bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Logistic Regression for Prediction of the Fate of
Staphylococcus aureus
in Pasteurized Milk in the Presence of Two Lytic Phages
Authors: Obeso José M. , García Pilar , Martínez Beatriz , Arroyo-López Francisco Noé , Garrido-Fernández Antonio , Rodriguez Ana 
Published: July 2010

ABSTRACT

The use of bacteriophages provides an attractive approach to the fight against food-borne pathogenic bacteria, since they can be found in different environments and are unable to infect humans, both characteristics of which support their use as biocontrol agents. Two lytic bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), previously isolated from the dairy environment inhibited the growth of
Staphylococcus aureus
. To facilitate the successful application of both bacteriophages as biocontrol agents, probabilistic models for predicting
S. aureus
inactivation by the phages in pasteurized milk were developed. A linear logistic regression procedure was used to describe the survival/death interface of
S. aureus
after 8 h of storage as a function of the initial phage titer (2 to 8 log
10
PFU/ml), initial bacterial contamination (2 to 6 log
10
CFU/ml), and temperature (15 to 37°C). Two successive models were built, with the first including only data from the experimental design and a global one in which results derived from the validation experiments were also included. The temperature, interaction temperature-initial level of bacterial contamination, and initial level of bacterial contamination-phage titer contributed significantly to the first model prediction. However, only the phage titer and temperature were significantly involved in the global model prediction. The predictions of both models were fail-safe and highly consistent with the observed
S. aureu
s responses. Nevertheless, the global model, deduced from a higher number of experiments (with a higher degree of freedom), was dependent on a lower number of variables and had an apparent better fit. Therefore, it can be considered a convenient evolution of the first model. Besides, the global model provides the minimum phage concentration (about 2 × 10
8
PFU/ml) required to inactivate
S. aureus
in milk at different temperatures, irrespective of the bacterial contamination level.
Transcriptional Regulation of the Terephthalate Catabolism Operon in
Comamonas
sp. Strain E6
Authors: Kasai Daisuke , Kitajima Masahiro , Fukuda Masao , Masai Eiji 
Published: July 2010

ABSTRACT

Two almost identical gene clusters,
tphR
I
C
I
A2
I
A3
I
B
I
A1
I
and
tphR
II
C
II
A2
II
A3
II
B
II
A1
II
, are responsible for the conversion of terephthalate (TPA) to protocatechuate in
Comamonas
sp. strain E6. In the present study, we investigated the transcriptional regulation of the
tphR
II
C
II
A2
II
A3
II
B
II
A1
II
gene cluster. Reverse transcription-PCR analysis suggested that the
tphR
II
C
II
A2
II
A3
II
B
II
A1
II
genes form two transcriptional units, the
tphC
II
A2
II
A3
II
B
II
A1
II
catabolism operon and
tphR
II
, with the latter encoding an IclR-type transcriptional regulator (ITTR). The transcription start site of the
tph
II
catabolism operon was mapped at 21 nucleotides upstream of the initiation codon of
tphC
II
. The
lacZ
transcriptional fusion experiments showed that
tphR
II
encodes a transcriptional activator of the
tph
II
catabolism operon and that TPA acts as an inducer. On the other hand, TphR
II
appeared to repress its own transcription regardless of the presence of TPA. The analysis of mutant derivatives of E6 indicated that
tphR
II
is essential for the transcriptional activation of the
tph
II
catabolism operon and the growth on TPA of a
tph
I
-deficient derivative of E6. Purified His-tagged TphR
II
bound specifically to the
tphR
II
-
tphC
II
intergenic region containing a 21-bp inverted repeat sequence. Alignment of the inverted repeat sequences in the binding sites for TphR
II
and other members of ITTRs revealed highly conserved nucleotides. The substitution of conserved nucleotides resulted in significantly reduced TPA-dependent transcriptional activation from the
tphC
II
promoter and reduced binding to His-tagged TphR
II
. These results clearly indicate that the conserved nucleotides are required for the inducible expression of the
tph
II
catabolism operon regulated by TphR
II
.
Use of Amino Acids as Inducers for High-Level Protein Expression in the Single-Protein Production System
Authors: Vaiphei S. Thangminlal , Mao Lili , Shimazu Tsutomu , Park Jung-Ho , Inouye Masayori 
Published: July 2010

