bluuebunny/crossref_metadata_2025 huggingface dataset:
Silencing of Host Genes Directed by Virus-Derived Short Interfering RNAs in Caenorhabditis elegans
Authors: Guo Xunyang , Li Wan-Xiang , Lu Rui
Published: August 2012

Small interfering RNAs (siRNAs) processed from viral replication intermediates by RNase III-like enzyme Dicer guide sequence-specific antiviral silencing in fungi, plants, and invertebrates. In plants, virus-derived siRNAs (viRNAs) can target and silence cellular transcripts and, in some cases, are responsible for the induction of plant diseases. Currently it remains unclear whether viRNAs are also capable of modulating the expression of cellular genes in the animal kingdom, although animal virus-encoded microRNAs (miRNAs) are known to guide efficient silencing of host genes, thereby facilitating virus replication. In this report, we showed that viRNAs derived from a modified nodavirus triggered potent silencing of homologous cellular transcripts produced by the endogenous gene or transgene in the nematode worm
Caenorhabditis elegans
. Like that found in plants, virus-induced gene silencing (VIGS) in
C. elegans
also involves RRF-1, a worm RNA-dependent RNA polymerase (RdRP) that is known to produce single-stranded secondary siRNAs in a Dicer-independent manner. We further demonstrated that VIGS in
C. elegans
is inheritable, suggesting that VIGS has the potential to generate profound epigenetic consequences in future generations. Altogether, these findings, for the first time, confirmed that viRNAs have the potential to modulate host gene expression in the animal kingdom. Most importantly, the success in uncoupling the trigger and the target of the antiviral silencing would allow for the exploration of novel features of virus-host interactions mediated by viRNAs in the animal kingdom.
Long-Term and Memory Immune Responses in Mice against Newcastle Disease Virus-Like Particles Containing Respiratory Syncytial Virus Glycoprotein Ectodomains
Authors: Schmidt Madelyn R. , McGinnes Lori W. , Kenward Sarah A. , Willems Kristen N. , Woodland Robert T. , Morrison Trudy G.
Published: August 2012

Although respiratory syncytial virus (RSV) is a significant human pathogen, no RSV vaccines are available. We have reported that a virus-like particle (VLP) RSV vaccine candidate stimulated, in mice, robust, protective anti-RSV glycoprotein T
H
1 biased immune responses without enhanced respiratory disease upon RSV challenge. We report here an analysis of long-term responses to these VLPs. BALB/c mice immunized, without adjuvant, with VLPs or with infectious RSV generated anti-F and anti-G protein serum antibody responses that were stable over 14 months. Neutralizing antibody titers stimulated by VLPs were robust and durable for 14 months, whereas those of RSV-immunized animals declined significantly by 3 months. F protein-specific antibody-secreting cells were detected in the bone marrows of VLP-immunized mice but not in the marrows of RSV-immunized mice. Adoptive transfer of enriched splenic B cells from VLP-immunized mice into immunodeficient
rag
−/−
mice resulted in anti-F and anti-G protein serum IgG antibody responses, in recipient mice, that were protective upon RSV challenge. In contrast, transfer of splenic B cells from RSV-immunized mice produced no detectable serum antibody in the recipients, nor could these mice inhibit RSV replication upon virus challenge. Immunization with VLPs stimulated the formation of germinal center GL7
+
B cells in normal mice. VLP immunization of TCR βδ
−/−
T-cell-deficient mice did not induce anti-RSV IgG antibodies, results consistent with T-cell-dependent immune responses. These results demonstrate that VLPs are effective in stimulating long-lived RSV-specific, T-cell-dependent neutralizing antibody-secreting cells and RSV-specific memory responses.
Large-Scale Chromatin Immunoprecipitation with Promoter Sequence Microarray Analysis of the Interaction of the NSs Protein of Rift Valley Fever Virus with Regulatory DNA Regions of the Host Genome
Authors: Benferhat Rima , Josse Thibaut , Albaud Benoit , Gentien David , Mansuroglu Zeyni , Marcato Vasco , Souès Sylvie , Le Bonniec Bernard , Bouloy Michèle , Bonnefoy Eliette
Published: August 2012

Rift Valley fever virus (RVFV) is a highly pathogenicPhlebovirusthat infects humans and ruminants. Initially confined to Africa, RVFV has spread outside Africa and presently represents a high risk to other geographic regions. It is responsible for high fatality rates in sheep and cattle. In humans, RVFV can induce hepatitis, encephalitis, retinitis, or fatal hemorrhagic fever. The nonstructural NSs protein that is the major virulence factor is found in the nuclei of infected cells where it associates with cellular transcription factors and cofactors. In previous work, we have shown that NSs interacts with the promoter region of the beta interferon gene abnormally maintaining the promoter in a repressed state. In this work, we performed a genome-wide analysis of the interactions between NSs and the host genome using a genome-wide chromatin immunoprecipitation combined with promoter sequence microarray, the ChIP-on-chip technique. Several cellular promoter regions were identified as significantly interacting with NSs, and the establishment of NSs interactions with these regions was often found linked to deregulation of expression of the corresponding genes. Among annotated NSs-interacting genes were present not only genes regulating innate immunity and inflammation but also genes regulating cellular pathways that have not yet been identified as targeted by RVFV. Several of these pathways, such as cell adhesion, axonal guidance, development, and coagulation were closely related to RVFV-induced disorders. In particular, we show in this work that NSs targeted and modified the expression of genes coding for coagulation factors, demonstrating for the first time that this hemorrhagic virus impairs the host coagulation cascade at the transcriptional level.
Polymorphisms in Toll-Like Receptor 4 Underlie Susceptibility to Tumor Induction by the Mouse Polyomavirus
Authors: Velupillai Palanivel , Sung Chang Kyoo , Andrews Erik , Moran Jennifer , Beier David , Kagan Jonathan , Benjamin Thomas
Published: August 2012

