of immune escape and reversion
Authors: Smith Miranda Z. , Fernandez Caroline S. , Chung Amy , Jane Dale C. , Rose Robert De , Lin Jie , Brooks Andrew G. , Krebs Kendall C. , Watkins David I. , O'Connor David H. , Davenport Miles P. , Kent Stephen J.
Published: August 2005

Abstract:  The pigtail macaque (Macaca nemestrina) is a common model for the study of AIDS. The pigtail major histocompatibility complex class I allele Mane‐A*10 restricts an immunodominant simian immunodeficiency virus (SIV) Gag epitope (KP9) which rapidly mutates to escape T cell recognition following acute simian/human immunodeficiency virus infection. Two technologies for the detection of Mane‐A*10 in outbred pigtail macaques were developed: reference strand‐mediated conformational analysis and sequence‐specific primer polymerase chain reaction. A Mane‐A*10/KP9 tetramer was then developed to quantify CD8+ T lymphocytes primed by multigenic DNA vaccination, which have previously been difficult to detect using standard interferon‐γ‐based T cell assays. We also demonstrate mutational escape at KP9 following acute SIV infection. Mane‐A*10+ animals have lower set point SIV levels than Mane‐A*10− animals, suggesting a significant fitness cost of escape. These studies pave the way for a more robust understanding of HIV vaccines in pigtail macaques.
Cytoplasmic Targeting of Mutant Poly(A)‐Binding Protein Nuclear 1 Suppresses Protein Aggregation and Toxicity in Oculopharyngeal Muscular Dystrophy
Authors: Abu‐Baker Aida , Laganiere Simon , Fan Xueping , Laganiere Janet , Brais Bernard , Rouleau Guy A.
Published: August 2005

Oculopharyngeal muscular dystrophy (OPMD) is an adult‐onset disorder characterized by progressive eyelid drooping, swallowing difficulties and proximal limb weakness. The autosomal dominant form of this disease is caused by a polyalanine expansion from 10 to 12–17 residues, located at the N‐terminus of the poly(A)‐binding protein nuclear 1 (PABPN1). A distinct pathological hallmark of OPMD is the presence of filamentous intranuclear aggregates in patients' skeletal muscle cells. Wildtype PABPN1 protein is expressed ubiquitously and was shown to be mostly concentrated in discrete nuclear domains called ‘speckles’. Using an established cell‐ culture model, we show that most mutant PABPN1‐ positive (alanine expanded form) intranuclear aggregates are structures distinct from intranuclear speckles. In contrast, the promyelocytic leukaemia protein, a major component of nuclear bodies, strongly colocalized to intranuclear aggregates of mutant PABPN1. Wildtype PABPN1 can freely shuttle between the nucleus and cytoplasm. We determined whether the nuclear environment is necessary for mutant PABPN1 inclusion formation and cellular toxicity. This was achieved by inactivating the mutant PABPN1 nuclear localization signal and by generating full‐length mutant PABPN1 fused to a strong nuclear export sequence. A green fluorescence protein tag inserted at the N‐terminus of both wildtype PABPN1 (ala10) and mutant PABPN1 (ala17) proteins allowed us to visualize their subcellular localization. Targeting mutant PABPN1 to the cytoplasm resulted in a significant suppression of both intranuclear aggregates formation and cellular toxicity, two histological consequences of OPMD. Our results indicate that the nuclear localization of mutant PABPN1 is crucial to OPMD pathogenesis.
Uncoupling of Brefeldin A‐Mediated Coatomer Protein Complex‐I Dissociation from Golgi Redistribution
Authors: Barzilay Eran , Ben‐Califa Nathalie , Hirschberg Koret , Neumann Drorit
Published: August 2005

