bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demonstration of Loss of Heterozygosity by Single-Nucleotide Polymorphism Microarray Analysis and Alterations in Strain Morphology in
Candida albicans
Strains during Infection
Authors: Forche Anja , May Georgiana , Magee P. T. 
Published: January 2005

ABSTRACT

Candida albicans
is a diploid yeast with a predominantly clonal mode of reproduction, and no complete sexual cycle is known. As a commensal organism, it inhabits a variety of niches in humans. It becomes an opportunistic pathogen in immunocompromised patients and can cause both superficial and disseminated infections. It has been demonstrated that genome rearrangement and genetic variation in isolates of
C. albicans
are quite common. One possible mechanism for generating genome-level variation among individuals of this primarily clonal fungus is mutation and mitotic recombination leading to loss of heterozygosity (LOH). Taking advantage of a recently published genome-wide single-nucleotide polymorphism (SNP) map (A. Forche, P. T. Magee, B. B. Magee, and G. May, Eukaryot. Cell 3:705-714, 2004), an SNP microarray was developed for 23 SNP loci residing on chromosomes 5, 6, and 7. It was used to examine 21 strains previously shown to have undergone mitotic recombination at the
GAL1
locus on chromosome 1 during infection in mice. In addition, karyotypes and morphological properties of these strains were evaluated. Our results show that during in vivo passaging, LOH events occur at observable frequencies, that such mitotic recombination events occur independently in different loci across the genome, and that changes in karyotypes and alterations of phenotypic characteristics can be observed alone, in combination, or together with LOH.
Mcl1p Is a Polymerase α Replication Accessory Factor Important for S-Phase DNA Damage Survival
Authors: Williams Dewight R. , McIntosh J. R. 
Published: January 2005

ABSTRACT

Mcl1p is an essential fission yeast chromatin-binding protein that belongs to a family of highly conserved eukaryotic proteins important for sister chromatid cohesion. The essential function is believed to result from its role as a Pol1p (polymerase α) accessory protein, a conclusion based primarily on analogy to Ctf4p's interaction with Pol1p. In this study, we show that Mcl1p also binds to Pol1p with high affinity for the N terminus of Pol1p during S phase and DNA damage. Characterization of an inducible allele of
mcl1
+
,

nmt41

mcl1-MH
, shows that altered expression levels of Mcl1p lead to sensitivity to DNA-damaging agents and synthetic lethality with the replication checkpoint mutations
rad3
Δ,
rqh1
Δ, and
hsk1
-
1312
. Further, we find that the overexpression of the S-phase checkpoint kinase, Cds1, or the loss of Hsk1 kinase activity can disrupt Mcl1p's interaction with chromatin and Pol1p during replication arrest with hydroxyurea. We take these data to mean that Mcl1p is a dynamic component of the polymerase α complex during replication and is important for the replication stress response in fission yeast.
Sphingosine Kinase Regulates the Sensitivity of
Dictyostelium discoideum
Cells to the Anticancer Drug Cisplatin
Authors: Min Junxia , Traynor David , Stegner Andrew L. , Zhang Lei , Hanigan Marie H. , Alexander Hannah , Alexander Stephen 
Published: January 2005

ABSTRACT

The drug cisplatin is widely used to treat a number of tumor types. However, resistance to the drug, which remains poorly understood, limits its usefulness. Previous work using
Dictyostelium discoideum
as a model for studying drug resistance showed that mutants lacking sphingosine-1-phosphate (S-1-P) lyase, the enzyme that degrades S-1-P, had increased resistance to cisplatin, whereas mutants overexpressing the enzyme were more sensitive to the drug. S-1-P is synthesized from sphingosine and ATP by the enzyme sphingosine kinase. We have identified two sphingosine kinase genes in
D. discoideum
—
sgkA
and
sgkB
—that are homologous to those of other species. The biochemical properties of the SgkA and SgkB enzymes suggest that they are the equivalent of the human Sphk1 and Sphk2 enzymes, respectively. Disruption of the kinases by homologous recombination (both single and double mutants) or overexpression of the
sgkA
gene resulted in altered growth rates and altered response to cisplatin. The null mutants showed increased sensitivity to cisplatin, whereas mutants overexpressing the sphingosine kinase resulted in increased resistance compared to the parental cells. The results indicate that both the SgkA and the SgkB enzymes function in regulating cisplatin sensitivity. The increase in sensitivity of the sphingosine kinase-null mutants was reversed by the addition of S-1-P, and the increased resistance of the sphingosine kinase overexpressor mutant was reversed by the inhibitor
N
,
N
-dimethylsphingosine. Parallel changes in sensitivity of the null mutants are seen with the platinum-based drug carboplatin but not with doxorubicin, 5-fluorouracil, and etoposide. This pattern of specificity is similar to that observed with the S-1-P lyase mutants and should be useful in designing therapeutic schemes involving more than one drug. This study identifies the sphingosine kinases as new drug targets for modulating the sensitivity to platinum-based drugs.
Transcriptional Network of Multiple Capsule and Melanin Genes Governed by theCryptococcus neoformansCyclic AMP Cascade
Authors: Pukkila-Worley Read , Gerrald Quincy D. , Kraus Peter R. , Boily Marie-Josée , Davis Matthew J. , Giles Steven S. , Cox Gary M. , Heitman Joseph , Alspaugh J. Andrew 
Published: January 2005

