bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Compounds with Bioactivity against the Nematode
Caenorhabditis elegans
by a Screen Based on the Functional Genomics of the Marine Bacterium
Pseudoalteromonas tunicata
D2
Authors: Ballestriero Francesco , Thomas Torsten , Burke Catherine , Egan Suhelen , Kjelleberg Staffan 
Published: July 2010

ABSTRACT

Marine bacteria are a rich, yet underexplored, resource of compounds with inhibitory bioactivity against a range of eukaryotic target organisms. Identification of those inhibitors, however, requires a culturable or genetically tractable producer strain, a prerequisite that is not often fulfilled. This study describes a novel functional genomic screen that is based on expression of inhibitors in a heterogeneous recombinant host (i.e.,
Escherichia coli
). Functional libraries were screened by selective grazing by the nematode
Caenorhabditis elegans
, in a simple, rapid, high-throughput manner. We applied our approach to discover inhibitors of
C. elegans
produced by the marine bacterium
Pseudoalteromonas tunicata
D2, a model organism for exploring a range of antagonistic activities between bacteria and eukaryotes and a known producer of several toxic compounds. Expression of
P. tunicata
DNA in
E. coli
and grazing selection by the nematode
Caenorhabditis elegans
identified two clones, with slow- and fast-killing modes of action. Genomic analysis of the slow-killing clone revealed that the activity was due to a small molecule, tambjamine, while the fast-killing activity involved a gene encoding for a novel protein. Microscopic analysis showed substantial colonization of the intestinal lumen, or rapid death of the nematode without colonization, for the two activities, respectively. The novel functional genomic screen presented here therefore detects new eukaryotic inhibitors with different chemical structures, kinetics, and predicted modes of actions.
Flavin Mononucleotide-Based Fluorescent Reporter Proteins Outperform Green Fluorescent Protein-Like Proteins as Quantitative
In Vivo
Real-Time Reporters
Authors: Drepper Thomas , Huber Robert , Heck Achim , Circolone Franco , Hillmer Anne-Kathrin , Büchs Jochen , Jaeger Karl-Erich 
Published: July 2010

ABSTRACT

Fluorescent proteins of the green fluorescent protein (GFP) family are commonly used as reporter proteins for quantitative analysis of complex biological processes in living microorganisms. Here we demonstrate that the fluorescence signal intensity of GFP-like proteins is affected under oxygen limitation and therefore does not reflect the amount of reporter protein in
Escherichia coli
batch cultures. Instead, flavin mononucleotide (FMN)-binding fluorescent proteins (FbFPs) are suitable for quantitative real-time
in vivo
assays under these conditions.
Allelic Exchange in
Actinomyces oris
with mCherry Fluorescence Counterselection
Authors: Wu Chenggang , Ton-That Hung 
Published: July 2010

ABSTRACT

Described here is a method for facile generation of markerless gene deletion mutants of
Actinomyces oris
. Homologous integration of a nonreplicative vector carrying a gene exchange cassette into the bacterial chromosome was selected for by using mCherry fluorescence and resistance to kanamycin. Completion of allelic replacement was counterselected for by using loss of fluorescence.
Suitability of Quantitative Real-Time PCR To Estimate the Biomass of Fungal Root Endophytes
Authors: Tellenbach Christoph , Grünig Christoph R. , Sieber Thomas N. 
Published: July 2010

