bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extraintestinal
Escherichia coli
Carrying Virulence Genes in Coastal Marine Sediments
Authors: Luna G. M. , Vignaroli C. , Rinaldi C. , Pusceddu A. , Nicoletti L. , Gabellini M. , Danovaro R. , Biavasco F. 
Published: July 2010

ABSTRACT

Despite the recognized potential of long-term survival or even growth of fecal indicators bacteria (FIB) in marine sediments, this compartment is largely ignored by health protection authorities. We conducted a large-scale study over approximately 50 km of the Marche coasts (Adriatic Sea) at depths ranging from 2 to 5 m. Total and fecal coliforms (FC) were counted by culture-based methods.
Escherichia coli
was also quantified using fluorescence
in situ
hybridization targeting specific 16S rRNA sequences, which yielded significantly higher abundances than culture-based methods, suggesting the potential importance of viable but nonculturable
E. coli
cells. Fecal coliforms displayed high abundances at most sites and showed a prevalence of
E. coli.
FC isolates (
n
= 113) were identified by API 20E, additional biochemical tests, and internal transcribed spacer-PCR.
E. coli
strains, representing 96% of isolates, were then characterized for genomic relatedness and phylogenetic group (A, B1, B2, and D) of origin by randomly amplified polymorphic DNA and multiplex-PCR. The results indicated that
E. coli
displayed a wide genotypic diversity, also among isolates from the same station, and that 44 of the 109
E. coli
isolates belonged to groups B2 and D. Further characterization of B2 and D isolates for the presence of 11 virulence factor genes (
pap
,
sfa/foc
,
afa
,
eaeA
,
ibeA
,
traT
,
hlyA
,
stx
1
,
stx
2
,
aer
, and
fyuA
) showed that 90% of B2 and 65% of D isolates were positive for at least one of these. Most of the variance of both
E. coli
abundance and assemblage composition (>62%) was explained by a combination of physical-chemical and trophic variables. These findings indicate that coastal sediments could represent a potential reservoir for commensal and pathogenic
E. coli
and that
E. coli
distribution in marine coastal sediments largely depends upon the physical and trophic status of the sediment. We conclude that future sampling designs aimed at monitoring the microbiological quality of marine coastal areas should not further neglect the analysis of the sediment and that monitoring of these environments can be improved by including molecular methods as a complement of culture-based techniques.
Central Role of Manganese in Regulation of Stress Responses, Physiology, and Metabolism in
Streptococcus pneumoniae
Authors: Ogunniyi Abiodun D. , Mahdi Layla K. , Jennings Michael P. , McEwan Alastair G. , McDevitt Christopher A. , Van der Hoek Mark B. , Bagley Christopher J. , Hoffmann Peter , Gould Katherine A. , Paton James C. 
Published: July 2010

ABSTRACT

The importance of Mn
2+
for pneumococcal physiology and virulence has been studied extensively. However, the specific cellular role(s) for which Mn
2+
is required are yet to be fully elucidated. Here, we analyzed the effect of Mn
2+
limitation on the transcriptome and proteome of
Streptococcus pneumoniae
D39. This was carried out by comparing a deletion mutant lacking the solute binding protein of the high-affinity Mn
2+
transporter, pneumococcal surface antigen A (PsaA), with its isogenic wild-type counterpart. We provide clear evidence for the Mn
2+
-dependent regulation of the expression of oxidative-stress-response enzymes SpxB and Mn
2+
-SodA and virulence-associated genes
pcpA
and
prtA
. We also demonstrate the upregulation of at least one oxidative- and nitrosative-stress-response gene cluster, comprising
adhC
,
nmlR
, and
czcD
, in response to Mn
2+
stress. A significant increase in 6-phosphogluconate dehydrogenase activity in the
psaA
mutant grown under Mn
2+
-replete conditions and upregulation of an oligopeptide ABC permease (AppDCBA) were also observed. Together, the results of transcriptomic and proteomic analyses provided evidence for Mn
2+
having a central role in activating or stimulating enzymes involved in central carbon and general metabolism. Our results also highlight the importance of high-affinity Mn
2+
transport by PsaA in pneumococcal competence, physiology, and metabolism and elucidate mechanisms underlying the response to Mn
2+
stress.
Analysis of the Role of the Type III Effector Inventory ofPseudomonas syringaepv. phaseolicola 1448a in Interaction with the Plant
Authors: Zumaquero Adela , Macho Alberto P. , Rufián José S. , Beuzón Carmen R. 
Published: July 2010