ABSTRACTCryptococcus neoformansis an opportunistic human fungal pathogen that elaborates several virulence attributes, including a polysaccharide capsule and melanin pigments. A conserved Gα protein/cyclic AMP (cAMP) pathway controls melanin and capsule production. To identify targets of this pathway, we used an expression profiling approach to define genes that are transcriptionally regulated by the Gα protein Gpa1. This approach revealed that Gpa1 transcriptionally regulates multiple genes involved in capsule assembly and identified two additional genes with a marked dependence on Gpa1 for transcription. The first is theLAC1gene, encoding the laccase enzyme that catalyzes a rate-limiting step in diphenol oxidation and melanin production. The second gene identified (LAC2) is adjacent to theLAC1gene and encodes a second laccase that shares 75% nucleotide identity withLAC1. Similar to theLAC1gene,LAC2is induced in response to glucose deprivation. However,LAC2basal transcript levels are much lower than those forLAC1. Accordingly, alac2mutation results in only a modest delay in melanin formation.LAC2overexpression suppresses the melanin defects ofgpa1andlac1mutants and partially restores virulence of these strains. These studies provide mechanistic insights into the regulation of capsule and melanin production by theC. neoformanscAMP pathway and demonstrate that multiple laccases contribute toC. neoformansmelanin production and pathogenesis.
Species Specificity in Ribosome Biogenesis: a Nonconserved Phosphoprotein Is Required for Formation of the Large Ribosomal Subunit in
Trypanosoma brucei
Authors: Jensen Bryan C. , Brekken Deirdre L. , Randall Amber C. , Kifer Charles T. , Parsons Marilyn 
Published: January 2005

ABSTRACT

In the protozoan parasite
Trypanosoma brucei
, the large rRNA, which is a single 3.4- to 5-kb species in most organisms, is further processed to form six distinct RNAs, two larger than 1 kb (LSU1 and LSU2) and four smaller than 220 bp. The small rRNA SR1 separates the two large RNAs, while the remaining small RNAs are clustered at the 3′ end of the precursor rRNA. One would predict that
T. brucei
possesses specific components to carry out these added processing events. We show here that the trypanosomatid-specific nucleolar phosphoprotein NOPP44/46 is involved in this further processing. Cells depleted of NOPP44/46 by RNA interference had a severe growth defect and demonstrated a defect in large-ribosomal-subunit biogenesis. Concurrent with this defect, a significant decrease in processing intermediates, particularly for SR1, was seen. In addition, we saw an accumulation of aberrant processing intermediates caused by cleavage within either LSU1 or LSU2. Though it is required for large-subunit biogenesis, we show that NOPP44/46 is not incorporated into the nascent particle. Thus, NOPP44/46 is an unusual protein in that it is both nonconserved and required for ribosome biogenesis.
Cryptococcus neoformansMitochondrial Superoxide Dismutase: an Essential Link between Antioxidant Function and High-Temperature Growth
Authors: Giles Steven S. , Batinić-Haberle Ines , Perfect John R. , Cox Gary M. 
Published: January 2005

