Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator.

PubMed

Huang, W; Pérez-García, P; Pokhilko, A; Millar, A J; Antoshechkin, I; Riechmann, J L; Mas, P

2012-04-06

In many organisms, the circadian clock is composed of functionally coupled morning and evening oscillators. In Arabidopsis, oscillator coupling relies on a core loop in which the evening oscillator component TIMING OF CAB EXPRESSION 1 (TOC1) was proposed to activate a subset of morning-expressed oscillator genes. Here, we show that TOC1 does not function as an activator but rather as a general repressor of oscillator gene expression. Repression occurs through TOC1 rhythmic association to the promoters of the oscillator genes. Hormone-dependent induction of TOC1 and analysis of RNA interference plants show that TOC1 prevents the activation of morning-expressed genes at night. Our study overturns the prevailing model of the Arabidopsis circadian clock, showing that the morning and evening oscillator loops are connected through the repressing activity of TOC1.

Importance of correlation between gene expression levels: application to the type I interferon signature in rheumatoid arthritis.

PubMed

Reynier, Frédéric; Petit, Fabien; Paye, Malick; Turrel-Davin, Fanny; Imbert, Pierre-Emmanuel; Hot, Arnaud; Mougin, Bruno; Miossec, Pierre

2011-01-01

The analysis of gene expression data shows that many genes display similarity in their expression profiles suggesting some co-regulation. Here, we investigated the co-expression patterns in gene expression data and proposed a correlation-based research method to stratify individuals. Using blood from rheumatoid arthritis (RA) patients, we investigated the gene expression profiles from whole blood using Affymetrix microarray technology. Co-expressed genes were analyzed by a biclustering method, followed by gene ontology analysis of the relevant biclusters. Taking the type I interferon (IFN) pathway as an example, a classification algorithm was developed from the 102 RA patients and extended to 10 systemic lupus erythematosus (SLE) patients and 100 healthy volunteers to further characterize individuals. We developed a correlation-based algorithm referred to as Classification Algorithm Based on a Biological Signature (CABS), an alternative to other approaches focused specifically on the expression levels. This algorithm applied to the expression of 35 IFN-related genes showed that the IFN signature presented a heterogeneous expression between RA, SLE and healthy controls which could reflect the level of global IFN signature activation. Moreover, the monitoring of the IFN-related genes during the anti-TNF treatment identified changes in type I IFN gene activity induced in RA patients. In conclusion, we have proposed an original method to analyze genes sharing an expression pattern and a biological function showing that the activation levels of a biological signature could be characterized by its overall state of correlation.

Profiling Antibody Responses to Infections by Chlamydia abortus Enables Identification of Potential Virulence Factors and Candidates for Serodiagnosis

PubMed Central

Forsbach-Birk, Vera; Foddis, Corinna; Simnacher, Ulrike; Wilkat, Max; Longbottom, David; Walder, Gernot; Benesch, Christiane; Ganter, Martin; Sachse, Konrad; Essig, Andreas

2013-01-01

Enzootic abortion of ewes (EAE) due to infection with the obligate intracellular pathogen Chlamydia (C.) abortus is an important zoonosis leading to considerable economic loss to agriculture worldwide. The pathogen can be transmitted to humans and may lead to serious infection in pregnant women. Knowledge about epidemiology, clinical course and transmission to humans is hampered by the lack of reliable diagnostic tools. Immunoreactive proteins, which are expressed in infected animals and humans, may serve as novel candidates for diagnostic marker proteins and represent putative virulence factors. In order to broaden the spectrum of immunogenic C. abortus proteins we applied 2D immunoblot analysis and screening of an expression library using human and animal sera. We have identified 48 immunoreactive proteins representing potential diagnostic markers and also putative virulence factors, such as CAB080 (homologue of the “macrophage infectivity potentiator”, MIP), CAB167 (homologue of the “translocated actin recruitment protein”, TARP), CAB712 (homologue of the “chlamydial protease-like activity factor”, CPAF), CAB776 (homologue of the “Polymorphic membrane protein D”, PmpD), and the “hypothetical proteins” CAB063, CAB408 and CAB821, which are predicted to be type III secreted. We selected two putative virulence factors for further characterization, i.e. CAB080 (cMIP) and CAB063, and studied their expression profiles at transcript and protein levels. Analysis of the subcellular localization of both proteins throughout the developmental cycle revealed CAB063 being the first C. abortus protein shown to be translocated to the host cell nucleus. PMID:24260366

Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory.

PubMed

Tanigaki, Yusuke; Higashi, Takanobu; Takayama, Kotaro; Nagano, Atsushi J; Honjo, Mie N; Fukuda, Hirokazu

2015-01-01

In plant factories, measurements of plant conditions are necessary at an early stage of growth to predict harvest times of high value-added crops. Moreover, harvest qualities depend largely on environmental stresses that elicit plant hormone responses. However, the complexities of plant hormone networks have not been characterized under nonstress conditions. In the present study, we determined temporal expression profiles of all genes and then focused on plant hormone pathways using RNA-Seq analyses of gene expression in tomato leaves every 2 h for 48 h. In these experiments, temporally expressed genes were found in the hormone synthesis pathways for salicylic acid, abscisic acid, ethylene, and jasmonic acid. The timing of CAB expression 1 (TOC1) and abscisic acid insensitive 1 (ABA1) and open stomata 1 (OST1) control gating stomata. In this study, compare with tomato and Arabidopsis thaliana, expression patterns of TOC1 have similarity. In contrast, expression patterns of tomato ABI1 and OST1 had expression peak at different time. These findings suggest that the regulation of gating stomata does not depend predominantly on TOC1 and significantly reflects the extracellular environment. The present data provide new insights into relationships between temporally expressed plant hormone-related genes and clock genes under normal sunlight conditions.

Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory

PubMed Central

Tanigaki, Yusuke; Higashi, Takanobu; Takayama, Kotaro; Nagano, Atsushi J.; Honjo, Mie N.; Fukuda, Hirokazu

2015-01-01

In plant factories, measurements of plant conditions are necessary at an early stage of growth to predict harvest times of high value-added crops. Moreover, harvest qualities depend largely on environmental stresses that elicit plant hormone responses. However, the complexities of plant hormone networks have not been characterized under nonstress conditions. In the present study, we determined temporal expression profiles of all genes and then focused on plant hormone pathways using RNA-Seq analyses of gene expression in tomato leaves every 2 h for 48 h. In these experiments, temporally expressed genes were found in the hormone synthesis pathways for salicylic acid, abscisic acid, ethylene, and jasmonic acid. The timing of CAB expression 1 (TOC1) and abscisic acid insensitive 1 (ABA1) and open stomata 1 (OST1) control gating stomata. In this study, compare with tomato and Arabidopsis thaliana, expression patterns of TOC1 have similarity. In contrast, expression patterns of tomato ABI1 and OST1 had expression peak at different time. These findings suggest that the regulation of gating stomata does not depend predominantly on TOC1 and significantly reflects the extracellular environment. The present data provide new insights into relationships between temporally expressed plant hormone-related genes and clock genes under normal sunlight conditions. PMID:26624004

LWD-TCP complex activates the morning gene CCA1 in Arabidopsis.

PubMed

Wu, Jing-Fen; Tsai, Huang-Lung; Joanito, Ignasius; Wu, Yi-Chen; Chang, Chin-Wen; Li, Yi-Hang; Wang, Ying; Hong, Jong Chan; Chu, Jhih-Wei; Hsu, Chao-Ping; Wu, Shu-Hsing

2016-10-13

A double-negative feedback loop formed by the morning genes CIRCADIAN CLOCK ASSOCIATED1 (CCA1)/LATE ELONGATED HYPOCOTYL (LHY) and the evening gene TIMING OF CAB EXPRESSION1 (TOC1) contributes to regulation of the circadian clock in Arabidopsis. A 24-h circadian cycle starts with the peak expression of CCA1 at dawn. Although CCA1 is targeted by multiple transcriptional repressors, including PSEUDO-RESPONSE REGULATOR9 (PRR9), PRR7, PRR5 and CCA1 HIKING EXPEDITION (CHE), activators of CCA1 remain elusive. Here we use mathematical modelling to infer a co-activator role for LIGHT-REGULATED WD1 (LWD1) in CCA1 expression. We show that the TEOSINTE BRANCHED 1-CYCLOIDEA-PCF20 (TCP20) and TCP22 proteins act as LWD-interacting transcriptional activators. The concomitant binding of LWD1 and TCP20/TCP22 to the TCP-binding site in the CCA1 promoter activates CCA1. Our study reveals activators of the morning gene CCA1 and provides an action mechanism that ensures elevated expression of CCA1 at dawn to sustain a robust clock.

LWD–TCP complex activates the morning gene CCA1 in Arabidopsis

PubMed Central

Wu, Jing-Fen; Tsai, Huang-Lung; Joanito, Ignasius; Wu, Yi-Chen; Chang, Chin-Wen; Li, Yi-Hang; Wang, Ying; Hong, Jong Chan; Chu, Jhih-Wei; Hsu, Chao-Ping; Wu, Shu-Hsing

2016-01-01

A double-negative feedback loop formed by the morning genes CIRCADIAN CLOCK ASSOCIATED1 (CCA1)/LATE ELONGATED HYPOCOTYL (LHY) and the evening gene TIMING OF CAB EXPRESSION1 (TOC1) contributes to regulation of the circadian clock in Arabidopsis. A 24-h circadian cycle starts with the peak expression of CCA1 at dawn. Although CCA1 is targeted by multiple transcriptional repressors, including PSEUDO-RESPONSE REGULATOR9 (PRR9), PRR7, PRR5 and CCA1 HIKING EXPEDITION (CHE), activators of CCA1 remain elusive. Here we use mathematical modelling to infer a co-activator role for LIGHT-REGULATED WD1 (LWD1) in CCA1 expression. We show that the TEOSINTE BRANCHED 1-CYCLOIDEA-PCF20 (TCP20) and TCP22 proteins act as LWD-interacting transcriptional activators. The concomitant binding of LWD1 and TCP20/TCP22 to the TCP-binding site in the CCA1 promoter activates CCA1. Our study reveals activators of the morning gene CCA1 and provides an action mechanism that ensures elevated expression of CCA1 at dawn to sustain a robust clock. PMID:27734958

The phosphoenolpyruvate/phosphate translocator is required for phenolic metabolism, palisade cell development, and plastid-dependent nuclear gene expression.

PubMed

Streatfield, S J; Weber, A; Kinsman, E A; Häusler, R E; Li, J; Post-Beittenmiller, D; Kaiser, W M; Pyke, K A; Flügge, U I; Chory, J

1999-09-01

The Arabidopsis chlorophyll a/b binding protein (CAB) gene underexpressed 1 (cue1) mutant underexpresses light-regulated nuclear genes encoding chloroplast-localized proteins. cue1 also exhibits mesophyll-specific chloroplast and cellular defects, resulting in reticulate leaves. Both the gene underexpression and the leaf cell morphology phenotypes are dependent on light intensity. In this study, we determine that CUE1 encodes the plastid inner envelope phosphoenolpyruvate/phosphate translocator (PPT) and define amino acid residues that are critical for translocator function. The biosynthesis of aromatics is compromised in cue1, and the reticulate phenotype can be rescued by feeding aromatic amino acids. Determining that CUE1 encodes PPT indicates the in vivo role of the translocator in metabolic partitioning and reveals a mesophyll cell-specific requirement for the translocator in Arabidopsis leaves. The nuclear gene expression defects in cue1 suggest that a light intensity-dependent interorganellar signal is modulated through metabolites dependent on a plastid supply of phosphoenolpyruvate.

Role of extracellular matrix protein CabA in resistance of Vibrio vulnificus biofilms to decontamination strategies.

PubMed

Park, Jin Hwan; Lee, Byungho; Jo, Youmi; Choi, Sang Ho

2016-11-07

Biofilms are recalcitrant and raise safety problems in the food industry. In this study, the role of CabA, an extracellular matrix protein, in the resistance of the biofilms of Vibrio vulnificus, a foodborne pathogen, to decontamination strategies was investigated. Biofilms of the cabA mutant revealed reduced resistance to detachment by vibration and disinfection by sodium hypochlorite compared to the biofilms of the parental wild type in vitro. The reduced resistance of the cabA mutant biofilms was complemented by introducing a recombinant cabA, indicating that the reduced resistance of the cabA mutant biofilms is caused by the inactivation of cabA. The expression of cabA was induced in cells bound to oyster, the primary vehicle of the pathogen. The cabA mutant biofilms on oyster are defective in biomass and resistance to detachment and disinfection. The bacterial cells in the wild-type biofilms are clustered by filaments which are not apparent in the cabA mutant biofilms. The combined results indicated that CabA contributes to the structural integrity of V. vulnificus biofilms possibly by forming filaments in the matrix and thus rendering the biofilms robust, suggesting that CabA could be a target to control V. vulnificus biofilms on oyster. Copyright © 2016 Elsevier B.V. All rights reserved.

microRNA-451a regulates colorectal cancer proliferation in response to radiation.

PubMed

Ruhl, Rebecca; Rana, Shushan; Kelley, Katherine; Espinosa-Diez, Cristina; Hudson, Clayton; Lanciault, Christian; Thomas, Charles R; Liana Tsikitis, V; Anand, Sudarshan

2018-05-03

Colorectal cancer (CRC) is a leading cause of cancer-related death. The biologic response of CRC to standard of care adjuvant therapies such as chemotherapy and radiation are poorly understood. MicroRNAs (miRs) have been shown to affect CRC progression and metastasis. Therefore, we hypothesized that specific miRs modulate CRC response to chemoradiation. In this study, we used miR expression profiling and discovered a set of microRNAs upregulated rapidly in response to either a single 2 Gy dose fraction or a 10 Gy dose of γ-radiation in mouse colorectal carcinoma models. We used gain and loss-of-function studies in 2D and 3Dcell proliferation assays and colony formation assays to understand the role of the top miR candidate from our profiling. We used Student's T-tests for simple comparisons and two-factor ANOVA for evaluating significance. The most upregulated candidate at early time points in our signature, miR-451a inhibited tumor cell proliferation and attenuated surviving fraction in longer-term cultures. Conversely, inhibition of miR-451a increased proliferation, tumorsphere formation, and surviving fraction of tumor cells. Using a bioinformatics approach, we identified four genes, CAB39, EMSY, MEX3C, and EREG, as targets of miR-451a. Transfection of miR-451a decreased both mRNA and protein levels of these targets. Importantly, we found miR-451a expression was high and CAB39, EMSY levels were low in a small subset of rectal cancer patients who had a partial response to chemoradiation when compared to patients that had no response. Finally, analysis of a TCGA colorectal cancer dataset revealed that CAB39 and EMSY are upregulated at the protein level in a significant number of CRC patients. Higher levels of CAB39 and EMSY correlated with poorer overall survival. Taken together, our data indicates miR-451a is induced by radiation and may influence colorectal carcinoma proliferation via CAB39 and EMSY pathways.

Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease in Lagerstroemia indica

PubMed Central

Shi, Weibing; Rinehart, Timothy

2015-01-01

Transcriptome analysis was conducted in two popular Lagerstroemia cultivars: “Natchez” (NAT), a white flower and powdery mildew resistant interspecific hybrid and “Carolina Beauty” (CAB), a red flower and powdery mildew susceptible L. indica cultivar. RNA-seq reads were generated from Erysiphe australiana infected leaves and de novo assembled. A total of 37,035 unigenes from 224,443 assembled contigs in both genotypes were identified. Approximately 85% of these unigenes have known function. Of them, 475 KEGG genes were found significantly different between the two genotypes. Five of the top ten differentially expressed genes (DEGs) involved in the biosynthesis of secondary metabolites (plant defense) and four in flavonoid biosynthesis pathway (antioxidant activities or flower coloration). Furthermore, 5 of the 12 assembled unigenes in benzoxazinoid biosynthesis and 7 of 11 in flavonoid biosynthesis showed higher transcript abundance in NAT. The relative abundance of transcripts for 16 candidate DEGs (9 from CAB and 7 from NAT) detected by qRT-PCR showed general agreement with the abundances of the assembled transcripts in NAT. This study provided the first transcriptome analyses in L. indica. The differential transcript abundance between two genotypes indicates that it is possible to identify candidate genes that are associated with the plant defenses or flower coloration. PMID:26247009

Changes in neuroendocrine elements in bronchial mucosa in chronic lung disease in adults.

PubMed

Pilmane, M; Luts, A; Sundler, F

1995-05-01

It is not clear whether there is any association between metaplasia of the bronchial epithelium and changes in the distribution of neuroendocrine cells. This study examined, by immunohistological techniques, the distribution of neuroendocrine cells and juxtamucoscal nerve fibres in bronchial biopsies showing metaplastic changes. Bronchial biopsies from 12 subjects with epithelial metaplasia associated with bronchiectasis and diffuse pulmonary fibrosis were examined by conventional light microscopy and immunohistological techniques for protein gene product 9.5 (PGP), chromogranin A and B (CAB), serotonin, vasoactive intestinal peptide (VIP), substance P (SP), calcitonin gene-related peptide (CGRP), calcitonin (CT), and gastrin releasing peptide (GRP). Regions of non-metaplastic epithelium contained numerous PGP and serotonin immunoreactive cells. Sub-populations of these cells displayed CAB, CGRP, CT, and GRP immunoreactivity. Metaplastic epithelium contained only a few weakly stained PGP, serotonin, CAB, GRP, CT and CGRP immunoreactive cells in six cases. Metaplastic epithelium was characterised by a high number of CAB-containing cells in six cases and in these biopsies prominent PGP-containing nerve bundles were seen in the subepithelial layer beneath the metaplastic epithelium. The distribution patterns of neuroendocrine cells and neuronal elements vary between areas of normal and metaplastic epithelium and within areas of metaplastic epithelium. Neuronal hyperplasia was associated with an increase in the number of CAB-containing cells within the metaplastic epithelium.

Changes in neuroendocrine elements in bronchial mucosa in chronic lung disease in adults.

PubMed Central

Pilmane, M.; Luts, A.; Sundler, F.

1995-01-01

BACKGROUND--It is not clear whether there is any association between metaplasia of the bronchial epithelium and changes in the distribution of neuroendocrine cells. This study examined, by immunohistological techniques, the distribution of neuroendocrine cells and juxtamucoscal nerve fibres in bronchial biopsies showing metaplastic changes. METHODS--Bronchial biopsies from 12 subjects with epithelial metaplasia associated with bronchiectasis and diffuse pulmonary fibrosis were examined by conventional light microscopy and immunohistological techniques for protein gene product 9.5 (PGP), chromogranin A and B (CAB), serotonin, vasoactive intestinal peptide (VIP), substance P (SP), calcitonin gene-related peptide (CGRP), calcitonin (CT), and gastrin releasing peptide (GRP). RESULTS--Regions of non-metaplastic epithelium contained numerous PGP and serotonin immunoreactive cells. Sub-populations of these cells displayed CAB, CGRP, CT, and GRP immunoreactivity. Metaplastic epithelium contained only a few weakly stained PGP, serotonin, CAB, GRP, CT and CGRP immunoreactive cells in six cases. Metaplastic epithelium was characterised by a high number of CAB-containing cells in six cases and in these biopsies prominent PGP-containing nerve bundles were seen in the subepithelial layer beneath the metaplastic epithelium. CONCLUSIONS--The distribution patterns of neuroendocrine cells and neuronal elements vary between areas of normal and metaplastic epithelium and within areas of metaplastic epithelium. Neuronal hyperplasia was associated with an increase in the number of CAB-containing cells within the metaplastic epithelium. Images PMID:7541167

A phosphate-regulated promoter for fine-tuned and reversible overexpression in Ostreococcus: application to circadian clock functional analysis.

PubMed

Djouani-Tahri, El Batoul; Sanchez, Frédéric; Lozano, Jean-Claude; Bouget, François-Yves

2011-01-01

The green picoalga Ostreococcus tauri (Prasinophyceae), which has been described as the smallest free-living eukaryotic organism, has minimal cellular ultra-structure and a very small genome. In recent years, O. tauri has emerged as a novel model organism for systems biology approaches that combine functional genomics and mathematical modeling, with a strong emphasis on light regulated processes and circadian clock. These approaches were made possible through the implementation of a minimal molecular toolbox for gene functional analysis including overexpression and knockdown strategies. We have previously shown that the promoter of the High Affinity Phosphate Transporter (HAPT) gene drives the expression of a luciferase reporter at high and constitutive levels under constant light. Here we report, using a luciferase reporter construct, that the HAPT promoter can be finely and reversibly tuned by modulating the level and nature of phosphate in culture medium. This HAPT regulation was additionally used to analyze the circadian clock gene Time of Cab expression 1 (TOC1). The phenotype of a TOC1ox/CCA1:Luc line was reverted from arrhythmic to rhythmic simply by adding phosphate to the culture medium. Furthermore, since the time of phosphate injection had no effect on the phase of CCA1:Luc expression, this study suggests further that TOC1 is a central clock gene in Ostreococcus. We have developed a phosphate-regulated expression system that allows fine gene function analysis in Ostreococcus. Recently, there has been a growing interest in microalgae as cell factories. This non-toxic phosphate-regulated system may prove useful in tuning protein expression levels quantitatively and temporally for biotechnological applications.

Characterization and Complementation of a Chlorophyll-Less Dominant Mutant GL1 in Lagerstroemia indica.

PubMed

Wang, Shu'an; Wang, Peng; Gao, Lulu; Yang, Rutong; Li, Linfang; Zhang, Enliang; Wang, Qing; Li, Ya; Yin, Zengfang

2017-05-01

Crape myrtle (Lagerstroemia indica) is a woody ornamental plant popularly grown because of its long-lasting, midsummer blooms and beautiful colors. The GL1 dominant mutant is the first chlorophyll-less mutant identified in crape myrtle. It was obtained from a natural yellow leaf bud mutation. We previously revealed that leaf color of the GL1 mutant is affected by light intensity. However, the mechanism of the GL1 mutant on light response remained unclear. The acclimation response of mutant and wild-type (WT) plants was assessed in a time series after transferring from low light (LL) to high light (HL) by analyzing chlorophyll synthesis precursor content, photosynthetic performance, and gene expression. In LL conditions, coproporphyrinogen III (Coprogen III) content had the greatest amount of accumulation in the mutant compared with WT, increasing by 100%. This suggested that the yellow leaf phenotype of the GL1 dominant mutant might be caused by disruption of coproporphyrinogen III oxidase (CPO) biosynthesis. Furthermore, the candidate gene, oxygen-independent CPO (HEMN), might only affect expression of upstream genes involved in chlorophyll metabolism in the mutant. Moreover, two genes, photosystem II (PSII) 10 kDa protein (psbR) and chlorophyll a/b binding protein gene (CAB1), had decreased mRNA levels in the GL1 mutant within the first 96 h following LL/HL transfer compared with the WT. Hierarchical clustering revealed that these two genes shared a similar expression trend as the oxygen-dependent CPO (HEMF). These findings provide evidence that GL1 is highly coordinated with PSII stability and chloroplast biogenesis.

Significant accumulation of C(4)-specific pyruvate, orthophosphate dikinase in a C(3) plant, rice.

PubMed

Fukayama, H; Tsuchida, H; Agarie, S; Nomura, M; Onodera, H; Ono, K; Lee, B H; Hirose, S; Toki, S; Ku, M S; Makino, A; Matsuoka, M; Miyao, M

2001-11-01

The C(4)-Pdk gene encoding the C(4) enzyme pyruvate, orthophosphate dikinase (PPDK) of maize (Zea mays cv Golden Cross Bantam) was introduced into the C(3) plant, rice (Oryza sativa cv Kitaake). When the intact maize C(4)-Pdk gene, containing its own promoter and terminator sequences and exon/intron structure, was introduced, the PPDK activity in the leaves of some transgenic lines was greatly increased, in one line reaching 40-fold over that of wild-type plants. In a homozygous line, the PPDK protein accounted for 35% of total leaf-soluble protein or 16% of total leaf nitrogen. In contrast, introduction of a chimeric gene containing the full-length cDNA of the maize PPDK fused to the maize C(4)-Pdk promoter or the rice Cab promoter only increased PPDK activity and protein level slightly. These observations suggest that the intron(s) or the terminator sequence of the maize gene, or a combination of both, is necessary for high-level expression. In maize and transgenic rice plants carrying the intact maize gene, the level of transcript in the leaves per copy of the maize C(4)-Pdk gene was comparable, and the maize gene was expressed in a similar organ-specific manner. These results suggest that the maize C(4)-Pdk gene behaves in a quantitatively and qualitatively similar way in maize and transgenic rice plants. The activity of the maize PPDK protein expressed in rice leaves was light/dark regulated as it is in maize. This is the first reported evidence for the presence of an endogenous PPDK regulatory protein in a C(3) plant.

CRISPRi-sRNA: Transcriptional-Translational Regulation of Extracellular Electron Transfer in Shewanella oneidensis.

PubMed

Cao, Yingxiu; Li, Xiaofei; Li, Feng; Song, Hao

2017-09-15

Extracellular electron transfer (EET) in Shewanella oneidensis MR-1, which is one of the most well-studied exoelectrogens, underlies many microbial electrocatalysis processes, including microbial fuel cells, microbial electrolysis cells, and microbial electrosynthesis. However, regulating the efficiency of EET remains challenging due to the lack of efficient genome regulation tools that regulate gene expression levels in S. oneidensis. Here, we systematically established a transcriptional regulation technology, i.e., clustered regularly interspaced short palindromic repeats interference (CRISPRi), in S. oneidensis MR-1 using green fluorescent protein (GFP) as a reporter. We used this CRISPRi technology to repress the expression levels of target genes, individually and in combination, in the EET pathways (e.g., the MtrCAB pathway and genes affecting the formation of electroactive biofilms in S. oneidensis), which in turn enabled the efficient regulation of EET efficiency. We then established a translational regulation technology, i.e., Hfq-dependent small regulatory RNA (sRNA), in S. oneidensis by repressing the GFP reporter and mtrA, which is a critical gene in the EET pathways in S. oneidensis. To achieve coordinated transcriptional and translational regulation at the genomic level, the CRISPRi and Hfq-dependent sRNA systems were incorporated into a single plasmid harbored in a recombinant S. oneidensis strain, which enabled an even higher efficiency of mtrA gene repression in the EET pathways than that achieved by the CRISPRi and Hfq-dependent sRNA system alone, as exhibited by the reduced electricity output. Overall, we developed a combined CRISPRi-sRNA method that enabled the synergistic transcriptional and translational regulation of target genes in S. oneidensis. This technology involving CRISPRi-sRNA transcriptional-translational regulation of gene expression at the genomic level could be applied to other microorganisms.

A novel biomarker associated with distress in humans: calcium-binding protein, spermatid-specific 1 (CABS1)

PubMed Central

Ritz, Thomas; Rosenfield, David; St. Laurent, Chris D.; Trueba, Ana F.; Werchan, Chelsey A.; Vogel, Pia D.; Auchus, Richard J.; Reyes-Serratos, Eduardo

2017-01-01

Calcium-binding protein spermatid-specific 1 (CABS1) is expressed in the human submandibular gland and has an anti-inflammatory motif similar to that in submandibular rat 1 in rats. Here, we investigate CABS1 in human saliva and its association with psychological and physiological distress and inflammation in humans. Volunteers participated across three studies: 1) weekly baseline measures; 2) a psychosocial speech and mental arithmetic stressor under evaluative threat; and 3) during academic exam stress. Salivary samples were analyzed for CABS1 and cortisol. Additional measures included questionnaires of perceived stress and negative affect; exhaled nitric oxide; respiration and cardiac activity; lung function; and salivary and nasal inflammatory markers. We identified a CABS1 immunoreactive band at 27 kDa in all participants and additional molecular mass forms in some participants. One week temporal stability of the 27-kDa band was satisfactory (test–retest reliability estimate = 0.62–0.86). Acute stress increased intensity of 18, 27, and 55 kDa bands; 27-kDa increases were associated with more negative affect and lower heart rate, sympathetic activity, respiration rate, and minute ventilation. In both acute and academic stress, changes in 27 kDa were positively associated with salivary cortisol. The 27-kDa band was also positively associated with VEGF and salivary leukotriene B4 levels. Participants with low molecular weight CABS1 bands showed reduced habitual stress and negative affect in response to acute stress. CABS1 is readily detected in human saliva and is associated with psychological and physiological indicators of stress. The role of CABS1 in inflammatory processes, stress, and stress resilience requires careful study. PMID:28381457

Two MYB-related transcription factors play opposite roles in sugar signaling in Arabidopsis.

PubMed

Chen, Yi-Shih; Chao, Yi-Chi; Tseng, Tzu-Wei; Huang, Chun-Kai; Lo, Pei-Ching; Lu, Chung-An

2017-02-01

Sugar regulation of gene expression has profound effects at all stages of the plant life cycle. Although regulation at the transcriptional level is one of the most prominent mechanisms by which gene expression is regulated, only a few transcription factors have been identified and demonstrated to be involved in the regulation of sugar-regulated gene expression. OsMYBS1, an R1/2-type MYB transcription factor, has been demonstrated to be involved in sugar- and hormone-regulated α-amylase gene expression in rice. Arabidopsis contains two OsMYBS1 homologs. In the present study, we investigate MYBS1 and MYBS2 in sugar signaling in Arabidopsis. Our results indicate that MYBS1 and MYBS2 play opposite roles in regulating glucose and ABA signaling in Arabidopsis during seed germination and early seedling development. MYB proteins have been classified into four subfamilies: R2R3-MYB, R1/2-MYB, 3R-MYB, and 4R-MYB. An R1/2-type MYB transcription factor, OsMYBS1, has been demonstrated to be involved in sugar- and hormone-regulated α-amylase genes expression in rice. In this study, two genes homologous to OsMYBS1, MYBS1 and MYBS2, were investigated in Arabidopsis. Subcellular localization analysis showed that MYBS1 and MYBS2 were localized in the nucleus. Rice embryo transient expression assays indicated that both MYBS1 and MYBS2 could recognize the sugar response element, TA-box, in the promoter and induced promoter activity. mybs1 mutant exhibited hypersensitivity to glucose, whereas mybs2 seedlings were hyposensitive to it. MYBS1 and MYBS2 are involved in the control of glucose-responsive gene expression, as the mybs1 mutant displayed increased expression of a hexokinase gene (HXK1), chlorophyll a/b-binding protein gene (CAB1), ADP-glucose pyrophosphorylase gene (APL3), and chalcone synthase gene (CHS), whereas the mybs2 mutant exhibited decreased expression of these genes. mybs1 also showed an enhanced response to abscisic acid (ABA) in the seed germination and seedling growth stages, while mybs2 showed reduced responses. The ABA biosynthesis inhibitor fluridone rescued the mybs1 glucose-hypersensitive phenotype. Moreover, the mRNA levels of three ABA biosynthesis genes, ABA1, NCED9, and AAO3, and three ABA signaling genes, ABI3, ABI4, and ABI5, were increased upon glucose treatment of mybs1 seedlings, but were decreased in mybs2 seedlings. These results indicate that MYBS1 and MYBS2 play opposite roles in regulating glucose and ABA signaling in Arabidopsis during seed germination and early seedling development.

Transcription of All amoC Copies Is Associated with Recovery ofNitrosomonas europaea from Ammonia Starvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berube, Paul M.; Samudrala, Ram; Stahl, David A.

2007-09-21

The chemolithotrophic ammonia-oxidizing bacteriumNitrosomonas europaea is known to be highly resistant to starvationconditions. The transcriptional response of N. europaea to ammoniaaddition following short- and long-term starvation was examined by primerextension and S1 nuclease protection analyses of genes encoding enzymesfor ammonia oxidation (amoCAB operons) and CO2 fixation (cbbLS), a third,lone copy of amoC (amoC3), and two representative housekeeping genes(glyA and rpsJ). Primer extension analysis of RNA isolated from growing,starved, and recovering cells revealed two differentially regulatedpromoters upstream of the two amoCAB operons. The distal sigma 70 typeamoCAB promoter was constitutively active in the presence of ammonia, butthe proximal promoter was onlymore » active when cells were recovering fromammonia starvation. The lone, divergent copy of amoC (amoC3) wasexpressed only during recovery. Both the proximal amoC1,2 promoter andthe amoC3 promoter are similar to gram-negative sigma E promoters, thusimplicating sigma E in the regulation of the recovery response. Althoughmodeling of subunit interactions suggested that a nonconservative prolinesubstitution in AmoC3 may modify the activity of the holoenzyme,characterization of a Delta amoC3 strain showed no significant differencein starvation recovery under conditions evaluated. In contrast to the amotranscripts, a delayed appearance of transcripts for a gene required forCO2 fixation (cbbL) suggested that its transcription is retarded untilsufficient energy is available. Overall, these data revealed a programmedexit from starvation likely involving regulation by sigma E and thecoordinated regulation of catabolic and anabolic genes.« less

Characterization of the glutathione S-transferase gene family through ESTs and expression analyses within common and pigmented cultivars of Citrus sinensis (L.) Osbeck.

PubMed

Licciardello, Concetta; D'Agostino, Nunzio; Traini, Alessandra; Recupero, Giuseppe Reforgiato; Frusciante, Luigi; Chiusano, Maria Luisa

2014-02-03

Glutathione S-transferases (GSTs) represent a ubiquitous gene family encoding detoxification enzymes able to recognize reactive electrophilic xenobiotic molecules as well as compounds of endogenous origin. Anthocyanin pigments require GSTs for their transport into the vacuole since their cytoplasmic retention is toxic to the cell. Anthocyanin accumulation in Citrus sinensis (L.) Osbeck fruit flesh determines different phenotypes affecting the typical pigmentation of Sicilian blood oranges. In this paper we describe: i) the characterization of the GST gene family in C. sinensis through a systematic EST analysis; ii) the validation of the EST assembly by exploiting the genome sequences of C. sinensis and C. clementina and their genome annotations; iii) GST gene expression profiling in six tissues/organs and in two different sweet orange cultivars, Cadenera (common) and Moro (pigmented). We identified 61 GST transcripts, described the full- or partial-length nature of the sequences and assigned to each sequence the GST class membership exploiting a comparative approach and the classification scheme proposed for plant species. A total of 23 full-length sequences were defined. Fifty-four of the 61 transcripts were successfully aligned to the C. sinensis and C. clementina genomes. Tissue specific expression profiling demonstrated that the expression of some GST transcripts was 'tissue-affected' and cultivar specific. A comparative analysis of C. sinensis GSTs with those from other plant species was also considered. Data from the current analysis are accessible at http://biosrv.cab.unina.it/citrusGST/, with the aim to provide a reference resource for C. sinensis GSTs. This study aimed at the characterization of the GST gene family in C. sinensis. Based on expression patterns from two different cultivars and on sequence-comparative analyses, we also highlighted that two sequences, a Phi class GST and a Mapeg class GST, could be involved in the conjugation of anthocyanin pigments and in their transport into the vacuole, specifically in fruit flesh of the pigmented cultivar.

Role of tissue transglutaminase type 2 in calbindin-D28k interaction with ataxin-1

PubMed Central

Vig, P.J.S.; Wei, J.; Shao, Q.; Hebert, M.D.; Subramony, S.H.; Sutton, L.T.

2007-01-01

Spinocerebellar ataxia-1 (SCA1) is caused by the expansion of a polyglutamine repeats within the disease protein, ataxin-1. The mutant ataxin-1 precipitates as large intranuclear aggregates in the affected neurons. These aggregates may protect neurons from mutant protein and/or trigger neuronal degeneration by encouraging recruitment of other essential proteins. Our previous studies have shown that calcium binding protein calbindin-D28k (CaB) associated with SCA1 pathogenesis is recruited to ataxin-1 aggregates in Purkinje cells of SCA1 mice. Since our recent findings suggest that tissue transglutaminase 2 (TG2) may be involved in cross-linking and aggregation of ataxin-1, the present study was initiated to determine if TG2 has any role in CaB-ataxin-1 interaction. The guinea pig TG2 covalently cross-linked purified rat brain CaB. Time dependent progressive increase in aggregation produced large multimers, which stayed on top of the gel. CaB interaction with ataxin-1 was studied using HeLa cell lysates expressing GFP and GFP tagged ataxin-1 with normal and expanded polyglutamine repeats (Q2, Q30 and Q82). The reaction products were analyzed by Western blots using anti- polyglutamine, CaB or GFP antibodies. CaB interacted with ataxin-1 independent of TG2 as the protein-protein cross-linker DSS stabilized CaB-ataxin-1 complex. TG2 cross-linked CaB preferentially with Q82 ataxin-1. The cross-linking was inhibited with EGTA or TG2 inhibitor cystamine. The present data indicate that CaB may be a TG2 substrate. In addition, aggregates of mutant ataxin-1 may recruit CaB via TG2 mediated covalent cross-linking, further supporting the argument that ataxin-1 aggregates may be toxic to neurons. PMID:17442486

Improvement of Arabidopsis Biomass and Cold, Drought and Salinity Stress Tolerance by Modified Circadian Clock-Associated PSEUDO-RESPONSE REGULATORs.

PubMed

Nakamichi, Norihito; Takao, Saori; Kudo, Toru; Kiba, Takatoshi; Wang, Yin; Kinoshita, Toshinori; Sakakibara, Hitoshi

2016-05-01

Plant circadian clocks control the timing of a variety of genetic, metabolic and physiological processes. Recent studies revealed a possible molecular mechanism for circadian clock regulation. Arabidopsis thaliana (Arabidopsis) PSEUDO-RESPONSE REGULATOR (PRR) genes, including TIMING OF CAB EXPRESSION 1 (TOC1), encode clock-associated transcriptional repressors that act redundantly. Disruption of multiple PRR genes results in drastic phenotypes, including increased biomass and abiotic stress tolerance, whereas PRR single mutants show subtle phenotypic differences due to genetic redundancy. In this study, we demonstrate that constitutive expression of engineered PRR5 (PRR5-VP), which functions as a transcriptional activator, can increase biomass and abiotic stress tolerance, similar to prr multiple mutants. Concomitant analyses of relative growth rate, flowering time and photosynthetic activity suggested that increased biomass of PRR5-VP plants is mostly due to late flowering, rather than to alterations in photosynthetic activity or growth rate. In addition, genome-wide gene expression profiling revealed that genes related to cold stress and water deprivation responses were up-regulated in PRR5-VP plants. PRR5-VP plants were more resistant to cold, drought and salinity stress than the wild type, whereas ft tsf and gi, well-known late flowering and increased biomass mutants, were not. These findings suggest that attenuation of PRR function by a single transformation of PRR-VP is a valuable method for increasing biomass as well as abiotic stress tolerance in Arabidopsis. Because the PRR gene family is conserved in vascular plants, PRR-VP may regulate biomass and stress responses in many plants, but especially in long-day annual plants. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A strategy of gene overexpression based on tandem repetitive promoters in Escherichia coli.

PubMed

Li, Mingji; Wang, Junshu; Geng, Yanping; Li, Yikui; Wang, Qian; Liang, Quanfeng; Qi, Qingsheng

2012-02-06

For metabolic engineering, many rate-limiting steps may exist in the pathways of accumulating the target metabolites. Increasing copy number of the desired genes in these pathways is a general method to solve the problem, for example, the employment of the multi-copy plasmid-based expression system. However, this method may bring genetic instability, structural instability and metabolic burden to the host, while integrating of the desired gene into the chromosome may cause inadequate transcription or expression. In this study, we developed a strategy for obtaining gene overexpression by engineering promoter clusters consisted of multiple core-tac-promoters (MCPtacs) in tandem. Through a uniquely designed in vitro assembling process, a series of promoter clusters were constructed. The transcription strength of these promoter clusters showed a stepwise enhancement with the increase of tandem repeats number until it reached the critical value of five. Application of the MCPtacs promoter clusters in polyhydroxybutyrate (PHB) production proved that it was efficient. Integration of the phaCAB genes with the 5CPtacs promoter cluster resulted in an engineered E.coli that can accumulate 23.7% PHB of the cell dry weight in batch cultivation. The transcription strength of the MCPtacs promoter cluster can be greatly improved by increasing the tandem repeats number of the core-tac-promoter. By integrating the desired gene together with the MCPtacs promoter cluster into the chromosome of E. coli, we can achieve high and stale overexpression with only a small size. This strategy has an application potential in many fields and can be extended to other bacteria.

Pseudomonas sax genes overcome aliphatic isothiocyanate-mediated non-host resistance in Arabidopsis

Treesearch

Jun Fan; Casey Crooks; Gary Creissen; Lionel Hill; Shirley Fairhurst; Peter Doerner; Chris Lamb

2011-01-01

Most plant-microbe interactions do not result in disease; natural products restrict non-host pathogens. We found that sulforaphane (4-methylsulfinylbutyl isothiocyanate), a natural product derived from aliphatic glucosinolates, inhibits growth in Arabidopsis of non-host Pseudomonas bacteria in planta. Multiple sax genes (saxCAB/F/D/G) were identified in Pseudomonas...

Time Course of mRNA Induction Elicited by Salt Stress in the Common Ice Plant (Mesembryanthemum crystallinum) 1

PubMed Central

Michalowski, Christine B.; Olson, Steven W.; Piepenbrock, Mechtild; Schmitt, Jürgen M.; Bohnert, Hans J.

1989-01-01

In the facultative halophyte Mesembryanthemum crystallinum (common ice plant), irrigation with solutions containing NaCl induces an alternate mode of carbon dioxide fixation, Crassulacean acid metabolism (CAM). The salt stress protocol which we have established facilitates the study of CAM induction and the correlation of changes in metabolism and gene expression. We have studied the time course of mRNA induction for phosphoenolpyruvate carboxylase (PEPCase) (gene: ppc) and several other enzymes of carbon metabolism during stress. While CAM is not fully established for at least 10 days after the start of stress, mRNA amounts for PEPCase and for other CAM enzymes, such as Pyruvate orthophosphate dikinase, increase between day 2 and 3 after stress induction. Increases continue for at least 5 days. Concomitant with the increase of CAM transcripts, fluctuations in the mRNA amounts for genes rbcS and cab were observed. Transcript levels for these proteins decreased several-fold during a 3 to 4 day period. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:16666626

Structural and regulatory mutations in Vibrio parahaemolyticus type III secretion systems display variable effects on virulence.

PubMed

Calder, Thomas; de Souza Santos, Marcela; Attah, Victoria; Klimko, John; Fernandez, Jessie; Salomon, Dor; Krachler, Anne-Marie; Orth, Kim

2014-12-01

The Gram-negative bacterium, Vibrio parahaemolyticus, is a major cause of seafood-derived food poisoning throughout the world. The pathogenicity of V. parahaemolyticus is attributed to several virulence factors, including two type III secretion systems (T3SS), T3SS1 and T3SS2. Herein, we compare the virulence of V. parahaemolyticus POR strains, which harbor a mutation in the T3SS needle apparatus of either system, to V. parahaemolyticus CAB strains, which harbor mutations in positive transcriptional regulators of either system. These strains are derived from the clinical RIMD 2210633 strain. We demonstrate that each mutation affects the virulence of the bacterium in a different manner. POR and CAB strains exhibited similar levels of swarming motility and T3SS effector production and secretion, but the CAB3 and CAB4 strains, which harbor a mutation in the T3SS2 master regulator gene, formed reduced biofilm growth under T3SS2 inducing conditions. Additionally, while the cytotoxicity of the POR and CAB strains was similar, the CAB2 (T3SS1 regulatory mutant) strain was strikingly more invasive than the comparable POR2 (T3SS1 structural mutant) strain. In summary, creating structural or regulatory mutations in either T3SS1 or T3SS2 causes differential downstream effects on other virulence systems. Understanding the biological differences of strains created from a clinical isolate is critical for interpreting and understanding the pathogenic nature of V. parahaemolyticus. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Regulation and function of the pepper pectin methylesterase inhibitor (CaPMEI1) gene promoter in defense and ethylene and methyl jasmonate signaling in plants.

PubMed

An, Soo Hyun; Choi, Hyong Woo; Hong, Jeum Kyu; Hwang, Byung Kook

2009-11-01

Analysis of the promoters of defense-related genes is valuable for determining stress signaling and transcriptional activation during pathogen infection. Here, we have isolated and functionally characterized the promoter region of the pepper (Capsicum annuum) pectin methylesterase inhibitor 1 (CaPMEI1) gene in transiently transformed tobacco plants and stably transformed Arabidopsis plants. Among four 5' deletion constructs analyzed, the -958-bp CaPMEI1 promoter induced a high level of GUS reporter activity in tobacco leaf tissue, driven by pathogen infection as well as by ethylene and methyl jasmonate (MeJA) treatment. The 204-bp region from -958 bp to -754 bp of the CaPMEI1 promoter is responsible for the stress-responsive expression. In addition, the pepper transcription factor CARAV1 activated the CaPMEI1 promoter in tobacco leaves, whereas the transcription factor CAbZIP1 did not. In the transgenic Arabidopsis plants, the -958 bp CaPMEI1 promoter was functionally regulated by developmental cues, bacterial and oomycete pathogen infections, and treatment with ethylene and MeJA. Histochemical GUS staining analyses of Arabidopsis tissues revealed that the CaPMEI1 promoter was mainly activated in leaf veins in response to various biotic and abiotic stimuli. Together, these results suggest that CaPMEI1 promoter activation may be a critical molecular event for host defense response and ethylene- and MeJA-mediated CaPMEI1 gene expression.

Inhibition of biphasic ethylene production enhances tolerance to abiotic stress by reducing the accumulation of reactive oxygen species in Nicotiana tabacum.

PubMed

Wi, Soo Jin; Jang, Su Jin; Park, Ky Young

2010-07-01

Reactive oxygen species (ROS), such as H(2)O(2), are important plant cell signaling molecules involved in responses to biotic and abiotic stresses and in developmental and physiological processes. Despite the well-known physiological functions of ethylene production and stress signaling via ROS during stresses, whether ethylene acts alone or in conjunction with ROS has not yet been fully elucidated. Therefore, we investigated the relationship between ethylene production and ROS accumulation during the response to abiotic stress. We used three independent transgenic tobacco lines, CAS-AS-2, -3 and -4, in which an antisense transcript of the senescence-related ACC synthase (ACS) gene from carnation flower (CARACC, Gen-Bank accession No. M66619) was expressed heterologously. Biphasic ethylene biosynthesis was reduced significantly in these transgenic plants, with or without H(2)O(2) treatment. These plants exhibited significantly reduced H(2)O(2)-induced gene-specific expression of ACS members, which were regulated in a time-dependent manner. The higher levels of NtACS1 expression in wild-type plants led to a second peak in ethylene production, which resulted in a more severe level of necrosis and cell death, as determined by trypan blue staining. In the transgenic lines, upregulated transcription of CAB, POR1 and RbcS resulted in increased photosynthetic performance following salt stress. This stress tolerance of H(2)O(2)-treated transgenic plants resulted from reduced ethylene biosynthesis, which decreased ROS accumulation via increased gene expression and activity of ROS-detoxifying enzymes, including MnSOD, CuZnSOD, and catalase. Therefore, it is suggested that ethylene plays a potentially critical role as an amplifier for ROS accumulation, implying a synergistic effect between biosynthesis of ROS and ethylene.

Characterization of the glutathione S-transferase gene family through ESTs and expression analyses within common and pigmented cultivars of Citrus sinensis (L.) Osbeck

PubMed Central

2014-01-01

Background Glutathione S-transferases (GSTs) represent a ubiquitous gene family encoding detoxification enzymes able to recognize reactive electrophilic xenobiotic molecules as well as compounds of endogenous origin. Anthocyanin pigments require GSTs for their transport into the vacuole since their cytoplasmic retention is toxic to the cell. Anthocyanin accumulation in Citrus sinensis (L.) Osbeck fruit flesh determines different phenotypes affecting the typical pigmentation of Sicilian blood oranges. In this paper we describe: i) the characterization of the GST gene family in C. sinensis through a systematic EST analysis; ii) the validation of the EST assembly by exploiting the genome sequences of C. sinensis and C. clementina and their genome annotations; iii) GST gene expression profiling in six tissues/organs and in two different sweet orange cultivars, Cadenera (common) and Moro (pigmented). Results We identified 61 GST transcripts, described the full- or partial-length nature of the sequences and assigned to each sequence the GST class membership exploiting a comparative approach and the classification scheme proposed for plant species. A total of 23 full-length sequences were defined. Fifty-four of the 61 transcripts were successfully aligned to the C. sinensis and C. clementina genomes. Tissue specific expression profiling demonstrated that the expression of some GST transcripts was 'tissue-affected' and cultivar specific. A comparative analysis of C. sinensis GSTs with those from other plant species was also considered. Data from the current analysis are accessible at http://biosrv.cab.unina.it/citrusGST/, with the aim to provide a reference resource for C. sinensis GSTs. Conclusions This study aimed at the characterization of the GST gene family in C. sinensis. Based on expression patterns from two different cultivars and on sequence-comparative analyses, we also highlighted that two sequences, a Phi class GST and a Mapeg class GST, could be involved in the conjugation of anthocyanin pigments and in their transport into the vacuole, specifically in fruit flesh of the pigmented cultivar. PMID:24490620

Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM

PubMed Central

Amin, N; Byrne, E; Johnson, J; Chenevix-Trench, G; Walter, S; Nolte, I M; Vink, J M; Rawal, R; Mangino, M; Teumer, A; Keers, J C; Verwoert, G; Baumeister, S; Biffar, R; Petersmann, A; Dahmen, N; Doering, A; Isaacs, A; Broer, L; Wray, N R; Montgomery, G W; Levy, D; Psaty, B M; Gudnason, V; Chakravarti, A; Sulem, P; Gudbjartsson, D F; Kiemeney, L A; Thorsteinsdottir, U; Stefansson, K; van Rooij, F J A; Aulchenko, Y S; Hottenga, J J; Rivadeneira, F R; Hofman, A; Uitterlinden, A G; Hammond, C J; Shin, S-Y; Ikram, A; Witteman, J C M; Janssens, A C J W; Snieder, H; Tiemeier, H; Wolfenbuttel, B H R; Oostra, B A; Heath, A C; Wichmann, E; Spector, T D; Grabe, H J; Boomsma, D I; Martin, N G; van Duijn, C M

2012-01-01

Coffee consumption is a model for addictive behavior. We performed a meta-analysis of genome-wide association studies (GWASs) on coffee intake from 8 Caucasian cohorts (N=18 176) and sought replication of our top findings in a further 7929 individuals. We also performed a gene expression analysis treating different cell lines with caffeine. Genome-wide significant association was observed for two single-nucleotide polymorphisms (SNPs) in the 15q24 region. The two SNPs rs2470893 and rs2472297 (P-values=1.6 × 10−11 and 2.7 × 10−11), which were also in strong linkage disequilibrium (r2=0.7) with each other, lie in the 23-kb long commonly shared 5′ flanking region between CYP1A1 and CYP1A2 genes. CYP1A1 was found to be downregulated in lymphoblastoid cell lines treated with caffeine. CYP1A1 is known to metabolize polycyclic aromatic hydrocarbons, which are important constituents of coffee, whereas CYP1A2 is involved in the primary metabolism of caffeine. Significant evidence of association was also detected at rs382140 (P-value=3.9 × 10−09) near NRCAM—a gene implicated in vulnerability to addiction, and at another independent hit rs6495122 (P-value=7.1 × 10−09)—an SNP associated with blood pressure—in the 15q24 region near the gene ULK3, in the meta-analysis of discovery and replication cohorts. Our results from GWASs and expression analysis also strongly implicate CAB39L in coffee drinking. Pathway analysis of differentially expressed genes revealed significantly enriched ubiquitin proteasome (P-value=2.2 × 10−05) and Parkinson's disease pathways (P-value=3.6 × 10−05). PMID:21876539

The role of abdominal compliance, the neglected parameter in critically ill patients - a consensus review of 16. Part 1: definitions and pathophysiology.