ABSTRACT

By taking advantage of MazF, an ACA codon-specific mRNA interferase,
Escherichia coli
cells can be converted into a bioreactor producing only a single protein of interest by using an ACA-less mRNA for the protein. In this single-protein production (SPP) system, we engineered MazF by replacing two tryptophan residues in positions 14 and 83 with Phe (W14F) and Leu (W83L), respectively. Upon the addition of an inducer (IPTG [isopropyl-β-
d
-thiogalactopyranoside]), the mutated MazF [MazF(ΔW)] can still be produced even in the absence of tryptophan in the medium by using a Trp auxotroph, while a target protein having Trp residues cannot be produced. However, at 3 h after the addition of IPTG, the addition of tryptophan to the medium exclusively induces production of the target protein at a high level. A similar SPP system was also constructed with the use of a His-less protein [MazF(ΔH)] and a His auxotroph. Using these dual-induction systems, isotopic enrichments of
13
C,
15
N, and
2
H were highly improved by almost complete suppression of the production of the unlabeled target protein. In both systems, isotopic incorporation reached more than 98% labeling efficiency, significantly reducing the background attributable to the unlabeled target protein.
Validation of a Self-Excising Marker in the Human Pathogen
Aspergillus fumigatus
by Employing the β-Rec/
six
Site-Specific Recombination System
Authors: Hartmann Thomas , Dümig Michaela , Jaber Basem M. , Szewczyk Edyta , Olbermann Patrick , Morschhäuser Joachim , Krappmann Sven 
Published: July 2010

ABSTRACT

Recyclable markers based on site-specific recombination allow repetitive gene targeting in filamentous fungi. Here we describe for the first time functionality of the bacterial recombination system employing β serine recombinase acting on
six
recognition sequences (β-rec/
six
) in a fungal host, the human pathogen
Aspergillus fumigatus
, and its use in establishing a self-excising resistance marker cassette for serial gene replacement.
Chitin Utilization by the Insect-Transmitted Bacterium
Xylella fastidiosa
Authors: Killiny Nabil , Prado Simone S. , Almeida Rodrigo P. P. 
Published: July 2010

ABSTRACT

Xylella fastidiosa
is an insect-borne bacterium that colonizes xylem vessels of a large number of host plants, including several crops of economic importance. Chitin is a polysaccharide present in the cuticle of leafhopper vectors of
X. fastidiosa
and may serve as a carbon source for this bacterium. Biological assays showed that
X. fastidiosa
reached larger populations in the presence of chitin. Additionally, chitin induced phenotypic changes in this bacterium, notably increasing adhesiveness. Quantitative PCR assays indicated transcriptional changes in the presence of chitin, and an enzymatic assay demonstrated chitinolytic activity by
X. fastidiosa
. An ortholog of the chitinase A gene (
chiA
) was identified in the
X. fastidiosa
genome. The
in silico
analysis revealed that the open reading frame of
chiA
encodes a protein of 351 amino acids with an estimated molecular mass of 40 kDa.
chiA
is in a locus that consists of genes implicated in polysaccharide degradation. Moreover, this locus was also found in the genomes of closely related bacteria in the genus
Xanthomonas
, which are plant but not insect associated.
X. fastidiosa
degraded chitin when grown on a solid chitin-yeast extract-agar medium and grew in liquid medium with chitin as the sole carbon source; ChiA was also determined to be secreted. The gene encoding ChiA was cloned into
Escherichia coli
, and endochitinase activity was detected in the transformant, showing that the gene is functional and involved in chitin degradation. The results suggest that
X. fastidiosa
may use its vectors' foregut surface as a carbon source. In addition, chitin may trigger
X. fastidiosa's
gene regulation and biofilm formation within vectors. Further work is necessary to characterize the role of chitin and its utilization in
X. fastidiosa
.
Effect of Earthworm Feeding Guilds on Ingested Dissimilatory Nitrate Reducers and Denitrifiers in the Alimentary Canal of the Earthworm
Authors: Depkat-Jakob Peter S. , Hilgarth Maik , Horn Marcus A. , Drake Harold L. 
Published: July 2010

