bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Phylogenetics of
Candida albicans
Authors: Odds Frank C. , Bougnoux Marie-Elisabeth , Shaw Duncan J. , Bain Judith M. , Davidson Amanda D. , Diogo Dorothée , Jacobsen Mette D. , Lecomte Maud , Li Shu-Ying , Tavanti Arianna , Maiden Martin C. J. , Gow Neil A. R. , d'Enfert Christophe 
Published: April 2007

ABSTRACT

We analyzed data on multilocus sequence typing (MLST), ABC typing, mating type-like locus (
MAT
) status, and antifungal susceptibility for a panel of 1,391
Candida albicans
isolates. Almost all (96.7%) of the isolates could be assigned by MLST to one of 17 clades. eBURST analysis revealed 53 clonal clusters. Diploid sequence type 69 was the most common MLST strain type and the founder of the largest clonal cluster, and examples were found among isolates from all parts of the world. ABC types and geographical origins showed statistically significant variations among clades by univariate analysis of variance, but anatomical source and antifungal susceptibility data were not significantly associated. A separate analysis limited to European isolates, thereby minimizing geographical effects, showed significant differences in the proportions of isolates from blood, commensal carriage, and superficial infections among the five most populous clades. The proportion of isolates with low antifungal susceptibility was highest for
MAT
homozygous
a
/
a
types and then α/α types and was lowest for heterozygous
a
/α types. The tree of clades defined by MLST was not congruent with trees generated from the individual gene fragments sequenced, implying a separate evolutionary history for each fragment. Analysis of nucleic acid variation among loci and within loci supported recombination. Computational haplotype analysis showed a high frequency of recombination events, suggesting that isolates had mixed evolutionary histories resembling those of a sexually reproducing species.
Further Characterization of the Signaling Proteolysis Step in theAspergillus nidulanspH Signal Transduction Pathway
Authors: Peñas María M. , Hervás-Aguilar América , Múnera-Huertas Tatiana , Reoyo Elena , Peñalva Miguel Á. , Arst Herbert N. , Tilburn Joan 
Published: April 2007

ABSTRACTTheAspergillus nidulanspH-responsive transcription factor PacC is modulated by limited, two-step proteolysis. The first, pH-regulated cleavage occurs in the 24-residue highly conserved “signaling protease box” in response to the alkaline pH signal. This is transduced by the Pal signaling pathway, containing the predicted calpain-like cysteine protease and likely signaling protease, PalB. In this work, we carried out classical mutational analysis of the putative signaling protease PalB, and we describe 9 missense and 18 truncating loss-of-function (including null) mutations. Mutations in the region of and affecting directly the predicted catalytic cysteine strongly support the deduction that PalB is a cysteine protease. Truncating and missense mutations affecting the C terminus highlight the importance of this region. Analysis of three-hemagglutinin-tagged PalB in Western blots demonstrates that PalB levels are independent of pH and Pal signal transduction. We have followed the processing of MYC3-tagged PacC in Western blots. We show unequivocally that PalB is essential for signaling proteolysis and is definitely not the processing protease. In addition, we have replaced 15 residues of the signaling protease box of MYC3-tagged PacC (pacC900) with alanine. The majority of these substitutions are silent. Leu481Ala, Tyr493Ala, and Gln499Ala result in delayed PacC processing in response to shifting from acidic to alkaline medium, as determined by Western blot analysis. Leu498Ala reduces function much more markedly, as determined by plate tests and processing recalcitrance. Excepting Leu498, this demonstrates that PacC signaling proteolysis is largely independent of sequence in the cleavage region.
Genomic and Biochemical Analysis of Lipid Biosynthesis in the Unicellular Rhodophyte
Cyanidioschyzon merolae
: Lack of a Plastidic Desaturation Pathway Results in the Coupled Pathway of Galactolipid Synthesis
Authors: Sato Naoki , Moriyama Takashi 
Published: April 2007