PubMed

Malbrain, Manu L N G; Roberts, Derek J; De Laet, Inneke; De Waele, Jan J; Sugrue, Michael; Schachtrupp, Alexander; Duchesne, Juan; Van Ramshorst, Gabrielle; De Keulenaer, Bart; Kirkpatrick, Andrew W; Ahmadi-Noorbakhsh, Siavash; Mulier, Jan; Ivatury, Rao; Pracca, Francisco; Wise, Robert; Pelosi, Paolo

2014-01-01

Over the last few decades, increasing attention has been paid to understanding the pathophysiology, aetiology, prognosis, and treatment of elevated intra-abdominal pressure (IAP) in trauma, surgical, and medical patients. However, there is presently a relatively poor understanding of intra-abdominal volume (IAV) and the relationship between IAV and IAP (i.e. abdominal compliance). Consensus definitions on Cab were discussed during the 5th World Congress on Abdominal Compartment Syndrome and a writing committee was formed to develop this article. During the writing process, a systematic and structured Medline and PubMed search was conducted to identify relevant studies relating to the topic. According to the recently updated consensus definitions of the World Society on Abdominal Compartment Syndrome (WSACS), abdominal compliance (Cab) is defined as a measure of the ease of abdominal expansion, which is determined by the elasticity of the abdominal wall and diaphragm. It should be expressed as the change in IAV per change in IAP (mL [mm Hg]⁻¹). Importantly, Cab is measured differently than IAP and the abdominal wall (and its compliance) is only a part of the total abdominal pressure-volume (PV) relationship. During an increase in IAV, different phases are encountered: the reshaping, stretching, and pressurisation phases. The first part of this review article starts with a comprehensive list of the different definitions related to IAP (at baseline, during respiratory variations, at maximal IAV), IAV (at baseline, additional volume, abdominal workspace, maximal and unadapted volume), and abdominal compliance and elastance (i.e. the relationship between IAV and IAP). An historical background on the pathophysiology related to IAP, IAV and Cab follows this. Measurement of Cab is difficult at the bedside and can only be done in a case of change (removal or addition) in IAV. The Cab is one of the most neglected parameters in critically ill patients, although it plays a key role in understanding the deleterious effects of unadapted IAV on IAP and end-organ perfusion. The definitions presented herein will help to understand the key mechanisms in relation to Cab and clinical conditions and should be used for future clinical and basic science research. Specific measurement methods, guidelines and recommendations for clinical management of patients with low Cab are published in a separate review.

Caffeinated Alcohol Consumption Profiles and Associations with Use Severity and Outcome Expectancies

PubMed Central

Lau-Barraco, Cathy; Milletich, Robert J.; Linden, Ashley N.

2014-01-01

Growing evidence suggests that the consumption of caffeinated alcoholic beverages (CAB) may be riskier than alcohol alone. Efforts to identify patterns of CAB use and the correlates of such drinking patterns could further our conceptualization of and intervention for this health issue. Consequently, the current study aimed to (1) identify distinct classes of CAB users, (2) examine differences between classes on measures of alcohol and caffeine problems, and (3) compare distinct classes of CAB users on caffeine and alcohol outcome expectancies. Participants were 583 (31% men) undergraduate students from a psychology research pool. Latent profile analysis models were derived using four indicators: CAB use quantity, CAB use frequency, alcohol use quantity, and alcohol use frequency. Finding revealed four classes of drinkers: High Alcohol/High CAB (6.00%), High Alcohol/Moderate CAB (5.15%), High Alcohol/Low CAB (22.99%), and Low Alcohol/Low CAB (65.87%). The Low Alcohol/Low CAB class reported the lowest relative levels of caffeine dependence symptoms, caffeine withdrawal, alcohol use problems, and heavy episodic drinking frequency. Further, results indicated differential expectancy endorsement based on use profiles. CAB users in the High Alcohol/Low CAB class endorsed more positive alcohol expectancies than the Low Alcohol/Low CAB group. Those in the High Alcohol/High CAB class endorsed stronger withdrawal symptoms caffeine expectancies than all other classes. Inclusion of substance-specific expectancies into larger theoretical frameworks in future work of CAB use may be beneficial. Findings may inform intervention efforts for those at greatest risk related to CAB consumption. PMID:24210683

Caffeinated alcohol consumption profiles and associations with use severity and outcome expectancies.

PubMed

Lau-Barraco, Cathy; Milletich, Robert J; Linden, Ashley N

2014-01-01

Growing evidence suggests that the consumption of caffeinated alcoholic beverages (CAB) may be riskier than alcohol alone. Efforts to identify patterns of CAB use and the correlates of such drinking patterns could further our conceptualization of and intervention for this health issue. Consequently, the current study aimed to (1) identify distinct classes of CAB users, (2) examine differences between classes on measures of alcohol and caffeine problems, and (3) compare distinct classes of CAB users on caffeine and alcohol outcome expectancies. Participants were 583 (31% men) undergraduate students from a psychology research pool. Latent profile analysis models were derived using four indicators: CAB use quantity, CAB use frequency, alcohol use quantity, and alcohol use frequency. Finding revealed four classes of drinkers: High Alcohol/High CAB (6.00%), High Alcohol/Moderate CAB (5.15%), High Alcohol/Low CAB (22.99%), and Low Alcohol/Low CAB (65.87%). The Low Alcohol/Low CAB class reported the lowest relative levels of caffeine dependence symptoms, caffeine withdrawal, alcohol use problems, and heavy episodic drinking frequency. Further, results indicated differential expectancy endorsement based on use profiles. CAB users in the High Alcohol/Low CAB class endorsed more positive alcohol expectancies than the Low Alcohol/Low CAB group. Those in the High Alcohol/High CAB class endorsed stronger withdrawal symptom caffeine expectancies than all other classes. Inclusion of substance-specific expectancies into larger theoretical frameworks in future work of CAB use may be beneficial. Findings may inform intervention efforts for those at greatest risk related to CAB consumption. © 2013.

Molecular cloning, expression and single nucleotide polymorphisms of protein phosphatase 1 (PP1) in mandarin fish (Siniperca chuatsi).

PubMed

Cheng, Xiao-Yan; He, Shan; Liang, Xu-Fang; Song, Yi; Yuan, Xiao-Chen; Li, Ling; Wen, Zheng-Yong; Cai, Wen-Jing; Tao, Ya-Xiong

2015-11-01

In the wild, mandarin fish (Siniperca chuatsi) only feed on live prey fish, refusing dead prey. When reared in ponds, training will result in some mandarin fish accepting artificial diets. However, little is currently known about the molecular mechanism of the individual difference. Serine/threonine protein phosphatase 1 (PP1) is a suppressor of learning and long-term memory (LTM) in mammals. In the present study, the relationship between PP1 and the individual difference in acceptance of artificial diets in mandarin fish was investigated. The complete CDS (coding sequence) of four PP1 isoforms (PP1caa, PP1cab, PP1cb and PP1cc) were cloned in mandarin fish. The amino acid sequences of these PP1 isoforms are highly conserved in different species. The mRNA expressions of PP1caa and PP1cb in brain of artificial diet feeders were significantly higher than those in nonfeeders, suggesting the deficiency in the maintenance of long-term memory of its natural food habit (live prey fish). The SNP loci in PP1caa and PP1cb were also found to be associated with the individual difference in acceptance of artificial diets in mandarin fish. These SNPs of PP1caa and PP1cb genes could be useful markers for gene-associated breeding of mandarin fish, which could accept artificial diets. In conclusion, different mRNA expression and SNPs of PP1caa and PP1cb genes in feeders and nonfeeders of artificial diets might contribute to understanding the molecular mechanism of individual difference in acceptance of artificial diets in mandarin fish. Copyright © 2015 Elsevier Inc. All rights reserved.

Characterization of Current Tower Cab Environments

DOT National Transportation Integrated Search

1977-11-01

This report describes the general tower cab environment in terms of: (a) the evolution of the tower cab, current cab classification and staffing levels, and the basic flow of ATC data relevant to cab operations, (b) a breakdown of functions performed...

Finite element analysis of ROPS for mechanical driving dump truck cab

NASA Astrophysics Data System (ADS)

Wang, Yong; Xie, Heping; Fang, Yuanbin; Feng, Handui; Dong, Lei

2018-02-01

For roll-over protective structures (ROPS) in a mechanical driving dump truck cab, it simulates the lateral, vertical and longitudinal loads of ROPS. It obtains stress and deformation of the cab that occurs to roll. For the relative weak position of ROPS in the cab, the structure of the cab is improved and verified according to the ISO 3164: 1995. The results show that the established finite element model can effectively predict the deformation and stress distribution of ROPS, and optimize the weak structure of the cab, which has important guiding significance for structural design of the cab and ROPS optimization of the mechanical driving dump truck cab.

Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant

PubMed Central

Hawkins, Angela K; Garza, Elyssa R; Dietz, Valerie A; Hernandez, Oscar J; Hawkins, W Daryl; Burrell, A Millie

2017-01-01

Abstract Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation. PMID:29220486

Novel Partial Reductive Pathway for 4-Chloronitrobenzene and Nitrobenzene Degradation in Comamonas sp. Strain CNB-1

PubMed Central

Wu, Jian-feng; Jiang, Cheng-ying; Wang, Bao-jun; Ma, Ying-fei; Liu, Zhi-pei; Liu, Shuang-jiang

2006-01-01

Comamonas sp. strain CNB-1 grows on 4-chloronitrobenzene (4-CNB) and nitrobenzene as sole carbon and nitrogen sources. In this study, two genetic segments, cnbB-orf2-cnbA and cnbR-orf1-cnbCaCbDEFGHI, located on a newly isolated plasmid, pCNB1 (ca. 89 kb), and involved in 4-CNB/nitrobenzene degradation, were characterized. Seven genes (cnbA, cnbB, cnbCa, cnbCb, cnbD, cnbG, and cnbH) were cloned and functionally expressed in recombinant Escherichia coli, and they were identified as encoding 4-CNB nitroreductase (CnbA), 1-hydroxylaminobenzene mutase (CnbB), 2-aminophenol 1,6-dioxygenase (CnbCab), 2-amino-5-chloromuconic semialdehyde dehydrogenase (CnbD), 2-hydroxy-5-chloromuconic acid (2H5CM) tautomerase, and 2-amino-5-chloromuconic acid (2A5CM) deaminase (CnbH). In particular, the 2A5CM deaminase showed significant identities (31 to 38%) to subunit A of Asp-tRNAAsn/Glu-tRNAGln amidotransferase and not to the previously identified deaminases for nitroaromatic compound degradation. Genetic cloning and expression of cnbH in Escherichia coli revealed that CnbH catalyzed the conversion of 2A5CM into 2H5CM and ammonium. Four other genes (cnbR, cnbE, cnbF, and cnbI) were tentatively identified according to their high sequence identities to other functionally identified genes. It was proposed that CnbH might represent a novel type of deaminase and be involved in a novel partial reductive pathway for chloronitrobenzene or nitrobenzene degradation. PMID:16517619

49 CFR 236.515 - Visibility of cab signals.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Visibility of cab signals. 236.515 Section 236.515..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.515 Visibility of cab signals. The cab signals...

49 CFR 236.515 - Visibility of cab signals.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Visibility of cab signals. 236.515 Section 236.515..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.515 Visibility of cab signals. The cab signals...

49 CFR 236.515 - Visibility of cab signals.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Visibility of cab signals. 236.515 Section 236.515..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.515 Visibility of cab signals. The cab signals...

49 CFR 236.515 - Visibility of cab signals.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Visibility of cab signals. 236.515 Section 236.515..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.515 Visibility of cab signals. The cab signals...

49 CFR 236.515 - Visibility of cab signals.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Visibility of cab signals. 236.515 Section 236.515..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.515 Visibility of cab signals. The cab signals...

49 CFR 230.87 - Cab lights.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Cab lights. 230.87 Section 230.87 Transportation... Signals, Sanders and Lights § 230.87 Cab lights. Each steam locomotive shall have cab lights that... readings from their usual and proper positions in the cab. These lights shall be so located and constructed...

49 CFR 230.87 - Cab lights.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Cab lights. 230.87 Section 230.87 Transportation... Signals, Sanders and Lights § 230.87 Cab lights. Each steam locomotive shall have cab lights that... readings from their usual and proper positions in the cab. These lights shall be so located and constructed...

49 CFR 230.87 - Cab lights.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Cab lights. 230.87 Section 230.87 Transportation... Signals, Sanders and Lights § 230.87 Cab lights. Each steam locomotive shall have cab lights that... readings from their usual and proper positions in the cab. These lights shall be so located and constructed...

49 CFR 230.87 - Cab lights.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Cab lights. 230.87 Section 230.87 Transportation... Signals, Sanders and Lights § 230.87 Cab lights. Each steam locomotive shall have cab lights that... readings from their usual and proper positions in the cab. These lights shall be so located and constructed...

49 CFR 230.87 - Cab lights.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Cab lights. 230.87 Section 230.87 Transportation... Signals, Sanders and Lights § 230.87 Cab lights. Each steam locomotive shall have cab lights that... readings from their usual and proper positions in the cab. These lights shall be so located and constructed...

49 CFR 393.203 - Cab and body components.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 5 2011-10-01 2011-10-01 false Cab and body components. 393.203 Section 393.203... NECESSARY FOR SAFE OPERATION Frames, Cab and Body Components, Wheels, Steering, and Suspension Systems § 393.203 Cab and body components. (a) The cab compartment doors or door parts used as an entrance or exist...

Low-fat yogurt consumption reduces biomarkers of chronic inflammation and inhibits markers of endotoxin exposure in healthy premenopausal women: a randomised controlled trial.

PubMed

Pei, Ruisong; DiMarco, Diana M; Putt, Kelley K; Martin, Derek A; Gu, Qinlei; Chitchumroonchokchai, Chureeporn; White, Heather M; Scarlett, Cameron O; Bruno, Richard S; Bolling, Bradley W

2017-12-01

The anti-inflammatory mechanisms of low-fat dairy product consumption are largely unknown. The objective of this study was to determine whether low-fat yogurt reduces biomarkers of chronic inflammation and endotoxin exposure in women. Premenopausal women (BMI 18·5-27 and 30-40 kg/m2) were randomised to consume 339 g of low-fat yogurt (yogurt non-obese (YN); yogurt obese (YO)) or 324 g of soya pudding (control non-obese; control obese (CO)) daily for 9 weeks (n 30/group). Fasting blood samples were analysed for IL-6, TNF-α/soluble TNF II (sTNF-RII), high-sensitivity C-reactive protein, 2-arachidonoyl glycerol, anandamide, monocyte gene expression, soluble CD14 (sCD14), lipopolysaccharide (LPS), LPS binding protein (LBP), IgM endotoxin-core antibody (IgM EndoCAb), and zonulin. BMI, waist circumference and blood pressure were also determined. After 9-week yogurt consumption, YO and YN had decreased TNF-α/sTNFR-RII. Yogurt consumption increased plasma IgM EndoCAb regardless of obesity status. sCD14 was not affected by diet, but LBP/sCD14 was lowered by yogurt consumption in both YN and YO. Yogurt intervention increased plasma 2-arachidonoylglycerol in YO but not YN. YO peripheral blood mononuclear cells expression of NF-κB inhibitor α and transforming growth factor β1 increased relative to CO at 9 weeks. Other biomarkers were unchanged by diet. CO and YO gained approximately 0·9 kg in body weight. YO had 3·6 % lower diastolic blood pressure at week 3. Low-fat yogurt for 9 weeks reduced biomarkers of chronic inflammation and endotoxin exposure in premenopausal women compared with a non-dairy control food. This trial was registered as NCT01686204.

Steering Control in a Low-Cost Driving Simulator: A Case for the Role of Virtual Vehicle Cab.

PubMed

Mecheri, Sami; Lobjois, Régis

2018-04-01

The aim of this study was to investigate steering control in a low-cost driving simulator with and without a virtual vehicle cab. In low-cost simulators, the lack of a vehicle cab denies driver access to vehicle width, which could affect steering control, insofar as locomotor adjustments are known to be based on action-scaled visual judgments of the environment. Two experiments were conducted in which steering control with and without a virtual vehicle cab was investigated in a within-subject design, using cornering and straight-lane-keeping tasks. Driving around curves without vehicle cab information made drivers deviate more from the lane center toward the inner edge in right (virtual cab = 4 ± 19 cm; no cab = 42 ± 28 cm; at the apex of the curve, p < .001) but not in left curves. More lateral deviation from the lane center toward the edge line was also found in driving without the virtual cab on straight roads (virtual cab = 21 ± 28 cm; no cab = 36 ± 27 cm; p < .001), whereas driving stability and presence ratings were not affected. In both experiments, the greater lateral deviation in the no-cab condition led to significantly more time driving off the lane. The findings strongly suggest that without cab information, participants underestimate the distance to the right edge of the car (in contrast to the left edge) and thus vehicle width. This produces considerable differences in the steering trajectory. Providing a virtual vehicle cab must be encouraged for more effectively capturing drivers' steering control in low-cost simulators.

Mining and expression analysis of candidate genes involved in regulating the chilling requirement fulfillment of Paeonia lactiflora 'Hang Baishao'.

PubMed

Zhang, Jiaping; Li, Danqing; Shi, Xiaohua; Zhang, Dong; Qiu, Shuai; Wei, Jianfen; Zhang, Jiao; Zhou, Jianghua; Zhu, Kaiyuan; Xia, Yiping

2017-12-22

The artificial enlargement of the planting area and ecological amplitude of ornamentals for horticultural and landscape applications are significant. Herbaceous peony (Paeonia lactiflora Pall.) is a world-famous ornamental with attractive and fragrant flowers and is mainly planted in temperate and cool areas. Comparatively higher winter temperatures in the subtropical and tropical Northern Hemisphere result in a deficit of chilling accumulation for bud dormancy release, which severely hinders "The southward plantation of herbaceous peony". Studies on the dormancy, chilling requirement (CR) and relevant molecular mechanisms of peony are needed to enhance our ability to extend the range of this valuable horticultural species. Based on natural and artificial chilling experiments, and chilling hour (CH) and chilling unit (CU) evaluation systems, the lowest CR of 'Hang Baishao' was between 504.00 and 672.00 CHs and the optimal CR was 672.00 CHs and 856.08 CUs for achieving strong sprouting, growth and flowering performance. Transcriptome sequencing and gene identification by RNA-Seq were performed on 'Hang Baishao' buds during the dormancy and sprouting periods. Six gene libraries were constructed, and 66 temperature- and photoperiod-associated unigenes were identified as the potential candidate genes that may regulate or possibly determine CR characteristics. The difference in the expression patterns of SUPPRESSPOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) between the winters of 2012-2013 and 2015-2016, and the difference of CR fulfillment periods also between these two winters represented the interesting congruent relationships. This correlation was also observed for WRKY DNA-BINDING PROTEIN 33 (WRKY 33). Combined with the results acquired from all of experiments, 'Hang Baishao' was confirmed to be a superb peony resource that have significantly low CR characteristics. The two genes of SOC1 and WRKY33 are likely involved in determining the CR amount and fulfillment period of 'Hang Baishao'. HEAT SHOCK PROTEIN, OSMOTIN and TIMING OF CAB EXPRESSION 1 also deserve attention for the CR research. This study could contribute to the knowledge of the deep factors and mechanisms that regulate CR characteristics, and may be beneficial for breeding new germplasms that have low CRs for landscape or horticulture applications in subtropical regions.

49 CFR 230.80 - Cabs.

Code of Federal Regulations, 2010 CFR

2010-10-01

... pipe, with properly rated valves and fittings. Live steam heating radiators must not be fastened to the cab. Exhaust steam radiators may be fastened to the cab. (c) Oil-burning steam locomotives. If the cab...

Enzymatic hydrolysis and fermentation of pretreated cashew apple bagasse with alkali and diluted sulfuric Acid for bioethanol production.

PubMed

Rocha, Maria Valderez Ponte; Rodrigues, Tigressa Helena Soares; de Macedo, Gorete Ribeiro; Gonçalves, Luciana R B

2009-05-01

The aim of this work was to optimize the enzymatic hydrolysis of the cellulose fraction of cashew apple bagasse (CAB) after diluted acid (CAB-H) and alkali pretreatment (CAB-OH), and to evaluate its fermentation to ethanol using Saccharomyces cerevisiae. Glucose conversion of 82 +/- 2 mg/g CAB-H and 730 +/- 20 mg/g CAB-OH was obtained when 2% (w/v) of solid and 30 FPU/g bagasse was used during hydrolysis at 45 degrees C, 2-fold higher than when using 15 FPU/g bagasse, 44 +/- 2 mg/g CAB-H, and 450 +/- 50 mg/g CAB-OH, respectively. Ethanol concentration and productivity, achieved after 6 h of fermentation, were 20.0 +/- 0.2 g L(-1) and 3.33 g L(-1) h(-1), respectively, when using CAB-OH hydrolyzate (initial glucose concentration of 52.4 g L(-1)). For CAB-H hydrolyzate (initial glucose concentration of 17.4 g L(-1)), ethanol concentration and productivity were 8.2 +/- 0.1 g L(-1) and 2.7 g L(-1) h(-1) in 3 h, respectively. Hydrolyzates fermentation resulted in an ethanol yield of 0.38 and 0.47 g/g glucose with pretreated CAB-OH and CAB-H, respectively. Ethanol concentration and productivity, obtained using CAB-OH hydrolyzate, were close to the values obtained in the conventional ethanol fermentation of cashew apple juice or sugar cane juice.

Myocardial Blood Flow in Man: Effects of Coronary Collateral Circulation and Coronary Artery Bypass Surgery

PubMed Central

Smith, Sidney C.; Gorlin, Richard; Herman, Michael V.; Taylor, Warren J.; Collins, John J.

1972-01-01

The effects of coronary artery bypass graft (CAB) and coronary collaterals (CC) on myocardial blood flow (MBF) were studied in 24 patients undergoing 29 CAB's. MBF after CAB was compared to preexisting MBF by intraoperatively injecting 133xenon via distal CAB with proximal CAB first occluded then open. Pressure gradients across bypassed obstructions were measured. The results were correlated with preoperative coronary arteriograms to determine the effects of CC on MBF and postobstructive perfusion pressures. Mean MBF was increased by CAB from 32±6 (se) ml/min per 100 g (CAB occluded) to 118±13 ml/min per 100 g (CAB open). The 133Xe clearance curves with CAB open were resolved into slow (19±2 ml/min per 100 g) and rapid (133±12 ml/min per 100 g) phases, suggesting that MBF remained heterogeneous after CAB. Vessels with less than 80% stenosis by angiography had pressure gradients less than 20 mm Hg across obstructions, high postobstructive perfusion pressures (75±7 mm Hg), and normal MBF (87±6 ml/min per 100 g) even with CAB occluded. Vessels with greater than 80% stenosis or total occlusion by angiography had significant pressure gradients with marked reduction of postobstructive MBF. No significant difference in postobstructive MBF was found when vessels with CC (21±4 ml/min per 100 g) were compared to those without CC (17±4 ml/min per 100 g) (P > 0.4). These studies demonstrate that (a) mean MBF increased 268% after CAB, (b) heterogeneous MBF persisted after CAB, (c) CC were not associated with significant increases in MBF, and (d) vessels with less than 80% stenosis had less than 20 mm Hg gradient with minimal effect on resting MBF. Images PMID:5056655

Clinical outcomes and nadir prostate-specific antigen (PSA) according to initial PSA levels in primary androgen deprivation therapy for metastatic prostate cancer.

PubMed

Kitagawa, Yasuhide; Ueno, Satoru; Izumi, Kouji; Kadono, Yoshifumi; Mizokami, Atsushi; Hinotsu, Shiro; Akaza, Hideyuki; Namiki, Mikio

2016-03-01

To investigate the clinical outcomes of metastatic prostate cancer patients and the relationship between nadir prostate-specific antigen (PSA) levels and different types of primary androgen deprivation therapy (PADT). This study utilized data from the Japan Study Group of Prostate Cancer registry, which is a large, multicenter, population-based database. A total of 2982 patients treated with PADT were enrolled. Kaplan-Meier analysis was used to compare progression-free survival (PFS) and overall survival (OS) in patients treated using combined androgen blockade (CAB) and non-CAB therapies. The relationships between nadir PSA levels and PADT type according to initial serum PSA levels were also investigated. Among the 2982 enrolled patients, 2101 (70.5 %) were treated with CAB. Although CAB-treated patients had worse clinical characteristics, their probability of PFS and OS was higher compared with those treated with a non-CAB therapy. These results were due to a survival benefit with CAB in patients with an initial PSA level of 500-1000 ng/mL. Nadir PSA levels were significantly lower in CAB patients than in non-CAB patients with comparable initial serum PSA levels. A small survival benefit for CAB in metastatic prostate cancer was demonstrated in a Japanese large-scale prospective cohort study. The clinical significance of nadir PSA levels following PADT was evident, but the predictive impact of PSA nadir on OS was different between CAB and non-CAB therapy.

Environmental context effects on craving among consumers of caffeinated alcohol beverages: Associations with aspects of impulsivity.

PubMed

Stamates, Amy L; Lau-Barraco, Cathy

2017-12-01

The present study primarily sought to (a) determine the effects of environmental context on subjective ratings of craving for alcohol and caffeinated alcohol beverages (CAB) and (b) test inhibitory control, a state behavioral aspect of impulsivity, as a mediator of the association between context and craving in a sample of consumers of CAB. A secondary aim was to examine the associations between trait impulsivity and subjective craving for alcohol and CAB. Participants were 143 (67.1% female) college CAB drinkers. Participants were randomized into either a simulated bar context condition or neutral context condition and completed measures of alcohol use, CAB use, trait impulsivity, inhibitory control on a go/no-go task, and subjective craving for alcohol and CAB. Findings revealed that participants in the simulated bar condition, as compared with those in the neutral condition, reported more subjective craving for alcohol and for CAB; however, alcohol and CAB-specific craving were not different overall or as a function of context. The association between context and subjective craving for alcohol was not mediated by inhibitory control. Trait impulsivity was positively associated with alcohol and CAB-specific craving at baseline and post context exposure, and this finding was similar across both conditions. Therefore, the current investigation suggests that consumers of CAB may be sensitive to alcohol contexts as indicated by greater responses in alcohol and CAB-specific craving. However, inhibitory control did not explain this association. Future research may benefit from examining other potential mechanisms that explain the relationship between context and craving among CAB consumers. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Locomotive cab design development. Volume 1 : analysis of locomotive cab environment & development of cab design alternatives

DOT National Transportation Integrated Search

1976-10-01

This report presents an analysis of the line haul freight : engineer's working and living environment, the resultant locomotive : cab design and design alternatives. The analysis is based on a : delineation of functional requirements found in current...

49 CFR 236.805 - Signal, cab.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Signal, cab. 236.805 Section 236.805..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Definitions § 236.805 Signal, cab. A signal located in engineman's compartment or cab, indicating a condition affecting the...

49 CFR 236.805 - Signal, cab.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Signal, cab. 236.805 Section 236.805..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Definitions § 236.805 Signal, cab. A signal located in engineman's compartment or cab, indicating a condition affecting the...

Locomotive cab design development. volume III: design application analysis - Interim report

DOT National Transportation Integrated Search

1976-10-01

In Volume II of this service of reports on Locomotive Cab Design Development, changes were recommended in the layout and equipment content of locomotive cabs. This report studies the impact of these changes on the interface of the cab with the rest o...

49 CFR 236.805 - Signal, cab.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Signal, cab. 236.805 Section 236.805..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Definitions § 236.805 Signal, cab. A signal located in engineman's compartment or cab, indicating a condition affecting the...

49 CFR 236.805 - Signal, cab.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Signal, cab. 236.805 Section 236.805..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Definitions § 236.805 Signal, cab. A signal located in engineman's compartment or cab, indicating a condition affecting the...

49 CFR 236.805 - Signal, cab.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Signal, cab. 236.805 Section 236.805..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Definitions § 236.805 Signal, cab. A signal located in engineman's compartment or cab, indicating a condition affecting the...

49 CFR 229.127 - Cab lights.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Cab lights. 229.127 Section 229.127 Transportation... lights. (a) Each locomotive shall have cab lights which will provide sufficient illumination for the... normal positions in the cab. These lights shall be located, constructed, and maintained so that light...

49 CFR 229.127 - Cab lights.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Cab lights. 229.127 Section 229.127 Transportation... lights. (a) Each locomotive shall have cab lights which will provide sufficient illumination for the... normal positions in the cab. These lights shall be located, constructed, and maintained so that light...

49 CFR 229.127 - Cab lights.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Cab lights. 229.127 Section 229.127 Transportation... lights. (a) Each locomotive shall have cab lights which will provide sufficient illumination for the... normal positions in the cab. These lights shall be located, constructed, and maintained so that light...

49 CFR 229.127 - Cab lights.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Cab lights. 229.127 Section 229.127 Transportation... lights. (a) Each locomotive shall have cab lights which will provide sufficient illumination for the... normal positions in the cab. These lights shall be located, constructed, and maintained so that light...

49 CFR 229.127 - Cab lights.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Cab lights. 229.127 Section 229.127 Transportation... lights. (a) Each locomotive shall have cab lights which will provide sufficient illumination for the... normal positions in the cab. These lights shall be located, constructed, and maintained so that light...

49 CFR 236.514 - Interconnection of cab signal system with roadway signal system.

Code of Federal Regulations, 2011 CFR

2011-10-01

... GOVERNING THE INSTALLATION, INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.514 Interconnection of cab signal system with roadway signal system. The automatic cab signal system shall be...

49 CFR 236.511 - Cab signals controlled in accordance with block conditions stopping distance in advance.

Code of Federal Regulations, 2011 CFR

2011-10-01

... INSTRUCTIONS GOVERNING THE INSTALLATION, INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards... automatic cab signal system shall be arranged so that cab signals will be continuously controlled in...

The Bacillus subtilis and Bacillus halodurans Aspartyl-tRNA Synthetases Retain Recognition of tRNA(Asn).

PubMed

Nair, Nilendra; Raff, Hannah; Islam, Mohammed Tarek; Feen, Melanie; Garofalo, Denise M; Sheppard, Kelly

2016-02-13

Synthesis of asparaginyl-tRNA (Asn-tRNA(Asn)) in bacteria can be formed either by directly ligating Asn to tRNA(Asn) using an asparaginyl-tRNA synthetase (AsnRS) or by synthesizing Asn on the tRNA. In the latter two-step indirect pathway, a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) attaches Asp to tRNA(Asn) and the amidotransferase GatCAB transamidates the Asp to Asn on the tRNA. GatCAB can be similarly used for Gln-tRNA(Gln) formation. Most bacteria are predicted to use only one route for Asn-tRNA(Asn) formation. Given that Bacillus halodurans and Bacillus subtilis encode AsnRS for Asn-tRNA(Asn) formation and Asn synthetases to synthesize Asn and GatCAB for Gln-tRNA(Gln) synthesis, their AspRS enzymes were thought to be specific for tRNA(Asp). However, we demonstrate that the AspRSs are non-discriminating and can be used with GatCAB to synthesize Asn. The results explain why B. subtilis with its Asn synthetase genes knocked out is still an Asn prototroph. Our phylogenetic analysis suggests that this may be common among Firmicutes and 30% of all bacteria. In addition, the phylogeny revealed that discrimination toward tRNA(Asp) by AspRS has evolved independently multiple times. The retention of the indirect pathway in B. subtilis and B. halodurans likely reflects the ancient link between Asn biosynthesis and its use in translation that enabled Asn to be added to the genetic code. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Semirational Approach for Ultrahigh Poly(3-hydroxybutyrate) Accumulation in Escherichia coli by Combining One-Step Library Construction and High-Throughput Screening.

PubMed

Li, Teng; Ye, Jianwen; Shen, Rui; Zong, Yeqing; Zhao, Xuejin; Lou, Chunbo; Chen, Guo-Qiang

2016-11-18

As a product of a multistep enzymatic reaction, accumulation of poly(3-hydroxybutyrate) (PHB) in Escherichia coli (E. coli) can be achieved by overexpression of the PHB synthesis pathway from a native producer involving three genes phbC, phbA, and phbB. Pathway optimization by adjusting expression levels of the three genes can influence properties of the final product. Here, we reported a semirational approach for highly efficient PHB pathway optimization in E. coli based on a phbCAB operon cloned from the native producer Ralstonia entropha (R. entropha). Rationally designed ribosomal binding site (RBS) libraries with defined strengths for each of the three genes were constructed based on high or low copy number plasmids in a one-pot reaction by an oligo-linker mediated assembly (OLMA) method. Strains with desired properties were evaluated and selected by three different methodologies, including visual selection, high-throughput screening, and detailed in-depth analysis. Applying this approach, strains accumulating 0%-92% PHB contents in cell dry weight (CDW) were achieved. PHB with various weight-average molecular weights (M w ) of 2.7-6.8 × 10 6 were also efficiently produced in relatively high contents. These results suggest that the semirational approach combining library design, construction, and proper screening is an efficient way to optimize PHB and other multienzyme pathways.

Subcellular localization and functional characterization of a fish IRF9 from crucian carp Carassius auratus.

PubMed

Shi, Jun; Zhang, Yi-Bing; Liu, Ting-Kai; Sun, Fan; Gui, Jian-Fang

2012-08-01

Mammalian interferon (IFN) regulatory factor 9 (IRF-9) has long been recognized as the DNA sequence recognition subunit of IFN-stimulated gene factor 3 (ISGF3) complex, which is critical for type I IFN to induce the expression of IFN-stimulated genes (ISGs) against viral infection. Recent studies have shown that fish IFN exerts antiviral effects by induction of a number of ISGs and also of itself; however, little is known about the role of fish IRF9 in IFN signaling. Here we identify a fish IRF9 orthologue (CaIRF9) from IFN-producing cell line, crucian carp Carassius auratus blastulae embryonic (CAB) cells. Analysis of subcellular distribution of CaIRF9-green fluorescent protein indicates that CaIRF9 is constitutively present in the nucleus, which is driven by two nuclear localization signals (NLS), one locating within DNA-binding domain (DBD) of CaIRF9 and the other immediately behind DBD, although human IRF9 contains only one NLS analogous to the former of CaIRF9. Overexpression of CaIRF9 together with CaSTAT2 not only activates ISRE-containing promoter but also upregulates the expression of fish ISGs. Strikingly, CaIRF9 together with CaSTAT2 also exhibits an ability to activate crucian carp IFN promoter, and blockade of cellular CaIRF9 attenuates IFN itself-induced activation of crucian carp IFN promoter. Taken together, these data suggest that crucian carp IFN induces the expression of ISGs and also of itself possibly by the JAK-STAT signaling pathway that is conserved from fish to mammals. Copyright © 2012 Elsevier Ltd. All rights reserved.

The molecular mechanisms of action of PPAR-γ agonists in the treatment of corneal alkali burns (Review)

PubMed Central

Zhou, Hongyan; Zhang, Wensong; Bi, Miaomiao; Wu, Jie

2016-01-01

Corneal alkali burns (CAB) are characterized by injury-induced inflammation, fibrosis and neovascularization (NV), and may lead to blindness. This review evaluates the current knowledge of the molecular mechanisms responsible for CAB. The processes of cytokine production, chemotaxis, inflammatory responses, immune response, cell signal transduction, matrix metalloproteinase production and vascular factors in CAB are discussed. Previous evidence indicates that peroxisome proliferator-activated receptor γ (PPAR-γ) agonists suppress immune responses, inflammation, corneal fibrosis and NV. This review also discusses the role of PPAR-γ as an anti-inflammatory, anti-fibrotic and anti-angiogenic agent in the treatment of CAB, as well as the potential role of PPAR-γ in the pathological process of CAB. There have been numerous studies evaluating the clinical profiles of CAB, and the aim of this systematic review was to summarize the evidence regarding the treatment of CAB with PPAR-γ agonists. PMID:27499172

49 CFR 236.512 - Cab signal indication when locomotive enters block where restrictive conditions obtain.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Cab signal indication when locomotive enters block... Systems Standards § 236.512 Cab signal indication when locomotive enters block where restrictive... within a block, wherein any condition described in § 236.205 obtains, the cab signals shall indicate...

49 CFR 238.447 - Train operator's controls and power car cab layout.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Train operator's controls and power car cab layout... layout. (a) Train operator controls in the power car cab shall be arranged so as to minimize the chance.... (d) Power car cab information displays shall be designed with the following characteristics: (1...

49 CFR 238.447 - Train operator's controls and power car cab layout.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Train operator's controls and power car cab layout... layout. (a) Train operator controls in the power car cab shall be arranged so as to minimize the chance.... (d) Power car cab information displays shall be designed with the following characteristics: (1...

49 CFR 238.447 - Train operator's controls and power car cab layout.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Train operator's controls and power car cab layout... layout. (a) Train operator controls in the power car cab shall be arranged so as to minimize the chance.... (d) Power car cab information displays shall be designed with the following characteristics: (1...

49 CFR 236.512 - Cab signal indication when locomotive enters block where restrictive conditions obtain.

Code of Federal Regulations, 2011 CFR

2011-10-01

... TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.512 Cab signal indication when locomotive enters block where restrictive conditions obtain. The automatic cab signal system shall be arranged so that when a locomotive enters or is...

Impulsivity and Alcohol Demand in relation to Combined Alcohol and Caffeine Use

PubMed Central

Amlung, Michael; Few, Lauren R.; Howland, Jonathan; Rohsenow, Damaris J.; Metrik, Jane; MacKillop, James

2014-01-01

Problematic alcohol use among college students continues to be a prominent concern in the United States, including the growing trend of consuming caffeine with alcoholic beverages (CABs). Epidemiologically, CAB use is associated with incremental risks from drinking, although these relationships could be due to common predisposing factors rather than specifically due to CABs. This study investigated the relationship between CAB use, alcohol misuse, and person-level characteristics including impulsive personality traits, delayed reward discounting, and behavioral economic demand for alcohol use. Participants were 273 regularly drinking undergraduate students. Frequency of CAB use was assessed over the past month. A multidimensional assessment of impulsivity included the UPPS-P questionnaire and a validated, questionnaire-based measure of delayed reward discounting. Demand was assessed via a hypothetical alcohol purchase task. Frequency of CAB consumption was significantly higher in males compared to females and was also associated with higher impulsivity on the majority of the UPPS-P subscales, steeper delayed reward discounting, and greater demand for alcohol. Significant correlations between CAB use and both alcohol demand and lack of premeditation remained present after including level of alcohol misuse in partial correlations. In a hierarchical linear regression incorporating demographic, demand, and impulsivity variables, CAB frequency continued to be a significant predictor of hazardous alcohol use. These results suggest that although there are significant associations between CAB consumption and gender, impulsivity, and alcohol demand, CAB use continues to be associated with alcohol misuse after controlling for these variables. PMID:24364537

Community Advisory Boards Guiding Engaged Research Efforts within a Clinical Translational Sciences Award: Key Contextual Factors Explored.

PubMed

Halladay, Jacqueline R; Donahue, Katrina E; Sleath, Betsy; Reuland, Dan; Black, Adina; Mitchell, C Madeline; Breland, Carol E; Coyne-Beasley, Tamera; Mottus, Kathleen; Watson, Sable Noelle; Lewis, Virginia; Wynn, Mysha; Corbie-Smith, Giselle

2017-01-01

Engaging stakeholders in research carries the promise of enhancing the research relevance, transparency, and speed of getting findings into practice. By describing the context and functional aspects of stakeholder groups, like those working as community advisory boards (CABs), others can learn from these experiences and operationalize their own CABs. Our objective is to describe our experiences with diverse CABs affiliated with our community engagement group within our institution's Clinical Translational Sciences Award (CTSA). We identify key contextual elements that are important to administering CABs. A group of investigators, staff, and community members engaged in a 6-month collaboration to describe their experiences of working with six research CABs. We identified the key contextual domains that illustrate how CABS are developed and sustained. Two lead authors, with experience with CABs and identifying contextual domains in other work, led a team of 13 through the process. Additionally, we devised a list of key tips to consider when devising CABs. The final domains include (1) aligned missions among stakeholders (2) resources/support, (3) defined operational processes/shared power, (4) well-described member roles, and (5) understanding and mitigating challenges. The tips are a set of actions that support the domains. Identifying key contextual domains was relatively easy, despite differences in the respective CAB's condition of focus, overall mission, or patient demographics represented. By contextualizing these five domains, other research and community partners can take an informed approach to move forward with CAB planning and engaged research.

Cabotegravir long acting injection protects macaques against intravenous challenge with SIVmac251.

PubMed

Andrews, Chasity D; Bernard, Leslie St; Poon, Amanda Yee; Mohri, Hiroshi; Gettie, Natanya; Spreen, William R; Gettie, Agegnehu; Russell-Lodrigue, Kasi; Blanchard, James; Hong, Zhi; Ho, David D; Markowitz, Martin

2017-02-20

We evaluated the effectiveness of cabotegravir (CAB; GSK1265744 or GSK744) long acting as preexposure prophylaxis (PrEP) against intravenous simian immunodeficiency virus (SIV) challenge in a model that mimics blood transfusions based on the per-act probability of infection. CAB long acting is an integrase strand transfer inhibitor formulated as a 200 mg/ml injectable nanoparticle suspension that is an effective PrEP agent against rectal and vaginal simian/human immunodeficiency virus transmission in macaques. Three groups of rhesus macaques (n = 8 per group) were injected intramuscularly with CAB long acting and challenged intravenously with 17 animal infectious dose 50% SIVmac251 on week 2. Group 1 was injected with 50 mg/kg on week 0 and 4 to evaluate the protective efficacy of the CAB long-acting dose used in macaque studies mimicking sexual transmission. Group 2 was injected with 50 mg/kg on week 0 to evaluate the necessity of the second injection of CAB long acting for protection against intravenous challenge. Group 3 was injected with 25 mg/kg on week 0 and 50 mg/kg on week 4 to correlate CAB plasma concentrations at the time of challenge with protection. Five additional macaques remained untreated as controls. CAB long acting was highly protective with 21 of the 24 CAB long-acting-treated macaques remaining aviremic, resulting in 88% protection. The plasma CAB concentration at the time of virus challenge appeared to be more important for protection than sustaining therapeutic plasma concentrations with the second CAB long acting injection. These results support the clinical investigation of CAB long acting as PrEP in people who inject drugs.

Waste Workers’ Exposure to Airborne Fungal and Bacterial Species in the Truck Cab and During Waste Collection

PubMed Central

Madsen, Anne Mette; Alwan, Taif; Ørberg, Anders; Uhrbrand, Katrine; Jørgensen, Marie Birk

2016-01-01

A large number of people work with garbage collection, and exposure to microorganisms is considered an occupational health problem. However, knowledge on microbial exposure at species level is limited. The aim of the study was to achieve knowledge on waste collectors’ exposure to airborne inhalable fungal and bacterial species during waste collection with focus on the transport of airborne microorganisms into the truck cab. Airborne microorganisms were collected with samplers mounted in the truck cab, on the workers’ clothes, and outdoors. Fungal and bacterial species were quantified and identified. The study showed that the workers were exposed to between 112 and 4.8×104 bacteria m−3 air and 326 and 4.6×104 fungi m−3 air. The personal exposures to bacteria and fungi were significantly higher than the concentrations measured in the truck cabs and in the outdoor references. On average, the fungal and bacterial concentrations in truck cabs were 111 and 7.7 times higher than outdoor reference measurements. In total, 23 fungal and 38 bacterial species were found and identified. Most fungal species belonged to the genus Penicillium and in total 11 Penicillium species were found. Identical fungal species were often found both in a personal sample and in the same person’s truck cab, but concentrations were on average 27 times higher in personal samples. Concentrations of fungal and bacterial species found only in the personal samples were lower than concentrations of species also found in truck cabs. Skin-related bacteria constituted a large fraction of bacterial isolates found in personal and truck cab samples. In total, six Staphylococcus species were found. In outdoor samples, no skin-related bacteria were found. On average, concentrations of bacterial species found both in the truck cab and personal samples were 77 times higher in personal samples than in truck cab samples. In conclusion, high concentrations of fungi were found in truck cabs, but the highest concentrations were found in personal samples; fungal and bacterial species found in high concentrations in personal samples were also found in truck cabs, but in lower concentrations indicating that both fungi and bacteria are transported by the workers into the truck cab, and are subsequently aerosolized in the truck cab. PMID:27098185

49 CFR 238.409 - Forward end structures of power car cabs.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Forward end structures of power car cabs. 238.409... II Passenger Equipment § 238.409 Forward end structures of power car cabs. This section contains requirements for the forward end structure of the cab of a power car. (A conceptual implementation of this end...

49 CFR 238.447 - Train operator's controls and power car cab layout.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Train operator's controls and power car cab layout... Specific Requirements for Tier II Passenger Equipment § 238.447 Train operator's controls and power car cab layout. (a) Train operator controls in the power car cab shall be arranged so as to minimize the chance...

49 CFR 238.409 - Forward end structures of power car cabs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Forward end structures of power car cabs. 238.409... II Passenger Equipment § 238.409 Forward end structures of power car cabs. This section contains requirements for the forward end structure of the cab of a power car. (A conceptual implementation of this end...

49 CFR 238.411 - Rear end structures of power car cabs.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Rear end structures of power car cabs. 238.411... II Passenger Equipment § 238.411 Rear end structures of power car cabs. The rear end structure of the cab of a power car shall be designed to include the following elements, or their structural equivalent...

49 CFR 238.411 - Rear end structures of power car cabs.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Rear end structures of power car cabs. 238.411... II Passenger Equipment § 238.411 Rear end structures of power car cabs. The rear end structure of the cab of a power car shall be designed to include the following elements, or their structural equivalent...

49 CFR 238.447 - Train operator's controls and power car cab layout.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Train operator's controls and power car cab layout... Specific Requirements for Tier II Passenger Equipment § 238.447 Train operator's controls and power car cab layout. (a) Train operator controls in the power car cab shall be arranged so as to minimize the chance...

49 CFR 238.411 - Rear end structures of power car cabs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Rear end structures of power car cabs. 238.411... II Passenger Equipment § 238.411 Rear end structures of power car cabs. The rear end structure of the cab of a power car shall be designed to include the following elements, or their structural equivalent...

49 CFR 238.409 - Forward end structures of power car cabs.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Forward end structures of power car cabs. 238.409... II Passenger Equipment § 238.409 Forward end structures of power car cabs. This section contains requirements for the forward end structure of the cab of a power car. (A conceptual implementation of this end...

49 CFR 238.411 - Rear end structures of power car cabs.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Rear end structures of power car cabs. 238.411... II Passenger Equipment § 238.411 Rear end structures of power car cabs. The rear end structure of the cab of a power car shall be designed to include the following elements, or their structural equivalent...

49 CFR 238.409 - Forward end structures of power car cabs.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Forward end structures of power car cabs. 238.409... II Passenger Equipment § 238.409 Forward end structures of power car cabs. This section contains requirements for the forward end structure of the cab of a power car. (A conceptual implementation of this end...

49 CFR 238.411 - Rear end structures of power car cabs.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Rear end structures of power car cabs. 238.411... II Passenger Equipment § 238.411 Rear end structures of power car cabs. The rear end structure of the cab of a power car shall be designed to include the following elements, or their structural equivalent...

49 CFR 238.409 - Forward end structures of power car cabs.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Forward end structures of power car cabs. 238.409... II Passenger Equipment § 238.409 Forward end structures of power car cabs. This section contains requirements for the forward end structure of the cab of a power car. (A conceptual implementation of this end...

The pepper Bs4C proteins are localized to the endoplasmic reticulum (ER) membrane and confer disease resistance to bacterial blight in transgenic rice.

PubMed

Wang, Jun; Zeng, Xuan; Tian, Dongsheng; Yang, Xiaobei; Wang, Lanlan; Yin, Zhongchao

2018-03-30

Transcription activator-like effector (TALE)-dependent dominant disease resistance (R) genes in plants, also referred to as executor R genes, are induced on infection by phytopathogenic bacteria of the genus Xanthomonas harbouring the corresponding TALE genes. Unlike the traditional R proteins, the executor R proteins do not determine the resistance specificity and may function broadly in different plant species. The executor R gene Bs4C-R in the resistant genotype PI 235047 of the pepper species Capsicum pubescens (CpBs4C-R) confers disease resistance to Xanthomonas campestris pv. vesicatoria (Xcv) harbouring the TALE genes avrBsP/avrBs4. In this study, the synthetic genes of CpBs4C-R and two other Bs4C-like genes, the susceptible allele in the genotype PI585270 of C. pubescens (CpBs4C-S) and the CaBs4C-R homologue gene in the cultivar 'CM334' of Capsicum annum (CaBs4C), were characterized in tobacco (Nicotiana benthamiana) and rice (Oryza sativa). The Bs4C genes induced cell death in N. benthamiana. The functional Bs4C-eCFP fusion proteins were localized to the endoplasmic reticulum (ER) membrane in the leaf epidermal cells of N. benthamiana. The Xa10 promoter-Bs4C fusion genes in transgenic rice conferred strain-specific disease resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight in rice, and were specifically induced by the Xa10-incompatible Xoo strain PXO99 A (pHM1avrXa10). The results indicate that the Bs4C proteins from pepper species function broadly in rice and the Bs4C protein-mediated cell death from the ER is conserved between dicotyledonous and monocotyledonous plants, which can be utilized to engineer novel and enhanced disease resistance in heterologous plants. © 2018 TEMASEK LIFE SCIENCES LABORATORY. MOLECULAR PLANT PATHOLOGY © 2018 JOHN WILEY & SONS LTD.

Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis

PubMed Central

2014-01-01

Background The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrained by environmental signals, such as light and temperature. In recent years, alternative splicing emerges as an important molecular mechanism that modulates the clock function in plants. Several clock genes are known to undergo alternative splicing in response to changes in environmental conditions, suggesting that the clock function is intimately associated with environmental responses via the alternative splicing of the clock genes. However, the alternative splicing events of the clock genes have not been studied at the molecular level. Results We systematically examined whether major clock genes undergo alternative splicing under various environmental conditions in Arabidopsis. We also investigated the fates of the RNA splice variants of the clock genes. It was found that the clock genes, including EARLY FLOWERING 3 (ELF3) and ZEITLUPE (ZTL) that have not been studied in terms of alternative splicing, undergo extensive alternative splicing through diverse modes of splicing events, such as intron retention, exon skipping, and selection of alternative 5′ splice site. Their alternative splicing patterns were differentially influenced by changes in photoperiod, temperature extremes, and salt stress. Notably, the RNA splice variants of TIMING OF CAB EXPRESSION 1 (TOC1) and ELF3 were degraded through the nonsense-mediated decay (NMD) pathway, whereas those of other clock genes were insensitive to NMD. Conclusion Taken together, our observations demonstrate that the major clock genes examined undergo extensive alternative splicing under various environmental conditions, suggesting that alternative splicing is a molecular scheme that underlies the linkage between the clock and environmental stress adaptation in plants. It is also envisioned that alternative splicing of the clock genes plays more complex roles than previously expected. PMID:24885185

Impulsivity and alcohol demand in relation to combined alcohol and caffeine use.

