bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Fur-like protein PerR regulates two oxidative stress response related operons dpr and metQIN in Streptococcus suis
Authors: Zhang Tengfei , Ding Yi , Li Tingting , Wan Yun , Li Wei , Chen Huanchun , Zhou Rui 
Published: September 2012

Abstract

Background
Metal ions are important micronutrients in cellular metabolism, but excess ions that cause toxic reactive oxygen species are harmful to cells. In bacteria, Fur family proteins such as Fur, Zur and PerR manage the iron and zinc uptake and oxidative stress responses, respectively. The single Fur-like protein (annotated as PerR) in Streptococcus suis has been demonstrated to be involved in zinc and iron uptake in previous studies, but the reports on oxidative stress response and gene regulation are limited.

Results
In the present study, the perR gene deletion mutant ΔperR was constructed in Streptococcus suis serotype 2 strain SC-19, and the mutant strain ΔperR exhibited less sensitivity to H2O2 stress compared to the wild-type. The dpr and metQIN were found to be upregulated in the ΔperR strain compared with SC-19. Electrophoretic mobility shift assays showed that the promoters of dpr and metQIN could be bound by the PerR protein. These results suggest that dpr and metQIN are members of the PerR regulon of S. suis. dpr encodes a Dps-like peroxide resistance protein, and the dpr knockout strains (Δdpr and ΔdprΔperR) were highly sensitive to H2O2. MetQIN is a methionine transporter, and the increased utilization of methionine in the ΔperR strain indirectly affected the peroxide resistance. Using a promoter–EGFP gene fusion reporting system, we found that the PerR regulon was induced by H2O2, and the induction was modulated by metal ions. Finally, we found that the pathogenicity of the perR mutant was attenuated and easily cleared by mice.

Conclusions
These data strongly suggest that the Fur-like protein PerR directly regulates dpr and metQIN and plays a crucial role in oxidative stress response in S. suis.
Facilitating knowledge transfer: decision support tools in environment and health
Authors: Liu Hai-Ying , Bartonova Alena , Neofytou Panagiotis , Yang Aileen , Kobernus Michael J , Negrenti Emanuele , Housiadas Christos 
Published: September 2012

Abstract
The HENVINET Health and Environment Network aimed to enhance the use of scientific knowledge in environmental health for policy making. One of the goals was to identify and evaluate Decision Support Tools (DST) in current use. Special attention was paid to four “priority” health issues: asthma and allergies, cancer, neurodevelopment disorders, and endocrine disruptors.
We identified a variety of tools that are used for decision making at various levels and by various stakeholders. We developed a common framework for information acquisition about DSTs, translated this to a database structure and collected the information in an online Metadata Base (MDB).
The primary product is an open access web-based MDB currently filled with 67 DSTs, accessible through the HENVINET networking portal http://www.henvinet.eu and http://henvinet.nilu.no. Quality assurance and control of the entries and evaluation of requirements to use the DSTs were also a focus of the work.
The HENVINET DST MDB is an open product that enables the public to get basic information about the DSTs, and to search the DSTs using pre-designed attributes or free text. Registered users are able to 1) review and comment on existing DSTs; 2) evaluate each DST’s functionalities, and 3) add new DSTs, or change the entry for their own DSTs.
Assessment of the available 67 DSTs showed: 1) more than 25% of the DSTs address only one pollution source; 2) 25% of the DSTs address only one environmental stressor; 3) almost 50% of the DSTs are only applied to one disease; 4) 41% of the DSTs can only be applied to one decision making area; 5) 60% of the DSTs’ results are used only by national authority and/or municipality/urban level administration; 6) almost half of the DSTs are used only by environmental professionals and researchers. This indicates that there is a need to develop DSTs covering an increasing number of pollution sources, environmental stressors and health end points, and considering links to other ‘Driving forces-Pressures-State-Exposure-Effects-Actions’ (DPSEEA) elements. Of interest to both researchers and decision makers should be the standardization of the way DSTs are described for easier access to the knowledge, and the identification of coverage gaps.
Double-donor complex in vertically coupled quantum dots in a threading magnetic field
Authors: Manjarres-García Ramón , Escorcia-Salas Gene Elizabeth , Manjarres-Torres Javier , Mikhailov Ilia D , Sierra-Ortega José 
Published: September 2012