ABSTRACT

The acyl lipids making up the plastid membranes in plants and algae are highly enriched in polyunsaturated fatty acids and are synthesized by two distinct pathways, known as the prokaryotic and eukaryotic pathways, which are located within the plastids and the endoplasmic reticulum, respectively. Here we report the results of biochemical as well as genomic analyses of lipids and fatty acids in the unicellular rhodophyte
Cyanidioschyzon merolae
. All of the glycerolipids usually found in photosynthetic algae were found, such as mono- and digalactosyl diacylglycerol, sulfolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol. However, the fatty acid composition was extremely simple. Only palmitic, stearic, oleic, and linoleic acids were found as major acids. In addition, 3-
trans
-hexadecanoic acid was found as a very minor component in phosphatidylglycerol. Unlike the case for most other photosynthetic eukaryotes, polyenoic fatty acids having three or more double bonds were not detected. These results suggest that polyunsaturated fatty acids are not necessary for photosynthesis in eukaryotes. Genomic analysis suggested that
C. merolae
lacks acyl lipid desaturases of cyanobacterial origin as well as stearoyl acyl carrier protein desaturase, both of which are major desaturases in plants and green algae. The results of labeling experiments with radioactive acetate showed that the desaturation leading to linoleic acid synthesis occurs on phosphatidylcholine located outside the plastids. Monogalactosyl diacylglycerol is therefore synthesized by the coupled pathway, using plastid-derived palmitic acid and endoplasmic reticulum-derived linoleic acid. These results highlight essential differences in lipid biosynthetic pathways between the red algae and the green lineage, which includes plants and green algae.
Genome of
Methylobacillus flagellatus
, Molecular Basis for Obligate Methylotrophy, and Polyphyletic Origin of Methylotrophy
Authors: Chistoserdova Ludmila , Lapidus Alla , Han Cliff , Goodwin Lynne , Saunders Liz , Brettin Tom , Tapia Roxanne , Gilna Paul , Lucas Susan , Richardson Paul M. , Lidstrom Mary E. 
Published: April 2007

ABSTRACT

Along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. The complete genome of a model obligate methanol and methylamine utilizer,
Methylobacillus flagellatus
(strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp, potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol and methylamine dehydrogenases and their specific electron transport chain components, the tetrahydromethanopterin-linked formaldehyde oxidation pathway and the assimilatory and dissimilatory ribulose monophosphate cycles, and by a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or nonidentical) copy. The obligate dependence on single-carbon compounds appears to be due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alpha-ketoglutarate, malate, or succinate dehydrogenases are identifiable. The genome of
M. flagellatus
was compared in terms of methylotrophy functions to the previously sequenced genomes of three methylotrophs,
Methylobacterium extorquens
(an alphaproteobacterium, 7 Mbp),
Methylibium petroleiphilum
(a betaproteobacterium, 4 Mbp), and
Methylococcus capsulatus
(a gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, the methylotrophy functions in
M. flagellatus
were more similar to those in
M. capsulatus
and
M. extorquens
than to the ones in the more closely related
M. petroleiphilum
species, providing the first genomic evidence for the polyphyletic origin of methylotrophy in
Betaproteobacteria
.
Colicin E2 Is Still in Contact with Its Receptor and Import Machinery When Its Nuclease Domain Enters the Cytoplasm
Authors: Duché Denis 
Published: April 2007

ABSTRACT

Colicins reach their targets in susceptible
Escherichia coli
strains through two envelope protein systems: the Tol system is used by group A colicins and the TonB system by group B colicins. Colicin E2 (ColE2) is a cytotoxic protein that recognizes the outer membrane receptor BtuB. After gaining access to the cytoplasmic membrane of sensitive
Escherichia coli
cells, ColE2 enters the cytoplasm to cleave DNA. After binding to BtuB, ColE2 interacts with the Tol system to reach its target. However, it is not known if the entire colicin or only the nuclease domain of ColE2 enters the cell. Here I show that preincubation of ColE2 with
Escherichia coli
cells prevents binding and translocation of pore-forming colicins of group A but not of group B. This inhibition persisted even when cells were incubated with ColE2 for 30 min before the addition of pore-forming colicins, indicating that ColE2 releases neither its receptor nor its translocation machinery when its nuclease domain enters the cells. These competition experiments enabled me to estimate the time required for ColE2 binding to its receptor and translocation.
SOS Induction in a Subpopulation of Structural Maintenance of Chromosome (Smc) Mutant Cells in
Bacillus subtilis
Authors: Britton Robert A. , Küster-Schöck Elke , Auchtung Thomas A. , Grossman Alan D. 
Published: April 2007