ABSTRACTInPseudomonas syringae, the type III secretion system (T3SS) is essential for disease in compatible hosts and for eliciting the hypersensitive response in incompatible hosts.P. syringaepathovars secrete a variable number of type III effectors that form their secretomes. The secretome ofPseudomonas syringaepv. phaseolicola 1448a (Pph1448a) currently includes 22 experimentally validated effectors, one HrpL-regulated candidate for which translocation results have been inconsistent, two translocated candidates for whichin plantaexpression has not been established, one bioinformatically identified candidate, and six candidates that have been experimentally discarded. We analyzed the translocation and/or expression of these and other candidates to complete thePph1448a effector inventory, bringing this inventory to 27 bona fide effectors, including a new one that does not belong to any of the previously described effector families. We developed a simple process for rapidly making single and double knockout mutants and apply it to the generation of an effector mutant collection that includes single knockouts for the majority of thePph1448a effector inventory. We also generated two double mutant strains containing effectors with potentially redundant functions and analyzed the virulence of the single and double mutant strains as well as strains expressing each of the effectors from a plasmid. We demonstrate that AvrB4-1 and AvrB4-2, as well as HopW1-1 and HopW1-2, are fully redundant and contribute to virulence in bean plants, thus validating this approach for dissecting the contribution of thePph1448a type III effector inventory to virulence. We also analyzed the effect that the expression of these four effectors fromPseudomonas syringaepv. tomato DC3000 (PtoDC3000) has during its interaction withArabidopsis thaliana, establishing that AvrB4-1, but not the others, determines a restriction of bacterial growth that takes place mostly independently of the salicylic acid (SA)-signaling pathway.
CrfA, a Small Noncoding RNA Regulator of Adaptation to Carbon Starvation in
Caulobacter crescentus
Authors: Landt Stephen G. , Lesley Joseph A. , Britos Leticia , Shapiro Lucy 
Published: July 2010

ABSTRACT

Small noncoding regulatory RNAs (sRNAs) play a key role in the posttranscriptional regulation of many bacterial genes. The genome of
Caulobacter crescentus
encodes at least 31 sRNAs, and 27 of these sRNAs are of unknown function. An overexpression screen for sRNA-induced growth inhibition along with sequence conservation in a related
Caulobacter
species led to the identification of a novel sRNA, CrfA, that is specifically induced upon carbon starvation. Twenty-seven genes were found to be strongly activated by CrfA accumulation. One-third of these target genes encode putative TonB-dependent receptors, suggesting CrfA plays a role in the surface modification of
C. crescentus
, facilitating the uptake of nutrients during periods of carbon starvation. The mechanism of CrfA-mediated gene activation was investigated for one of the genes predicted to encode a TonB-dependent receptor, CC3461. CrfA functions to stabilize the CC3461 transcript. Complementarity between a region of CrfA and the terminal region of the CC3461 5′-untranslated region (5′-UTR) and also the behavior of a deletion of this region and a site-specific base substitution and a 3-base deletion in the CrfA complementary sequence suggest that CrfA binds to a stem-loop structure upstream of the CC3461 Shine-Dalgarno sequence and stabilizes the transcript.
Whole Genome Sequences of Two
Xylella fastidiosa
Strains (M12 and M23) Causing Almond Leaf Scorch Disease in California
Authors: Chen J. , Xie G. , Han S. , Chertkov O. , Sims D. , Civerolo E. L. 
Published: July 2010

ABSTRACT

Xylella fastidiosa
is a Gram-negative plant-pathogenic bacterium causing many economically important diseases, including almond leaf scorch disease (ALSD) in California. Genome information greatly facilitates research on this nutritionally fastidious organism. Here we report the complete genome sequences of two ALSD strains of this bacterium, M12 and M23.
Complete Genome Sequence of
Beijerinckia indica
subsp.
indica
Authors: Tamas Ivica , Dedysh Svetlana N. , Liesack Werner , Stott Matthew B. , Alam Maqsudul , Murrell J. Colin , Dunfield Peter F. 
Published: July 2010

