bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted Access to the Genomes of Low-Abundance Organisms in Complex Microbial Communities
Authors: Podar Mircea , Abulencia Carl B. , Walcher Marion , Hutchison Don , Zengler Karsten , Garcia Joseph A. , Holland Trevin , Cotton David , Hauser Loren , Keller Martin 
Published: March 2007

ABSTRACT
Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequencies, especially those representing yet-uncultured taxa, which include the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms isolated directly from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community's metabolic potential.
Control of Ammonium Permease Expression and Filamentous Growth by the GATA Transcription Factors
GLN3
and
GAT1
in
Candida albicans
Authors: Dabas Neelam , Morschhäuser Joachim 
Published: March 2007

ABSTRACT

In response to nitrogen starvation, the human fungal pathogen
Candida albicans
switches from yeast to filamentous growth. This morphogenetic switch is controlled by the ammonium permease Mep2p, whose expression is induced under limiting nitrogen conditions. In order to understand in more detail how nitrogen starvation-induced filamentous growth is regulated in
C. albicans
, we identified the
cis
-acting sequences in the
MEP2
promoter that mediate its induction in response to nitrogen limitation. We found that two putative binding sites for GATA transcription factors have a central role in
MEP2
expression, as deletion of the region containing these sites or mutation of the GATAA sequences in the full-length
MEP2
promoter strongly reduced
MEP2
expression. To investigate whether the GATA transcription factors
GLN3
and
GAT1
regulate
MEP2
expression, we constructed mutants of the
C. albicans
wild-type strain SC5314 lacking one or both of these transcription factors. Expression of Mep2p was strongly reduced in
gln3
Δ and
gat1
Δ single mutants and abolished in
gln3
Δ
gat1
Δ double mutants. Deletion of
GLN3
strongly inhibited filamentous growth under limiting nitrogen conditions, but the filamentation defect of
gln3
Δ mutants could be rescued by constitutive expression of
MEP2
from the
ADH1
promoter. In contrast, inactivation of
GAT1
had no effect on filamentation, and we found that filamentation became independent of the presence of a functional
MEP2
gene in the
gat1
Δ mutants, indicating that the loss of
GAT1
function results in the activation of other pathways inducing filamentous growth. These results demonstrate that the GATA transcription factors
GLN3
and
GAT1
control expression of the
MEP2
ammonium permease and that
GLN3
is also an important regulator of nitrogen starvation-induced filamentous growth in
C. albicans
.
The SsrA-SmpB Ribosome Rescue System Is Important for Growth ofBacillus subtilisat Low and High Temperatures
Authors: Shin Ji-Hyun , Price Chester W. 
Published: March 2007

ABSTRACTBacillus subtilishas multiple stress response systems whose integrated action promotes growth and survival under unfavorable conditions. Here we address the function and transcriptional organization of a five-gene cluster containingssrA, previously known to be important for growth at high temperature because of the role of its tmRNA product in rescuing stalled ribosomes. Reverse transcription-PCR experiments detected a single message for thesecG-yvaK-rnr-smpB-ssrAcluster, suggesting that it constitutes an operon. However, rapid amplification of cDNA ends-PCR andlacZfusion experiments indicated that operon transcription is complex, with at least five promoters controlling different segments of the cluster. One σA-like promoter precededsecG(P1), and internal σA-like promoters were found in both thernr-smpB(P2) andsmpB-ssrAintervals (P3and PHS). Another internal promoter lay in thesecG-yvaKintercistronic region, and this activity (PB) was dependent on the general stress factor σB. Null mutations in the four genes downstream from PBwere tested for their effects on growth. Loss ofyvaK(carboxylesterase E) orrnr(RNase R) caused no obvious phenotype. By contrast,smpBwas required for growth at high temperature (52°C), as anticipated if its product (a small ribosomal binding protein) is essential for tmRNA (ssrA) function. Notably,smpBandssrAwere also required for growth at low temperature (16°C), a phenotype not previously associated with tmRNA activity. These results extend the known high-temperature role ofssrAand indicate that the ribosome rescue system is important at both extremes of theB. subtilistemperature range.
Identification of the
l
,
d
-Transpeptidases Responsible for Attachment of the Braun Lipoprotein to
Escherichia coli
Peptidoglycan
Authors: Magnet Sophie , Bellais Samuel , Dubost Lionel , Fourgeaud Martine , Mainardi Jean-Luc , Petit-Frère Sébastien , Marie Arul , Mengin-Lecreulx Dominique , Arthur Michel , Gutmann Laurent 
Published: March 2007