The Golgi complex functions in transport of molecules from the endoplasmic reticulum (ER) to the plasma membrane and other distal organelles as well as in retrograde transport to the ER. The fungal metabolite brefeldin A (BFA) promotes dissociation of ADP‐ribosylation‐factor‐1 (ARF1) and the coatomer protein complex‐I (COP‐I) from Golgi membranes, followed by Golgi tubulation and fusion with the ER. Here we demonstrate that the cationic ionophore monensin inhibited the BFA‐mediated Golgi redistribution to the ER without interfering with ARF1 and COP‐I dissociation. Preservation of a perinuclear Golgi despite COP‐I and ARF1 dissociation enables addressing the involvement of these proteins in anterograde ER to Golgi transport. The thermo‐reversible folding mutant of vesicular stomatitis virus G protein (VSVGtsO45) was retained in the ER in the presence of both monensin and BFA, thus supporting ARF1/COP‐I participation in ER‐exit processes. Live‐cell imaging revealed that BFA‐induced Golgi tubulation persisted longer in the presence of monensin, suggesting that monensin inhibits tubule fusion with the ER. Moreover, monensin also augmented Golgi‐derived tubules that contained the ER‐Golgi‐intermediate compartment marker, p58, in the absence of BFA, signifying the generality of this effect. Taken together, we propose that monensin inhibits membrane fusion processes in the presence or absence of BFA.
Come FLY with us: toward understanding fragile X syndrome
Authors: Zarnescu D. C. , Shan G. , Warren S. T. , Jin P.
Published: August 2005

The past few years have seen an increased number of articles using Drosophila as a model system to study fragile X syndrome. Phenotypic analyses have demonstrated an array of neuronal and behavioral defects similar to the phenotypes reported in mouse models as well as human patients. The availability of both cellular and molecular tools along with the power of genetics makes the tiny fruit fly a premiere model in elucidating the molecular basis of fragile X syndrome. Here, we summarize the advances made in recent years in the characterization of fragile X Drosophila models and the identification of new molecular partners in neural development.
K4, K9 and K18 in human histone H3 are targets for biotinylation by biotinidase
Authors: Kobza Keyna , Camporeale Gabriela , Rueckert Brian , Kueh Alice , Griffin Jacob B. , Sarath Gautam , Zempleni Janos
Published: August 2005

Histones are modified post‐translationally, e.g. by methylation of lysine and arginine residues, and by phosphorylation of serine residues. These modifications regulate processes such as gene expression, DNA repair, and mitosis and meiosis. Recently, evidence has been provided that histones are also modified by covalent binding of the vitamin biotin. The aims of this study were to identify biotinylation sites in histone H3, and to investigate the crosstalk among histone biotinylation, methylation and phosphorylation. Synthetic peptides based on the sequence of human histone H3 were used as substrates for enzymatic biotinylation by biotinidase; biotin in peptides was probed using streptavidin peroxidase. These studies provided evidence that K4, K9 and K18 in histone H3 are good targets for biotinylation; K14 and K23 are relatively poor targets. Antibodies were generated to histone H3, biotinylated either at K4, K9 or K18. These antibodies localized to nuclei in human placental cells in immunocytochemistry and immunoblotting experiments, suggesting that lysines in histone H3 are biotinylated in vivo. Dimethylation of R2, R8 and R17 increased biotinylation of K4, K9 and K18, respectively, by biotinidase; phosphorylation of S10 abolished biotinylation of K9. These observations are consistent with crosstalk between biotinylation of histones and other known modifications of histones. We speculate that this crosstalk provides a link to known roles for biotin in gene expression and cell proliferation.
Mitochondrial calcium signalling in cell death
Authors: Leo Sara , Bianchi Katiuscia , Brini Marisa , Rizzuto Rosario
Published: August 2005

The development of targeted probes (based on the molecular engineering of luminescent or fluorescent proteins) has allowed the specific measurement of [Ca2+] in intracellular organelles or cytoplasmic subdomains. This approach gave novel information on different aspects of cellular Ca2+ homeostasis. Regarding mitochondria, it was possible to demonstrate that, upon physiological stimulation of cells, Ca2+ is rapidly accumulated in the matrix. We will discuss the basic characteristics of this process, its role in modulating physiological and pathological events, such as the regulation of aerobic metabolism and the induction of cell death, and new insight into the regulatory mechanisms operating in vivo.
Primary Headache Disorders and Circadian Biology: A Clinical, Imaging, and Therapy Perspective
Authors: Cohen Anna S. , Kaube Holger
Published: August 2005