Abstract
We consider a model of hydrogen-like artificial molecule formed by two vertically coupled quantum dots in the shape of axially symmetrical thin layers with on-axis single donor impurity in each of them and with the magnetic field directed along the symmetry axis. We present numerical results for energies of some low-lying levels as functions of the magnetic field applied along the symmetry axis for different quantum dot heights, radii, and separations between them. The evolution of the Aharonov-Bohm oscillations of the energy levels with the increase of the separation between dots is analyzed.
Relay on-off threshold for NDF protocol with distributed orthogonal space-time block codes
Authors: Jin Dong-Sup , Jin Xianglan , No Jong-Seon , Shin Dong-Joon 
Published: September 2012

Abstract
In this article, a relay on-off threshold (ROT) based on symbol error rate is derived for the cooperative communication networks with multiple antennas, where the non-orthogonal decode-and-forward (NDF) protocol with source antenna switching and linear combining decoding are used as the relaying protocol and decoding scheme, respectively. The optimal ROT for the cases using distributed orthogonal space-time block codes is derived for high signal to noise ratio (SNR) region and also a suboptimal ROT is provided for low SNR region. Finally, the diversity order of the NDF protocol using the relay on-off scheme with the proposed ROT is derived and its performance is verified through numerical analysis.
Medicinal use of fauna by a traditional community in the Brazilian Amazonia
Authors: Barros Flávio B , Varela Susana AM , Pereira Henrique M , Vicente Luís 
Published: September 2012

AbstractBackgroundZootherapy inventories are important as they contribute to the world documentation of the prevalence, importance and diversity of the medicinal use of animals in traditional human communities. The present study aims to contribute with a more valuable example of the zootherapy practices of a traditional community in the Brazilian Amazonia – the “Riozinho do Anfrísio” Extractive Reserve, in Northern Brazil.MethodsWe used the methods of participant observation and semi-structured interviews, applied to 25 informants. We employed the combined properties of two indices to measure the medicinal importance of each cited species to the studied community, as well as their versatility in the treatment of diseases: the well known Use Value (UV) and the Medicinal Applications Value (MAV) that we developed.ResultsWe recorded 31 species of medicinal animals from six taxonomic categories, seven of which are new to science. The species are used for the treatment of 28 diseases and one species is used as an amulet against snakebites. The five species with the highest UV indices are the most popular and valued by the studied community. Their contrasting MAV indices indicate that they have different therapeutic properties: specific (used for the treatment of few diseases; low versatility) and all-purpose (several diseases; high versatility). Similarly, the most cited diseases were also those that could be treated with a larger number of animal species. Ten species are listed in the CITES appendices and 21 are present in the IUCN Red List. The knowledge about the medicinal use of the local fauna is distributed evenly among the different age groups of the informants.ConclusionsThis study shows that the local fauna represents an important medicinal resource for the inhabitants of the protected area. The combined use of the UV and MAV indices allowed identifying the species with the highest therapeutic potential. This type of information about a species may be of interest to pharmacological research, and is crucial to its conservation, since it helps signaling the species that may undergo higher hunting pressures. Data on zootherapy can also be of interesting to ecologists by contributing to indicators of local biodiversity richness.
PCR identification of culicoid biting midges (Diptera, Ceratopogonidae) of the Obsoletus complex including putative vectors of bluetongue and Schmallenberg viruses
Authors: Lehmann Kathrin , Werner Doreen , Hoffmann Bernd , Kampen Helge 
Published: September 2012

Abstract

Background
Biting midges of the Obsoletus species complex of the ceratopogonid genus Culicoides were assumed to be the major vectors of bluetongue virus (BTV) in northern and central Europe during the 2006 outbreak of bluetongue disease (BT). Most recently, field specimens of the same group of species have also been shown to be infected with the newly emerged Schmallenberg virus (SBV) in Europe. A reliable identification of the cryptic species of this group is fundamental for both understanding the epidemiology of the diseases and for targeted vector control. In the absence of classical morphological characters unambiguously identifying the species, DNA sequence-based tests have been established for the distinction of selected species in some parts of Europe. Since specificity and sensitivity of these tests have been shown to be in need of improvement, an alternative PCR assay targeting the mitochondrial cytochrome oxidase subunit I (COI) gene was developed for the identification of the three Obsoletus complex species endemic to Germany (C. obsoletus, C. scoticus, C. chiopterus) plus the isomorphic species C. dewulfi.