ABSTRACT

The
l
,
d
-transpeptidase Ldt
fm
catalyzes peptidoglycan cross-linking in β-lactam-resistant mutant strains of
Enterococcus faecium
. Here, we show that in
Escherichia coli
Ldt
fm
homologues are responsible for the attachment of the Braun lipoprotein to murein, indicating that evolutionarily related domains have been tailored to use muropeptides or proteins as acyl acceptors in the
l
,
d
-transpeptidation reaction.
Septum-Localized Protein Required for Filament Integrity and Diazotrophy in the Heterocyst-Forming Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Flores Enrique , Pernil Rafael , Muro-Pastor Alicia M. , Mariscal Vicente , Maldener Iris , Lechno-Yossef Sigal , Fan Qing , Wolk C. Peter , Herrero Antonia 
Published: March 2007

ABSTRACT

Heterocysts, formed when filamentous cyanobacteria, such as
Anabaena
sp. strain PCC 7120, are grown in the absence of combined nitrogen, are cells that are specialized in fixing atmospheric nitrogen (N
2
) under oxic conditions and that transfer fixed nitrogen to the vegetative cells of the filament.
Anabaena
sp. mutants whose
sepJ
gene (open reading frame
alr2338
of the
Anabaena
sp. genome) was affected showed filament fragmentation and arrested heterocyst differentiation at an early stage. In a
sepJ
insertional mutant, a layer similar to a heterocyst polysaccharide layer was formed, but the heterocyst-specific glycolipids were not synthesized. The
sepJ
mutant did not exhibit nitrogenase activity even when assayed under anoxic conditions. In contrast to proheterocysts produced in the wild type, those produced in the
sepJ
mutant still divided. SepJ is a multidomain protein whose N-terminal region is predicted to be periplasmic and whose C-terminal domain resembles an export permease. Using a green fluorescent protein translationally fused to the carboxyl terminus of SepJ, we observed that in mature heterocysts and vegetative cells, the protein is localized at the intercellular septa, and when cell division starts, it is localized in a ring whose position is similar to that of a Z ring. SepJ is a novel composite protein needed for filament integrity, proper heterocyst development, and diazotrophic growth.
Regulation of
dev
, an Operon That Includes Genes Essential for
Myxococcus xanthus
Development and CRISPR-Associated Genes and Repeats
Authors: Viswanathan Poorna , Murphy Kimberly , Julien Bryan , Garza Anthony G. , Kroos Lee 
Published: March 2007

ABSTRACT

Expression of
dev
genes is important for triggering spore differentiation inside
Myxococcus xanthus
fruiting bodies. DNA sequence analysis suggested that
dev
and
cas
(
C
RISPR-
as
sociated) genes are cotranscribed at the
dev
locus, which is adjacent to CRISPR (
c
lustered
r
egularly
i
nterspaced
s
hort
p
alindromic
r
epeats). Analysis of RNA from developing
M. xanthus
confirmed that
dev
and
cas
genes are cotranscribed with a short upstream gene and at least two repeats of the downstream CRISPR, forming the
dev
operon. The operon is subject to strong, negative autoregulation during development by DevS. The
dev
promoter was identified. Its −35 and −10 regions resemble those recognized by
M. xanthus
σ
A
RNA polymerase, the homolog of
Escherichia coli
σ
70
, but the spacer may be too long (20 bp); there is very little expression during growth. Induction during development relies on at least two positive regulatory elements located in the coding region of the next gene upstream. At least two positive regulatory elements and one negative element lie downstream of the
dev
promoter, such that the region controlling
dev
expression spans more than 1 kb. The results of testing different fragments for
dev
promoter activity in wild-type and
devS
mutant backgrounds strongly suggest that upstream and downstream regulatory elements interact functionally. Strikingly, the 37-bp sequence between the two CRISPR repeats that, minimally, are cotranscribed with
dev
and
cas
genes exactly matches a sequence in the bacteriophage Mx8
intP
gene, which encodes a form of the integrase needed for lysogenization of
M. xanthus
.
Transcription Activation Mediated by a Cyclic AMP Receptor Protein from
Thermus thermophilus
HB8
Authors: Shinkai Akeo , Kira Satoshi , Nakagawa Noriko , Kashihara Aiko , Kuramitsu Seiki , Yokoyama Shigeyuki 
Published: March 2007

