bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social Interactions and Distribution of
Bacillus subtilis
Pherotypes at Microscale
Authors: Stefanic Polonca , Mandic-Mulec Ines 
Published: December 2008

ABSTRACT

Bacillus subtilis
strains communicate through the
comQXPA
quorum sensing (QS) system, which regulates genes expressed during early stationary phase. A high polymorphism of
comQXP
′ loci was found in closely related strains isolated from desert soil samples separated by distances ranging from meters to kilometers. The observed polymorphism comprised four communication groups (pherotypes), such that strains belonging to the same pherotype exchanged information efficiently but strains from different pherotypes failed to communicate. To determine whether the same level of polymorphism in the
comQXP
′ QS system could be detected at microscale,
B. subtilis
isolates were obtained from two separate 1-cm
3
soil samples, which were progressively divided into smaller sections. Cross-activation studies using pherotype-responsive reporter strains indicated the same number of communication pherotypes at microscale as previously determined at macroscale. Sequencing of the housekeeping gene
gyrA
and the QS
comQ
gene confirmed different evolutionary rates of these genes. Furthermore, an asymmetric communication response was detected inside the two pherotype clusters, suggesting continuous evolution of the QS system and possible development of new languages. To our knowledge, this is the first microscale study demonstrating the presence of different QS languages among isolates of one species, and the implications of this microscale diversity for microbial interactions are discussed.
Three
Mycobacterium tuberculosis
Rel Toxin-Antitoxin Modules Inhibit Mycobacterial Growth and Are Expressed in Infected Human Macrophages
Authors: Korch Shaleen B. , Contreras Heidi , Clark-Curtiss Josephine E. 
Published: December 2008

ABSTRACT

Mycobacterium tuberculosis
protein pairs Rv1246c-Rv1247c, Rv2865-Rv2866, and Rv3357-Rv3358, here named RelBE, RelFG, and RelJK, respectively, were identified based on homology to the
Escherichia coli
RelBE toxin:antitoxin (TA) module. In this study, we have characterized each Rel protein pair and have established that they are functional TA modules. Overexpression of individual
M. tuberculosis rel
toxin genes
relE
,
relG
, and
relK
induced growth arrest in
Mycobacterium smegmatis
; a phenotype that was completely reversible by expression of their cognate antitoxin genes,
relB
,
relF
, and
relJ
, respectively. We also provide evidence that RelB and RelE interact directly, both in vitro and in vivo. Analysis of the genetic organization and regulation established that
relBE
,
relFG
, and
relJK
form bicistronic operons that are cotranscribed and autoregulated, in a manner unlike typical TA modules. RelB and RelF act as transcriptional activators, inducing expression of their respective promoters. However, RelBE, RelFG, and RelJK (together) repress expression to basal levels of activity, while RelJ represses promoter activity altogether. Finally, we have determined that all six
rel
genes are expressed in broth-grown
M. tuberculosis
, whereas
relE
,
relF
, and
relK
are expressed during infection of human macrophages. This is the first demonstration of
M. tuberculosis
expressing TA modules in broth culture and during infection of human macrophages.
Analysis of ColE1 MbeC Unveils an Extended Ribbon-Helix-Helix Family of Nicking Accessory Proteins
Authors: Varsaki Athanasia , Moncalián Gabriel , del Pilar Garcillán-Barcia Maria , Drainas Constantin , de la Cruz Fernando 
Published: December 2008

ABSTRACT

MbeC is a 13-kDa ColE1-encoded protein required for efficient mobilization of ColE1, a plasmid widely used in cloning vector technology. MbeC protein was purified and used for in vitro DNA binding, which showed that it binds specifically double-stranded DNA (dsDNA) containing the ColE1
oriT
. Amino acid sequence comparison and secondary structure prediction imply that MbeC is related to the ribbon-helix-helix (RHH) protein family. Alignment with RHH members pointed to a conserved arginine (R13 in MbeC) that was mutated to alanine. The mutant MbeC(R13A) was unable to bind either single-stranded DNA or dsDNA. Limited proteolysis fragmented MbeC in two stable folding domains: the N-terminal domain, which contains the RHH motif, and the C-terminal domain, which comprises a signature shared by nicking accessory proteins. The results indicate that MbeC plays a similar role in conjugation as TraY and TrwA of plasmids F and R388, respectively. Thus, it appears that an extended, possibly universal mechanism of DNA conjugative processing exists, in which
oriT
-processing is carried out by relaxases assisted by homologous nicking accessory proteins. This mechanism seems to be shared by all major conjugative systems analyzed thus far.
Role of Conjugative Elements in the Evolution of the Multidrug-Resistant Pandemic CloneStreptococcus pneumoniaeSpain23FST81
Authors: Croucher Nicholas J. , Walker Danielle , Romero Patricia , Lennard Nicola , Paterson Gavin K. , Bason Nathalie C. , Mitchell Andrea M. , Quail Michael A. , Andrew Peter W. , Parkhill Julian , Bentley Stephen D. , Mitchell Tim J. 
Published: December 2008

