bluuebunny/crossref_metadata_2025_split huggingface dataset:
MODELING OF THICKNESS FOR SEMISOLID FOODS
Authors: TERPSTRA MARJOLEIN E.J. , JANSSEN ANKE M. , PRINZ JON F. , DE WIJK RENÉ A. , WEENEN HUGO , VAN DER LINDEN ERIK 
Published: June 2005

ABSTRACT We investigated the relationship between orally perceived thickness and calculated shear stress on the tongue for mayonnaise and custard. To this end, the applicability of the models of Kokini et al. (1977), describing the mechanical breakdown in the mouth, have been tested. Within a limited range of shear stresses (mayonnaise < 150 Pa; custard < 30 Pa), there was a linear relationship between shear stress and thickness, in accordance with the work of Kokini et al. (1977). Beyond this range, the linear relationship breaks down and the thickness levels off with shear stress for both mayonnaise and custard. The relationship over the entire range of shear stresses used in this paper can be satisfactorily described by a semilogarithmic (Fechner) relation. For both types of products, the quality of the thickness prediction by the decreasing‐height model and the constant‐height model of Kokini et al. (1977) is similar. For most mayonnaises, the contribution of the lateral movement of the tongue to the shear stress in the decreasing‐height model of Kokini et al. (1977) is orders of magnitude larger than the contribution of the squeezing or compression movement of the tongue towards the palate. This difference in magnitude is affected by the low value measured for the compression force and by the high values for material consistency K. The values for K are high because yield‐stress behavior has been neglected when the flow curves were analyzed. For custard, the models of Kokini et al. (1977) are found to be less adequate. It is proposed that this is because the models ignore interactions with saliva. Several routes to improve the modeling by incorporating viscoelastic behavior were unsuccessful. Elongational stress and yield stress were neglected in all tested models.
ACE2
,
CBK1
, and
BUD4
in Budding and Cell Separation
Authors: Voth Warren P. , Olsen Aileen E. , Sbia Mohammed , Freedman Karen H. , Stillman David J. 
Published: June 2005

ABSTRACT

Mutations in the RAM network genes, including
CBK1
,
MOB2
,
KIC1
,
HYM1
, and
TAO3
, cause defects in bud site selection, asymmetric apical growth, and mating projections. Additionally, these mutants show altered colony morphology, cell separation defects, and reduced
CTS1
expression, phenotypes also seen by mutating the Ace2 transcription factor. We show that an
ACE2
multicopy plasmid suppresses the latter three defects of RAM network mutations, demonstrating that Ace2 is downstream of the RAM network and suggesting that these phenotypes are caused by reduced expression of Ace2 target genes. We show that wild-type W303 strains have a
bud4
mutation and that combining
bud4
with either
ace2
or
cbk1
in haploids results in altered colony morphology. We describe a timed sedimentation assay that allows quantitation of cytokinesis defects and subtle changes in budding pattern and cell shape. Experiments examining budding patterns and sedimentation rates both show that Ace2 and Cbk1 have independent functions in addition to their common pathway in transcription of genes such as
CTS1
.
SWI5
encodes a transcription factor paralogous to
ACE2
. Additive effects are seen in
cbk1 swi5
strains, and we show that activation of some target genes, such as
EGT2
, requires either Swi5 or Ace2 with Cbk1. The relative roles and interactions of Ace2, Cbk1, and Bud4 in bud site selection, polarized growth, and cell separation are discussed.
A Novel Assay for Protein Phosphatase 2A (PP2A) Complexes In Vivo Reveals Differential Effects of Covalent Modifications on Different
Saccharomyces cerevisiae
PP2A Heterotrimers
Authors: Gentry Matthew S. , Li Yikun , Wei Huijun , Syed Farhana F. , Patel Sameer H. , Hallberg Richard L. , Pallas David C. 
Published: June 2005