ABSTRACT

Beijerinckia indica
subsp.
indica
is an aerobic, acidophilic, exopolysaccharide-producing, N
2
-fixing soil bacterium. It is a generalist chemoorganotroph that is phylogenetically closely related to facultative and obligate methanotrophs of the genera
Methylocella
and
Methylocapsa
. Here we report the full genome sequence of this bacterium.
MiRNA-196 Is Upregulated in Glioblastoma But Not in Anaplastic Astrocytoma and Has Prognostic Significance
Authors: Guan Yanlei , Mizoguchi Masahiro , Yoshimoto Koji , Hata Nobuhiro , Shono Tadahisa , Suzuki Satoshi O. , Araki Yukie , Kuga Daisuke , Nakamizo Akira , Amano Toshiyuki , Ma Xinlong , Hayashi Kenshi , Sasaki Tomio 
Published: July 2010

Abstract
Purpose: MicroRNAs (miRNA) are short noncoding RNAs that can play critical roles in diverse biological processes. They are implicated in tumorigenesis and function both as tumor suppressors and as oncogenes. The clinical significance of miRNA expression profiles in malignant gliomas remains unclear.
Experimental Design: In this study, we examined the expression levels of 365 mature human miRNAs in 12 malignant gliomas, including 8 glioblastomas and 4 anaplastic astrocytomas, using TaqMan real-time quantitative PCR arrays. A validation study was done to corroborate a subset of the results, including expression levels of miR-196a, -196b, -21, and -15b, by analyzing 92 malignant gliomas by conventional real-time PCR. We modeled the relationship between the expression levels of these miRNAs and the survival rate of 39 glioblastoma patients by Kaplan-Meier method and multivariate analysis.
Results: Expression profiles in glioblastomas and anaplastic astrocytomas suggested that 16 miRNAs were candidate markers associated with the malignant progression of gliomas. Among them, miR-196a showed the most significant difference (P = 0.0038), with miR-196b also having a high significance (P = 0.0371). Both miRNAs showed increased expression levels in glioblastomas relative to both anaplastic astrocytomas and normal brains in the validation study. Furthermore, patients with high miR-196 expression levels showed significantly poorer survival by the Kaplan-Meier method (P = 0.0073). Multivariate analysis showed that miR-196 expression levels were an independent predictor of overall survival in all 39 glioblastoma patients (P = 0.021; hazard ratio, 2.81).
Conclusions: Our results suggest that miR-196 may play a role in the malignant progression of gliomas and may be a prognostic predictor in glioblastomas. Clin Cancer Res; 16(16); 4289–97. ©2010 AACR.
Diminished Sensitivity of Chronic Lymphocytic Leukemia Cells to ABT-737 and ABT-263 Due to Albumin Binding in Blood
Authors: Vogler Meike , Furdas Silviya D. , Jung Manfred , Kuwana Tomomi , Dyer Martin J.S. , Cohen Gerald M. 
Published: July 2010

AbstractPurpose: Inhibition of the antiapoptotic BCL2 family is one of the most promising areas of anticancer drug development. However, ABT-737, a specific BCL2 inhibitor, is neither orally bioavailable nor metabolically stable. To overcome these problems, the structurally related molecule ABT-263 was synthesized and recently entered clinical trials in hematologic malignancies, including chronic lymphocytic leukemia (CLL). Almost all laboratory studies have been carried out with ABT-737 rather than ABT-263, the drug being used in clinical trials. Currently there are no published data on the comparative effects of these inhibitors. To gain insight into the potential value or limitations of ABT-263 in the clinic, we assessed its ability to induce apoptosis in clinically relevant cellular models of CLL.Experimental Design: The susceptibility of freshly isolated primary CLL cells to these inhibitors was compared in standard culture conditions and in conditions that more closely mimic in vivo conditions in a whole blood assay system.Results: ABT-737 was more potent than ABT-263 at inducing apoptosis in CLL cells. In whole blood, ∼100-fold higher concentrations of both drugs were required to induce apoptosis. We found that ABT-263 was highly bound by albumin and that an increased albumin binding of ABT-263 as compared with ABT-737 accounted for the differential sensitivity of CLL cells.Conclusions: Our data indicate that the exquisite in vitro sensitivity of CLL cells to BCL2 inhibitors may be lost in vivo due to high cell densities and the albumin binding of ABT-263. Modification of ABT-263 may yield a BCL2 inhibitor with greater bioavailability and more favorable pharmacokinetics. Clin Cancer Res; 16(16); 4217–25. ©2010 AACR.
The Law and Role of Contracts in The Muscovite Tsardom
Authors: Weickhardt George 
Published: July 2010