ABSTRACTThe earthworm gut is an anoxic nitrous oxide (N2O)-emitting microzone in aerated soils.In situconditions of the gut might stimulate ingested nitrate-reducing soil bacteria linked to this emission. The objective of this study was to determine if dissimilatory nitrate reducers and denitrifiers in the alimentary canal were affected by feeding guilds (epigeic [Lumbricus rubellus], anecic [Lumbricus terrestris], and endogeic [Aporrectodea caliginosa]). Genes and gene transcripts ofnarG(encodes a subunit of nitrate reductase and targets both dissimilatory nitrate reducers and denitrifiers) andnosZ(encodes a subunit of N2O reductase and targets denitrifiers) were detected in guts and soils. Gut-derived sequences were similar to those of cultured and uncultured soil bacteria and to soil-derived sequences obtained in this study. Gut-derivednarGsequences andnarGterminal restriction fragments (TRFs) were affiliated mainly with Gram-positive organisms (Actinobacteria). The majority of gut- and uppermost-soil-derivednarGtranscripts were affiliated withMycobacterium(Actinobacteria). In contrast,narGsequences indicative of Gram-negative organisms (Proteobacteria) were dominant in mineral soil. MostnosZsequences andnosZTRFs were affiliated withBradyrhizobium(Alphaproteobacteria) and uncultured soil bacteria. TRF profiles indicated thatnosZtranscripts were more affected by earthworm feeding guilds than werenosZgenes, whereasnarGtranscripts were less affected by earthworm feeding guilds than werenarGgenes.narGandnosZtranscripts were different and less diverse in the earthworm gut than in mineral soil. The collective results indicate that dissimilatory nitrate reducers and denitrifiers in the earthworm gut are soil derived and that ingestednarG- andnosZ-containing taxa were not uniformly stimulated in the guts of worms from different feeding guilds.
The Novel Two-Component Regulatory System BfiSR Regulates Biofilm Development by Controlling the Small RNArsmZthrough CafA
Authors: Petrova Olga E. , Sauer Karin 
Published: July 2010

ABSTRACTThe formation of biofilms by the opportunistic pathogenPseudomonas aeruginosais a developmental process governed by a novel signal transduction system composed of three two-component regulatory systems (TCSs), BfiSR, BfmSR, and MifSR. Here, we show that BfiSR-dependent arrest of biofilm formation coincided with reduced expression of genes involved in virulence, posttranslational/transcriptional modification, and Rhl quorum sensing but increased expression ofrhlABand the small regulatory RNAsrsmYZ. Overexpression ofrsmZ, but notrsmY, coincided with impaired biofilm development similar to inactivation ofbfiSandretS. We furthermore show that BfiR binds to the 5′ untranslated region ofcafAencoding RNase G. Lack ofcafAexpression coincided with impaired biofilm development and increasedrsmYZlevels during biofilm growth compared to the wild type. Overexpression ofcafArestored ΔbfiSbiofilm formation to wild-type levels and reducedrsmZabundance. Moreover, inactivation ofbfiSresulted in reduced virulence, as revealed by two plant models of infection. This work describes the regulation of a committed biofilm developmental step following attachment by the novel TCS BfiSR through the suppression of sRNArsmZvia the direct regulation of RNase G in a biofilm-specific manner, thus underscoring the importance of posttranscriptional mechanisms in controlling biofilm development and virulence.
The Insertion Sequences of
Anabaena
sp. Strain PCC 7120 and Their Effects on Its Open Reading Frames
Authors: Wolk C. Peter , Lechno-Yossef Sigal , Jäger Karin M. 
Published: July 2010

ABSTRACT

Anabaena
sp. strain PCC 7120, widely studied, has 145 annotated transposase genes that are part of transposable elements called insertion sequences (ISs). To determine the entirety of the ISs, we aligned transposase genes and their flanking regions; identified the ISs' possible terminal inverted repeats, usually flanked by direct repeats; and compared IS-interrupted sequences with homologous sequences. We thereby determined both ends of 87 ISs bearing 110 transposase genes in eight IS families (
http://www-is.biotoul.fr/
) and in a cluster of unclassified ISs, and of hitherto unknown miniature inverted-repeat transposable elements. Open reading frames were then identified to which ISs contributed and others—some encoding proteins of predictable function, including protein kinases, and restriction endonucleases—that were interrupted by ISs.
Anabaena
sp. ISs were often more closely related to exogenous than to other endogenous ISs, suggesting that numerous variant ISs were not degraded within PCC 7120 but transferred from without. This observation leads to the expectation that further sequencing projects will extend this and similar analyses. We also propose an adaptive role for poly(A) sequences in ISs.
Evidence for VirB4-Mediated Dislocation of Membrane-Integrated VirB2 Pilin during Biogenesis of the
Agrobacterium
VirB/VirD4 Type IV Secretion System
Authors: Kerr Jennifer E. , Christie Peter J. 
Published: July 2010

