bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Molecules Secreted by
Lactobacillus acidophilus
Strain La-5 on
Escherichia coli
O157:H7 Colonization
Authors: Medellin-Peña Maira J. , Griffiths Mansel W. 
Published: December 2008

ABSTRACT

The probiotic bacterium
Lactobacillus acidophilus
strain La-5 is a gut-colonizing microorganism that, when established, becomes an important part of the gastrointestinal (GI) tract microbiota. It has been shown to be effective against enterohemorrhagic
Escherichia coli
(EHEC) O157:H7 infection. We have previously shown that molecules released by probiotic strain La-5 influence the transcription of EHEC genes involved in colonization and quorum sensing. In this work, we report on the ability of these molecules to prevent the adherence of EHEC to epithelial cells and on its capacity to concentrate F-actin at adhesion sites. With a fluorescein-labeled phallotoxin, it was shown that La-5 cell-free spent medium (CFSM) fractions remarkably reduced attaching and effacing lesions in HeLa cells. We also observed a significant inhibition of bacterial adhesion to Hep-2 cells when they were treated with the same La-5 CFSM fractions. In order to observe if La-5 CFSM fractions exhibited the same effect in vivo, we studied the ability of luminescent EHEC constructs (
LEE1
::
luxCDABE
) to adhere to intestinal epithelial cells of specific-pathogen-free ICR mice following intragastric inoculation. Colonization of the GI tract by luminescent EHEC O157:H7 was monitored in real time with a slow-scan charge-coupled device camera. At the same time, fecal shedding of EHEC was studied. Following oral gavage of the La-5 active fraction, we observed a reduced amount of bioluminescence signal along with a decrease in fecal shedding by mice, indicating an effect on the ability of the organism to colonize the GI tract. Our results confirm past evidence of the possibility of blocking or interfering with EHEC's virulence by active molecules contained in the probiotic CFSM and identify novel therapeutic alternatives to antibiotic treatments in the fight against food-borne pathogens.
Community-Level Analysis of
psbA
Gene Sequences and Irgarol Tolerance in Marine Periphyton
Authors: Eriksson K. M. , Clarke A. K. , Franzen L.-G. , Kuylenstierna M. , Martinez K. , Blanck H. 
Published: December 2008

ABSTRACT

This study analyzes
psbA
gene sequences, predicted D1 protein sequences, species relative abundance, and pollution-induced community tolerance in marine periphyton communities exposed to the antifouling compound Irgarol 1051. The mechanism of action of Irgarol is the inhibition of photosynthetic electron transport at photosystem II by binding to the D1 protein. The metagenome of the communities was used to produce clone libraries containing fragments of the
psbA
gene encoding the D1 protein. Community tolerance was quantified with a short-term test for the inhibition of photosynthesis. The communities were established in a continuous flow of natural seawater through microcosms with or without added Irgarol. The selection pressure from Irgarol resulted in an altered species composition and an inducted community tolerance to Irgarol. Moreover, there was a very high diversity in the
psbA
gene sequences in the periphyton, and the composition of
psbA
and D1 fragments within the communities was dramatically altered by increased Irgarol exposure. Even though tolerance to this type of compound in land plants often depends on a single amino acid substitution (Ser
264
→Gly) in the D1 protein, this was not the case for marine periphyton species. Instead, the tolerance mechanism likely involves increased degradation of D1. When we compared sequences from low and high Irgarol exposure, differences in nonconserved amino acids were found only in the so-called PEST region of D1, which is involved in regulating its degradation. Our results suggest that environmental contamination with Irgarol has led to selection for high-turnover D1 proteins in marine periphyton communities at the west coast of Sweden.
Atypical Biosynthetic Properties of a Δ
12
/ν+3 Desaturase from the Model Basidiomycete
Phanerochaete chrysosporium
Authors: Minto Robert E. , Blacklock Brenda J. , Younus Hina , Pratt Andrew C. 
Published: December 2008