PubMed

Amlung, Michael; Few, Lauren R; Howland, Jonathan; Rohsenow, Damaris J; Metrik, Jane; MacKillop, James

2013-12-01

Problematic alcohol use among college students continues to be a prominent concern in the United States, including the growing trend of consuming caffeinated alcoholic beverages (CABs). Epidemiologically, CAB use is associated with incremental risks from drinking, although these relationships could be due to common predisposing factors rather than specifically due to CABs. This study investigated the relationship between CAB use, alcohol misuse, and person-level characteristics, including impulsive personality traits, delayed reward discounting, and behavioral economic demand for alcohol use. Participants were 273 regularly drinking undergraduate students. Frequency of CAB use was assessed over the past month. A multidimensional assessment of impulsivity included the UPPS-P questionnaire, which measures positive and negative urgency, premeditation (lack thereof), perseverance (lack thereof), and sensation seeking (Lynam, Smith, Whiteside, & Cyders, 2007), and a validated questionnaire-based measure of delayed reward discounting. Demand was assessed via a hypothetical alcohol purchase task. Frequency of CAB consumption was significantly higher in men than in women and was also associated with higher impulsivity on the majority of the UPPS-P subscales, steeper delayed reward discounting, and greater demand for alcohol. Significant correlations between CAB use and both alcohol demand and lack of premeditation remained present after including level of alcohol misuse in partial correlations. In a hierarchical linear regression incorporating demographic, demand, and impulsivity variables, CAB frequency continued to be a significant predictor of hazardous alcohol use. These results suggest that although there are significant associations between CAB consumption and gender, impulsivity, and alcohol demand, CAB use continues to be associated with alcohol misuse after controlling for these variables.

Enhanced enzymatic hydrolysis and ethanol production from cashew apple bagasse pretreated with alkaline hydrogen peroxide.

PubMed

da Costa, Jessyca Aline; Marques, José Edvan; Gonçalves, Luciana Rocha Barros; Rocha, Maria Valderez Ponte

2015-03-01

The effect of combinations and ratios between different enzymes has been investigated in order to assess the optimal conditions for hydrolysis of cashew apple bagasse pretreated with alkaline hydrogen peroxide (the solids named CAB-AHP). The separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) processes were evaluated in the ethanol production. The enzymatic hydrolysis conducted with cellulase complex and β-glucosidase in a ratio of 0.61:0.39, enzyme loading of 30FPU/g(CAB-AHP) and 66CBU/g(CAB-AHP), respectively, using 4% cellulose from CAB-AHP, turned out to be the most effective conditions, with glucose and xylose yields of 511.68 mg/g(CAB-AHP) and 237.8 mg/g(CAB-AHP), respectively. Fermentation of the pure hydrolysate by Kluyveromyces marxianus ATCC 36907 led to an ethanol yield of 61.8kg/ton(CAB), corresponding to 15 g/L ethanol and productivity of 3.75 g/( Lh). The ethanol production obtained for SSF process using K. marxianus ATCC 36907 was 18 g/L corresponding to 80% yield and 74.2kg/ton(CAB). Copyright © 2014 Elsevier Ltd. All rights reserved.

49 CFR Appendix F to Part 238 - Alternative Dynamic Performance Requirements for Front End Structures of Cab Cars and MU Locomotives

Code of Federal Regulations, 2013 CFR

2013-10-01

... of cab cars and MU locomotives with shaped-noses or crash energy management designs, or both. In any... Front End Structures of Cab Cars and MU Locomotives F Appendix F to Part 238 Transportation Other... Performance Requirements for Front End Structures of Cab Cars and MU Locomotives As specified in § 238.209(b...

49 CFR Appendix F to Part 238 - Alternative Dynamic Performance Requirements for Front End Structures of Cab Cars and MU Locomotives

Code of Federal Regulations, 2012 CFR

2012-10-01

... of cab cars and MU locomotives with shaped-noses or crash energy management designs, or both. In any... Front End Structures of Cab Cars and MU Locomotives F Appendix F to Part 238 Transportation Other... Performance Requirements for Front End Structures of Cab Cars and MU Locomotives As specified in § 238.209(b...

49 CFR Appendix F to Part 238 - Alternative Dynamic Performance Requirements for Front End Structures of Cab Cars and MU Locomotives

Code of Federal Regulations, 2011 CFR

2011-10-01

... of cab cars and MU locomotives with shaped-noses or crash energy management designs, or both. In any... Front End Structures of Cab Cars and MU Locomotives F Appendix F to Part 238 Transportation Other... Performance Requirements for Front End Structures of Cab Cars and MU Locomotives As specified in § 238.209(b...

49 CFR Appendix F to Part 238 - Alternative Dynamic Performance Requirements for Front End Structures of Cab Cars and MU Locomotives

Code of Federal Regulations, 2014 CFR

2014-10-01

... of cab cars and MU locomotives with shaped-noses or crash energy management designs, or both. In any... Front End Structures of Cab Cars and MU Locomotives F Appendix F to Part 238 Transportation Other... Performance Requirements for Front End Structures of Cab Cars and MU Locomotives As specified in § 238.209(b...

49 CFR Appendix F to Part 238 - Alternative Dynamic Performance Requirements for Front End Structures of Cab Cars and MU Locomotives

Code of Federal Regulations, 2010 CFR

2010-10-01

... Front End Structures of Cab Cars and MU Locomotives F Appendix F to Part 238 Transportation Other... Performance Requirements for Front End Structures of Cab Cars and MU Locomotives As specified in § 238.209(b... and allow for the application of dynamic performance criteria to cab cars and MU locomotives as an...

Comparison of Adverse Events and Hospital Length of Stay Associated With Various Amphotericin B Formulations

PubMed Central

Wade, Rolin L.; Chaudhari, Paresh; Natoli, Jaime L.; Taylor, Robert J.; Nathanson, Brian H.; Horn, David

2013-01-01

Purpose: Patients with invasive fungal infections are often treated initially with conventional amphotericin B deoxycholate (CAB), followed by a switch to lipid-based formulations of amphotericin B (LF-AMB). Our study examined adverse events and hospital length of stay (LOS) among adults who received LF-AMB exclusively or CAB followed by LF-AMB (CAB/LF-AMB). Methods: Data were extracted from the Cerner Health Facts database. The study included adults with evidence of infection by Aspergillus, Candida, or Cryptococcus in addition to either renal insufficiency, a clinical condition suggesting intolerance to CAB, or CAB exposure within 90 days of admission. Nephrotoxicity was defined as a serum creatinine (SCr) level exceeding a 100% increase from baseline and an absolute level above 1.2 mg/dL. We used a hierarchical mixed-effect logistic regression model with nephrotoxicity as the outcome for the multivariate analysis. Results: The study included 327 LF-AMB and 81 CAB/LF-AMB patients with similar demographics and baseline SCr values. The mean pre-to-post percentage increase in SCr levels was greater for CAB/LF-AMB (122.9%) compared with LF-AMB (62.2%) (P < 0.001). The multivariate-adjusted odds ratio of nephrotoxicity was 5.93, for a 95% confidence interval of 2.92 to 12.05 (P < 0.001) for CAB/LF-AMB compared with LF-AMB. Hypokalemia, hypomagnesemia, and infusion-related reactions were more frequent with CAB/LF-AMB. Compared with the LF-AMB group, the CAB/LF-AMB patients had a longer post-amphotericin B LOS (24.1 days vs. 15.7 days, respectively; P < 0.001), with a marginal effect of 4.5 days longer for those receiving CAB/LF-AMB (P = 0.016). Conclusion: In this retrospective study, we noted a significantly longer post-amphotericin B LOS and a greater frequency of adverse events, including nephrotoxicity, for patients whose initial treatment was CAB and who were switched to LF-AMB, compared with patients who received LF-AMB only. PMID:23946621

The use of caffeinated alcoholic beverages among underage drinkers: Results of a national survey

PubMed Central

Kponee, Kalé Z.; Siegel, Michael; Jernigan, David H.

2013-01-01

Objective The mixing of alcoholic beverages with caffeine has been identified as a public health problem among college students; however, little is known about the consumption of such drinks among younger adolescents. We estimated the prevalence of caffeinated alcoholic beverage (CAB) use among a wide age range of underage drinkers, examined differences in traditional (i.e. self-mixed alcoholic beverages with soda, coffee and tea) and non-traditional CAB use (pre-mixed caffeinated alcoholic beverages or self-mixed alcoholic beverages with energy drinks or energy shots) among underage drinkers by age and other demographic characteristics, and examined differences in hazardous drinking behavior between CAB and non-CAB users. Methods We used an existing internet panel maintained by Knowledge Networks, Inc. to assess the use of pre-mixed and self-mixed CABs in the past 30 days among a national sample of 1,031 youth drinkers ages 13–20. We conducted logistic regression analyses to estimate the relationship between traditional and non-traditional CAB use and risky drinking behavior as well as adverse outcomes of drinking, while controlling for age, gender, race/ethnicity, income, and general risk-taking (seat belt use). Results The overall prevalence of CAB use in the sample of underage drinkers was 52.4% (95% confidence interval [CI], 47.4%–57.4%). CAB prevalence was 48.4% among 13–15 year-old drinkers, 45.3% among 16–18 year-old drinkers, and 58.4% among 19–20 year-old drinkers. After controlling for other variables, we found a continuum of risk with non-traditional CAB use most significantly associated with binge drinking (odds ratio [OR] = 6.3), fighting (OR = 4.4), and alcohol-related injuries (OR = 5.6) Conclusions The problem of caffeinated alcoholic beverage use is not restricted to college-aged youth. The prevalence of CAB use among underage drinkers is higher than previously thought and begins in early adolescence. Adolescents who consume CABs, and particularly non-traditional CABs, are at increased risk of adverse outcomes. PMID:24161375

Field Assessment of Enclosed Cab Filtration System Performance Using Particle Counting Measurements

PubMed Central

Organiscak, John A.; Cecala, Andrew B.; Noll, James D.

2015-01-01

Enclosed cab filtration systems are typically used on mobile mining equipment to reduce miners’ exposure to airborne dust generated during mining operations. The National Institute for Occupational Safety and Health (NIOSH) Office of Mine Safety and Health Research (OMSHR) has recently worked with a mining equipment manufacturer to examine a new cab filtration system design for underground industrial minerals equipment. This cab filtration system uses a combination of three particulate filters to reduce equipment operators’ exposure to dust and diesel particulates present in underground industrial mineral mines. NIOSH initially examined this cab filtration system using a two-instrument particle counting method at the equipment company’s manufacturing shop facility to assess several alternative filters. This cab filtration system design was further studied on several pieces of equipment during a two- to seven-month period at two underground limestone mines. The two-instrument particle counting method was used outside the underground mine at the end of the production shifts to regularly test the cabs’ long-term protection factor performance with particulates present in the ambient air. This particle counting method showed that three of the four cabs achieved protection factors greater than 1,000 during the field studies. The fourth cab did not perform at this level because it had a damaged filter in the system. The particle counting measurements of submicron particles present in the ambient air were shown to be a timely and useful quantification method in assessing cab performance during these field studies. PMID:23915268

CABS-flex predictions of protein flexibility compared with NMR ensembles

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2014-01-01

Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes. Availability and implementation: The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex. Contact: sekmi@chem.uw.edu.pl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24735558

Secretory cargo sorting by Ca2+-dependent Cab45 oligomerization at the trans-Golgi network

PubMed Central

Blank, Birgit; Maiser, Andreas; Emin, Derya; Prescher, Jens; Beck, Gisela; Kienzle, Christine; Bartnik, Kira; Habermann, Bianca; Pakdel, Mehrshad; Leonhardt, Heinrich; Lamb, Don C.

2016-01-01

Sorting and export of transmembrane cargoes and lysosomal hydrolases at the trans-Golgi network (TGN) are well understood. However, elucidation of the mechanism by which secretory cargoes are segregated for their release into the extracellular space remains a challenge. We have previously demonstrated that, in a reaction that requires Ca2+, the soluble TGN-resident protein Cab45 is necessary for the sorting of secretory cargoes at the TGN. Here, we report that Cab45 reversibly assembles into oligomers in the presence of Ca2+. These Cab45 oligomers specifically bind secretory proteins, such as COMP and LyzC, in a Ca2+-dependent manner in vitro. In intact cells, mutation of the Ca2+-binding sites in Cab45 impairs oligomerization, as well as COMP and LyzC sorting. Superresolution microscopy revealed that Cab45 colocalizes with secretory proteins and the TGN Ca2+ pump (SPCA1) in specific TGN microdomains. These findings reveal that Ca2+-dependent changes in Cab45 mediate sorting of specific cargo molecules at the TGN. PMID:27138253

CABS-flex predictions of protein flexibility compared with NMR ensembles.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2014-08-01

Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes. The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex. sekmi@chem.uw.edu.pl Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Identification of a novel endophytic Bacillus sp. from Capsicum annuum with highly efficient and broad spectrum plant probiotic effect.

PubMed

Jasim, B; Mathew, J; Radhakrishnan, E K

2016-10-01

The study mainly aimed the isolation and characterization of plant probiotic endophytic bacteria from Capsicum annuum to explore its multipotent agricultural applications. Endophytic bacteria were isolated from the surface sterilized fruit tissue. The isolates were then subjected to PCR-based screening for the presence of potential biosynthetic gene clusters. The PCR positive isolate was then analysed for its inhibitory effect towards fungal and bacterial pathogens. The compounds responsible for the antimicrobial activity was purified from large scale culture and subjected to identification by LC-MS/MS. The ability of the selected isolate in plant growth enhancement was also done using Vigna radiata seedlings. In this study, an endophytic bacterium isolated from C. annuum was found to have the phenotypic and genetic basis for broad antimicrobial property. PCR-based sequence analysis has resulted in the identification of nonribosomal peptide synthases, PKS Type I, Iturin, surfactin, DAPG and gacA genes in the selected isolate CaB 5. The bioactivity-guided fractionation using column and HPLC purification of active fraction followed by LC-MS/MS analysis has proved the presence of surfactin derivatives (M+H(+) - 1008 & 1036) and iturin (M+H(+) - 1058) as the basis of antimicrobial activity of CaB 5. The isolate was identified as a novel Bacillus sp. because of its low (76%) identity to the reported sequences. Endophytes are considered to have the genetic basis for a diverse array of bioactive metabolites which can have significant applications in both pharmaceutical industry and agriculture. The identification of CaB 5 with broad bioactivity and excellent plant growth enhancement on taxonomically distinct plant species as explained in current study and our previous reports highlights its plant probiotic applicability. This proves the potential of the isolate obtained in the study to be an excellent plant probiotic. © 2016 The Society for Applied Microbiology.

49 CFR 393.203 - Cab and body components.

Code of Federal Regulations, 2010 CFR

2010-10-01

... NECESSARY FOR SAFE OPERATION Frames, Cab and Body Components, Wheels, Steering, and Suspension Systems § 393... a roof exit. (b) Bolts or brackets securing the cab or the body of the vehicle to the frame shall...

From molecular salt to pseudo CAB cocrystal: Expanding solid-state landscape of carboxylic acids based on charge-assisted COOH⋯COO- hydrogen bonds

NASA Astrophysics Data System (ADS)

Lou, Benyong; Perumalla, Sathyanarayana Reddy; Sun, Changquan Calvin

2015-11-01

Using three carboxylic acids, we show that the COOH⋯COO- synthon is robust for directing the cocrystallization between a carboxylic acid and a carboxylate of either the same or a chemically different molecule to form a CAB or pseudo CAB cocrystal, respectively. For a given carboxylic acid and a counterion, only one salt could be prepared. However, additional one CAB cocrystals and two pseudo CAB cocrystals could be prepared based on the COOH⋯COO- synthon. The same synthon has the potential to enable the preparation of additional molecular pseudo CAB cocrystals using other chemically distinct carboxylic acids. This significantly increased number of solid forms highlights the values of charge-assisted synthons, such as COOH⋯COO-, in crystal engineering for expanding the range of material properties of a given molecule for optimum performance in product design.

Evaluation of the driver's cab in the Rc5 engine.

PubMed

Hedberg, G

1987-03-01

The opinion of engine drivers concerning the design of the cab in a new engine (Rc5, ASEA, Sweden) is surveyed in the present study, which is aimed at recommendations for further improvements of the new cab. Fifty engine drivers from the northern part of Sweden (Ange, Vannas and Boden), who had been driving the new engine, were selected at random to answer a specially designed questionnaire. Most of the drivers considered the new cab as better than the old one (Rc4) in several respects. Particularly appreciated was an adjustable footrest, on which the safety regulator pedal was fitted, which enabled an individually adjusted position for driving. They also preferred the automatic brake valve located close to the driver and with its movements in a sagittal direction. A number of proposals for further improvement of the cab are presented in order to attain an optimally designed driver's cab.

Juvenile onset depression alters cardiac autonomic balance in response to psychological and physical challenges

PubMed Central

Bylsma, Lauren M.; Yaroslavsky, Ilya; Rottenberg, Jonathan; Jennings, J. Richard; George, Charles J.; Kiss, Enikő; Kapornai, Krisztina; Halas, Kitti; Dochnal, Roberta; Lefkovics, Eszter; Benák, István; Baji, Ildikó; Vetró, Ágnes; Kovacs, Maria

2015-01-01

Cardiac autonomic balance (CAB) indexes the ratio of parasympathetic to sympathetic activation (Berntson, Norman, Hawkley, & Cacioppo, 2008), and is believed to reflect overall autonomic flexibility in the face of environmental challenges. However, CAB has not been examined in depression. We examined changes in CAB and other physiological variables in 179 youth with a history of juvenile onset depression (JOD) and 161 healthy controls, in response to two psychological (unsolvable puzzle, sad film) and two physical (handgrip, and forehead cold pressor) challenges. In repeated measures analyses, controls showed expected reductions in CAB for both the handgrip and unsolvable puzzle, reflecting a shift to sympathetic relative to parasympathetic activation. By contrast, JOD youth showed increased CAB from baseline for both tasks (ps<.05). No effects were found for the forehead cold pressor or sad film tasks, suggesting that CAB differences may arise under conditions requiring greater attentional control or sustained effort. PMID:26225465

Locomotive crashworthiness research : volume 5 : cab car crashworthiness report

DOT National Transportation Integrated Search

1996-03-01

Models used to analyze locomotive crashworthiness are modified for application to control cab cars of the types used for intercity and commuter rail passenger service. An existing control cab car is analyzed for crashworthiness based on scenarios dev...

Atlanta Tower Cab and TRACON Equipment Integration Analysis

DOT National Transportation Integrated Search

1980-10-01

This report presents an analysis of how the new Terminal Information Processing System (TIPS) and Consolidated Cab Display (CCD) equipments might appear to Air Traffic personnel if they were installed in the tower cab and TRACON at Hartsfield-Atlanta...

ARC-1997-AC97-0295-14

NASA Image and Video Library

1997-09-03

N-257 CVSRF: control rooms for 747 and ACSF cabs - LEFT SIDE; EOS - ACFS (Advanced Cab Flight Simulator) w. (l-r) Victor Loesche, Hector Reyes & Eric Jacobs and RIGHT SIDE; EOS - 747 Cab with (l-r) David Brown and Cindy Nguyen

Quantifying the foodscape: A systematic review and meta-analysis of the validity of commercially available business data.

PubMed

Lebel, Alexandre; Daepp, Madeleine I G; Block, Jason P; Walker, Renée; Lalonde, Benoît; Kestens, Yan; Subramanian, S V

2017-01-01

This paper reviews studies of the validity of commercially available business (CAB) data on food establishments ("the foodscape"), offering a meta-analysis of characteristics associated with CAB quality and a case study evaluating the performance of commonly-used validity indicators describing the foodscape. Existing validation studies report a broad range in CAB data quality, although most studies conclude that CAB quality is "moderate" to "substantial". We conclude that current studies may underestimate the quality of CAB data. We recommend that future validation studies use density-adjusted and exposure measures to offer a more meaningful characterization of the relationship of data error with spatial exposure.

Quantifying the foodscape: A systematic review and meta-analysis of the validity of commercially available business data

PubMed Central

Lebel, Alexandre; Daepp, Madeleine I. G.; Block, Jason P.; Walker, Renée; Lalonde, Benoît; Kestens, Yan; Subramanian, S. V.

2017-01-01

This paper reviews studies of the validity of commercially available business (CAB) data on food establishments (“the foodscape”), offering a meta-analysis of characteristics associated with CAB quality and a case study evaluating the performance of commonly-used validity indicators describing the foodscape. Existing validation studies report a broad range in CAB data quality, although most studies conclude that CAB quality is “moderate” to “substantial”. We conclude that current studies may underestimate the quality of CAB data. We recommend that future validation studies use density-adjusted and exposure measures to offer a more meaningful characterization of the relationship of data error with spatial exposure. PMID:28358819

Country analysis briefs: 1994. Profiles of major world energy producers, consumers, and transport centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-05-01

Country Analysis Briefs: 1994 is a compilation of country profiles prepared by the Energy Markets and Contingency Information Division (EMCID) of the Office of Energy Markets and End Use. EMCID maintains Country Analysis Briefs (CABs) for specific countries or geographical areas that are important to world energy markets. As a general rule, CABs are prepared for all members of the Organization of Petroleum Exporting Countries (OPEC), major non-OPEC oil producers (i.e., the North Sea, Russia), major energy transit areas (i.e., Ukraine), and other areas of current interest to energy analysts and policy makers. As of January 1995, EMCID maintained overmore » 40 CABs, updated on an annual schedule and subject to revision as events warrant. This report includes 25 CABs updated during 1994. All CABs contain a profile section, a map showing the country`s location, and a narrative section. The profile section includes outlines of the country`s economy, energy sector, and environment. The narrative provides further information and discussion of these topics. Some CABs also include a detailed map displaying locations of major oil and gas fields, pipelines, ports, etc. These maps were created as a result of special individual requests and so are not typically a standard feature of the CABs. They are presented here wherever available as a supplement to the information contained in the CABs.« less

Human Factors Guidelines for the Evaluation of the Locomotive Cab

DOT National Transportation Integrated Search

1995-09-01

This document presents human factors guidelines for the evaluation of the locomotive cab. These guidelines are part of : an effort to evaluate working conditions and safety in the locomotive cab. The guidelines will serve as a decision : making tool ...

Executive Summary : Tower Cab System Integration Analysis

DOT National Transportation Integrated Search

1978-08-01

This report summarizes the principal results of the study of the integration into the tower cab of the systems being developed under the Major Systems Development Program (MSDP). The impact of these systems on the tower cab is analyzed from several p...

Plasma endotoxin core antibody concentration and linear growth are unrelated in rural Malawian children aged 2-5 years.

PubMed

Benzoni, Nicole; Korpe, Poonum; Thakwalakwa, Chrissie; Maleta, Ken; Stephenson, Kevin; Manary, Micah; Manary, Mark

2015-06-24

Environmental enteropathy is subclinical inflammation of the upper gastrointestinal tract associated with reduced linear growth in developing countries. Usually investigators have used biopsy or a dual sugar absorption test to assess environmental enteropathy. Such tests are time and resource intensive, restricting their utility as screening methods. Serum endotoxin core antibody (EndoCab) concentration is a potential indicator of intestinal inflammation and integrity, and thus may be useful to predict environmental enteropathy. We analyzed the association of serum EndoCab levels versus linear growth and lactulose-mannitol assay results in 2-5 year old rural Malawian children. This was an observational study of 388 rural, asymptomatic Malawian children who had anthropometric measurements taken at least every 3 months since birth. In June and July 2011, dual sugar permeability tests were performed and serum samples were drawn for EndoCab assays. Pearson correlation, Student's t test and multivariable linear regression were used to compare ln EndoCab concentrations with height-for-age z scores (HAZ) at time of sampling and 3 months later. Identical analysis was also performed for ln EndoCab versus measurements from dual sugar permeability testing performed in conjunction with serum sampling. In a subgroup of children with anthropometric data in the months prior to serum sampling, Pearson correlation was used to estimate the relationship between ln EndoCab and recent linear growth. Ln EndoCab concentrations were not correlated with HAZ at time of measurement (B = -0.078, P = 0.14) nor change in HAZ over the subsequent 3 months HAZ (B = -0.018, P = 0.27). EndoCab concentration was not associated with %lactulose excretion (B < 0.001, P = 0.98) nor the lactulose:mannitol ratio (B = 0.021, P = 0.62). Subgroup analysis also did not reveal any significant association between EndoCab and recent growth. EndoCab titers were not correlated with measurements of growth or intestinal permeability in rural pre-school aged Malawian children.

Establishment of a Community Advisory Board (CAB) for tuberculosis control and research in the Inanda, Ntuzuma and KwaMashu (INK) area of KwaZulu-Natal, South Africa.

PubMed

Ntshanga, Sbongile P; Ngcobo, Paulos S; Mabaso, Musawenkosi L H

2010-05-01

To strengthen community mobilization, education, awareness and involvement in research to improve Tuberculosis (TB) control, by building partnership between communities and the health sector through the establishment of a Community Advisory Board (CAB) in the Inanda, Ntuzuma and KwaMashu (INK) area. Key stakeholders from multiple sectors of the target community were identified. Two workshops were held with the aim of communicating the need for CAB and selecting its members. A 22 member INK CAB with representatives from different sectors in the community was selected. CAB members were trained through a 2-day workshop on TB and research. Various activities were successfully initiated and spearheaded by the INK CAB, and these involved training of Traditional Healers, recruiting of more TB tracer teams, organizing awareness campaigns during TB World Day, establishing TB school peer educators and links with NGOs to support impoverished TB patients all with positive outcomes. The INK CAB is a successful example of providing a mechanism for community consultation and participation that contributes to promoting and facilitating relevant research and TB control activities. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

In-vitro dissolution rate and molecular docking studies of cabergoline drug with β-cyclodextrin

NASA Astrophysics Data System (ADS)

Shanmuga priya, Arumugam; Balakrishnan, Suganya bharathi; Veerakanellore, Giri Babu; Stalin, Thambusamy

2018-05-01

The physicochemical properties and dissolution profile of cabergoline drug (CAB) with β-cyclodextrin (β-CD) inclusion complex were investigated by the UV spectroscopy. The inclusion complex has used to calculate the stability constant and gives the stoichiometry molar ratio is 1:1 between CAB and β-CD. The phase solubility diagram and the aqueous solubility of CAB (60%) was found to be enhanced by β-CD. In addition, the phase solubility profile of CAB with β-CD was classified as AL-type. Binary systems of CAB with β-CD were prepared by Physical mixture, Kneading and solvent evaporation methods. The solid-state properties of the inclusion complex were characterized by Fourier transformation-infrared spectroscopy, Differential scanning calorimetry, Powder X-ray diffractometric patterns and Scanning electron microscopic techniques. Theoretically, β-CD and CAB inclusion complex obtained by molecular docking studies, it is in good correlation with the results obtained through experimental methods using the Schrödinger software program. In-vitro dissolution profiles of the inclusion complexes were carried out and obvious increase in dissolution rate was observed when compared with pure CAB drug and the complexes.

Systems Integration Analysis for Future Tower Cab Configurations/Systems

DOT National Transportation Integrated Search

1978-06-01

This report presents the results of the analysis of various aspects of the integration of future ATC systems into the tower cab. The impact on the tower cab environment is analyzed from several points of view: how the systems information and displays...

Locomotive cab design development. volume 2 : operator's manual - Interim Report

DOT National Transportation Integrated Search

1976-10-01

Locomotive Cab 913 designed as a result of Contract DOT-TSC- 913 has been built as a hard mock-up. This Operator's Manual is to familiarize the user with the mock-up. Normal and emergency procedures and cab facilities are described.

Selection of the Next Generation of Air Traffic Control Specialists: Aptitude Requirements for the Air Traffic Control Tower Cab in 2018

DTIC Science & Technology

2013-03-01

Sequencing; and 5) Taxi Routing (with Conformance Monitoring). Third, the impact of these DSTs on tower cab operational activities, sub-activities...keystroke or interface level. Fourth, the impact of the DSTs on aptitudes required of controllers is evaluated. The importance of the following aptitudes...Analysis of Mid-Term NextGen Impact on Aptitudes Required in the ATCT Cab ---------------- 36 Mid-Term DST Impact on Tower Cab Controller Roles

Taxi Cab Syndrome: A Review of the Extensive Genitourinary Pathology Experienced by Taxi Cab Drivers and What We Can Do to Help

PubMed Central

Mass, Alon Y; Goldfarb, David S; Shah, Ojas

2014-01-01

This review consolidates knowledge regarding the extensive genitourinary pathology experienced by taxi cab drivers. Taxi cab, livery, truck, and other drivers all objectively and subjectively may have more voiding dysfunction, infertility, urolithiasis, bladder cancer, and urinary infections as compared with nonprofessional drivers; this is called taxi cab syndrome. Together with governmental and medical assistance, simple interventions—such as education, the addition of taxi relief stations, and possibly the use of sanitary urinary collection devices—to curb the progression of genitourinary disease in taxi drivers should be prospectively studied. It is postulated that many of these interventions may also benefit other groups of occupationally related infrequent voiders. PMID:25337038

49 CFR 230.81 - Cab aprons.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Cab aprons. 230.81 Section 230.81 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION STEAM LOCOMOTIVE INSPECTION AND MAINTENANCE STANDARDS Steam Locomotives and Tenders Cabs, Warning Signals, Sanders and Lights §...

Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model.

PubMed

Pulawski, Wojciech; Jamroz, Michal; Kolinski, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2016-11-28

The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics, and interactions). Here we introduce an extension of the CABS representation and force field (CABS-membrane) to the modeling of the effect of the biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane. In the resulting trajectories, we have found models close to the experimental membrane structures. We also attempted to select the correctly folded models using simple filtering followed by structural clustering combined with reconstruction to the all-atom representation and all-atom scoring. The CABS-membrane model is a promising approach for further development toward modeling of large protein-membrane systems.

49 CFR 236.513 - Audible indicator.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.513 Audible indicator. (a) The automatic cab signal... control system shall have a distinctive sound and be clearly audible throughout the cab under all...

49 CFR 236.513 - Audible indicator.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.513 Audible indicator. (a) The automatic cab signal... control system shall have a distinctive sound and be clearly audible throughout the cab under all...

Prototype design of a collision protection system for cab car engineers.

DOT National Transportation Integrated Search

2013-03-01

The objective of this project was to develop and analyze a passive system to protect a cab car engineer from secondary impact injuries that might be experienced due to impact with the cab console. The primary requirement for the system was the abilit...

Analysis of colliding vehicle interactions for the passenger rail train-to-train impact test

DOT National Transportation Integrated Search

2004-04-06

A full-scale train-to-train impact test was performed in : which a cab car-led passenger train traveling at 30 mph collided : with a standing locomotive-led train. During the test, the lead : cab car overrode the cab of the standing locomotive, susta...

77 FR 32594 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-01

... Advisors). The Bureau seeks to collect selection-related information from nominees to the CAB, such as... for other Advisory Groups, members of other Advisory Groups, and Special Advisors to CAB and other... obtain information on the qualifications of individuals nominated to the CAB and will aid the Bureau in...

49 CFR 229.121 - Locomotive cab noise.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Locomotive cab noise. 229.121 Section 229.121... § 229.121 Locomotive cab noise. (a) Performance standards for locomotives. (1) When tested for static noise in accordance with paragraph (a)(3) of this section, all locomotives of each design or model that...

49 CFR 235.5 - Changes requiring filing of application.

Code of Federal Regulations, 2010 CFR

2010-10-01

... system, automatic train stop, train control, or cab signal system or other similar appliance or device..., automatic train stop, train control, or cab signal system; or (3) The modification of a block signal system, interlocking, traffic control system, automatic train stop, train control, or cab signal system. (b) [Reserved...

49 CFR 235.5 - Changes requiring filing of application.

Code of Federal Regulations, 2011 CFR

2011-10-01

... system, automatic train stop, train control, or cab signal system or other similar appliance or device..., automatic train stop, train control, or cab signal system; or (3) The modification of a block signal system, interlocking, traffic control system, automatic train stop, train control, or cab signal system. (b) [Reserved...

A crush zone design for an existing passenger rail cab car

DOT National Transportation Integrated Search

2005-11-05

A Crash Energy Management (CEM) cab car crush zone : design has been developed for retrofit onto an existing Budd : M1 cab car. This design is to be used in the upcoming fullscale : train-to-train test of a CEM consist impacting a standing : freight ...

Promising evidence of impact on road safety by changing at-risk behavior process at Union Pacific

DOT National Transportation Integrated Search

2008-06-01

Changing At-risk Behavior (CAB) is a safety process that is being conducted at Union Pacifics San Antonio Service Unit with the aim of improving locomotive cab safety related to constraining signals. CAB is an example of a risk reduction method th...

Passenger cab car grade crossing impact test report : rail passenger equipment impact tests

DOT National Transportation Integrated Search

2007-10-01

Two full-scale oblique grade crossing impact tests were conducted in June 2002 to compare the crashworthiness performance of alternative corner post designs on rail passenger cab cars. On June 4, 2002, a cab car fitted with an end frame built to pre-...

CABS-flex: server for fast simulation of protein structure fluctuations

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model–based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics—a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions. PMID:23658222

CABS-flex: Server for fast simulation of protein structure fluctuations.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-07-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions.

Immunohistochemical and radiological characterization of wound healing in porcine liver after radiofrequency ablation.

PubMed

Stadlbauer, Vanessa; Lang-Olip, Ingrid; Leber, Bettina; Mayrhauser, Ursula; Koestenbauer, Sonja; Tawdrous, Monika; Moche, Michael; Sereinigg, Michael; Seider, Daniel; Iberer, Florian; Wiederstein-Grasser, Iris; Portugaller, Rupert Horst; Stiegler, Philipp

2016-01-01

Radiofrequency ablation (RFA) is a minimal invasive therapeutic option for patients with hepatocellular carcinoma or liver metastases. We investigated RFA-induced cellular changes in the liver of pigs. Healthy pigs (n=18) were sacrificed between day 0 and 3 months after RFA. The wound healing process was evaluated by computed tomography (CT), chromotrope anilinblue (CAB) staining of large-scale and standard tissue sections. Immunohistochemistry (IHC) for heat shock protein 70, Caspase-3, Ki67, Reelin, Vinculin, Vimentin and α-SMA was perfomed. One day after RFA, CAB staining showed cell damage and massive hyperaemia. All IHC markers were predominantly expressed at the outer borders of the lesion, except Reelin, which was mainly detected in untreated liver regions. By staining for Hsp70, the heat stress during RFA was monitored, which was most distinct 1-2 days after RFA. CT revealed decreased lesion size after one week. Development of a Vimentin and α-SMA positive fibrotic capsule was observed. In the early phase signs of cell damage, apoptosis and proliferation are dominant. Reduced expression of Reelin suggests a minor role of hepatic stellate cells in the RFA zone. After one week myofibroblasts become prominent and contribute to the development of the fibrotic capsule. This elucidates the pathophysiology of RFA and could contribute to the future optimization of RFA procedures.

Material decomposition images generated from spectral CT: detectability of urinary calculi and influencing factors.

PubMed

Lv, Peijie; Zhang, Yonggao; Liu, Jie; Ji, Lijuan; Chen, Yan; Gao, Jianbo

2014-01-01

To evaluate the detectability of urinary calculi on material decomposition (MD) images generated from spectral computed tomography (CT) and identify the influencing factors. Forty-six patients were examined with true nonenhanced (TNE) CT and spectral CT urography in the excretory phase. The contrast medium was removed from excretory phase images using water-based (WB) and calcium-based (CaB) MD analysis. The sensitivity for detection on WB and CaB images was evaluated using TNE results as the reference standard. The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) on MD images were evaluated. Using logistic regression, the influences of image noise, attenuation, stone size, and patient's body mass index (BMI) were assessed. Threshold values with maximal sensitivity and specificity were calculated by means of receiver operating characteristic analyses. One hundred thirty-six calculi were detected on TNE images; 98 calculi were identified on WB images (sensitivity, 72.06%) and 101 calculi on CaB images (sensitivity, 74.26%). Sensitivities were 76.92% for the 3-5-mm stones and 84.51% for the 5-mm or larger stones on both WB and CaB images but reduced to 46.15% on WB images and 53.85% on CaB images for small calculi (<3 mm). Compared to WB images, CaB images showed lower image noise, higher SNR but similar CNR. Larger stone sizes (both >2.71 mm on WB and CaB) and greater CT attenuation (>280 Hounsfield units [HU] on WB, >215 HU on CaB) of the urinary stones were significantly associated with higher stone visibility rates on WB and CaB images (P ≤ .003). Image noise and BMI showed no impact on the stone detection. MD images generated from spectral CT showed good reliability for the detection of large (>2.71 mm) and hyperattenuating (>280 HU on WB, >215 HU on CaB) urinary calculi. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

ABC versus CAB for cardiopulmonary resuscitation: a prospective, randomized simulator-based trial.

PubMed

Marsch, Stephan; Tschan, Franziska; Semmer, Norbert K; Zobrist, Roger; Hunziker, Patrick R; Hunziker, Sabina

2013-09-06

After years of advocating ABC (Airway-Breathing-Circulation), current guidelines of cardiopulmonary resuscitation (CPR) recommend CAB (Circulation-Airway-Breathing). This trial compared ABC with CAB as initial approach to CPR from the arrival of rescuers until the completion of the first resuscitation cycle. 108 teams, consisting of two physicians each, were randomized to receive a graphical display of either the ABC algorithm or the CAB algorithm. Subsequently teams had to treat a simulated cardiac arrest. Data analysis was performed using video recordings obtained during simulations. The primary endpoint was the time to completion of the first resuscitation cycle of 30 compressions and two ventilations. The time to execution of the first resuscitation measure was 32 ± 12 seconds in ABC teams and 25 ± 10 seconds in CAB teams (P = 0.002). 18/53 ABC teams (34%) and none of the 55 CAB teams (P = 0.006) applied more than the recommended two initial rescue breaths which caused a longer duration of the first cycle of 30 compressions and two ventilations in ABC teams (31 ± 13 vs.23 ± 6 sec; P = 0.001). Overall, the time to completion of the first resuscitation cycle was longer in ABC teams (63 ± 17 vs. 48 ± 10 sec; P <0.0001). This randomized controlled trial found CAB superior to ABC with an earlier start of CPR and a shorter time to completion of the first 30:2 resuscitation cycle. These findings endorse the change from ABC to CAB in international resuscitation guidelines.

30 CFR 75.1710 - Canopies or cabs; diesel-powered and electric face equipment.

Code of Federal Regulations, 2013 CFR

2013-07-01

...-powered and electric face equipment, including shuttle cars, be provided with substantially constructed... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Canopies or cabs; diesel-powered and electric... Miscellaneous § 75.1710 Canopies or cabs; diesel-powered and electric face equipment. In any coal mine where the...

30 CFR 75.1710 - Canopies or cabs; diesel-powered and electric face equipment.

Code of Federal Regulations, 2012 CFR

2012-07-01

...-powered and electric face equipment, including shuttle cars, be provided with substantially constructed... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Canopies or cabs; diesel-powered and electric... Miscellaneous § 75.1710 Canopies or cabs; diesel-powered and electric face equipment. In any coal mine where the...

30 CFR 75.1710 - Canopies or cabs; diesel-powered and electric face equipment.

Code of Federal Regulations, 2014 CFR

2014-07-01

...-powered and electric face equipment, including shuttle cars, be provided with substantially constructed... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Canopies or cabs; diesel-powered and electric... Miscellaneous § 75.1710 Canopies or cabs; diesel-powered and electric face equipment. In any coal mine where the...

30 CFR 75.1710 - Canopies or cabs; diesel-powered and electric face equipment.

Code of Federal Regulations, 2011 CFR

2011-07-01

...-powered and electric face equipment, including shuttle cars, be provided with substantially constructed... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Canopies or cabs; diesel-powered and electric... Miscellaneous § 75.1710 Canopies or cabs; diesel-powered and electric face equipment. In any coal mine where the...

30 CFR 75.1710 - Canopies or cabs; diesel-powered and electric face equipment.

Code of Federal Regulations, 2010 CFR

2010-07-01

...-powered and electric face equipment, including shuttle cars, be provided with substantially constructed... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Canopies or cabs; diesel-powered and electric... Miscellaneous § 75.1710 Canopies or cabs; diesel-powered and electric face equipment. In any coal mine where the...

49 CFR 223.11 - Requirements for existing locomotives.

Code of Federal Regulations, 2010 CFR

2010-10-01

... be equipped with certified glazing in all locomotive cab windows after June 30, 1984. (d) Each... vandalism has a locomotive cab window that is broken or damaged so that the window fails to permit good... broken or damaged window is a part of the windshield of the locomotive cab, all of the forward and...

Mechanical and thermal properties of eco-friendly poly(propylene carbonate)/cellulose acetate butyrate blends.

PubMed

Xing, Chenyang; Wang, Hengti; Hu, Qiaoqiao; Xu, Fenfen; Cao, Xiaojun; You, Jichun; Li, Yongjin

2013-02-15

The eco-friendly poly(propylene carbonate) (PPC)/cellulose acetate butyrate (CAB) blends were prepared by melt-blending in a batch mixer for the first time. PPC and CAB were partially miscible because of the drastically shifted glass transition temperatures of both PPC and CAB, which originated from the specific interactions between carbonyl groups and hydroxyl groups. The incorporation of CAB into PPC matrix enhanced not only tensile strength and modulus of PPC dramatically, but also improved heat resistance and thermal stability of PPC significantly. The tensile strength and the modulus of PPC/CAB=50/50 blend are 27.7 MPa and 1.24 GPa, which are 21 times and 28 times higher than those of the unmodified PPC, respectively. Moreover, the elongation at break of PPC/CAB=50/50 blend is as high as 117%. In addition, the obtained blends exhibited good transparency, which is very important for the package materials. The results in this work pave new possibility for the massive application of eco-friendly polymer materials. Copyright © 2012 Elsevier Ltd. All rights reserved.

Effects of an Encapsulated Fruit and Vegetable Juice Concentrate on Obesity-Induced Systemic Inflammation: A Randomised Controlled Trial

PubMed Central

Williams, Evan J.; Baines, Katherine J.; Berthon, Bronwyn S.; Wood, Lisa G.

2017-01-01

Phytochemicals from fruit and vegetables reduce systemic inflammation. This study examined the effects of an encapsulated fruit and vegetable (F&V) juice concentrate on systemic inflammation and other risk factors for chronic disease in overweight and obese adults. A double-blinded, parallel, randomized placebo-controlled trial was conducted in 56 adults aged ≥40 years with a body mass index (BMI) ≥28 kg/m2. Before and after eight weeks daily treatment with six capsules of F&V juice concentrate or placebo, peripheral blood gene expression (microarray, quantitative polymerase chain reaction (qPCR)), plasma tumour necrosis factor (TNF)α (enzyme-linked immunosorbent assay (ELISA)), body composition (Dual-energy X-ray absorptiometry (DEXA)) and lipid profiles were assessed. Following consumption of juice concentrate, total cholesterol, low-density lipoprotein (LDL) cholesterol and plasma TNFα decreased and total lean mass increased, while there was no change in the placebo group. In subjects with high systemic inflammation at baseline (serum C-reactive protein (CRP) ≥3.0 mg/mL) who were supplemented with the F&V juice concentrate (n = 16), these effects were greater, with decreased total cholesterol, LDL cholesterol and plasma TNFα and increased total lean mass; plasma CRP was unchanged by the F&V juice concentrate following both analyses. The expression of several genes involved in lipogenesis, the nuclear factor-κB (NF-κB) and 5′ adenosine monophosphate-activated protein kinase (AMPK) signalling pathways was altered, including phosphomevalonate kinase (PMVK), zinc finger AN1-type containing 5 (ZFAND5) and calcium binding protein 39 (CAB39), respectively. Therefore, F&V juice concentrate improves the metabolic profile, by reducing systemic inflammation and blood lipid profiles and, thus, may be useful in reducing the risk of obesity-induced chronic disease. PMID:28208713

Leukemia-associated gene MLAA-34 reduces arsenic trioxide-induced apoptosis in HeLa cells via activation of the Wnt/β-catenin signaling pathway.

PubMed

Zhang, Pengyu; Zhao, Xuan; Zhang, Wenjuan; He, Aili; Lei, Bo; Zhang, Wanggang; Chen, Yinxia

2017-01-01

Our laboratory previously used the SEREX method in U937 cells and identified a novel leukemia-associated gene MLAA-34, a novel splice variant of CAB39L associated with acute monocytic leukemia, that exhibited anti-apoptotic activities in U937 cells. Whether MLAA-34 has an anti-apoptotic role in other tumor cells has not yet been reported. We explored whether MLAA-34 exhibited anti-apoptotic effects in HeLa cervical cancer cells and the possible mechanism of action. We generated a HeLa cell line stably expressing MLAA-34 and found that MLAA-34 overexpression had no effect on the growth, apoptosis and cell cycle of HeLa cells. However, upon treatment with arsenic trioxide (ATO) to induce apoptosis, the cell viability and colony formation ability of ATO-treated MLAA-34 stable HeLa cells were significantly higher than that of ATO-treated controls, and the apoptosis rate and proportion of G2/M cells also decreased. We found that ATO treatment of HeLa cells resulted in significant decreases in the expression of β-catenin mRNA and protein and the downstream target factors c-Myc, cyclin B1, and cyclin D1 in the Wnt signaling pathway. Notably, ATO-treated MLAA-34 stable HeLa cells showed a significant reduction in the ATO-mediated downregulation of these factors. In addition, MLAA-34 overexpression significantly increased the expression of nuclear β-catenin protein in ATO-treated cells compared with HeLa cells treated only with ATO. Thus, here we have found that the Wnt/β-catenin signaling pathway is involved in ATO-induced apoptosis in HeLa cells. MLAA-34 reduces ATO-induced apoptosis and G2/M arrest, and the anti-apoptotic effect may be achieved by activating the Wnt/β-catenin signaling pathway in HeLa cells.

Leukemia-associated gene MLAA-34 reduces arsenic trioxide-induced apoptosis in HeLa cells via activation of the Wnt/β-catenin signaling pathway

PubMed Central

Zhao, Xuan; Zhang, Wenjuan; He, Aili; Lei, Bo; Zhang, Wanggang; Chen, Yinxia

2017-01-01

Our laboratory previously used the SEREX method in U937 cells and identified a novel leukemia-associated gene MLAA-34, a novel splice variant of CAB39L associated with acute monocytic leukemia, that exhibited anti-apoptotic activities in U937 cells. Whether MLAA-34 has an anti-apoptotic role in other tumor cells has not yet been reported. We explored whether MLAA-34 exhibited anti-apoptotic effects in HeLa cervical cancer cells and the possible mechanism of action. We generated a HeLa cell line stably expressing MLAA-34 and found that MLAA-34 overexpression had no effect on the growth, apoptosis and cell cycle of HeLa cells. However, upon treatment with arsenic trioxide (ATO) to induce apoptosis, the cell viability and colony formation ability of ATO-treated MLAA-34 stable HeLa cells were significantly higher than that of ATO-treated controls, and the apoptosis rate and proportion of G2/M cells also decreased. We found that ATO treatment of HeLa cells resulted in significant decreases in the expression of β-catenin mRNA and protein and the downstream target factors c-Myc, cyclin B1, and cyclin D1 in the Wnt signaling pathway. Notably, ATO-treated MLAA-34 stable HeLa cells showed a significant reduction in the ATO-mediated downregulation of these factors. In addition, MLAA-34 overexpression significantly increased the expression of nuclear β-catenin protein in ATO-treated cells compared with HeLa cells treated only with ATO. Thus, here we have found that the Wnt/β-catenin signaling pathway is involved in ATO-induced apoptosis in HeLa cells. MLAA-34 reduces ATO-induced apoptosis and G2/M arrest, and the anti-apoptotic effect may be achieved by activating the Wnt/β-catenin signaling pathway in HeLa cells. PMID:29059232

Effects of MERV 16 filters and routine work practices on enclosed cabs for reducing respirable dust and DPM exposures in an underground limestone mine

PubMed Central

Noll, J.D.; Cecala, A.B.; J.A.Organiscak; Rider, J.P.

2015-01-01

An effective technique to minimize miners’ respirable dust and diesel exposure on mobile mining equipment is to place mine operators in enclosed cabs with designed filtration and pressurization systems. Many factors affect the performance of these enclosed cab systems, and one of the most significant factors is the effectiveness of the filtration system. High-efficiency particulate air (HEPA)-type filters are typically used because they are highly efficient at capturing all types and sizes of particles, including those in the submicron range such as diesel particulate matter (DPM). However, in laboratory tests, minimum efficiency reporting value (MERV) 16 filters have proven to be highly efficient for capturing DPM and respirable dust. Also, MERV 16 filters can be less restrictive to cab airflow and less expensive than HEPA filters. To verify their effectiveness in the field, MERV 16 filters were used in the enclosed cab filtration system on a face drill and roof bolting mining machine and tested at an underground limestone mine. Test results showed that DPM and respirable dust concentrations were reduced by more than 90% when the cabs were properly sealed. However, when the cab door was opened periodically throughout the shift, the reduction efficiency of the MERV 16 filters was reduced to 80% on average. PMID:26236044

49 CFR 236.511 - Cab signals controlled in accordance with block conditions stopping distance in advance.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Cab signals controlled in accordance with block conditions stopping distance in advance. 236.511 Section 236.511 Transportation Other Regulations Relating to... § 236.511 Cab signals controlled in accordance with block conditions stopping distance in advance. The...

49 CFR 236.566 - Locomotive of each train operating in train stop, train control or cab signal territory; equipped.

Code of Federal Regulations, 2010 CFR

2010-10-01

... OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and... controlled, of each train operating in automatic train stop, train control, or cab signal territory shall be..., train control or cab signal territory; equipped. 236.566 Section 236.566 Transportation Other...

49 CFR 236.566 - Locomotive of each train operating in train stop, train control or cab signal territory; equipped.

Code of Federal Regulations, 2011 CFR

2011-10-01

... OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and... controlled, of each train operating in automatic train stop, train control, or cab signal territory shall be..., train control or cab signal territory; equipped. 236.566 Section 236.566 Transportation Other...

49 CFR 236.568 - Difference between speeds authorized by roadway signal and cab signal; action required.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Difference between speeds authorized by roadway... Systems Rules and Instructions; Locomotives § 236.568 Difference between speeds authorized by roadway signal and cab signal; action required. If for any reason a cab signal authorizes a speed different from...

49 CFR 236.568 - Difference between speeds authorized by roadway signal and cab signal; action required.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Difference between speeds authorized by roadway... Systems Rules and Instructions; Locomotives § 236.568 Difference between speeds authorized by roadway signal and cab signal; action required. If for any reason a cab signal authorizes a speed different from...

Epidemiology, microbiology and mortality associated with community-acquired bacteremia in northeast Thailand: a multicenter surveillance study.