Methods
Biting midges of the genus Culicoides caught by UV light traps all over Germany were morphologically pre-identified to species or complex level. The COI region was amplified from their extracted DNA and sequenced. Final species assignment was done by sequence comparison to GenBank entries and to morphologically identified males. Species-specific consensus sequences were aligned and polymorphisms were utilized to design species-specific primers to PCR-identify specimens when combined with a universal primer.

Results
The newly developed multiplex PCR assay was successfully tested on genetically defined Obsoletus complex material as well as on morphologically pre-identified field material. The intended major advantage of the assay as compared to other PCR approaches, namely the production of only one single characteristic band for each species, could be realized with high specificity and sensitivity.

Conclusion
To elucidate the biological characteristics of potential vectors of disease agents, such as ecology, behaviour and vector competence, and the role of these haematophagous arthropods in the epidemiology of the diseases, simple, cost-effective and, most importantly, reliable identification techniques are necessary. The PCR assay presented will help to identify culicoid vector species and therefore add to bluetongue and Schmallenberg disease research including vector control and monitoring.
Bioluminescent imaging of Trypanosoma cruzi infection in Rhodnius prolixus
Authors: Henriques Cristina , Castro Daniele P , Gomes Leonardo HF , Garcia Eloi S , de Souza Wanderley 
Published: September 2012

Abstract

Background
Usually the analysis of the various developmental stages of Trypanosoma cruzi in the experimentally infected vertebrate and invertebrate hosts is based on the morphological observations of tissue fragments from animals and insects. The development of techniques that allow the imaging of animals infected with parasites expressing luciferase open up possibilities to follow the fate of bioluminescent parasites in infected vectors.

Methods
D-luciferin (60 μg) was injected into the hemocoel of the whole insect before bioluminescence acquisition. In dissected insects, the whole gut was incubated with D-luciferin in PBS (300 μg/ml) for ex vivo bioluminescence acquisition in the IVIS® Imaging System, Xenogen.

Results
Herein, we describe the results obtained with the luciferase gene integrated into the genome of the Dm28c clone of T. cruzi, and the use of these parasites to follow, in real time, the infection of the insect vector Rhodnius prolixus, by a non- invasive method. The insects were evaluated by in vivo bioluminescent imaging on the feeding day, and on the 7 th, 14 th, 21 st and 28 th days after feeding. To corroborate the bioluminescent imaging made in vivo, and investigate the digestive tract region, the insects were dissected. The bioluminescence emitted was proportional to the number of protozoans in regions of the gut. The same digestive tracts were also macerated to count the parasites in distinct morphological stages with an optical microscope, and for bioluminescence acquisition in a microplate using the IVIS® Imaging System. A positive correlation of parasite numbers and bioluminescence in the microplate was obtained.

Conclusions
This is the first report of bioluminescent imaging in Rhodnius prolixus infected with trypomastigotes of the Dm28c-luc stable strain, expressing firefly luciferase. In spite of the distribution limitations of the substrate (D-luciferin) in the insect body, longitudinal evaluation of infected insects by bioluminescent imaging is a valuable tool. Bioluminescent imaging of the digestive tract infected with Dm28c-luc is highly sensitive and accurate method to track the fate of the parasite in the vector, in the crop, intestine and rectum. This methodology is useful to gain a better understanding of the parasite – insect vector interactions.
RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
Authors: Kim Joonhoon , Reed Jennifer L 
Published: September 2012