ABSTRACT

The model white-rot basidiomycete
Phanerochaete chrysosporium
contains a single integral membrane Δ
12
-desaturase FAD2 related to the endoplasmic reticular plant FAD2 enzymes. The fungal
fad2
-like gene was cloned and distinguished itself from plant homologs by the presence of four introns and a significantly larger coding region. The coding sequence exhibits ca. 35% sequence identity to plant homologs, with the highest sequence conservation found in the putative catalytic and major structural domains. In vivo activity of the heterologously expressed enzyme favors C
18
substrates with ν+3 regioselectivity, where the site of desaturation is three carbons carboxy-distal to the reference position of a preexisting double bond (ν). Linoleate accumulated to levels in excess of 12% of the total fatty acids upon heterologous expression of
P. chrysosporium
FAD2 in
Saccharomyces cerevisiae
. In contrast to the behavior of the plant FAD2 enzymes, this oleate desaturase does not 12-hydroxylate lipids and is the first example whose activity increases at higher temperatures (30°C versus 15°C). Thus, while maintaining the hallmark activity of the fatty acyl Δ
12
-desaturase family, the basidiomycete
fad2
genes appear to have evolved substantially from an ancestral desaturase.
Molecular and Biochemical Characterization of a β-Fructofuranosidase from
Xanthophyllomyces dendrorhous
Authors: Linde Dolores , Macias Isabel , Fernández-Arrojo Lucía , Plou Francisco J. , Jiménez Antonio , Fernández-Lobato María 
Published: December 2008

ABSTRACT

An extracellular β-fructofuranosidase from the yeast
Xanthophyllomyces dendrorhous
was characterized biochemically, molecularly, and phylogenetically. This enzyme is a glycoprotein with an estimated molecular mass of 160 kDa, of which the N-linked carbohydrate accounts for 60% of the total mass. It displays optimum activity at pH 5.0 to 6.5, and its thermophilicity (with maximum activity at 65 to 70°C) and thermostability (with a
T
50
in the range 66 to 71°C) is higher than that exhibited by most yeast invertases. The enzyme was able to hydrolyze fructosyl-β-(2→1)-linked carbohydrates such as sucrose, 1-kestose, or nystose, although its catalytic efficiency, defined by the
k
cat
/

K
m

ratio, indicates that it hydrolyzes sucrose approximately 4.2 times more efficiently than 1-kestose. Unlike other microbial β-fructofuranosidases, the enzyme from
X. dendrorhous
produces neokestose as the main transglycosylation product, a potentially novel bifidogenic trisaccharide. Using a 41% (wt/vol) sucrose solution, the maximum fructooligosaccharide concentration reached was 65.9 g liter
−1
. In addition, we isolated and sequenced the
X. dendrorhous
β-fructofuranosidase gene (
Xd-INV
), showing that it encodes a putative mature polypeptide of 595 amino acids and that it shares significant identity with other fungal, yeast, and plant β-fructofuranosidases, all members of family 32 of the glycosyl-hydrolases. We demonstrate that the
Xd-INV
could functionally complement the
suc2
mutation of
Saccharomyces cerevisiae
and, finally, a structural model of the new enzyme based on the homologous invertase from
Arabidopsis thaliana
has also been obtained.
From Local Surveys to Global Surveillance: Three High-Throughput Genotyping Methods for Epidemiological Monitoring of
Xanthomonas citri
pv. citri Pathotypes
Authors: Bui Thi Ngoc Lan , Vernière Christian , Jarne Philippe , Brisse Sylvain , Guérin Fabien , Boutry Sébastien , Gagnevin Lionel , Pruvost Olivier 
Published: December 2008

ABSTRACT

Asiatic citrus canker is a major disease worldwide, and its causal agent,
Xanthomonas citri
pv. citri, is listed as a quarantine organism in many countries. Analysis of the molecular epidemiology of this bacterium is hindered by a lack of molecular typing techniques suitable for surveillance and outbreak investigation. We report a comparative evaluation of three typing techniques, amplified fragment length polymorphism (AFLP) analysis, insertion sequence ligation-mediated PCR (IS-LM-PCR) typing, and multilocus variable-number tandem-repeat analysis (MLVA), with 234 strains originating from Asia, the likely center of origin of the pathogen, and reference strains of pathotypes A, A*, and A
w
, which differ in host range. The typing techniques were congruent in describing the diversity of this strain collection, suggesting that the evolution pattern of the bacterium may be clonal. Based on a hierarchical analysis of molecular variance, the AFLP method best described the genetic variation found among pathotypes whereas MLVA best described the variation found among individual strains from the same countries or groups of neighboring countries. IS-LM-PCR data suggested that the transposition of insertion sequences in the genome of
X. citri
pv. citri occurs rarely enough not to disturb the phylogenetic signal. This technique may be useful for the global surveillance of non-epidemiologically related strains. Although pathological characteristics of strains could be most often predicted from genotyping data, we report the occurrence in the Indian peninsula of strains genetically related to pathotype A* strains but with a host range similar to that of pathotype A, which makes the classification of this bacterium even more complicated.
On the impact of combinatorial structure on congestion games
Authors: Ackermann Heiner , Röglin Heiko , Vöcking Berthold 
Published: December 2008