ABSTRACT

Agrobacterium
VirB2 pilin is required for assembly of the VirB/VirD4 type IV secretion system (T4SS). The propilin is processed by signal sequence cleavage and covalent linkage of the N and C termini, and the cyclized pilin integrates into the inner membrane (IM) as a pool for assembly of the secretion channel and T pilus. Here, by use of the substituted cysteine accessibility method (SCAM), we defined the VirB2 IM topology and then identified distinct contributions of the T4SS ATPase subunits to the pilin structural organization. Labeling patterns of Cys-substituted pilins exposed to the membrane-impermeative, thiol-reactive reagent 3-(
N
-maleimidopropionyl)biocytin (MPB) supported a topology model in which two hydrophobic stretches comprise transmembrane domains, an intervening hydrophilic loop (residues 90 to 94) is cytoplasmic, and the hydrophilic N and C termini joined at residues 48 and 121 form a periplasmic loop. Interestingly, the VirB4 ATPase, but not a Walker A nucleoside triphosphate (NTP) binding motif mutant, induced (i) MPB labeling of Cys94, a residue that in the absence of the ATPase is located in the cytoplasmic loop, and (ii) release of pilin from the IM upon osmotic shock. These findings, coupled with evidence for VirB2-VirB4 complex formation by coimmunoprecipitation, support a model in which VirB4 functions as a dislocation motor to extract pilins from the IM during T4SS biogenesis. The VirB11 ATPase functioned together with VirB4 to induce a structural change in the pilin that was detectable by MPB labeling, suggestive of a role for VirB11 as a modulator of VirB4 dislocase activity.
Use of a wire extender during neuroprotected vertebral artery angioplasty and stenting
Authors: Lesley Walter S , Kumar Ravi , Rangaswamy Rajesh 
Published: July 2010

BackgroundThe off-label use of an extender wire during vertebral artery stenting and angioplasty with or with neuroprotection has not been previously reported.Material and MethodsRetrospective, single-patient, technical report.ResultsAfter monorail balloon angioplasty was performed on a proximal left vertebral artery stenosis, the 190 cm long Accunet neuroprotection filter device was not long enough for delivery of an over-the-wire stent. After mating a 145 cm long, 0.014 inch extension wire to the filter device, a balloon-mounted Liberté stent was implanted with good angiographic and clinical results.ConclusionThe off-label use of an extender wire permits successful over-the-wire stenting on a monorail neuroprotection device for vertebral artery endosurgery.
Beyond the 'Long Partition'. From Divisive Geographies of Korea to the Korean 'Meta-Culture'
Authors: Gelézeau Valérie 
Published: July 2010

AbstractThis paper addresses the importance of the post-colonial division of Korea between North and South in shaping not only territorial structures, but also geographical interpretations of contemporary Korea. After a critical analysis of the Korean 'meta-border', the paper discusses how traditional approaches in Korean geography consider the 'long partition' as a backdrop affecting South and North Korean societies. Until the 1990s, this divisive paradigm was expressed in South Korea by the focus on various embodiments of the developmental state at the national scale with great attention on Seoul, or its alternative, the regional problem (chiyok munje). Recent trends in Korean studies acknowledge the peculiarities of the Korean socio-spatial dimensions that disturb multi-scaled borders and boundaries, geographical, national or ethnic. The paper argues that, in the classical paradigm, the division between North and South Korea, internalised at all levels of the socio-spatial spheres, acted as an essential matrix for shaping not only both societies but their narratives in the social sciences. This requires a new geographical approach to Korea, going beyond the partition, from territorial borders between North and South to epistemological borders within Korean geographies, or Korean studies themselves, in order to better grasp the notion of a 'Korean meta-culture'.
Constructing a New Image. Hallyu in Taiwan
Authors: Sung Sang-Yeon 
Published: July 2010