ABSTRACT

A nested single-copy locus-based quantitative PCR (qPCR) assay and a multicopy locus-based qPCR assay were developed to estimate endophytic biomass of fungal root symbionts belonging to the
Phialocephala fortinii
sensu lato-
Acephala applanata
species complex (PAC). Both assays were suitable for estimation of endophytic biomass, but the nested assay was more sensitive and specific for PAC. For mycelia grown in liquid cultures, the correlation between dry weight and DNA amount was strong and statistically significant for all three examined strains, allowing accurate prediction of fungal biomass by qPCR. For mycelia colonizing cellophane or Norway spruce roots, correlation between biomass estimated by qPCR and microscopy was strain dependent and was affected by the abundance of microsclerotia. Fungal biomass estimated by qPCR and microscopy correlated well for one strain with poor microsclerotia formation but not for two strains with high microsclerotia formation. The accuracy of qPCR measurement is constrained by the variability of cell volumes, while the accuracy of microscopy can be hampered by overlapping fungal structures and lack of specificity for PAC. Nevertheless, qPCR is preferable because it is highly specific for PAC and less time-consuming than quantification by microscopy. There is currently no better method than qPCR-based quantification using calibration curves obtained from pure mycelia to predict PAC biomass in substrates. In this study, the DNA amount of
A. applanata
extracted from 15 mm of Norway spruce fine root segments (mean diameter, 610 μm) varied between 0.3 and 45.5 ng, which corresponds to a PAC biomass of 5.1 ± 4.5 μg (estimate ± 95% prediction interval) and 418 ± 264 μg.
Display of Recombinant Proteins on
Bacillus subtilis
Spores, Using a Coat-Associated Enzyme as the Carrier
Authors: Potot Sébastien , Serra Cláudia R. , Henriques Adriano O. , Schyns Ghislain 
Published: July 2010

ABSTRACT

The display of proteins such as feed enzymes at the surface of bacterial spore systems has a great potential use for animal feed. Feed enzymes increase the digestibility of nutrients, leading to greater efficiency in the manufacturing of animal products and minimizing the environmental impact of increased animal production. To deliver their full potential in the gut, feed enzymes must survive the harsh conditions of the feed preparation and the gastrointestinal tract. The well-documented resistance of spores to harsh environments, together with the ability to use proteins that compose the spore as carriers for the display of passenger proteins, suggests that spores could be used as innovative tools to improve the formulation of bioactive molecules. Although some successful examples have been reported, in which abundant structural proteins of the
Bacillus subtilis
spore outer-coat layer were used as carriers for the display of recombinant proteins, only one convincing example resulted in the display of functional enzymes. In addition, no examples are available about the use of an inner-coat protein for the display of an active passenger enzyme. In our study, we show that the inner-coat oxalate decarboxylase (OxdD) can expose an endogenous phytase, a commonly used feed enzyme for monogastric animals, in an active form at the spore surface. Importantly, despite the higher abundance of CotG outer-coat protein, an OxdD-Phy fusion was more represented at the spore surface. The potential of OxdD as a carrier protein is further documented through the spore display of a bioactive heterologous passenger, the tetrameric β-glucuronidase enzyme from
Escherichia coli
.
Two Internal Origins of Replication in
Streptomyces
Linear Plasmid pFRL1
Authors: Zhang Ran , Peng Shiyuan , Qin Zhongjun 
Published: July 2010

ABSTRACT

Previous reports showed that
Streptomyces
linear plasmids usually contain one internal replication locus. Here, we identified two new replication loci on pFRL1, one (
rep1A-ncs1
) next to a telomere and another (
rep2A-ncs2
) ∼10 kb from it. The
rep1A-ncs1
locus was able to direct replication independently in both linear and circular modes, whereas
rep2A-ncs2
required an additional locus,
rlrA-rorA
, in order to direct propagation in linear mode. Rep1A protein bound to
ncs1 in vitro
. By quantitative reverse transcription-PCR and Northern hybridization, we showed that transcription of
rep1A
and
rep2A
varied during development and that each dominated at different time points. pFRL1-derived linear plasmids were inherited through spores more stably than circular plasmids and were more stable with pSLA2 telomeres than with pFRL1 telomeres in
Streptomyces lividans
.
Analysis of RuvABC and RecG Involvement in the
Escherichia coli
Response to the Covalent Topoisomerase-DNA Complex
Authors: Sutherland Jeanette H. , Tse-Dinh Yuk-Ching 
Published: July 2010

