bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome
Authors: Biers Erin J. , Sun Shulei , Howard Erinn C. 
Published: February 2009

ABSTRACT

The
Sorcerer II
Global Ocean Sampling (GOS) sequencing effort has vastly expanded the landscape of metagenomics, providing an opportunity to study the genetic potential of surface ocean water bacterioplankton on a global scale. Here we describe the habitat-based microbial diversity, both taxon evenness and taxon richness, for each GOS site and estimate genome characteristics of a typical free-living, surface ocean water bacterium. While
Alphaproteobacteria
and particularly SAR11 dominate the 0.1- to 0.8-μm size fraction of surface ocean water bacteria (43% and 31%, respectively), the proportions of other taxa varied with ocean habitat type. Within each habitat type, lower-bound estimates of phylum richness ranged between 18 and 59 operational taxonomic units (OTUs). However, OTU richness was relatively low in the hypersaline lagoon community at every taxonomic level, and open-ocean communities had much more microdiversity than any other habitat. Based on the abundance of single-copy eubacterial genes from the same data set, we estimate that the genome of an average free-living surface ocean water bacterium (sized between 0.1 and 0.8 μm) contains ∼1,019 genes and 1.8 copies of the 16S rRNA gene, suggesting that these bacteria have relatively streamlined genomes in comparison to those of cultured bacteria and bacteria from other habitats (e.g., soil or acid mine drainage).
Dynamic Model of Heat Inactivation Kinetics for Bacterial Adaptation
Authors: Corradini Maria G. , Peleg Micha 
Published: February 2009

ABSTRACT

The Weibullian-log logistic (WeLL) inactivation model was modified to account for heat adaptation by introducing a logistic adaptation factor, which rendered its “rate parameter” a function of both temperature and heating rate. The resulting model is consistent with the observation that adaptation is primarily noticeable in slow heat processes in which the cells are exposed to sublethal temperatures for a sufficiently long time. Dynamic survival patterns generated with the proposed model were in general agreement with those of
Escherichia coli
and
Listeria monocytogenes
as reported in the literature. Although the modified model's rate equation has a cumbersome appearance, especially for thermal processes having a variable heating rate, it can be solved numerically with commercial mathematical software. The dynamic model has five survival/adaptation parameters whose determination will require a large experimental database. However, with assumed or estimated parameter values, the model can simulate survival patterns of adapting pathogens in cooked foods that can be used in risk assessment and the establishment of safe preparation conditions.
Plasticity and Evolution of Aeruginosin Biosynthesis in Cyanobacteria
Authors: Ishida Keishi , Welker Martin , Christiansen Guntram , Cadel-Six Sabrina , Bouchier Christiane , Dittmann Elke , Hertweck Christian , Tandeau de Marsac Nicole 
Published: February 2009

ABSTRACT

Aeruginosins are bioactive oligopeptides that are produced in high structural diversity by strains of the bloom-forming cyanobacterial genera
Microcystis
and
Planktothrix
. A hallmark of aeruginosins is the unusual Choi moiety central to the tetrapeptides, while other positions are occupied by variable moieties in individual congeners. Here we report on three aeruginosin synthetase gene clusters (
aer
) of
Microcystis aeruginosa
(strains PCC 7806, NIES-98, and NIES-843). The analysis and comparison the
aer
gene clusters provide the first insight into the molecular basis of biosynthetic and structural plasticity in aeruginosin pathways. Major parts of the
aer
gene clusters are highly similar in all strains, particularly the genes coding for the first three nonribosomal peptide synthetase (NRPS) modules except for the region coding for the second adenylation domain. However, the gene clusters differ largely in genes coding for tailoring enzymes such as halogenases and sulfotransferases, reflecting structural peculiarities in aeruginosin congeners produced by the individual strains. Significant deviations were further observed in the C-terminal NRPS modules, suggesting two distinct release mechanisms. The architecture of the gene clusters is in agreement with the particular aeruginosin variants that are produced by individual strains, the structures of two of which (aeruginosins 686 A and 686 B) were elucidated. The
aer
gene clusters of
Microcystis
and
Planktothrix
are proposed to originate from a common ancestor and to have evolved to their present-day diversity largely through horizontal gene transfer and recombination events.
Reciprocal Expression of Integration Host Factor and HU in the Developmental Cycle and Infectivity of
Legionella pneumophila
Authors: Morash Michael G. , Brassinga Ann Karen C. , Warthan Michelle , Gourabathini Poornima , Garduño Rafael A. , Goodman Steven D. , Hoffman Paul S. 
Published: February 2009