AbstractMuscovite law, which was advanced and well-articulated in many areas, developed no coherent theory of contracts. Even the Law Code of 1649 contains few provisions on contracts and virtually none on the sale of goods or free (non-serf, non-slave) labor. The Muscovite tsardom did, however, adopt some simple provisions that served to reduce the possibility of disputes about whether there was a contract and what its terms were, such as requiring all important contracts to be in writing. Muscovite law also made it clear that consent to a contract had to be freely given, without duress or fraud. The article attempts to explain the lack of any law regulating the sale of goods and free labor.
How Muscovy Governed: Seventeenth-Century Russian Central Administration
Authors: Brown Peter 
Published: July 2010

AbstractThe modern Russian state's first governmental administration, the chancellery system (prikaznaia sistema), guided Muscovy from the 1470s to the 1710s. A handful of state secretaries (d'iaki), subordinate clerks (pod'iachie), and several nascent bureaus matured into over ten permanent, well-codified bodies with decision-making boards, archives, professional hierarchies, and merit-based hiring and promotion by the 1550s. By the 1670s there were 60 chancelleries, and their Moscow staffs by the 1690s had increased to about 3,000, from the highest civil ranks (boyars and okol'niche) through the professional administrative ranks: duma state secretaries (dumnye d'iaki), the state secretaries, and clerks. The chancelleries (prikazy) discharged an array of state, royal court, and church functions, but military concerns were foremost. An arresting internal complexity typified the larger, more important chancelleries, like the Military and Foreign Affairs Chancelleries, divided into sub-units. The chancellery system was entirely homegrown, owning nothing to Roman Imperial and Medieval Latin traditions. The Russians borrowed some paperwork (scrolls) and zealous attention to that from the Mongols, as they did Byzantine and Lithuanian legal elements. Documentary language was a vernacular, Middle Russian register, with burgeoning specialized vocabulary and phraseology. Strict oaths guided conduct, though judicial bureau personnel were notorious for bribe-taking. Foreign travel accounts commented on the obsequiousness of documentary format wherein petitioners referred to themselves as “slaves” (kholopy) and used first-name diminutives. Seventeenth-century Muscovite centralized administration acquired Weber's hallmark features of a bureaucracy; the prikazy guided Muscovy and acculturated its subjects, from tsar to peasant, into its rationale, mechanisms, and operations. Weathering major social traumas and challenges, such as Ivan the Terrible's Oprichnina, the Time of Troubles, the Thirteen Years' War, and the 1682 Musketeers' Uprising, the chancelleries provided the bureaucratic continuity for the Imperial Russian and Soviet states.
"Revolutionary Church" or "Church Revolution"? Some Recent Studies on the History of the Russian Orthodox Church in 1917
Authors: Leont'eva Tatiana 
Published: July 2010

AbstractContemporary Russian scholars usually try to abstain from any criticism to Russian Orthodox Church' actions in past and present. Meanwhile a situation in 1917 was very confused: the Holy Synod supported the abdication of its formal head – the Tsar. So historians discussed: what it was – "revolutionary Church" or "revolution inside Church"? One of them insists that bishops become "liberals", another argue that they operated accordingly old religious canons. In reality the full scale revolution inside Church took place: believers tried to overthrow the "reactionary" and "counterrevolutionary" bishops and priests as "serfs of old regime", rank and file clergy supported them.
Memory of the Revolution as a trauma inflicted on contemporary social conscience in Russia
Authors:   Prokhorov
Published: July 2010

AbstractMany painful ideological problems existing in contemporary Russia are determined by the inadequacy of perception of the country's revolutionary past. This misperception stems from both the consequences of the decades-long mythologization of the October Revolution and its leaders and from the more recent attempts to get rid of the dependence on Bolshevik propaganda. Contemporary historic memory in Russia is beset with one major contradiction: the desire to part with the myth, and the inability to do so. Although, traditionally, images of the past are usually adapted in order to suit the needs of modernity, this task has become much easier in contemporary society with its powerful mass media fitted with visual networks. Historic memory, previously shaped by legends, folklore, rites and rituals, now comes under relentless fire from the dilettantes pretending to have discovered some "true" vision of the past, and illustrating this vision by incongruous video footage. As a result, images of the past inevitably lose their former edifying role and become a means of inculcation by propagating political and moral stereotypes advantageous to the authorities. The wave of discussions on the Russian Revolution, which rose in connection with its current anniversary, was yet another indication that today's ideologists, with their inept denunciations, are only aggravating the trauma inflicted on social conscience.
The oldest fossil strepsipteran larva (Insecta: Strepsiptera) from the Geisel Valley, Germany (Eocene)
Authors: Pohl Hans 
Published: July 2010