ABSTRACT

Protein phosphatase 2A (PP2A) catalytic subunit can be covalently modified at its carboxy terminus by phosphorylation or carboxymethylation. Determining the effects of these covalent modifications on the relative amounts and functions of different PP2A heterotrimers is essential to understanding how these modifications regulate PP2A-controlled cellular processes. In this study we have validated and used a novel in vivo assay for assessing PP2A heterotrimer formation in
Saccharomyces cerevisiae
: the measurement of heterotrimer-dependent localization of green fluorescent protein-PP2A subunits. This assay relies on the fact that the correct cellular localization of PP2A requires that it be fully assembled. Thus, reduced localization would occur as the result of the inability to assemble a stable heterotrimer. Using this assay, we determined the effects of PP2A C-subunit phosphorylation mimic mutations and reduction or loss of PP2A methylation on the formation and localization of PP2A
B/Cdc55p
and PP2A
B
′
/Rts1p
heterotrimers. Collectively, our findings demonstrate that phosphorylation and methylation of the PP2A catalytic subunit can influence its function both by regulating the total amount of specific PP2A heterotrimers within a cell and by altering the relative proportions of PP2A
B/Cdc55p
and PP2A
B
′
/Rts1p
heterotrimers up to 10-fold. Thus, these posttranslational modifications allow flexible, yet highly coordinated, regulation of PP2A-dependent signaling pathways that in turn modulate cell growth and function.
Role of Integrase in Reverse Transcription of the
Saccharomyces cerevisiae
Retrotransposon Ty1
Authors: Wilhelm M. , Wilhelm F.-X. 
Published: June 2005

ABSTRACT

Reverse transcriptase (RT) with its associated RNase H (RH) domain and integrase (IN) are key enzymes encoded by retroviruses and retrotransposons. Several studies have implied a functional role of the interaction between IN and RT during the replication of retroviral and retrotransposon genomes. In this study, IN deletion mutants were used to investigate the role of IN on the RT activity of the yeast
Saccharomyces cerevisiae
retrotransposon Ty1. We have identified two domains of Ty1 integrase which have effects on RT activity in vivo. The deletion of a domain spanning amino acid residues 233 to 520 of IN increases the exogenous specific activity of RT up to 20-fold, whereas the removal of a region rich in acidic amino acid residues between residues 521 and 607 decreases its activity. The last result complements our observation that an active recombinant RT protein can be obtained if a small acidic tail mimicking the acidic domain of IN is fused to the RT-RH domain. We suggest that interaction between these acidic amino acid residues of IN and a basic region of RT could be critical for the correct folding of RT and for the formation of an active conformation of the enzyme.
A Rac Homolog Functions Downstream of Ras1 To Control Hyphal Differentiation and High-Temperature Growth in the Pathogenic Fungus
Cryptococcus neoformans
Authors: Vallim Marcelo A. , Nichols Connie B. , Fernandes Larissa , Cramer Kari L. , Alspaugh J. Andrew 
Published: June 2005

ABSTRACT

The
Cryptococcus neoformans
Ras1 protein serves as a central regulator for several signaling pathways. Ras1 controls the induction of the mating pheromone response cascade as well as a distinct signaling pathway that allows this pathogenic fungus to grow at human physiological temperature. To characterize elements of the Ras1-dependent high-temperature growth pathway, we performed a multicopy suppressor screen, identifying genes whose overexpression allows the
ras1
mutant to grow at 37°C. Using this genetic technique, we identified a
C. neoformans
gene encoding a Rac homolog that suppresses multiple
ras1
mutant phenotypes. Deletion of the
RAC1
gene does not affect high-temperature growth. However, a
rac1
mutant strain demonstrates a profound defect in haploid filamentation as well as attenuated mating. In a yeast two-hybrid assay, Rac1 physically interacts with the PAK kinase Ste20, which similarly regulates hyphal formation in this fungus. Similar to Rac1, overexpression of the
STE20α
gene also restores high-temperature growth to the
ras1
mutant. These results support a model in which the small G protein Rac1 acts downstream of Ras proteins and coordinately with Ste20 to control high-temperature growth and cellular differentiation in this human fungal pathogen.
Calcium- and Calcineurin-Independent Roles for Calmodulin in
Cryptococcus neoformans
Morphogenesis and High-Temperature Growth
Authors: Kraus Peter R. , Nichols Connie B. , Heitman Joseph 
Published: June 2005