PERA/Ei (PE) mice are susceptible to tumor induction by polyomavirus (Py), while C57BR/cdJ (BR) mice are resistant. Antigen-presenting cells from BR mice respond to the virus with interleukin-12 (IL-12) and those from PE mice with IL-10. These polarized cytokine responses underlie the development of effective antitumor immunity in BR mice and the lack thereof in PE mice. Anex vivocytokine production assay using spleen cells from infected [PE × BR] F2 mice together with a genome-wide SNP (single-nucleotide polymorphism)-based QTL (quantitative trait locus) analysis was used to map the determinant of cytokine production to a region of chromosome 4 carrying the Toll-like receptor 4 (TLR4) gene. Genotyping of infected F2 mice showed concordance of TLR4 allele-specific DNA sequences with the cytokine profile. Cytokine responses elicited by Py are MyD88 dependent. Bacterial lipopolysaccharide (LPS), a known TLR4 ligand, induced the same polarized responses as the virus in these host strains. Spleen cells from C3H/HeJ and C57BL/10ScNJ LPS-nonresponsive mice challengedin vitrowith Py showed an impaired IL-12 response but were unaffected in IL-10 production. TLR4s of strains PE and BR differ by 3 amino acid substitutions, 2 in the extracellular domain and 1 in the intracellular domain. cDNAs encoding the TLR4s signaled equally to an NF-κB reporter in 293 cells in a ligand-independent manner. When introduced intoTLR2/TLR4double-knockout macrophages, the TLR4 cDNA from BR mice conferred a robust IL-12 response to Py and no IL-10 response. The TLR4 cDNA from PE mice failed to confer a response with either cytokine. These results establish TLR4 as a key mediator of the cytokine response governing susceptibility to tumor induction by Py.
A Virus-Like Particle That Elicits Cross-Reactive Antibodies to the Conserved Stem of Influenza Virus Hemagglutinin
Authors: Schneemann Anette , Speir Jeffrey A. , Tan Gene S. , Khayat Reza , Ekiert Damian C. , Matsuoka Yumiko , Wilson Ian A.
Published: August 2012

The discovery of broadly neutralizing antibodies that recognize highly conserved epitopes in the membrane-proximal region of influenza virus hemagglutinin (HA) has revitalized efforts to develop a universal influenza virus vaccine. This effort will likely require novel immunogens that contain these epitopes but lack the variable and immunodominant epitopes located in the globular head of HA. As a first step toward developing such an immunogen, we investigated whether the 20-residue A-helix of the HA2 chain that forms the major component of the epitope of broadly neutralizing antibodies CR6261, F10, and others is sufficient by itself to elicit antibodies with similarly broad antiviral activity. Here, we report the multivalent display of the A-helix on icosahedral virus-like particles (VLPs) derived from the capsid of Flock House virus. Mice immunized with VLPs displaying 180 copies/particle of the A-helix produced antibodies that recognized trimeric HA and the elicited antibodies had binding characteristics similar to those of CR6261 and F10: they recognized multiple HA subtypes from group 1 but not from group 2. However, the anti-A-helix antibodies did not neutralize influenza virus. These results indicate that further engineering of the transplanted peptide is required and that display of additional regions of the epitope may be necessary to achieve protection.
Viperin, MTAP44, and Protein Kinase R Contribute to the Interferon-Induced Inhibition of Bunyamwera Orthobunyavirus Replication
Authors: Carlton-Smith Charles , Elliott Richard M.
Published: August 2012

The first line of defense against viral infection is the interferon (IFN) response, which culminates in the expression of hundreds of proteins with presumed antiviral activity, and must be overcome by a virus for successful replication. The nonstructural NSs protein is the primary IFN antagonist encoded by Bunyamwera virus (BUNV), the prototype of the
Orthobunyavirus
genus and the family
Bunyaviridae
. The NSs protein interferes with RNA polymerase II-mediated transcription, thereby inhibiting cellular mRNA production, including IFN mRNAs. A recombinant virus, rBUNdelNSs, that is unable to express the NSs protein does not inhibit cellular transcription and is a strong IFN inducer. We report here that cells stimulated into the antiviral state by IFN-β treatment were protected against wild-type BUNV and rBUNdelNSs infection but addition of IFN-β after infection had little effect on the replication cycle of either virus. By screening a panel of cell lines that overexpressed individual IFN-stimulated genes, we found that protein kinase R (PKR), MTAP44, and particularly viperin appreciably restricted BUNV replication. The enzymatic activities of PKR and viperin were required for their inhibitory activities. Taken together, our data show that the restriction of BUNV replication mediated by IFN is an accumulated effect of at least three IFN-stimulated genes that probably act on different stages of the viral replication cycle.
Broadly Neutralizing Immune Responses against Hepatitis C Virus Induced by Vectored Measles Viruses and a Recombinant Envelope Protein Booster
Authors: Reyes-del Valle Jorge , de la Fuente Cynthia , Turner Mallory A. , Springfeld Christoph , Apte-Sengupta Swapna , Frenzke Marie E. , Forest Amelie , Whidby Jillian , Marcotrigiano Joseph , Rice Charles M. , Cattaneo Roberto
Published: August 2012