AbstractThe only known fossil strepsipteran first-instar larva from Eocene brown coal is re-examined and redescribed, and photographs together with a detailed interpretative illustration are presented. The original preparation of the minute larva in a 1-mm-thick piece of brown coal of the Geisel valley precludes a detailed examination. After remounting, additional details of the larva are recognisable. A cladistic analysis of 60 morphological characters of 24 recent first-instar strepsipteran larva and the fossil larva confirm the placement in Strepsiptera and in Stylopidia with good support. A placement in Myrmecolacidae or even in the recent genus Stichotrema is rejected. Thus, Pseudococcites Haupt, 1950 comb.rev. is re-established and †Pseudococcites eocaenicus is moved to Stylopidia as incertae sedis.
A taxonomic review of Pelidnoptera Rondani (Diptera: Sciomyzoidea), with discovery of a related new genus and species from Asia
Authors: Ghorpadé Kumar , Knutson Lloyd , Sueyoshi Masahiro 
Published: July 2010

AbstractThe genus Pelidnoptera Rondani is taxonomically reviewed based on examination of the type series. Pelidnoptera triangularis, sp.n. from Japan, the Russian Far East and Nepal, and Akebono vernalis, gen. & sp.n. from Japan are described and illustrated. The lectotype of P. leptiformis (Schiner) is designated here based on the examination of syntypes in the Naturhistorisches Museum, Wien.
Public Consultation and GMO Policy—A Very British Experiment
Authors: Macrory Richard 
Published: July 2010

AbstractThis article describes the UK experience with public consultation procedures in the field of environmental policy and law. It analyses the different challenges for such procedures, particularly on issues where there seems to be a conflict between scientific information on environmental or health risks and deeply held public values. As a conscious departure from established practices GM Nation tried to engage the public in a new form of debate about the risks and benefits associated with GM agriculture. The article describes how this exercise was conducted, how it actually worked out in practice and also discusses some of the criticisms raised and problems encountered.
Moving Towards Phase III—Key Elements of the Review of the EU Emissions Trading Scheme
Authors: Marr Simon , Enzmann Johannes 
Published: July 2010

AbstractWith the Climate and Energy Package the European Commission has also published its draft for a revised EU Emissions Trading Scheme from 2013 onwards. The draft revision of the EU ETS serves as the EU's main pillar to fight climate change in that it requires a reduction of mainly CO2 of 21% below 2005 figures for the EU's major emissions sources in the energy and industry sectors. In addition, most notably the EU is proposing an EU wide cap and harmonised allocation rules, in order to exploit the full potential of emissions trading making national allocation plans ghosts of the past. The revised EU ETS gives investors into CDM projects the necessary long time planning security for investments into projects. At the same time it sends out a strong signal to the international negotiations for a post-2012 climate agreement in that it allows the use of more project based generated credits within the EU ETS once an ambitious post 2012 agreement is concluded.
The European Carbon Market in Action: Lessons from the First Trading Period
Authors: Ellerman Denny , Convery Frank , de Perthuis Christian 
Published: July 2010

AbstractThrough its Emissions Trading Scheme (EU ETS), the European Union is leading the world's first effort to mobilize market forces to tackle global climate change. This article, examines how the EU ETS has performed thus far, at the conclusion of the scheme's first trading phase (2005–2007). Insights drawn from this analysis may inform not only the scheme's future operation, but also the establishment of greenhouse gas trading programs outside Europe. This interim analysis finds that Phase I of the EU ETS (2005–2007) has successfully established a carbon price for significant segments of economic activity in Europe, as well as the necessary trading infrastructure and experience; that the price on carbon has so far had limited impact on the industrial competitiveness of European industry; that it has provided an important stimulus to greenhouse gas emission reductions outside of Europe, primarily through the Clean Development Mechanism; and that the EU ETS provides useful lessons for other countries seeking to limit GHG emissions and for future global climate negotiations.