ABSTRACT

Legionella pneumophila
is an intracellular parasite of protozoa that differentiates late in infection into metabolically dormant cysts that are highly infectious. Regulation of this process is poorly understood. Here we report that the small DNA binding regulatory proteins integration host factor (IHF) and HU are reciprocally expressed over the developmental cycle, with HU expressed during exponential phase and IHF expressed postexponentially. To assess the role of these regulatory proteins in development, chromosomal deletions were constructed. Single (
ihfA
or
ihfB
) and double deletion (Δ
ihf
) IHF mutants failed to grow in
Acanthamoeba castellanii
unless complemented in
trans
when expressed temporally from the
ihfA
promoter but not under P
tac
(isopropyl-β-
d
-thiogalactopyranoside). In contrast, IHF mutants were infectious for HeLa cells, though electron microscopic examination revealed defects in late-stage cyst morphogenesis (thickened cell wall, intracytoplasmic membranes, and inclusions of poly-β-hydroxybutyrate), and were depressed for the developmental marker MagA. Green fluorescent protein promoter fusion assays indicated that IHF and the stationary-phase sigma factor RpoS were required for full postexponential expression of
magA
. Finally, defects in cyst morphogenesis noted for Δ
ihf
mutants in HeLa cells correlated with a loss of both detergent resistance and hyperinfectivity compared with results for wild-type cysts. These studies establish IHF and HU as markers of developmental stages and show that IHF function is required for both differentiation and full virulence of
L. pneumophila
in natural amoebic hosts.
Mesophilic and Psychrotrophic Bacteria from Meat and Their Spoilage Potential In Vitro and in Beef
Authors: Ercolini Danilo , Russo Federica , Nasi Antonella , Ferranti Pasquale , Villani Francesco 
Published: February 2009

ABSTRACT

Mesophilic and psychrotrophic populations from refrigerated meat were identified in this study, and the spoilage potential of microbial isolates in packaged beef was evaluated by analyzing the release of volatile organic compounds (VOC) by gas chromatography-mass spectrometry (GC/MS). Fifty mesophilic and twenty-nine psychrotrophic isolates were analyzed by random amplified polymorphic DNA-PCR, and representative strains were identified by 16S rRNA gene sequencing.
Carnobacterium maltaromaticum
and
C. divergens
were the species most frequently found in both mesophilic and psychrotrophic populations.
Acinetobacter baumannii
,
Buttiauxella
spp. and
Serratia
spp. were identified among the mesophilic isolates, while
Pseudomonas
spp. were commonly identified among the psychrotrophs. The isolates were further characterized for their growth at different temperatures and their proteolytic activity in vitro on meat proteins extracts at 7°C. Selected proteolytic strains of
Serratia proteamaculans
,
Pseudomonas fragi
, and
C. maltaromaticum
were used to examine their spoilage potential in situ. Single strains of these species and mixtures of these strains were used to contaminate beef chops that were packed and stored at 7°C. At time intervals up to 1 month, viable counts were determined, and VOC were identified by GC/MS. Generally, the VOC concentrations went to increase during the storage of the contaminated meats, and the profiles of the analyzed meat changed dramatically depending on the contaminating microbial species. About 100 volatiles were identified in the different contaminated samples. Among the detected volatiles, some specific molecules were identified only when the meat was contaminated by a specific microbial species. Compounds such as 2-ethyl-1-hexanol, 2-buten-1-ol, 2-hexyl-1-octanol, 2-nonanone, and 2-ethylhexanal were detectable only for
C. maltaromaticum
, which also produced the highest number of aldehydes, lactones, and sulfur compounds. The highest number of alcohols and ketons were detected in the headspace of meat samples contaminated by
P. fragi
, whereas the highest concentrations of some alcohols, such as 1-octen-3-ol, and some esters, such as isoamyl acetate, were produced by
S. proteamaculans
. In conclusion, different microbial species can contribute to meat spoilage with release of different volatile compounds that concur to the overall quality decrease of spoiling meat.
Role of
Acinetobacter baylyi
Crc in Catabolite Repression of Enzymes for Aromatic Compound Catabolism
Authors: Zimmermann Tina , Sorg Tobias , Siehler Simone Yasmin , Gerischer Ulrike 
Published: February 2009