ABSTRACT

The extremely thermophilic bacterium
Thermus thermophilus
HB8, which belongs to the phylum
Deinococcus
-
Thermus
, has an open reading frame encoding a protein belonging to the cyclic AMP (cAMP) receptor protein (CRP) family present in many bacteria. The protein named
T. thermophilus
CRP is highly homologous to the CRP family proteins from the phyla
Firmicutes
,
Actinobacteria
, and
Cyanobacteria
, and it forms a homodimer and interacts with cAMP. CRP mRNA and intracellular cAMP were detected in this strain, which did not drastically fluctuate during cultivation in a rich medium. The expression of several genes was altered upon disruption of the
T. thermophilus
CRP gene. We found six CRP-cAMP-dependent promoters in in vitro transcription assays involving DNA fragments containing the upstream regions of the genes exhibiting decreased expression in the CRP disruptant, indicating that the CRP is a transcriptional activator. The consensus
T. thermophilus
CRP-binding site predicted upon nucleotide sequence alignment is 5′-(C/T)NNG(G/T)(G/T)C(A/C)N(A/T)NNTCACAN(G/C)(G/C)-3′. This sequence is unique compared with the known consensus binding sequences of CRP family proteins. A putative −10 hexamer sequence resides at 18 to 19 bp downstream of the predicted
T. thermophilus
CRP-binding site. The CRP-regulated genes found in this study comprise clustered regularly interspaced short palindromic repeat (CRISPR)-associated (
cas
) ones, and the genes of a putative transcriptional regulator, a protein containing the exonuclease III-like domain of DNA polymerase, a GCN5-related acetyltransferase homolog, and
T. thermophilus
-specific proteins of unknown function. These results suggest a role for cAMP signal transduction in
T. thermophilus
and imply the
T. thermophilus
CRP is a cAMP-responsive regulator.
Identification and Characterization of Genes Encoding a Putative ABC-Type Transporter Essential for Utilization of γ-Hexachlorocyclohexane in
Sphingobium japonicum
UT26
Authors: Endo Ryo , Ohtsubo Yoshiyuki , Tsuda Masataka , Nagata Yuji 
Published: March 2007

ABSTRACT

Sphingobium japonicum
UT26 utilizes γ-hexachlorocyclohexane (γ-HCH) as its sole source of carbon and energy. In our previous studies, we cloned and characterized genes encoding enzymes for the conversion of γ-HCH to β-ketoadipate in UT26. In this study, we analyzed a mutant obtained by transposon mutagenesis and identified and characterized new genes encoding a putative ABC-type transporter essential for the utilization of γ-HCH in strain UT26. This putative ABC transporter consists of four components, permease, ATPase, periplasmic protein, and lipoprotein, encoded by
linK
,
linL
,
linM
, and
linN
, respectively. Mutation and complementation analyses indicated that all the
linKLMN
genes are required, probably as a set, for γ-HCH utilization in UT26. Furthermore, the mutant cells deficient in this putative ABC transporter showed (i) higher γ-HCH degradation activity and greater accumulation of the toxic dead-end product 2,5-dichlorophenol (2,5-DCP), (ii) higher sensitivity to 2,5-DCP itself, and (iii) higher permeability of hydrophobic compounds than the wild-type cells. These results strongly suggested that LinKLMN are involved in γ-HCH utilization by controlling membrane hydrophobicity. This study clearly demonstrated that a cellular factor besides catabolic enzymes and transcriptional regulators is essential for utilization of xenobiotic compounds in bacterial cells.
Complex patterns of chromosome 9 alterations including the p16INK4alocus in Wilms tumours
Authors: Natrajan R , Warren W , Messahel B , Reis-Filho J S , Brundler M-A , Dome J S , Grundy P E , Vujanic G , Pritchard-Jones K , Jones C 
Published: March 2007