ABSTRACT

Topoisomerases form a covalent enzyme-DNA intermediate after initial DNA cleavage. Trapping of the cleavage complex formed by type IIA topoisomerases initiates the bactericidal action of fluoroquinolones. It should be possible also to identify novel antibacterial lead compounds that act with a similar mechanism on type IA bacterial topoisomerases. The cellular response and repair pathways for trapped topoisomerase complexes remain to be fully elucidated. The RuvAB and RecG proteins could play a role in the conversion of the initial protein-DNA complex to double-strand breaks and also in the resolution of the Holliday junction during homologous recombination.
Escherichia coli
strains with
ruvA
and
recG
mutations are found to have increased sensitivity to low levels of norfloxacin treatment, but the mutations had more pronounced effects on survival following the accumulation of covalent complexes formed by mutant topoisomerase I defective in DNA religation. Covalent topoisomerase I and DNA gyrase complexes are converted into double-strand breaks for SOS induction by the RecBCD pathway. SOS induction following topoisomerase I complex accumulation is significantly lower in the
ruvA
and
recG
mutants than in the wild-type background, suggesting that RuvAB and RecG may play a role in converting the initial single-strand DNA-protein cleavage complex into a double-strand break prior to repair by homologous recombination. The use of a
ruvB
mutant proficient in homologous recombination but not in replication fork reversal demonstrated that the replication fork reversal function of RuvAB is required for SOS induction by the covalent complex formed by topoisomerase I.
The Gene
ssl3076
Encodes a Protein Mediating the Salt-Induced Expression of
ggpS
for the Biosynthesis of the Compatible Solute Glucosylglycerol in
Synechocystis
sp. Strain PCC 6803
Authors: Klähn Stephan , Höhne Antje , Simon Elke , Hagemann Martin 
Published: July 2010

ABSTRACT

Acclimation to high salt concentrations involves concerted changes in gene expression. For the majority of salt-regulated genes, the mechanism underlying the induction process is not known. The gene
ggpS
(
sll1566
), which encodes the glucosylglycerol-phosphate synthase responsible for the synthesis of the compatible solute glucosylglycerol (GG), is specifically induced by salt in the cyanobacterial model strain
Synechocystis
sp. strain PCC 6803. To identify mechanisms mediating this salt-specific gene regulation, the
ggpS
promoter was analyzed in more detail. 5′ rapid amplification of cDNA ends (5′-RACE) experiments revealed that the adjacent open reading frame (ORF), which is annotated as unknown protein Ssl3076, overlaps with the transcriptional start site of the
ggpS
gene. Reporter gene expression analyses indicated an essential role for the intact
ssl3076
gene in the salt-regulated transcription of a
gfp
reporter gene. Promoter fragments containing a mutated
ssl3076
lost the salt regulation; similarly, a frameshift mutation in
ssl3076
resulted in a high level of
ggpS
expression under low-salt conditions, thereby establishing this small ORF, named
ggpR
, as a negative regulator of
ggpS
. Interestingly, small ORFs were also found adjacent to
ggpS
genes in the genomes of other GG-accumulating cyanobacteria. These results suggest that the GgpR protein represses
ggpS
expression under low-salt conditions, whereas in salt-shocked and salt-acclimated cells a stress-proportional
ggpS
expression occurs, leading to GG accumulation.
Genome Sequence of the Oligotrophic Marine Gammaproteobacterium HTCC2143, Isolated from the Oregon Coast
Authors: Oh Hyun-Myung , Kang Ilnam , Ferriera Steve , Giovannoni Stephen J. , Cho Jang-Cheon 
Published: July 2010

ABSTRACT

Strain HTCC2143 was isolated from Oregon Coast surface waters using dilution-to-extinction culturing. Here we present the genome of strain HTCC2143 from the BD1-7 clade of the oligotrophic marine
Gammaproteobacteria
group. The genome of HTCC2143 contains genes for carotenoid biosynthesis and proteorhodopsin and for proteins that have potential biotechnological significance: epoxide hydrolases, Baeyer-Villiger monooxygenases, and polyketide synthases.
Ophrynon (Hymenoptera: Orussidae) in California: diversity, distribution and phylogeny
Authors: Smith David , Vilhelmsen Lars , Blank Stephan 
Published: July 2010