ABSTRACT

Here, we describe for the first time the Crc (
c
atabolite
r
epression
c
ontrol) protein from the soil bacterium
Acinetobacter baylyi
. Expression of
A. baylyi crc
varied according to the growth conditions. A strain with a disrupted
crc
gene showed the same growth as the wild type on a number of carbon sources. Carbon catabolite repression by acetate and succinate of protocatechuate 3,4-dioxygenase, the key enzyme of protocatechuate breakdown, was strongly reduced in the
crc
strain, whereas in the wild-type strain it underwent strong catabolite repression. This strong effect was not based on transcriptional regulation because the transcription pattern of the
pca-qui
operon (encoding protocatechuate 3,4-dioxygenase) did not reflect the derepression in the absence of Crc.
pca-qui
transcript abundance was slightly increased in the
crc
strain. Lack of Crc dramatically increased the mRNA stability of the
pca-qui
transcript (up to 14-fold), whereas two other transcripts (
pobA
and
catA
) remained unaffected.
p
-Hydroxybenzoate hydroxylase activity, encoded by
pobA
, was not significantly different in the absence of Crc, as protocatechuate 3,4-dioxygenase was. It is proposed that
A. baylyi
Crc is involved in the determination of the transcript stability of the
pca-qui
operon and thereby effects catabolite repression.
Role of RsbU in Controlling SigB Activity inStaphylococcus aureusfollowing Alkaline Stress
Authors: Pané-Farré Jan , Jonas Beate , Hardwick Steven W. , Gronau Katrin , Lewis Richard J. , Hecker Michael , Engelmann Susanne 
Published: February 2009

ABSTRACTSigB is an alternative sigma factor that controls a large regulon inStaphylococcus aureus. Activation of SigB requires RsbU, a protein phosphatase 2C (PP2C)-type phosphatase. In a closely related organism,Bacillus subtilis, RsbU activity is stimulated upon interaction with RsbT, a kinase, which following an activating stimulus switches from a 25S high-molecular-weight complex, the stressosome, to the N-terminal domain of RsbU. Active RsbU dephosporylates RsbV and thereby triggers the release of SigB from its inhibitory complex with RsbW. While RsbU, RsbV, RsbW, and SigB are conserved inS. aureus, proteins similar to RsbT and the components of the stressosome are not, raising the question of how RsbU activity and hence SigB activity are controlled inS. aureus. We found that in contrast to the case inB. subtilis, the induced expression of RsbU was sufficient to stimulate SigB-dependent transcription inS. aureus. However, activation of SigB-dependent transcription following alkaline stress did not lead to a clear accumulation of SigB and its regulators RsbV and RsbW or to a change in the RsbV/RsbV-P ratio inS. aureus. When expressed inB. subtilis, theS. aureusRsbU displayed a high activity even in the absence of an inducing stimulus. This high activity could be transferred to the PP2C domain of theB. subtilisRsbU protein by a fusion to the N-terminal domain of theS. aureusRsbU. Collectively, the data suggest that the activity of theS. aureusRsbU and hence SigB may be subjected to different regulation in comparison to that inB. subtilis.
Activation of the
Campylobacter jejuni
FlgSR Two-Component System Is Linked to the Flagellar Export Apparatus
Authors: Joslin Stephanie N. , Hendrixson David R. 
Published: February 2009