Primary headache syndromes such as hypnic headache, and trigeminal autonomic cephalgias (TACs) such as cluster headache, paroxysmal hemicrania, and SUNCT (Short‐lasting Unilateral Neuralgiform headache attacks with Conjunctival injection and Tearing), are associated with varying degrees with attacks that occur with circadian rhythmicity. In hypnic headache, the attacks occur exclusively during sleep, and in cluster headache the attacks predominate in sleep in 75% of patients. The TACs, especially cluster headache and SUNCT, have been associated on functional imaging with activation of the hypothalamus during attacks. There is also evidence in patients with cluster headache of altered secretory rhythms of a variety of hypophyseal hormone systems including melatonin, cortisol, and others. Given the role of the suprachiasmatic nucleus in the diurnal cycle, the hypothalamus is implicated as a generator of headaches with a prominent circadian rhythm. This article discusses the physiological and biochemical mechanisms that implicate the hypothalamus in the generation of a variety of primary headache disorders.
Ecology and Distribution of Melastomataceae in African Rain Forest Inselbergs1
Authors: Parmentier Ingrid
Published: August 2005

The ecology and distribution of thirty‐seven Melastomataceae species found on 29 inselbergs in the rain forest of Equatorial Guinea, Gabon, and Cameroon are described. The relative contributions of climatic determinism, and stochastic and historical processes to the present distribution of the species amongst the study sites are investigated. Inselbergs are rock outcrops enduring very harsh edaphic and microclimatic conditions, forming “xeric islands” in the rain forest, where natural grasslands develop. For each Melastomataceae species, the habitats where they were collected on the inselbergs and in other biotopes were listed, and their phytogeographical distribution was established. Three species are restricted to rock outcrops. Most species are distributed inside the Guineo‐Congolian Region. Three species have disjunct distributions on rain forest inselbergs and have their main distribution area outside the forested zone. The distribution of the species amongst the inselbergs is correlated to the altitude and the annual rainfall of the sites, and to inselberg geographical location. This correlation of the species distribution with the geographical location of the inselberg is attributed to the spatial autocorrelation of environmental variables and to the combined effects of the history of past vegetation changes due to climatic fluctuations and dispersal limitation.
Epiphyte Orchid Establishment on Termite Carton Trails1
Authors: Flores‐Palacios Alejandro , Ortiz‐Pulido Raúl
Published: August 2005

In the coastal zone of central Veracruz, Mexico, we recorded the abundance of orchid plants growing on termite carton trails or directly on the peeling bark of Bursera fagaroides. Although only 19 percent of the surveyed trees contained termite carton trails, trees with termites hosted 92 percent of all orchid individuals. A disproportionate number of orchid seedlings occurred on termite cartons given the relative availability of carton and bark substrate. Our results show for the first time that orchids can establish on termite trails, and we discuss the potential for termite facilitation of orchid populations.
Nocturnal Fungi: Airborne Spores in the Canopy and Understory of a Tropical Rain Forest1
Authors: Gilbert Gregory S. , Reynolds Don R.
Published: August 2005

Pathogens and other symbiotic fungi that infect above‐ground plant parts commonly disperse as airborne spores. Here we present diel patterns of the density of airborne fungal spores in the canopy and understory of a tropical rain forest. Spores were 52‐fold more abundant in the understory than in the canopy. Additionally, spores were 5‐ to 35‐fold more abundant at night than during the day, associated with environmental conditions conducive to germination and plant infection.
The Citreoline Trogon as an Ecosystem Engineer1
Authors: Valdivia‐Hoeflich Talía , Vega Rivera Jorge H. , Stoner Kathryn E.
Published: August 2005

The western Mexican endemic Citreoline Trogon (Trogon citreolus) builds its nest cavities in arboreal termitaria. We studied the reuse of these holes by other organisms after the trogons abandoned them in the tropical dry forest of western Mexico. Of the 24 cavities examined, 19 were occupied (5 by mammals and 14 by arthropods). We found two western Mexico endemic mammals (Marmosa canescens and Xenomys nelsoni) using these spaces. Our results suggest that the T. citreolus provides a critical role in creating necessary cavities for many organisms in tropical dry forests.
ASSESSMENT OF RIPENESS/DAMAGE IN BANANA (MUSA PARADISIACAL) BY ACOUSTIC RESONANCE SPECTROSCOPY
Authors: JAGANNATH J.H. , DAS GUPTA D.K. , BAWA A.S. , SEBASTIN R. , VISHNU B.
Published: August 2005