ABSTRACT

The function of calcium as a signaling molecule is conserved in eukaryotes from fungi to humans. Previous studies have identified the calcium-activated phosphatase calcineurin as a critical factor in governing growth of the human pathogenic fungus
Cryptococcus neoformans
at mammalian body temperature. Here, we employed insertional mutagenesis to identify new genes required for growth at 37°C. One insertion mutant,
cam1-ts
, that displayed a growth defect at 37°C and hypersensitivity to the calcineurin inhibitor FK506 at 25°C was isolated. Both phenotypes were linked to the dominant marker in genetic crosses, and molecular analysis revealed that the insertion occurred in the 3′ untranslated region of the gene encoding the calcineurin activator calmodulin (
CAM1
) and impairs growth at 37°C by significantly reducing calmodulin mRNA abundance. The
CAM1
gene was demonstrated to be essential using genetic analysis of a
CAM1
/
cam1
Δ diploid strain. In the absence of calcineurin function, the
cam1-ts
mutant displayed a severe morphological defect with impaired bud formation. Expression of a calmodulin-independent calcineurin mutant did not suppress the growth defect of the
cam1-ts
mutant at 37°C, indicating that calmodulin promotes growth at high temperature via calcineurin-dependent and -independent pathways. In addition, a Ca
2+
-binding-defective allele of
CAM1
complemented the 37°C growth defect, FK506 hypersensitivity, and morphogenesis defect of the
cam1-ts
mutant. Our findings reveal that calmodulin performs Ca
2+
- and calcineurin-independent and -dependent roles in controlling
C. neoformans
morphogenesis and high-temperature growth.
Contribution of Horizontal Gene Transfer to the Evolution of
Saccharomyces cerevisiae
Authors: Hall Charles , Brachat Sophie , Dietrich Fred S. 
Published: June 2005

ABSTRACT

The genomes of the hemiascomycetes
Saccharomyces cerevisiae
and
Ashbya gossypii
have been completely sequenced, allowing a comparative analysis of these two genomes, which reveals that a small number of genes appear to have entered these genomes as a result of horizontal gene transfer from bacterial sources. One potential case of horizontal gene transfer in
A. gossypii
and 10 potential cases in
S. cerevisiae
were identified, of which two were investigated further. One gene, encoding the enzyme dihydroorotate dehydrogenase (DHOD), is potentially a case of horizontal gene transfer, as shown by sequencing of this gene from additional bacterial and fungal species to generate sufficient data to construct a well-supported phylogeny. The DHOD-encoding gene found in
S. cerevisiae
,
URA1
(YKL216W), appears to have entered the
Saccharomycetaceae
after the divergence of the
S. cerevisiae
lineage from the
Candida albicans
lineage and possibly since the divergence from the
A. gossypii
lineage. This gene appears to have come from the
Lactobacillales
, and following its acquisition the endogenous eukaryotic DHOD gene was lost. It was also shown that the bacterially derived horizontally transferred DHOD is required for anaerobic synthesis of uracil in
S. cerevisiae.
The other gene discussed in detail is
BDS1
, an aryl- and alkyl-sulfatase gene of bacterial origin that we have shown allows utilization of sulfate from several organic sources. Among the eukaryotes, this gene is found in
S. cerevisiae
and
Saccharomyces bayanus
and appears to derive from the alpha-proteobacteria.
Constitutive Signal Transduction by Mutant Ssy5p and Ptr3p Components of the SPS Amino Acid Sensor System in
Saccharomyces cerevisiae
Authors: Poulsen Peter , Wu Boqian , Gaber Richard F. , Kielland-Brandt Morten C. 
Published: June 2005

ABSTRACT

Amino acids in the environment of
Saccharomyces cerevisiae
can transcriptionally activate a third of the amino acid permease genes through a signal that originates from the interaction between the extracellular amino acids and an integral plasma membrane protein, Ssy1p. Two plasma membrane-associated proteins, Ptr3p and Ssy5p, participate in the sensing, which results in cleavage of the transcription factors Stp1p and Stp2p, removing 10 kDa of the N terminus of each of them. This confers the transcription factors with the ability to gain access to the nucleus and activate transcription of amino acid permease genes. To extend our understanding of the role of Ptr3p and Ssy5p in this amino acid sensing process, we have isolated constitutive gain-of-function mutants in these two components by using a genetic screening in which potassium uptake is made dependent on amino acid signaling. Mutants which exhibit inducer-independent processing of Stp1p and activation of the amino acid permease gene
AGP1
were obtained. For each component of the SPS complex, constitutive signaling by a mutant allele depended on the presence of wild-type alleles of the other two components. Despite the signaling in the absence of inducer, the processing of Stp1p was more complete in the presence of inducer. Dose response assays showed that the median effective concentration for Stp1p processing in the mutant cells was decreased; i.e., a lower inducer concentration is needed for signaling in the mutant cells. These results suggest that the three sensor components interact intimately in a complex rather than in separate reactions and support the notion that the three components function as a complex.
Class I and Class II Chitin Synthases Are Involved in Septum Formation in the Filamentous Fungus
Aspergillus nidulans
Authors: Ichinomiya Masayuki , Yamada Emi , Yamashita Shuichi , Ohta Akinori , Horiuchi Hiroyuki 
Published: June 2005