ABSTRACT

The structural maintenance of chromosome (Smc) protein is highly conserved and involved in chromosome compaction, cohesion, and other DNA-related processes. In
Bacillus subtilis
,
smc
null mutations cause defects in DNA supercoiling, chromosome compaction, and chromosome partitioning. We investigated the effects of
smc
mutations on global gene expression in
B. subtilis
using DNA microarrays. We found that an
smc
null mutation caused partial induction of the SOS response, including induction of the defective prophage PBSX. Analysis of SOS and phage gene expression in single cells indicated that approximately 1% of
smc
mutants have fully induced SOS and PBSX gene expression while the other 99% of cells appear to have little or no expression. We found that induction of PBSX was not responsible for the chromosome partitioning or compaction defects of
smc
mutants. Similar inductions of the SOS response and PBSX were observed in cells depleted of topoisomerase I, an enzyme that relaxes negatively supercoiled DNA.
Citrate Sensing by the C
4
-Dicarboxylate/Citrate Sensor Kinase DcuS of
Escherichia coli
: Binding Site and Conversion of DcuS to a C
4
-Dicarboxylate- or Citrate-Specific Sensor
Authors: Krämer J. , Fischer J. D. , Zientz E. , Vijayan V. , Griesinger C. , Lupas A. , Unden G. 
Published: April 2007

ABSTRACT

The histidine protein kinase DcuS of
Escherichia coli
senses C
4
-dicarboxylates and citrate by a periplasmic domain. The closely related sensor kinase CitA binds citrate, but no C
4
-dicarboxylates, by a homologous periplasmic domain. CitA is known to bind the three carboxylate and the hydroxyl groups of citrate by sites C1, C2, C3, and H. DcuS requires the same sites for C
4
-dicarboxylate sensing, but only C2 and C3 are highly conserved. It is shown here that sensing of citrate by DcuS required the same sites. Binding of citrate to DcuS, therefore, was similar to binding of C
4
-dicarboxylates but different from that of citrate binding in CitA. DcuS could be converted to a C
4
-dicarboxylate-specific sensor (DcuS
DC
) by mutating residues of sites C1 and C3 or of some DcuS-subtype specific residues. Mutations around site C1 aimed at increasing the size and accessibility of the site converted DcuS to a citrate-specific sensor (DcuS
Cit
). DcuS
DC
and DcuS
Cit
had complementary effector specificities and responded either to C
4
-dicarboxylates or to citrate and mesaconate. The results imply that DcuS binds citrate (similar to the C
4
-dicarboxylates) via the C
4
-dicarboxylate part of the molecule. Sites C2 and C3 are essential for binding of two carboxylic groups of citrate or of C
4
-dicarboxylates; sites C1 and H are required for other essential purposes.
Role of RNA Structure and Susceptibility to RNase E in Regulation of a Cold Shock mRNA,
cspA
mRNA
Authors: Hankins Janet S. , Zappavigna Christopher , Prud'homme-Généreux Annie , Mackie George A. 
Published: April 2007

ABSTRACT

Degradation of the
cspA
mRNA in vivo is very rapid at temperatures greater than 30°C and is moderately dependent on RNase E. Investigations in vitro show that degradosomes prepared from normal or cold-shocked cultures cleave the
cspA
mRNA preferentially at a single site in vitro between two stem-loops ∼24 residues 3′ to the termination codon and ∼31 residues from the 3′ end. The site of cleavage is independent of the temperature and largely independent of the phosphorylation status of the 5′ end of
cspA
mRNA. A 5′ stem-loop, potential occlusion of the initiation and termination codons, temperature-dependent translational efficiency, and the position of the RNase E cleavage site can explain the differential stability of the
cspA
mRNA.
Heterocyst Development and Diazotrophic Metabolism in Terminal Respiratory Oxidase Mutants of the Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Valladares Ana , Maldener Iris , Muro-Pastor Alicia M. , Flores Enrique , Herrero Antonia 
Published: April 2007