Hepatitis C virus (HCV) infection remains a serious public health problem worldwide. Treatments are limited, and no preventive vaccine is available. Toward developing an HCV vaccine, we engineered two recombinant measles viruses (MVs) expressing structural proteins from the prototypic HCV subtype 1a strain H77. One virus directs the synthesis of the HCV capsid (C) protein and envelope glycoproteins (E1 and E2), which fold properly and form a heterodimer. The other virus expresses the E1 and E2 glycoproteins separately, with each one fused to the cytoplasmic tail of the MV fusion protein. Although these hybrid glycoproteins were transported to the plasma membrane, they were not incorporated into MV particles. Immunization of MV-susceptible, genetically modified mice with either vector induced neutralizing antibodies to MV and HCV. A boost with soluble E2 protein enhanced titers of neutralizing antibody against the homologous HCV envelope. In animals primed with MV expressing properly folded HCV C-E1-E2, boosting also induced cross-neutralizating antibodies against two heterologous HCV strains. These results show that recombinant MVs retain the ability to induce MV-specific humoral immunity while also eliciting HCV neutralizing antibodies, and that anti-HCV immunity can be boosted with a single dose of purified E2 protein. The use of MV vectors could have advantages for pediatric HCV vaccination.
Full-Length HIV-1 Immunogens Induce Greater Magnitude and Comparable Breadth of T Lymphocyte Responses to Conserved HIV-1 Regions Compared with Conserved-Region-Only HIV-1 Immunogens in Rhesus Monkeys
Authors: Stephenson Kathryn E. , SanMiguel Adam , Simmons Nathaniel L. , Smith Kaitlin , Lewis Mark G. , Szinger James J. , Korber Bette , Barouch Dan H.
Published: August 2012

A global HIV-1 vaccine will likely need to induce immune responses against conserved HIV-1 regions to contend with the profound genetic diversity of HIV-1. Here we evaluated the capacity of immunogens consisting of only highly conserved HIV-1 sequences that are aimed at focusing cellular immune responses on these potentially critical regions. We assessed in rhesus monkeys the breadth and magnitude of T lymphocyte responses elicited by adenovirus vectors expressing either full-length HIV-1 Gag/Pol/Env immunogens or concatenated immunogens consisting of only highly conserved HIV-1 sequences. Surprisingly, we found that the full-length immunogens induced comparable breadth (
P
= 1.0) and greater magnitude (
P
= 0.01) of CD8
+
T lymphocyte responses against conserved HIV-1 regions compared with the conserved-region-only immunogens. Moreover, the full-length immunogens induced a 5-fold increased total breadth of HIV-1-specific T lymphocyte responses compared with the conserved-region-only immunogens (
P
= 0.007). These results suggest that full-length HIV-1 immunogens elicit a substantially increased magnitude and breadth of cellular immune responses compared with conserved-region-only HIV-1 immunogens, including greater magnitude and comparable breadth of responses against conserved sequences.
Specific Dietary Oligosaccharides Increase Th1 Responses in a Mouse Respiratory Syncytial Virus Infection Model
Authors: Schijf Marcel A. , Kruijsen Debby , Bastiaans Jacqueline , Coenjaerts Frank E. J. , Garssen Johan , van Bleek Grada M. , van't Land Belinda
Published: August 2012

Breast feeding reduces the risk of developing severe respiratory syncytial virus (RSV) infections in infants. In addition to maternal antibodies, other immune-modulating factors in human milk contribute to this protection. Specific dietary prebiotic oligosaccharides, similar to oligosaccharides present in human milk, were evaluated in a C57BL/6 mouse RSV infection model. During primary RSV infection, increased numbers of RSV-specific CD4
+
T cells producing gamma interferon (IFN-γ) were found in the lungs at days 8 to 10 postinfection in mice receiving diet containing short-chain galactooligosacharides, long-chain fructooligosaccharides, and pectin-derived acidic oligosaccharides (termed scGOS/lcFOS/pAOS). In a Th2-skewed formalin-inactivated (FI)-RSV vaccination model, the prebiotic diet reduced RSV-specific Th2 cytokine (interleukin-4 [IL-4], IL-5, and IL-13)-producing CD4
+
T cells in the lung and the magnitude of airway eosinophilia at day 4 and 6 after infection. This was accompanied by a decreased influx of inflammatory dendritic cells (CD11b
+
/CD11c
+
) and increased numbers of IFN-γ-producing CD4
+
and CD8
+
T cells at day 8 after viral challenge. These findings suggest that specific dietary oligosaccharides can influence trafficking and/or effector functions of innate immune, CD4
+
, and CD8
+
T cell subsets in the lungs of RSV-infected mice. In our models, scGOS/lcFOS/pAOS had no effect on weight but increased viral clearance in FI-RSV-vaccinated mice 8 days after infection. The increased systemic Th1 responses potentiated by scGOS/lcFOS/pAOS might contribute to an accelerated Th1/Th2 shift of the neonatal immune system, which might favor protective immunity against viral infections with a high attack rate in early infancy, such as RSV.
Genome-wide identification, evolutionary and expression analyses of putative Fe–S biogenesis genes in rice (Oryza sativa)
Authors: Kesawat Mahipal Singh , Das Basanta Kumar , Bhaganagare Govindraj Ramakantrao , Manorama
Published: August 2012