ABSTRACT

The class II and class I chitin synthases of the filamentous fungus
Aspergillus nidulans
are encoded by
chsA
and
chsC
, respectively. Previously, we presented several lines of evidence suggesting that ChsA and ChsC have overlapping functions in maintaining cell wall integrity. In order to determine the functions of these chitin synthases, we employed electron and fluorescence microscopy and investigated in detail the cell wall of a Δ
chsA
Δ
chsC
double mutant (ΔAC mutant) along with the localization of ChsA and ChsC. In the lateral cell wall of the ΔAC mutant, electron-transparent regions were thickened. Septa of the ΔAC mutant were aberrantly thick and had a large pore. Some septa were located abnormally close to adjacent septa. A functional hemagglutinin (HA)-tagged ChsA (HA-ChsA) and a functional FLAG-tagged ChsC (FLAG-ChsC) were each localized to a subset of septation sites. Comparison with the localization pattern of actin, which is known to localize at forming septa, suggested that ChsA and ChsC transiently exist at the septation sites during and shortly after septum formation. Double staining of HA-ChsA and FLAG-ChsC indicated that their localizations were not identical but partly overlapped at the septation sites. Fluorescence of FLAG-ChsC, but not of HA-ChsA, was also observed at hyphal tips. These data indicate that ChsA and ChsC share overlapping roles in septum formation.
Unique Mitochondrial Genome Structure in Diplonemids, the Sister Group of Kinetoplastids
Authors: Marande William , Lukeš Julius , Burger Gertraud 
Published: June 2005

ABSTRACT

Kinetoplastid flagellates are characterized by uniquely massed mitochondrial DNAs (mtDNAs), the kinetoplasts. Kinetoplastids of the trypanosomatid group possess two types of mtDNA molecules: maxicircles bearing protein and mitoribosomal genes and minicircles specifying guide RNAs, which mediate uridine insertion/deletion RNA editing. These circles are interlocked with one another to form dense networks. Whether these peculiar mtDNA features are restricted to kinetoplastids or prevail throughout Euglenozoa (euglenids, diplonemids, and kinetoplastids) is unknown. Here, we describe the mitochondrial genome and the mitochondrial ultrastructure of
Diplonema papillatum
, a member of the diplonemid flagellates, the sister group of kinetoplastids. Fluorescence and electron microscopy show a single mitochondrion per cell with an ultrastructure atypical for Euglenozoa. In addition, DNA is evenly distributed throughout the organelle rather than compacted. Molecular and electron microscopy studies distinguish numerous 6- and 7-kbp-sized mitochondrial chromosomes of monomeric circular topology and relaxed conformation in vivo. Remarkably, the
cox1
gene (and probably other mitochondrial genes) is fragmented, with separate gene pieces encoded on different chromosomes. Generation of the contiguous
cox1
mRNA requires
trans
-splicing, the precise mechanism of which remains to be determined. Taken together, the mitochondrial gene/genome structure of
Diplonema
is not only different from that of kinetoplastids but unique among eukaryotes as a whole.
Eukaryotic UDP-Galactopyranose Mutase (
GLF
Gene) in Microbial and Metazoal Pathogens
Authors: Beverley Stephen M. , Owens Katherine L. , Showalter Melissa , Griffith Cara L. , Doering Tamara L. , Jones Victoria C. , McNeil Michael R. 
Published: June 2005

ABSTRACT

Galactofuranose (Gal

f

) is a novel sugar absent in mammals but present in a variety of pathogenic microbes, often within glycoconjugates that play critical roles in cell surface formation and the infectious cycle. In prokaryotes, Gal

f

is synthesized as the nucleotide sugar UDP-Gal

f

by UDP-galactopyranose mutase (UGM) (gene
GLF
). Here we used a combinatorial bioinformatics screen to identify a family of candidate eukaryotic
GLF
s that had previously escaped detection.
GLF
s from three pathogens, two protozoa (
Leishmania major
and
Trypanosoma cruzi
) and one fungus (
Cryptococcus neoformans
), had UGM activity when expressed in
Escherichia coli
and assayed in vivo and/or in vitro. Eukaryotic
GLF
s are closely related to each other but distantly related to prokaryotic
GLF
s, showing limited conservation of core residues around the substrate-binding site and flavin adenine dinucleotide binding domain. Several eukaryotes not previously investigated for Gal