AbstractThree new species of Ophrynon Middlekauff, 1983, O. dominiqueae, O. martini and O. patricki, are added to the only species known previously, O. levigatus Middlekauff, 1983. All species are described, illustrated and keyed. Cladistic analyses under different weighting conditions retrieved Ophrynon as monophyletic, but the topologies produced for the higher ophrynopine taxa are quite variable. The possible closest relatives of Ophrynon are Argentophrynopus Vilhelmsen & D.R. Smith, 2002 and Kulcania Benson, 1935. The internal phylogeny of Ophrynon is O. martini + (O. levigatus + (O. dominiqueae + O. patricki)). The distribution of Ophrynon is restricted to central and southern California. Supposedly, the species belong to the californo-eremial distribution type and are the result of a comparatively recent speciation process.
The implementation of the IPPC Directive from a comparative perspective and lessons for its recast (Part1 )
Authors: Bohne Eberhard 
Published: July 2010

AbstractThis essay presents a comparative empirical and legal evaluation of the implementation of the IPPC Directive in eight EU member states focusing on the integrated approach of the directive. The national transpositions left existing national administrative structures and procedures basically unchanged. Holistic integrated permitting does not occur in any of the countries under study. Explaining the findings with incremental political theory, they serve as the basis for some reflections on the planned recast of the IPPC Directive and the prospects for better regulation. This first part of the article displays the basic shortcomings of the IPPC review process (1.) the concepts of integration under the Directive (2.) and the empirical analysis of the national approaches to integrated permitting (3.1 – 3.3). The second part which will be published in the subsequent JEEPL issue explains and evaluates the findings with regard to the pending revision of the Directive.
Public Participation in the Establishment and Management of the Natura 2000 Network—Legal Framework and Administrative Practices in Selected Member States
Authors: Unnerstall Herwig 
Published: July 2010

AbstractThe Natura 2000 network is one of the most important instruments for biodiversity conservation in the EU. Public participation at its establishment and its management is an idea often promoted for improving implementation and hence conservation results. The Habitats Directive being the legal basis for the network does not pay attention to the issue of public participation—leaving the task to the Member States. This paper analyses and compares the legal basis and administrative practices of a number of Member States in regard to public participation at different stages of development of the network. It distinguishes different of types of public participation and makes a preliminary evaluation of them.
Classification, Labelling and Packaging: implementation of the Globally Harmonised System
Authors: Holmqvist Jenny , Blainey Mark 
Published: July 2010

AbstractThe European Commission has proposed a new Regulation on Classification Labelling and Packaging to replace the current Directives on classification and to implement the Globally Harmonised System for Classification and Labelling (GHS). The proposal is slowly making its way through the co-decision process and has raised a number of questions with the Council and Parliament that need to be addressed before a compromise can be found.
Including aviation in the EU Emissions Trading Scheme: prepare for take-off
Authors: Barton Jane 
Published: July 2010

AbstractSince the advent of civil aviation, air transport has experienced almost continuous growth. However this growth has also led to an increase in emissions which contribute to climate change. The exclusion of international aviation emissions from the targets under the Kyoto Protocol means that little action has been taken to address this impact. In 2005, the European Commission set out its comprehensive approach for addressing aviation's impact on climate change and in December 2006 made a legislative proposal for the inclusion of aviation in the EU Emissions Trading Scheme. Both the Council and the European Parliament broadly support the Commission's proposal but have proposed detailed amendments to the proposed legislation. This Article analyses the position adopted by each institution so far and the next steps for the adoption of the legislation.
State Aid for Environmental Protection—The Commission's new Guidelines and the new General Block Exemption Regulation
Authors: Schatz Felix , Soltész Ulrich 
Published: July 2010

AbstractWith its new guidelines on State aid for environmental protection, the European Commission seeks to further implement the roadmap for state aid reform 2005–2009 laid down in its State Aid Action Plan and thus to strive for "less and better targeted aid" in the field of environmental protection. Another important change in the legal regime applicable to State aid for environmental protection is brought about by the new General Block Exemption Regulation which, for the first time, contains several block exemption provisions for aid in this field. The new Guidelines—together with the respective provisions in the new General Block Exemption Regulation—are a remarkable step in that they entail a considerable increase in regulatory density and are thereby increasing "red tape" in this field. The new Guidelines are evidence of a more and more palpable tendency of the European Commission to use its power to examine aid for its compatibility with the common market under Article 87(3) EC to regulate in areas of law in which it is not competent to legislate. In doing so, it does not only interfere with competences of the Member States and of the other Community institutions but also risks contradiction to its own decisions in other fields.
Using Green Public Procurement (GPP) for sustainable consumption and production
Authors: Burja Alenka 
Published: July 2010