ABSTRACTStreptococcus pneumoniaeis a human commensal and pathogen able to cause a variety of diseases that annually result in over a million deaths worldwide. TheS. pneumoniaeSpain23Fsequence type 81 lineage was among the first recognized pandemic clones and was responsible for almost 40% of penicillin-resistant pneumococcal infections in the United States in the late 1990s. Analysis of the chromosome sequence of a representative strain, and comparison with other available genomes, indicates roles for integrative and conjugative elements in the evolution of pneumococci and, more particularly, the emergence of the multidrug-resistant Spain 23F ST81 lineage. A number of recently acquired loci within the chromosome appear to encode proteins involved in the production of, or immunity to, antimicrobial compounds, which may contribute to the proficiency of this strain at nasopharyngeal colonization. However, further sequencing of other pandemic clones will be required to establish whether there are any general attributes shared by these strains that are responsible for their international success.
Regulation of Expression of the Region 3 Promoter of theEscherichia coliK5 Capsule Gene Cluster Involves H-NS, SlyA, and a Large 5′ Untranslated Region
Authors: Xue Peng , Corbett David , Goldrick Marie , Naylor Clare , Roberts Ian S. 
Published: December 2008

ABSTRACTEscherichia coligroup 2 capsule gene clusters are temperature regulated, being expressed at 37°C but not at 20°C. Expression is regulated at the level of transcription by two convergent promoters, PR1 and PR3. In this paper, we show that regulation of transcription from PR3 involves a number of novel features including H-NS, SlyA, and a large 741-bp 5′ untranslated region (UTR). H-NS represses transcription from PR3 at 20°C and binds both 5′ and 3′ of the transcription start site. The 3′ downstream regulatory element (DRE) was essential for temperature-dependent H-NS repression. At 37°C, SlyA activates transcription independent of H-NS but maximal transcription requires H-NS. The UTR is present between the transcription start site and the first gene in the operon,kpsM. We demonstrate that the UTR, as well as containing the H-NS DRE, functions to moderate the extent of transcription that reacheskpsMand allows the binding of antitermination factor RfaH.
Characterization of theEscherichia coliO157:H7 Sakai GadE Regulon
Authors: Kailasan Vanaja Sivapriya , Bergholz Teresa M. , Whittam Thomas S. 
Published: December 2008

ABSTRACTIntegrating laterally acquired virulence genes into the backbone regulatory network is important for the pathogenesis ofEscherichia coliO157:H7, which has captured many virulence genes through horizontal transfer during evolution. GadE is an essential transcriptional activator of the glutamate decarboxylase (GAD) system, the most efficient acid resistance (AR) mechanism inE. coli. The full contribution of GadE to the AR and virulence ofE. coliO157:H7 remains largely unknown. We inactivatedgadEinE. coliO157:H7 Sakai and compared global transcription profiles of the mutant with that of the wild type in the exponential and stationary phases of growth. Inactivation ofgadEsignificantly altered the expression of 60 genes independently of the growth phase and of 122 genes in a growth phase-dependent manner. Inactivation ofgadEmarkedly downregulated the expression ofgadA, gadB, andgadCand of many acid fitness island genes. Nineteen genes encoded on the locus of enterocyte effacement (LEE), includingler, showed a significant increase in expression upongadEinactivation. Inactivation oflerin the ΔgadEstrain reversed the effect ofgadEdeletion on LEE expression, indicating that Ler is necessary for LEE repression by GadE. GadE is also involved in downregulation of LEE expression under conditions of moderately acidic pH. Characterization of AR of the ΔgadEstrain revealed that GadE is indispensable for a functional GAD system and for survival ofE. coliO157:H7 in a simulated gastric environment. Altogether, these data indicate that GadE is critical for the AR ofE. coliO157:H7 and that it plays an important role in virulence by downregulating expression of LEE.
TtgV Represses Two Different Promoters by Recognizing Different Sequences
Authors: Fillet Sandy , Vélez Marisela , Lu Duo , Zhang Xiaodong , Gallegos María-Trinidad , Ramos Juan L. 
Published: December 2008