Acoustic resonance spectroscopy was used to assess ripeness of bananas at various stages of maturity. Two distinctly different varieties of bananas were selected for the study. Bananas were also bruised, and an acoustic response spectrum was taken before and after bruising. A dynamic impact force was applied to the base over which the fruit was kept horizontally with the help of a coupling agent. The output response was picked up by a hydrophone coupled, in turn to the base to the top (vertically opposite) of the fruit coupled. The signal was analyzed using Fast Fourier Transform. Response resonance frequencies decreased while damping ratio increased as the fruit ripened. Bruising of fruits resulted in decreased resonance frequency due to tissue damage. The values of resonance frequency and damping ratio could be correlated to the color changes due to ripeness of fruits as a result of either increased rates of respiration or external damage of tissue from mechanical or temperature abuse.
CENTRIFUGAL YIELD AND FURTHER MICROSCOPIC CHARACTERIZATION OF SEA BUCKTHORN JUICE PRODUCTS
Authors: BEVERIDGE T.H.J. , HARRISON J.E.
Published: August 2005

Yields of press juice for Hippophae rhamnoides ssp. sinensis and ssp. mongolica cv. Indian Summer were 69.2% and 62.8%, respectively. Centrifugation of the press juices at 4C, 4480 × g for 15 min provided yields of cream, serum and pellet of 1.72, 95.6 and 0.68% for ssp. sinensis, and 5.4, 92.3 and 0.32% for ssp. mongolica cv. Indian Summer. All percentages are percentage (w/w). The particulate of each juice was characterized microscopically and the particulate of cv. Indian Summer was much larger than that of ssp. sinensis. Much more oil was apparent microscopically in the cv. Indian Summer cream as expected from the yield data mentioned above. Pellet material was not distinguishable between the two ssp. Trichomes were visualized in greater detail, a particular particle that may be exclusive to cv. Indian Summer was described and the presence of crystalline material in aggregated particles was observed.
INFLUENCE OF 1‐METHYLCYCLOPROPENE AND NATURESEAL ON THE QUALITY OF FRESH‐CUT “EMPIRE” AND “CRISPIN” APPLES
Authors: RUPASINGHE H.P. VASANTHA , MURR DENNIS P. , DeELL JENNIFER R. , ODUMERU JOSEPH
Published: August 2005

Wounding during processing triggers physiological reactions that limits shelf life of fresh‐cut apples. Exposure of “Empire” and “Crispin” apples at harvest to the ethylene antagonist, 1‐methylcyclopropene (1‐MCP), on the maintenance of fresh‐cut quality was evaluated in combination with post‐cut dipping of NatureSealTMEfficacy of 1‐MCP on fresh‐cut physiology and quality depended on the storage duration and apple cultivar. Ethylene production of apple slices was inhibited by 1‐MCP but not by NatureSeal. Total volatiles produced by fresh‐cut apples were not affected by NatureSeal but by 1‐MCP when 1‐month stored “Crispin” apples were used. 1‐MCP influenced the quality attributes of fresh‐cut slices prepared from apples stored either 4 months in cold storage or 6 months in controlled atmosphere. Enzymatic browning and softening of the cut‐surface, TSS and total microbial growth were suppressed by 1‐MCP in “Empire” apples. The influence of 1‐MCP on quality attributes in “Crispin” apple slices was marginal.
Tetracycline-Inducible Gene Expression and Gene Deletion in
Candida albicans
Authors: Park Yang-Nim , Morschhäuser Joachim
Published: August 2005