We study the impact of combinatorial structure in congestion games on the complexity of computing pure Nash equilibria and the convergence time of best response sequences. In particular, we investigate which properties of the strategy spaces of individual players ensure a polynomial convergence time. We show that if the strategy space of each player consists of the bases of a matroid over the set of resources, then the lengths of all best response sequences are polynomially bounded in the number of players and resources. We also prove that this result is tight, that is, the matroid property is a necessary and sufficient condition on the players' strategy spaces for guaranteeing polynomial-time convergence to a Nash equilibrium.
In addition, we present an approach that enables us to devise hardness proofs for various kinds of combinatorial games, including first results about the hardness of market sharing games and congestion games for overlay network design. Our approach also yields a short proof for the PLS-completeness of network congestion games. In particular, we show that network congestion games are PLS-complete for directed and undirected networks even in case of linear latency functions.
Starring Nero as Nero: Poetry, Role-Playing and Identity in Juvenal 8.215-21
Authors: Cowan Robert 
Published: December 2008

AbstractJuvenal's synkrisis between Orestes and Nero climaxes with the statement that the former never played Orestes; the implied antithesis, that Nero did play Nero, gains point from the princeps' practice of wearing masks resembling his own face. This blurring of the distinction between 'playing Nero' and 'playing Orestes' problematizes the princeps' identity. This problematization is furthered by the peculiarities of Orestes, who in various tragic plots repeatedly either plays other roles or is himself impersonated. This is part of Satire 8's wider exploration of identity as underdetermined by ancestry and the inadequacy of names as signifiers. The further statement that Orestes never wrote a Troica is illuminated by its intertextual engagement with Callimachus Epigr. 59 G-P, in which the poet's loss of his 'Pyladeses' through writing a play contrasts with Orestes' omission of this final act of madness. The Callimachean Orestes thus keeps distinct the roles of tragedian and tragic hero, poet and character, thereby foregrounding Nero's failure to maintain this distinction. By blurring his identity with that of Paris in both his epic and his alleged burning of Rome, Nero confuses the categories of artist and perpetrator, creator and character, just as he and Orestes confuse those of actor and role.
Plato Theaetetus 182e1-2: The Meaning of μενειν
Authors: Boter Gerard 
Published: December 2008

AbstractIn Pl. Tht. 182c1-183b5 Socrates deals with the implications of the Heraclitean doctrine of flux for the thesis (attributed to Protagoras) that knowledge is perception. After having illustrated that, according to the flux theory, the perceived object is subject to constant change (182d1-5), he deals with perception itself (182e1-2): μενειν ποτε εν αυτω τω οραν η ακουειν. It is generally believed that this phrase means that sight, for instance, does not remain within the domain of sight, but changes into another kind of perception. Thus the words εν αυτω τω οραν η ακουειν are taken as an obligatory constituent belonging to μενειν; the whole phrase is supposed to mean, 'Shall we say that it ever stays in the condition of seeing or hearing?' (Sedley). This contribution shows why this interpretation is untenable. As an alternative, it is argued that μενειν is used absolutely as 'remain as one was'; the phrase εν αυτω τω οραν η ακουειν serves to indicate that a perception, while constantly changing, does remain within its own domain; that is, sight is never stable, but it does remain within the domain of sight. The whole sentence means, 'Does it ever remain the same within sight or hearing itself?'
“The Idumaeans” in Josephus' The Jewish War
Authors: Appelbaum Alan 
Published: December 2008