Background:Previous data implicating genetic and epigenetic events on chromosome 9, including theCDKN2A/2Blocus, as molecular predictors of Wilms tumour relapse, have been conflicting.Aims:To clarify this using genome-wide and focused molecular genetic analysis.Methods:Microarray-based comparative genomic hybridisation (aCGH) using genome-wide coverage was applied to 76 favourable histology Wilms tumours. Additional investigation of the 9p21 locus was carried out using loss of heterozygosity (LOH) and fluorescence in situ hybridisation (FISH), as well as immunohistochemistry for CDKN2A/p16INK4aon a paediatric renal tumour tissue microarray.Results:Approximately half of the tumours were found to show chromosome 9 copy number changes. Those cases which harboured alterations comprised at least four distinct patterns: gain of the entire chromosome, loss of 9p, gain of 9q34, or a more complex combination of gains/losses. None of these tumour groups showed any statistically significant correlation with clinicopathological variables. Deletion mapping of 9p by LOH revealed several regions of overlap, including theCDKN2A/2Blocus in 4/34 (11.8%) tumours, which was confirmed to represent hemizygous deletions by FISH. CDKN2A/p16INK4aprotein expression was predominantly negative in Wilms tumours as assessed by immunohistochemistry on a tissue array, reflecting the expression pattern in normal kidney. However, 38/236 (16.1%) non-anaplastic Wilms tumours, 4/9 (44.4%) anaplastic Wilms tumours, 5/7 (71.4%) rhabdoid tumours of the kidney, and 4/10 (40%) clear cell sarcomas of the kidney showed nuclear CDKN2A/p16INK4aimmunoreactivity.Conclusions:These data reveal the complex nature of genetic alterations on chromosome 9 in Wilms tumours, but do not provide evidence for their involvement in or association with treatment failure.
Images of Hope: Representations of the Death of the Virgin, East and West
Authors: Walsh Elizabeth 
Published: March 2007

AbstractChristianity has existed for nearly two thousand years, yet its divergent forms and rituals almost belie its existence. Perhaps the best image to express its reality is the cross, but that too has many interpretations. Is there any image that can be said to represent all that Christianity intends? The Death of the Virgin, which was first represented in art in the tenth century, is an image which includes all of the basic elements of the Christian faith: incarnation, death, and resurrection. The story of this icon spans much of Christian history as the icon evolved through legend, liturgy, art, and theology. It is an imaginative rendition of centuries of speculation, study, discussion, prayer, and devotion. Although Christian unity is more of a desire than a reality, this image transcends the divisions and separation which have marred the religion and stands as a sign of hope and unity. In order to understand the icon, it seems necessary to trace the process of its signification. Icons of Mary's death occur in eastern and western art; thus, they represent a call to be mindful of the essential unity of the Christian faith. This article will focus especially on the categories of legend, liturgy, and art.
Shakespeare's Grand Deception: The Merchant of Venice—Anti-Semitism as "Uncanny Causality" and the Catholic-Protestant Problem
Authors: Coonradt Nicole 
Published: March 2007

AbstractConsidering the notion of poetry in Early Modern drama as a veil for political commentary during a perilously censorious time, this essay closely examines Shakespeare's The Merchant of Venice in its previously ignored historical context while providing a brief survey of the play's critical heritage to show how the play's anti-Judaism effects reader response. Within an emerging new vein of Dissident Theory that explores formerly overlooked historical facts in England's troubled Reformation history, this essay provides an alternate interpretation reading "otherwise" to discover how Shylock haunts our interpretations of the play, which is not, as this essay's title suggests, so much about the Jewish Question, but the Christian one as found in the Catholic-Protestant crisis, as crisis it undoubtedly was. This reading offers a measured departure from most existing scholarship by exploring the play poststructurally as the site of a metaphoric, performative conversion where Shakespeare employs the trope of anti-Semitism ironically to convey a coded message about the moral incoherence in popular Christianity—specifically concerning aroused anxieties about Christian identity as seen in forced conversions and the complete violation of the basic tenets of mercy and justice which highlight the hypocrisy in Christianity as Shakespeare saw it practiced.
Introduction to Special Focus
Authors: Kopanski Ataullah Bogdan , Idriz Mesut 
Published: March 2007