ABSTRACTExpression of the multidrug efflux pumpttgDEFandttgGHIoperons is modulated in vivo mainly by the TtgV repressor. TtgV is a multidrug recognition repressor that exhibits a DNA binding domain with a long interaction helix comprising residues 47 to 64. The pattern of expression of the two pumps is different inPseudomonas putida: in the absence of effectors, the promoter for thettgDgene is silent, whereas thettgGgene is expressed at a high basal level. This correlates with the fact that TtgV exhibits a higher affinity for thettgDoperator (KD= 10 ± 1 nM) than for thettgG(KD= 19 ± 1 nM) operator. Sequence analysis revealed that both operators are 40% identical, and mutational analysis of thettgDandttgGoperators combined with electrophoretic mobility shift assays and in vivo expression analysis suggests that TtgV recognizes an inverted repeat with a high degree of palindromicity around the central axis. We generated a collection of alanine substitution mutants with substitutions between residues 47 and 64 of TtgV. The results of extensive combinations of promoter variants with these TtgV alanine substitution mutants revealed that TtgV modulates expression fromttgDandttgGpromoters through the recognition of both common and different sequences in the two promoters. In this regard, we found that TtgV mutants at residues 48, 50, 53, 54, 60, and 61 failed to bindttgGbut recognized thettgDoperator. TtgV residues R47, R52, L57, and T49 are critical for binding to both operators. Based on three-dimensional models, we propose that these residues contact nucleotides within the major groove of DNA.
Complete Genome Sequence of the Anaerobic, Protein-Degrading Hyperthermophilic Crenarchaeon
Desulfurococcus kamchatkensis
Authors: Ravin Nikolai V. , Mardanov Andrey V. , Beletsky Alexey V. , Kublanov Ilya V. , Kolganova Tatiana V. , Lebedinsky Alexander V. , Chernyh Nikolai A. , Bonch-Osmolovskaya Elizaveta A. , Skryabin Konstantin G. 
Published: December 2008

ABSTRACT

Desulfurococcus kamchatkensis
is an anaerobic organotrophic hyperthermophilic crenarchaeon isolated from a terrestrial hot spring. Its genome consists of a single circular chromosome of 1,365,223 bp with no extrachromosomal elements. A total of 1,474 protein-encoding genes were annotated, among which 205 are exclusive for
D. kamchatkensis
. The search for a replication origin site revealed a single region coinciding with a global extreme of the nucleotide composition disparity curve and containing a set of crenarchaeon-type origin recognition boxes. Unlike in most archaea, two genes encoding homologs of the eukaryotic initiator proteins Orc1 and Cdc6 are located distantly from this site. A number of mobile elements are present in the genome, including seven transposons representing IS
607
and IS
200
/IS
605
families and multiple copies of miniature inverted repeat transposable elements. Two large clusters of regularly interspaced repeats are present; none of the spacer sequences matches known archaeal extrachromosomal elements, except one spacer matches the sequence of a resident gene of
D. kamchatkensis
. Many of the predicted metabolic enzymes are associated with the fermentation of peptides and sugars, including more than 30 peptidases with diverse specificities, a number of polysaccharide degradation enzymes, and many transporters. Consistently, the genome encodes both enzymes of the modified Embden-Meyerhof pathway of glucose oxidation and a set of enzymes needed for gluconeogenesis. The genome structure and content reflect the organism's nutritionally diverse, competitive natural environment, which is periodically invaded by viruses and other mobile elements.
Oxygen-Limiting Conditions Enrich for Fimbriate Cells of UropathogenicProteus mirabilisandEscherichia coli
Authors: Lane M. Chelsea , Li Xin , Pearson Melanie M. , Simms Amy N. , Mobley Harry L. T. 
Published: December 2008