ABSTRACT

Heterocyst development was analyzed in mutants of the heterocyst-forming cyanobacterium
Anabaena
sp. strain PCC 7120 bearing inactivated
cox2
and/or
cox3
genes, encoding heterocyst-specific terminal respiratory oxidases. At the morphological level, the
cox2 cox3
double mutant (strain CSAV141) was impaired in membrane reorganization involving the so-called honeycomb system that in the wild-type strain is largely or exclusively devoted to respiration, accumulated glycogen granules at conspicuously higher levels than the wild type (in both vegetative cells and heterocysts), and showed a delay in carboxysome degradation upon combined nitrogen deprivation. Consistently, chemical analysis confirmed higher accumulation of glycogen in strain CSAV141 than in the wild type. No impairment was observed in the formation of the glycolipid or polysaccharide layers of the heterocyst envelope, consistent with the chemical detection of heterocyst-specific glycolipids, or in the expression of the heterocyst-specific genes
nifHDK
and
fdxH
. However, nitrogenase activity under oxic conditions was impaired in strain CSAV135 (
cox3
) and undetectable in strain CSAV141 (
cox2 cox3
). These results show that these dedicated oxidases are required for normal development and performance of the heterocysts and indicate a central role of Cox2 and, especially, of Cox3 in the respiratory activity of the heterocysts, decisively contributing to protection of the N
2
fixation machinery against oxygen. However, in contrast to the case for other diazotrophic bacteria, expression of
nif
genes in
Anabaena
seems not to be affected by oxygen.
Molecular Analysis of Genes in
Nostoc punctiforme
Involved in Pilus Biogenesis and Plant Infection
Authors: Duggan Paula S. , Gottardello Priscila , Adams David G. 
Published: April 2007

ABSTRACT

Hormogonia are the infective agents in many cyanobacterium-plant symbioses. Pilus-like appendages are expressed on the hormogonium surface, and mutations in
pil
-like genes altered surface piliation and reduced symbiotic competency. This is the first molecular evidence that pilus biogenesis in a filamentous cyanobacterium requires a type IV pilus system.
Predation by
Bdellovibrio bacteriovorus
HD100 Requires Type IV Pili
Authors: Evans Katy J. , Lambert Carey , Sockett R. Elizabeth 
Published: April 2007

ABSTRACT

Early electron microscopy and more recent studies in our laboratory of
Bdellovibrio bacteriovorus
cells indicated the presence of narrow fibers at the nonflagellar pole of this unusual predatory bacterium. Analysis of the
B. bacteriovorus
HD100 genome showed a complete set of genes potentially encoding type IV pili and an incomplete gene set for Flp pili; therefore, the role of type IV pili in the predatory life cycle of
B. bacteriovorus
HD100 was investigated. Alignment of the predicted PilA protein with known type IV pilins showed the characteristic conserved N terminus common to type IVa pilins. The
pilA
gene, encoding the type IV pilus fiber protein, was insertionally inactivated in multiple
Bdellovibrio
replicate cultures, and the effect upon the expression of other pilus genes was monitored by reverse transcriptase PCR. Interruption of
pilA
in replicate isolates abolished
Bdellovibrio
predatory capability in liquid prey cultures and on immobilized yellow fluorescent protein-labeled prey, but the mutants could be cultured prey independently. Expression patterns of
pil
genes involved in the formation of type IV pili were profiled across the predatory life cycle from attack phase predatory
Bdellovibrio
throughout the intraperiplasmic bdelloplast stages to prey lysis and in prey-independent growth. Taken together, the data show that type IV pili play a critical role in
Bdellovibrio
predation.
Religion, Secularism and the Promise of Public Theology
Authors: Maddox Marion 
Published: April 2007