PubMed

Kanoksil, Manas; Jatapai, Anchalee; Peacock, Sharon J; Limmathurotsakul, Direk

2013-01-01

National statistics in developing countries are likely to underestimate deaths due to bacterial infections. Here, we calculated mortality associated with community-acquired bacteremia (CAB) in a developing country using routinely available databases. Information was obtained from the microbiology and hospital database of 10 provincial hospitals in northeast Thailand, and compared with the national death registry from the Ministry of Interior, Thailand for the period between 2004 and 2010. CAB was defined in patients who had pathogenic organisms isolated from blood taken within 2 days of hospital admission without a prior inpatient episode in the preceding 30 days. A total of 15,251 CAB patients identified, of which 5,722 (37.5%) died within 30 days of admission. The incidence rate of CAB between 2004 and 2010 increased from 16.7 to 38.1 per 100,000 people per year, and the mortality rate associated with CAB increased from 6.9 to 13.7 per 100,000 people per year. In 2010, the mortality rate associated with CAB was lower than that from respiratory tract infection, but higher than HIV disease or tuberculosis. The most common causes of CAB were Escherichia coli (23.1%), Burkholderia pseudomallei (19.3%), and Staphylococcus aureus (8.2%). There was an increase in the proportion of Extended-Spectrum Beta-Lactamases (ESBL) producing E. coli and Klebsiella pneumoniae over time. This study has demonstrated that national statistics on causes of death in developing countries could be improved by integrating information from readily available databases. CAB is neglected as an important cause of death, and specific prevention and intervention is urgently required to reduce its incidence and mortality.

Epidemiology, Microbiology and Mortality Associated with Community-Acquired Bacteremia in Northeast Thailand: A Multicenter Surveillance Study

PubMed Central

Kanoksil, Manas; Jatapai, Anchalee; Peacock, Sharon J.; Limmathurotsakul, Direk

2013-01-01

Background National statistics in developing countries are likely to underestimate deaths due to bacterial infections. Here, we calculated mortality associated with community-acquired bacteremia (CAB) in a developing country using routinely available databases. Methods/Principal Findings Information was obtained from the microbiology and hospital database of 10 provincial hospitals in northeast Thailand, and compared with the national death registry from the Ministry of Interior, Thailand for the period between 2004 and 2010. CAB was defined in patients who had pathogenic organisms isolated from blood taken within 2 days of hospital admission without a prior inpatient episode in the preceding 30 days. A total of 15,251 CAB patients identified, of which 5,722 (37.5%) died within 30 days of admission. The incidence rate of CAB between 2004 and 2010 increased from 16.7 to 38.1 per 100,000 people per year, and the mortality rate associated with CAB increased from 6.9 to 13.7 per 100,000 people per year. In 2010, the mortality rate associated with CAB was lower than that from respiratory tract infection, but higher than HIV disease or tuberculosis. The most common causes of CAB were Escherichia coli (23.1%), Burkholderia pseudomallei (19.3%), and Staphylococcus aureus (8.2%). There was an increase in the proportion of Extended-Spectrum Beta-Lactamases (ESBL) producing E. coli and Klebsiella pneumoniae over time. Conclusions This study has demonstrated that national statistics on causes of death in developing countries could be improved by integrating information from readily available databases. CAB is neglected as an important cause of death, and specific prevention and intervention is urgently required to reduce its incidence and mortality. PMID:23349954

Using Community Advisory Boards to Reduce Environmental Barriers to Health in American Indian Communities, Wisconsin, 2007–2012

PubMed Central

Scott, Jamie R.; Prince, Ron; Williamson, Amy

2014-01-01

Background American Indian communities have a high prevalence of chronic diseases including diabetes, obesity, cardiovascular disease, and cancer. Innovative community-based approaches are needed to identify, prioritize, and create sustainable interventions to reduce environmental barriers to healthy lifestyles and ultimately improve health. Community Context Healthy Children, Strong Families was a family-based and community-based intervention to increase healthy lifestyles on Wisconsin American Indian reservations. This intervention arose from a long-standing partnership between University of Wisconsin researchers and 3 of these American Indian communities. Methods In each community, community advisory boards (CABs) were established by the residents and university partners. CAB meetings were open and held at various times and locations to increase member participation. CABs featured continual, snowball recruitment; internal and external expert consultation; and coordination with standing tribal committees. Meetings initially focused on understanding community supports for and barriers to healthy lifestyles but quickly turned toward community action for change. Outcome CAB interventions decreased environmental barriers to health at each site and improved options for healthy lifestyle choices. Over 5 years, 71 CAB meetings occurred with a total of 1,070 participants. Successful CAB interventions included planting community gardens and an apple orchard, conducting gardening and canning workshops, instituting food-related policies and dog control regulations, building an environmentally friendly playground, and providing access to recreational facilities. The CABs are now self-sustaining. Interpretation CABs can be highly effective action teams capable of improving community environments. Our experience shows that academic researchers can partner with community residents to generate programs and policies that will expand access to local food, increase people’s choices for engaging in physical activity, and encourage local policy changes that improve overall community health. PMID:25232747

Community engagement on the Thai–Burmese border: rationale, experience and lessons learnt

PubMed Central

Cheah, Phaik Yeong; Lwin, Khin Maung; Phaiphun, Lucy; Maelankiri, Ladda; Parker, Michael; Day, Nicholas P.; White, Nicholas J.; Nosten, François

2012-01-01

Community engagement is increasingly promoted in developing countries, especially in international health research, but there is little published experience. The Shoklo Malaria Research Unit (SMRU) conducts research with refugees, migrant workers, displaced people, and day migrants on the Thai-Burmese border, and has recently facilitated the set up of the Tak Province Border Community Ethics Advisory Board (T-CAB). Valuable lessons have been learnt from consultation with the T-CAB especially in the area of participant recruitment and the informed consent process. A lot of new research questions have emerged from consultation with the T-CAB. This paper describes our experience, lessons learnt and the unique challenges faced working with the T-CAB from its initial conception to date. We conclude that consultation with the T-CAB has made improvements in our research in particular operational and ethical aspects of our studies. PMID:22984375

49 CFR Figure 1 to Subpart E of... - Power Car Cab Forward End Structure Conceptual Implementation

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Power Car Cab Forward End Structure Conceptual Implementation 1 Figure 1 to Subpart E of Part 238 Transportation Other Regulations Relating to Transportation... Subpart E of Part 238—Power Car Cab Forward End Structure Conceptual Implementation ER12MY99.000 ...

49 CFR Figure 1 to Subpart E of... - Power Car Cab Forward End Structure Conceptual Implementation

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Power Car Cab Forward End Structure Conceptual Implementation 1 Figure 1 to Subpart E of Part 238 Transportation Other Regulations Relating to Transportation... Subpart E of Part 238—Power Car Cab Forward End Structure Conceptual Implementation ER12MY99.000 ...

Alternative Fuels Data Center: Happy Cab Fuels Taxi Fleet With CNG

Science.gov Websites

Happy Cab Fuels Taxi Fleet With CNG Find out how a cab company in Omaha, Nebraska, saves money fueling Go Electric in Florida Feb. 15, 2014 Renzenberger Inc Saves Money With Propane Vans Feb. 1, 2014 Gas School Buses Help Kansas City Save Money Nov. 12, 2011 Metropolitan Utilities District Fuels

Alternative Fuels Data Center: Yellow Cab Converts Taxis to Propane in

Science.gov Websites

electric car. College Students Engineer Efficient Vehicles in EcoCAR 2 Competition Aug. 2, 2014 Photo of a Columbus, OhioA> Yellow Cab Converts Taxis to Propane in Columbus, Ohio to someone by E-mail how Yellow Cab is overhauling their fleet in Columbus, Ohio, with propane power. For information about

49 CFR Figure 1 to Subpart E of... - Power Car Cab Forward End Structure Conceptual Implementation

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Power Car Cab Forward End Structure Conceptual Implementation 1 Figure 1 to Subpart E of Part 238 Transportation Other Regulations Relating to Transportation... Subpart E of Part 238—Power Car Cab Forward End Structure Conceptual Implementation ER12MY99.000 ...

Measuring and modeling air exchange rates inside taxi cabs in Los Angeles, California

NASA Astrophysics Data System (ADS)

Shu, Shi; Yu, Nu; Wang, Yueyan; Zhu, Yifang

2015-12-01

Air exchange rates (AERs) have a direct impact on traffic-related air pollutant (TRAP) levels inside vehicles. Taxi drivers are occupationally exposed to TRAP on a daily basis, yet there is limited measurement of AERs in taxi cabs. To fill this gap, AERs were quantified in 22 representative Los Angeles taxi cabs including 10 Prius, 5 Crown Victoria, 3 Camry, 3 Caravan, and 1 Uplander under realistic driving (RD) conditions. To further study the impacts of window position and ventilation settings on taxi AERs, additional tests were conducted on 14 taxis with windows closed (WC) and on the other 8 taxis with not only windows closed but also medium fan speed (WC-MFS) under outdoor air mode. Under RD conditions, the AERs in all 22 cabs had a mean of 63 h-1 with a median of 38 h-1. Similar AERs were observed under WC condition when compared to those measured under RD condition. Under WC-MFS condition, AERs were significantly increased in all taxi cabs, when compared with those measured under RD condition. A General Estimating Equation (GEE) model was developed and the modeling results showed that vehicle model was a significant factor in determining the AERs in taxi cabs under RD condition. Driving speed and car age were positively associated with AERs but not statistically significant. Overall, AERs measured in taxi cabs were much higher than typical AERs people usually encounter in indoor environments such as homes, offices, and even regular passenger vehicles.

Conceptual design study for an advanced cab and visual system, volume 2

NASA Technical Reports Server (NTRS)

Rue, R. J.; Cyrus, M. L.; Garnett, T. A.; Nachbor, J. W.; Seery, J. A.; Starr, R. L.

1980-01-01

The performance, design, construction and testing requirements are defined for developing an advanced cab and visual system. The rotorcraft system integration simulator is composed of the advanced cab and visual system and the rotorcraft system motion generator, and is part of an existing simulation facility. User's applications for the simulator include rotorcraft design development, product improvement, threat assessment, and accident investigation.

Towards a covariance matrix of CAB model parameters for H(H2O)

NASA Astrophysics Data System (ADS)

Scotta, Juan Pablo; Noguere, Gilles; Damian, José Ignacio Marquez

2017-09-01

Preliminary results on the uncertainties of hydrogen into light water thermal scattering law of the CAB model are presented. It was done through a coupling between the nuclear data code CONRAD and the molecular dynamic simulations code GROMACS. The Generalized Least Square method was used to adjust the model parameters on evaluated data and generate covariance matrices between the CAB model parameters.

The tae-miR408-Mediated Control of TaTOC1 Genes Transcription Is Required for the Regulation of Heading Time in Wheat1[OPEN

PubMed Central

Zhao, Xiang Yu; Hong, Po; Chen, Xiang Bin; Ye, Xing Guo; Pan, Yan You; Wang, Jian

2016-01-01

Timing of flowering is not only an interesting topic in developmental biology, but it also plays a significant role in agriculture for its effects on the maturation time of seed. The hexaploid wheat (Triticum aestivum) is one of the most important crop species whose flowering time, i.e. heading time, greatly influences yield. However, it remains unclear whether and how microRNAs regulate heading time in it. In our current study, we identified the tae-miR408 in wheat and its targets in vivo, including Triticum aestivum TIMING OF CAB EXPRESSION-A1 (TaTOC-A1), TaTOC-B1, and TaTOC-D1. The tae-miR408 levels were reciprocal to those of TaTOC1s under long-day and short-day conditions. Wheat plants with a knockdown of TaTOC1s via RNA interference and overexpression of tae-miR408 showed early-heading phenotype. Furthermore, TaTOC1s expression was down-regulated by the tae-miR408 in the hexaploid wheat. In addition, other important agronomic traits in wheat, such as plant height and flag leaf angle, were regulated by both tae-miR408 and TaTOC1s. Thus, our results suggested that the tae-miR408 functions in the wheat heading time by mediating TaTOC1s expression, and the study provides important new information on the mechanism underlying heading time regulation in wheat. PMID:26768600

The tae-miR408-Mediated Control of TaTOC1 Genes Transcription Is Required for the Regulation of Heading Time in Wheat.

PubMed

Zhao, Xiang Yu; Hong, Po; Wu, Ji Yun; Chen, Xiang Bin; Ye, Xing Guo; Pan, Yan You; Wang, Jian; Zhang, Xian Sheng

2016-03-01

Timing of flowering is not only an interesting topic in developmental biology, but it also plays a significant role in agriculture for its effects on the maturation time of seed. The hexaploid wheat (Triticum aestivum) is one of the most important crop species whose flowering time, i.e. heading time, greatly influences yield. However, it remains unclear whether and how microRNAs regulate heading time in it. In our current study, we identified the tae-miR408 in wheat and its targets in vivo, including Triticum aestivum TIMING OF CAB EXPRESSION-A1 (TaTOC-A1), TaTOC-B1, and TaTOC-D1. The tae-miR408 levels were reciprocal to those of TaTOC1s under long-day and short-day conditions. Wheat plants with a knockdown of TaTOC1s via RNA interference and overexpression of tae-miR408 showed early-heading phenotype. Furthermore, TaTOC1s expression was down-regulated by the tae-miR408 in the hexaploid wheat. In addition, other important agronomic traits in wheat, such as plant height and flag leaf angle, were regulated by both tae-miR408 and TaTOC1s. Thus, our results suggested that the tae-miR408 functions in the wheat heading time by mediating TaTOC1s expression, and the study provides important new information on the mechanism underlying heading time regulation in wheat. © 2016 American Society of Plant Biologists. All Rights Reserved.

ALP conversion and the soft X-ray excess in the outskirts of the Coma cluster

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kraljic, David; Rummel, Markus; Conlon, Joseph P., E-mail: David.Kraljic@physics.ox.ac.uk, E-mail: Markus.Rummel@physics.ox.ac.uk, E-mail: j.conlon1@physics.ox.ac.uk

2015-01-01

It was recently found that the soft X-ray excess in the center of the Coma cluster can be fitted by conversion of axion-like-particles (ALPs) of a cosmic axion background (CAB) to photons. We extend this analysis to the outskirts of Coma, including regions up to 5 Mpc from the center of the cluster. We extract the excess soft X-ray flux from ROSAT All-Sky Survey data and compare it to the expected flux from ALP to photon conversion of a CAB. The soft X-ray excess both in the center and the outskirts of Coma can be simultaneously fitted by ALP tomore » photon conversion of a CAB. Given the uncertainties of the cluster magnetic field in the outskirts we constrain the parameter space of the CAB. In particular, an upper limit on the CAB mean energy and a range of allowed ALP-photon couplings are derived.« less

Formation of CaB6 in the thermal decomposition of the hydrogen storage material Ca(BH4)2.

PubMed

Sahle, Christoph J; Sternemann, Christian; Giacobbe, Carlotta; Yan, Yigang; Weis, Christopher; Harder, Manuel; Forov, Yury; Spiekermann, Georg; Tolan, Metin; Krisch, Michael; Remhof, Arndt

2016-07-20

Using a combination of high resolution X-ray powder diffraction and X-ray Raman scattering spectroscopy at the B K- and Ca L2,3-edges, we analyzed the reaction products of Ca(BH4)2 after annealing at 350 °C and 400 °C under vacuum conditions. We observed the formation of nanocrystalline/amorphous CaB6 mainly and found only small contributions from amorphous B for annealing times larger than 2 h. For short annealing times of 0.5 h at 400 °C we observed neither CaB12H12 nor CaB6. The results indicate a reaction pathway in which Ca(BH4)2 decomposes to B and CaH2 and finally reacts to form CaB6. These findings confirm the potential of using Ca(BH4)2 as a hydrogen storage medium and imply the desired cycling capabilities for achieving high-density hydrogen storage materials.

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

PubMed Central

Kurcinski, Mateusz; Jamroz, Michal; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

2015-01-01

Protein–peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein–peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein–peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. PMID:25943545

Histological and Transcriptomic Analysis of Adult Japanese Medaka Sampled Onboard the International Space Station

PubMed Central

Murata, Yasuhiko; Yasuda, Takako; Watanabe-Asaka, Tomomi; Oda, Shoji; Mantoku, Akiko; Takeyama, Kazuhiro; Chatani, Masahiro; Kudo, Akira; Uchida, Satoko; Suzuki, Hiromi; Tanigaki, Fumiaki; Shirakawa, Masaki; Fujisawa, Koichi; Hamamoto, Yoshihiko; Terai, Shuji; Mitani, Hiroshi

2015-01-01

To understand how humans adapt to the space environment, many experiments can be conducted on astronauts as they work aboard the Space Shuttle or the International Space Station (ISS). We also need animal experiments that can apply to human models and help prevent or solve the health issues we face in space travel. The Japanese medaka (Oryzias latipes) is a suitable model fish for studying space adaptation as evidenced by adults of the species having mated successfully in space during 15 days of flight during the second International Microgravity Laboratory mission in 1994. The eggs laid by the fish developed normally and hatched as juveniles in space. In 2012, another space experiment (“Medaka Osteoclast”) was conducted. Six-week-old male and female Japanese medaka (Cab strain osteoblast transgenic fish) were maintained in the Aquatic Habitat system for two months in the ISS. Fish of the same strain and age were used as the ground controls. Six fish were fixed with paraformaldehyde or kept in RNA stabilization reagent (n = 4) and dissected for tissue sampling after being returned to the ground, so that several principal investigators working on the project could share samples. Histology indicated no significant changes except in the ovary. However, the RNA-seq analysis of 5345 genes from six tissues revealed highly tissue-specific space responsiveness after a two-month stay in the ISS. Similar responsiveness was observed among the brain and eye, ovary and testis, and the liver and intestine. Among these six tissues, the intestine showed the highest space response with 10 genes categorized as oxidation–reduction processes (gene ontogeny term GO:0055114), and the expression levels of choriogenin precursor genes were suppressed in the ovary. Eleven genes including klf9, klf13, odc1, hsp70 and hif3a were upregulated in more than four of the tissues examined, thus suggesting common immunoregulatory and stress responses during space adaptation. PMID:26427061

Histological and Transcriptomic Analysis of Adult Japanese Medaka Sampled Onboard the International Space Station.

PubMed

Murata, Yasuhiko; Yasuda, Takako; Watanabe-Asaka, Tomomi; Oda, Shoji; Mantoku, Akiko; Takeyama, Kazuhiro; Chatani, Masahiro; Kudo, Akira; Uchida, Satoko; Suzuki, Hiromi; Tanigaki, Fumiaki; Shirakawa, Masaki; Fujisawa, Koichi; Hamamoto, Yoshihiko; Terai, Shuji; Mitani, Hiroshi

2015-01-01

To understand how humans adapt to the space environment, many experiments can be conducted on astronauts as they work aboard the Space Shuttle or the International Space Station (ISS). We also need animal experiments that can apply to human models and help prevent or solve the health issues we face in space travel. The Japanese medaka (Oryzias latipes) is a suitable model fish for studying space adaptation as evidenced by adults of the species having mated successfully in space during 15 days of flight during the second International Microgravity Laboratory mission in 1994. The eggs laid by the fish developed normally and hatched as juveniles in space. In 2012, another space experiment ("Medaka Osteoclast") was conducted. Six-week-old male and female Japanese medaka (Cab strain osteoblast transgenic fish) were maintained in the Aquatic Habitat system for two months in the ISS. Fish of the same strain and age were used as the ground controls. Six fish were fixed with paraformaldehyde or kept in RNA stabilization reagent (n = 4) and dissected for tissue sampling after being returned to the ground, so that several principal investigators working on the project could share samples. Histology indicated no significant changes except in the ovary. However, the RNA-seq analysis of 5345 genes from six tissues revealed highly tissue-specific space responsiveness after a two-month stay in the ISS. Similar responsiveness was observed among the brain and eye, ovary and testis, and the liver and intestine. Among these six tissues, the intestine showed the highest space response with 10 genes categorized as oxidation-reduction processes (gene ontogeny term GO:0055114), and the expression levels of choriogenin precursor genes were suppressed in the ovary. Eleven genes including klf9, klf13, odc1, hsp70 and hif3a were upregulated in more than four of the tissues examined, thus suggesting common immunoregulatory and stress responses during space adaptation.

Caffeinated and Non-caffeinated Alcohol Use and Indirect Aggression: The Impact of Self-regulation

PubMed Central

Sheehan, Brynn E.; Linden-Carmichael, Ashley N.; Lau-Barraco, Cathy

2016-01-01

Research shows that heavier alcohol use is associated with physical aggression. Scant research has examined the way in which alcohol relates to other forms of aggression, such as indirect aggression (e.g., malicious humor, social exclusion). Given the possible negative consequences of indirect aggression and the limited evidence suggesting alcohol use can elicit indirectly aggressive responses, research is needed to further investigate the association between drinking behavior and indirect aggression. Additionally, specific alcoholic beverages, such as caffeinated alcoholic beverages (CABs; e.g., Red Bull and vodka), may potentiate aggression above the influence of typical use, thus warrant examination with regard to indirect aggression. One factor that may impact the strength of the alcohol-indirect aggression and CAB-indirect aggression relationships is one's level of self-regulation. Consequently, our study examined the relationships between (1) alcohol use and indirect aggression, (2) CAB use and indirect aggression, and (3) self-regulation as a moderator. Participants were 733 (67.6% female) undergraduate students who reported their CAB and alcohol use, self-regulation, and aggressive behaviors. Results revealed that heavier alcohol use was associated with more frequent indirect aggression after controlling for dispositional aggression. Heavier CAB use was related to more frequent indirect aggression after accounting for typical use and dispositional aggression. Self-regulation moderated these associations such that for those with lower self-regulation, greater alcohol and CAB consumption was associated with greater indirect aggression. Our findings suggest that heavier alcohol and CAB consumption may be risk factors for engaging in indirect aggression and this risk is impacted by one's regulatory control. PMID:26905765

Lack of effect of oral cabotegravir on the pharmacokinetics of a levonorgestrel/ethinyl oestradiol‐containing oral contraceptive in healthy adult women

PubMed Central

Trezza, Christine; Ford, Susan L.; Gould, Elizabeth; Lou, Yu; Huang, Chuyun; Ritter, James M.; Buchanan, Ann M.; Spreen, William

2017-01-01

Aims This study aimed to investigate whether cabotegravir (CAB), an integrase inhibitor in development for treatment and prevention of human immunodeficiency virus‐1, influences the pharmacokinetics (PK) of a levonorgestrel (LNG) and ethinyl oestradiol (EO)–containing oral contraceptive (OC) in healthy women. Methods In this open‐label, fixed‐sequence crossover study, healthy female subjects received LNG 0.15 mg/EO 0.03 mg tablet once daily Days 1–10 alone and with oral CAB 30 mg once daily Days 11–21. At the end of each treatment period, subjects underwent predose sampling for concentrations of follicle‐stimulating hormone, luteinizing hormone, and progesterone and serial PK sampling for plasma LNG, EO, and CAB concentrations. Results Twenty women were enrolled, and 19 completed the study. One subject was withdrawn due to an adverse event unrelated to study medications. Geometric least squares mean ratios (90% confidence interval) of LNG + CAB vs. LNG alone for LNG area under the plasma concentration–time curve over the dosing interval of duration τ and maximum observed plasma concentration were 1.12 (1.07–1.18) and 1.05 (0.96–1.15), respectively. Geometric least squares mean ratio (90% confidence interval) of EO + CAB vs. EO alone for EO area under the plasma concentration–time curve over the dosing interval of duration τ and maximum observed plasma concentration were 1.02 (0.97–1.08) and 0.92 (0.83–1.03), respectively. Steady‐state CAB PK parameters were comparable to historical values. There was no apparent difference in mean luteinizing hormone, follicle‐stimulating hormone, and progesterone concentrations between periods. No clinically significant trends in laboratory values, vital signs, or electrocardiography values were observed. Conclusions Repeat doses of oral CAB had no significant effect on LNG/EO PK or pharmacodynamics, which supports CAB coadministration with LNG/EO OCs in clinical practice. PMID:28087972

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both single and multi-domain comparisons. The CAB-align software is freely available to academic users as stand-alone software at http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html.

Assessment of Proposed Cab Glass Coating for FAA Control Towers

DTIC Science & Technology

2015-11-16

report would be prepared after the initial coating and evaluation (with sprayed water) and then a final report after the 6 month study period to assess...Distribution A: Approved for public release. AFRL-RH-WP-TR-2015-0074 Assessment of Proposed Cab Glass Coating for FAA Control...REPORT TYPE Interim 3. DATES COVERED (From - To) 30 Jun 2014 – 1 Nov 2015 4. TITLE AND SUBTITLE Assessment of Proposed Cab Glass Coating

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

PubMed

Kuriata, Aleksander; Gierut, Aleksandra Maria; Oleniecki, Tymoteusz; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kurcinski, Mateusz; Kmiecik, Sebastian

2018-05-14

Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.

CABS-fold: Server for the de novo and consensus-based prediction of protein structure.

PubMed

Blaszczyk, Maciej; Jamroz, Michal; Kmiecik, Sebastian; Kolinski, Andrzej

2013-07-01

The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold.

CABS-fold: server for the de novo and consensus-based prediction of protein structure

PubMed Central

Blaszczyk, Maciej; Jamroz, Michal; Kmiecik, Sebastian; Kolinski, Andrzej

2013-01-01

The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold. PMID:23748950

[Genetic modification of Methylobacterium extorquens G10 producer strain of polyhydroxybutyrate].

PubMed

Fedorov, D N; Zamakhaeva, S A; Ezhov, V A; Doronina, N V; Trotsenko, Iu A

2014-01-01

The effect of the increased copy number of polyhydroxybutyrate (PHB) biosynthesis genes in pink-pigmented methylobacterium Methylobacterium extorquens G10 on properties of the biopolymer was studied. The activity of poly-3-hydroxybutyril-synthase (PHB-synthase) was shown to increase and the molecular weight of synthesized PHB decreases twofold (150 --> 79 kDa) after insertion of extra copies of phaC and phaCAB genes into cells of the producer strain, whereas the physicochemical properties of the plastic changed insignificantly. White mutant M. extorquens G10-W with disrupted synthesis of the carotenoid pigment (defect by the crtI gene, which codes for phytoene desaturase) was established to have the same rate of growth and level of PHB accumulation as the initial strain G10. The G10-W strain is a promising producer of PHB, with decreased expenses for purification and PHB biosynthesis.

Protection of the vehicle cab environment against bacteria, fungi and endotoxins in composting facilities.

PubMed

Schlosser, O; Huyard, A; Rybacki, D; Do Quang, Z

2012-06-01

Microbial quality of air inside vehicle cabs is a major occupational health risk management issue in composting facilities. Large differences and discrepancies in protection factors between vehicles and between biological agents have been reported. This study aimed at estimating the mean protection efficiency of the vehicle cab environment against bioaerosols with higher precision. In-cab measurement results were also analysed to ascertain whether or not these protection systems reduce workers' exposure to tolerable levels. Five front-end loaders, one mobile mixer and two agricultural tractors pulling windrow turners were investigated. Four vehicles were fitted with a pressurisation and high efficiency particulate air (HEPA) filtration system. The four others were only equipped with pleated paper filter without pressurisation. Bacteria, fungi and endotoxins were measured in 72 pairs of air samples, simultaneously collected inside the cab and on the outside of the cab with a CIP 10-M sampler. A front-end loader, purchased a few weeks previously, fitted with a pressurisation and high efficiency particulate air (HEPA) filtration system, and with a clean cab, exhibited a mean protection efficiency of between 99.47% CI 95% [98.58-99.97%] and 99.91% [99.78-99.98%] depending on the biological agent. It is likely that the lower protection efficiency demonstrated in other vehicles was caused by penetration through the only moderately efficient filters, by the absence of pressurisation, by leakage in the filter-sealing system, and by re-suspension of particles which accumulated in dirty cabs. Mean protection efficiency in regards to bacteria and endotoxins ranged between 92.64% [81.87-97.89%] and 98.61% [97.41-99.38%], and between 92.68% [88.11-96.08%] and 98.43% [97.44-99.22%], respectively. The mean protection efficiency was the lowest when confronted with fungal spores, from 59.76% [4.19-90.75%] to 94.71% [91.07-97.37%]. The probability that in-cab exposure to fungi exceeded the benchmark value for short-term respiratory effects suggests that front-end loaders and mobile mixers in composting facilities should be fitted with a pressurisation and HEPA filtration system, regardless of whether or not the facility is indoors or outdoors. Regarding the tractors, exposure inside the cabs was not significantly reduced. However, in this study, there was a less than 0.01% risk of exceeding the bench mark value associated with fungi related short-term respiratory effects during an 1-h per day windrow turning operation. Pressurisation and a HEPA filtration system can provide safe working conditions inside loaders and mobile mixer with regard to airborne bacteria, fungi and endotoxins in composting facilities. However, regular thorough cleaning of the vehicle cab, as well as overalls and shoes cleaning, and mitigation of leakage in the filter-sealing system are necessary to achieve high levels of protection efficiency. Copyright © 2012 Elsevier Ltd. All rights reserved.

Cloning of phaCAB genes from thermophilic Caldimonas manganoxidans in Escherichia coli for poly(3-hydroxybutyrate) (PHB) production.

PubMed

Lin, Ji-Hong; Lee, Ming-Chieh; Sue, You-Sheng; Liu, Yung-Chuan; Li, Si-Yu

2017-08-01

PHB biosynthesis pathway, consisting of three open reading frames (ORFs) that encode for β-ketothiolase (phaA Cma , 1179 bp), acetoacetyl-CoA reductase (phaB Cma , 738 bp), and PHA synthase (phaC Cma , 1694 bp), of Caldimonas manganoxidans was identified. The functions of PhaA, PhaB, and PhaC were demonstrated by successfully reconstructing PHB biosynthesis pathway of C. manganoxidans in Escherichia coli, where PHB production was confirmed by OD 600 , gas chromatography, Nile blue stain, and transmission electron microscope (TEM). The protein sequence alignment of PHB synthases revealed that phaC Cma shares at least 60% identity with those of class I PHB synthase. The effects of PhaA, PhaB, and PhaC expression levels on PHB production were investigated. While the overexpression of PhaB is found to be important in recombinant E. coli, performances of PHB production can be quantified as follows: PHB concentration of 16.8 ± 0.6 g/L, yield of 0.28 g/g glucose, content of 74%, productivity of 0.28 g/L/h, and Mw of 1.41 MDa.

Dual mechanism controls asymmetric spindle position in ascidian germ cell precursors.

PubMed

Prodon, François; Chenevert, Janet; Hébras, Céline; Dumollard, Rémi; Faure, Emmanuel; Gonzalez-Garcia, Jose; Nishida, Hiroki; Sardet, Christian; McDougall, Alex

2010-06-01

Mitotic spindle orientation with respect to cortical polarity cues generates molecularly distinct daughter cells during asymmetric cell division (ACD). However, during ACD it remains unknown how the orientation of the mitotic spindle is regulated by cortical polarity cues until furrowing begins. In ascidians, the cortical centrosome-attracting body (CAB) generates three successive unequal cleavages and the asymmetric segregation of 40 localized postplasmic/PEM RNAs in germ cell precursors from the 8-64 cell stage. By combining fast 4D confocal fluorescence imaging with gene-silencing and classical blastomere isolation experiments, we show that spindle repositioning mechanisms are active from prometaphase until anaphase, when furrowing is initiated in B5.2 cells. We show that the vegetal-most spindle pole/centrosome is attracted towards the CAB during prometaphase, causing the spindle to position asymmetrically near the cortex. Next, during anaphase, the opposite spindle pole/centrosome is attracted towards the border with neighbouring B5.1 blastomeres, causing the spindle to rotate (10 degrees /minute) and migrate (3 microm/minute). Dynamic 4D fluorescence imaging of filamentous actin and plasma membrane shows that precise orientation of the cleavage furrow is determined by this second phase of rotational spindle displacement. Furthermore, in pairs of isolated B5.2 blastomeres, the second phase of rotational spindle displacement was lost. Finally, knockdown of PEM1, a protein localized in the CAB and required for unequal cleavage in B5.2 cells, completely randomizes spindle orientation. Together these data show that two separate mechanisms active during mitosis are responsible for spindle positioning, leading to precise orientation of the cleavage furrow during ACD in the cells that give rise to the germ lineage in ascidians.

Effect of cabergoline on metabolism in prolactinomas.

PubMed

Auriemma, Renata S; Granieri, Luciana; Galdiero, Mariano; Simeoli, Chiara; Perone, Ylenia; Vitale, Pasquale; Pivonello, Claudia; Negri, Mariarosaria; Mannarino, Teresa; Giordano, Carla; Gasperi, Maurizio; Colao, Annamaria; Pivonello, Rosario

2013-01-01

Hyperprolactinemia has been implicated in the pathogenesis of obesity and glucose intolerance and is reportedly associated with an impaired metabolic profile. The current study aimed at investigating the effects of 12- and 60-month treatment with cabergoline (CAB) on metabolic syndrome (MetS) in patients with prolactinomas. 61 patients with prolactinomas (13 men, 48 women, 41 with microadenoma, 20 with macroadenoma), aged 34.4 ± 10.3 years, entered the study. In all patients, prolactin (PRL) and metabolic parameters were assessed at diagnosis and after 12 and 60 months of continuous CAB treatment. MetS was diagnosed according to NCEP-ATP III criteria. Compared to baseline, CAB induced a significant decrease in PRL with complete normalization in 93% of patients after the 60-month treatment. At baseline, MetS prevalence was significantly higher in patients with PRL above (34.5%) than in those with PRL lower (12.5%) than the median (129 μg/l, p = 0.03). MetS prevalence significantly decreased after 12 (11.5%, p = 0.039) and 60 (5.0%, p = 0.001) months compared to baseline (28.0%). At both evaluations the lipid profile significantly improved compared to baseline. Fasting insulin and homeostatic model assessment of insulin resistance significantly decreased after 1 year of CAB (p = 0.012 and p = 0.002, respectively) and further improved after 60 months (p = 0.000). The visceral adiposity index significantly decreased after the 60-month treatment (p = 0.000) compared to baseline. At the 5-year evaluation CAB dose was the best predictor of percent decrease in fasting insulin (t = 2.35, p = 0.022). CAB significantly reduces MetS prevalence and improves the adipose tissue dysfunction index. The improvement in PRL, insulin sensitivity and other metabolic parameters might reflect the direct effect of CAB. © 2013 S. Karger AG, Basel.

Evaluation of welfare advice in primary care: effect on practice workload and prescribing for mental health.

PubMed

Krska, Janet; Palmer, Sharon; Dalzell-Brown, Annette; Nicholl, Pat

2013-07-01

To determine Citizen's Advice Bureaux (CAB) and general practice staff perceptions on the impact of a CAB Health Outreach (CABHO) service on staff workload. To quantify the frequency of mental health issues among patients referred to the CABHO service. To measure any impact of the CABHO service on appointments, referrals and prescribing for mental health. GPs and practice managers perceive that welfare rights services, provided by CAB, reduce practice staff workload, but this has not been quantified. Interviews with practice managers and GPs hosting and CAB staff providing an advisory service in nine general practices. Comparison of frequency of GP and nurse appointments, mental health referrals and prescriptions for hypnotics/anxiolytics and antidepressants issued before and after referral to the CABHO service, obtained from medical records of referred patients. Most GPs and CAB staff perceived the service reduced practice staff workload, although practice managers were less certain. CAB staff believed that many patients referred to them had mental health issues. Data were obtained for 148/250 referrals of whom 46% may have had a mental health issue. There were statistically significant reductions in the number of GP appointments and prescriptions for hypnotics/anxiolytics during the six months after referral to CABHO compared with six months before. There were also non-significant reductions in nurse appointments and prescriptions for antidepressants, but no change in appointments or referrals for mental health problems. The quantitative findings therefore confirmed perceptions among both CAB and practice staff of reduced workload and in addition suggest that prescribing may be reduced, although further larger-scale studies are required to confirm this.

Controlling microbial PHB synthesis via CRISPRi.

PubMed

Li, Dan; Lv, Li; Chen, Jin-Chun; Chen, Guo-Qiang

2017-07-01

Microbial polyhydroxyalkanoates (PHA) are a family of biopolyesters with properties similar to petroleum plastics such as polyethylene (PE) or polypropylene (PP). Polyhydroxybutyrate (PHB) is the most common PHA known so far. Clustered regularly interspaced short palindromic repeats interference (CRISPRi), a technology recently developed to control gene expression levels in eukaryotic and prokaryotic genomes, was employed to regulate PHB synthase activity influencing PHB synthesis. Recombinant Escherichia coli harboring an operon of three PHB synthesis genes phaCAB cloned from Ralstonia eutropha, was transformed with various single guided RNA (sgRNA with its guide sequence of 20-23 bases) able to bind to various locations of the PHB synthase PhaC, respectively. Depending on the binding location and the number of sgRNA on phaC, CRISPRi was able to control the phaC transcription and thus PhaC activity. It was found that PHB content, molecular weight, and polydispersity were approximately in direct and reverse proportion to the PhaC activity, respectively. The higher the PhaC activity, the more the intracellular PHB accumulation, yet the less the PHB molecular weights and the wider the polydispersity. This study allowed the PHB contents to be controlled in the ranges of 1.47-75.21% cell dry weights, molecular weights from 2 to 6 millions Dalton and polydispersity of 1.2 to 1.43 in 48 h shake flask studies. This result will be very important for future development of ultrahigh molecular weight PHA useful to meet high strength application requirements.

A Light-Responsive Self-Assembly Formed by a Cationic Azobenzene Derivative and SDS as a Drug Delivery System

NASA Astrophysics Data System (ADS)

Geng, Shengyong; Wang, Yuzhu; Wang, Liping; Kouyama, Tsutomu; Gotoh, Toshiaki; Wada, Satoshi; Wang, Jin-Ye

2017-01-01

The structure of a self-assembly formed from a cationic azobenzene derivative, 4-cholesterocarbonyl-4‧-(N,N,N-triethylamine butyloxyl bromide) azobenzene (CAB) and surfactant sodium dodecyl sulfate (SDS) in aqueous solution was studied by cryo-TEM and synchrotron radiation small-angle X-ray scattering (SAXS). Both unilamellar and multilamellar vesicles could be observed. CAB in vesicles were capable to undergo reversible trans-to-cis isomerization upon UV or visible light irradiation. The structural change upon UV light irradiation could be catched by SAXS, which demonstrated that the interlamellar spacing of the cis-multilamellar vesicles increased by 0.2-0.3 nm. Based on this microstructural change, the release of rhodamine B (RhB) and doxorubicin (DOX) could be triggered by UV irradiation. When incubated NIH 3T3 cells and Bel 7402 cells with DOX-loaded CAB/SDS vesicles, UV irradiation induced DOX release decreased the viability of both cell lines significantly compared with the non-irradiated cells. The in vitro experiment indicated that CAB/SDS vesicles had high efficiency to deliver loaded molecules into cells. The in vivo experiment showed that CAB/SDS vesicles not only have high drug delivery efficiency into rat retinas, but also could maintain high drug concentration for a longer time. CAB/SDS catanionic vesicles may find potential applications as a smart drug delivery system for controlled release by light.

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.

PubMed

Kurcinski, Mateusz; Jamroz, Michal; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

2015-07-01

Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein-peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Study participants incentives, compensation and reimbursement in resource-constrained settings.

PubMed

Mduluza, Takafira; Midzi, Nicholas; Duruza, Donold; Ndebele, Paul

2013-01-01

Controversies still exists within the research fraternity on the form and level of incentives, compensation and reimbursement to study participants in resource-constrained settings. While most research activities contribute significantly to advancement of mankind, little has been considered in rewarding directly the research participants from resource-constrained areas. A study was conducted in Zimbabwe to investigate views and expectations of various stakeholders on study participation incentives, compensation and reimbursement issues. Data was collected using various methods including a survey of about 1,008 parents/guardians of school children participating in various immunological cohort studies and parasitology surveys. Community advisory boards (CABs) at 9 of the sites were also consulted. Further, information was gathered during discussions held at a basic research ethics training workshop. The workshop had 45 participants that including 40 seasoned Zimbabwean researchers and 5 international research collaborators. About 90% (907) of the study participants and guardians expected compensation of reasonable value, in view of the researchers' value and comparison to other sites regardless of economic status of the community. During discussion with researchers at a basic ethics training workshop, about 80% (32) believed that decisions on level of compensation should be determined by the local research ethics committees. While, the few international research collaborators were of the opinion that compensation should be in accordance with local guidelines, and incentives should be in line with funding. Both the CAB members and study participants expressed that there should be a clear distinction between study incentive and compensation accorded to individual and community expectations on benefits from studies. However, CABs expressed that their suggestions on incentives and compensation are often moderated by the regulatory authorities who cite fear of unknown concerns. Overall, both personal and community benefits need to be considered collectively in future studies to be conducted in resource-constrained communities. There is projected fear that recruitment in future may be a challenge, now that almost every community, has somehow been reached and participated in some form of studies. A major concern on reimbursement, compensation or incentives should be internationally pegged regardless of different economic status of the individuals or communities where the study is to be conducted.

Intelligent Shuttle Management and Routing Algorithm

NASA Astrophysics Data System (ADS)

Thomas, Toshen M.; Subashanthini, S.

2017-11-01

Nowadays, most of the big Universities and campuses have Shuttle cabs running in them to cater the transportational needs of the students and faculties. While some shuttle services ask for a meagre sum to be paid for the usage, no digital payment system is onboard these vehicles to go truly cashless. Even more troublesome is the fact that sometimes during the day, some of these cabs run with bare number of passengers, which can result in unwanted budget loss to the shuttle operator. The main purpose of this paper is to create a system with two types of applications: A web portal and an Android app, to digitize the Shuttle cab industry. This system can be used for digital cashless payment feature, tracking passengers, tracking cabs and more importantly, manage the number of shuttle cabs in every route to maximize profit. This project is built upon an ASP.NET website connected to a cloud service along with an Android app that tracks and reads the passengers ID using an attached barcode reader along with the current GPS coordinates, and sends these data to the cloud for processing using the phone’s internet connectivity.

Monogamy equality in 2⊗2⊗d quantum systems

NASA Astrophysics Data System (ADS)

Chi, Dong Pyo; Choi, Jeong Woon; Jeong, Kabgyun; San Kim, Jeong; Kim, Taewan; Lee, Soojoon

2008-11-01

There is an interesting property about multipartite entanglement, called the monogamy of entanglement. The property can be shown by the monogamy inequality, called the Coffman-Kundu-Wootters inequality [Phys. Rev. A 61, 052306 (2000); Coffman-Kundu-WoottersPhys. Rev. Lett. 96, 220503 (2006)], and more explicitly by the monogamy equality in terms of the concurrence and the concurrence of assistance, CA(BC)2=CAB2+(CACa)2, in the three-qubit system. In this paper, we consider the monogamy equality in 2⊗2⊗d quantum systems. We show that CA(BC)=CAB if and only if CACa=0 and also show that if CA(BC)=CACa, then CAB=0, while there exists a state in a 2⊗2⊗d system such that CAB=0 but CA(BC)>CACa.

Regulation of the scp Genes in the Cyanobacterium Synechocystis sp. PCC 6803--What is New?

PubMed

Cheregi, Otilia; Funk, Christiane

2015-08-12

In the cyanobacterium Synechocystis sp. PCC 6803 there are five genes encoding small CAB-like (SCP) proteins, which have been shown to be up-regulated under stress. Analyses of the promoter sequences of the scp genes revealed the existence of an NtcA binding motif in two scp genes, scpB and scpE. Binding of NtcA, the key transcriptional regulator during nitrogen stress, to the promoter regions was shown by electrophoretic mobility shift assay. The metabolite 2-oxoglutarate did not increase the affinity of NtcA for binding to the promoters of scpB and scpE. A second motif, the HIP1 palindrome 5' GGCGATCGCC 3', was detected in the upstream regions of scpB and scpC. The transcription factor encoded by sll1130 has been suggested to recognize this motif to regulate heat-responsive genes. Our data suggest that HIP1 is not a regulatory element within the scp genes. Further, the presence of the high light regulatory (HLR1) motif was confirmed in scpB-E, in accordance to their induced transcriptions in cells exposed to high light. The HLR1 motif was newly discovered in eight additional genes.

ISOL@: an Italian SOLAnaceae genomics resource.

PubMed

Chiusano, Maria Luisa; D'Agostino, Nunzio; Traini, Alessandra; Licciardello, Concetta; Raimondo, Enrico; Aversano, Mario; Frusciante, Luigi; Monti, Luigi

2008-03-26

Present-day '-omics' technologies produce overwhelming amounts of data which include genome sequences, information on gene expression (transcripts and proteins) and on cell metabolic status. These data represent multiple aspects of a biological system and need to be investigated as a whole to shed light on the mechanisms which underpin the system functionality. The gathering and convergence of data generated by high-throughput technologies, the effective integration of different data-sources and the analysis of the information content based on comparative approaches are key methods for meaningful biological interpretations. In the frame of the International Solanaceae Genome Project, we propose here ISOLA, an Italian SOLAnaceae genomics resource. ISOLA (available at http://biosrv.cab.unina.it/isola) represents a trial platform and it is conceived as a multi-level computational environment.ISOLA currently consists of two main levels: the genome and the expression level. The cornerstone of the genome level is represented by the Solanum lycopersicum genome draft sequences generated by the International Tomato Genome Sequencing Consortium. Instead, the basic element of the expression level is the transcriptome information from different Solanaceae species, mainly in the form of species-specific comprehensive collections of Expressed Sequence Tags (ESTs). The cross-talk between the genome and the expression levels is based on data source sharing and on tools that enhance data quality, that extract information content from the levels' under parts and produce value-added biological knowledge. ISOLA is the result of a bioinformatics effort that addresses the challenges of the post-genomics era. It is designed to exploit '-omics' data based on effective integration to acquire biological knowledge and to approach a systems biology view. Beyond providing experimental biologists with a preliminary annotation of the tomato genome, this effort aims to produce a trial computational environment where different aspects and details are maintained as they are relevant for the analysis of the organization, the functionality and the evolution of the Solanaceae family.

Lack of effect of oral cabotegravir on the pharmacokinetics of a levonorgestrel/ethinyl oestradiol-containing oral contraceptive in healthy adult women.

PubMed

Trezza, Christine; Ford, Susan L; Gould, Elizabeth; Lou, Yu; Huang, Chuyun; Ritter, James M; Buchanan, Ann M; Spreen, William; Patel, Parul

2017-07-01

This study aimed to investigate whether cabotegravir (CAB), an integrase inhibitor in development for treatment and prevention of human immunodeficiency virus-1, influences the pharmacokinetics (PK) of a levonorgestrel (LNG) and ethinyl oestradiol (EO)-containing oral contraceptive (OC) in healthy women. In this open-label, fixed-sequence crossover study, healthy female subjects received LNG 0.15 mg/EO 0.03 mg tablet once daily Days 1-10 alone and with oral CAB 30 mg once daily Days 11-21. At the end of each treatment period, subjects underwent predose sampling for concentrations of follicle-stimulating hormone, luteinizing hormone, and progesterone and serial PK sampling for plasma LNG, EO, and CAB concentrations. Twenty women were enrolled, and 19 completed the study. One subject was withdrawn due to an adverse event unrelated to study medications. Geometric least squares mean ratios (90% confidence interval) of LNG + CAB vs. LNG alone for LNG area under the plasma concentration-time curve over the dosing interval of duration τ and maximum observed plasma concentration were 1.12 (1.07-1.18) and 1.05 (0.96-1.15), respectively. Geometric least squares mean ratio (90% confidence interval) of EO + CAB vs. EO alone for EO area under the plasma concentration-time curve over the dosing interval of duration τ and maximum observed plasma concentration were 1.02 (0.97-1.08) and 0.92 (0.83-1.03), respectively. Steady-state CAB PK parameters were comparable to historical values. There was no apparent difference in mean luteinizing hormone, follicle-stimulating hormone, and progesterone concentrations between periods. No clinically significant trends in laboratory values, vital signs, or electrocardiography values were observed. Repeat doses of oral CAB had no significant effect on LNG/EO PK or pharmacodynamics, which supports CAB coadministration with LNG/EO OCs in clinical practice. © 2017 ViiV Healthcare. British Journal of Clinical Pharmacology published by John Wiley & Sons Ltd on behalf of British Pharmacological Society.

Improved Mapping of Carbon, Water and Energy Land-Surface Fluxes Using Remotely Sensed Indicators of Canopy Light Use Efficiency

NASA Astrophysics Data System (ADS)

Schull, M. A.; Anderson, M. C.; Kustas, W.; Cammalleri, C.; Houborg, R.

2012-12-01

A light-use-efficiency (LUE) based model of canopy resistance has been embedded into a thermal-based Two-Source Energy Balance (TSEB) model to facilitate coupled simulations of transpiration and carbon assimilation. The model assumes that deviations of the observed canopy LUE from a nominal stand-level value (LUEn - typically indexed by vegetation class) are due to varying conditions of light, humidity, CO2 concentration and leaf temperature. The deviations are accommodated by adjusting an effective LUE that responds to the varying conditions. The challenge to monitoring fluxes on a larger scale is to capture the physiological responses due to changing conditions. This challenge can be met using remotely sensed leaf chlorophyll (Cab). Since Cab is a vital pigment for absorbing light for use in photosynthesis, it has been recognized as a key parameter for quantifying photosynthetic functioning that are sensitive to these conditions. Recent studies have shown that it is sensitive to changes in LUE, which defines how efficiently a plant can assimilate carbon dioxide (CO2) given the absorbed Photosynthetically Active Radiation (PAR) and is therefore useful for monitoring carbon fluxes. We investigate the feasibility of leaf chlorophyll to capture these variations in LUEn using remotely sensed data. To retrieve Cab from remotely sensed data we use REGFLEC, a physically based tool that translates at-sensor radiances in the green, red and NIR spectral regions from multiple satellite sensors into realistic maps of LAI and Cab. Initial results show that Cab is exponentially correlated to light use efficiency. Incorporating nominal light use efficiency estimated from Cab is shown to improve fluxes of carbon, water and energy most notably in times of stressed vegetation. The result illustrates that Cab is sensitive to changes in plant physiology and can capture plant stress needed for improved estimation of fluxes. The observed relationship and initial results demonstrate the need for integrating remotely sensed Cab to facilitate improved mapping of coupled carbon, water, and energy fluxes across vegetated landscapes.

Equipment boxes (later addition) one level down from antenna cab, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Equipment boxes (later addition) one level down from antenna cab, looking southwest. - Western Union Telegraph Company, Jennerstown Relay, Laurel Summit Road off U.S. 30, Laughlintown, Westmoreland County, PA

Antenna cab interior showing equipment rack and fiberglass antenna panels, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Antenna cab interior showing equipment rack and fiberglass antenna panels, looking west. - Western Union Telegraph Company, Jennerstown Relay, Laurel Summit Road off U.S. 30, Laughlintown, Westmoreland County, PA

Antenna cab interior showing equipment rack and fiberglass antenna panels, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Antenna cab interior showing equipment rack and fiberglass antenna panels, looking southeast. - Western Union Telegraph Company, Jennerstown Relay, Laurel Summit Road off U.S. 30, Laughlintown, Westmoreland County, PA

Chemical weathering in response to tectonic uplift and denudation rate in a semi-arid environment, southeast Spain

NASA Astrophysics Data System (ADS)

Ameijeiras-Mariño, Yolanda; Opfergelt, Sophie; Schoonejans, Jérôme; Vanacker, Veerle; Sonnet, Philippe; Delmelle, Pierre

2014-05-01

Soil thickness reflects the balance between soil production and denudation by chemical weathering and physical erosion. At topographic steady state, the soil weathering intensity is expected to be higher at low denudation rate (transport-limited) than at high denudation rate (weathering-limited). We tested this hypothesis for the first time in a semi-arid environment where chemical weathering processes are generally slow. The study site is the Internal Zone of the Betic Cordillera in Southeast Spain, Almeria province. The lithology is mainly mica-schist and quartzite with local presence of phyllite. Three catchments (EST, FIL, CAB) were selected upstream local faults along a gradient of increasing uplift rates (10-170 mm/kyr) and increasing denudation rates (20-250 mm/kyr), following the sequence EST

12. ELEVATOR DOORS AND CAB. Hot Springs National Park, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. ELEVATOR DOORS AND CAB. - Hot Springs National Park, Bathhouse Row, Fordyce Bathhouse: Mechanical & Piping Systems, State Highway 7, 1 mile north of U.S. Highway 70, Hot Springs, Garland County, AR

Antenna cab interior showing waveguide from external parabolic antenna (later ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Antenna cab interior showing waveguide from external parabolic antenna (later addition), looking north. - Western Union Telegraph Company, Jennerstown Relay, Laurel Summit Road off U.S. 30, Laughlintown, Westmoreland County, PA

View of 175 ton hoisthouse from northeast. Hoist operator's cab ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

View of 175 ton hoist-house from northeast. Hoist operator's cab is in foreground center. - Marshall Space Flight Center, Saturn V Dynamic Test Facility, East Test Area, Huntsville, Madison County, AL

Capillary-Driven Microfluidic Chips for Miniaturized Immunoassays: Patterning Capture Antibodies Using Microcontact Printing and Dry-Film Resists.