Iron–sulfur (Fe–S) proteins are ubiquitous in nature and carry Fe–S clusters (ISCs) as prosthetic groups that are essential in maintaining basic biological processes such as photosynthesis, respiration, nitrogen fixation, and DNA repair. In the present investigation, a comprehensive genome-wide analysis was carried out to find all the genes involved in the formation of ISCs in rice ( Oryza sativa L.) through a systematic EST and genomic DNA sequence data mining. This analysis profiled 44 rice ISC genes (OsISCs) that were identified using in silico analysis. Multiple sequence alignment and phylogenetic analysis revealed that these genes were highly conserved among bacteria, fungi, animals, and plants. EST analysis and RT–PCR assays demonstrated that all OsISCs were active and that the transcript abundance of some OsISCs was tissue specific. The results of this study will assist further investigations to identify and elucidate the structural components involved in the assembly, biogenesis, and regulation of OsISCs. Thus, the outcome of the present study provides basic genomic information for the OsISC and will pave the way for elucidating the precise role of OsISCs in plant growth and development in the future. Also, it may enable us in the future to enhance the crop yield, uptake of Fe, and protection against abiotic and biotic stress.
Molecular bases of the postzygotic barriers in interspecific crosses between the wild potato speciesSolanum acauleandSolanum commersonii
Authors: Cornejo P. , Camadro E.L. , Masuelli R.W.
Published: August 2012

To investigate the molecular bases of postzygotic hybridization barriers in tuber-bearing Solanums, the wild species Solanum commersonii Dunal ex Poir. (cmm, 2n = 2x = 24, 1EBN) and Solanum acaule Bitter (acl, 2n = 4x = 48, 2EBN) were crossed in intra- and interspecific genotypic combinations, and the transcriptome of immature seeds was analyzed by using the cDNA-AFLP technique. From a total of 423 analyzed cDNA fragments, 107 (25.3%) were differentially regulated in the compatible (acl × acl and cmm × cmm) versus incompatible (acl × cmm) crosses. DNA sequence data were obtained from 21 fragments and RT–PCR analyses were carried out with five fragments to validate the cDNA-AFLP differential pattern. Sequence analysis suggested a possible role for the differentially expressed sequences in cytokinesis, cell cycle, secondary and hormonal metabolism, biodegradation, and transport. In situ hybridization experiments with fragments encoding an ubiquitin-fold modifier 1 precursor and a possible vesicle transport protein revealed expression of these genes in the embryo and endosperm. The results suggest that the collapse of the embryo and endosperm in incompatible crosses may be related to alterations in cell cycle and cytokinesis.
Potential role of tRNAs in wheat and Lolium mitochondrial rps7 transcript processing
Authors: Byers Evan , Bonen Linda
Published: August 2012

The wheat mitochondrial gene for ribosomal protein S7 exhibits multiple transcripts that share the same 3′ terminus but range in overall length from 3.4 to 0.7 kb because of 5′end-maturation events. The longest detectable precursor RNA maps precisely to the 3′ end of a chloroplast-origin tRNA-Phe gene, consistent with it providing signals for endonucleolytic cleavage. Steady-state levels of precursor RNAs were seen to be lower in seedlings than in germinating embryos, although the degree of editing within untranslated regions (UTRs) was higher in seedlings. In another grass, Lolium multiflorum Lam., rps7 displays transcripts of 1.3 and 0.7 kb, and although the distal 5′ UTRs are unrelated in sequence to those of wheat, the 5′ terminus of the longer transcript also maps to a tRNA gene, in this case the native mitochondrial-type tRNA-Ser. Our findings illustrate the plasticity of plant mitochondrial transcriptional units and the recruitment of chloroplast-origin sequences for the expression of mitochondrial genes.
Adiponectin and osteocalcin: relation to insulin sensitivity
Authors: Zhang Yanjun , Zhou Peng , Kimondo Julia Wanjiru
Published: August 2012

Obesity and osteoporosis have grave consequences for human health, quality of life, and even the efficiency of the labor force. Interestingly, these diseases share several features including a genetic predisposition and a common progenitor cell. Recent findings show that high adipocyte count in bone marrow is directly related to bone loss, as fat cells replace osteoblasts resulting in reduced bone mineral density and increased propensity towards osteoporosis. This close relationship has a positive aspect, whereby higher osteocalcin levels results in increased adiponectin production while the presence of adiponectin influences osteoblast proliferation and differentiation in a positive way. We focus on how osteoblasts and adipocytes affect each other and ultimately insulin resistance through the hormones they produce. This approach to whole animal physiology is the main stay of Alternative Medicine. It is assumed that the body is linked together intricately, and treating one is equal to treating the whole body. As we go further into bone and adipocytes physiology, it is evident that these organs affect each other. Therefore, elucidation on the actions of fat on bone and vice versa will unravel the complex mechanism of insulin resistance.
Daphnetin methylation stabilizes the activity of phosphoribulokinase in wheat during cold acclimation
Authors: Kane Khalil , Moheb Amira , Fukushi Yukihara , Roy René , Hüner Norman P.A , Ibrahim Ragai K. , Sarhan Fathey
Published: August 2012

The methylation of daphnetin (7,8-dihydroxycoumarin) to its 8-methyl derivative is catalyzed by a wheat (Triticum aestivum L.) O-methyltransferase (TaOMT1). This enzyme is regulated by cold and photosystem II excitation pressure (plastid redox state). Here, we investigated the biological significance of this methylation and its potential role in modulating the activity of kinases in wheat. To identify the potential kinases that may interact with daphnetin in wheat, the soluble protein extract from aerial parts of cold-acclimated wheat was purified by DEAE-cellulose separation and affinity chromatography on a daphnetin derivative (7,8-dihydroxy-4-coumarin acetic acid)-EAH sepharose column. Mass spectrometric analysis indicated that wheat phosphoribulokinase (TaPRK) is the major kinase that binds to daphnetin. This TaPRK plays an important role in regulating the flow of carbon through the Calvin cycle, by catalyzing the final step in the regeneration of ribulose 1,5-bisphosphate from ribulose-5-phosphate (Ru5P) and ATP. The activities of TaPRK, endogenous or recombinant, are inhibited by daphnetin in a specific and dose-dependent manner, but not by its monomethyl derivative (7-methyl, 8-hydroxycoumarin). Furthermore, HPLC-MS analysis of wheat extracts reveals that 7,8-dimethoxycoumarin is more abundant than its monomethyl derivative. The results also show that cold acclimation does not alter the level of TaPRK mRNA or its enzyme activity, and thus ensures the stable generation of ribulose 1,5-biphosphate.
ON INTEGRAL RICCI CURVATURE AND TOPOLOGY OF FINSLER MANIFOLDS
Authors: WU B. Y.
Published: August 2012