Abstract“The Idumaeans” constitute a single, although collective, character in Josephus' The Jewish War. This article discusses whom Josephus meant by “the Idumaeans,” and considers whether, in his mind, they were, as others have suggested, “Jews” from Idumaea or a separate nation or ethnic group. It argues that the character “the Idumaeans” is not in fact a representative picture of Idumaeans of Josephus' time, but may be understood in terms of modern ethnic stereotyping, and that Josephus' stereotype of “the Idumaeans” as bloodthirsty hooligans is ultimately drawn from a continuous Idumaean military tradition. The article concludes by re-reading the War stripped of Josephus' ethnic prejudice against Idumaeans to learn more about the role of Idumaean fighting men in the first war against Rome.
Ritual Baths Adjacent to Tombs: An Analysis of the Archaeological Evidence in Light of the Halakhic Sources
Authors: Adler Yonatan 
Published: December 2008

AbstractThis study surveys the archaeological evidence of Jewish ritual baths (miqwa'ot) built adjacent to tombs, dating variously from the late Second Temple period through the 3rd-4th centuries C.E., and analyses this evidence in light of the halakhic sources. At first glance, this archaeological phenomenon would seem to stand at odds with normative halakhah, which mandates miqweh ablutions for corpse-impurity only at the end of a seven-day purification process. A careful reading of the scriptural and rabbinic sources, however, reveals that while a seven-day purification process is required for one who has contracted impurity directly from a corpse or a grave, impurity conveyed through an intermediary source (i.e. physical contact with one who has contracted direct corpse-impurity) may be purged through ablutions on the same day that the impurity was incurred. This study suggests that miqwa'ot adjacent to tombs were utilized at the conclusion of burial ceremonies by funeral participants who had contracted such “second-degree” impurity.
Will Satan Be Saved? Reconsidering Origen's Theory of Volition in Peri Archon
Authors: Holliday Lisa 
Published: December 2008

AbstractThough the list of Origen's mistakes varies among authors, perhaps one of the most notorious accusations is that he proposed salvation for the devil, despite his protestations to the contrary. Though in PArch his discussion of Satan is secondary to his larger aims, Origen does provide evidence that validates his claim that the devil could not be saved, especially in his exploration of volition. By considering the devil within Origen's stance on volition and the nature of the soul, it is clear that while the devil technically retained the possibility of salvation, he did not wish to attain it, due to the degree to which he pursued his own desires.
Intracellular cotrafficking of factor VIII and von Willebrand factor type 2N variants to storage organelles
Authors: van den Biggelaar Maartje , Meijer Alexander B. , Voorberg Jan , Mertens Koen 
Published: December 2008

AbstractWeibel-Palade bodies (WPBs) are the endothelial storage organelles that are formed upon von Willebrand factor (VWF) expression. Apart from VWF, WPBs contain a variety of hemostatic and inflammatory proteins. Some of these are thought to be targeted to WPBs by directly interacting with VWF in the secretory pathway. Previous studies have demonstrated that coexpression of factor VIII (FVIII) with VWF results in costorage of both proteins. However, whether cotrafficking is driven by intracellular FVIII-VWF assembly has remained unclear. We now have addressed this issue using recombinant VWF type 2N variants that are known to display reduced FVIII binding in the circulation. Binding studies using purified fluorescent FVIII and VWF type 2N variants revealed FVIII binding defects varying from moderate (Arg854Gln, Cys1060Arg) to severe (Arg763Gly, Thr791Met, Arg816Trp). Upon expression in HEK293 cells, all VWF variants induced formation of WPB-like organelles that were able to recruit P-selectin, as well as FVIII. WPBs containing FVIII did not display their typical elongated shape, suggesting that FVIII affects the organization of VWF tubules therein. The finding that VWF type 2N variants are still capable of cotargeting FVIII to storage granules implies that trafficking of WPB cargo proteins does not necessarily require high-affinity assembly with VWF.
Characterization of the ompL1 gene of pathogenic Leptospira species in China and cross-immunogenicity of the OmpL1 protein
Authors: Dong Haiyan , Hu Ye , Xue Feng , Sun Dexter , Ojcius David M , Mao Yafei , Yan Jie 
Published: December 2008

Abstract

Background
The usefulness of available vaccine and serological tests for leptospirosis is limited by the low cross-reactivity of antigens from numerous serovars of pathogenic Leptospira spp. Identification of genus-specific protein antigens (GP-Ag) of Leptospira would be important for development of universal vaccines and serodiagnostic methods. OmpL1, a transmembrane porin of pathogenic leptospires, was identified as a possible GP-Ag, but its sequence diversity and immune cross-reactivity among different serovars of pathogenic leptospires remains largely unknown.