AbstractPredicting cellular responses to perturbations is an important task in systems biology. We report a new approach, RELATCH, which uses flux and gene expression data from a reference state to predict metabolic responses in a genetically or environmentally perturbed state. Using the concept of relative optimality, which considers relative flux changes from a reference state, we hypothesize a relative metabolic flux pattern is maintained from one state to another, and that cells adapt to perturbations using metabolic and regulatory reprogramming to preserve this relative flux pattern. This constraint-based approach will have broad utility where predictions of metabolic responses are needed.
Examination of ERα Signaling Pathways in Bone of Mutant Mouse Models Reveals the Importance of ERE-Dependent Signaling
Authors: Chokalingam Kumar , Roforth Matthew M. , Nicks Kristy M. , McGregor Ulrike , Fraser Daniel , Khosla Sundeep , Monroe David G. 
Published: September 2012

AbstractThe mechanisms of estrogen receptor (ER)-α activity can be categorized into those involving direct (classical) or indirect (nonclassical) DNA binding. Although various mouse models have demonstrated the importance of ERα in bone, the specific gene expression patterns affected by these modes of ERα action are unknown. In this report, the gene expression patterns of ERα-deficient (ERKO) mice and nonclassical ER knock-in (NERKI) mice, which can function only by nonclassical means, were analyzed. Three-month-old mice were ovariectomized and implanted with estrogen pellets for 1 month to normalize estrogen levels. Microarray analysis of flushed cortical bone revealed 28% (210 of 763) of the genes differentially expressed in ERKO mice were altered in NERKI mice, suggesting estrogen response element-dependent regulation of these genes in bone. Pathway analysis revealed alterations in genes involved in focal adhesion and extracellular matrix interactions. However, the majority of genes regulated in ERKO mice (72%) were unique (i.e. not altered in NERKI mice), suggesting these are regulated by nonclassical mechanisms. To further explore the pathways affected in ERKO mice, we performed focused quantitative PCR arrays for genes involved in various aspects of bone physiology. Genes involved in bone formation, senescence, apoptosis, and autophagy were significantly regulated. Overall, the majority of the genes regulated by ERα in bone are via nonclassical pathways. However, because NERKI mice display an osteoporotic phenotype, it can be deduced that the minority of the estrogen response element-dependent genes/pathways play critical roles in the regulation of bone physiology. These data demonstrate the importance of classical ERα signaling in regulating bone metabolism.
Interactions between ICAM-5 and β1 integrins regulate neuronal synapse formation
Authors: Ning Lin , Tian Li , Smirnov Sergei , Vihinen Helena , Llano Olaya , Vick Kyle , Davis Ronald L. , Rivera Claudio , Gahmberg Carl G. 
Published: September 2012

SummaryIntercellular adhesion molecule-5 (ICAM-5) is a dendrite-specific adhesion molecule, which functions in both the immune and nervous systems. ICAM-5 is the only negative regulator that has been identified for maturation of dendritic spines so far. Shedding of the ICAM-5 ectodomain promotes spine maturation and enhances synaptic activity. However, the mechanism by which ICAM-5 regulates spine development remains poorly understood. In this study, we found that ablation of ICAM5 expression resulted in a significant increase in the formation of synaptic contacts and the frequency of miniature excitatory post-synaptic currents, an indicator of pre-synaptic release probability. Antibodies against ICAM-5 and β1 integrins altered spine maturation. Furthermore, we found that β1 integrins serve as binding partners for ICAM-5. β1 integrins were immunoprecipitated with ICAM-5 from mouse brain and the binding region in ICAM-5 was localized to the two first Ig domains. β1 integrins were juxtaposed to filopodia tips at the early stage of synaptic formation, but as synapses matured, β1 integrins covered the mushroom spines. Loss of β1 integrins from the pre-synaptic sites affected the morphology of the post-synaptic structures. ICAM-5 ectodomain cleavage decreased or increased when the interaction between ICAM-5 and β1 integrins was potentiated or weakened, respectively, using antibodies. These results suggest that the interaction between ICAM-5 and β1 integrins is important in formation of functional synapses.
Poc1A and Poc1B act together in human cells to ensure centriole integrity
Authors: Venoux Magali , Tait Xavier , Hames Rebecca S. , Straatman Kees R. , Woodland Hugh R. , Fry Andrew M. 
Published: September 2012