We establish a relative volume comparison theorem for minimal volume form of Finsler manifolds under integral Ricci curvature bound. As its applications, we obtain some results on integral Ricci curvature and topology of Finsler manifolds. These results generalize the corresponding properties with pointwise Ricci curvature bound in the literatures.
STRUCTURE SCALARS IN CHARGED PLANE SYMMETRY
Authors: SHARIF M. , ZAEEM UL HAQ BHATTI M.
Published: August 2012

We consider non-adiabatic flow of the fluid possessing dissipation in the form of shearing viscosity in electromagnetic field. The scalar functions (structure scalars) for charged plane symmetry are formulated and are related with the physical variables of the fluid. We also develop a relationship between the Weyl tensor and other physical variables by using Taub mass formalism. The role of electric charge as well as its physical significance for the evolution of the shear tensor and expansion scalar are also explored. Finally, we discuss a special case for dust with cosmological constant.
THE LEPTON FLAVOR VIOLATING DECAYS Z→li lj IN THE SIMPLEST LITTLE HIGGS MODEL
Authors: HAN XIAO-FANG , WANG LEI
Published: August 2012

In the simplest little Higgs model the new flavor-changing interactions between heavy neutrinos and the Standard Model leptons can generate contributions to some lepton flavor violating decays of Z-boson at one-loop level, such as Z→τ±μ∓, Z→τ±e∓ and Z→μ±e∓. We examine the decay modes and find that the branching ratios can reach 10-7 for the three decays, which should be accessible at the GigaZ option of the ILC.
(ANTI-)STRANGE DENSITY AND CONTRIBUTION OF HEAVY FLAVOR, $F_2^c$, TO THE NUCLEON STRUCTURE FUNCTION IN THE CHIRAL QUARK MODEL
Authors: NEMATOLLAHI HODA , YAZDANPANAH MOHAMMAD MEHDI , MIRJALILI ABOLFAZL
Published: August 2012

A new approach is employed to provide the required expressions for the bare constituent quark densities in the proton. In this approach, we assume the bare quark densities take a Gaussian form in four-momentum space, which fulfill more properly the desired constrains of parton densities inside the proton. Using the modified chiral quark model and the related convolutions, the parton densities inside the proton are obtained. By evolving the gluon density to high energy scale, the contribution of charm quark to the proton structure function can be extracted and it is found in good agreement with the available experimental data. Sea quark ((anti-)strange) densities are calculated and compared with the ones from some phenomenological and experimental groups in which consistent results are obtained. What makes the results more valuable is that the initial framework is completely theoretical and we do not need to resort to any parametrizations in our calculations.
OPTIMAL ASSEMBLY OF SUPPORT VECTOR REGRESSORS WITH APPLICATION TO SYSTEM MONITORING
Authors: ALAMANIOTIS MILTIADIS , IKONOMOPOULOS ANDREAS , TSOUKALAS LEFTERI H.
Published: August 2012

Power plants are high complexity systems running risks of low frequency but high consequence. The field of machine learning appears to offer the necessary tools for developing automated instrument surveillance systems supporting decision-making in critical systems such as power stations. A novel prediction method is presented with the aim to enhance system safety and performance by making an ahead-of-time prediction of the status of fundamental system components and subsequent detection of abnormalities. The utilization of a linear assembly of support vector regressors employing unique kernels is proposed in a hybrid computational scheme that encompasses the formulation of a multi-objective optimization problem addressed with an evolutionary algorithm that employs Pareto theory to identify an optimal solution. The approach is tested on the ahead of time prediction of the crack length in power plant turbine blades utilizing historical data. The results obtained highlight the efficiency of the proposed methodology since better performance over the standalone support vector regressors is observed.
JUST.ASK — A MULTI-PRONGED APPROACH TO QUESTION ANSWERING
Authors: MENDES ANA CRISTINA , COHEUR LUÍSA , SILVA JOÃO , RODRIGUES HUGO
Published: August 2012

In the last decades, several research areas experienced key improvements due to the appearance of numerous tools made available to the scientific community. For instance, Moses plays an important role in recent developments in machine translation and Lucene is, with no doubt, a widespread tool in information retrieval. The existence of these systems allows an easy development of baselines and, therefore, researchers can focus on improving preliminary results, instead of spending time in developing software from scratch. In addition, the existence of appropriate test collections leads to a straightforward comparison of systems and of their specific components.