ABSTRACT

Activation of σ
54
-dependent gene expression essential for formation of flagella in
Campylobacter jejuni
requires the components of the inner membrane-localized flagellar export apparatus and the FlgSR two-component regulatory system. In this study, we characterized the FlgS sensor kinase and how activation of the protein is linked to the flagellar export apparatus. We found that FlgS is localized to the
C. jejuni
cytoplasm and that His141 of FlgS is essential for autophosphorylation, phosphorelay to the cognate FlgR response regulator, motility, and expression of σ
54
-dependent flagellar genes. Mutants with incomplete flagellar export apparatuses produced wild-type levels of FlgS and FlgR, but they were defective for signaling through the FlgSR system. By using genetic approaches, we found that FlgSR activity is linked to and downstream of the flagellar export apparatus in a regulatory cascade that terminates in expression of σ
54
-dependent flagellar genes. By analyzing defined
flhB
and
fliI
mutants of
C. jejuni
that form flagellar export apparatuses that are secretion incompetent, we determined that formation of the apparatus is required to contribute to the signal sensed by FlgS to terminate in activation of expression of σ
54
-dependent flagellar genes. Considering that the flagellar export apparatuses of
Escherichia coli
and
Salmonella
species influence σ
28
-dependent flagellar gene expression, our work expands the signaling activity of the apparatuses to include σ
54
-dependent pathways of
C. jejuni
and possibly other motile bacteria. This study indicates that these apparatuses have broader functions beyond flagellar protein secretion, including activation of essential two-component regulatory systems required for expression of σ
54
-dependent flagellar genes.
Sporulation and Enterotoxin (CPE) Synthesis Are Controlled by the Sporulation-Specific Sigma Factors SigE and SigK inClostridium perfringens
Authors: Harry Kathryn H. , Zhou Ruanbao , Kroos Lee , Melville Stephen B. 
Published: February 2009

ABSTRACTClostridium perfringensis the third most frequent cause of bacterial food poisoning annually in the United States. IngestedC. perfringensvegetative cells sporulate in the intestinal tract and produce an enterotoxin (CPE) that is responsible for the symptoms of acute food poisoning. Studies ofBacillus subtilishave shown that gene expression during sporulation is compartmentalized, with different genes expressed in the mother cell and the forespore. The cell-specific RNA polymerase sigma factors σF, σE, σG, and σKcoordinate much of the developmental process. TheC. perfringens cpegene, encoding CPE, is transcribed from three promoters, where P1 was proposed to be σKdependent, while P2 and P3 were proposed to be σEdependent based on consensus promoter recognition sequences. In this study, mutations were introduced into thesigEandsigKgenes ofC. perfringens. With thesigEandsigKmutants,gusAfusion assays indicated that there was no expression ofcpein either mutant. Results fromgusAfusion assays and immunoblotting experiments indicate that σE-associated RNA polymerase and σK-associated RNA polymerase coregulate each other's expression. Transcription and translation of thespoIIIDgene inC. perfringenswere not affected by mutations insigEandsigK, which differs fromB. subtilis, in whichspoIIIDtranscription requires σE-associated RNA polymerase. The results presented here show that the regulation of developmental events in the mother cell compartment ofC. perfringensis not the same as that inB. subtilisandClostridium acetobutylicum.
The unbearable lightness of diagnostic testing: time to contain inappropriate test ordering
Authors: Schattner A 
Published: February 2009

Abstract
The numbers of tests, imaging and diagnostic procedures ordered by doctors in primary care and hospital settings alike are rising. According to established guidelines, many of these tests may be unnecessary. Various non-clinical factors often underlie test ordering, and multiple prevalent problems associated with tests and their interpretation are often under-appreciated. These include the significant potential for cascades of further testing and patient harm. Multifaceted strategies may improve test-ordering behaviour. Brief reconsideration of several points by the clinician before ordering the test is advisable.
Looking at the Sky: On Nature and Contemplation
Authors: Baracchi Claudia 
Published: February 2009

AbstractThe essay focuses on human self-understanding as it arises from out of the experience of nature—the experience of a relatedness to nature that is at once a belonging in nature. At stake, then, is not a conceptual approach to the question of nature but rather the emergence of the human within the embrace of what presents itself as a mystery irreducible to the human, inhuman in the sense of other-than-human.The experience of nature “hiding itself” (as Heraclitus said) gave rise to the longing for mastery (e.g., the rationalistic-scientific project) as well as to a celebration of the mystery in its wonder and beauty. The juxtaposition of Giordano Bruno's cosmological vision and Renaissance painting (Tiziano Vecellio, Raphaël, and Leonardo da Vinci) illuminates this latter perspective, disclosing mystery not so much as that which would lie beyond appearances, but as that which inhabits appearances and in them becomes manifest as such.
What Is Living and What Is Dead in Attention?
Authors: Marder Michael 
Published: February 2009