AbstractThis paper discusses how hallyu—the recent influx of Korean popular culture in Taiwan—has transformed the image of South Korea among the people of Taiwan. South Korea and Taiwan share a similar historical past. Nevertheless, the Taiwanese did not have a positive image of South Korea after 1992, when South Korea broke off diplomatic relations with Taiwan in order to establish diplomatic relations with mainland China. This work is based on ethnographic research done in Taiwan and South Korea from 2001–2003 and 2007–2009. It explores how hallyu has contributed to the rebuilding of the image of South Korea in Taiwan. It discusses Taiwanese perceptions of this image and the role of the South Korean government in improving it. It focuses on how a once-held negative image of South Korea has been transformed. The hallyu boom inspired many Taiwanese to remark on the influence of South Korean dramas and pop music in renewing their relationship with South Korea. It has provided an opportunity for Taiwan and South Korea to build positive relationships after the break-up of their diplomatic relations. Through hallyu, South Korea became a country that Taiwanese want to emulate, a model nation for Taiwan today.
The Right to Survival in the Democratic People's Republic of Korea
Authors: Song Jiyoung 
Published: July 2010

AbstractFor the past decade, the author has examined North Korean primary public documents and concludes that there have been changes of identities and ideas in the public discourse of human rights in the DPRK: from strong post-colonialism to Marxism-Leninism, from there to the creation of Juche as the state ideology and finally 'our style' socialism. This paper explains the background to Kim Jong Il's 'our style' human rights in North Korea: his broader framework, 'our style' socialism, with its two supporting ideational mechanisms, named 'virtuous politics' and 'military-first politics'. It analyses how some of these characteristics have disappeared while others have been reinforced over time. Marxism has significantly withered away since the end of the Cold War, and communism was finally deleted from the latest 2009 amended Socialist Constitution, whereas the concept of sovereignty has been strengthened and the language of duties has been actively employed by the authority almost as a relapse to the feudal Confucian tradition. The paper also includes some first-hand accounts from North Korean defectors interviewed in South Korea in October–December 2008. They show the perception of ordinary North Koreans on the ideas of human rights.
The Taiwanese Fishing Industry. The Military and Political Complex
Authors: Ta-Yuan Chen 
Published: July 2010

AbstractTaiwan was subjected to the longest period of martial law in history, from 1948 to 1987, and for this period of time the fishing industry of Taiwan was closely controlled and monitored by the government and the military. From 1951 to 1982, the fisheries authorities of Taiwan were controlled to a large extent by high-ranking military officers. Besides this, the military also used a variety of methods to track the movement of fishermen in distant waters. Under such strict control and surveillance of the government, only a few politicians were willing to speak on behalf of the interests of Taiwan's fishing industry. The situation did not improve until two young men from the local fishing industry were elected into the national parliaments in 1972.
The BBC Arabic Service: Changing Political Mediascapes
Authors: Baumann Gerd , el Issawi Fatima 
Published: July 2010

AbstractLaunched in 1938 as the BBC's first foreign language radio service, 80 years later, in 2008, the BBC Arabic Service also became the first tri-media platform at the World Service offering news and current affairs not only on radio and on online, but also via a fully fledged TV Channel in Arabic. This article traces the intervening transformations by exploring two critical moments in detail and examines why broadcasting to the Middle East has assumed such a pivotal position in the BBC's history. The first step examines selected internal communications between the British government and the BBC during World War Two, and the second outlines the BBC's current choices and strategy of combining the provision of 'impartial' news with new kinds of interactive programming and establishing opportunities for participation in mediated debates among audiences and users across the Middle East and the Arabic-speaking diasporas. Drawing on archival research, observational, and interview data, this article indicates enduring issues and themes that run through the history of the BBC Arabic services. The most important of these concern the dilemma of providing impartial news at the same time as promoting British diplomatic goals and strategic interests in the Greater Middle East.
Broadcasting to Afghanistan: A history of the BBC Pashto Service
Authors: Sreberny Annabelle , Torfeh Massoumeh 
Published: July 2010

AbstractThis paper traces the history of BBC World Service (BBCWS) broadcasts to Afghanistan and the political struggles that led to the establishment of a Pashto language service to complement BBC broadcasting in Persian. The complex linguistic, ethnic, and tribal diversity of Afghanistan makes providing appropriate and relevant news, and an information service in the right language, accent, and idiom for Afghanistan, a daunting task. The paper analyzes the relationship between the Foreign and Commonwealth Office and the BBC, and the impetus behind the launch of a Pashto service for Afghans. It also explores the tensions between providing impartial news and engaging in communications for development purposes.