PubMed

Temiz, Yuksel; Lovchik, Robert D; Delamarche, Emmanuel

2017-01-01

The miniaturization of immunoassays using microfluidic devices is attractive for many applications, but an important challenge remains the patterning of capture antibodies (cAbs) on the surface of microfluidic structures. Here, we describe how to pattern cAbs on planar poly(dimethylsiloxane) (PDMS) stamps and how to microcontact print the cAbs on a dry-film resist (DFR). DFRs are new types of photoresists having excellent chemical resistance and good mechanical, adhesive, and optical properties. Instead of being liquid photoresists, DFRs are thin layers that are easy to handle, cut, photo-pattern, and laminate over surfaces. We show how to perform a simple fluorescence immunoassay using anti-biotin cAbs patterned on a 50-μm-thick DF-1050 DFR, Atto 647N-biotin analytes, and capillary-driven chips fabricated in silicon.

Consortium for Algal Biofuel Commercialization (CAB-COMM) Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayfield, Stephen P.

The Consortium for Algal Biofuel Commercialization (CAB-Comm) was established in 2010 to conduct research to enable commercial viability of alternative liquid fuels produced from algal biomass. The main objective of CAB-Comm was to dramatically improve the viability of algae as a source of liquid fuels to meet US energy needs, by addressing several significant barriers to economic viability. To achieve this goal, CAB-Comm took a diverse set of approaches on three key aspects of the algal biofuels value chain: crop protection; nutrient utilization and recycling; and the development of genetic tools. These projects have been undertaken as collaboration between sixmore » academic institutions and two industrial partners: University of California, San Diego; Scripps Institution of Oceanography; University of Nebraska, Lincoln; Rutgers University; University of California, Davis; Johns Hopkins University; Sapphire Energy; and Life Technologies.« less

The Child Adolescent Bullying Scale (CABS): Psychometric evaluation of a new measure.

PubMed

Strout, Tania D; Vessey, Judith A; DiFazio, Rachel L; Ludlow, Larry H

2018-06-01

While youth bullying is a significant public health problem, healthcare providers have been limited in their ability to identify bullied youths due to the lack of a reliable, and valid instrument appropriate for use in clinical settings. We conducted a multisite study to evaluate the psychometric properties of a new 22-item instrument for assessing youths' experiences of being bullied, the Child Adolescent Bullying Scale (CABS). The 20 items summed to produce the measure's score were evaluated here. Diagnostic performance was assessed through evaluation of sensitivity, specificity, predictive values, and area under receiver operating characteristic (AUROC) curve. A sample of 352 youths from diverse racial, ethnic, and geographic backgrounds (188 female, 159 male, 5 transgender, sample mean age 13.5 years) were recruited from two clinical sites. Participants completed the CABS and existing youth bullying measures. Analyses grounded in classical test theory, including assessments of reliability and validity, item analyses, and principal components analysis, were conducted. The diagnostic performance and test characteristics of the CABS were also evaluated. The CABS is comprised of one component, accounting for 67% of observed variance. Analyses established evidence of internal consistency reliability (Cronbach's α = 0.97), construct and convergent validity. Sensitivity was 84%, specificity was 65%, and the AUROC curve was 0.74 (95% CI: 0.69-0.80). Findings suggest that the CABS holds promise as a reliable, valid tool for healthcare provider use in screening for bullying exposure in the clinical setting. © 2018 Wiley Periodicals, Inc.

Development, characterization and dissolution behavior of calcium-aluminoborate glass wasteforms to immobilize rare-earth oxides.

PubMed

Kim, Miae; Corkhill, Claire L; Hyatt, Neil C; Heo, Jong

2018-03-28

Calcium-aluminoborate (CAB) glasses were developed to sequester new waste compositions made of several rare-earth oxides generated from the pyrochemical reprocessing of spent nuclear fuel. Several important wasteform properties such as waste loading, processability and chemical durability were evaluated. The maximum waste loading of the CAB compositions was determined to be ~56.8 wt%. Viscosity and the electrical conductivity of the CAB melt at 1300 °C were 7.817 Pa·s and 0.4603 S/cm, respectively, which satisfies the conditions for commercial cold-crucible induction melting (CCIM) process. Addition of rare-earth oxides to CAB glasses resulted in dramatic decreases in the elemental releases of B and Ca in aqueous dissolution experiments. Normalized elemental releases from product consistency standard chemical durability test were <3.62·10 -5  g·m -2 for Nd, 0.009 g·m -2 for Al, 0.067 g·m -2 for B and 0.073 g·m -2 for Ca (at 90, after 7 days, for SA/V = 2000m -1 ); all meet European and US regulation limits. After 20 d of dissolution, a hydrated alteration layer of ~ 200-nm-thick, Ca-depleted and Nd-rich, was formed at the surface of CAB glasses with 20 mol% Nd 2 O 3 whereas boehmite [AlO(OH)] secondary crystalline phases were formed in pure CAB glass that contained no Nd 2 O 3 .

Biomechanical effects of mobile computer location in a vehicle cab.

PubMed

Saginus, Kyle A; Marklin, Richard W; Seeley, Patricia; Simoneau, Guy G; Freier, Stephen

2011-10-01

The objective of this research is to determine the best location to place a conventional mobile computer supported by a commercially available mount in a light truck cab. U.S. and Canadian electric utility companies are in the process of integrating mobile computers into their fleet vehicle cabs. There are no publications on the effect of mobile computer location in a vehicle cab on biomechanical loading, performance, and subjective assessment. The authors tested four locations of mobile computers in a light truck cab in a laboratory study to determine how location affected muscle activity of the lower back and shoulders; joint angles of the shoulders, elbows, and wrist; user performance; and subjective assessment. A total of 22 participants were tested in this study. Placing the mobile computer closer to the steering wheel reduced low back and shoulder muscle activity. Joint angles of the shoulders, elbows, and wrists were also closer to neutral angle. Biomechanical modeling revealed substantially less spinal compression and trunk muscle force. In general, there were no practical differences in performance between the locations. Subjective assessment indicated that users preferred the mobile computer to be as close as possible to the steering wheel. Locating the mobile computer close to the steering wheel reduces risk of injuries, such as low back pain and shoulder tendonitis. Results from the study can guide electric utility companies in the installation of mobile computers into vehicle cabs. Results may also be generalized to other industries that use trucklike vehicles, such as construction.

Early modulation of the cecal microbial activity in the young rabbit with rapidly fermentable fiber: impact on health and growth.

PubMed

Jacquier, V; Combes, S; Oswald, I P; Rogel-Gaillard, C; Gidenne, T

2014-12-01

This study aimed at comparing various diets predicted to induce different stimulations of the cecal microbial activity of the young rabbit fed ad libitum from 16 to 70 d of age: i) a diet enriched with rapidly fermentable fiber expected to stimulate the cecal microbial activity (RFF group); ii) a control diet with a standard composition (C group); iii) and the same control diet with tiamulin and apramycin antibiotics, expected to inhibit the microbial activity (C+AB group). A total of 398 rabbits were used from 42 litters and weaned at 28 d of age. An in vivo digestibility trial was performed on 36 rabbits of 42 to 46 d of age housed in individual metabolic cages. The feed intake and growth rates were lower in the RFF group compared with the C+AB group (-15% in ADFI and -11% in ADG, P<0.001), with a lower weight of -183 g at 70 d (P<0.001). No significant difference was found on ADG and final BW between the RFF and the C groups, but the RFF diet allowed a better G:F ratio at postweaning (P<0.01). The digestion of soluble fiber (total dietary fiber minus NDF) was greater for the RFF group. The C+AB diet had a positive effect on the postweaning morbidity rate (P<0.05) but did not affect the mortality rate and the health risk index (morbidity and mortality). Conversely, the RFF diet appeared to reduce the mortality rate compared with the C+AB diet, especially before 41 d of age. Concerning the cecal microbial activity, a supply of RFF in the diet increased the cecal VFA concentrations (+28% vs. C+AB and +22% vs. C, P<0.001) and lowered the pH. The VFA pattern was affected at 45 and 60 d, with a dominance of acetate in the RFF group (+4% vs. C+AB and C groups, P<0.001) instead of butyrate in the C+AB and C groups (-3.6% and -5% vs. C+AB and C, respectively, P<0.001). Antibiotics addition (C+AB group) reduced the VFA concentration, but only after weaning (-25% at 45 d of age) without changing the fermentation pattern. In conclusion, early intake of RFF in young rabbits stimulated the cecal microbial activity, and reduced the voluntary feed intake, leading to a reduced G:F ratio.

Safety of first-line triple therapy with a potassium-competitive acid blocker for Helicobacter pylori eradication in children.

PubMed

Kusano, Chika; Gotoda, Takuji; Suzuki, Sho; Ikehara, Hisatomo; Moriyama, Mitsuhiko

2018-06-01

Helicobacter pylori infection is a risk factor for gastric cancer, and it has been reported that eradication of H. pylori is effective for preventing such cancer. Recently, H. pylori eradication has been performed in children as first-line therapy against gastric cancer. Here, we report use of triple therapy with a potassium-competitive acid blocker (P-CAB) for H. pylori eradication in children. H. pylori infection testing and eradication therapy began in fiscal year 2015 in junior high school students located in Yurihonjo city and Nikaho city, Akita prefecture, Japan. Urine-based immunochromatography, stool antigen enzyme-linked immunosorbent assay tests, and serum antibody tests were performed as the initial screening examination. Those who tested positive on one of the three examinations then underwent a urea breath test ( 13 C-UBT). Those who tested positive on 13 C-UBT and expressed the desire to undergo H. pylori eradication then received eradication therapy comprising 20 mg P-CAB, 750 mg amoxicillin, and 200 mg clarithromycin twice a day for 7 days. At least 8 weeks after treatment, eradication success was evaluated using 13 C-UBT. A total of 118 students received eradication therapy. Eradication rates were 81.3% (95% confidence interval: 74.3-88.4, 96/118) in ITT analysis and 85.7% (95% confidence interval: 79.1-92.9 96/112) in PP analysis. Adverse effects associated with eradication therapy were observed in 25 of 118 subjects (21.1%), seven of whom required hospital treatment (rash in five, vomiting in two). All seven subjects either discontinued therapy or were administered anti-allergy drugs, which resulted in swift alleviation of symptoms. First-line triple therapy with a P-CAB for H. pylori eradication in children was found to be safe.

Quantifying the Stress Responses of Brassica Rapa Genotypes, With Experimental Drought in Two Nitrogen Treatments

NASA Astrophysics Data System (ADS)

Hickerson, J. L.; Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B. E.; Weinig, C.

2014-12-01

In a greenhouse study designed to quantify and compare stress responses of four genotypes of Brassica rapa, broccolette (bro), cabbage (cab), turnip (tur), and oil, leaf water potential and net CO2 assimilations were measured. Individuals from each genotype, grown either with high or low nitrogen, were exposed to experimental drought of the same duration. One hypothesis was that the genotypes would differ significantly in their responses to periodic drought. The other hypothesis was that the nitrogen treatment versus no nitrogen treatment would play a significant role in the stress responses during drought. It would be expected that the nitrogen treated would have greater dry leaf mass. A LI-6400 XT portable photosynthesis system was used to obtain A/Ci curves (net CO2 assimilation rate versus substomatal CO2) for each treatment group. Predawn and midday water potentials were obtained throughout the hydrated and drought periods using a Model 670 pressure chamber. The dry leaf mass was significantly greater among the high nitrogen group versus the low nitrogen group for each genotype. Nitrogen and genotype were both determinants in variation of water potentials and net CO2 assimilation. Bro and cab genotypes with high nitrogen showed the highest net CO2 assimilation rates during hydration, but the assimilation rates dropped to the lowest during droughts. The water potentials for bro and cab were lower than values for tur and oil. Nitrogen treated genotypes had lower water potentials, but higher net CO2 assimilation rates. Bayesian ecophysiological modeling with the TREES model showed significant differences in trait expression, quantified in terms of differences in model parameter posteriors, among the four genotypes.

Locomotive cab occupant protection

DOT National Transportation Integrated Search

2003-11-15

The effectiveness of fitting a locomotive cab with a passive inflatable restraint system utilizing inflatable structures, and interior padding to protect the operator has been evaluated for the in-line collision scenario. It is a challenge to design ...

Evaluation of cab car crashworthiness design modifications

DOT National Transportation Integrated Search

1997-03-01

A study was conducted to evaluate the effectiveness of structural : modifications to rail cab cars for increased crashworthiness protection in train collisions. The crashworthiness benefits were calculated based on a particular design's ability to pr...

Clean Cities case study : Barwood Cab Fleet study summary

DOT National Transportation Integrated Search

1999-05-21

Barwood Cab Fleet Study Summary is the second in a new series called 'Alternative Fuel Information Case Studies', designed to present real-world experiences with alternative fuels to fleet managers and other industry stakeholders.

The Effects of Curtain Airbag on Occupant Kinematics and Injury Index in Rollover Crash

PubMed Central

Li, Hongyun; Cui, Dong; Lu, Shuang

2018-01-01

Background Occupant injuries in rollover crashes are associated with vehicle structural performance, as well as the restraint system design. For a better understanding of the occupant kinematics and injury index in certain rollover crash, it is essential to carry out dynamic vehicle rollover simulation with dummy included. Objective This study focused on effects of curtain airbag (CAB) parameters on occupant kinematics and injury indexes in a rollover crash. Besides, optimized parameters of the CAB were proposed for the purpose of decreasing the occupant injuries in such rollover scenario. Method and Material The vehicle motion from the physical test was introduced as the input for the numerical simulation, and the 50% Hybrid III dummy model from the MADYMO database was imported into a simulation model. The restraint system, including a validated CAB module, was introduced for occupant kinematics simulation and injury evaluation. TTF setting, maximum inflator pressure, and protection area of the CAB were analysed. Results After introducing the curtain airbag, the maximum head acceleration was reduced from 91.60 g to 49.52 g, and the neck Mx and neck Fz were reduced significantly. Among these CAB parameters, the TTF setting had the largest effect on the head acceleration which could reduce 8.6 g furthermore after optimization. The neck Fz was decreased from 3766.48 N to 2571.77 N after optimization of CAB protection area. Conclusions Avoiding hard contact is critical for the occupant protection in the rollover crashes. The simulation results indicated that occupant kinematics and certain injury indexes were improved with the help of CAB in such rollover scenario. Appropriate TTF setting and inflator selection could benefit occupant kinematics and injury indexes. Besides, it was advised to optimize the curtain airbag thickness around the head contact area to improve head and neck injury indexes. PMID:29765463

Effects of an Encapsulated Fruit and Vegetable Juice Concentrate on Obesity-Induced Systemic Inflammation: A Randomised Controlled Trial.

PubMed

Williams, Evan J; Baines, Katherine J; Berthon, Bronwyn S; Wood, Lisa G

2017-02-08

Phytochemicals from fruit and vegetables reduce systemic inflammation. This study examined the effects of an encapsulated fruit and vegetable (F&V) juice concentrate on systemic inflammation and other risk factors for chronic disease in overweight and obese adults. A double-blinded, parallel, randomized placebo-controlled trial was conducted in 56 adults aged ≥40 years with a body mass index (BMI) ≥28 kg/m². Before and after eight weeks daily treatment with six capsules of F&V juice concentrate or placebo, peripheral blood gene expression (microarray, quantitative polymerase chain reaction (qPCR)), plasma tumour necrosis factor (TNF)α (enzyme-linked immunosorbent assay (ELISA)), body composition (Dual-energy X-ray absorptiometry (DEXA)) and lipid profiles were assessed. Following consumption of juice concentrate, total cholesterol, low-density lipoprotein (LDL) cholesterol and plasma TNFα decreased and total lean mass increased, while there was no change in the placebo group. In subjects with high systemic inflammation at baseline (serum C-reactive protein (CRP) ≥3.0 mg/mL) who were supplemented with the F&V juice concentrate ( n = 16), these effects were greater, with decreased total cholesterol, LDL cholesterol and plasma TNFα and increased total lean mass; plasma CRP was unchanged by the F&V juice concentrate following both analyses. The expression of several genes involved in lipogenesis, the nuclear factor-κB (NF-κB) and 5' adenosine monophosphate-activated protein kinase (AMPK) signalling pathways was altered, including phosphomevalonate kinase (PMVK), zinc finger AN1-type containing 5 (ZFAND5) and calcium binding protein 39 (CAB39), respectively. Therefore, F&V juice concentrate improves the metabolic profile, by reducing systemic inflammation and blood lipid profiles and, thus, may be useful in reducing the risk of obesity-induced chronic disease.

Next generation locomotive cab task 5 summary report : control stand design.

DOT National Transportation Integrated Search

2010-07-01

This report discusses the development of a user-centered control stand for the Federal Railroad Administrations Next Generation Locomotive Cab Demonstration Program. A modified Association of American Railroads 105 side-mounted control stand...

Cab technology integration laboratory demonstration with moving map technology

DOT National Transportation Integrated Search

2013-03-31

A human performance study was conducted at the John A. Volpe National Transportation Systems Center (Volpe Center) using a locomotive research simulatorthe Cab Technology Integration Laboratory (CTIL)that was acquired by the Federal Railroad Ad...

Protective effect of active perfusion in porcine models of acute myocardial ischemia

PubMed Central

Feng, Zanxiang; Mao, Zhifu; Dong, Shengjun; Liu, Baohui

2016-01-01

Mortality rates associated with off-pump coronary artery bypass (CAB) are relatively high, as the majority of patients requiring CAB are at a high risk for cardiac events. The present study aimed to establish porcine models of acute myocardial ischemia, and evaluate the protective role of shunt and active perfusion. A total of 30 pigs were randomly assigned to five groups, as follows: i) Sham (control); ii) A1 (shunt; stenosis rate, 55%); iii) A2 (shunt; stenosis rate, 75%); iv) B1 (active perfusion; stenosis rate, 55%); and v) B2 (active perfusion; stenosis rate, 75%) groups. Aortic pressure (P0), left anterior descending coronary pressure (P1), and coronary effective perfusion pressure (P1/P0) were measured. The expression levels of tumor necrosis factor-α (TNF-α), cardiac troponin (cTnI), creatine kinase-myocardial band (CK-MB), interleukin (IL)-6, IL-10, B-cell lymphoma 2 (Bcl-2), and caspase-3 were detected using enzyme-linked immunosorbent assay or western blotting. The myocardial apoptosis rate was determined using the terminal deoxynucleotidyl transferase dUTP nick end labeling assay. Ischemia models with stenosis rates of 55 and 75% were successfully constructed following suturing of the descending artery. Compared with the control, the 55 and 75% stenosis groups demonstrated significantly decreased P1/P0, increased expression levels of TNF-α, cTnI, CK-MB, IL-6, IL-10 and caspase-3, an increased rate of myocardial apoptosis, and a decreased expression level of anti-apoptotic protein, Bcl-2. At 30 min following successful establishment of the model (ST segment elevation to 1 mm), group B demonstrated significantly increased P1/P0, decreased expression levels of TNF-α, cTnI, CK-MB, IL-6, IL-10 and caspase-3, a decreased rate of myocardial apoptosis, and an increased expression level of anti-apoptotic protein, Bcl-2. Furthermore, the current study indicated that active perfusion was more efficacious in maintaining myocardial perfusion and alleviating ischemic injury when compared with traditional shunt perfusion. PMID:27573177

The influence of crystal habit on the prediction of dry powder inhalation formulation performance using the cohesive-adhesive force balance approach.

PubMed

Hooton, Jennifer C; Jones, Matthew D; Harris, Haggis; Shur, Jagdeep; Price, Robert

2008-09-01

The aim of this investigation was to study the influence of crystalline habit of active pharmaceutical ingredients on the cohesive-adhesive force balance within model dry powder inhaler (DPI) formulations and the corresponding affect on DPI formulation performance. The cohesive-adhesive balance (CAB) approach to colloid probe atomic force microscopy (AFM) was employed to determine the cohesive and adhesive interactions of micronized budesonide particles against the {102} and {002} faces of budesonide single crystals and crystalline substrates of different sugars (cyclodextrin, lactose, trehalose, raffinose, and xylitol), respectively. These data were used to measure the relative level of cohesion and adhesion via CAB and the possible influence on in vitro performance of a carrier-based DPI formulation. Varying the crystal habit of the drug had a significant effect on the cohesive measurement of micronized budesonide probes, with the cohesive values on the {102} faces being approximately twice that on the {002} crystal faces. However, although different CAB values were measured with the sugars with respect to the crystal faces chosen for the cohesive-based measurement, the overall influence on the rank order of the CAB values was not directly influenced. For these data sets, the CAB gradient indicated that a decrease in the dominance of the adhesive forces led to a concomitant increase in fine particle delivery, reaching a plateau as the cohesive forces became dominant. The study suggested that crystal habit of the primary drug crystals influences the cohesive interactions and the resulting force balance measurements of colloid probe CAB analysis.

U.S. truck driver anthropometric study and multivariate anthropometric models for cab designs.

PubMed

Guan, Jinhua; Hsiao, Hongwei; Bradtmiller, Bruce; Kau, Tsui-Ying; Reed, Matthew R; Jahns, Steven K; Loczi, Josef; Hardee, H Lenora; Piamonte, Dominic Paul T

2012-10-01

This study presents data from a large-scale anthropometric study of U.S. truck drivers and the multivariate anthropometric models developed for the design of next-generation truck cabs. Up-to-date anthropometric information of the U.S. truck driver population is needed for the design of safe and ergonomically efficient truck cabs. We collected 35 anthropometric dimensions for 1,950 truck drivers (1,779 males and 171 females) across the continental United States using a sampling plan designed to capture the appropriate ethnic, gender, and age distributions of the truck driver population. Truck drivers are heavier than the U.S.general population, with a difference in mean body weight of 13.5 kg for males and 15.4 kg for females. They are also different in physique from the U.S. general population. In addition, the current truck drivers are heavier and different in physique compared to their counterparts of 25 to 30 years ago. The data obtained in this study provide more accurate anthropometric information for cab designs than do the current U.S. general population data or truck driver data collected 25 to 30 years ago. Multivariate anthropometric models, spanning 95% of the current truck driver population on the basis of a set of 12 anthropometric measurements, have been developed to facilitate future cab designs. The up-to-date truck driver anthropometric data and multivariate anthropometric models will benefit the design of future truck cabs which, in turn, will help promote the safety and health of the U.S. truck drivers.

A randomized cross-over study comparing cabergoline and quinagolide in the treatment of hyperprolactinemic patients.

PubMed

De Luis, D A; Becerra, A; Lahera, M; Botella, J I; Valero; Varela, C

2000-01-01

Quinagolide (QUI) and cabergoline (CAB) are dopamine agonists recently introduced for the treatment of hyperprolactinemia. In the present study, these drugs have been compared in terms of effectiveness and tolerability. Twenty patients (18 females and 2 males) with hyperprolactinemia (8 with microprolactinomas, 6 with idiopathic hyperprolactinemia and 6 with empty sella turcica syndrome) were treated with oral QUI (75 microg once daily) and CAB (0,5 mg twice weekly), in a randomized cross-over trial with placebo between both drugs. Each drug was administered for 12 weeks, separated by other 12 weeks with placebo. PRL levels decreased with both drugs at 2 or 4 weeks of starting the treatment, without differences between both drugs at weeks 4, 8 and 12. At week 12, normal PRL levels (<20 ng/ml) were attained in 90% patients with CAB and only in 75% patients with QUI (p<0.05). After discontinuation of treatment, significant increase in serum PRL was higher after QUI withdrawal than after CAB. Clinical efficacy of both treatments was similar in terms of improvement amenorrhea, oligomenorrhea, galactorrhea, and impotence. All patients completed both cycles of treatment, and the most frequent side-effects were nausea, headache and dizziness, without significant differences between CAB (30%) and QUI (55%). Our study indicates that, at the doses employed here, CAB showed a high percentage of patients with normal PRL at the end of treatment and long-lasting efficacy in the levels of PRL. Clinical response and side-effects were similar in both drugs.

Measuring the Performance of Attention Networks with the Dalhousie Computerized Attention Battery (DalCAB): Methodology and Reliability in Healthy Adults.

PubMed

Jones, Stephanie A H; Butler, Beverly C; Kintzel, Franziska; Johnson, Anne; Klein, Raymond M; Eskes, Gail A

2016-01-01

Attention is an important, multifaceted cognitive domain that has been linked to three distinct, yet interacting, networks: alerting, orienting, and executive control. The measurement of attention and deficits of attention within these networks is critical to the assessment of many neurological and psychiatric conditions in both research and clinical settings. The Dalhousie Computerized Attention Battery (DalCAB) was created to assess attentional functions related to the three attention networks using a range of tasks including: simple reaction time, go/no-go, choice reaction time, dual task, flanker, item and location working memory, and visual search. The current study provides preliminary normative data, test-retest reliability (intraclass correlations) and practice effects in DalCAB performance 24-h after baseline for healthy young adults (n = 96, 18-31 years). Performance on the DalCAB tasks demonstrated Good to Very Good test-retest reliability for mean reaction time, while accuracy and difference measures (e.g., switch costs, interference effects, and working memory load effects) were most reliable for tasks that require more extensive cognitive processing (e.g., choice reaction time, flanker, dual task, and conjunction search). Practice effects were common and pronounced at the 24-h interval. In addition, performance related to specific within-task parameters of the DalCAB sub-tests provides preliminary support for future formal assessment of the convergent validity of our interpretation of the DalCAB as a potential clinical and research assessment tool for measuring aspects of attention related to the alerting, orienting, and executive control networks.

A new approach in gastroretentive drug delivery system using cholestyramine.

PubMed

Umamaheshwari, R B; Jain, Subheet; Jain, N K

2003-01-01

We prepared cellulose acetate butyrate (CAB)-coated cholestyramine microcapsules as a intragastric floating drug delivery system endowed with floating ability due to the carbon dioxide generation when exposed to the gastric fluid. The microcapsules also have a mucoadhesive property. Ion-exchange resin particles can be loaded with bicarbonate followed by acetohydroxamic acid (AHA) and coated with CAB by emulsion solvent evaporation method. The drug concentration was monitored to maintain the floating property and minimum effective concentration. The effect of CAB: drug-resin ratio (2:1, 4:1, 6:1 w/w) on the particle size, floating time, and drug release was determined. Cholestyramine microcapsules were characterized for shape, surface characteristics, and size distribution; cholestyramine/acetohydroxamic acid interactions inside microcapsules were investigated by X-ray diffractometry. The buoyancy time of CAB-coated formulations was better than that of uncoated resin particles. Also, a longer floating time was observed with a higher polymer:drug resin complex ratio (6:1). With increasing coating thickness the particle size was increased but drug release rate was decreased. The drug release rate was higher in simulated gastric fluid (SGF) than in simulated intestinal fluid (SIF). The in vivo mucoadhesion studies were performed with rhodamine-isothiocyanate (RITC) by fluorescent probe method. The amount of CAB-coated cholestyramine microcapsules that remained in the stomach was slightly lower than that of uncoated resin particles. Cholestyramine microcapsules were distributed throughout the stomach and exhibited prolonged gastric residence via mucoadhesion. These results suggest that CAB-coated microcapsules could be a floating as well as a mucoadhesive drug delivery system. Thus, it has promise in the treatment of Helicobacter pylori.

Evaluation of railroad cab car end beam designs.

DOT National Transportation Integrated Search

2003-06-01

This report presents the results of an experimental study to establish the strength and energy absorption capability of railroad cab car corner structures built to current requirements and for structures modified to carry higher loads and absorb more...

3. Missile transporter/erector, front of cab, erector fully extended, view ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

3. Missile transporter/erector, front of cab, erector fully extended, view from left rear towards east - Ellsworth Air Force Base, Delta Flight, 10 mile radius around Exit 127 off Interstate 90, Interior, Jackson County, SD

Tower-Related Major System Development Programs

DOT National Transportation Integrated Search

1978-03-01

This report is devoted to the present and near future states of the tower cab environment, addresses those MSDP systems which may have an impact on the current tower cab environment, systems and/or operations. The systems included are: Discrete Addre...

Identification and Categorization of Accidents and Injuries in Cabs of Locomotives

DOT National Transportation Integrated Search

1972-09-01

A review and categorization is made of available published locomotive cab accident reports and statistics, as well as of unpublished accident reports from a number of individual railroads. Major hazards related to locomotive control compartment accid...

49 CFR 236.714 - Cab.

Code of Federal Regulations, 2010 CFR

2010-10-01

... TRANSPORTATION RULES, STANDARDS, AND INSTRUCTIONS GOVERNING THE INSTALLATION, INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Definitions § 236.714 Cab. The compartment of a locomotive from which the propelling power and power brakes of the train are manually...

Modeling material failure during cab car end frame impact

DOT National Transportation Integrated Search

2009-03-03

New standards have been proposed to increase the strength requirements for cab car end structures and impose further requirements on their ability to absorb energy during a grade-crossing collision. This conference paper reports on a set of full-scal...

Mergers and Anti-trust Issues in Recent CAB Cases

NASA Technical Reports Server (NTRS)

Andrews, A. M.

1972-01-01

The airline industry is surveyed-particularly domestic trunklines-in relation to collective approaches to industry concerns. These actions are classified by the apparent degree of anti-trust issue present. Recent route merger cases are considered from the CAB staff viewpoint.

Air flow testing on aerodynamic truck

NASA Technical Reports Server (NTRS)

1975-01-01

After leasing a cab-over tractor-trailer from a Southern California firm, Dryden researchers added sheet metal modifications like those shown here. They rounded the front corners and edges, and placed a smooth fairing on the cab's roofs and sides extending back to the trailer. During the investigation of truck aerodynamics, the techniques honed in flight research proved highly applicable. By closing the gap between the cab and the trailer, for example, researchers discovered a significant reduction in aerodynamic drag, one resulting in 20 to 25 percent less fuel consumption than the standard design. Many truck manufacturers subsequently incorporated similar modifications on their products.

Improvement of CO2/N2 separation performance by polymer matrix cellulose acetate butyrate

NASA Astrophysics Data System (ADS)

Lee, R. J.; Jawad, Z. A.; Ahmad, A. L.; Ngo, J. Q.; Chua, H. B.

2017-06-01

With the rapid development of modern civilization, carbon dioxide (CO2) is produced in large quantities and mainly generated from industrial sectors. The gas emission is the major contributor to global warming. To address this issue, the membrane technology is implemented for the CO2 removal, due to the energy efficiency and economic advantages presented. Cellulose acetate butyrate (CAB) is selected as the polymeric material, due to the excellent film-forming properties and capable of developing a defect-free layer of neat membrane. This study described the fabrication development of CAB using a wet phase inversion method with different casting conditions. Where the composition of the casting solutions (3-5 wt %) and solvent evaporation time (4-6 min) were determined. The outcomes of these dominant parameters were then used to determine the best CAB membrane for CO2/Nitrogen (N2) separation and supported by the characterization i.e. scanning electron micrograph. Gas permeation measurements showed satisfactory performance for CAB membrane fabricated with 5 min evaporation time and 4 wt% polymer composition (M2). Where, its permeance and selectivity are 120.19 GPU and 3.17, respectively. In summary, this study showed a brief outlined of the future direction and perspective of CAB membrane for CO2/N2 separation.

Pathogenesis of Potassium-Competitive Acid Blocker-Resistant Non-Erosive Reflux Disease.

PubMed

Kawami, Noriyuki; Hoshino, Shintaro; Hoshikawa, Yoshimasa; Takenouchi, Nana; Umezawa, Mariko; Hanada, Yuriko; Kaise, Mitsuru; Iwakiri, Katsuhiko

2018-06-05

The present study examined the pathogenesis of potassium-competitive acid blocker (P-CAB)-resistant non-erosive reflux disease (NERD). Forty-three patients with NERD, who had persistent reflux symptoms despite the administration of P-CAB, were included in this study. After excluding eosinophilic esophagitis and primary esophageal motility disorders, esophageal impedance-pH monitoring was performed. In symptom index (SI)-positive patients, the mechanism of SI-positivity and percent time with intragastric pH > 4 and with esophageal pH < 4 were investigated according to the presence or absence of Helicobacter pylori infection. One (2.3%) of 43 patients had a primary esophageal motility disorder (Jackhammer esophagus). Eighteen (41.9%) and 3 (7%) patients were SI-positive for liquid and gas-only reflux, respectively, and the remaining 21 patients who were SI-negative (48.8%) had functional heartburn. All patients SI-positive for liquid reflux were SI-positive for weakly acidic reflux. Gastric acid was sufficiently suppressed by P-CAB, regardless of the presence or absence of H. pylori infection. The pathogenesis of -P-CAB-resistant NERD was elucidated in 51% of patients. Symptoms in all patients SI-positive for liquid reflux were related to weakly acidic reflux, and symptoms related to acid reflux may be ruled out by the administration of P-CAB. © 2018 S. Karger AG, Basel.

Prototype design and test of a collision protection system for cab car engineers.

DOT National Transportation Integrated Search

2014-12-01

Advancements in the design of rail cars can : potentially prevent the structural collapse of : space occupied by a cab car engineer : during a train collision. With adequate : survival space maintained, the next : crashworthiness objective is to mini...

Rail vehicle cab car collision and corner post designs according to APTA-S-034 requirements

DOT National Transportation Integrated Search

2003-11-16

The American Public Transportation Association standard for rail passenger equipment, S-034, includes requirements for the collision and corner posts of cab cars that are consistent with new federal requirements and substantially different than what ...

Prototype design of a collision protection system for cab car engineers - fabrication and test.

DOT National Transportation Integrated Search

2015-06-01

Advancements in the structural crashworthiness of passenger rail cars now make it possible to preserve the compartmentalized : space occupied by a cab car engineer during a train collision. In order to translate this additional protection into improv...

Study for every other day administration of vonoprazan in maintenance treatment of erosive GERD: study protocol for a multicentre randomised cross-over study.

PubMed

Kato, Mototsugu; Ito, Noriko; Demura, Mamiko; Kubo, Kimitoshi; Mabe, Katsuhiro; Harada, Naohiko

2018-01-01

The first drug selected for treatment of gastro-oesophageal reflux disease (GERD) and prevention of the recurrence is a proton pump inhibitor (PPI), but recently, a potassium-competitive acid blocker (P-CAB) was put on the market in Japan. Its onset of effect is faster than PPI, and it takes more than 2 days to recover acid secretion after the withdrawal period. Therefore, unlike PPI, the usefulness of every other day administration or discontinuous administration is expected. This study is a prospective, multicentre, open-label, two-period randomised cross-over study to compare the efficacy and safety of PPI every other day administration and P-CAB every other day administration in 120 patients who receive erosive GERD maintenance therapy with PPI. Patients will be randomly allocated to receive 4 weeks P-CAB or PPI followed by 4 weeks cross over, where those on P-CAB will receive PPI and vice versa. The primary endpoint is proportion of asymptomatic patients. Secondary endpoints are suppressive effect of GERD symptoms, proportion of asymptomatic patients at each time point, safety and cost-saving effect of P-CAB every other day administration, compliance with every other day administration, and proportion of asymptomatic patients at the first month of study drug administration. This study was approved by the National Hospital Organization Central Review Board for Clinical Trials (5 December 2017). If P-CAB every other day administration is established as one of GERD maintenance therapies, there is merit in both medical cost reduction and the safety to alleviate elevation in serum gastrin. UMIN000034701.

Study for every other day administration of vonoprazan in maintenance treatment of erosive GERD: study protocol for a multicentre randomised cross-over study

PubMed Central

Kato, Mototsugu; Ito, Noriko; Demura, Mamiko; Kubo, Kimitoshi; Mabe, Katsuhiro; Harada, Naohiko

2018-01-01

Introduction The first drug selected for treatment of gastro-oesophageal reflux disease (GERD) and prevention of the recurrence is a proton pump inhibitor (PPI), but recently, a potassium-competitive acid blocker (P-CAB) was put on the market in Japan. Its onset of effect is faster than PPI, and it takes more than 2 days to recover acid secretion after the withdrawal period. Therefore, unlike PPI, the usefulness of every other day administration or discontinuous administration is expected. Methods and analysis This study is a prospective, multicentre, open-label, two-period randomised cross-over study to compare the efficacy and safety of PPI every other day administration and P-CAB every other day administration in 120 patients who receive erosive GERD maintenance therapy with PPI. Patients will be randomly allocated to receive 4 weeks P-CAB or PPI followed by 4 weeks cross over, where those on P-CAB will receive PPI and vice versa. The primary endpoint is proportion of asymptomatic patients. Secondary endpoints are suppressive effect of GERD symptoms, proportion of asymptomatic patients at each time point, safety and cost-saving effect of P-CAB every other day administration, compliance with every other day administration, and proportion of asymptomatic patients at the first month of study drug administration. Ethics and dissemination This study was approved by the National Hospital Organization Central Review Board for Clinical Trials (5 December 2017). Discussion If P-CAB every other day administration is established as one of GERD maintenance therapies, there is merit in both medical cost reduction and the safety to alleviate elevation in serum gastrin. Trial registration number UMIN000034701. PMID:29527318

a Simplified Method to Design Suspended Cabs for Counterbalance Trucks

NASA Astrophysics Data System (ADS)

LEMERLE, P.; BOULANGER, P.; POIROT, R.

2002-05-01

A “low-frequency” suspension system, placed between the driving cab and chassis of an existing fork lift truck was designed. The aim of this project was to develop a design procedure which is easy to implement and suitable for all types of fork lift trucks. It was also to show how the use of numerical simulation could be helpful to optimize the efficiency of such suspension systems. The cab specifications were: (1) to achieve a vertical vibration attenuation of at least 50% when this truck is tested under severe but realistic conditions, (2) to operate with no specific adjustment for drivers weighing between 60 and 100 kg, (3) to be efficient with a reasonable dynamic stroke (about 3 cm maximum). The suspended cab was modelled using ADAMS software. In the simplified method, the input acceleration signals (at the four fixing points of the cab) were not computed from a vehicle model (chassis and wheels) but directly measured under various driving conditions (passage of two or four wheels over an obstacle with a loaded or unloaded fork lift truck). This model allowed evaluation of the theoretical attenuation, obtained below the driver's seat along the three axes, in comparison with an infinitely rigid suspension. The attenuation ratio was calculated for several values of the characteristics of the suspension components (stiffness and damping). Similarly, for every design value tested, the design constraints were evaluated and at the end of this parametrical study, optimal suspension components were found. Finally, the suspended cab was built according to the results of the parametrical study and measurements subsequently confirmed that the attenuation of vertical accelerations was more than 50%.

Locomotive cab design development. Volume 5 : performance evaluation tests

DOT National Transportation Integrated Search

1976-09-01

This document reports on a preiiminary evaluation o f the Buman : Factors design proposed for a line haul freight locomotive : cab . The program was conducted using a full scale hard mock-up : o f the proposed design and the evaluation was provided b...

A numerical evaluation of protection strategies for cab car crashworthiness

DOT National Transportation Integrated Search

1999-11-15

The operator and passengers in cab cars are particularly vulnerable to collisions with objects or with other trains because of their proximity to the point of collision. We present one part of a larger study in which we examined several strategies fo...

Rail-car impact tests with steel coil: collision dynamics

DOT National Transportation Integrated Search

2003-04-22

Two full-scale oblique grade-crossing impact tests were conducted in June 2002 to compare the crashworthiness performance of alternative corner post designs on rail passenger cab cars. On June 4, 2002 a cab car fitted with an end structure built to p...

Development of conventional passenger cab car end structure designs for full scale testing

DOT National Transportation Integrated Search

2006-12-01

The Volpe Center is supporting the Federal Railroad Administration's full-scale testing program to understand and improve rail vehicle cashworthiness. The objectie of one of the sets of tests in this program is determining the behavior of cab car end...

Airport Shared-Ride Taxi Programs in New York, Chicago and Boston

DOT National Transportation Integrated Search

1987-12-01

This report summarizes the development and operation of three shared-ride taxi operations at major U.S. airports. These are: New York's LaGuardia Airport Share-A-Cab; Super Saver Taxi in Chicago; and Share-A-Cab service at Boston's Logan Airport. The...

49 CFR 236.534 - Entrance to equipped territory; requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... INSTALLATION, INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Rules and Instructions; Roadway § 236.534... not exceed restricted speed, the automatic train stop, train control, or cab signal device shall be...

49 CFR 236.526 - Roadway element not functioning properly.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Rules and Instructions; Roadway § 236.526 Roadway..., train control or cab signal system is not functioning as intended, the signal associated with such...

49 CFR 236.534 - Entrance to equipped territory; requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... INSTALLATION, INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Rules and Instructions; Roadway § 236.534... not exceed restricted speed, the automatic train stop, train control, or cab signal device shall be...

49 CFR 236.526 - Roadway element not functioning properly.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Rules and Instructions; Roadway § 236.526 Roadway..., train control or cab signal system is not functioning as intended, the signal associated with such...

49 CFR 236.587 - Departure test.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Inspection and Tests; Locomotive § 236.587 Departure test. (a) The automatic train stop, train control, or cab signal apparatus on each locomotive, except a locomotive or a...

21 CFR 26.36 - Listing of CAB's.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Listing of CAB's. 26.36 Section 26.36 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL MUTUAL RECOGNITION OF PHARMACEUTICAL GOOD MANUFACTURING PRACTICE REPORTS, MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS...

Review of severe deformation recommended practice through analyses - comparison of two cab car end frame designs

DOT National Transportation Integrated Search

2005-03-16

Non-linear large deformation analyses have been conducted : to evaluate the performance of the cab car corner and collision : posts of the Federal Railroad Administration's (FRA) : sponsored state-of-the-art (SOA) end frame design and the : Bombardie...

49 CFR 236.516 - Power supply.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Power supply. 236.516 Section 236.516..., Train Control and Cab Signal Systems Standards § 236.516 Power supply. Automatic cab signal, train stop, or train control device hereafter installed shall operate from a separate or isolated power supply...

49 CFR 236.516 - Power supply.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Power supply. 236.516 Section 236.516..., Train Control and Cab Signal Systems Standards § 236.516 Power supply. Automatic cab signal, train stop, or train control device hereafter installed shall operate from a separate or isolated power supply...

49 CFR 229.115 - Slip/slide alarms.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., DEPARTMENT OF TRANSPORTATION RAILROAD LOCOMOTIVE SAFETY STANDARDS Safety Requirements Cabs and Cab Equipment § 229.115 Slip/slide alarms. (a) Except for MU locomotives, each locomotive used in road service shall... road service, or continue in road service following a daily inspection, unless the wheel slip/slide...

49 CFR 229.115 - Slip/slide alarms.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., DEPARTMENT OF TRANSPORTATION RAILROAD LOCOMOTIVE SAFETY STANDARDS Safety Requirements Cabs and Cab Equipment § 229.115 Slip/slide alarms. (a) Except for MU locomotives, each locomotive used in road service shall... road service, or continue in road service following a daily inspection, unless the wheel slip/slide...

49 CFR 236.590 - Pneumatic apparatus.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Pneumatic apparatus. 236.590 Section 236.590..., Train Control and Cab Signal Systems Inspection and Tests; Locomotive § 236.590 Pneumatic apparatus. Automatic train stop, train control, or cab signal pneumatic apparatus shall be inspected, cleaned, and the...

49 CFR 236.590 - Pneumatic apparatus.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Pneumatic apparatus. 236.590 Section 236.590..., Train Control and Cab Signal Systems Inspection and Tests; Locomotive § 236.590 Pneumatic apparatus. Automatic train stop, train control, or cab signal pneumatic apparatus shall be inspected, cleaned, and the...

10. DETAIL, CAB SIDE. DETAIL, END OF BOOM. DETAIL, LOWER ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. DETAIL, CAB SIDE. DETAIL, END OF BOOM. DETAIL, LOWER PART OF TOWER, SHOWING METAL WHEELS AND CABLE SPOOLS. DETAIL, LOOKING UP AT THE UNDERSIDE OF THE REVOLVING PLATFORM ATOP THE TOWER. - United Engineering Company Shipyard, Crane, 2900 Main Street, Alameda, Alameda County, CA

Evaluation of EA-934NA with 2.5 percent Cab-O-Sil

NASA Technical Reports Server (NTRS)

Caldwell, Gordon A.

1990-01-01

Currently, Hysol adhesive EA-934NA is used to bond the Field Joint Protection System on the Shuttle rocket motors at Kennedy Space Center. However, due to processing problems, an adhesive with a higher viscosity is needed to alleviate these difficulties. One possible solution is to add Cab-O-Sil to the current adhesive. The adhesive strength and bond strengths that can be obtained when 2.5 percent Cab-O-Sil is added to adhesive EA-934NA are examined and tested over a range of test temperatures from -20 to 300 F. Tensile adhesion button and lap shear specimens were bonded to D6AC steel and uniaxial tensile specimens (testing for strength, initial tangent modulus, elongation and Poisson's ratio) were prepared using Hysol adhesive EA-934NA with 2.5 percent Cab-O-Sil added. These specimens were tested at -20, 20, 75, 100, 125, 150, 200, 250, and 300 F, respectively. Additional tensile adhesion button specimens bonding Rust-Oleum primed and painted D6AC steel to itself and to cork using adhesive EA-934NA with 2.5 percent Cab-O-Sil added were tested at 20, 75, 125, 200, and 300 F, respectively. Results generally show decreasing strength values with increasing test temperatures. The bond strengths obtained using cork as a substrate were totally dependent on the cohesive strength of the cork.

Decreases in collision risk and derailments attributed to changing at-risk behavior process at Union Pacific.

DOT National Transportation Integrated Search

2009-09-01

Changing At-Risk Behavior (CAB) is a safety process that is being conducted at Union Pacifics San Antonio Service Unit (SASU) with the aim of improving road and yard safety. CAB is an example of a proactive safety risk-reduction method, called Cle...

49 CFR 236.586 - Daily or after trip test.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Inspection and Tests; Locomotive § 236.586 Daily or after trip test..., each locomotive equipped with an automatic cab signal or train stop or train control device operating...

49 CFR 236.588 - Periodic test.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Inspection and Tests; Locomotive § 236.588 Periodic test. Except as provided in § 236.586, periodic test of the automatic train stop, train control, or cab signal apparatus...

49 CFR 236.509 - Two or more locomotives coupled.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.509 Two or more locomotives coupled. The automatic train stop, train control or cab signal apparatus shall be arranged so that when two or...

49 CFR 236.557 - Receiver; location with respect to rail.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Rules and Instructions; Locomotives § 236.557 Receiver... automatic cab signal, train stop, or train control device of locomotive equipped with onboard test equipment...

49 CFR 236.586 - Daily or after trip test.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Inspection and Tests; Locomotive § 236.586 Daily or after trip test..., each locomotive equipped with an automatic cab signal or train stop or train control device operating...

49 CFR 236.509 - Two or more locomotives coupled.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES, AND APPLIANCES Automatic Train Stop, Train Control and Cab Signal Systems Standards § 236.509 Two or more locomotives coupled. The automatic train stop, train control or cab signal apparatus shall be arranged so that when two or...

41 CFR 101-26.501-2 - Standardized buying programs.

Code of Federal Regulations, 2011 CFR

2011-07-01

... and 6×4 cab-chassis, stake, van, dump, and truck-tractor; 19,000 to 60,000 pounds GVWR. (ii) 4×4 and 6×4 cab-chassis, stake, dump, and truck-tractor; 26,000 to 52,000 pounds GVWR. (iii) 1,200 and 2,000...

49 CFR 236.514 - Interconnection of cab signal system with roadway signal system.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Interconnection of cab signal system with roadway signal system. 236.514 Section 236.514 Transportation Other Regulations Relating to Transportation... GOVERNING THE INSTALLATION, INSPECTION, MAINTENANCE, AND REPAIR OF SIGNAL AND TRAIN CONTROL SYSTEMS, DEVICES...

49 CFR 236.588 - Periodic test.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Periodic test. 236.588 Section 236.588..., Train Control and Cab Signal Systems Inspection and Tests; Locomotive § 236.588 Periodic test. Except as provided in § 236.586, periodic test of the automatic train stop, train control, or cab signal apparatus...

49 CFR 236.588 - Periodic test.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Periodic test. 236.588 Section 236.588..., Train Control and Cab Signal Systems Inspection and Tests; Locomotive § 236.588 Periodic test. Except as provided in § 236.586, periodic test of the automatic train stop, train control, or cab signal apparatus...

2008 Tactical Wheeled Vehicles Conference (TWV) Volume 1

DTIC Science & Technology

2008-02-05

additional LSAC cabs FMTV Gunners Restraint (2,022 LSAC; 1,855 RACK) Counterweight bumper for M1078 Cargo with LSAC Cab and GPK 3 Jan 08NDIA TWV Conference...Objective Gunner Protection Kits to support Up-Armored HMMWV’s GPK Upgrade Program. Partnerships: Ensured partnerships with commercial manufacturers

Themes Found in High Performing Schools: The CAB Model

ERIC Educational Resources Information Center

Sanders, Brenda

2010-01-01

This study examines the CAB [Cooperativeness, Accountability, and Boundlessness] model of high performing schools by developing case studies of two Portland, Oregon area schools. In pursuing this purpose, this study answers the following three research questions: 1) To what extent is the common correlate cooperativeness demonstrated or absent in…

Train-to-Train Impact Test of Crash-Energy Management Passenger Rail Equipment: Structural Results

DOT National Transportation Integrated Search

2006-01-01

On March 23, 2006, a full-scale test was conducted on a : passenger rail train retrofitted with newly developed cab end : and non-cab end crush zone designs. This test was conducted : as part of a larger testing program to establish the degree of : e...

Characterization of the Novel DNA-Binding Activity of p270, a hSWI/SNF Protein Frequently Downregulated in Breast Cancer

DTIC Science & Technology

2005-07-01

M62324), MRF2 (M73837), RRPe (P24374), RBP1L1 (NP 057458), Jumonji (92833), SMoX (L25270), SMCY (Nok004644), RBP2 (S66431), and PLU-1 (CAB43532). Aoic...associated with specific aspects of cell cycle 2 regulation. Expression of the cell cycle inhibitor p21 CIP1/WAF1 has been repeatedly identified as 3 BRG1...Histone H1, Ascorbic acid, P-glycerol phosphate, and protease inhibitors were obtained from 6 Sigma Chemical Co. (St. Louis, MO), and G418 from Gibco

Improved safety culture and labor-management relations attributed to changing at-risk behavior process at Union Pacific.