AbstractThe goal of this article is to outline a triangular nexus between life, death, and attention. Not only does the act of attending animate or enliven consciousness in the passage from inactional and indeterminate potentiality to the actional determination of a noema but it also coincides with intentionality, itself the form of life proper to consciousness. Upon outlining the “enlivening” element in attention and the overlap between attention and psychic life as such, I will discuss its deadening aspects understood both in terms of the petrifaction resulting from a fixed, attentive, captivated gaze and, more positively, in terms of the potentiality of the inactional mode, in which consciousness lies dormant.
Dead Transcendence: Blanchot, Heidegger, and the Reverse of Language
Authors: Allen William S. 
Published: February 2009

AbstractIn this essay I will examine the development of the notion of transcendence in Blanchot's early critical writings. Doing so indicates the radical way that Blanchot reconfigures this central ontological and theological term by way of his readings of the literary use of language. In turn this exposes the essential relation between finitude and literature, something which the second part of the essay will examine by way of Heidegger's study of the myth of Er.
Religion, Theology, and Philosophy on the Way to Being and Time: Heidegger, the Hermeneutical, the Factical, and the Historical with Respect to Dilthey and Early Christianity
Authors: Fehér István M. 
Published: February 2009

AbstractMy aim in the present paper is to show the significance of Heidegger's phenomenology of religion as an important step on his way to his magnum opus. First, I wish to exhibit traits characteristic of Heidegger's path of thinking in terms of his confrontation with phenomenology, historicism, hermeneutics, and Lebensphilosophie. I will then argue, in a second step, that it was with an eye to, and drawing upon, his previous understanding of religion and religious life, as well as of the relation between faith and theology, that Heidegger was to conceive of philosophy and its relation to human existence in Being and Time. Both theology and philosophy offer a conceptual elaboration of something previously enacted or lived (a sort of having-been) and, in doing so, are at the same time meant to refer back to and reinforce what they grow out of—faith or factical life.
Health, Wealth or Wisdom? Religion and the Paradox of Prosperity
Authors: Graham Elaine 
Published: February 2009

AbstractThe so-called 'happiness hypothesis', associated with the work of the economist Richard Layard, has attracted much public debate over recent years. Its main contention is that despite rising levels of material prosperity in the west, incidence of recorded happiness and greater quality of life has not increased accordingly. In considering the major contributory factors to happiness and well-being, however, Layard is not alone in identifying the significance of religious values and participation in religion for positive and enduring levels of happiness. In response, this article critiques some of the evidence correlating religion and well-being, as well as considering the broader and much more vexed question of how far public policy is capable of incorporating questions of belief and value into its indicators of happiness and the good life. Drawing on traditions of virtue ethics as the cultivation of 'the life well-lived', I ask whether specifically Christian accounts of human flourishing and the good life still have any bearing in the wider public domain, and what 'rules of engagement' might need to be articulated in any dialogue between Christian values and the discourse of theology and a pluralist society.
Welfare, Church and the Pursuit of Justice in the Land of the Long White Cloud
Authors: Dancer Anthony 
Published: February 2009

AbstractThe relationship between Christianity and social development in New Zealand has been an historically complex one. Many of the early settlers to these islands came to escape a life of poverty in their mother country. Yet wherever there is wealth, there is poverty social problems, and they cast a long shadow over the promised land for the early colonizers and the indigenous Maori. The emergence of the welfare state in the 1930s paved the way for significant social transformation. It was understood by some to express 'applied Christianity'. With the comparatively recent demise of the Welfare State in New Zealand at the hands of neo-liberalism it is reasonable to consider whether this can equally be understood to indicate the demise of the Christianity's social import. Yet an appreciation of the church's predominantly informal social involvement throughout the history of these islands provides both a helpful interpretative key to the past and the future. Aotearoa New Zealand history may be one signifier that the priority for the pursuit of justice is to be found primarily at the margins amidst the informality of the ordinary, and far less at the centre of formality, systems and political institutions, and that the role of intentional Christian community in this might be as significant to the identity of the church as it is to the state.