ABSTRACTManganese superoxide dismutase is an essential component of the mitochondrial antioxidant defense system of most eukaryotes. In the present study, we used a reverse-genetics approach to assess the contribution of theCryptococcus neoformansmanganese superoxide dismutase (Sod2) for antioxidant defense. Strains with mutations in theSOD2gene exhibited increased susceptibility to oxidative stress as well as poor growth at elevated temperatures compared to isogenic wild-type strains. Thesod2Δ mutants were also avirulent in a murine model of inhaled cryptococcosis. Reconstitution of asod2Δ mutant restored Sod2 activity, eliminated the oxidative stress and temperature-sensitive (ts) phenotypes, and complemented the virulence phenotype. Characterization of the ts phenotype revealed a dependency between Sod2 antioxidant activity and the ability ofC. neoformanscells to adapt to growth at elevated temperatures. The ts phenotype could be suppressed by the addition of either ascorbic acid (10 mM) or Mn salen (200 μM) at 30°C, but not at 37°C. Furthermore,sod2Δ mutant cells that were incubated for 24 h at 37°C under anaerobic, but not aerobic, conditions were viable when shifted to the permissive conditions of 25°C in the presence of air. These data suggest that theC. neoformansSod2 is a major component of the antioxidant defense system in this human fungal pathogen and that adaptation to growth at elevated temperatures is also dependent on Sod2 activity.
Loss of Meiotic Rereplication Block in
Saccharomyces cerevisiae
Cells Defective in Cdc28p Regulation
Authors: Rice Lyndi M. , Plakas Constantine , Nickels Joseph T. 
Published: January 2005

ABSTRACT

Cdc28p is the major cyclin-dependent kinase in
Saccharomyces cerevisiae
. Its activity is required for blocking the reinitiation of DNA replication during mitosis. Here, we show that under conditions where Cdc28p activity is improperly regulated—either through the loss of function of the
Schizosaccharomyces pombe wee1
ortholog Swe1p or through the expression of a dominant
CDC28
allele,
CDC28AF
—diploid yeast cells are able to complete several rounds of premeiotic DNA replication within a single meiotic cell cycle. Moreover, a percentage of mutant cells exhibit a “multispore” phenotype, possessing the ability to package more than four spores within a single ascus. These multispored asci contain both even and odd numbers of viable spores. In order for meiotic rereplication and multispore formation to occur, cells must initiate homologous recombination and maintain proper chromosome cohesion during meiosis I. Rad9p- or Rad17p-dependent checkpoint mechanisms are not required for multispore formation and neither are the B-type cyclin Clb6p and the cyclin-dependent kinase inhibitor Sic1p. Finally, we present evidence of a possible role for a Cdc55p-dependent protein phosphatase 2A in initiating meiotic replication.
Tor and Cyclic AMP-Protein Kinase A: Two Parallel Pathways Regulating Expression of Genes Required for Cell Growth
Authors: Zurita-Martinez Sara A. , Cardenas Maria E. 
Published: January 2005

ABSTRACT

In the budding yeast
Saccharomyces cerevisiae
, the Tor and cyclic AMP-protein kinase A (cAMP-PKA) signaling cascades respond to nutrients and regulate coordinately the expression of genes required for cell growth, including ribosomal protein (RP) and stress-responsive (STRE) genes. The inhibition of Tor signaling by rapamycin results in repression of the RP genes and induction of the STRE genes. Mutations that hyperactivate PKA signaling confer resistance to rapamycin and suppress the repression of RP genes imposed by rapamycin. By contrast, partial inactivation of PKA confers rapamycin hypersensitivity but only modestly affects RP gene expression. Complete inactivation of PKA impairs RP gene expression and concomitantly enhances STRE gene expression; remarkably, this altered transcriptional pattern is still sensitive to rapamycin and thus subject to Tor control. These findings illustrate how the Tor and cAMP-PKA signaling pathways respond to nutrient signals to govern gene expression required for cell growth via two parallel routes, and they have broad implication for our understanding of analogous regulatory networks in normal and neoplastic mammalian cells.
Exposure of Cells to a Cell Number-Counting Factor Decreases the Activity of Glucose-6-Phosphatase To Decrease Intracellular Glucose Levels in
Dictyostelium discoideum
Authors: Jang Wonhee , Gomer Richard H. 
Published: January 2005