Results
PCR analysis demonstrated that the ompL1 gene existed in all 15 official Chinese standard strains as well as 163 clinical strains of pathogenic leptospires isolated in China. In the standard strains, the ompL1 gene could be divided into three groups (ompL1/1, ompL1/2 and ompL1/3) according to their sequence identities. Immune electron microscopy demonstrated that all products of the different gene types of ompL1 are located on the surface of leptospires. The microscopic agglutination test revealed extensive yet distinct cross-immunoagglutination among the antisera against recombinant OmpL1 (rOmpL1) and leptospiral strains belonging to different ompL1 gene types. These cross-immunoreactions were further verified by ELISAs using the OmpL1 proteins as the coated antigens in serum samples from 385 leptospirosis patients. All the antisera against rOmpL1 proteins could inhibit L. interrogans strain Lai from adhering to J774A.1 cells. Furthermore, immunization of guinea pigs with each of the rOmpL1 proteins could cause cross-immunoprotection against lethal challenge with leptospires from different ompL1 gene types.

Conclusion
Three types of the ompL1 gene are present in pathogenic leptospires in China. OmpL1 is an immunoprotective GP-Ag which should be considered in the design of new universal vaccines and serodiagnostic methods against leptospirosis.
Response of the cytoplasmic and membrane proteome of Corynebacterium glutamicum ATCC 13032 to pH changes
Authors: Barriuso-Iglesias Mónica , Schluesener Daniela , Barreiro Carlos , Poetsch Ansgar , Martín Juan F 
Published: December 2008

Abstract

Background

C. glutamicum has traditionally been grown in neutral-pH media for amino acid production, but in a previous article we reported that this microorganism is a moderate alkaliphile since it grows optimally at pH 7.0–9.0, as shown in fermentor studies under tightly controlled pH conditions. We determined the best pH values to study differential expression of several genes after acidic or basic pH conditions (pH 6.0 for acidic expression and pH 9.0 for alkaline expression). Thus, it was interesting to perform a detailed analysis of the pH-adaptation response of the proteome of C. glutamicum ATCC 13032 to clarify the circuits involved in stress responses in this bacterium. In this paper we used the above indicated pH conditions, based on transcriptional studies, to confirm that pH adaptation results in significant changes in cytoplasmatic and membrane proteins.

Results
The cytoplasmatic and membrane proteome of Corynebacterium glutamicum ATCC 13032 at different pH conditions (6.0, 7.0 and 9.0) was analyzed by classical 2D-electrophoresis, and by anion exchange chromatography followed by SDS-PAGE (AIEC/SDS-PAGE). A few cytoplasmatic proteins showed differential expression at the three pH values with the classical 2D-technique including a hypothetical protein cg2797, L-2.3-butanediol dehydrogenase (ButA), and catalase (KatA). The AIEC/SDS-PAGE technique revealed several membrane proteins that respond to pH changes, including the succinate dehydrogenase complex (SdhABCD), F0F1-ATP synthase complex subunits b, α and δ (AtpF, AtpH and AtpA), the nitrate reductase II α subunit (NarG), and a hypothetical secreted/membrane protein cg0752. Induction of the F0F1-ATP synthase complex β subunit (AtpD) at pH 9.0 was evidenced by Western analysis. By contrast, L-2.3-butanediol dehydrogenase (ButA), an ATPase with chaperone activity, the ATP-binding subunit (ClpC) of an ATP-dependent protease complex, a 7 TMHs hypothetical protein cg0896, a conserved hypothetical protein cg1556, and the dihydrolipoamide acyltransferase SucB, were clearly up-regulated at pH 6.0.

Conclusion
The observed protein changes explain the effect of the extracellular pH on the growth and physiology of C. glutamicum. Some of the proteins up-regulated at alkaline pH respond also to other stress factors suggesting that they serve to integrate the cell response to different stressing conditions.