AbstractDuring the 20th century, there have been numerous scholarly attempts in studying, analyzing and even to some extent, criticizing the issues pertaining to the contacts, impacts and relations between the Muslim world and the West. However, when dealing with these issues, the geography should not be limited to the Muslim world and the West, Europe in particular, but it should cover both Europe and Asia taken together where the earliest civilizations took place and by the 7th century, Islamic civilization flourished in the center of domain civilizations. With a wider and more positive look, the four articles by the academicians, (namely Danial M. Yosuf, Ali Çaksu, Anke Iman Bouzenita and Mesut Idriz), selected to be featured in this edition will contribute not only to this field of study but also avoid or remove the barriers and concentrate on the bridges between the Islamic world and the Eurasia. All the articles are original works and published for the first time in this volume The focus of this special edition is on the paradoxes between the Islamic and Eurasian worlds.
Davutoglu's Paradigm, Winkel's Epistemé and Political Science in Malaysia
Authors: Yusof Danial Mohd 
Published: March 2007

AbstractHusserlian phenomenology and its terminology are utilised to justify the sociology of Islam and its essentialist response through the course of transcultural exchanges and sedimentation with the irreconcilable weltanshauung of the West. At the same time, the issue of structure and reliable knowledge is considered through the difficult relationship between revivalist religion and state politics where political legitimacy and the development of institutions is a feature of socio-political fact. Here, Malaysian political culture and democracy is used as an example. It makes out that sociopolitical realities, if not co-incidental with discourses of reliable knowledge and moral society, are representations of the conciliation of interests with specific value orientation with regards to alternative conceptions of moral society.
Ibn Khaldun and Hegel on Causality in History: Aristotelian Legacy Reconsidered
Authors: Çaksu Ali 
Published: March 2007

AbstractThere have been several attempts to identify the 'four causes' of history in Ibn Khaldun and Hegel. These attempts have been inspired by the presupposition that both Ibn Khaldun and Hegel are basically Aristotelian in their outlook, and that Aristotle's four causes, which, for him, pertained to physics and metaphysics, were simply extended to the domain of history by Ibn Khaldun and Hegel. However, it is the main thesis of this study that Ibn Khaldun's and Hegel's approaches to causality cannot be reduced to a mechanical application of Aristotelian doctrine and that in developing their philosophies of history, both Ibn Khaldun and Hegel transformed the Aristotelian doctrine of the four basic causes. Their transformations of this doctrine were so profound that it is an oversimplification and a distortion to simply impose the Aristotelian scheme on their systems.
From a Local Tradition to a Universal Practice: Ijāzah as a Muslim Educational Tradition (With Special Reference to a 19th Century Idrīs Fahmī b. Sālih's Ijāzah Issued in the Balkans and Its Annotated English Translation)
Authors: Idriz Mesut 
Published: March 2007

AbstractThe ijāzah tradition is recognized as having a long history in Muslim educational life. The term 'ijāzah' in Islamic pedagogy generally signifies a 'licence to teach', and more specifically refers to a certificate issued by a professor in an institution of higher learning to a student who has attended a course of lecturers to the professor's satisfaction, and who has been deemed henceforth as qualified to transmit the same subject to his own students. The ijāzah tradition developed in Muslim education life as early as the 4th century A.H. (10th century A.D.) and became a universally applied educational procedure in all Muslim lands. Originally, it was a tradition developed by Muslims under the influence of Islamic sciences, such as hadīth and tafsīr. Some two centuries later, in the second half of the 12th century, ijāzah made its appearance in the Latin West or Christian Europe. It was a licence to teach, a so-called 'licentia docendi', which is the same as ijāzah. Licentia docendi was the earliest form of certificate in the West. But throughout history, the term 'licentia docendi' has been altered, according to the university system, into certificate, diploma, degree, etc. Whereas the term ijāzah has remained almost the same since the time it was developed, from the early years of Islam up until today, with a few exceptions in some areas. The various ijāzahs in Islamic sciences and in other fields demonstrate the religious, cultural and educational unity of Muslims in the past, despite their geographical differences. In this article, we will have an attempt to study the ijāzah tradition in the Balkans by analyzing an ijāzah issued in the 19th century in the famous city of Üsküp (Skopje), then translating the same ijāzah into English.