ABSTRACT

The development of
Dictyostelium discoideum
is a model for tissue size regulation, as these cells form groups of ≈2 × 10
4
cells. The group size is regulated in part by a negative feedback pathway mediated by a secreted multipolypeptide complex called counting factor (CF). CF signal transduction involves decreasing intracellular CF glucose levels. A component of CF, countin, has the bioactivity of the entire CF complex, and an 8-min exposure of cells to recombinant countin decreases intracellular glucose levels. To understand how CF regulates intracellular glucose, we examined the effect of CF on enzymes involved in glucose metabolism. Exposure of cells to CF has little effect on amylase or glycogen phosphorylase, enzymes involved in glucose production from glycogen. Glucokinase activity (the first specific step of glycolysis) is inhibited by high levels of CF but is not affected by an 8-min exposure to countin. The second enzyme specific for glycolysis, phosphofructokinase, is not regulated by CF. There are two corresponding enzymes in the gluconeogenesis pathway, fructose-1,6-bisphosphatase and glucose-6-phosphatase. The first is not regulated by CF or countin, whereas glucose-6-phosphatase is regulated by both CF and an 8-min exposure to countin. The countin-induced changes in the

K
m

and
V
max
of glucose-6-phosphatase cause a decrease in glucose production that can account for the countin-induced decrease in intracellular glucose levels. It thus appears that part of the CF signal transduction pathway involves inhibiting the activity of glucose-6-phosphatase, decreasing intracellular glucose levels and affecting the levels of other metabolites, to regulate group size.
Broad Sensitivity of
Saccharomyces cerevisiae
Lacking Ribosome-Associated Chaperone Ssb or Zuo1 to Cations, Including Aminoglycosides
Authors: Kim So-Young , Craig Elizabeth A. 
Published: January 2005

ABSTRACT

The Hsp70 Ssb and J protein Zuo1 of
Saccharomyces cerevisiae
are ribosome-associated molecular chaperones, proposed to be involved in the folding of newly synthesized polypeptide chains. Cells lacking Ssb and/or Zuo1 have been reported to be hypersensitive to cationic aminoglycoside protein synthesis inhibitors that affect translational fidelity and to NaCl. Since we found that Δ
ssb1
Δ
ssb2
(Δ
ssb1
,
2
), Δ
zuo1
, and wild-type cells have very similar levels of translational misreading in the absence of aminoglycosides, we asked whether the sensitivities to aminoglycosides and NaCl represent a general increase in sensitivity to cations. We found that Δ
ssb1
,
2
and Δ
zuo1
cells are hypersensitive to a wide range of cations. This broad sensitivity is similar to that of cells having lowered activity of major plasma membrane transporters, such as the major K
+
transporters Trk1 and Trk2 or their regulators Hal4 and Hal5. Like Δ
hal4
,
5
cells, Δ
ssb1
,
2
and Δ
zuo1
cells have increased intracellular levels of Na
+
and Li
+
upon challenge with higher-than-normal levels of these cations, due to an increased rate of influx. In the presence of aminoglycosides, Δ
ssb1
,
2
, Δ
zuo1
, and Δ
hal 4
,
5
cells have similarly increased levels of translational misreading. We conclude that, in vivo, the major cause of the aminoglycoside sensitivity of cells lacking ribosome-associated molecular chaperones is a general increase in cation influx, perhaps due to altered maturation of membrane proteins.
The G
1
Cyclin Cln3 Regulates Morphogenesis in
Candida albicans
Authors: Chapa y Lazo Bernardo , Bates Steven , Sudbery Peter 
Published: January 2005

ABSTRACT

In
Saccharomyces cerevisiae
, the G
1
cyclin Cln3 initiates the Start of a mitotic cell cycle in response to size and nutrient inputs. Loss of Cln3 delays but does not prevent Start, due to the eventual Cln3-independent transcription of
CLN1
and
CLN2.
When unbudded cells of the human pathogen
Candida albicans
were depleted of the G
1
cyclin Cln3 they increased in size but did not bud. Thus, unlike
S. cerevisiae
, Cln3 is essential for budding in
C. albicans.
However, eventually the large unbudded cells spontaneously produced filamentous forms. The morphology was growth medium dependent; on nutritionally poor medium the polarized outgrowths fulfilled the formal criteria for true hyphae. This state is stable, and continued growth leads to a hyphal mycelium, which invades the agar substratum. Interestingly, it is also required for normal hyphal development, as Cln3-depleted cells develop morphological abnormalities if challenged with hyphal inducing signals such as serum or neutral pH. Taken together, these results show that, in
C. albicans
, Cln3 has assumed a critical role in coordinating mitotic cell division with differentiation.
Cyclin Cln3p Links G
1
Progression to Hyphal and Pseudohyphal Development in
Candida albicans
Authors: Bachewich Catherine , Whiteway Malcolm 
Published: January 2005