The genetic analysis of
Candida albicans
, the major fungal pathogen of humans, is hampered by its diploid genome, the absence of a normal sexual cycle, and a nonstandard codon usage. Although effective methods to study gene function have been developed in the past years, systems to control gene expression in
C. albicans
are limited. We have established a system that allows induction of gene expression in
C. albicans
by the addition of tetracycline (Tet). By fusing genetically modified versions of the reverse Tet repressor from
Escherichia coli
and the transcription activation domain of the Gal4 protein from
Saccharomyces cerevisiae
, a
C. albicans
-adapted reverse Tet-dependent transactivator (rtTA) was created that was expressed from the constitutive
ADH1
or the opaque-specific
OP4
promoter. To monitor Tet-inducible gene expression, the
caGFP
reporter gene was placed under the control of a Tet-dependent promoter, obtained by fusing a minimal promoter from
C. albicans
to seven copies of the Tet operator sequence. Fluorescence of the cells demonstrated that gene expression could be efficiently induced by the addition of doxycycline in yeast, hyphal, and opaque cells of
C. albicans
. The Tet-inducible gene expression system was then used to manipulate the behavior of the various growth forms of
C. albicans
. Tet-induced expression of a dominant-negative
CDC42
allele resulted in growth arrest as large, multinucleate cells. Filamentous growth was efficiently inhibited under all tested hyphal-growth-promoting conditions by Tet-inducible expression of the
NRG1
repressor. Tet-induced expression of the
MTL
a
1
gene in opaque cells of an
MTL
α strain forced the cells to switch to the white phase, whereas Tet-induced expression of the
MTL
a
2
transcription factor induced shmooing. When the
ecaFLP
gene, encoding the site-specific recombinase FLP, was placed under the control of the Tet-dependent promoter, Tet-inducible deletion of genes which were flanked by the FLP target sequences was achieved with high efficiency to generate conditional null mutants. In combination with the dominant selection marker
caSAT1
, the Tet-inducible gene expression system was also applied in
C. albicans
wild-type strains, including drug-resistant clinical isolates that overexpressed the
MDR1
,
CDR1
, and
CDR2
multidrug efflux pumps. This system, therefore, allows a growth medium-independent, Tet-inducible expression and deletion of genes in
C. albicans
and provides a convenient, versatile new tool to study gene function and manipulate cellular behavior in this model pathogenic fungus.
Polarized Morphogenesis Regulator Spa2 Is Required for the Function of Putative Stretch-Activated Ca
2+
-Permeable Channel Component Mid1 in
Saccharomyces cerevisiae
Authors: Noma Shigeko , Iida Kazuko , Iida Hidetoshi
Published: August 2005

Mid1 is a putative stretch-activated Ca
2+
channel component and is required for the maintenance of viability in the mating process. In response to mating pheromone, the
mid1
mutant normally forms a pointed mating projection but eventually dies. This phenotype is called the mid phenotype. To identify a protein regulating Mid1 or regulated by Mid1, we isolated a multicopy suppressor that rescues the
mid1
-
1
mutant from mating pheromone-induced death and found that it encodes a truncated Spa2 protein lacking an amino-terminal region responsible for interaction with components of the mitogen-activated protein kinase cascades. One of these
SPA2
alleles was
SPA2
Δ
N
, whose product lacked the region from Ser
5
to Leu
230
.
SPA2
Δ
N
on a multicopy plasmid (YEpSPA2ΔN) complemented the mid phenotype but not another phenotype, low Ca
2+
accumulation, of the
mid1
-
1
mutant. Neither
SPA2
Δ
N
on a low-copy plasmid nor wild-type
SPA2
on a multicopy plasmid had suppressive activity. The
SPA2
gene is involved in the formation of a pointed mating projection, and cells of the
spa2
Δ mutant lacking Spa2 are viable and develop a peanut shell-like structure when exposed to mating pheromone. Like the
spa2
Δ mutant, the
mid1
-
1 spa2
Δ double mutant and the
mid1
-
1/
YEpSPA2ΔN strain developed the peanut shell-like structure. The
mid1
-
1 spa2
Δ double mutant did not have the mid phenotype, indicating that
SPA2
is epistatic to
MID1
. Overexpression of Spa2ΔN abolished the localization of Spa2-green fluorescent protein to the tip of the mating projection. These results suggest that the Spa2ΔN protein interferes with the localization of the normal Spa2 protein and thereby prevents cells from entering the mating process. Therefore, we suggest that Mid1 function is influenced by Spa2 function through polarized morphogenesis.
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

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

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

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

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

The 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

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

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

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
.
Explicit solutions of the Manning equation for partially filled circular pipes
Authors: Akgiray Ömer
Published: August 2005

The application of the Manning equation to partly filled circular channels is considered. The four types of problem that require iterative calculations are elucidated, and explicit solutions proposed in the literature are reviewed. New and improved equations are presented for one type of problem. Explicit analytical equations are developed for the two types of problem for which no explicit solutions could be found in the literature. For each type of problem, two cases are considered: (i) constant Manning roughness coefficient, and (ii) variable Manning roughness coefficient that depends on the depth of flow. Separate equations are presented for each case. The accuracy of each equation is demonstrated by calculating and reporting its maximum deviation from the exact solution within its range of applicability. In addition to obviating the need for iterative calculations, these equations facilitate the calculation of both solutions when the problem at hand has two distinct solutions (two possible flow depths). The proposed equations are accurate enough to be used in computer calculations and sufficiently simple to be used with a hand-held calculator. Key words: explicit solution, hydraulics, Manning equation, free-surface flow, roughness coefficient, sewer design.
Modeling uncertainty with an integrated simulation system
Authors: Song Lingguang , Al-Battaineh Hussien T , AbouRizk Simaan M
Published: August 2005