In this paper we describe Just.Ask, a multi-pronged approach to open-domain question answering. Just.Ask combines rule- with machine learning-based components and implements several state-of-the-art strategies in question answering. Also, it has a flexible architecture that allows for further extensions. Moreover, in this paper we report a detailed evaluation of each one of Just.Ask components. The evaluation is split into two parts: in the first one, we use a manually built test collection — the GoldWebQA — that intends to evaluate Just.Ask performance when the information source in use is the Web, without having to deal with its constant changes; in the second one, we use a set of questions gathered from the TREC evaluation forum, having a closed text collection, locally indexed and stored, as information source. Therefore, this paper contributes with a benchmark for research on question answering, since both Just.Ask and the GoldWebQA corpus are freely available for the scientific community.
A WEIGHTED COMBINER OF STACKING BASED METHODS
Authors: ROONEY NIALL
Published: August 2012

In this paper we present a novel method that forms a weighted combination of a range of Stacking based methods for regression problems, without adding any major computational overhead in comparison to stacking itself. The intention of the technique is to benefit from the variation in performance of individual Stacking methods as demonstrated with different data sets, in order to provide a more robust technique overall. We detail an empirical analysis of the technique referred to as weighted Meta–Combiner (wMetaComb) and compare its performance to its underlying techniques.
Ethanol stimulates epithelial sodium channels by elevating reactive oxygen species
Authors: Bao Hui-Fang , Song John Z. , Duke Billie J. , Ma He-Ping , Denson Donald D. , Eaton Douglas C.
Published: August 2012

Alcohol affects total body sodium balance, but the molecular mechanism of its effect remains unclear. We used single-channel methods to examine how ethanol affects epithelial sodium channels (ENaC) in A6 distal nephron cells. The data showed that ethanol significantly increased both ENaC open probability ( Po) and the number of active ENaC in patches ( N). 1-Propanol and 1-butanol also increased ENaC activity, but iso-alcohols did not. The effects of ethanol were mimicked by acetaldehyde, the first metabolic product of ethanol, but not by acetone, the metabolic product of 2-propanol. Besides increasing open probability and apparent density of active channels, confocal microscopy and surface biotinylation showed that ethanol significantly increased α-ENaC protein in the apical membrane. The effects of ethanol on ENaC Po and N were abolished by a superoxide scavenger, 4-hydroxy-2,2,6,6-tetramethylpiperidinyloxy (TEMPOL) and blocked by the phosphatidylinositol 3-kinase inhibitor LY294002. Consistent with an effect of ethanol-induced reactive oxygen species (ROS) on ENaC, primary alcohols and acetaldehyde elevated intracellular ROS, but secondary alcohols did not. Taken together with our previous finding that ROS stimulate ENaC, the current results suggest that ethanol stimulates ENaC by elevating intracellular ROS probably via its metabolic product acetaldehyde.
Deletion of Slc26a6 alters the stoichiometry of apical Cl−/HCO3− exchange in mouse pancreatic duct
Authors: Song Ying , Yamamoto Akiko , Steward Martin C. , Ko Shigeru B. H. , Stewart Andrew K. , Soleimani Manoocher , Liu Bai-Chun , Kondo Takaharu , Jin Chun-Xiang , Ishiguro Hiroshi
Published: August 2012

To define the stoichiometry and molecular identity of the Cl−/HCO3− exchanger in the apical membrane of pancreatic duct cells, changes in luminal pH and volume were measured simultaneously in interlobular pancreatic ducts isolated from wild-type and Slc26a6-null mice. Transepithelial fluxes of HCO3− and Cl− were measured in the presence of anion gradients favoring rapid exchange of intracellular HCO3− with luminal Cl− in cAMP-stimulated ducts. The flux ratio of Cl− absorption/HCO3− secretion was ∼0.7 in wild-type ducts and ∼1.4 in Slc26a6−/− ducts where a different Cl−/HCO3− exchanger, most likely SLC26A3, was found to be active. Interactions between Cl−/HCO3− exchange and cystic fibrosis transmembrane conductance regulator (CFTR) in cAMP-stimulated ducts were examined by measuring the recovery of intracellular pH after alkali-loading by acetate prepulse. Hyperpolarization induced by luminal application of CFTRinh-172 enhanced HCO3− efflux across the apical membrane via SLC26A6 in wild-type ducts but significantly reduced HCO3− efflux in Slc26a6−/− ducts. In microperfused wild-type ducts, removal of luminal Cl−, or luminal application of dihydro-4,4′-diisothiocyanatostilbene-2,2′-disulphonic acid to inhibit SLC26A6, caused membrane hyperpolarization, which was abolished in Slc26a6−/− ducts. In conclusion, we have demonstrated that deletion of Slc26a6 alters the apparent stoichiometry of apical Cl−/HCO3− exchange in native pancreatic duct. Our results are consistent with SLC26A6 mediating 1:2 Cl−/HCO3− exchange, and the exchanger upregulated in its absence, most probably SLC26A3, mediating 2:1 exchange.
Satellite cell depletion does not inhibit adult skeletal muscle regrowth following unloading-induced atrophy
Authors: Jackson Janna R. , Mula Jyothi , Kirby Tyler J. , Fry Christopher S. , Lee Jonah D. , Ubele Margo F. , Campbell Kenneth S. , McCarthy John J. , Peterson Charlotte A. , Dupont-Versteegden Esther E.
Published: August 2012

Resident muscle stem cells, known as satellite cells, are thought to be the main mediators of skeletal muscle plasticity. Satellite cells are activated, replicate, and fuse into existing muscle fibers in response to both muscle injury and mechanical load. It is generally well-accepted that satellite cells participate in postnatal growth, hypertrophy, and muscle regeneration following injury; however, their role in muscle regrowth following an atrophic stimulus remains equivocal. The current study employed a genetic mouse model (Pax7-DTA) that allowed for the effective depletion of >90% of satellite cells in adult muscle upon the administration of tamoxifen. Vehicle and tamoxifen-treated young adult female mice were either hindlimb suspended for 14 days to induce muscle atrophy or hindlimb suspended for 14 days followed by 14 days of reloading to allow regrowth, or they remained ambulatory for the duration of the experimental protocol. Additionally, 5-bromo-2′-deoxyuridine (BrdU) was added to the drinking water to track cell proliferation. Soleus muscle atrophy, as measured by whole muscle wet weight, fiber cross-sectional area, and single-fiber width, occurred in response to suspension and did not differ between satellite cell-depleted and control muscles. Furthermore, the depletion of satellite cells did not attenuate muscle mass or force recovery during the 14-day reloading period, suggesting that satellite cells are not required for muscle regrowth. Myonuclear number was not altered during either the suspension or the reloading period in soleus muscle fibers from vehicle-treated or satellite cell-depleted animals. Thus, myonuclear domain size was reduced following suspension due to decreased cytoplasmic volume and was completely restored following reloading, independent of the presence of satellite cells. These results provide convincing evidence that satellite cells are not required for muscle regrowth following atrophy and that, instead, the myonuclear domain size changes as myofibers adapt.
VIP17/MAL expression modulates epithelial cyst formation and ciliogenesis
Authors: Takiar Vinita , Mistry Kavita , Carmosino Monica , Schaeren-Wiemers Nicole , Caplan Michael J.
Published: August 2012