AbstractThe phrase 'religion and politics' conjures unsettling images of fiery-eyed zealots, in Protestant America or the Muslim Middle-East. Such religiously-inspired political activity is usually assumed to be a feature of societies where religion is prominent in national and cultural life. The presumed antidote, particularly from a European point of view, has been secularization: surely, if people in general cared less about religion, religious politics would fade from public life and its threatened disruptions would disappear. This view rests too much on historical specificities. Very secular societies can foster their own varieties of religious extremism, entering the public square in ways which are covert rather than overt, but no less unsettling for that. Very secular societies also pose searching questions for those wishing to develop theologically-based contributions to such societies' public debate. What legitimacy can a theologically-based contribution claim where Christianity commands no automatic attention? How should theologically-grounded voices pitch themselves in order to be heard, without succumbing to either (a) nostalgia for a time when Christian/Christendom assumptions could enter the public sphere uncontested or (b) covert hegemonic aspirations? Recent Australian politics provides a case study of both pitfalls and prospects.
'Glocalization' as a Key to the Interplay between Christianity and Asian Cultures: The Vision of Francis Wei in Early Twentieth Century China
Authors: Ng Peter Tze Ming 
Published: April 2007

AbstractThis article aims to apply the concept of 'glocalization' to the study of theology and culture. China is chosen as a case study, with particular focus on a Chinese theologians discussion of the interplay between Christianity and Chinese Culture in the early twentieth century China. Francis Wei was the first Chinese President of Huazhong University in Wuhan, 1929–1952, and he was appointed as the first Henry Luce Visiting Professor of World Christianity in 1945–46. Wei's conviction was that Christianity and Chinese culture could be complementary. He held that China needed Christianity for a better understanding of God's nature and the way human beings could communicate with God, while maintaining that Christianity needed China to move beyond western denominationalism. Moreover, Christianity could not become a universal religion without including China. This article argues that Wei's work is relevant to the contemporary discussion about interaction between globalization and localization, known as 'glocalization'.
The Singing Coachman or, The Road and Russia's Ethnographic Invention in Early Modern Times
Authors: Randolph John 
Published: April 2007

AbstractScholars agree that the first modern ethnographic traditions surrounding Russia developed in travel accounts written by foreigners in the 16th, 17th, and 18th centuries. These laid the foundations for a 'national turn' in Russian belles-lettres in the late 18th century. Yet scholars have paid relatively little attention to the history of the coach system, known as the iam, that made travel writing about Muscovy possible. Many foreign travelers—as well as Imperial Russian hommes des lettres —were fascinated by the figures of Russia's iamshchiki, the state peasants who manned the state-organized coach system. The lives and expressions of these coachmen were often taken as proxies for Russia's national character. This article describes this process, demonstrating how the iam system provided a practical as well as a symbolic frame for the making of early conceptions of Russian nationality.
Slave Trade in the Early Modern Crimea From the Perspective of Christian, Muslim, and Jewish Sources
Authors: Kizilov Mikhail 
Published: April 2007

AbstractThe Crimea, a peninsula on the border between the Christian West and the Muslim East, was a place where merchants from all over the Black Sea region, East and West Mediterranean, Anatolia, Turkey, Russia, and West European countries came to buy, sell, and exchange their goods. In this trade "live merchandise"—reluctant travellers, seized by the Tatars during their raids to adjacent countries—was one of the main objects to be negotiated. Numerous published and archival sources (accounts of European and Ottoman travellers, letters and memoirs of captives, Turkish defters [registers], Russian and Ottoman chronicles to mention some of them) composed by Muslim, Christian, and Jewish authors provide not only a detailed account of the slave trade in the region in the Early Modern times, but also a discussion of some moral implications related to this sort of commercial activity. While most of the authors expressed their disapproval of the Tatar predatory raids and cruel treatment of the captives, none of them, it seems, objected to the existence of the slave trade per se, considering it just another off shoot of the international trade. Another issue often discussed in the sources was the problem of the slaves' conversion.
Möglichkeiten einer literaturwissenschaftlichen Antisemitismusforschung. ,,Tod eines Kritikers" im Werkkontext
Authors: Lorenz Matthias N. 
Published: April 2007

AbstractMartin Walser's reflections on German self-identity have made him a controversial author: whereas critics have raised charges of ,,literary anti-Semitism", his defenders consider him – as a writer who since the early 1960s has shown a preoccupation with his country's Nazi past – immune to such criticism. Taking both arguments seriously, Matthias N. Lorenz has reviewed Walser's allegedly untenable positions on the Holocaust in his book ,,Auschwitz drängt uns auf einen Fleck": Judendarstellung und Auschwitzdiskurs bei Martin Walser. In this essay the author concisely presents the main theses and thoughts of Lorenz's widely discussed Ph.D. dissertation.