DOT National Transportation Integrated Search

2009-09-01

Changing At-Risk Behavior (CAB) is a safety process that is being conducted at Union Pacifics San Antonio Service Unit (SASU) with the aim of improving road and yard safety. CAB is an example of a proactive safety risk-reduction method called Clea...

Fabrication of Tunable Submicro- or Nano-structured Polyethylene Materials form Immiscible Blends with Cellulose Acetate Butyrate

USDA-ARS?s Scientific Manuscript database

Low density polyethylene (LDPE) was prepared into micro- or submicro-spheres or nanofibers via melt blending or extrusion of cellulose acetate butyrate (CAB)/LDPE immiscible blends and subsequent removal of the CAB matrix. The sizes of the PE spheres or fibers can be successfully controlled by varyi...

Heavy vehicle driver workload assessment. Task 7A, in-cab text message system and cellular phone use by heavy vehicle drivers on road

DOT National Transportation Integrated Search

This report covers the seventh in a series of tasks involving the assessment of driver workload in heavy vehicle operation associated with in-cab devices or systems. This report addresses the application of a workload assessment protocol and measurem...

KSC-04PD-1042

NASA Technical Reports Server (NTRS)

2004-01-01

KENNEDY SPACE CENTER, FLA. -- STS-114 Mission Specialist Andrew Thomas takes a look inside one of the cabs on a Crawler- Transporter. The crawlers had recent modifications to the cab and muffler system. The STS-114 mission is Logistics Flight 1, which is scheduled to deliver supplies and equipment plus the external stowage platform to the International Space Station.

Carbonic anhydrase activators: activation of the archaeal beta-class (Cab) and gamma-class (Cam) carbonic anhydrases with amino acids and amines.

PubMed

Innocenti, Alessio; Zimmerman, Sabrina A; Scozzafava, Andrea; Ferry, James G; Supuran, Claudiu T

2008-12-01

Activation of the archaeal beta-class (Cab) and gamma-class (Cam) carbonic anhydrases (CAs, EC 4.2.1.1) with a series of natural and non-natural amino acids and aromatic/heterocyclic amines has been investigated. Cab, Zn-Cam and Co-Cam showed an activation profile with natural, L- and D-amino acids very different of those of the alpha-class enzymes CA I, II and III. Most of these compounds showed medium efficacy as archaeal CA activators, except for D-Phe and L-Tyr which were effective Cab activators (K(A)s of 10.3-10.5 microM), 2-pyridylmethylamine and 1-(2-aminoethyl)-piperazine which effectively activated Zn-Cam (K(A)s of 10.1-11.4 microM) and serotonin, L-adrenaline and 2-pyridylmethylamine which were the best Co-Cam activators (K(A)s of 0.97-8.9 microM). We prove here that the activation mechanisms of the alpha-, beta-, and gamma-class CAs are similar, although the activation profiles with various compounds differ dramatically between these diverse enzymes.

Optimized Hyper Beamforming of Linear Antenna Arrays Using Collective Animal Behaviour

PubMed Central

Ram, Gopi; Mandal, Durbadal; Kar, Rajib; Ghoshal, Sakti Prasad

2013-01-01

A novel optimization technique which is developed on mimicking the collective animal behaviour (CAB) is applied for the optimal design of hyper beamforming of linear antenna arrays. Hyper beamforming is based on sum and difference beam patterns of the array, each raised to the power of a hyperbeam exponent parameter. The optimized hyperbeam is achieved by optimization of current excitation weights and uniform interelement spacing. As compared to conventional hyper beamforming of linear antenna array, real coded genetic algorithm (RGA), particle swarm optimization (PSO), and differential evolution (DE) applied to the hyper beam of the same array can achieve reduction in sidelobe level (SLL) and same or less first null beam width (FNBW), keeping the same value of hyperbeam exponent. Again, further reductions of sidelobe level (SLL) and first null beam width (FNBW) have been achieved by the proposed collective animal behaviour (CAB) algorithm. CAB finds near global optimal solution unlike RGA, PSO, and DE in the present problem. The above comparative optimization is illustrated through 10-, 14-, and 20-element linear antenna arrays to establish the optimization efficacy of CAB. PMID:23970843

Second-line treatment for metastatic clear cell renal cell cancer: experts' consensus algorithms.

PubMed

Rothermundt, C; von Rappard, J; Eisen, T; Escudier, B; Grünwald, V; Larkin, J; McDermott, D; Oldenburg, J; Porta, C; Rini, B; Schmidinger, M; Sternberg, C N; Putora, P M

2017-04-01

Second-line systemic treatment options for metastatic clear cell renal cell cancer (mccRCC) are diverse and treatment strategies are variable among experts. Our aim was to investigate the approach for the second-line treatment after first-line therapy with a tyrosine kinase inhibitor (TKI). Recently two phase III trials have demonstrated a potential role for nivolumab (NIV) and cabozantinib (CAB) in this setting. We aimed to estimate the impact of these trials on clinical decision making. Eleven international experts were asked to provide their treatment strategies for second-line systemic therapy for mccRCC in the current setting and once NIV and CAB will be approved and available. The treatment strategies were analyzed with the objective consensus approach. The analysis of the decision trees revealed everolimus (EVE), axitinib (AXI), NIV and TKI switch (sTKI) as therapeutic options after first-line TKI therapy in the current situation and mostly NIV and CAB in the future setting. The most commonly used criteria for treatment decisions were duration of response, TKI tolerance and zugzwang a composite of several related criteria. In contrast to the first-line setting, recommendations for second-line systemic treatment of mccRCC among experts were not as heterogeneous. The agents mostly used after disease progression on a first-line TKI included: EVE, AXI, NIV and sTKI. In the future setting of NIV and CAB availability, NIV was the most commonly chosen drug, whereas several experts identified situations where CAB would be preferred.

Determination of the effect of brand and product identification on consumer palatability ratings of ground beef patties.

PubMed

Wilfong, A K; McKillip, K V; Gonzalez, J M; Houser, T A; Unruh, J A; Boyle, E A E; O'Quinn, T G

2016-11-01

The objective of this study was to determine the effect of brand and product identification on consumer palatability ratings of ground beef patties. Six treatments were used in the study: 90/10 Certified Angus Beef (CAB) ground sirloin, 90/10 ground beef, 80/20 CAB ground chuck, 80/20 ground chuck, 80/20 ground beef, and 73/27 CAB ground beef. Ground beef was processed into 151.2-g patties using a patty former with 2 consecutively formed patties assigned to blind consumer testing and the following 2 assigned to informed testing. Following cooking to 74°C, patties were cut into quarters and served to consumers. Consumers ( = 112) evaluated samples in 2 rounds for tenderness, juiciness, flavor liking, texture liking, and overall liking. Each trait was also rated as either acceptable or unacceptable. In the first round of testing, samples were blind evaluated, with no information about the treatments provided to consumers, but in the second round, product type and brand were disclosed prior to sample evaluation. Additionally, texture profile and shear force analyses were performed on patties from each treatment. Few differences were observed for palatability traits during blind consumer testing; however, during informed testing, 90/10 CAB ground sirloin was rated greatest ( < 0.05) for all palatability traits other than juiciness. Also, 90/10 CAB ground sirloin had increased ( < 0.05; (consumer informed score - consumer blind score)/consumer blind score) ratings for tenderness (17.4%), juiciness (36.5%), flavor liking (23.3%), texture liking (18.2%), and overall liking (24.7%) due to brand disclosure. Increased ( < 0.05) ratings were found for CAB products for multiple traits due to treatment disclosure, whereas the only non-CAB-branded product that received increased ( < 0.05) ratings during informed testing was 90/10 ground beef for tenderness and juiciness. Texture results indicated that decreased fat level increased hardness, cohesiveness, gumminess, and chewiness. These results indicate that when sampling ground beef without brand and product information, few consumers find differences in eating quality among ground beef treatments; however, when consumers are aware of the brand, fat level, and subprimal blend prior to sampling, these factors have a large impact on consumer eating satisfaction.

Multiple heat priming enhances thermo-tolerance to a later high temperature stress via improving subcellular antioxidant activities in wheat seedlings.

PubMed

Wang, Xiao; Cai, Jian; Liu, Fulai; Dai, Tingbo; Cao, Weixing; Wollenweber, Bernd; Jiang, Dong

2014-01-01

Seedlings of winter wheat (Triticum aestivum L.) were firstly twice heat-primed at 32/24 °C, and subsequently subjected to a more severe high temperature stress at 35/27 °C. The later high temperature stress significantly decreased plant biomass and leaf total soluble sugars concentration. However, plants experienced priming (PH) up-regulated the Rubisco activase B encoding gene RcaB, which was in accordance with the higher photosynthesis rate in relation to the non-primed plants (NH) under the later high temperature stress. In relation to NH, the major chlorophyll a/b-binding protein gene Cab was down-regulated in PH plants, implying a reduction of the light absorption to protect the photosystem II from excitation energy under high temperature stress. At the same time, under the later high temperature stress PH plants showed significantly higher actual photochemical efficiency, indicating an improvement of light use efficiency due to the priming pre-treatment. Under the later high temperature stress, PH could be maintained a better redox homeostasis than NH, as exemplified by the higher activities of superoxide dismutase (SOD) in chloroplasts and glutathione reductase (GR), and of peroxidase (POD) in mitochondria, which contributed to the lower superoxide radical production rate and malondialdehyde concentration in both chloroplasts and mitochondria. The improved antioxidant capacity in chloroplasts and mitochondria was related to the up-regulated expressions of Cu/Zn-SOD, Mn-SOD and GR in PH. Collectively, heat priming effectively improved thermo-tolerance of wheat seedlings subjected to a later high temperature stress, which could be largely ascribed to the enhanced anti-oxidation at the subcellular level. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

KSC-04PD-1043

NASA Technical Reports Server (NTRS)

2004-01-01

KENNEDY SPACE CENTER, FLA. -- STS-114 Pilot James Kelly (left) talks with NASA Systems Engineer Robert Rokobauer inside one of the cabs on a Crawler-Transporter. The crawlers had recent modifications to the cab and muffler system. The STS-114 mission is Logistics Flight 1, which is scheduled to deliver supplies and equipment plus the external stowage platform to the International Space Station.

Controlled and high throughput fabrication of poly(trimethylene terephthalate) nanofibers via melt extrusion of immiscible blends

USDA-ARS?s Scientific Manuscript database

Immiscible blends of cellulose acetate butyrate (CAB) and poly(trimethylene terephthalate) (PTT) were melt extruded through a two strand rod die. The extrudates were hot-drawn at the die exit at different draw ratios. PTT fibers were obtained by removal of the CAB matrix from the drawn extrudates, a...

Controlled and high throughput fabrication of poly(trimethylene terphthalate) nanofibers via melt extrusion of immiscible blends

USDA-ARS?s Scientific Manuscript database

Immiscible blends of cellulose acetate butyrate (CAB) and poly(trimethylene terephthalate) (PTT) were melt extruded through a two strand rod die. The extrudates were hot-drawn at the die exit at different draw ratios. PTT fibers were obtained by removal of the CAB matrix from the drawn extrudates, a...

49 CFR 238.405 - Longitudinal static compressive strength.

Code of Federal Regulations, 2012 CFR

2012-10-01

... crash refuge for crewmembers occupying the cab of a power car, the underframe of the cab of a power car... volumes of a power car or a trailer car designed to crush as part of the crash energy management design...) The underframe of the occupied volume of each trailer car shall resist a minimum longitudinal static...

49 CFR 238.405 - Longitudinal static compressive strength.

Code of Federal Regulations, 2014 CFR

2014-10-01

... crash refuge for crewmembers occupying the cab of a power car, the underframe of the cab of a power car... volumes of a power car or a trailer car designed to crush as part of the crash energy management design...) The underframe of the occupied volume of each trailer car shall resist a minimum longitudinal static...

49 CFR 238.405 - Longitudinal static compressive strength.

Code of Federal Regulations, 2013 CFR

2013-10-01

... crash refuge for crewmembers occupying the cab of a power car, the underframe of the cab of a power car... volumes of a power car or a trailer car designed to crush as part of the crash energy management design...) The underframe of the occupied volume of each trailer car shall resist a minimum longitudinal static...

21 CFR 26.68 - Withdrawal of listed conformity assessment bodies.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 1 2011-04-01 2011-04-01 false Withdrawal of listed conformity assessment bodies... EUROPEAN COMMUNITY âFrameworkâ Provisions § 26.68 Withdrawal of listed conformity assessment bodies. The... assessment body (CAB): (a) A party proposing to withdraw a CAB listed in subpart B of this part shall forward...

Predictions of the Electronic Structure and Related Properties of Cubic Calcium Hexaboride (CaB6)

DTIC Science & Technology

2010-06-01

not display a currently valid OMB control number. 1. REPORT DATE JUN 2010 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE...TERAKURA, AND T. MIYAKE . 2002. Abnormal Quasiparticle shifts in CaB6. Phys. Rev. B. 66: 121103-1-121103-4. LEE, BYOUNGHAK, AND LIN-WANG WANG. 2005

A New Conception of Bucket Wheel Excavator Cab and Seat Mounting

NASA Astrophysics Data System (ADS)

Blekta, J.; Mevald, J.; Petríková, I.; Petříček, J.; Lufinka, A.

One of the most important problem of coal mining by bucket wheel excavators is how to minimize influence of vibrations on driver's body. Project of Ministry of Trade and Industry of the Czech Republic solved in Technical University of Liberec was engaged in this problem. The aim of this project was to design a new cab and seat mounting of wheel excavator Schrs 1320. A suitable possibilities of cab suspensions were investigated to minimize driver body vibrations and to improve influence of mining process to drivers health. After optimization one concept was chosen. A new methodic of measured data evaluation was created for using in excavators as well as in laboratory. The new concept of dynamic seat absorber were designed also.

Ethanol production from cashew apple bagasse: improvement of enzymatic hydrolysis by microwave-assisted alkali pretreatment.

PubMed

Rodrigues, Tigressa Helena Soares; Rocha, Maria Valderez Ponte; de Macedo, Gorete Ribeiro; Gonçalves, Luciana R B

2011-07-01

In this work, the potential of microwave-assisted alkali pretreatment in order to improve the rupture of the recalcitrant structures of the cashew able bagasse (CAB), lignocellulosic by-product in Brazil with no commercial value, is obtained from cashew apple process to juice production, was studied. First, biomass composition of CAB was determined, and the percentage of glucan and lignin was 20.54 ± 0.70% and 33.80 ± 1.30%, respectively. CAB content in terms of cellulose, hemicelluloses, and lignin, 19.21 ± 0.35%, 12.05 ± 0.37%, and 38.11 ± 0.08%, respectively, was also determined. Results showed that, after enzymatic hydrolysis, alkali concentration exerted influence on glucose formation, after pretreatment with 0.2 and 1.0 mo L(-1) of NaOH (372 ± 12 and 355 ± 37 mg g(glucan)(-1) ) when 2% (w/v) of cashew apple bagasse pretreated by microwave-assisted alkali pretreatment (CAB-M) was used. On the other hand, pretreatment time (15-30 min) and microwave power (600-900 W) exerted no significant effect on hydrolysis. On enzymatic hydrolysis step, improvement on solid percentage (16% w/v) and enzyme load (30 FPU g (CAB-M) (-1) ) increased glucose concentration to 15 g L(-1). The fermentation of the hydrolyzate by Saccharomyces cerevesiae resulted in ethanol concentration and productivity of 5.6 g L(-1) and 1.41 g L(-1) h(-1), respectively.

Genetic interrelationships among phosphorus, nitrogen, calcium, and energy bioavailability in a growing chicken population.

PubMed

Ankra-Badu, G A; Pesti, G M; Aggrey, S E

2010-11-01

A random-mating population was used to study the genetic interrelationship between phytate P (PPB), Ca (CaB), N (NB), and energy bioavailability (EB), BW at 4 wk of age, relative growth (RG), and feed conversion ratio (FCR). Heritability estimates for PPB, CaB, NB, and EB were 0.09, 0.13, 0.16, and 0.10, respectively, and those of BW, RG, and FCR were 0.66, 0.15, and 0.10, respectively. Genetic correlations between PPB and BW, and FCR were moderate and negative, suggesting that improvement in PPB will impair growth. The genetic correlations between PPB and CaB, and EB and RG were positive and moderate, indicating that improvement in PPB would also lead to improved CaB, EB, and RG. Energy bioavailability was positively correlated with CaB, NB, PPB, and BW. Even though the genetic correlation between EB and the other traits measured, except RG and FCR, ranged from low to moderate, improving the ability of birds to utilize caloric energy in the feed would consequently improve PPB as well as growth. Improving PPB would reduce the amount of P in excreta and provide an additional savings if exogenous phytase were not added to poultry feed. The genetic correlation between PPB and NB was low but positive, whereas NB had a positive genetic correlation with BW. Therefore, selecting on NB will result in positive correlated responses in BW and PPB. Improving PPB and NB will not only improve productivity, but also reduce the polluting effects of P and N on the environment.

Understanding Disproportionate Representation in Special Education by Examining Group Differences in Behavior Ratings

ERIC Educational Resources Information Center

Peters, Christina D.; Kranzler, John H.; Algina, James; Smith, Stephen W.; Daunic, Ann P.

2014-01-01

The aim of the current study was to examine mean-group differences on behavior rating scales and variables that may predict such differences. Sixty-five teachers completed the Clinical Assessment of Behavior-Teacher Form (CAB-T) for a sample of 982 students. Four outcome variables from the CAB-T were assessed. Hierarchical linear modeling was used…

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

49 CFR Appendix H to Part 229 - Static Noise Test Protocols-In-Cab Static

Code of Federal Regulations, 2010 CFR

2010-10-01

... Federal Railroad Administration, Docket Room, 1200 New Jersey Avenue, SE., Washington, DC 20950, or at the... measured at each of the following locations: (A) 30 inches above the center of the left seat; (B) Centered in the middle of the cab between the right and left seats, and 56 inches above the floor; (C) 30...

The Compensatory ADHD Behaviors Scale (CABS): Development and Initial Validation.

PubMed

Castagna, Peter J; Roye, Scott; Calamia, Matthew

2018-05-01

Several measures are available that assess inattention, hyperactivity/impulsivity, and executive functioning deficits. Treatments for adults with attention-deficit/hyperactivity disorder (ADHD) and skill-based academic interventions focus on improving compensatory strategies to ameliorate functional impairment; however, no measure exists that examines the compensatory behaviors adults utilize to compensate for the functional deficits associated with inattention and hyperactivity/impulsivity. The current study aimed to determine the psychometric properties of the Compensatory ADHD Behaviors Scale (CABS). Five-hundred participants ( M age = 36.83, SD = 11.57) completed measures of ADHD symptomatology, executive functioning, functional impairment, mood disorder symptoms, and the CABS. Analyses revealed that scales assessing both use and effectiveness of compensatory behaviors subscales had similar factor structures, reflecting present- and future-oriented behaviors. The present-, but not future-oriented, behaviors significantly related to ADHD symptomatology, executive dysfunction, and functional impairment; effectiveness of present-oriented compensatory behaviors demonstrated incremental validity in predicting impairment. Compensatory strategies may be a useful variable to measure when examining functional impairment associated with inattention and hyperactivity/impulsivity. The current study provides preliminary evidence of the ability of CABS to validly measure various strategies associated with (clinical and subclinical) ADHD symptomatology, executive functioning, and overall impairment.

CABS: Green Energy for Our Nation's Future (A "Life at the Frontiers of Energy Research" contest entry from the 2011 Energy Frontier Research Centers (EFRCs) Summit and Forum)

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

"CABS: Green Energy for our Nation's Future" was submitted by the Center for Advanced Biofuel Systems (CABS) to the "Life at the Frontiers of Energy Research" video contest at the 2011 Science for Our Nation's Energy Future: Energy Frontier Research Centers (EFRCs) Summit and Forum. Twenty-six EFRCs created short videos to highlight their mission and their work. CABS, an EFRC directed by Jan Jaworski at the Donald Danforth Plant Science Center is a partnership of scientists from five institutions: Donald Danforth Plant Science Center (lead), Michigan State University, the University of Nebraska, New Mexico Consortium/LANL, and Washington State University. Themore » Office of Basic Energy Sciences in the U.S. Department of Energy's Office of Science established the 46 Energy Frontier Research Centers (EFRCs) in 2009. These collaboratively-organized centers conduct fundamental research focused on 'grand challenges' and use-inspired 'basic research needs' recently identified in major strategic planning efforts by the scientific community. The overall purpose is to accelerate scientific progress toward meeting the nation's critical energy challenges.« less

[Simulation of vegetation indices optimizing under retrieval of vegetation biochemical parameters based on PROSPECT + SAIL model].

PubMed

Wu, Ling; Liu, Xiang-Nan; Zhou, Bo-Tian; Liu, Chuan-Hao; Li, Lu-Feng

2012-12-01

This study analyzed the sensitivities of three vegetation biochemical parameters [chlorophyll content (Cab), leaf water content (Cw), and leaf area index (LAI)] to the changes of canopy reflectance, with the effects of each parameter on the wavelength regions of canopy reflectance considered, and selected three vegetation indices as the optimization comparison targets of cost function. Then, the Cab, Cw, and LAI were estimated, based on the particle swarm optimization algorithm and PROSPECT + SAIL model. The results showed that retrieval efficiency with vegetation indices as the optimization comparison targets of cost function was better than that with all spectral reflectance. The correlation coefficients (R2) between the measured and estimated values of Cab, Cw, and LAI were 90.8%, 95.7%, and 99.7%, and the root mean square errors of Cab, Cw, and LAI were 4.73 microg x cm(-2), 0.001 g x cm(-2), and 0.08, respectively. It was suggested that to adopt vegetation indices as the optimization comparison targets of cost function could effectively improve the efficiency and precision of the retrieval of biochemical parameters based on PROSPECT + SAIL model.

Conceptual design study for an advanced cab and visual system, volume 1

NASA Technical Reports Server (NTRS)

Rue, R. J.; Cyrus, M. L.; Garnett, T. A.; Nachbor, J. W.; Seery, J. A.; Starr, R. L.

1980-01-01

A conceptual design study was conducted to define requirements for an advanced cab and visual system. The rotorcraft system integration simulator is for engineering studies in the area of mission associated vehicle handling qualities. Principally a technology survey and assessment of existing and proposed simulator visual display systems, image generation systems, modular cab designs, and simulator control station designs were performed and are discussed. State of the art survey data were used to synthesize a set of preliminary visual display system concepts of which five candidate display configurations were selected for further evaluation. Basic display concepts incorporated in these configurations included: real image projection, using either periscopes, fiber optic bundles, or scanned laser optics; and virtual imaging with helmet mounted displays. These display concepts were integrated in the study with a simulator cab concept employing a modular base for aircraft controls, crew seating, and instrumentation (or other) displays. A simple concept to induce vibration in the various modules was developed and is described. Results of evaluations and trade offs related to the candidate system concepts are given, along with a suggested weighting scheme for numerically comparing visual system performance characteristics.

Tannase Production by Solid State Fermentation of Cashew Apple Bagasse

NASA Astrophysics Data System (ADS)

Podrigues, Tigressa H. S.; Dantas, Maria Alcilene A.; Pinto, Gustavo A. S.; Gonçalves, Luciana R. B.

The ability of Aspergillus oryzae for the production of tannase by solid state fermentation was investigated using cashew apple bagasse (CAB) as substrate. The effect of initial water content was studied and maximum enzyme production was obtained when 60 mL of water was added to 100.0 g of CAB. The fungal strain was able to grow on CAB without any supplementation but a low enzyme activity was obtained, 0.576 U/g of dry substrate (gds). Optimization of process parameters such as supplementation with tannic acid, phosphorous, and different organic and inorganic nitrogen sources was studied. The addition of tannic acid affected the enzyme production and maximum tannase activity (2.40 U/gds) was obtained with 2.5% (w/w) supplementation. Supplementation with ammonium nitrate, peptone, and yeast extract exerted no influence on tannase production. Ammonium sulphate improved the enzyme production in 3.75-fold compared with control. Based on the experimental results, CAB is a promising substrate for solid state fermentation, enabling A. oryzae growth and the production of tannase, with a maximum activity of 3.42 U/gds and enzyme productivity of 128.5×10-3 U·gds -1·h-1.

Electro-deposition painting process improvement of cab truck by Six Sigma concept

NASA Astrophysics Data System (ADS)

Kawitu, Kitiya; Chutima, Parames

2017-06-01

The case study company is a manufacturer of trucks and currently facing a high rework cost due to the thickness of the electro-deposited paint (EDP) of the truck cab is lower than standard. In addition, the process capability is very low. The Six Sigma concept consisting of 5 phases (DMAIC) is applied to determine new parameter settings for each significant controllable factor. After the improvement, EDP thickness of the truck cab increases from 17.88μ to 20μ (i.e. standard = 20 ± 3μ). Moreover, the process capability indexes (Cp and Cpk) are increased from 0.9 to 1.43, and from 0.27 to 1.43, respectively. This improvement could save the rework cost about 1.6M THB per year.

Tectonic uplift and denudation rate influence soil chemical weathering intensity in a semi-arid environment, southeast Spain: physico-chemical and mineralogical evidence

NASA Astrophysics Data System (ADS)

Ameijeiras-Mariño, Yolanda; Opfergelt, Sophie; Schoonejans, Jérôme; Vanacker, Veerle; Sonnet, Philippe; Delmelle, Pierre

2015-04-01

Tectonic uplift is known to influence denudation rates. Denudation, including chemical weathering and physical erosion, affects soil production rates and weathering intensities. At topographic steady state, weathering can be transport- or weathering-limited. In the transport-limited regime, low denudation rates should lead to comparatively high weathering intensities, while in the weathering-limited case high denudation rates are associated with lower weathering intensities. Here, we test if this relationship applies to semi-arid environments where chemical weathering is generally slow. Three catchments (EST, FIL and CAB) were studied in the Internal Zone of the Betic Cordillera in southeast Spain, spanning a range of increasing uplift rates (10-170 mm/kyr) and increasing denudation rates (20-250 mm/kyr) from EST to CAB. In each catchment, two ridgetop soil profiles were sampled down to the bedrock. The three catchments have similar vegetation and climatic conditions, with precipitation of 250- 315 mm/yr and mean annual temperature of 15-17 °C. The mineralogy of the bedrock, as determined by XRD, is similar across the three catchments and is characterized by the presence of quartz, muscovite, clinochlore, biotite and plagioclase. This primary mineral assemblage is also found in the catchment soils, indicating that the soils studied derive from the same parent material. The soil clay-size fraction is dominated by kaolinite, vermiculite and illite. However, the proportions of the soil primary and secondary minerals vary between the catchment sites. The abundance of biotite decreases from CAB (14%) to EST (4%), whereas the quartz and clay contents show an opposite tendency (from 30 to 69% and 9.9 to 14.3%, respectively). Further, the abundance of vermiculite increases from CAB to EST. The results are interpreted in terms of increasing weathering intensity from CAB to EST by weathering of biotite into vermiculite and enrichment of soils on more weathering resistant quartz. Soil weathering intensity in each catchment was assessed previously [1] using three independent weathering indices: the Total Reserve in Bases (TRB = [Ca2+] + [Na+] + [K+] + [Mg2+]), soil Fed/Fet ratio (Fe-oxides/total Fe), and Cation Exchange Capacity (CEC). In agreement with the soil mineralogy, the physico-chemical analyses revealed increasing weathering intensity from CAB to EST. We postulate that the higher chemical weathering intensity in EST reflects lower denudation and uplift rates compared to CAB and therefore, soil chemical weathering intensity in this semi-arid environment may be controlled by denudation and uplift rates [1] Ameijeiras-Mariño et al, EGU 2014-9714-1

Concomitant Carotid and Coronary Artery Reconstruction

PubMed Central

Craver, Joseph M.; Murphy, Douglas A.; Jones, Ellis L.; Curling, Patrick E.; Bone, David K.; Smith, Robert B.; Perdue, Garland D.; Hatcher, Charles R.; Kandrach, Michael

1982-01-01

Data are presented on 68 patients who underwent concomitant carotid endarterectomy (CE) and coronary artery bypass surgery (CAB) at Emory University Hospital from January 1974 to February 1981. This group is then compared with a randomly selected, matched population without known carotid disease who underwent CAB alone. Asymptomatic bruit was the reason for investigation in 40 patients (59%); another 23 patients (34%) experienced transient cerebral ischemic attacks (TIAs); and five patients (7%) had TIA and prior stroke. Carotid stenoses (>75% luminal narrowing) were demonstrated as follows: isolated left, 24 patients; isolated right, 27 patients; and bilateral lesions, 16 patients. One patient had innominate artery stenosis. Associated total occlusion of one or both vertebral arteries was demonstrated in six patients. Ninety-seven per cent of patients had disabling angina pectoris prior to operation; the angina was unstable in 57%, 15% had congestive heart failure, and 54% had had at least one prior myocardial infarction (MI). Single-vessel coronary disease was present in 12.5% of patients, double in 37.5%, triple in 41.1%, and left main stenosis in 9%; 43% of patients had abnormal ventricular contractility. CE was performed on 67 patients (36 left and 31 right); aortocarotid bypass was performed on one. The CE procedures were performed immediately prior to the sternotomy for CAB under the same anesthesia. CAB consisted of single bypass in eight patients (11.8%); double in 16 patients (23.5%); triple in 22 patients (32.4%); and quadruple or more in 22 patients (32.4%) (mean = 2.9 grafts per patient). There was no hospital mortality. Perioperative MI occurred in 2.0% and stroke with residual deficit in 1.3%. Cumulative survival is 98.5% at two years. Sixty-three patients (92%) reported improvement or elimination of anginal symptoms after operation. Rehospitalization for stroke was necessary in 3.7% patients. Postoperative activity levels are; self-care only, 3.9%; normal daily activity only, 17.6%; moderate exercise capability, 45%; and vigorous exercise capability, 33%. Comparison was made with a group of 84 randomly selected patients who underwent CAB alone during the same time interval. Data revealed no significant difference between the groups regarding sex, angina subset, ventricular function, coronary anatomy, vessels grafted, perioperative stroke or MI, mortality, or postoperative activity capability. Older age (59.8 vs. 55.6, p < 0.01) and less complete coronary revascularization possible (66 vs. 84%, p < 0.05) in the CECAB group were the only significant differences. Carotid stenosis co-existing in patients requiring CAB should be concomitantly corrected with the same risk and results expected from CAB alone. PMID:7082063

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery

PubMed Central

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-01-01

Background DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. Results GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. Conclusion GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at . PMID:19728865

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.

PubMed

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-09-03

DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at http://cgs.pharm.kyoto-u.ac.jp/services/network.

Multiphase materials with lignin. VI. Effect of cellulose derivative structure on blend morphology with lignin

Treesearch

Timothy G. Rials; Wolfgang G. Glasser

1989-01-01

Polymeric blends of lignin with ethyl cellulose (EC) and cellulose acetate/butyrate (CAB) prepared by solution casting from dioxane. Fracture surface analysis by scanning electron microscopy revealed phase separation when the lignin content exceeded 10% for blends with EC and 5% in the CAB system. While this phase behavior is as predicted for the EC blends, a greater...

Structure Inference from Mobility Encounters

DTIC Science & Technology

2013-10-20

world dataset, which contains 230K trajectories of taxi cabs in Beijing . Our algorithm extracts a pathlet dictionary containing around 130K...data set, frequently used pathlets in the dictionary represent driving segments chosen by many taxi cab drivers in Beijing , reflecting the joint wisdom...limitations on storage and communication bandwidth. For instance, 50% of the Beijing Taxi Trajectories we employed in this study have at most one

Emission estimates of HCFCs and HFCs in California from the 2010 CalNex study

NASA Astrophysics Data System (ADS)

Barletta, Barbara; Carreras-Sospedra, Marc; Cohan, Alex; Nissenson, Paul; Dabdub, Donald; Meinardi, Simone; Atlas, Elliot; Lueb, Rich; Holloway, John S.; Ryerson, Thomas B.; Pederson, James; VanCuren, Richard A.; Blake, Donald R.

2013-02-01

The CalNex 2010 (California Research at the Nexus of Air Quality and Climate Change) study was designed to evaluate the chemical composition of air masses over key source regions in California. During May to June 2010, air samples were collected on board a National Oceanic and Atmospheric Administration (NOAA) WP-3D aircraft over the South Coast Air Basin of California (SoCAB) and the Central Valley (CV). This paper analyzes six effective greenhouse gases—chlorodifluoromethane (HCFC-22), 1,1-dichloro-1-fluoroethane (HCFC-141b), 1-chloro-1,1-difluoroethane (HCFC-142b), 2-chloro-1,1,1,2-tetrafluoroethane (HCFC-124), 1,1,1,2-tetrafluoroethane (HFC-134a), and 1,1-difluoroethane (HFC-152a)—providing the most comprehensive characterization of chlorofluorocarbon (CFC) replacement compound emissions in California. Concentrations of measured HCFCs and HFCs are enhanced greatly throughout the SoCAB and CV, with highest levels observed in the SoCAB: 310 ± 92 pptv for HCFC-22, 30.7 ± 18.6 pptv for HCFC-141b, 22.9 ± 2.0 pptv for HCFC-142b, 4.86 ± 2.56 pptv for HCFC-124, 109 ± 46.4 pptv for HFC-134a, and 91.2 ± 63.9 pptv for HFC-152a. Annual emission rates are estimated for all six compounds in the SoCAB using the measured halocarbon to carbon monoxide (CO) mixing ratios and CO emissions inventories. Emission rates of 3.05 ± 0.70 Gg for HCFC-22, 0.27 ± 0.07 Gg for HCFC-141b, 0.06 ± 0.01 Gg for HCFC-142b, 0.11 ± 0.03 Gg for HCFC-124, 1.89 ± 0.43 Gg for HFC-134a, and 1.94 ± 0.45 Gg for HFC-152b for the year 2010 are calculated for the SoCAB. These emissions are extrapolated from the SoCAB region to the state of California using population data. Results from this study provide a baseline emission rate that will help future studies determine if HCFC and HFC mitigation strategies are successful.

Organohalogen contaminants and metabolites in beluga whale (Delphinapterus leucas) liver from two Canadian populations.

PubMed

McKinney, Melissa A; De Guise, Sylvain; Martineau, Daniel; Béland, Pierre; Lebeuf, Michel; Letcher, Robert J

2006-05-01

Contaminants described as organochlorines (OCs; e.g., polychlorinated biphenyls [PCBs]) are present in tissues of marine mammals, including beluga whales (Delphinapterus leucas), but the complexity of contaminant exposure often is not fully known. The PCBs, OC pesticides, polybrominated diphenyl ether (PBDE) flame retardants, methylsulfonyl (MeSO2)- and hydroxy (OH)-PCB metabolites, and OH-PBDEs and methoxylated (MeO)-PBDEs were determined in the liver of beluga whales from two Canadian populations: the St. Lawrence Estuary (SLB; n=6), and western Hudson Bay in the Canadian Arctic (CAB; n=11). The sigmaPCB, sigmaDDT, and sigmaPBDE concentrations were higher (p < 0.05) in SLB versus CAB. Of 18 detectable OH-PCBs in SLB (mainly 4-OH-CB107, 4-OH-CB112, and 4'-OH-CB120), only 4'-OH-CB120 was found in CAB. The sigmaOH-PCB concentrations were less than 0.2% of the sigmaPCBs in both populations but were higher (p < 0.05) in SLB (65 +/- 22 ng/g lipid wt) than in CAB (3.1 +/- 0.5 ng/g lipid wt). The sigmaMeSO2-PCB concentrations were higher in SLB (3801 +/- 1322 ng/g lipid wt) relative to CAB (77 +/- 23 ng/g lipid wt) and were 11 and 4%, respectively, of the sigmaPCB concentrations. Of the 15 OH-PBDEs, only two congeners were detectable, but not quantifiable (notably 2'-OH-BDE 68 and 6-OH-BDE 47), in animals from both populations. Of the 15 MeO-PBDEs, 4'-MeO-BDE 17 and 6-MeO-BDE 47 in the SLB (n=2) and 2'-MeO-BDE 68 and 6-MeO-BDE 47 in the CAB (n=2) had concentrations from 20 to 100 ng/g lipid weight. The OH-PBDEs and MeO-PBDEs most likely are of natural origin and accumulated in beluga whales, whereas the OH-PCBs and MeSO2-PCBs are metabolites derived from accumulated PCBs. Canadian beluga whale liver contains previously unidentified organohalogen contaminants and metabolites and, thus, a complexity of contaminant exposure that may be impacting the health of Canadian beluga whale populations.

Neighboring Genes Show Correlated Evolution in Gene Expression

PubMed Central

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

PubMed Central

Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

2013-01-01

The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

Neighboring Genes Show Correlated Evolution in Gene Expression.

PubMed

Ghanbarian, Avazeh T; Hurst, Laurence D

2015-07-01

When considering the evolution of a gene's expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sleeper Cab Climate Control Load Reduction for Long-Haul Truck Rest Period Idling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lustbader, J. A.; Kreutzer, C.; Adelman, S.

2015-04-29

Annual fuel use for long-haul truck rest period idling is estimated at 667 million gallons in the United States. The U.S. Department of Energy’s National Renewable Energy Laboratory’s CoolCab project aims to reduce heating, ventilating, and air conditioning (HVAC) loads and resulting fuel use from rest period idling by working closely with industry to design efficient long-haul truck climate control systems while maintaining occupant comfort. Enhancing the thermal performance of cab/sleepers will enable smaller, lighter, and more cost-effective idle reduction solutions. In order for candidate idle reduction technologies to be implemented at the original equipment manufacturer and fleet level, theirmore » effectiveness must be quantified. To address this need, a number of promising candidate technologies were evaluated through experimentation and modeling to determine their effectiveness in reducing rest period HVAC loads. For this study, load reduction strategies were grouped into the focus areas of solar envelope, occupant environment, and conductive pathways. The technologies selected for a complete-cab package of technologies were “ultra-white” paint, advanced insulation, and advanced curtains. To measure the impact of these technologies, a nationally-averaged solar-weighted reflectivity long-haul truck paint color was determined and applied to the baseline test vehicle. Using the complete-cab package of technologies, electrical energy consumption for long-haul truck daytime rest period air conditioning was reduced by at least 35% for summer weather conditions in Colorado. The National Renewable Energy Laboratory's CoolCalc model was then used to extrapolate the performance of the thermal load reduction technologies nationally for 161 major U.S. cities using typical weather conditions for each location over an entire year.« less

HFC-152a and HFC-134a emission estimates and characterization of CFCs, CFC replacements, and other halogenated solvents measured during the 2008 ARCTAS campaign (CARB phase) over the South Coast Air Basin of California

NASA Astrophysics Data System (ADS)

Barletta, B.; Nissenson, P.; Meinardi, S.; Dabdub, D.; Sherwood Rowland, F.; Vancuren, R. A.; Pederson, J.; Diskin, G. S.; Blake, D. R.

2011-03-01

This work presents results from the NASA Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) study. Whole air samples were obtained on board research flights that flew over California during June 2008 and analyzed for selected volatile organic compounds, including several halogenated species. Samples collected over the South Coast Air Basin of California (SoCAB), which includes much of Los Angeles (LA) County, were compared with samples from inflow air masses over the Pacific Ocean. The levels of many halocarbon species were enhanced significantly over the SoCAB, including compounds regulated by the Montreal Protocol and subsequent amendments. Emissions estimates of HFC-152a (1,1-difluoroethane, CH3CHF2; 0.82 ± 0.11 Gg) and HFC-134a (1,1,1,2-tetrafluoroethane, CH2FCF3; 1.16 ± 0.22 Gg) in LA County for 2008 were obtained using the observed HFC:carbon monoxide (CO) enhancement ratio. Emission rates also were calculated for the SoCAB (1.60 ± 0.22 Gg yr-1 for HFC-152a and 2.12 ± 0.28 Gg yr-1 for HFC-134a) and then extrapolated to the United States (32 ± 4 Gg yr-1 for HFC-152a and 43 ± 6 Gg yr-1 for HFC-134a) using population data. In addition, emission rates of the two HFCs in LA County and SoCAB were calculated by a second method that utilizes air quality modeling. Emissions estimates obtained using both methods differ by less than 25% for the LA County and less than 45% for the SoCAB.

Rapid and sensitive sandwich enzyme-linked immunosorbent assay for detection of staphylococcal enterotoxin B in cheese.

PubMed Central

Morissette, C; Goulet, J; Lamoureux, G

1991-01-01

A rapid and sensitive screening sandwich enzyme-linked immunosorbent assay (ELISA) was developed for the detection of staphylococcal enterotoxin B (SEB) in cheese by using a highly avid anti-SEB antibody (Ab) as the capture Ab (CAb) and as the biotinylated Ab conjugate. The glutaraldehyde fixation method for the immobilization of CAb on polystyrene dipsticks was superior to the adsorption fixation and the adsorption-glutaraldehyde fixation methods. The glutaraldehyde fixation method resulted in a higher surface-saturating CAb concentration as evaluated by the peroxidase saturation technique and by the ability of the CAb-coated dipstick to discriminate between positive and negative controls (index of discrimination). Of nine blocking agents used alone or in pairs, lysine-human serum albumin, bovine serum albumin, human serum albumin, and gelatin effectively saturated available sites on the CAb-coated dipsticks without causing interference with the antigen-Ab reactions. The addition of 1% polyethylene glycol to the diluent of the biotinylated anti-SEB Ab conjugate improved the detection of SEB. A concentration of 4% polyethylene glycol allowed a 5-min reaction time for the streptavidin-biotin-horseradish peroxidase conjugate. Cheddar cheese homogenate reduced the sensitivity of the SEB assay; however, the sensitivity was restored when 1.6% (wt/vol) of either a nonionic detergent (Mega-9) or two zwitterionic detergents (Zwittergent 3-10 and 3-12 detergent) was added to the diluent. By using the rapid sandwich ELISA, a minimum of 0.5 to 1.0 ng of SEB per ml was detected within 45 min. The whole procedure for the analysis of the cheddar cheese samples was completed within 1 h.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2039234

Driving to Better Health: Cancer and Cardiovascular Risk Assessment among Taxi Cab Operators in Chicago

PubMed Central

Apantaku-Onayemi, Funmi; Baldyga, William; Amuwo, Shaffdeen; Adefuye, Adedeji; Mason, Terry; Mitchell, Robin; Blumenthal, Daniel S.

2014-01-01

While a number of investigations of the health of taxi cab drivers have been conducted in Europe, Asia, and Africa, virtually none have been conducted in the United States. We undertook a survey of taxi cab operators in the Chicago area to understand better their health status and health promotion practices. The survey was completed by a convenience sample of 751 Chicago taxi drivers. Taxi drivers had low rates of insurance coverage, fruit and vegetable consumption, and physical activity compared with the general Chicago population. Participation in cancer screening tests was also lower for this group. A high proportion of taxi drivers are immigrants. They tend to be highly educated and report a readiness to engage in more health-promoting behaviors. Further research is needed to develop a targeted intervention for this population. PMID:22643623

Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods.

PubMed

Chang, Dan; Duda, Thomas F

2014-06-05

Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components ('conotoxins'), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species' 'venom gene space'. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species. We modified community phylogenetics approaches to incorporate phylogenetic history and disparity of genes and their expression profiles to determine patterns of venom gene space utilization. Less than half of the A-superfamily gene repertoire of these species is expressed, and only a few orthologous genes are coexpressed among species. Species exhibit substantially distinct expression strategies, with some expressing sets of closely related loci ('under-dispersed' expression of available genes) while others express sets of more disparate genes ('over-dispersed' expression). In addition, expressed genes show higher dN/dS values than either unexpressed or ancestral genes; this implies that expression exposes genes to selection and facilitates rapid evolution of these genes. Few recent lineage-specific gene duplicates are expressed simultaneously, suggesting that expression divergence among redundant gene copies may be established shortly after gene duplication. Our study demonstrates that venom gene space is explored differentially by Conus species, a process that effectively permits the independent and rapid evolution of venoms in these species.

Elucidating the Role of cAb1 and the Abi-Family of cAB1 Target Proteins in Cancer Development and Progression

DTIC Science & Technology

2000-07-01

1996;87:2252. members. J Biol Chem. 1996;271:31,704. SH2 regulatory domain in a non-phosphotyro- 36. DiNoto R, LoRardo C, Schiavone EM, et al. Stem 11...Information Center (DTIC-OCA), 8725 John J. Kingman Road, Fort Belvoir, VA 22060-6218 SUBJECT: Request Change in Distribution Statement 1. The U.S. Army

Thermal Comfort Testing for Vehicle Operator/Passenger Workspaces (Truck Cabs)

DTIC Science & Technology

2007-10-09

This TOP describes the procedure to quantify the thermal comfort of a truck cab in temperatures as hot and humid as possible. Facilities, instrumentation, health and safety, test conditions, test procedures, data required, and presentation of data will be discussed in this TOP. This TOP will supplement the following TOPs: TOP 1-1-006, TOP 2-2-508, TOP 2-4-001, and TOP 10-1-003.

PBF Reactor Building (PER620). Camera is in cab of electricpowered ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

PBF Reactor Building (PER-620). Camera is in cab of electric-powered rail crane and facing east. Reactor pit and storage canal have been shaped. Floors for wings on east and west side are above and below reactor in view. Photographer: Larry Page. Date: August 23, 1967. INEEL negative no. 67-4403 - Idaho National Engineering Laboratory, SPERT-I & Power Burst Facility Area, Scoville, Butte County, ID

Human Factors Engineering Guidelines for Overhead Cranes

NASA Technical Reports Server (NTRS)

Chandler, Faith; Delgado, H. (Technical Monitor)

2001-01-01

This guideline provides standards for overhead crane cabs that can be applied to the design and modification of crane cabs to reduce the potential for human error due to design. This guideline serves as an aid during the development of a specification for purchases of cranes or for an engineering support request for crane design modification. It aids human factors engineers in evaluating existing cranes during accident investigations or safety reviews.

Can the democratic ideal of participatory research be achieved? An inside look at an academic-indigenous community partnership.

PubMed

Cargo, Margaret; Delormier, Treena; Lévesque, Lucie; Horn-Miller, Kahente; McComber, Alex; Macaulay, Ann C

2008-10-01

Democratic or equal participation in decision making is an ideal that community and academic stakeholders engaged in participatory research strive to achieve. This ideal, however, may compete with indigenous peoples' right to self-determination. Study objectives were to assess the perceived influence of multiple community (indigenous) and academic stakeholders engaged in the Kahnawake Schools Diabetes Prevention Project (KSDPP) across six domains of project decision making and to test the hypothesis that KSDPP would be directed by community stakeholders. Self-report surveys were completed by 51 stakeholders comprising the KSDPP Community Advisory Board (CAB), KSDPP staff, academic researchers and supervisory board members. KSDPP staff were perceived to share similar levels of influence with (i) CAB on maintaining partnership ethics and CAB activities and (ii) academic researchers on research and dissemination activities. KSDPP staff were perceived to carry significantly more influence than other stakeholders on decisions related to annual activities, program operations and intervention activities. CAB and staff were the perceived owners of KSDPP. The strong community leadership aligns KSDPP with a model of community-directed research and suggests that equitable participation-distinct from democratic or equal participation-is reflected by indigenous community partners exerting greater influence than academic partners in decision making.

Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals

PubMed Central

White, Gaye F.; Shi, Zhi; Shi, Liang; Wang, Zheming; Dohnalkova, Alice C.; Marshall, Matthew J.; Fredrickson, James K.; Zachara, John M.; Butt, Julea N.; Richardson, David J.; Clarke, Thomas A.

2013-01-01

The mineral-respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decaheme cytochromes, MtrC and MtrA, brought together inside a transmembrane porin, MtrB, to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system containing a pool of internalized electron carriers was used to investigate how the topology of the MtrCAB complex relates to its ability to transport electrons across a lipid bilayer to externally located Fe(III) oxides. With MtrA facing the interior and MtrC exposed on the outer surface of the phospholipid bilayer, the established in vivo orientation, electron transfer from the interior electron carrier pool through MtrCAB to solid-phase Fe(III) oxides was demonstrated. The rates were 103 times higher than those reported for reduction of goethite, hematite, and lepidocrocite by S. oneidensis, and the order of the reaction rates was consistent with those observed in S. oneidensis cultures. In contrast, established rates for single turnover reactions between purified MtrC and Fe(III) oxides were 103 times lower. By providing a continuous flow of electrons, the proteoliposome experiments demonstrate that conduction through MtrCAB directly to Fe(III) oxides is sufficient to support in vivo, anaerobic, solid-phase iron respiration. PMID:23538304

Quantifying the Loss of Processed Natural Gas Within California's South Coast Air Basin Using Long-term Measurements of Ethane and Methane

NASA Astrophysics Data System (ADS)

Wunch, D.; Toon, G. C.; Hedelius, J.; Vizenor, N.; Roehl, C. M.; Saad, K.; Blavier, J. F.; Blake, D. R.; Wennberg, P. O.

2016-12-01

In California's South Coast Air Basin (SoCAB), the methane emissions inferred from atmospheric measurements exceed estimates based on inventories. We seek to provide insight into the sources of the discrepancy with two records of atmospheric trace gas total column abundances in the SoCAB: one temporally sparse dataset that began in the late 1980s, and a temporally dense dataset that began in 2012. We use their measurements of ethane and methane to partition the sources of the excess methane. The early few years of the sparse record show a rapid decline in ethane emissions at a much faster rate than decreasing vehicle exhaust or natural gas and crude oil production can explain. Between 2010 and 2015, ethane emissions have grown gradually, which is in contrast to the steady production of natural gas liquids over that time. Since 2012, ethane to methane ratios in the natural gas withdrawn from a storage facility within the SoCAB have been increasing; these ratios are tracked in our atmospheric measurements with about half of the rate of increase. From this, we infer that about half of the excess methane in the SoCAB between 2012-­2015 is attributable to losses from the natural gas infrastructure.

Pleural tissue hyaluronan produced by postmortem ventilation in rabbits.

PubMed

Wang, P M; Lai-Fook, S J

2000-01-01

We developed a method that used Alcian blue bound to hyaluronan to measure pleural hyaluronan in rabbits postmortem. Rabbits were killed, then ventilated with 21% O2--5% CO2--74% N2 for 3 h. The pleural liquid was removed by suction and 5 ml Alcian blue stock solution (0.33 mg/ml, 3.3 pH) was injected into each chest cavity. After 10 min, the Alcian blue solution was removed and the unbound Alcian blue solution (supernatant) separated by centrifugation and filtration. The supernatant transmissibility (T) was measured spectrophotometrically at 613 nm. Supernatant Alcian blue concentration (Cab) was obtained from a calibration curve of T versus dilutions of stock solution Cab. Alcian blue bound to pleural tissue hyaluronan was obtained by subtracting supernatant Cab from stock solution Cab. Pleural tissue hyaluronan was obtained from a calibration curve of hyaluronan versus Alcian blue bound to hyaluronan. Compared with control rabbits, pleural tissue hyaluronan (0.21 +/- 0.04 mg/kg) increased twofold, whereas pleural liquid volume decreased by 30% after 3 h of ventilation. Pleural effusions present 3 h postmortem without ventilation did not change pleural tissue hyaluronan from control values. Thus ventilation-induced pleural liquid shear stress, not increased filtration, was the stimulus for the increased hyaluronan produced from pleural mesothelial cells.