The polarized organization of epithelial cells is required for vectorial solute transport and may be altered in renal cystic diseases. Vesicle integral protein of 17 kDa (VIP17/MAL) is involved in apical vesicle transport. VIP17/MAL overexpression in vivo results in renal cystogenesis of unknown etiology. Renal cystogenesis can occur as a consequence of defects of the primary cilium. To explore the role of VIP17/MAL in renal cystogenesis and ciliogenesis, we examined the polarization and ciliary morphology of wild-type and VIP17/MAL overexpressing Madin-Darby canine kidney renal epithelial cells grown in two-dimensional (2D) and three-dimensional (3D) cyst culture. VIP17/MAL is apically localized when expressed in cells maintained in 2D and 3D culture. VIP17/MAL overexpressing cells produce more multilumen cysts compared with controls. While the distributions of basolateral markers are not affected, VIP17/MAL expression results in aberrant sorting of the apical marker gp135 to the primary cilium. VIP17/MAL overexpression is also associated with shortened or absent cilia. Immunofluorescence analysis performed on kidney sections from VIP17/MAL transgenic mice also demonstrates fewer and shortened cilia within dilated lumens ( P < 0.01). These studies demonstrate that VIP17/MAL overexpression results in abnormal cilium and cyst development, in vitro and in vivo, suggesting that VIP17/MAL overexpressing mice may develop cysts secondary to a ciliary defect.
Renal afferent arteriolar and tubuloglomerular feedback reactivity in mice with conditional deletions of adenosine 1 receptors
Authors: Li Lingli , Lai En Yin , Huang Yuning , Eisner Christoph , Mizel Diane , Wilcox Christopher S. , Schnermann Jurgen
Published: August 2012

Adenosine 1 receptors (A1AR) have been shown in previous experiments to play a major role in the tubuloglomerular feedback (TGF) constrictor response of afferent arterioles (AA) to increased loop of Henle flow. Overexpression studies have pointed to a critical role of vascular A1AR, but it has remained unclear whether selective deletion of A1AR from smooth muscle cells is sufficient to abolish TGF responsiveness. To address this question, we have determined TGF response magnitude in mice in which vascular A1AR deletion was achieved using the loxP recombination approach with cre recombinase being controlled by a smooth muscle actin promoter (SmCre/A1ARff). Effective vascular deletion of A1AR was affirmed by absence of vasoconstrictor responses to adenosine or cyclohexyl adenosine (CHA) in microperfused AA. Elevation of loop of Henle flow from 0 to 30 nl/min caused a 22.1 ± 3.1% reduction of stop flow pressure in control mice and of 7.2 ± 1.5% in SmCre/A1ARff mice ( P < 0.001). Maintenance of residual TGF activity despite absence of A1AR-mediated responses in AA suggests participation of extravascular A1AR in TGF. Support for this notion comes from the observation that deletion of A1ARff by nestin-driven cre causes an identical TGF response reduction (7.3 ± 2.4% in NestinCre/A1ARff vs. 20.3 ± 2.7% in controls), whereas AA responsiveness was reduced but not abolished. A1AR on AA smooth muscle cells are primarily responsible for TGF activation, but A1AR on extravascular cells, perhaps mesangial cells, appear to contribute to the TGF response.
Bladder smooth muscle organ culture preparation maintains the contractile phenotype
Authors: Wang Tanchun , Kendig Derek M. , Chang Shaohua , Trappanese Danielle M. , Chacko Samuel , Moreland Robert S.
Published: August 2012

Smooth muscle cells, when subjected to culture, modulate from a contractile to a secretory phenotype. This has hampered the use of cell culture for molecular techniques to study the regulation of smooth muscle biology. The goal of this study was to develop a new organ culture model of bladder smooth muscle (BSM) that would maintain the contractile phenotype and aid in the study of BSM biology. Our results showed that strips of BSM subjected to up to 9 days of organ culture maintained their contractile phenotype, including the ability to achieve near-control levels of force with a temporal profile similar to that of noncultured tissues. The technical aspects of our organ culture preparation that were responsible, in part, for the maintenance of the contractile phenotype were a slight longitudinal stretch during culture and subjection of the strips to daily contraction-relaxation. The tissues contained viable cells throughout the cross section of the strips. There was an increase in extracellular collagenous matrix, resulting in a leftward shift in the passive length-tension relationship. There were no significant changes in the content of smooth muscle-specific α-actin, calponin, h-caldesmon, total myosin heavy chain, protein kinase G, Rho kinase-I, or the ratio of SM1 to SM2 myosin isoforms. Moreover the organ cultured tissues maintained functional voltage-gated calcium channels and large-conductance calcium-activated potassium channels. Therefore, we propose that this novel BSM organ culture model maintains the contractile phenotype and will be a valuable tool for the use in cellular/molecular biology studies of bladder myocytes.
Acetic acid modulates spike rate and spike latency to salt in peripheral gustatory neurons of rats
Authors: Breza Joseph M. , Contreras Robert J.
Published: August 2012