f

synthesis also showed strong
GLF
homologs with conservation of key residues. These included other fungi, the alga
Chlamydomonas
and the algal phleovirus
Feldmannia irregularis
, parasitic nematodes (
Brugia
,
Onchocerca
, and
Strongyloides
) and
Caenorhabditis elegans
, and the urochordates
Halocynthia
and
Cionia
. The
C. elegans
open reading frame was shown to encode UGM activity. The
GLF
phylogenetic distribution suggests that Gal

f

synthesis may occur more broadly in eukaryotes than previously supposed. Overall,
GLF
/Gal

f

synthesis in eukaryotes appears to occur with a disjunct distribution and often in pathogenic species, similar to what is seen in prokaryotes. Thus, UGM inhibition may provide an attractive drug target in those eukaryotes where Gal

f

plays critical roles in cellular viability and virulence.
The
RIM101/pacC
Homologue from the Basidiomycete
Ustilago maydis
Is Functional in Multiple pH-Sensitive Phenomena
Authors: Aréchiga-Carvajal Elva T. , Ruiz-Herrera José 
Published: June 2005

ABSTRACT

A homologue of the gene encoding the transcription factor Rim101 (PacC), involved in pH signal transduction in fungi, was identified in the pathogenic basidiomycete
Ustilago maydis
. The gene (
RIM101
) encodes a protein of 827 amino acid residues, which shows highest similarity to PacC proteins from
Fusarium oxysporum
and
Aspergillus niger
. The gene had the capacity to restore protease activity to
rim101
mutants from
Yarrowia lipolytica
, confirming its homologous function, and was expressed at both acid and neutral pH. Null
Δrim101
mutants were not affected in the in vitro pH-induced dimorphic transition, their growth rate, resistance to hypertonic sorbitol or KCl stress, and pathogenicity. However, similar to
pacC
(
rim101
) mutants in other fungi, they displayed a pleiotropic phenotype with alterations in morphogenesis, impairment in protease secretion, and increased sensitivity to Na
+
and Li
+
ions. Other phenotypic characteristics not previously reported in fungal
pacC
(
rim101
) mutants (morphological changes, increased sensitivity to lytic enzymes, and augmented polysaccharide secretion) were also observed in
U. maydis
mutants. All these modifications were alleviated by transformation with the wild-type gene, confirming that all were the result of mutation in
RIM101
. These data indicate that the Pal/Rim pathway is functional in
U. maydis
(and probably in other basidiomycetes) and plays complex roles in pH-sensing phenomena, as occurs in ascomycetes and deuteromycetes.
Unraveling the Secret Lives of Bacteria: Use of In Vivo Expression Technology and Differential Fluorescence Induction Promoter Traps as Tools for Exploring Niche-Specific Gene Expression
Authors: Rediers Hans , Rainey Paul B. , Vanderleyden Jos , De Mot René 
Published: June 2005

SUMMARYA major challenge for microbiologists is to elucidate the strategies deployed by microorganisms to adapt to and thrive in highly complex and dynamic environments. In vitro studies, including those monitoring genomewide changes, have proven their value, but they can, at best, mimic only a subset of the ensemble of abiotic and biotic stimuli that microorganisms experience in their natural habitats. The widely used gene-to-phenotype approach involves the identification of altered niche-related phenotypes on the basis of gene inactivation. However, many traits contributing to ecological performance that, upon inactivation, result in only subtle or difficult to score phenotypic changes are likely to be overlooked by this otherwise powerful approach. Based on the premise that many, if not most, of the corresponding genes will be induced or upregulated in the environment under study, ecologically significant genes can alternatively be traced using the promoter trap techniques differential fluorescence induction and in vivo expression technology (IVET). The potential and limitations are discussed for the different IVET selection strategies and system-specific variants thereof. Based on a compendium of genes that have emerged from these promoter-trapping studies, several functional groups have been distinguished, and their physiological relevance is illustrated with follow-up studies of selected genes. In addition to confirming results from largely complementary approaches such as signature-tagged mutagenesis, some unexpected parallels as well as distinguishing features of microbial phenotypic acclimation in diverse environmental niches have surfaced. On the other hand, by the identification of a large proportion of genes with unknown function, these promoter-trapping studies underscore how little we know about the secret lives of bacteria and other microorganisms.