Uncertainty inevitably affects the performance of a construction project. The ability to identify uncertainty and quantitatively evaluate its impact on the project performance can significantly enhance the accuracy and reliability of a project plan. This paper describes a methodology to classify, model, and reduce uncertainty. This method was implemented within an integrated simulation framework capable of capturing physical features of the facility to be constructed, uncertainty in the working environment, and the construction processes. A "virtual" steel fabrication shop model was developed using the proposed framework to model uncertainty in a steel fabrication shop environment. The artificial neural network (ANN) modeling technique, which plays a significant role in the simulation model, was used to model activity duration based on the identified productivity influencing factors and data collected through a time study project conducted in the fabrication shop. The virtual shop model with the embedded ANN model proved to be more accurate than the traditional approach of modeling activity duration using statistical distributions.Key words: uncertainty, classification, modeling, simulation, neural networks.
Évaluation des conséquences de rupture d'un barrage : calculs détaillés ou méthode simplifiée ?
Authors: Marche C , Oriac Anne
Published: August 2005

Quebec's Dam Safety Act demands a safety assessment for all dams, whatever their capacity. The capacity only affects the detail level of the study to qualify the consequences of a potential dam failure, and thus determine the dam's classification. In practical terms, it is difficult to qualify the consequences of a failure flood if a complete hydraulic calculation of the failure flood is not performed. If consequences are not significant, this complicated specialized work can be deemed unnecessary by the dam owner, who normally has to defray the cost. This paper compares results of a complete dynamic calculation to those of three "simplified" methods. It shows, in two specific cases, that flow depth errors are significant, even after eliminating the greater part of this error generated by the discharge evaluation at the breach. The paper also shows that work involved when using "simplified" methods is not significantly decreased with relation to the work required for the complete calculation when time comes to interpret the data to assess correctly the consequences of a possible dam failure.Key words: dam, rupture, consequences, simplified assessment, complete calculation.[Journal translation]
Epigenetic regulation of lymphoid specific gene sets
Authors: Györy Ildikó , Minarovits Janos
Published: August 2005

Coregulation of lymphoid-specific gene sets is achieved by a series of epigenetic mechanisms. Association with higher-order chromosomal structures (nuclear subcompartments repressing or favouring gene expression) and locus control regions affects recombination and transcription of clonotypic antigen receptors and expression of a series of other lymphoid-specific genes. Locus control regions can regulate DNA methylation patterns in their vicinity. They may induce tissue- and site-specific DNA demethylation and affect, thereby, accessibility to recombination-activating proteins, transcription factors, and enzymes involved in histone modifications. Both DNA methylation and the Polycomb group of proteins (PcG) function as alternative systems of epigenetic memory in lymphoid cells. Complexes of PcG proteins mark their target genes by covalent histone tail modifications and influence lymphoid development and rearrangement of IgH genes. Ectopic expression of protein noncoding microRNAs may affect the generation of B-lineage cells, too, by guiding effector complexes to sites of heterochromatin assembly. Coregulation of lymphoid and viral promoters is also possible. EBNA 2, a nuclear protein encoded by episomal Epstein-Barr virus genomes, binds to the cellular protein CBF1 (C promoter binding factor 1) and operates, thereby, a regulatory network to activate latent viral promoters and cellular promoters associated with CBF1 binding sites.Key words : lymphoid cells, coregulation of gene batteries, epigenetic regulation, nuclear subcompartment switch, locus control region, DNA methylation, Polycomb group of proteins, histone modifications, microRNA, Epstein-Barr virus, EBNA 2, regulatory network.
Many players, one goal: how chromatin states are inherited during cell division
Authors: Santoro Raffaella , De Lucia Filomena
Published: August 2005