ABSTRACTMR/P fimbriae of uropathogenicProteus mirabilisundergo invertible element-mediated phase variation whereby an individual bacterium switches between expressing fimbriae (phase ON) and not expressing fimbriae (phase OFF). Under different conditions, the percentage of fimbriate bacteria within a population varies and could be dictated by either selection (growth advantage of one phase) or signaling (preferentially converting one phase to the other in response to external signals). Expression of MR/P fimbriae increases in a cell-density dependent manner in vitro and in vivo. However, rather than the increased cell density itself, this increase in fimbrial expression is due to an enrichment of fimbriate bacteria under oxygen limitation resulting from increased cell density. Our data also indicate that the persistence of MR/P fimbriate bacteria under oxygen-limiting conditions is a result of both selection (of MR/P fimbrial phase variants) and signaling (via modulation of expression of the MrpI recombinase). Furthermore, themrpJtranscriptional regulator encoded within themrpoperon contributes to phase switching. Type 1 fimbriae ofEscherichia coli, which are likewise subject to phase variation via an invertible element, also increase in expression during reduced oxygenation. These findings provide evidence to support a mechanism for persistence of fimbriate bacteria under oxygen limitation, which is relevant to disease progression within the oxygen-restricted urinary tract.
Genome Sequence of the
Wolbachia
Endosymbiont of
Culex quinquefasciatus
JHB
Authors: Salzberg Steven L. , Puiu Daniela , Sommer Daniel D. , Nene Vish , Lee Norman H. 
Published: December 2008

ABSTRACT

Wolbachia
species are endosymbionts of a wide range of invertebrates, including mosquitoes, fruit flies, and nematodes. The
w
Pip strains can cause cytoplasmic incompatibility in some strains of the
Culex
mosquito. Here we describe the genome sequence of a
Wolbachia
strain that was discovered in the whole-genome sequencing data for the mosquito
Culex quinquefasciatus
strain JHB.
Low-cost and robust evaluation of information retrieval systems
Authors: Carterette Benjamin A. 
Published: December 2008

Research in Information Retrieval has progressed against a background of rapidly increasing corpus size and heterogeneity, with every advance in technology quickly followed by a desire to organize and search more unstructured, more heterogeneous, and even bigger corpora. But as retrieval problems get larger and more complicated, evaluating the ranking performance of a retrieval engine gets harder: evaluation requires human judgments of the relevance of documents to queries, and for very large corpora the cost of acquiring these judgments may be insurmountable. This cost limits the types of problems researchers can study as well as the data they can be studied on.
We present methods for understanding performance differences between retrieval engines in the presence of missing and noisy relevance judgments. The work introduces a model of the cost of experimentation that incorporates the cost of human judgments as well as the cost of drawing incorrect conclusions about differences between engines in both the training and testing phases of engine development. Through adopting a view of evaluation that is more concerned with distributions over performance differences rather than estimates of absolute performance, the expected cost can be minimized so as to reliably differentiate between engines with less than 1% of the human effort that has been used in past experiments.
An aspect-oriented approach to the undergraduate programming language curriculum
Authors: Sheldon Mark A. , Turbak Franklyn 
Published: December 2008

Three key forces are shaping the modern Computer Science (CS) curriculum: (1) new topics/courses are squeezing out existing ones; (2) a focus on "big picture" and interdisciplinary aspects of CS is leading to curricula in which the traditional core courses + electives model is being superseded by a more flexible approach based on tracks/threads; and (3) project-based courses are increasingly relying on a notion of
just-in-time
teaching in which particular skills are not bundled into a particular course, but are covered at a point when they are needed for particular project work.

The undergraduate programming language curriculum is feeling the pressure of these forces. Core courses on programming languages and compilers are being changed to electives, relegated to a software/systems track, or phased out altogether. Particular programming languages and programming language concepts are being taught in a more piecemeal fashion on an as-needed basis. Unfortunately, these changes make it increasingly likely that CS majors can graduate without being exposed to certain "big ideas" of programming languages.
Programming languages (along with many other subdisciplines of CS) contains ideas that every well-educated computer scientist needs to know and which are relevant to a wide variety of projects/careers. In a CS curriculum based on tracks and projects, how can we ensure that vital intellectual components are not lost in the shuffle?