ABSTRACT

G
1
cyclins coordinate environmental conditions with growth and differentiation in many organisms. In the pathogen
Candida albicans
, differentiation of hyphae is induced by environmental cues but in a cell cycle-independent manner. Intriguingly, repressing the G
1
cyclin Cln3p under yeast growth conditions caused yeast cells to arrest in G
1
, increase in size, and then develop into hyphae and pseudohyphae, which subsequently resumed the cell cycle. Differentiation was dependent on Efg1p, Cph1p, and Ras1p, but absence of Ras1p was also synthetically lethal with repression of
CLN3
. In contrast, repressing
CLN3
in environment-induced hyphae did not inhibit growth or the cell cycle, suggesting that yeast and hyphal cell cycles may be regulated differently. Therefore, absence of a G
1
cyclin can activate developmental pathways in
C. albicans
and uncouple differentiation from the normal environmental controls. The data suggest that the G
1
phase of the cell cycle may therefore play a critical role in regulating hyphal and pseudohyphal development in
C. albicans
.
LEONARD PAIRS AND THE ASKEY–WILSON RELATIONS
Authors: TERWILLIGER PAUL , VIDUNAS RAIMUNDAS 
Published: January 2005

Let K denote a field and let V denote a vector space over K with finite positive dimension. We consider an ordered pair of linear transformations A:V→V and A*:V→V which satisfy the following two properties:(i) There exists a basis for V with respect to which the matrix representing A is irreducible tridiagonal and the matrix representing A* is diagonal.(ii) There exists a basis for V with respect to which the matrix representing A* is irreducible tridiagonal and the matrix representing A is diagonal.We call such a pair a Leonard pair on V. Referring to the above Leonard pair, we show there exists a sequence of scalars β,γ,γ*,ϱ,ϱ*,ω,η,η* taken from K such that both [Formula: see text] The sequence is uniquely determined by the Leonard pair provided the dimension of V is at least 4. The equations above are called the Askey–Wilson relations.
Tense, aspect and the passive voice in L1 and L2 academic texts
Authors: Hinkel Eli 
Published: January 2005

This study analyses specific written discourse production in which NNSs’ usage of English tenses and voice appears to be dramatically different from that of NSs. The data for the study narrowly focuses on a small number of verb phrase features, such as tenses, aspects and the passive voice, examining how they are presented in writing instruction texts and identifying areas of L2 learning in need of intensive instruction. The main goal of the analysis is to identify the patterns and median frequency rates of L1 and L2 uses of three English tenses (the present, the past and the future), two aspects (the progressive and the perfect), and passive verb structures encountered in a NS and NNS corpus of L1 and L2 academic student academic texts (746 essays/226,054 words). The results of the study demonstrate that even after many years of L2 learning and use, advanced NNS students may have difficulty with the conventionalized uses of tenses, aspects and the passive voice in written academic discourse. The paper also offers a few practical techniques to improve NNS students’ production of passable L2 written academic prose. Therefore, the types of texts and contexts in which NNSs may choose to use particular tenses, aspects and voice (or to avoid them) represent an important research venue because such investigations can lead to new insights into learners’ real-life L2 skills. In particular, in academic writing that all NNS students in universities in English-speaking countries must produce in copious quantities, the issues of tense, aspect and specifically passive voice usage are usually seen as very important (Michaelis, 1994; Nehls, 1988, 1992; Swales and Feak, 2000). The study presented here analyses specific written discourse production in which NNSs’ usage of English tense and voice appears to be dramatically different from that of NSs. The data for the study narrowly focuses on a small number of verb phrase features, such as tenses, aspects and the passive voice, with the goal of identifying areas of L2 learning in need of intensive instruction, in light of the fact that these important features of academic text are barely even mentioned in most writing instructional texts. The paper also offers a few practical techniques to improve NNS students’ production of passable L2 written academic prose. The research goal of this study is to analyse the patterns and median frequency rates of L1 and L2 uses of three English tenses (the present, the past and the future with both will- and would-constructions), two aspects (the progressive and the perfect) and passive verb structures encountered in a NS and NNS corpus of L1 and L2 academic student academic texts (746 essays/226,054 words).