AbstractEach year public authorities spend approximately 2 trillion euros (17% of the EU's Gross Domestic Product) on purchasing a variety of goods, services and works. If they can be encouraged to purchase environmentally friendly products and services instead of conventional ones with the same functions, they can save energy, natural resources and water, reduce harmful emissions and hazardous substances, generate less waste, improve health and stimulate behavioural change towards sustainable consumption and production. In this way, public authorities will be promoting modes of production that are more environmentally friendly and stimulate the supply of green goods and services. Politically GPP has been widely recognised as a powerful voluntary instrument in most of the Member States. At EU level European Commission sets a target that, by 2010, 50% of all tendering procedures should be green, where green means compliant with endorsed common core GPP criteria. Also, GPP guidance tools have been developed, together with common criteria for 10 priority product groups, and translated into all EU languages. However, in order to make GPP a standard practice of procurement procedure, more needs to be done to develop further common GPP criteria, and to train procurement officials, and possibly to establish a product database at EU level.
Public participation in the preparation of plans and programs: some reflections on the scope of obligations under Article 7 of the Aarhus Convention
Authors: Jendrośka Jerzy 
Published: July 2010

AbstractThe article aims to present the main legal issues related to implementation of the provisions of Article 7 of the Aarhus Convention regarding public participation in the preparations of plans and programs. The analysis is presented against the background of an overview of the legal nature and scope of obligations stemming from the second pillar of the Convention. The article attempts to identify the scope of application of Article 7 and the main elements of the framework for public participation included therein. The legal analysis is based, where appropriate, on the respective opinions of the Aarhus Convention Compliance Committee. The implementation of the Aarhus Convention in EU law will be addressed in this respect in a separate article in the forthcoming issue of the journal.
Implementing EC environmental law. Compliance promotion and enforcement by the European Commission
Authors: Koller Peter , Cashman Liam 
Published: July 2010

AbstractIt is widely acknowledged that only by ensuring the correct implementation of European environmental law will it be possible to achieve the EU's ambitious environmental objectives. Implementation has therefore become a strategic priority for the European Commission in recent years. This article presents a short overview of the main challenges in implementing EC environmental law and the Commission's compliance promotion and legal enforcement activities in this field. It deals with the Commission's priority-setting for its legal enforcement actions and presents briefly recent developments and new approaches in the Commission's complaints and infringements handling.
REACH, still being developed!
Authors: Blainey Mark 
Published: July 2010

AbstractA number of changes have occurred since REACH came into force in June 2007. These changes included modifications to the Regulation itself as well as the adoption of 4 Commission Regulations on test methods, fees, the qualifications of the European Chemical Agency's board of appeal, and the rules on the organisation and procedure of that body. In addition, changes to Annexes IV, V and XI of REACH have been adopted by the Commission. The review of Annex I has been completed whilst the review of Annex XIII is still ongoing, although a change to Annex XIII is likely XIII. In addition, REACH is undergoing its first challenge in the European Court if Justice. These changes are unlikely to be the last with further reviews of REACH and the European Chemicals Agency on the horizon in 2012.
Pit Stop Poznan. An Analysis of Negotiations on the Bali Action Plan at the Stopover to Copenhagen
Authors: Ott Hermann , Rudolph Frederic , Kiyar Dagmar , Mersmann Florian , Arens Christof , Eichhorst Urda , Santarius Tilman , Sterk Wolfgang , Watanabe Rie 
Published: July 2010

AbstractThis paper analyzes the international climate negotiations that took place at the 14th Conference of the Parties to the UNFCCC (COP) and the 4th Meeting of the Parties to the Kyoto Protocol (CMP) held in Poznan, December 1–12, 2008. It works out the main issues at stake in the negotiations, contrasts divergences in interests amongst negotiating Parties, and summarizes the main results achieved in Poznan. Furthermore, it contextualizes the Poznan negotiations within the broader political and economic context, which has shaped climate policy making throughout 2008. The paper ends with an outlook on the tasks ahead in 2009, until the next COP/CMP in December 2009 in Copenhagen.