Porous structures of polymer films prepared by spin coating with mixed solvents under humid condition.

PubMed

Park, Min Soo; Joo, Wonchul; Kim, Jin Kon

2006-05-09

We investigate the effects of interfacial energy between water and solvent as well as polymer concentration on the formation of porous structures of polymer films prepared by spin coating of cellulose acetate butyrate (CAB) in mixed solvent of tetrahydrofuran (THF) and chloroform under humid condition. The interfacial energy between water and the solvent was gradually changed by the addition of chloroform to the solvent. At a high polymer concentration (0.15 g/cm3 in THF), porous structures were limited only at the top surfaces of CAB films, regardless of interfacial energies, due to the high viscosity of the solution. At a medium concentration (approximately 0.08 g/cm3 in THF), CAB film had relatively uniform pores at the top surface and very small pores inside the film because of the mixing of the water droplets with THF solution. When chloroform was added to THF, pores at the inner CAB film had a comparable size with those at the top surface because of the reduced degree of the mixing between the water droplets and the mixed solvent. A further decrease in polymer concentration (0.05 g/cm3 in THF) caused the final films to have a two-layer porous structure, and the size of pores at each layer was almost the same.

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

The asparagine-transamidosome from Helicobacter pylori: a dual-kinetic mode in non-discriminating aspartyl-tRNA synthetase safeguards the genetic code

PubMed Central

Fischer, Frédéric; Huot, Jonathan L.; Lorber, Bernard; Diss, Guillaume; Hendrickson, Tamara L.; Becker, Hubert D.; Lapointe, Jacques; Kern, Daniel

2012-01-01

Helicobacter pylori catalyzes Asn-tRNAAsn formation by use of the indirect pathway that involves charging of Asp onto tRNAAsn by a non-discriminating aspartyl-tRNA synthetase (ND-AspRS), followed by conversion of the mischarged Asp into Asn by the GatCAB amidotransferase. We show that the partners of asparaginylation assemble into a dynamic Asn-transamidosome, which uses a different strategy than the Gln-transamidosome to prevent the release of the mischarged aminoacyl-tRNA intermediate. The complex is described by gel-filtration, dynamic light scattering and kinetic measurements. Two strategies for asparaginylation are shown: (i) tRNAAsn binds GatCAB first, allowing aminoacylation and immediate transamidation once ND-AspRS joins the complex; (ii) tRNAAsn is bound by ND-AspRS which releases the Asp-tRNAAsn product much slower than the cognate Asp-tRNAAsp; this kinetic peculiarity allows GatCAB to bind and transamidate Asp-tRNAAsn before its release by the ND-AspRS. These results are discussed in the context of the interrelation between the Asn and Gln-transamidosomes which use the same GatCAB in H. pylori, and shed light on a kinetic mechanism that ensures faithful codon reassignment for Asn. PMID:22362756

The asparagine-transamidosome from Helicobacter pylori: a dual-kinetic mode in non-discriminating aspartyl-tRNA synthetase safeguards the genetic code.

PubMed

Fischer, Frédéric; Huot, Jonathan L; Lorber, Bernard; Diss, Guillaume; Hendrickson, Tamara L; Becker, Hubert D; Lapointe, Jacques; Kern, Daniel

2012-06-01

Helicobacter pylori catalyzes Asn-tRNA(Asn) formation by use of the indirect pathway that involves charging of Asp onto tRNA(Asn) by a non-discriminating aspartyl-tRNA synthetase (ND-AspRS), followed by conversion of the mischarged Asp into Asn by the GatCAB amidotransferase. We show that the partners of asparaginylation assemble into a dynamic Asn-transamidosome, which uses a different strategy than the Gln-transamidosome to prevent the release of the mischarged aminoacyl-tRNA intermediate. The complex is described by gel-filtration, dynamic light scattering and kinetic measurements. Two strategies for asparaginylation are shown: (i) tRNA(Asn) binds GatCAB first, allowing aminoacylation and immediate transamidation once ND-AspRS joins the complex; (ii) tRNA(Asn) is bound by ND-AspRS which releases the Asp-tRNA(Asn) product much slower than the cognate Asp-tRNA(Asp); this kinetic peculiarity allows GatCAB to bind and transamidate Asp-tRNA(Asn) before its release by the ND-AspRS. These results are discussed in the context of the interrelation between the Asn and Gln-transamidosomes which use the same GatCAB in H. pylori, and shed light on a kinetic mechanism that ensures faithful codon reassignment for Asn.

FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data.

PubMed

Manijak, Mieszko P; Nielsen, Henrik B

2011-06-11

Although, systematic analysis of gene annotation is a powerful tool for interpreting gene expression data, it sometimes is blurred by incomplete gene annotation, missing expression response of key genes and secondary gene expression responses. These shortcomings may be partially circumvented by instead matching gene expression signatures to signatures of other experiments. To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700 Arabidopsis microarray experiments. Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. The server is available at http://www.cbs.dtu.dk/services/faro/.

Digital gene expression analysis of the zebra finch genome

PubMed Central

2010-01-01

Background In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates. PMID:20359325

Molecular Dynamics Simulation of Calbindin D9k in Apo, Singly and Doubly Loaded States in Various Side-Chains

NASA Astrophysics Data System (ADS)

Thapa, Mahendra Bahadur

Calbindin D9k (CAB) is a single domain calcium-binding protein and is the smallest members of the calmodulin superfamily, possessing a pair of calcium-binding EF-hands, and structures for all four states have been determined and extensively characterized experimentally. Because of the tremendous advancement in hardware and software computer technologies in recent years, longer and more realistic molecular dynamics (MD) simulations of a protein are possible now in reasonable periods of time. These advances were exploited to generate multiple, all-atom MD simulations of CAB via the AMBER software package, and the resulting trajectories were employed to calculate backbone order parameters of the apo, the singly and the doubly loaded states of calcium in CAB. The results are in very good agreement with corresponding experimental NMR-based (Nuclear Magnetic Resonance spectroscopy) results, and are improved in comparison to those calculated over a decade ago; use of modified force fields played a key role in the observed improvements. The apo state is the most flexible, and the singly loaded and the doubly loaded states are similar, thus supporting positive cooperativity in line with the experimental results. Further, B-factor calculations of backbone atoms for these calcium-binding states of calbindin D9k also support such cooperativity. Although changes in side-chain motions are not necessarily correlated to changes in protein backbone mobility, past studies on the comparison of experimental and simulated methyl side-chain NMR relaxation parameters of CAB for the doubly-loaded state reported significant improvements in the quantitative representation of side-chain motion by MD simulation. In this project, the order parameters for various side chains in apo, singly loaded and doubly loaded states of CAB were calculated. The primary goal of this work was to determine whether or not the allosteric effect of calcium binding, as observed via the backbone order parameters, also extended to the amino acid side chains, and if so, to what extent. Such information could be useful in better understanding the physical basis of cooperative calcium binding in CAB. Most of the residues which provide ligands to bind calcium at the binding sites support positive cooperativity, as observed when Ca-Cß, Cß-C?, C-C bond and C-O bonds of COO groups of aspartic and glutamic acid residues, the C-N bond of the side-chain amide group in asparagine and glutamine residues, and the N-H bonds of amide (NH2) group order parameters were studied. There are only a few residues containing methyl groups that are involved in providing ligands to the calcium, and the studies of order parameters of C-C bond and C-H bond of these methyl groups did not exhibit the cooperativity effect upon calcium binding; the simulated C-C bond order parameter of the methyl group symmetry axis did correlate well with the experimental results for the fully loaded state of CAB (4ICB). Analysis of the MD trajectories using GSATools and MutInf, provided valuable insights into possible pathways for communicating allosteric effects between the two calcium-binding sites of CAB.

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data.

PubMed

Bikel, Shirley; Jacobo-Albavera, Leonor; Sánchez-Muñoz, Fausto; Cornejo-Granados, Fernanda; Canizales-Quinteros, Samuel; Soberón, Xavier; Sotelo-Mundo, Rogerio R; Del Río-Navarro, Blanca E; Mendoza-Vargas, Alfredo; Sánchez, Filiberto; Ochoa-Leyva, Adrian

2017-01-01

In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays. We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6-10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR). From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment. Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments.

Differential gene expression analysis in glioblastoma cells and normal human brain cells based on GEO database.

PubMed

Wang, Anping; Zhang, Guibin

2017-11-01

The differentially expressed genes between glioblastoma (GBM) cells and normal human brain cells were investigated to performed pathway analysis and protein interaction network analysis for the differentially expressed genes. GSE12657 and GSE42656 gene chips, which contain gene expression profile of GBM were obtained from Gene Expression Omniub (GEO) database of National Center for Biotechnology Information (NCBI). The 'limma' data packet in 'R' software was used to analyze the differentially expressed genes in the two gene chips, and gene integration was performed using 'RobustRankAggreg' package. Finally, pheatmap software was used for heatmap analysis and Cytoscape, DAVID, STRING and KOBAS were used for protein-protein interaction, Gene Ontology (GO) and KEGG analyses. As results: i) 702 differentially expressed genes were identified in GSE12657, among those genes, 548 were significantly upregulated and 154 were significantly downregulated (p<0.01, fold-change >1), and 1,854 differentially expressed genes were identified in GSE42656, among the genes, 1,068 were significantly upregulated and 786 were significantly downregulated (p<0.01, fold-change >1). A total of 167 differentially expressed genes including 100 upregulated genes and 67 downregulated genes were identified after gene integration, and the genes showed significantly different expression levels in GBM compared with normal human brain cells (p<0.05). ii) Interactions between the protein products of 101 differentially expressed genes were identified using STRING and expression network was established. A key gene, called CALM3, was identified by Cytoscape software. iii) GO enrichment analysis showed that differentially expressed genes were mainly enriched in 'neurotransmitter:sodium symporter activity' and 'neurotransmitter transporter activity', which can affect the activity of neurotransmitter transportation. KEGG pathway analysis showed that the differentially expressed genes were mainly enriched in 'protein processing in endoplasmic reticulum', which can affect protein processing in endoplasmic reticulum. The results showed that: i) 167 differentially expressed genes were identified from two gene chips after integration; and ii) protein interaction network was established, and GO and KEGG pathway analyses were successfully performed to identify and annotate the key gene, which provide new insights for the studies on GBN at gene level.

Discovery and validation of a glioblastoma co-expressed gene module

PubMed Central

Dunwoodie, Leland J.; Poehlman, William L.; Ficklin, Stephen P.; Feltus, Frank Alexander

2018-01-01

Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors. Among the proneural, neural, mesenchymal, and classical glioblastoma subtypes, these genes are most-highly expressed in the mesenchymal subtype. Furthermore, high expression of these genes is associated with decreased survival across each glioblastoma subtype. These genes are of interest to glioblastoma biology and our gene interaction discovery and validation workflow can be used to discover and validate co-expressed gene modules derived from any co-expression network. PMID:29541392

Discovery and validation of a glioblastoma co-expressed gene module.

PubMed

Dunwoodie, Leland J; Poehlman, William L; Ficklin, Stephen P; Feltus, Frank Alexander

2018-02-16

Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors. Among the proneural, neural, mesenchymal, and classical glioblastoma subtypes, these genes are most-highly expressed in the mesenchymal subtype. Furthermore, high expression of these genes is associated with decreased survival across each glioblastoma subtype. These genes are of interest to glioblastoma biology and our gene interaction discovery and validation workflow can be used to discover and validate co-expressed gene modules derived from any co-expression network.

A Cost Analysis for Life-Cycle Preventive Maintenance, Administrative Storage, and Condition-Based Maintenance for the U.S. Marine Corps Medium Tactical Vehicle Replacement

DTIC Science & Technology

2013-12-04

Table 3. Monthly PMCS Actions and Labor Required Task Hours Task Hours Inspect cab and hood 1.0 Inspect turbocharger 0.5 Inspect fuel tank 0.1 Inspect...Annual PMCS Actions and Labor Required Task Hours Task Hours Inspect cab and hood 1.0 Air intake system 0.2 Inspect fuel Tank 0.1 Inspect turbocharger

"Dammed Taxi Cab"--How Silent Communication in Questionnaires Can Be Understood and Used to Give Voice to Children's Experiences

ERIC Educational Resources Information Center

Alerby, E.; Kostenius, C.

2011-01-01

"Dammed taxi cab"--a 12-year-old boy wrote these words in the margins of a questionnaire, and within this paper they will serve as a point of departure for the discussion of the use of questionnaires as a way to voice children's experiences. The overall aim of this paper is to enable understanding of and discuss the use of questionnaires as a way…

High speed variable delivery helical screw compressor/expander automotive air conditioning and waste heat energy recovery system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gagnon, J.A.; Schaefer, D.D.; Shaw, D.N.

1980-09-02

A compact, helical screw compressor/expander unit is described that is mounted in a vehicle and connected to the vehicle engine driven drive shaft has inlet and outlet ports and a capacity control slide valve and a pressure matching or volume ratio slide valve, respectively, for said ports. A refrigerant loop includes the compressor, a condenser mounted in the path of air flow over the engine and an evaporator mounted in a fresh air/cab return air flow duct for the occupant. Heat pipes thermally connect the cab air flow duct to the engine exhaust system which also bears the vapor boiler.more » Selectively operated damper valves control the fresh air/cab return air for passage selectively over the evaporator coil and the heat pipes as well as the exhaust gas flow over opposite ends of the heat pipes and the vapor boiler.« less

Cardiac Autonomic Balance vs. Cardiac Regulatory Capacity

PubMed Central

Berntson, Gary G.; Norman, Greg J.; Hawkley, Louise C.; Cacioppo, John T.

2013-01-01

The concept of autonomic balance views autonomic states along a bipolar continuum from sympathetic (S) to parasympathetic (P) dominance, whereas regulatory capacity models emphasize overall autonomic flexibility as a marker of the capacity for regulation. These two concepts were evaluated for their utility in characterizing patterns of autonomic control. Measures of P (high frequency heart rate variability, HF) and S (pre-ejection period, PEP) cardiac control were obtained. A measure of cardiac autonomic balance (CAB) was derived as the difference in the normalized P index minus the S index, and a measure of cardiac autonomic regulation (CAR) was derived as the normalized P index plus the S index. Results reveal that CAR, but not CAB, was a significant predictor of the prior occurrence of a myocardial infarction, net of demographic and other variables, whereas CAB, but not CAR, was a significant predictor of concurrent diabetes. PMID:18282204

Improving a workstation in an existing cab by means of a participatory approach: the case of subway operators' workstations.

PubMed

Bellemare, Marie; Beaugrand, Sylvie; Larue, Christian; Champoux, Danièle

2009-01-01

A study was conducted to identify possible solutions for redesigning a subway cab in order to improve the posture of drivers working in a restricted space. The approach used included the participation of a working group comprised of operations, maintenance, and engineering managers as well as several drivers. After 6 meetings in which different simulation techniques were used, the working group proposed changes for increasing the available space inside the cab and three seat designs. The involvement of the actors from the three departments affected by the changes, as well as the operators, throughout the process, was a determining factor in the advancement and acceptance of the projects. The fact that 400 cars are currently in service and must be modified means that it will take several years to implement the modifications in the entire fleet.

Thermal properties and cycling performance of Ca(BH4)2/MgH2 composite for energy storage

NASA Astrophysics Data System (ADS)

Li, Yang; Li, Ping; Tan, Qiwei; Zhang, Zongliang; Wan, Qi; Liu, Zhiwei; Subramanian, Arunprabaharan; Qu, Xuanhui

2018-05-01

Here we report the thermal properties and cycling performance of Ca(BH4)2/MgH2. The reaction enthalpy is 48 kJ mol-1 H2 and equilibrium pressure at 350 °C is 0.4981 MPa. We add NbF5 into Ca(BH4)2/MgH2to figure out the degradation mechanism because of its catalytic ability. Ca(BH4)2/MgH2 follows the dehydrogenation path to form CaH2, CaB6 and Mg. The degradation of Ca(BH4)2/MgH2 composite during cycling is due to the particle aggregation and the reduction of CaB6 product. NbF5 can promote the forming of CaB6 and prevent microstructural coarsening in Ca(BH4)2/MgH2 during cycling, which leads to better reversibility.

Analysis of Vibration and Noise of Construction Machinery Based on Ensemble Empirical Mode Decomposition and Spectral Correlation Analysis Method

NASA Astrophysics Data System (ADS)

Chen, Yuebiao; Zhou, Yiqi; Yu, Gang; Lu, Dan

In order to analyze the effect of engine vibration on cab noise of construction machinery in multi-frequency bands, a new method based on ensemble empirical mode decomposition (EEMD) and spectral correlation analysis is proposed. Firstly, the intrinsic mode functions (IMFs) of vibration and noise signals were obtained by EEMD method, and then the IMFs which have the same frequency bands were selected. Secondly, we calculated the spectral correlation coefficients between the selected IMFs, getting the main frequency bands in which engine vibration has significant impact on cab noise. Thirdly, the dominated frequencies were picked out and analyzed by spectral analysis method. The study result shows that the main frequency bands and dominated frequencies in which engine vibration have serious impact on cab noise can be identified effectively by the proposed method, which provides effective guidance to noise reduction of construction machinery.

Enabling the Tablet Product Development of 5-Fluorocytosine by Conjugate Acid Base Cocrystals.

PubMed

Perumalla, Sathyanarayana R; Paul, Shubhajit; Sun, Changquan C

2016-06-01

5-Fluorocytosine (FC) is a high-dose antifungal drug that challenges the development of a tablet product due to poor solid-state stability and tabletability. Using 2 pharmaceutically acceptable conjugate acid base (CAB) cocrystals of FC with HCl and acesulfame, we have developed commercially viable high loading FC tablets. The tablets were prepared by direct compression using nano-coated microcrystalline cellulose Avicel PH105 as a tablet binder, which provided both excellent tabletability and good flowability. Commercial manufacturability of formulations based on both CAB cocrystals was verified on a compaction simulator. The results from an expedited friability study were used to set the compaction force, which yielded tablets with sufficient mechanical strength and rapid tablet disintegration. This work demonstrates the potential value of CAB cocrystals in drug product development. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Taxicab tipping and sunlight

PubMed Central

2017-01-01

Does the level of sunlight affect the tipping percentage in taxicab rides in New York City? We examined this question using data on 13.82 million cab rides from January to October in 2009 in New York City combined with data on hourly levels of solar radiation. We found a small but statistically significant positive relationship between sunlight and tipping, with an estimated tipping increase of 0.5 to 0.7 percentage points when transitioning from a dark sky to full sunshine. The findings are robust to two-way clustering of standard errors based on hour-of-the-day and day-of-the-year and controlling for day-of-the-year, month-of-the-year, cab driver fixed effects, weather conditions, and ride characteristics. The NYC cab ride context is suitable for testing the association between sunlight and tipping due to the largely random assignment of riders to drivers, direct exposure to sunlight, and low confounding from variation in service experiences. PMID:28594917

Taxicab tipping and sunlight.

PubMed

Devaraj, Srikant; Patel, Pankaj C

2017-01-01

Does the level of sunlight affect the tipping percentage in taxicab rides in New York City? We examined this question using data on 13.82 million cab rides from January to October in 2009 in New York City combined with data on hourly levels of solar radiation. We found a small but statistically significant positive relationship between sunlight and tipping, with an estimated tipping increase of 0.5 to 0.7 percentage points when transitioning from a dark sky to full sunshine. The findings are robust to two-way clustering of standard errors based on hour-of-the-day and day-of-the-year and controlling for day-of-the-year, month-of-the-year, cab driver fixed effects, weather conditions, and ride characteristics. The NYC cab ride context is suitable for testing the association between sunlight and tipping due to the largely random assignment of riders to drivers, direct exposure to sunlight, and low confounding from variation in service experiences.

Gender-Specific Gene Expression in Post-Mortem Human Brain: Localization to Sex Chromosomes

PubMed Central

Vawter, Marquis P; Evans, Simon; Choudary, Prabhakara; Tomita, Hiroaki; Meador-Woodruff, Jim; Molnar, Margherita; Li, Jun; Lopez, Juan F; Myers, Rick; Cox, David; Watson, Stanley J; Akil, Huda; Jones, Edward G; Bunney, William E

2011-01-01

Gender differences in brain development and in the prevalence of neuropsychiatric disorders such as depression have been reported. Gender differences in human brain might be related to patterns of gene expression. Microarray technology is one useful method for investigation of gene expression in brain. We investigated gene expression, cell types, and regional expression patterns of differentially expressed sex chromosome genes in brain. We profiled gene expression in male and female dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum using the Affymetrix oligonucleotide microarray platform. Differentially expressed genes between males and females on the Y chromosome (DBY, SMCY, UTY, RPS4Y, and USP9Y) and X chromosome (XIST) were confirmed using real-time PCR measurements. In situ hybridization confirmed the differential expression of gender-specific genes and neuronal expression of XIST, RPS4Y, SMCY, and UTY in three brain regions examined. The XIST gene, which silences gene expression on regions of the X chromosome, is expressed in a subset of neurons. Since a subset of neurons express gender-specific genes, neural subpopulations may exhibit a subtle sexual dimorphism at the level of differences in gene regulation and function. The distinctive pattern of neuronal expression of XIST, RPS4Y, SMCY, and UTY and other sex chromosome genes in neuronal subpopulations may possibly contribute to gender differences in prevalence noted for some neuropsychiatric disorders. Studies of the protein expression of these sex- chromosome-linked genes in brain tissue are required to address the functional consequences of the observed gene expression differences. PMID:14583743

Non-Compliance and Follow-Up in Swedish Official and Private Animal Welfare Control of Dairy Cows

PubMed Central

Hultgren, Jan; Röcklinsberg, Helena; Wahlberg, Birgitta

2018-01-01

Simple Summary In many cases, different animal welfare inspections are taking place at an animal farm over time, as the farmer has to comply with both the legislation and with various private standards. In this study, we compared official inspections carried out by CAB (the County Administrative Board, a governmental agency) with private inspections carried out by Arla Foods (a private company) on dairy farms in one Swedish county. For example, we looked at seasonal effects and compared the incidence of different non-compliances. This study shows that long time periods were sometimes allowed for correction, that follow-up systems are diverse, and that there were differences in the inspection result between CAB and Arla due to different focuses during the inspections. Dirty dairy cattle were, however, a common non-compliance found by both CAB and Arla. Tie-stall housing and winter season (Dec–Feb) were risk factors for non-compliance, while the risk was lower for both CAB and Arla to find non-compliances at organic farms compared to conventional farms. We conclude that the presence of both similarities and differences between different control systems underlines the need for transparency, predictability, and clarity of inspections. Abstract Farmers often have to comply with several sets of animal welfare regulations, since private standards have been developed in addition to legislation. Using an epidemiological approach, we analysed protocols from animal welfare inspections carried out in Swedish dairy herds by the County Administrative Board (CAB; official control of legislation) and by the dairy company Arla Foods (private control of Arlagården standard) during 2010–2013 in the county of Västra Götaland. CAB and Arla inspections were not carried out simultaneously. We aimed to identify common non-compliances, quantify risk factors of non-compliance, and investigate if non-compliances were based on animal-, resource-, or management-based requirements, as well as determining the time period allowed for achieving compliance. Non-compliance was found in 58% of CAB cases, and 51% of Arla cases (each case comprising a sequence of one or several inspections). Dirty dairy cattle was one of the most frequent non-compliances in both control systems. However, the differences in control results were large, suggesting a difference in focus between the two systems. Tie-stall housing and winter season (Dec–Feb) were common risk factors for non-compliance, and overall organic farms had a lower predicted number of non-compliances compared to conventional farms. The presence of both similarities and differences between the systems underlines the need for transparency, predictability, and clarity of inspections. PMID:29738491

Gene expression variability in human hepatic drug metabolizing enzymes and transporters.

PubMed

Yang, Lun; Price, Elvin T; Chang, Ching-Wei; Li, Yan; Huang, Ying; Guo, Li-Wu; Guo, Yongli; Kaput, Jim; Shi, Leming; Ning, Baitang

2013-01-01

Interindividual variability in the expression of drug-metabolizing enzymes and transporters (DMETs) in human liver may contribute to interindividual differences in drug efficacy and adverse reactions. Published studies that analyzed variability in the expression of DMET genes were limited by sample sizes and the number of genes profiled. We systematically analyzed the expression of 374 DMETs from a microarray data set consisting of gene expression profiles derived from 427 human liver samples. The standard deviation of interindividual expression for DMET genes was much higher than that for non-DMET genes. The 20 DMET genes with the largest variability in the expression provided examples of the interindividual variation. Gene expression data were also analyzed using network analysis methods, which delineates the similarities of biological functionalities and regulation mechanisms for these highly variable DMET genes. Expression variability of human hepatic DMET genes may affect drug-gene interactions and disease susceptibility, with concomitant clinical implications.

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data

PubMed Central

Bikel, Shirley; Jacobo-Albavera, Leonor; Sánchez-Muñoz, Fausto; Cornejo-Granados, Fernanda; Canizales-Quinteros, Samuel; Soberón, Xavier; Sotelo-Mundo, Rogerio R.; del Río-Navarro, Blanca E.; Mendoza-Vargas, Alfredo; Sánchez, Filiberto

2017-01-01

Background In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays. Methods We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6–10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR). Results From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment. Discussion Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments. PMID:29230367

Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior.

PubMed

Schrader, Lukas; Helanterä, Heikki; Oettler, Jan

2017-03-01

Plastic gene expression underlies phenotypic plasticity and plastically expressed genes evolve under different selection regimes compared with ubiquitously expressed genes. Social insects are well-suited models to elucidate the evolutionary dynamics of plastic genes for their genetically and environmentally induced discrete polymorphisms. Here, we study the evolution of plastically expressed genes in the ant Cardiocondyla obscurior-a species that produces two discrete male morphs in addition to the typical female polymorphism of workers and queens. Based on individual-level gene expression data from 28 early third instar larvae, we test whether the same evolutionary dynamics that pertain to plastically expressed genes in adults also pertain to genes with plastic expression during development. In order to quantify plasticity of gene expression over multiple contrasts, we develop a novel geometric measure. For genes expressed during development, we show that plasticity of expression is positively correlated with evolutionary rates. We furthermore find a strong correlation between expression plasticity and expression variation within morphs, suggesting a close link between active and passive plasticity of gene expression. Our results support the notion of relaxed selection and neutral processes as important drivers in the evolution of adaptive plasticity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Analysis of multiplex gene expression maps obtained by voxelation.

PubMed

An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

2009-04-29

Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum. The experimental results confirm the hypothesis that genes with similar gene expression maps might have similar gene functions. The voxelation data takes into account the location information of gene expression level in mouse brain, which is novel in related research. The proposed approach can potentially be used to predict gene functions and provide helpful suggestions to biologists.

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.

PubMed

Li, Lin; Briskine, Roman; Schaefer, Robert; Schnable, Patrick S; Myers, Chad L; Flagel, Lex E; Springer, Nathan M; Muehlbauer, Gary J

2016-11-04

Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant subgenome. However, the landscape of co-expression network divergence of duplicate genes in maize is still largely uncharacterized. To address the consequence of gene duplication on co-expression network divergence, we developed a gene co-expression network from RNA-seq data derived from 64 different tissues/stages of the maize reference inbred-B73. WGD, tandem and inserted gene duplications exhibited distinct regulatory divergence. Inserted duplicate genes were more likely to be singletons in the co-expression networks, while WGD duplicate genes were likely to be co-expressed with other genes. Tandem duplicate genes were enriched in the co-expression pattern where co-expressed genes were nearly identical for the duplicates in the network. Older gene duplications exhibit more extensive co-expression variation than younger duplications. Overall, non-syntenic genes primarily from inserted duplications show more co-expression divergence. Also, such enlarged co-expression divergence is significantly related to duplication age. Moreover, subgenome dominance was not observed in the co-expression networks - maize1 and maize2 exhibit similar levels of intra subgenome correlations. Intriguingly, the level of inter subgenome co-expression was similar to the level of intra subgenome correlations, and genes from specific subgenomes were not likely to be the enriched in co-expression network modules and the hub genes were not predominantly from any specific subgenomes in maize. Our work provides a comprehensive analysis of maize co-expression network divergence for three different types of gene duplications and identifies potential relationships between duplication types, duplication ages and co-expression consequences.

Seasonal variability in size-segregated airborne bacterial particles and their characterization at different source-sites.

PubMed

Agarwal, Smita

2017-05-01

Size-segregated aerosol samplings were carried out near the potential sources of airborne biological particles i.e. at a landfill site, an agricultural field and a road side restaurant-cluster site in winter, spring and summer seasons during 2013-2015 in New Delhi. The culturable airborne bacterial (CAB) concentrations showed significant seasonal variation from higher to moderate in spring and winter seasons and lowest during summer. Highest CAB concentrations were observed at the Okhla landfill site followed by restaurant-cluster area and agriculture site. The CAB particles showed bimodal size distribution, abundant in the size ranges of 1.1-2.1, 2.1-3.3 and 4.7-5.8 μm. However, substantial concentrations were also observed in the size bins of 0.43-0.65 and <0.43 μm, which are important for cloud condensation nuclei (CCN) activity of aerosols in addition to their adverse health effects. In spring, bacterial particles were also maximized in size ranges between 5.8 and >9.0 μm. Fine mode proportions of CAB were found to be higher in winter than other two seasons. Bacterial identification was done by 16s rDNA sequencing, and most abundant identified strains were Bacillus cereus (16%), Bacillus licheniformis (11%), Bacillus thuringiensis (9%), Micrococcus sp. (7%) and Acinetobacter sp. (9%).

Tissue Non-Specific Genes and Pathways Associated with Diabetes: An Expression Meta-Analysis.

PubMed

Mei, Hao; Li, Lianna; Liu, Shijian; Jiang, Fan; Griswold, Michael; Mosley, Thomas

2017-01-21

We performed expression studies to identify tissue non-specific genes and pathways of diabetes by meta-analysis. We searched curated datasets of the Gene Expression Omnibus (GEO) database and identified 13 and five expression studies of diabetes and insulin responses at various tissues, respectively. We tested differential gene expression by empirical Bayes-based linear method and investigated gene set expression association by knowledge-based enrichment analysis. Meta-analysis by different methods was applied to identify tissue non-specific genes and gene sets. We also proposed pathway mapping analysis to infer functions of the identified gene sets, and correlation and independent analysis to evaluate expression association profile of genes and gene sets between studies and tissues. Our analysis showed that PGRMC1 and HADH genes were significant over diabetes studies, while IRS1 and MPST genes were significant over insulin response studies, and joint analysis showed that HADH and MPST genes were significant over all combined data sets. The pathway analysis identified six significant gene sets over all studies. The KEGG pathway mapping indicated that the significant gene sets are related to diabetes pathogenesis. The results also presented that 12.8% and 59.0% pairwise studies had significantly correlated expression association for genes and gene sets, respectively; moreover, 12.8% pairwise studies had independent expression association for genes, but no studies were observed significantly different for expression association of gene sets. Our analysis indicated that there are both tissue specific and non-specific genes and pathways associated with diabetes pathogenesis. Compared to the gene expression, pathway association tends to be tissue non-specific, and a common pathway influencing diabetes development is activated through different genes at different tissues.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

PubMed

Hurst, Laurence D; Ghanbarian, Avazeh T; Forrest, Alistair R R; Huminiecki, Lukasz

2015-12-01

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

PubMed Central

Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R. R.; Huminiecki, Lukasz

2015-01-01

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution. PMID:26685068

Validating internal controls for quantitative plant gene expression studies.

PubMed

Brunner, Amy M; Yakovlev, Igor A; Strauss, Steven H

2004-08-18

Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression levels for reference genes are adequately consistent among the samples used, nor compare alternative genes to assess which are most reliable for the experimental conditions analyzed. Using real-time RT-PCR to study the expression of 10 poplar (genus Populus) housekeeping genes, we demonstrate a simple method for determining the degree of stability of gene expression over a set of experimental conditions. Based on a traditional method for analyzing the stability of varieties in plant breeding, it defines measures of gene expression stability from analysis of variance (ANOVA) and linear regression. We found that the potential internal control genes differed widely in their expression stability over the different tissues, developmental stages and environmental conditions studied. Our results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression. The method we demonstrated facilitates statistical and graphical evaluation of gene expression stability. Selection of the best reference gene for a given set of experimental conditions should enable detection of biologically significant changes in gene expression that are too small to be revealed by less precise methods, or when highly variable reference genes are unknowingly used in real-time RT-PCR experiments.

Lanthanide, yttrium, and zirconium anomalies in the Fire Clay coal bed, Eastern Kentucky

USGS Publications Warehouse

Hower, J.C.; Ruppert, L.F.; Eble, C.F.

1999-01-01

The Fire Clay coal bed in the Central Appalachian basin region contains a laterally-persistent tonstein that is found in the coal throughout most of its areal extent. The tonstein contains an array of minerals, including sanidine, ??-quartz, anatase and euhedral zircon, thhat constitutes strong evidence for a volcanic origin of the parting. For this study, five samples of the tonstein and four sets of coal samples underlying the tonstein were collected from five sites in eastern Kentucky. Inductively coupled plasma-mass spectroscopy (ICP-MS) analysis of the tonstein and underlying coal collected from four sites in eastern Kentucky show that although Zr concentrations are high in the tonstein (570-1820 ppm on a coal-ash basis (cab)), they are highest in the coal directly underlying the tonstein (2870-4540 ppm (cab)). A similar enrichment pattern is observed in the concentration of Y plus the sum of the rare earth elements (Y + ??REE): total Y + ??REE concentrations in the five tonstein samples range from 511 to 565 ppm (cab). However, Y + ??REE contents are highest in the coals directly underlying the tonsteins: values range from 1965 to 4198 ppm (cab). Scanning electron microscopy of samples from coal which directly underlies two of the tonstein samples show that REE-rich phosphate, tentatively identified as monazite, commonly infills cracks in clays and cells in clarain and vitrain. Zircon is rare and commonly subhedral. On the basis of coal chemistry and grain morphology, we suggest that volcanic components in the tonstein were leached by ground water. The leachate, rich in Y and REE precipitated as authigenic mineral phases in the underlying coal.The Fire Clay coal bed in the Central Appalachian basin region contains a laterally-persistent tonstein that is found in the coal throughout most of its areal extent. The tonstein contains an array of minerals, including sanidine, ??-quartz, anatase and euhedral zircon, that constitutes strong evidence for a volcanic origin of the parting. For this study, five samples of the tonstein and four sets of coal samples underlying the tonstein were collected from five sites in eastern Kentucky. Inductively coupled plasma-mass spectroscopy (ICP-MS) analysis of the tonstein and underlying coal collected from four sites in eastern Kentucky show that although Zr concentrations are high in the tonstein (570-1820 ppm on a coal-ash basis (cab)), they are highest in the coal directly underlying the tonstein (2870-4540 ppm (cab)). A similar enrichment pattern is observed in the concentration of Y plus the sum of the rare earth elements (Y+???REE): total Y+???REE concentrations in the five tonstein samples range from 511 to 565 ppm (cab). However, Y+???REE contents are highest in the coals directly underlying the tonsteins: values range from 1965 to 4198 ppm (cab). Scanning electron microscopy of samples from coal which directly underlies two of the tonstein samples show that REE-rich phosphate, tentatively identified as monazite, commonly infills cracks in clays and cells in clarain and vitrain. Zircon is rare and commonly subhedral. On the basis of coal chemistry and grain morphology, we suggest that volcanic components in the tonstein were leached by ground water. The leachate, rich in Y and REE precipitated as authigenic mineral phases in the underlying coal.

General statistics of stochastic process of gene expression in eukaryotic cells.

PubMed Central

Kuznetsov, V A; Knott, G D; Bonner, R F

2002-01-01

Thousands of genes are expressed at such very low levels (< or =1 copy per cell) that global gene expression analysis of rarer transcripts remains problematic. Ambiguity in identification of rarer transcripts creates considerable uncertainty in fundamental questions such as the total number of genes expressed in an organism and the biological significance of rarer transcripts. Knowing the distribution of the true number of genes expressed at each level and the corresponding gene expression level probability function (GELPF) could help resolve these uncertainties. We found that all observed large-scale gene expression data sets in yeast, mouse, and human cells follow a Pareto-like distribution model skewed by many low-abundance transcripts. A novel stochastic model of the gene expression process predicts the universality of the GELPF both across different cell types within a multicellular organism and across different organisms. This model allows us to predict the frequency distribution of all gene expression levels within a single cell and to estimate the number of expressed genes in a single cell and in a population of cells. A random "basal" transcription mechanism for protein-coding genes in all or almost all eukaryotic cell types is predicted. This fundamental mechanism might enhance the expression of rarely expressed genes and, thus, provide a basic level of phenotypic diversity, adaptability, and random monoallelic expression in cell populations. PMID:12136033

The changes of gene expression profiling between segmental vitiligo, generalized vitiligo and healthy individual.

PubMed

Wang, Ping; Li, Yong; Nie, Huiqiong; Zhang, Xiaoyan; Shao, Qiongyan; Hou, Xiuli; Xu, Wen; Hong, Weisong; Xu, Aie

2016-10-01

Vitiligo is a common acquired depigmentation skin disease characterized by loss or dysfunction of melanocytes within the skin lesion, but its pathologenesis is far from lucid. The gene expression profiling of segmental vitiligo (SV) and generalized vitiligo (GV) need further investigation. To better understanding the common and distinct factors, especially in the view of gene expression profile, which were involved in the diseases development and maintenance of segmental vitiligo (SV) and generalized vitiligo (GV). Peripheral bloods were collected from SV, GV and healthy individual (HI), followed by leukocytes separation and total RNA extraction. The high-throughput whole genome expression microarrays were used to assay the gene expression profiles between HI, SV and GV. Bioinformatics tools were employed to annotated the biological function of differently expressed genes. Quantitative PCR assay was used to validate the gene expression of array. Compared to HI, 239 over-expressed genes and 175 down-expressed genes detected in SV, 688 over-expressed genes and 560 down-expressed genes were found in GV, following the criteria of log2 (fold change)≥0.585 and P value<0.05. In these differently expressed genes, 60 over-expressed genes and 60 down-expressed genes had similar tendency in SV and GV. Compared to SV, 223 genes were up regulated and 129 genes were down regulated in GV. In the SV with HI as control, the differently expressed genes were mainly involved in the adaptive immune response, cytokine-cytokine receptor interaction, chemokine signaling, focal adhesion and sphingolipid metabolism. The differently expressed genes between GV and HI were mainly involved in the innate immune, autophagy, apoptosis, melanocyte biology, ubiquitin mediated proteolysis and tyrosine metabolism, which was different from SV. While the differently expressed genes between SV and GV were mainly involved in the metabolism pathway of purine, pyrimidine, glycolysis and sphingolipid. Above results suggested that they not only shared part bio-process and signal pathway, but more important, they utilized different biological mechanism in their pathogenesis and maintenance. Our results provide a comprehensive view on the gene expression profiling change between SV and GV especially in the side of leukocytes, and may facilitate the future study on their molecular mechanism and theraputic targets. Copyright © 2016 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights reserved.

Mechanical Demolition of Buildings with Concrete Asbestos Board Siding: Methodology, Precautions, and Results at the Hanford Central Plateau - 12417

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kehler, Kurt

Since the start of its contract in 2008, the CH2M Hill Plateau Remediation Company (CH2M HILL) has demolished 25 buildings with concrete asbestos board (CAB) siding using mechanical means. While the asbestos contained in CAB siding is not friable in its manufactured form, concerns persist that mechanical methods of demolition have the potential to render the asbestos friable and airborne, therefore posing a health risk to demolition workers and the public. CH2M HILL's experience demonstrates that when carefully managed, mechanical demolition of CAB siding can be undertaken safely, successfully, and in compliance with regulatory requirements for the disposal of Classmore » II Asbestos-Containing Material (ACM). While the number of buildings demolished at Hanford and the number of samples collected does not make a conclusive argument that CAB cannot be made friable with normal demolition techniques, it certainly provides a significant body of evidence for the success of the approach. Of course, there are many factors that affect how to demolish a structure and dispose of the waste. These factors will impact the success depending on each site. The most obvious factors which contribute to this success at Hanford are: 1. The availability of onsite waste disposal where the handling and cost of asbestos-containing waste is not much different than other potentially contaminated waste. Therefore, segregation of demolition debris from the potential asbestos contamination is not necessary from a debris handling or asbestos disposal aspect. 2. The space between structures is typically significant enough to allow for large exclusion zones. There are not many restrictions due to cohabitation issues or potential contamination of adjacent facilities. 3. The willingness of the regulators and client to understand the industrial safety issues associated with manual CAB removal. (authors)« less

DEMOLISHING A COLD WARE ERA FULE STORAGE BASIN SUPERSTRUCTURE LADEN WITH ASBESTOS

DOE Office of Scientific and Technical Information (OSTI.GOV)

LLOYD ER; STEVENS JM; DAGAN EB

The K East (KE) Basin facilities are located near the north end of the Hanford Site's 100 K area. The facilities were built in 1950 as part of the KE Reactor complex and constructed within 400 meters of the Columbia River, which is the largest river in the Pacific Northwest and by volume the fourth largest river in the United States. The basin, located adjacent to the reactor, was used for the underwater storage of irradiated nuclear fuel discharged from the reactor. The basin was covered by a superstructure comprising steel columns and beams, concrete, and cement asbestos board (CAB)more » siding. The project's mission was to complete demolition of the structure over the KE Basin within six months of turnover from facility deactivation activities. The demolition project team applied open-air demolition techniques to bring the facility to slab-on-grade. Several innovative techniques were used to control contamination and maintain contamination control within the confines of the demolition exclusion zone. The techniques, which focused on a defense-in-depth approach, included spraying fixatives on interior and exterior surfaces before demolition began; applying fixatives during the demolition; misting using a fine spray of water during demolition; and demolishing the facility systematically. Another innovative approach that made demolition easier was to demolish the building with the non-friable CAB remaining in place. The CAB siding covered the exterior of the building and portions of the interior walls, and was an integral part of the multiple-layered roof. The project evaluated the risks involved in removing the CAB material in a radiologically contaminated environment and determined that radiological dose rates and exposure to radiological contamination and industrial hazards would be significantly reduced by using heavy equipment to remove the CAB during demolition. The ability to perform this demolition safely and without spreading contamination (radiological or asbestos) demonstrates that contaminated structures can be torn down successfully using similar open-air demolition techniques.« less

DEMOLISHING A COLD-WAR-ERA FUEL STORAGE BASIN SUPERSTRUCTURE LADEN WITH ASBESTOS

DOE Office of Scientific and Technical Information (OSTI.GOV)

LLOYD ER; ORGILL TK; DAGAN EB

The K East (KE) Basin facilities are located near the north end of the Hanford Site's 100 K area. The facilities were built in 1950 as part of the KE Reactor complex and constructed within 400 meters of the Columbia River, which is the largest river in the Pacific Northwest and by volume the fourth largest river in the United States. The basin, located adjacent to the reactor, was used for the underwater storage of irradiated nuclear fuel discharged from the reactor. The basin was covered by a superstructure comprising steel columns and beams, concrete, and cement asbestos board (CAB)more » siding. The project's mission was to complete demolition of the structure over the K East basin within six months of tumover from facility deactivation activities. The demolition project team implemented open-air demolition techniques to demolish the facility to slab-on-grade. Several innovative techniques were used to control contamination and maintain contamination control within the confines of the demolition exclusion zone. The techniques, which focused on a defense-in-depth approach, included spraying fixatives on interior and exterior surfaces before demolition began; applying fixatives; misting using a fine spray of water during demolition; and demolishing the facility systematically. Another innovation that aided demolition was to demolish the building with the non-friable CAB remaining in place. The CAB siding covered the exterior of the building, portions of the interior walls, and was an integral part of the multiple layered roof. The project evaluated the risks involved in removing the CAB material in a radiologically contaminated environment and determined that radiological dose rates and exposure to radiological contamination and industrial hazards would be significantly reduced by removing the CAB during demolition using heavy equipment. The ability to perform this demolition safely and without spreading contamination (radiological or asbestos) demonstrates that similar open-air demolition ofcontaminated structures can be performed successfully.« less

Top-down estimate of methane emissions in California using a mesoscale inverse modeling technique: The South Coast Air Basin

DOE PAGES

Cui, Yu Yan; Brioude, Jerome; McKeen, Stuart A.; ...

2015-07-28

Methane (CH 4) is the primary component of natural gas and has a larger global warming potential than CO 2. Some recent top-down studies based on observations showed CH 4 emissions in California's South Coast Air Basin (SoCAB) were greater than those expected from population-apportioned bottom-up state inventories. In this study, we quantify CH 4 emissions with an advanced mesoscale inverse modeling system at a resolution of 8 km × 8 km, using aircraft measurements in the SoCAB during the 2010 Nexus of Air Quality and Climate Change campaign to constrain the inversion. To simulate atmospheric transport, we use themore » FLEXible PARTicle-Weather Research and Forecasting (FLEXPART-WRF) Lagrangian particle dispersion model driven by three configurations of the Weather Research and Forecasting (WRF) mesoscale model. We determine surface fluxes of CH 4 using a Bayesian least squares method in a four-dimensional inversion. Simulated CH4 concentrations with the posterior emission inventory achieve much better correlations with the measurements (R2 = 0.7) than using the prior inventory (U.S. Environmental Protection Agency's National Emission Inventory 2005, R 2 = 0.5). The emission estimates for CH 4 in the posterior, 46.3 ± 9.2 Mg CH 4/h, are consistent with published observation-based estimates. Changes in the spatial distribution of CH 4 emissions in the SoCAB between the prior and posterior inventories are discussed. Missing or underestimated emissions from dairies, the oil/gas system, and landfills in the SoCAB seem to explain the differences between the prior and posterior inventories. Furthermore, we estimate that dairies contributed 5.9 ± 1.7 Mg CH 4/h and the two sectors of oil and gas industries (production and downstream) and landfills together contributed 39.6 ± 8.1 Mg CH 4/h in the SoCAB.« less

Identification of reference genes in human myelomonocytic cells for gene expression studies in altered gravity.

PubMed

Thiel, Cora S; Hauschild, Swantje; Tauber, Svantje; Paulsen, Katrin; Raig, Christiane; Raem, Arnold; Biskup, Josefine; Gutewort, Annett; Hürlimann, Eva; Unverdorben, Felix; Buttron, Isabell; Lauber, Beatrice; Philpot, Claudia; Lier, Hartwin; Engelmann, Frank; Layer, Liliana E; Ullrich, Oliver

2015-01-01

Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes ("housekeeping genes") are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity.

Adaptation of Musca domestica L. Field Population to Laboratory Breeding Causes Transcriptional Alterations

PubMed Central

Højland, Dorte H.; Jensen, Karl-Martin Vagn; Kristensen, Michael

2014-01-01

Background The housefly, Musca domestica, has developed resistance to most insecticides applied for its control. Expression of genes coding for detoxification enzymes play a role in the response of the housefly when encountered by a xenobiotic. The highest level of constitutive gene expression of nine P450 genes was previously found in a newly-collected susceptible field population in comparison to three insecticide-resistant laboratory strains and a laboratory reference strain. Results We compared gene expression of five P450s by qPCR as well as global gene expression by RNAseq in the newly-acquired field population (845b) in generation F1, F13 and F29 to test how gene expression changes following laboratory adaption. Four (CYP6A1, CYP6A36, CYP6D3, CYP6G4) of five investigated P450 genes adapted to breeding by decreasing expression. CYP6D1 showed higher female expression in F29 than in F1. For males, about half of the genes accessed in the global gene expression were up-regulated in F13 and F29 in comparison with the F1 population. In females, 60% of the genes were up-regulated in F13 in comparison with F1, while 33% were up-regulated in F29. Forty potential P450 genes were identified. In most cases, P450 gene expression was decreased in F13 flies in comparison with F1. Gene expression then increased from F13 to F29 in males and decreased further in females. Conclusion The global gene expression changes massively during adaptation to laboratory breeding. In general, global expression decreased as a result of laboratory adaption in males, while female expression was not unidirectional. Expression of P450 genes was in general down-regulated as a result of laboratory adaption. Expression of hexamerin, coding for a storage protein was increased, while gene expression of genes coding for amylases decreased. This suggests a major impact of the surrounding environment on gene response to xenobiotics and genetic composition of housefly strains. PMID:24489682

An RNA-Seq based gene expression atlas of the common bean.

PubMed

O'Rourke, Jamie A; Iniguez, Luis P; Fu, Fengli; Bucciarelli, Bruna; Miller, Susan S; Jackson, Scott A; McClean, Philip E; Li, Jun; Dai, Xinbin; Zhao, Patrick X; Hernandez, Georgina; Vance, Carroll P

2014-10-06

Common bean (Phaseolus vulgaris) is grown throughout the world and comprises roughly 50% of the grain legumes consumed worldwide. Despite this, genetic resources for common beans have been lacking. Next generation sequencing, has facilitated our investigation of the gene expression profiles associated with biologically important traits in common bean. An increased understanding of gene expression in common bean will improve our understanding of gene expression patterns in other legume species. Combining recently developed genomic resources for Phaseolus vulgaris, including predicted gene calls, with RNA-Seq technology, we measured the gene expression patterns from 24 samples collected from seven tissues at developmentally important stages and from three nitrogen treatments. Gene expression patterns throughout the plant were analyzed to better understand changes due to nodulation, seed development, and nitrogen utilization. We have identified 11,010 genes differentially expressed with a fold change ≥ 2 and a P-value < 0.05 between different tissues at the same time point, 15,752 genes differentially expressed within a tissue due to changes in development, and 2,315 genes expressed only in a single tissue. These analyses identified 2,970 genes with expression patterns that appear to be directly dependent on the source of available nitrogen. Finally, we have assembled this data in a publicly available database, The Phaseolus vulgaris Gene Expression Atlas (Pv GEA), http://plantgrn.noble.org/PvGEA/ . Using the website, researchers can query gene expression profiles of their gene of interest, search for genes expressed in different tissues, or download the dataset in a tabular form. These data provide the basis for a gene expression atlas, which will facilitate functional genomic studies in common bean. Analysis of this dataset has identified genes important in regulating seed composition and has increased our understanding of nodulation and impact of the nitrogen source on assimilation and distribution throughout the plant.

Particle damping applied research on mining dump truck vibration control

NASA Astrophysics Data System (ADS)

Song, Liming; Xiao, Wangqiang; Guo, Haiquan; Yang, Zhe; Li, Zeguang

2018-05-01

Vehicle vibration characteristics has become an important evaluation indexes of mining dump truck. In this paper, based on particle damping technology, mining dump truck vibration control was studied by combining the theoretical simulation with actual testing, particle damping technology was successfully used in mining dump truck cab vibration control. Through testing results analysis, with a particle damper, cab vibration was reduced obviously, the methods and basis were provided for vehicle vibration control research and particle damping technology application.

Analysis of bHLH coding genes using gene co-expression network approach.

PubMed

Srivastava, Swati; Sanchita; Singh, Garima; Singh, Noopur; Srivastava, Gaurava; Sharma, Ashok

2016-07-01

Network analysis provides a powerful framework for the interpretation of data. It uses novel reference network-based metrices for module evolution. These could be used to identify module of highly connected genes showing variation in co-expression network. In this study, a co-expression network-based approach was used for analyzing the genes from microarray data. Our approach consists of a simple but robust rank-based network construction. The publicly available gene expression data of Solanum tuberosum under cold and heat stresses were considered to create and analyze a gene co-expression network. The analysis provide highly co-expressed module of bHLH coding genes based on correlation values. Our approach was to analyze the variation of genes expression, according to the time period of stress through co-expression network approach. As the result, the seed genes were identified showing multiple connections with other genes in the same cluster. Seed genes were found to be vary in different time periods of stress. These analyzed seed genes may be utilized further as marker genes for developing the stress tolerant plant species.