Summary
Proteomic studies in unicellular eukaryotes identified a set of centriolar proteins that included proteome of centriole 1 (Poc1). Functional studies in these organisms implicated Poc1 in centriole duplication and length control, as well as ciliogenesis. Using isoform-specific antibodies and RNAi depletion, we have examined the function of the two related human proteins, Poc1A and Poc1B. We find that Poc1A and Poc1B each localize to centrioles and spindle poles, but do so independently and with different dynamics. However, although loss of one or other Poc1 protein does not obviously disrupt mitosis, depletion of both proteins leads to defects in spindle organization with the generation of unequal or monopolar spindles. Our data indicate that, once incorporated, a fraction of Poc1A and Poc1B remains stably associated with parental centrioles, but that depletion prevents incorporation into nascent centrioles. Nascent centrioles lacking both Poc1A and Poc1B exhibit loss of integrity and maturation, and fail to undergo duplication. Thus, when Poc1A and Poc1B are co-depleted, new centrosomes capable of maturation cannot assemble and unequal spindles result. Interestingly, Poc1B, but not Poc1A, is phosphorylated in mitosis, and depletion of Poc1B alone was sufficient to perturb cell proliferation. Hence, Poc1A and Poc1B play redundant, but essential, roles in generation of stable centrioles, but Poc1B may have additional independent functions during cell cycle progression.
Clathrin is not required for SNX-BAR-retromer-mediated carrier formation
Authors: McGough Ian J. , Cullen Peter J. 
Published: September 2012

Summary
Clathrin has been implicated in retromer-mediated trafficking, but its precise function remains elusive. Given the importance of retromers for efficient endosomal sorting, we have sought to clarify the relationship between clathrin and the SNX-BAR retromer. We find that the retromer SNX-BARs do not interact directly or indirectly with clathrin. In addition, we observe that SNX-BAR-retromer tubules and carriers are not clathrin coated. Furthermore, perturbing clathrin function, by overexpressing a dominant-negative clathrin or through suppression of clathrin expression, has no detectable effect on the frequency of SNX-BAR-retromer tubulation. We propose that SNX-BAR-retromer-mediated membrane deformation and carrier formation does not require clathrin, and hence the role of clathrin in SNX-BAR-retromer function would appear to lie in pre-SNX-BAR-retromer cargo sorting.
Understanding the Performance of the Long Chain and Sparse Designs in Process Flexibility
Authors: Simchi-Levi David , Wei Yehua 
Published: September 2012

The long chain has been an important concept in the design of flexible processes. This design concept, as well as other sparse designs, have been applied by the automotive and other industries as a way to increase flexibility in order to better match available capacities with variable demands. Numerous empirical studies have validated the effectiveness of these designs. However, there is little theory that explains the effectiveness of the long chain, except when the system size is large, i.e., by applying an asymptotic analysis. Our attempt in this paper is to develop a theory that explains the effectiveness of long chain designs for finite size systems. First, we uncover a fundamental property of long chains, supermodularity, that serves as an important building block in our analysis. This property is used to show that the marginal benefit, i.e., the increase in expected sales, increases as the long chain is constructed, and the largest benefit is always achieved when the chain is closed by adding the last arc to the system. Then, supermodularity is used to show that the performance of the long chain is characterized by the difference between the performances of two open chains. This characterization immediately leads to the optimality of the long chain among 2-flexibility designs. Finally, under independent and identically distributed (i.i.d.) demand, this characterization gives rise to three developments: (i) an effective algorithm to compute the performances of long chains using only matrix multiplications; (ii) a result that the gap between the fill rate of full flexibility and that of the long chain increases with system size, thus implying that the effectiveness of the long chain relative to full flexibility increases as the number of products decreases; (iii) a risk-pooling result implying that the fill rate of a long chain increases with the number of products, but this increase converges to zero exponentially fast.