Sour and salt taste interactions are not well understood in the peripheral gustatory system. Therefore, we investigated the interaction of acetic acid and NaCl on taste processing by rat chorda tympani neurons. We recorded multi-unit responses from the severed chorda tympani nerve (CT) and single-cell responses from intact narrowly tuned and broadly tuned salt-sensitive neurons in the geniculate ganglion simultaneously with stimulus-evoked summated potentials to signal when the stimulus contacted the lingual epithelium. Artificial saliva served as the rinse and solvent for all stimuli [0.3 M NH4Cl, 0.5 M sucrose, 0.1 M NaCl, 0.01 M citric acid, 0.02 M quinine hydrochloride (QHCl), 0.1 M KCl, 0.003–0.1 M acetic acid, and 0.003–0.1 M acetic acid mixed with 0.1 M NaCl]. We used benzamil to assess NaCl responses mediated by the epithelial sodium channel (ENaC). The CT nerve responses to acetic acid/NaCl mixtures were less than those predicted by summing the component responses. Single-unit analyses revealed that acetic acid activated acid-generalist neurons exclusively in a concentration-dependent manner: increasing acid concentration increased response frequency and decreased response latency in a parallel fashion. Acetic acid suppressed NaCl responses in ENaC-dependent NaCl-specialist neurons, whereas acetic acid-NaCl mixtures were additive in acid-generalist neurons. These data suggest that acetic acid attenuates sodium responses in ENaC-expressing-taste cells in contact with NaCl-specialist neurons, whereas acetic acid-NaCl mixtures activate distinct receptor/cellular mechanisms on taste cells in contact with acid-generalist neurons. We speculate that NaCl-specialist neurons are in contact with type I cells, whereas acid-generalist neurons are in contact with type III cells in fungiform taste buds.
Depolarizing bipolar cell dysfunction due to a Trpm1 point mutation
Authors: Peachey Neal S. , Pearring Jillian N. , Bojang Pasano , Hirschtritt Matthew E. , Sturgill-Short Gwen , Ray Thomas A. , Furukawa Takahisa , Koike Chieko , Goldberg Andrew F. X. , Shen Yin , McCall Maureen A. , Nawy Scott , Nishina Patsy M. , Gregg Ronald G.
Published: August 2012

Mutations in TRPM1 are found in humans with an autosomal recessive form of complete congenital stationary night blindness (cCSNB). The Trpm1−/− mouse has been an important animal model for this condition. Here we report a new mouse mutant, tvrm27, identified in a chemical mutagenesis screen. Genetic mapping of the no b-wave electroretinogram (ERG) phenotype of tvrm27 localized the mutation to a chromosomal region that included Trpm1. Complementation testing with Trpm1−/− mice confirmed a mutation in Trpm1. Sequencing identified a nucleotide change in exon 23, converting a highly conserved alanine within the pore domain to threonine (p.A1068T). Consistent with prior studies of Trpm1−/− mice, no anatomical changes were noted in the Trpm1 tvrm27/tvrm27 retina. The Trpm1 tvrm27/tvrm27 phenotype is distinguished from that of Trpm1−/− by the retention of TRPM1 expression on the dendritic tips of depolarizing bipolar cells (DBCs). While ERG b-wave amplitudes of Trpm1+/− heterozygotes are comparable to wild type, those of Trpm1+/ tvrm27 mice are reduced by 32%. A similar reduction in the response of Trpm1+/ tvrm27 DBCs to LY341495 or capsaicin is evident in whole cell recordings. These data indicate that the p.A1068T mutant TRPM1 acts as a dominant negative with respect to TRPM1 channel function. Furthermore, these data indicate that the number of functional TRPM1 channels at the DBC dendritic tips is a key factor in defining DBC response amplitude. The Trpm1 tvrm27/tvrm27 mutant will be useful for elucidating the role of TRPM1 in DBC signal transduction, for determining how Trpm1 mutations impact central visual processing, and for evaluating experimental therapies for cCSNB.
Dynamics of abducens nucleus neurons in the awake mouse
Authors: Stahl John S. , Thumser Zachary C.
Published: August 2012

The mechanics of the eyeball and orbital tissues (the “ocular motor plant”) are a fundamental determinant of ocular motor signal processing. The mouse is used increasingly in ocular motor physiology, but little is known about its plant mechanics. One way to characterize the mechanics is to determine relationships between extraocular motoneuron firing and eye movement. We recorded abducens nucleus neurons in mice executing compensatory eye movements during 0.1- to 1.6-Hz oscillation in the light. We analyzed firing rates to extract eye position and eye velocity sensitivities, from which we determined time constants of a viscoelastic model of the plant. The majority of abducens neurons were already active with the eye in its central rest position, with only 6% recruited at more abducted positions. Firing rates exhibited largely linear relationships to eye movement, although there was a nonlinearity consisting of increasing modulation in proportion to eye movement as eye amplitudes became small (due to reduced stimulus amplitude or reduced alertness). Eye position and velocity sensitivities changed with stimulus frequency as expected for an ocular motor plant dominated by cascaded viscoelasticities. Transfer function poles lay at approximately 0.1 and 0.9 s. Compared with previously studied animal species, the mouse plant is stiffer than the rabbit but laxer than cat and rhesus. Differences between mouse and rabbit can be explained by scaling for eye size (allometry). Differences between the mouse and cat or rhesus can be explained by differing ocular motor repertoires of animals with and without a fovea or area centralis.