Replication of genomic material is a process that requires not only high fidelity in the duplication of DNA sequences but also inheritance of the chromatin states. In the last few years enormous effort has been put into elucidating the mechanisms involved in the correct propagation of chromatin states. From all these studies it emerges that an epigenetic network is at the base of this process. A coordinated interplay between histone modifications and histone variants, DNA methylation, RNA components, ATP-dependent chromatin remodeling, and histone-specific assembly factors regulates establishment of the replication timing program, initiation of replication, and propagation of chromatin domains. The aim of this review is to examine, in light of recent findings, how so many players can be coordinated with each other to achieve the same goal, a correct inheritance of the chromatin state.Key words: replication, histone variants, histone modification, DNA methylation, chromatin remodeling factors.
An epigenetic code for DNA damage repair pathways?
Authors: Hassa Paul O , Hottiger Michael O
Published: August 2005

Exposure of living cells to intracellular or external mutagens results in DNA damage. Accumulation of DNA damage can lead to serious consequences because of the deleterious mutation rate resulting in genomic instability, cellular senescence, and cell death. To counteract genotoxic stress, cells have developed several strategies to detect defects in DNA structure. The eukaryotic genomic DNA is packaged through histone and nonhistone proteins into a highly condensed structure termed chromatin. Therefore the cellular enzymatic machineries responsible for DNA replication, recombination, and repair must circumvent this natural barrier in order to gain access to the DNA. Several studies have demonstrated that histone/chromatin modifications such as acetylation, methylation, and phosphorylation play crucial roles in DNA repair processes. This review will summarize the recent data that suggest a regulatory role of the epigenetic code in DNA repair processes. We will mainly focus on different covalent reversible modifications of histones as an initial step in early response to DNA damage and subsequent DNA repair. Special focus on a potential epigenetic histone code for these processes will be given in the last section. We also discuss new technologies and strategies to elucidate the putative epigenetic code for each of the DNA repair processes discussed.Key words: epigenetic code, histone modifications, DNA repair pathways, ChIP, MS/MS, acetylation, methylation, phosphorylation and mono(ADP-ribosyl)ation.
The role of poly(ADP-ribose) in the DNA damage signaling network
Authors: Malanga Maria , Althaus Felix R
Published: August 2005

DNA damage signaling is crucial for the maintenance of genome integrity. In higher eukaryotes a NAD+-dependent signal transduction mechanism has evolved to protect cells against the genome destabilizing effects of DNA strand breaks. The mechanism involves 2 nuclear enzymes that sense DNA strand breaks, poly(ADP-ribose) polymerase-1 and -2 (PARP-1 and PARP-2). When activated by DNA breaks, these PARPs use NAD+to catalyze their automodification with negatively charged, long and branched ADP-ribose polymers. Through recruitment of specific proteins at the site of damage and regulation of their activities, these polymers may either directly participate in the repair process or coordinate repair through chromatin unfolding, cell cycle progression, and cell survival – cell death pathways. A number of proteins, including histones, DNA topoisomerases, DNA methyltransferase-1 as well as DNA damage repair and checkpoint proteins (p23, p21, DNA-PK, NF-kB, XRCC1, and others) can be targeted in this manner; the interaction involves a specific poly(ADP-ribose)-binding sequence motif of 20–26 amino acids in the target domains.Key words: PARP; polymer binding; non-covalent interaction; p53; DNA topoisomerase I.
Poly(ADP-ribosylation) and genomic stability
Authors: Oei Shiao Li , Keil Claudia , Ziegler Mathias
Published: August 2005

Poly(ADP-ribose) polymerases (PARPs) catalyze the synthesis of ADP-ribose polymers and attach them to specific target proteins. To date, 6 members of this protein family in humans have been characterized. The best-known PARP, PARP-1, is located within the nucleus and has a major function in DNA repair but also in the execution of cell death pathways. Other PARP enzymes appear to carry out highly specific functions. Most prominently, the tankyrases modify telomere-binding proteins and thereby regulate telomere maintenance. Since only a single enzyme, poly(ADP-ribose) glycohydrolase (PARG), has been identified, which degrades poly(ADP-ribose), it is expected that this protein has important roles in PARP-mediated regulatory processes. This review summarizes recent observations indicating that poly(ADP-ribosylation) represents a major mechanism to regulate genomic stability both when DNA is damaged by exogenous agents and during cell division.Key words: DNA repair, PARP, PARG, tankyrase, telomere maintenance.