One way to think about this problem is to view the CS curriculum as a collection of
aspects
that can be combined in different arrangements to produce various projects/courses. In this paper, we consider the benefits and challenges of an aspect-oriented view of the CS curriculum, particularly in regard to programming language concepts.
The Perspective of Ebina Danjō's Japanized Christianity: A Historical Case Study
Authors: Iwai Shuma 
Published: December 2008

AbstractThis article approaches the topic of Japanese Christianity during the Meiji era (1868-1912). Missionaries introduced Protestant Christianity to the Japanese people after the end of Japanese national seclusion, and many of them converted to Christianity. This paper particularly focuses on Ebina Danjō, a Japanese theologian and a Christian leader. It examines his syncretistic Christianity, in which he combined some Japanese traditional religions with Christianity. This study first presents a historical background of Christianity in Japan during the Meiji era and biographical information of Ebina Danjō. It then explores Ebina's formation of his theological foundation. Finally, it discusses and evaluates how he established syncretistic Christianity.
Local Unity and Global Communion: An Analysis of the Ecumenical Scene in African Roman Catholicism
Authors: Uzochukwu Peter Uche 
Published: December 2008

AbstractCorrelating the general ecumenical directory from Rome and that of the Southern African region, both within the Catholic Church, the current study tends to bring to the fore, once again, the tension that exists between the local and universal spheres of the church. If the tension is not properly balanced up, the pursuit of global vision might tend to dwarf grassroots initiatives; thus engendering a dilemma of interests or a split in fidelities, especially among young churches like those in Africa. To realise their full essence, as I intend to posit here, however, both global policies and local praxis should mutually complement each other; empowering genuine and enriching diversity at the grass roots without disconnecting same from the global goal of the ecumenical movement.
Dyspnea—A Bad Prognosis Symptom at the End of Life
Authors: Cuervo Pinna Miguel Ángel , Mota Vargas Rafael , Redondo Moralo María José , Sánchez Correas Miguel Ángel , Pera Blanco Guillem 
Published: December 2008

Purposes: Dyspnea as refractory symptom leading to sedation at the end of life and the place of death. Survival study in population with dyspnea. Methods: Longitudinal study of terminally ill patients in a year (n = 195). We divided populations as (a) population with dyspnea: prevalent and incident dyspnea and (b) population without dyspnea. We used the statistical program Stata9 (Kaplan-Meier and Cox logistic regression models). Results: The probability of being sedated was 5 times higher in population with dyspnea. Dying in hospital odds ratio was 2.13 in patients with dyspnea. The average survival time was 52 days in patients with dyspnea and 69 in non-dyspnea patients. The average survival was similar between both groups. Patients with incident dyspnea showed a higher average survival than those with prevalent dyspnea. Conclusions: The connection between dyspnea and sedation was clearly shown. There were significant differences between prevalent dyspnea and incident dyspnea groups.
The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH
Authors: Furuya Tomoko , Uchiyama Tetsuji , Adachi Atsushi , Okada Takae , Nakao Motonao , Oga Atsunori , Yang Song-Ju , Kawauchi Shigeto , Sasaki Kohsuke 
Published: December 2008

Abstract

Background
The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome) mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers.

Methods
Initially, the DNA copy number aberrations (DCNAs) were analyzed by array-based comparative genomic hybridization (aCGH) in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a clone-by-clone comparison of the frequency of the DNA copy number aberrations selected 26 clones to estimate the disease states.

Results
By spotting these 50 clones together with 26 frequently or rarely involved clones and 62 reference clones, a mini-array was made to estimate the above parameters, and the diagnostic performance of the mini-array was evaluated for an independent set of 30 gastric cancers (blinded – sample set). In comparison to the clinicopathological features, the overall accuracy was 66.7% for node metastasis, 86.7% for liver metastasis, 86.7% for peritoneal dissemination, and 96.7% for depth of tumor invasion. The intratumoral heterogeneity barely affected the diagnostic performance of the mini-array.

Conclusion
These results suggest that the mini-array makes it possible to determine an optimal treatment for each of the patients with gastric adenocarcinoma.