Inhibition of the light-independent synthesis of chlorophyll in pine cotyledons at low temperature.

PubMed

Muramatsu, S; Kojima, K; Igasaki, T; Azumi, Y; Shinohara, K

2001-08-01

Cotyledons of Japanese black pine (Pinus thunbergii) were yellow when they developed in darkness at 8 degrees C since the light-independent synthesis of chlorophyll was almost completely inhibited in these cotyledons. The level of chlorophyll in dark-grown cotyledons was less than one-twentieth of that in light-grown cotyledons at the same temperature. In the yellow cotyledons, levels of transcripts of cab, rbcS, rbcL and psbA genes were quite high. The large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase were also detected at relatively high levels in yellow cotyledons. However, the accumulation of the two apoproteins of the light-harvesting chlorophyll a/b-binding protein of PSII was limited because of the limited supply of chlorophyll.

Validating internal controls for quantitative plant gene expression studies

PubMed Central

Brunner, Amy M; Yakovlev, Igor A; Strauss, Steven H

2004-01-01

Background Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression levels for reference genes are adequately consistent among the samples used, nor compare alternative genes to assess which are most reliable for the experimental conditions analyzed. Results Using real-time RT-PCR to study the expression of 10 poplar (genus Populus) housekeeping genes, we demonstrate a simple method for determining the degree of stability of gene expression over a set of experimental conditions. Based on a traditional method for analyzing the stability of varieties in plant breeding, it defines measures of gene expression stability from analysis of variance (ANOVA) and linear regression. We found that the potential internal control genes differed widely in their expression stability over the different tissues, developmental stages and environmental conditions studied. Conclusion Our results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression. The method we demonstrated facilitates statistical and graphical evaluation of gene expression stability. Selection of the best reference gene for a given set of experimental conditions should enable detection of biologically significant changes in gene expression that are too small to be revealed by less precise methods, or when highly variable reference genes are unknowingly used in real-time RT-PCR experiments. PMID:15317655

Characterization of basal gene expression trends over a diurnal cycle in Xiphophorus maculatus skin, brain and liver.

PubMed

Lu, Yuan; Reyes, Jose; Walter, Sean; Gonzalez, Trevor; Medrano, Geraldo; Boswell, Mikki; Boswell, William; Savage, Markita; Walter, Ronald

2018-06-01

Evolutionarily conserved diurnal circadian mechanisms maintain oscillating patterns of gene expression based on the day-night cycle. Xiphophorus fish have been used to evaluate transcriptional responses after exposure to various light sources and it was determined that each source incites distinct genetic responses in skin tissue. However, basal expression levels of genes that show oscillating expression patterns in day-night cycle, may affect the outcomes of such experiments, since basal gene expression levels at each point in the circadian path may influence the profile of identified light responsive genes. Lack of knowledge regarding diurnal fluctuations in basal gene expression patterns may confound the understanding of genetic responses to external stimuli (e.g., light) since the dynamic nature of gene expression implies animals subjected to stimuli at different times may be at very different stages within the continuum of genetic homeostasis. We assessed basal gene expression changes over a 24-hour period in 200 select Xiphophorus gene targets known to transcriptionally respond to various types of light exposure. We identified 22 genes in skin, 36 genes in brain and 28 genes in liver that exhibit basal oscillation of expression patterns. These genes, including known circadian regulators, produced the expected expression patterns over a 24-hour cycle when compared to circadian regulatory genes identified in other species, especially human and other vertebrate animal models. Our results suggest the regulatory network governing diurnal oscillating gene expression is similar between Xiphophorus and other vertebrates for the three Xiphophorus organs tested. In addition, we were able to categorize light responsive gene sets in Xiphophorus that do, and do not, exhibit circadian based oscillating expression patterns. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification of Reference Genes in Human Myelomonocytic Cells for Gene Expression Studies in Altered Gravity

PubMed Central

Thiel, Cora S.; Hauschild, Swantje; Tauber, Svantje; Paulsen, Katrin; Raig, Christiane; Raem, Arnold; Biskup, Josefine; Gutewort, Annett; Hürlimann, Eva; Philpot, Claudia; Lier, Hartwin; Engelmann, Frank; Layer, Liliana E.

2015-01-01

Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes (“housekeeping genes”) are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity. PMID:25654098

Life-cycle and growth-phase-dependent regulation of the ubiquitin genes of Trypanosoma cruzi.

PubMed

Manning-Cela, Rebeca; Jaishankar, Sobha; Swindle, John

2006-07-01

Trypanosoma cruzi, the causative agent of Chagas disease, exhibits a complex life cycle that is accompanied by the stage-specific gene expression. At the molecular level, very little is known about gene regulation in trypanosomes. Complex gene organizations coupled with polycistronic transcription units make the analysis of regulated gene expression difficult in trypanosomes. The ubiquitin genes of T. cruzi are a good example of this complexity. They are organized as a single cluster containing five ubiquitin fusion (FUS) and five polyubiquitin (PUB) genes that are polycistronically transcribed but expressed differently in response to developmental and environmental changes. Gene replacements were used to study FUS and PUB gene expression at different stages of growth and at different points in the life cycle of T. cruzi. Based on the levels of reporter gene expression, it was determined that FUS1 expression was downregulated as the parasites approached stationary phase, whereas PUB12.5 polyubiquitin gene expression increased. Conversely, FUS1 expression increases when epimastigotes and amastigotes differentiate into trypomastigotes, whereas the expression of PUB12.5 decreases when epimastigotes differentiate into amastigotes and trypomastigotes. Although the level of CAT activity in logarithmic growing epimastigotes is six- to seven-fold higher when the gene was expressed from the FUS1 locus than when expressed from the PUB12.5 locus, the rate of transcription from the two loci was the same implying that post-transcriptional mechanisms play a dominant role in the regulation of gene expression.

A two-component signal transduction pathway regulates manganese homeostasis in Synechocystis 6803, a photosynthetic organism.

PubMed

Ogawa, Teruo; Bao, Ding Hui; Katoh, Hirokazu; Shibata, Mari; Pakrasi, Himadri B; Bhattacharyya-Pakrasi, Maitrayee

2002-08-09

Elemental manganese is essential for the production of molecular oxygen by cyanobacteria, plants, and algae. In the cyanobacterium Synechocystis sp. PCC 6803, transcription of the mntCAB operon, encoding a high affinity Mn transporter, occurs under Mn starvation (nm Mn) conditions but not in Mn-sufficient (microm Mn) growth medium. Using a strain in which the promoter of this operon directs the transcription of the luxAB reporter genes, we determined that inactivation of the slr0640 gene, which encodes a histidine kinase sensor protein component of a two-component signal transduction system, resulted in constitutive high levels of lux luminescence. Systematic targeted inactivation mutagenesis also identified slr1837 as the gene encoding the corresponding response regulator protein. We have named these two genes manS (manganese-sensor) and manR (manganese-regulator), respectively. A polyhistidine-tagged form of the ManS protein was localized in the Synechocystis 6803 cell membrane. Directed replacement of the conserved catalytic His-205 residue of this protein by Leu abolished its activity, although the mutated protein was present in cyanobacterial membrane. This mutant also showed suboptimal rates of Mn uptake under either Mn-starved or Mn-sufficient growth condition. These data suggest that the ManS/ManR two-component system plays a central role in the homeostasis of manganese in Synechocystis 6803 cells.

Gene expression changes with age in skin, adipose tissue, blood and brain.

PubMed

Glass, Daniel; Viñuela, Ana; Davies, Matthew N; Ramasamy, Adaikalavan; Parts, Leopold; Knowles, David; Brown, Andrew A; Hedman, Asa K; Small, Kerrin S; Buil, Alfonso; Grundberg, Elin; Nica, Alexandra C; Di Meglio, Paola; Nestle, Frank O; Ryten, Mina; Durbin, Richard; McCarthy, Mark I; Deloukas, Panagiotis; Dermitzakis, Emmanouil T; Weale, Michael E; Bataille, Veronique; Spector, Tim D

2013-07-26

Previous studies have demonstrated that gene expression levels change with age. These changes are hypothesized to influence the aging rate of an individual. We analyzed gene expression changes with age in abdominal skin, subcutaneous adipose tissue and lymphoblastoid cell lines in 856 female twins in the age range of 39-85 years. Additionally, we investigated genotypic variants involved in genotype-by-age interactions to understand how the genomic regulation of gene expression alters with age. Using a linear mixed model, differential expression with age was identified in 1,672 genes in skin and 188 genes in adipose tissue. Only two genes expressed in lymphoblastoid cell lines showed significant changes with age. Genes significantly regulated by age were compared with expression profiles in 10 brain regions from 100 postmortem brains aged 16 to 83 years. We identified only one age-related gene common to the three tissues. There were 12 genes that showed differential expression with age in both skin and brain tissue and three common to adipose and brain tissues. Skin showed the most age-related gene expression changes of all the tissues investigated, with many of the genes being previously implicated in fatty acid metabolism, mitochondrial activity, cancer and splicing. A significant proportion of age-related changes in gene expression appear to be tissue-specific with only a few genes sharing an age effect in expression across tissues. More research is needed to improve our understanding of the genetic influences on aging and the relationship with age-related diseases.

Differential expression profiles and pathways of genes in sugarcane leaf at elongation stage in response to drought stress

PubMed Central

Li, Changning; Nong, Qian; Solanki, Manoj Kumar; Liang, Qiang; Xie, Jinlan; Liu, Xiaoyan; Li, Yijie; Wang, Weizan; Yang, Litao; Li, Yangrui

2016-01-01

Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, a pot experiment was performed with the sugarcane variety GT21 at three water-deficit levels (mild, moderate, and severe) during the elongation stage and gene expression was analyzed using microarray technology. Physiological parameters of sugarcane showed significant alterations in response to drought stress. Based on the expression profile of 15,593 sugarcane genes, 1,501 (9.6%) genes were differentially expressed under different water-level treatments; 821 genes were upregulated and 680 genes were downregulated. A gene similarity analysis showed that approximately 62.6% of the differentially expressed genes shared homology with functional proteins. In a Gene Ontology (GO) analysis, 901 differentially expressed genes were assigned to 36 GO categories. Moreover, 325 differentially expressed genes were classified into 101 pathway categories involved in various processes, such as the biosynthesis of secondary metabolites, ribosomes, carbon metabolism, etc. In addition, some unannotated genes were detected; these may provide a basis for studies of water-deficit tolerance. The reliability of the observed expression patterns was confirmed by RT-PCR. The results of this study may help identify useful genes for improving drought tolerance in sugarcane. PMID:27170459

GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

PubMed

Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

2018-01-01

When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

Circular RNA and gene expression profiles in gastric cancer based on microarray chip technology.

PubMed

Sui, Weiguo; Shi, Zhoufang; Xue, Wen; Ou, Minglin; Zhu, Ying; Chen, Jiejing; Lin, Hua; Liu, Fuhua; Dai, Yong

2017-03-01

The aim of the present study was to screen gastric cancer (GC) tissue and adjacent tissue for differences in mRNA and circular (circRNA) expression, to analyze the differences in circRNA and mRNA expression, and to investigate the circRNA expression in gastric carcinoma and its mechanism. circRNA and mRNA differential expression profiles generated using Agilent microarray technology were analyzed in the GC tissues and adjacent tissues. qRT-PCR was used to verify the differential expression of circRNAs and mRNAs according to the interactions between circRNAs and miRNAs as well as the possible existence of miRNA and mRNA interactions. We found that: i) the circRNA expression profile revealed 1,285 significant differences in circRNA expression, with circRNA expression downregulated in 594 samples and upregulated in 691 samples via interactions with miRNAs. The qRT-PCR validation experiments showed that hsa_circRNA_400071, hsa_circRNA_000543 and hsa_circRNA_001959 expression was consistent with the microarray analysis results. ii) 29,112 genes were found in the GC tissues and adjacent tissues, including 5,460 differentially expressed genes. Among them, 2,390 differentially expressed genes were upregulated and 3,070 genes were downregulated. Gene Ontology (GO) analysis of the differentially expressed genes revealed these genes involved in biological process classification, cellular component classification and molecular function classification. Pathway analysis of the differentially expressed genes identified 83 significantly enriched genes, including 28 upregulated genes and 55 downregulated genes. iii) 69 differentially expressed circRNAs were found that might adsorb specific miRNAs to regulate the expression of their target gene mRNAs. The conclusions are: i) differentially expressed circRNAs had corresponding miRNA binding sites. These circRNAs regulated the expression of target genes through interactions with miRNAs and might become new molecular biomarkers for GC in the future. ii) Differentially expressed genes may be involved in the occurrence of GC via a variety of mechanisms. iii) CD44, CXXC5, MYH9, MALAT1 and other genes may have important implications for the occurrence and development of GC through the regulation, interaction, and mutual influence of circRNA-miRNA-mRNA via different mechanisms.

A P-Norm Robust Feature Extraction Method for Identifying Differentially Expressed Genes

PubMed Central

Liu, Jian; Liu, Jin-Xing; Gao, Ying-Lian; Kong, Xiang-Zhen; Wang, Xue-Song; Wang, Dong

2015-01-01

In current molecular biology, it becomes more and more important to identify differentially expressed genes closely correlated with a key biological process from gene expression data. In this paper, based on the Schatten p-norm and Lp-norm, a novel p-norm robust feature extraction method is proposed to identify the differentially expressed genes. In our method, the Schatten p-norm is used as the regularization function to obtain a low-rank matrix and the Lp-norm is taken as the error function to improve the robustness to outliers in the gene expression data. The results on simulation data show that our method can obtain higher identification accuracies than the competitive methods. Numerous experiments on real gene expression data sets demonstrate that our method can identify more differentially expressed genes than the others. Moreover, we confirmed that the identified genes are closely correlated with the corresponding gene expression data. PMID:26201006

A P-Norm Robust Feature Extraction Method for Identifying Differentially Expressed Genes.

PubMed

Liu, Jian; Liu, Jin-Xing; Gao, Ying-Lian; Kong, Xiang-Zhen; Wang, Xue-Song; Wang, Dong

2015-01-01

In current molecular biology, it becomes more and more important to identify differentially expressed genes closely correlated with a key biological process from gene expression data. In this paper, based on the Schatten p-norm and Lp-norm, a novel p-norm robust feature extraction method is proposed to identify the differentially expressed genes. In our method, the Schatten p-norm is used as the regularization function to obtain a low-rank matrix and the Lp-norm is taken as the error function to improve the robustness to outliers in the gene expression data. The results on simulation data show that our method can obtain higher identification accuracies than the competitive methods. Numerous experiments on real gene expression data sets demonstrate that our method can identify more differentially expressed genes than the others. Moreover, we confirmed that the identified genes are closely correlated with the corresponding gene expression data.

Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti

PubMed Central

Wang, Xu; Werren, John H.; Clark, Andrew G.

2015-01-01

There is extraordinary diversity in sexual dimorphism (SD) among animals, but little is known about its epigenetic basis. To study the epigenetic architecture of SD in a haplodiploid system, we performed RNA-seq and whole-genome bisulfite sequencing of adult females and males from two closely related parasitoid wasps, Nasonia vitripennis and Nasonia giraulti. More than 75% of expressed genes displayed significantly sex-biased expression. As a consequence, expression profiles are more similar between species within each sex than between sexes within each species. Furthermore, extremely male- and female-biased genes are enriched for totally different functional categories: male-biased genes for key enzymes in sex-pheromone synthesis and female-biased genes for genes involved in epigenetic regulation of gene expression. Remarkably, just 70 highly expressed, extremely male-biased genes account for 10% of all transcripts in adult males. Unlike expression profiles, DNA methylomes are highly similar between sexes within species, with no consistent sex differences in methylation found. Therefore, methylation changes cannot explain the extensive level of sex-biased gene expression observed. Female-biased genes have smaller sequence divergence between species, higher conservation to other hymenopterans, and a broader expression range across development. Overall, female-biased genes have been recruited from genes with more conserved and broadly expressing “house-keeping” functions, whereas male-biased genes are more recently evolved and are predominately testis specific. In summary, Nasonia accomplish a striking degree of sex-biased expression without sex chromosomes or epigenetic differences in methylation. We propose that methylation provides a general signal for constitutive gene expression, whereas other sex-specific signals cause sex-biased gene expression. PMID:26100871

Extent and character of circadian gene expression in Drosophila melanogaster: identification of twenty oscillating mRNAs in the fly head.

PubMed

Van Gelder, R N; Bae, H; Palazzolo, M J; Krasnow, M A

1995-12-01

Although mRNAs expressed with a circadian rhythm have been isolated from many species, the extent and character of circadianly regulated gene expression is unknown for any animal. In Drosophila melanogaster, only the period (per) gene, an essential component of the circadian pacemaker, is known to show rhythmic mRNA expression. Recent work suggests that the encoded Per protein controls its own transcription by an autoregulatory feedback loop. Per might also control the rhythmic expression of other genes to generate circadian behavior and physiology. The goals of this work were to evaluate the extent and character of circadian control of gene expression in Drosophila, and to identify genes dependent on per for circadian expression. A large collection of anonymous, independent cDNA clones was used to screen for transcripts that are rhythmically expressed in the fly head. 20 of the 261 clones tested detected mRNAs with a greater than two-fold daily change in abundance. Three mRNAs were maximally expressed in the morning, whereas 17 mRNAs were most abundant in the evening--when per mRNA is also maximally expressed (but when the flies are inactive). Further analysis of the three 'morning' cDNAs showed that each has a unique dependence on the presence of a light-dark cycle, on timed feeding, and on the function of the per gene for its oscillation. These dependencies were different from those determined for per and for a novel 'evening' gene. Sequence analysis indicated that all but one of the 20 cDNAs identified previously uncloned genes. Diurnal control of gene expression is a significant but limited phenomenon in the fly head, which involves many uncharacterized genes. Diurnal control is mediated by multiple endogenous and exogenous mechanisms, even at the level of individual genes. A subset of circadianly expressed genes are predominantly or exclusively dependent on per for their rhythmic expression. The per gene can therefore influence the expression of genes other than itself, but for many rhythmically expressed genes, per functions in conjunction with external inputs to control their daily expression patterns.

Polycistronic gene expression in Aspergillus niger.

PubMed

Schuetze, Tabea; Meyer, Vera

2017-09-25

Genome mining approaches predict dozens of biosynthetic gene clusters in each of the filamentous fungal genomes sequenced so far. However, the majority of these gene clusters still remain cryptic because they are not expressed in their natural host. Simultaneous expression of all genes belonging to a biosynthetic pathway in a heterologous host is one approach to activate biosynthetic gene clusters and to screen the metabolites produced for bioactivities. Polycistronic expression of all pathway genes under control of a single and tunable promoter would be the method of choice, as this does not only simplify cloning procedures, but also offers control on timing and strength of expression. However, polycistronic gene expression is a feature not commonly found in eukaryotic host systems, such as Aspergillus niger. In this study, we tested the suitability of the viral P2A peptide for co-expression of three genes in A. niger. Two genes descend from Fusarium oxysporum and are essential to produce the secondary metabolite enniatin (esyn1, ekivR). The third gene (luc) encodes the reporter luciferase which was included to study position effects. Expression of the polycistronic gene cassette was put under control of the Tet-On system to ensure tunable gene expression in A. niger. In total, three polycistronic expression cassettes which differed in the position of luc were constructed and targeted to the pyrG locus in A. niger. This allowed direct comparison of the luciferase activity based on the position of the luciferase gene. Doxycycline-mediated induction of the Tet-On expression cassettes resulted in the production of one long polycistronic mRNA as proven by Northern analyses, and ensured comparable production of enniatin in all three strains. Notably, gene position within the polycistronic expression cassette matters, as, luciferase activity was lowest at position one and had a comparable activity at positions two and three. The P2A peptide can be used to express at least three genes polycistronically in A. niger. This approach can now be applied to heterologously express entire secondary metabolite gene clusters polycistronically or to co-express any genes of interest in equimolar amounts.

Global remote sensing of water-chlorophyll ratio in terrestrial plant leaves.

PubMed

Kushida, Keiji

2012-10-01

I evaluated the use of global remote sensing techniques for estimating plant leaf chlorophyll a + b (C(ab); μg cm(-2)) and water (C(w); mg cm(-2)) concentrations as well as the ratio of C(w)/C(ab) with the PROSAIL model under possible distributions for leaf and soil spectra, leaf area index (LAI), canopy geometric structure, and leaf size. First, I estimated LAI from the normalized difference vegetation index. I found that, at LAI values <2, C(ab), C(w), and C(w)/C(ab) could not be reliably estimated. At LAI values >2, C(ab) and C(w) could be estimated for only restricted ranges of the canopy structure; however, the ratio of C(w)/C(ab) could be reliably estimated for a variety of possible canopy structures with coefficients of determination (R(2)) ranging from 0.56 to 0.90. The remote estimation of the C(w)/C(ab) ratio from satellites offers information on plant condition at a global scale.

Assessment of Plant-Probiotic Performance of Novel Endophytic Bacillus sp. in Talc-Based Formulation.

PubMed

Basheer, Jasim; Ravi, Aswani; Mathew, Jyothis; Krishnankutty, Radhakrishnan Edayileveettil

2018-01-25

Endophytic bacteria are considered to have a plethora of plant growth promoting and anti-phytopathogenic traits to live within the plants. Hence, they have immense promises for plant probiotic development. In the current study, plant probiotic endophytic Bacillus sp. CaB5 which has been previously isolated from Capsicum annuum was investigated for its performance in talc-based formulation. For this, CaB5 was made into formulation with sterile talc, calcium carbonate, and carboxymethyl cellulose. The viability analysis of the formulation by standard plate count and fluorescence methods has confirmed the stable microbial count up to 45 days. Plant probiotic performance of the prepared formulation was analyzed on cowpea (Vigna unguiculata) and lady's finger (Abelmoschus esculentus). The results showed the formulation treatment to have enhancement effect on seed germination as well as plant growth in both selected plants. The results highlight the potential of CaB5-based formulation for field application to enhance growth of economically important plants.

Design and Analysis of a Novel Centrifugal Braking Device for a Mechanical Antilock Braking System.

PubMed

Yang, Cheng-Ping; Yang, Ming-Shien; Liu, Tyng

2015-06-01

A new concept for a mechanical antilock braking system (ABS) with a centrifugal braking device (CBD), termed a centrifugal ABS (C-ABS), is presented and developed in this paper. This new CBD functions as a brake in which the output braking torque adjusts itself depending on the speed of the output rotation. First, the structure and mechanical models of the entire braking system are introduced and established. Second, a numerical computer program for simulating the operation of the system is developed. The characteristics of the system can be easily identified and can be designed with better performance by using this program to studying the effects of different design parameters. Finally, the difference in the braking performance between the C-ABS and the braking system with or without a traditional ABS is discussed. The simulation results indicate that the C-ABS can prevent the wheel from locking even if excessive operating force is provided while still maintaining acceptable braking performance.

Pet dogs and child physical activity: the role of child-dog attachment.

PubMed

Gadomski, A M; Scribani, M B; Krupa, N; Jenkins, P

2017-10-01

Dog ownership has been associated with increased physical activity in children which in turn may mitigate childhood obesity. To measure the association between child-dog attachment and child physical activity and screen time. Cross-sectional study including 370 children (ages 4-10) who had pet dogs in the home. Parents completed the DartScreen, a web-based screener, before a well-child visit. Screener domains included child body mass index (BMI), physical activity, screen time and dog-related questions. The Companion Animal Bonding Scale (CABS) was used to measure child attachment to the dog. Clinic nurses weighed and measured the children. Associations between CABS, BMI z-score, screen time and physical activity were estimated. CABS was strongly associated with time spent being active with the dog (F = 22.81, p < 0.0001), but not with BMI z-score or screen time. A higher level of child attachment to a pet dog is associated with increased child physical activity. © 2016 World Obesity Federation.

Synergism and Physicochemical Properties of Anionic/Amphoteric Surfactant Mixtures with Nonionic Surfactant of Amine Oxide Type

NASA Astrophysics Data System (ADS)

Blagojević, S. M.; Pejić, N. D.; Blagojević, S. N.

2017-12-01

The physicochemical properties of initial formulation, that is anionic/amphoteric surfactants mixture SLES/AOS/CAB (sodium lauryl ether sulfate (SLES), α-olefin sulfonates (AOS) and cocamidopropyl betaine (CAB) at ratio 80 : 15 : 5) with nonionic surfactant of amine oxide type (lauramine oxide (AO)) in various concentration (1-5%) were studied. To characterize the surfactants mixture, the critical micelle concentration (CMC), surface tension (γ), foam volume, biodegradability and irritability were determined. This study showed that adding of AO in those mixtures lowered both γ and CMC as well as enhanced SLES/AOS/CAB foaming properties, but did not significantly affect biodegradability and irritability of initial formulation. Moreover, an increase in AO concentration has a meaningful synergistic effect on the initial formulation properties. All those results indicates that a nonionic surfactant of amine oxide type significantly improves the performance of anionic/amphoteric mixed micelle systems, and because of that anionic/amphoteric/nonionic mixture can be used in considerably lower concentrations as a cleaning formulation.

Intracellular high cholesterol content disorders the clock genes, apoptosis-related genes and fibrinolytic-related genes rhythmic expressions in human plaque-derived vascular smooth muscle cells.

PubMed

Lin, Changpo; Tang, Xiao; Xu, Lirong; Qian, Ruizhe; Shi, Zhenyu; Wang, Lixin; Cai, Tingting; Yan, Dong; Fu, Weiguo; Guo, Daqiao

2017-07-10

The clock genes are involved in regulating cardiovascular functions, and their expression disorders would lead to circadian rhythm disruptions of clock-controlled genes (CCGs), resulting in atherosclerotic plaque formation and rupture. Our previous study revealed the rhythmic expression of clock genes were attenuated in human plaque-derived vascular smooth muscle cells (PVSMCs), but failed to detect the downstream CCGs expressions and the underlying molecular mechanism. In this study, we examined the difference of CCGs rhythmic expression between human normal carotid VSMCs (NVSMCs) and PVSMCs. Furthermore, we compared the cholesterol and triglycerides levels between two groups and the link to clock genes and CCGs expressions. Seven health donors' normal carotids and 19 carotid plaques yielded viable cultured NVSMCs and PVSMCs. The expression levels of target genes were measured by quantitative real-time PCR and Western-blot. The intracellular cholesterol and triglycerides levels were measured by kits. The circadian expressions of apoptosis-related genes and fibrinolytic-related genes were disordered. Besides, the cholesterol levels were significant higher in PVSMCs. After treated with cholesterol or oxidized low density lipoprotein (ox-LDL), the expressions of clock genes were inhibited; and the rhythmic expressions of clock genes, apoptosis-related genes and fibrinolytic-related genes were disturbed in NVSMCs, which were similar to PVSMCs. The results suggested that intracellular high cholesterol content of PVSMCs would lead to the disorders of clock genes and CCGs rhythmic expressions. And further studies should be conducted to demonstrate the specific molecular mechanisms involved.

Double-filter identification of vascular-expressed genes using Arabidopsis plants with vascular hypertrophy and hypotrophy.

PubMed

Ckurshumova, Wenzislava; Scarpella, Enrico; Goldstein, Rochelle S; Berleth, Thomas

2011-08-01

Genes expressed in vascular tissues have been identified by several strategies, usually with a focus on mature vascular cells. In this study, we explored the possibility of using two opposite types of altered tissue compositions in combination with a double-filter selection to identify genes with a high probability of vascular expression in early organ primordia. Specifically, we generated full-transcriptome microarray profiles of plants with (a) genetically strongly reduced and (b) pharmacologically vastly increased vascular tissues and identified a reproducible cohort of 158 transcripts that fulfilled the dual requirement of being underrepresented in (a) and overrepresented in (b). In order to assess the predictive value of our identification scheme for vascular gene expression, we determined the expression patterns of genes in two unbiased subsamples. First, we assessed the expression patterns of all twenty annotated transcription factor genes from the cohort of 158 genes and found that seventeen of the twenty genes were preferentially expressed in leaf vascular cells. Remarkably, fifteen of these seventeen vascular genes were clearly expressed already very early in leaf vein development. Twelve genes with published leaf expression patterns served as a second subsample to monitor the representation of vascular genes in our cohort. Of those twelve genes, eleven were preferentially expressed in leaf vascular tissues. Based on these results we propose that our compendium of 158 genes represents a sample that is highly enriched for genes expressed in vascular tissues and that our approach is particularly suited to detect genes expressed in vascular cell lineages at early stages of their inception. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Increased gene expression noise in human cancers is correlated with low p53 and immune activities as well as late stage cancer.

PubMed

Han, Rongfei; Huang, Guanqun; Wang, Yejun; Xu, Yafei; Hu, Yueming; Jiang, Wenqi; Wang, Tianfu; Xiao, Tian; Zheng, Duo

2016-11-01

Gene expression in metazoans is delicately organized. As genetic information transmits from DNA to RNA and protein, expression noise is inevitably generated. Recent studies begin to unveil the mechanisms of gene expression noise control, but the changes of gene expression precision in pathologic conditions like cancers are unknown. Here we analyzed the transcriptomic data of human breast, liver, lung and colon cancers, and found that the expression noise of more than 74.9% genes was increased in cancer tissues as compared to adjacent normal tissues. This suggested that gene expression precision controlling collapsed during cancer development. A set of 269 genes with noise increased more than 2-fold were identified across different cancer types. These genes were involved in cell adhesion, catalytic and metabolic functions, implying the vulnerability of deregulation of these processes in cancers. We also observed a tendency of increased expression noise in patients with low p53 and immune activity in breast, liver and lung caners but not in colon cancers, which indicated the contributions of p53 signaling and host immune surveillance to gene expression noise in cancers. Moreover, more than 53.7% genes had increased noise in patients with late stage than early stage cancers, suggesting that gene expression precision was associated with cancer outcome. Together, these results provided genomic scale explorations of gene expression noise control in human cancers.

[Differential expression genes of bone tissues surrounding implants in diabetic rats by gene chip].

PubMed

Wang, Xin-xin; Ma, Yue; Li, Qing; Jiang, Bao-qi; Lan, Jing

2012-10-01

To compare mRNA expression profiles of bone tissues surrounding implants between normal rats and rats with diabetes using microarray technology. Six Wistar rats were randomly selected and divided into normal model group and diabetic group. Diabetic model condition was established by injecting Streptozotocin into peritoneal space. Titanium implants were implanted into the epiphyseal end of the rats' tibia. Bone tissues surrounding implant were harvested and sampled after 3 months to perform comprehensive RNA gene expression profiling, including 17983 for genome-wide association study.GO analysis was used to compare different gene expression and real-time PCR was used to confirm the results on core samples. The results indicated that there were 1084 differential gene expression. In the diabetic model, there were 352 enhanced expression genes, 732 suppressed expression genes. GO analysis involved 1154 different functional type. Osteoblast related gene expressions in bone tissue samples of diabetic rats were decreased, and lipid metabolism pathway related gene expression was increased.

Gene Architectures that Minimize Cost of Gene Expression.

PubMed

Frumkin, Idan; Schirman, Dvir; Rotman, Aviv; Li, Fangfei; Zahavi, Liron; Mordret, Ernest; Asraf, Omer; Wu, Song; Levy, Sasha F; Pilpel, Yitzhak

2017-01-05

Gene expression burdens cells by consuming resources and energy. While numerous studies have investigated regulation of expression level, little is known about gene design elements that govern expression costs. Here, we ask how cells minimize production costs while maintaining a given protein expression level and whether there are gene architectures that optimize this process. We measured fitness of ∼14,000 E. coli strains, each expressing a reporter gene with a unique 5' architecture. By comparing cost-effective and ineffective architectures, we found that cost per protein molecule could be minimized by lowering transcription levels, regulating translation speeds, and utilizing amino acids that are cheap to synthesize and that are less hydrophobic. We then examined natural E. coli genes and found that highly expressed genes have evolved more forcefully to minimize costs associated with their expression. Our study thus elucidates gene design elements that improve the economy of protein expression in natural and heterologous systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection

PubMed Central

2012-01-01

Background Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection. Results We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Several genes showed differential expression between control and stress conditions. Gene ontology (GO) enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs) were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with differential gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks). The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5) apoptosis and cell death categories were enriched. Of the 287 positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments. Conclusions Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study. PMID:22853646

Functional clustering of time series gene expression data by Granger causality

PubMed Central

2012-01-01

Background A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes. Results In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its consequence. Conclusions This kind of analysis can be used as a complementary approach for functional clustering, wherein genes would be clustered not solely based on their expression similarity but on their topological proximity built according to the intensity of Granger causality among them. PMID:23107425

Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression

PubMed Central

Richter, Karin; Wirta, Valtteri; Dahl, Lina; Bruce, Sara; Lundeberg, Joakim; Carlsson, Leif; Williams, Cecilia

2006-01-01

Background Expression of the LIM-homeobox gene Lhx2 in murine hematopoietic cells allows for the generation of hematopoietic stem cell (HSC)-like cell lines. To address the molecular basis of Lhx2 function, we generated HSC-like cell lines where Lhx2 expression is regulated by a tet-on system and hence dependent on the presence of doxycyclin (dox). These cell lines efficiently down-regulate Lhx2 expression upon dox withdrawal leading to a rapid differentiation into various myeloid cell types. Results Global gene expression of these cell lines cultured in dox was compared to different time points after dox withdrawal using microarray technology. We identified 267 differentially expressed genes. The majority of the genes overlapping with HSC-specific databases were those down-regulated after turning off Lhx2 expression and a majority of the genes overlapping with those defined as late progenitor-specific genes were the up-regulated genes, suggesting that these cell lines represent a relevant model system for normal HSCs also at the level of global gene expression. Moreover, in situ hybridisations of several genes down-regulated after dox withdrawal showed overlapping expression patterns with Lhx2 in various tissues during embryonic development. Conclusion Global gene expression analysis of HSC-like cell lines with inducible Lhx2 expression has identified genes putatively linked to self-renewal / differentiation of HSCs, and function of Lhx2 in organ development and stem / progenitor cells of non-hematopoietic origin. PMID:16600034

Integrated analysis of gene expression and methylation profiles of 48 candidate genes in breast cancer patients.

PubMed

Li, Zibo; Heng, Jianfu; Yan, Jinhua; Guo, Xinwu; Tang, Lili; Chen, Ming; Peng, Limin; Wu, Yepeng; Wang, Shouman; Xiao, Zhi; Deng, Zhongping; Dai, Lizhong; Wang, Jun

2016-11-01

Gene-specific methylation and expression have shown biological and clinical importance for breast cancer diagnosis and prognosis. Integrated analysis of gene methylation and gene expression may identify genes associated with biology mechanism and clinical outcome of breast cancer and aid in clinical management. Using high-throughput microfluidic quantitative PCR, we analyzed the expression profiles of 48 candidate genes in 96 Chinese breast cancer patients and investigated their correlation with gene methylation and associations with breast cancer clinical parameters. Breast cancer-specific gene expression alternation was found in 25 genes with significant expression difference between paired tumor and normal tissues. A total of 9 genes (CCND2, EGFR, GSTP1, PGR, PTGS2, RECK, SOX17, TNFRSF10D, and WIF1) showed significant negative correlation between methylation and gene expression, which were validated in the TCGA database. Total 23 genes (ACADL, APC, BRCA2, CADM1, CAV1, CCND2, CST6, EGFR, ESR2, GSTP1, ICAM5, NPY, PGR, PTGS2, RECK, RUNX3, SFRP1, SOX17, SYK, TGFBR2, TNFRSF10D, WIF1, and WRN) annotated with potential TFBSs in the promoter regions showed negative correlation between methylation and expression. In logistics regression analysis, 31 of the 48 genes showed improved performance in disease prediction with combination of methylation and expression coefficient. Our results demonstrated the complex correlation and the possible regulatory mechanisms between DNA methylation and gene expression. Integration analysis of methylation and expression of candidate genes could improve performance in breast cancer prediction. These findings would contribute to molecular characterization and identification of biomarkers for potential clinical applications.

Genome-wide profiling identifies a subset of methamphetamine (METH)-induced genes associated with METH-induced increased H4K5Ac binding in the rat striatum

PubMed Central

2013-01-01

Background METH is an illicit drug of abuse that influences gene expression in the rat striatum. Histone modifications regulate gene transcription. Methods We therefore used microarray analysis and genome-scale approaches to examine potential relationships between the effects of METH on gene expression and on DNA binding of histone H4 acetylated at lysine 4 (H4K5Ac) in the rat dorsal striatum of METH-naïve and METH-pretreated rats. Results Acute and chronic METH administration caused differential changes in striatal gene expression. METH also increased H4K5Ac binding around the transcriptional start sites (TSSs) of genes in the rat striatum. In order to relate gene expression to histone acetylation, we binned genes of similar expression into groups of 100 genes and proceeded to relate gene expression to H4K5Ac binding. We found a positive correlation between gene expression and H4K5Ac binding in the striatum of control rats. Similar correlations were observed in METH-treated rats. Genes that showed acute METH-induced increased expression in saline-pretreated rats also showed METH-induced increased H4K5Ac binding. The acute METH injection caused similar increases in H4K5Ac binding in METH-pretreated rats, without affecting gene expression to the same degree. Finally, genes that showed METH-induced decreased expression exhibited either decreases or no changes in H4K5Ac binding. Conclusion Acute METH injections caused increased gene expression of genes that showed increased H4K5Ac binding near their transcription start sites. PMID:23937714

Genome-wide profiling identifies a subset of methamphetamine (METH)-induced genes associated with METH-induced increased H4K5Ac binding in the rat striatum.

PubMed

Cadet, Jean Lud; Jayanthi, Subramaniam; McCoy, Michael T; Ladenheim, Bruce; Saint-Preux, Fabienne; Lehrmann, Elin; De, Supriyo; Becker, Kevin G; Brannock, Christie

2013-08-12

METH is an illicit drug of abuse that influences gene expression in the rat striatum. Histone modifications regulate gene transcription. We therefore used microarray analysis and genome-scale approaches to examine potential relationships between the effects of METH on gene expression and on DNA binding of histone H4 acetylated at lysine 4 (H4K5Ac) in the rat dorsal striatum of METH-naïve and METH-pretreated rats. Acute and chronic METH administration caused differential changes in striatal gene expression. METH also increased H4K5Ac binding around the transcriptional start sites (TSSs) of genes in the rat striatum. In order to relate gene expression to histone acetylation, we binned genes of similar expression into groups of 100 genes and proceeded to relate gene expression to H4K5Ac binding. We found a positive correlation between gene expression and H4K5Ac binding in the striatum of control rats. Similar correlations were observed in METH-treated rats. Genes that showed acute METH-induced increased expression in saline-pretreated rats also showed METH-induced increased H4K5Ac binding. The acute METH injection caused similar increases in H4K5Ac binding in METH-pretreated rats, without affecting gene expression to the same degree. Finally, genes that showed METH-induced decreased expression exhibited either decreases or no changes in H4K5Ac binding. Acute METH injections caused increased gene expression of genes that showed increased H4K5Ac binding near their transcription start sites.

Integrative clinical genomics of advanced prostate cancer.

PubMed

Robinson, Dan; Van Allen, Eliezer M; Wu, Yi-Mi; Schultz, Nikolaus; Lonigro, Robert J; Mosquera, Juan-Miguel; Montgomery, Bruce; Taplin, Mary-Ellen; Pritchard, Colin C; Attard, Gerhardt; Beltran, Himisha; Abida, Wassim; Bradley, Robert K; Vinson, Jake; Cao, Xuhong; Vats, Pankaj; Kunju, Lakshmi P; Hussain, Maha; Feng, Felix Y; Tomlins, Scott A; Cooney, Kathleen A; Smith, David C; Brennan, Christine; Siddiqui, Javed; Mehra, Rohit; Chen, Yu; Rathkopf, Dana E; Morris, Michael J; Solomon, Stephen B; Durack, Jeremy C; Reuter, Victor E; Gopalan, Anuradha; Gao, Jianjiong; Loda, Massimo; Lis, Rosina T; Bowden, Michaela; Balk, Stephen P; Gaviola, Glenn; Sougnez, Carrie; Gupta, Manaswi; Yu, Evan Y; Mostaghel, Elahe A; Cheng, Heather H; Mulcahy, Hyojeong; True, Lawrence D; Plymate, Stephen R; Dvinge, Heidi; Ferraldeschi, Roberta; Flohr, Penny; Miranda, Susana; Zafeiriou, Zafeiris; Tunariu, Nina; Mateo, Joaquin; Perez-Lopez, Raquel; Demichelis, Francesca; Robinson, Brian D; Schiffman, Marc; Nanus, David M; Tagawa, Scott T; Sigaras, Alexandros; Eng, Kenneth W; Elemento, Olivier; Sboner, Andrea; Heath, Elisabeth I; Scher, Howard I; Pienta, Kenneth J; Kantoff, Philip; de Bono, Johann S; Rubin, Mark A; Nelson, Peter S; Garraway, Levi A; Sawyers, Charles L; Chinnaiyan, Arul M

2015-05-21

Toward development of a precision medicine framework for metastatic, castration-resistant prostate cancer (mCRPC), we established a multi-institutional clinical sequencing infrastructure to conduct prospective whole-exome and transcriptome sequencing of bone or soft tissue tumor biopsies from a cohort of 150 mCRPC affected individuals. Aberrations of AR, ETS genes, TP53, and PTEN were frequent (40%-60% of cases), with TP53 and AR alterations enriched in mCRPC compared to primary prostate cancer. We identified new genomic alterations in PIK3CA/B, R-spondin, BRAF/RAF1, APC, β-catenin, and ZBTB16/PLZF. Moreover, aberrations of BRCA2, BRCA1, and ATM were observed at substantially higher frequencies (19.3% overall) compared to those in primary prostate cancers. 89% of affected individuals harbored a clinically actionable aberration, including 62.7% with aberrations in AR, 65% in other cancer-related genes, and 8% with actionable pathogenic germline alterations. This cohort study provides clinically actionable information that could impact treatment decisions for these affected individuals. Copyright © 2015 Elsevier Inc. All rights reserved.

Integrative clinical genomics of advanced prostate cancer

PubMed Central

Dan, Robinson; Van Allen, Eliezer M.; Wu, Yi-Mi; Schultz, Nikolaus; Lonigro, Robert J.; Mosquera, Juan-Miguel; Montgomery, Bruce; Taplin, Mary-Ellen; Pritchard, Colin C; Attard, Gerhardt; Beltran, Himisha; Abida, Wassim M.; Bradley, Robert K.; Vinson, Jake; Cao, Xuhong; Vats, Pankaj; Kunju, Lakshmi P.; Hussain, Maha; Feng, Felix Y.; Tomlins, Scott A.; Cooney, Kathleen A.; Smith, David C.; Brennan, Christine; Siddiqui, Javed; Mehra, Rohit; Chen, Yu; Rathkopf, Dana E.; Morris, Michael J.; Solomon, Stephen B.; Durack, Jeremy C.; Reuter, Victor E.; Gopalan, Anuradha; Gao, Jianjiong; Loda, Massimo; Lis, Rosina T.; Bowden, Michaela; Balk, Stephen P.; Gaviola, Glenn; Sougnez, Carrie; Gupta, Manaswi; Yu, Evan Y.; Mostaghel, Elahe A.; Cheng, Heather H.; Mulcahy, Hyojeong; True, Lawrence D.; Plymate, Stephen R.; Dvinge, Heidi; Ferraldeschi, Roberta; Flohr, Penny; Miranda, Susana; Zafeiriou, Zafeiris; Tunariu, Nina; Mateo, Joaquin; Lopez, Raquel Perez; Demichelis, Francesca; Robinson, Brian D.; Schiffman, Marc A.; Nanus, David M.; Tagawa, Scott T.; Sigaras, Alexandros; Eng, Kenneth W.; Elemento, Olivier; Sboner, Andrea; Heath, Elisabeth I.; Scher, Howard I.; Pienta, Kenneth J.; Kantoff, Philip; de Bono, Johann S.; Rubin, Mark A.; Nelson, Peter S.; Garraway, Levi A.; Sawyers, Charles L.; Chinnaiyan, Arul M.

2015-01-01

SUMMARY Toward development of a precision medicine framework for metastatic, castration resistant prostate cancer (mCRPC), we established a multi-institutional clinical sequencing infrastructure to conduct prospective whole exome and transcriptome sequencing of bone or soft tissue tumor biopsies from a cohort of 150 mCRPC affected individuals. Aberrations of AR, ETS genes, TP53 and PTEN were frequent (40–60% of cases), with TP53 and AR alterations enriched in mCRPC compared to primary prostate cancer. We identified novel genomic alterations in PIK3CA/B, R-spondin, BRAF/RAF1, APC, β-catenin and ZBTB16/PLZF. Aberrations of BRCA2, BRCA1 and ATM were observed at substantially higher frequencies (19.3% overall) than seen in primary prostate cancers. 89% of affected individuals harbored a clinically actionable aberration including 62.7% with aberrations in AR, 65% in other cancer-related genes, and 8% with actionable pathogenic germline alterations. This cohort study provides evidence that clinical sequencing in mCRPC is feasible and could impact treatment decisions in significant numbers of affected individuals. PMID:26000489

Thermodynamic, Kinetic, and Equilibrium Parameters for the Removal of Lead and Cadmium from Aqueous Solutions with Calcium Alginate Beads

PubMed Central

Alfaro-Cuevas-Villanueva, Ruth; Hidalgo-Vázquez, Aura Roxana; Cortés Penagos, Consuelo de Jesús; Cortés-Martínez, Raúl

2014-01-01

The sorption of cadmium (Cd) and lead (Pb) by calcium alginate beads (CAB) from aqueous solutions in batch systems was investigated. The kinetic and thermodynamic parameters, as well as the sorption capacities of CAB in each system at different temperatures, were evaluated. The rate of sorption for both metals was rapid in the first 10 minutes and reached a maximum in 50 minutes. Sorption kinetic data were fitted to Lagergren, pseudo-second-order and Elovich models and it was found that the second-order kinetic model describes these data for the two metals; comparing kinetic parameters for Cd and Pb sorption a higher kinetic rate (K 2) for Pb was observed, indicating that the interaction between lead cations and alginate beads was faster than for cadmium. Similarly, isotherm data were fitted to different models reported in literature and it was found that the Langmuir-Freundlich (L-F) and Dubinin-Radushkevich (D-R) models describe the isotherms in all cases. CAB sorption capacity for cadmium was 27.4 mg/g and 150.4 mg/g for lead, at 25°C. Sorption capacities of Cd and Pb increase as temperature rises. According to the thermodynamic parameters, the cadmium and lead adsorption process was spontaneous and endothermic. It was also found that pH has an important effect on the adsorption of these metals by CAB, as more were removed at pH values between 6 and 7. PMID:24587740

What are the fluxes of greenhouse gases from the greater Los Angeles area as inferred from top-down remote sensing studies?

NASA Astrophysics Data System (ADS)

Hedelius, J.; Wennberg, P. O.; Wunch, D.; Roehl, C. M.; Podolske, J. R.; Hillyard, P.; Iraci, L. T.

2017-12-01

Greenhouse gas (GHG) emissions from California's South Coast Air Basin (SoCAB) have been studied extensively using a variety of tower, aircraft, remote sensing, emission inventory, and modeling studies. It is impractical to survey GHG fluxes from all urban areas and hot-spots to the extent the SoCAB has been studied, but it can serve as a test location for scaling methods globally. We use a combination of remote sensing measurements from ground (Total Carbon Column Observing Network, TCCON) and space-based (Observing Carbon Observatory-2, OCO-2) sensors in an inversion to obtain the carbon dioxide flux from the SoCAB. We also perform a variety of sensitivity tests to see how the inversion performs using different model parameterizations. Fluxes do not significantly depend on the mixed layer depth, but are sensitive to the model surface layers (<5 m). Carbon dioxide fluxes are larger than those from bottom-up inventories by about 20%, and along with CO has a significant weekend:weekday effect. Methane fluxes have little weekend changes. Results also include flux estimates from sub-regions of the SoCAB. Larger top-down than bottom-up fluxes highlight the need for additional work on both approaches. Higher top-down fluxes could arise from sampling bias, model bias, or may show bottom-up values underestimate sources. Lessons learned here may help in scaling up inversions to hundreds of urban systems using space-based observations.

Mobile Geochemistry Instrument Package Facility (MGIPF) for In Situ Mineralogical and Chemical Analysis of Planetary Surface Material

NASA Astrophysics Data System (ADS)

Klingelhöfer, G.; Romstedt, J.; Henkel, H.; Michaelis, H.; Brückner, J.; D'Uston, C.

A first order requirement for any spacecraft mission to land on a solid planetary or moon surface is instrumentation for in-situ mineralogical and chemical analysis 2 Such analysis provide data needed for primary classification and characterization of surface materials present We will discuss a mobile instrument package we have developed for in-situ investigations under harsh environmental conditions like on Mercury or Mars This Geochemistry Instrument Package Facility is a compact box also called payload cab containing three small advanced geochemistry mineralogy instruments the chemical spectrometer APXS the mineralogical M o ssbauer spectrometer MIMOS II 3 and a textural imager close-up camera The payload cab is equipped with two actuating arms with two degrees of freedom permitting precision placement of all instruments at a chosen sample This payload cab is the central part of the small rover Nanokhod which has the size of a shoebox 1 The Nanokhod rover is a tethered system with a typical operational range of sim 100 m Of course the payload cab itself can be attached by means of its arms to any deployment device of any other rover or deployment device 1 Andre Schiele Jens Romstedt Chris Lee Sabine Klinkner Rudi Rieder Ralf Gellert G o star Klingelh o fer Bodo Bernhardt Harald Michaelis The new NANOKHOD Engineeering model for extreme cold environments 8th International symposium on Artificial Intelligence Robotics and Automation in Space 5 - 9 September 2005

Operators' perception of comfort in two tractor cabs.

PubMed

Ferrari, E; Cavallo, E

2013-01-01

Workspace characteristics affect the perceived comfort level of the operator and uncomfortable working conditions have been found to have a negative impact on productivity and safety. The comfort of the operator is increasingly recognized by manufacturers as a product's added value. Comfort can positively distinguish a product and increase its competitiveness. The concept of comfort is controversial, and a clear operational definition is missing. Nevertheless, it is widely accepted that comfort is a subjective phenomenon that can be evaluated by the final users. In this study, comfort aspects of the tractor workspace interior (i.e., the cab) were investigated. Users with various levels of expertise and two medium-power utility tractors of different brands were used in a 2 x 2 mixed-factorial experimental design. Participants were involved in a dynamic assessment of the cabs, and their opinions about the different workspaces were collected through a questionnaire. Additionally, objective measurements were taken on both tractors, and subjective data were compared with objective data. Results indicate significant differences in terms of the ease of locating and operating the controls (i.e., rear-mounted three-point linkage, hydraulic system, and power take-off), the ease of starting the tractor, the ease exiting the cab, the required level of concentration in executing the tasks, the adequacy of lateral visibility from the driving station, and the level of noise at the operator's position. This article provides guidance for improving the comfort of tractor workspace interiors. Agricultural machinery manufactures would benefit from research results, differentiating themselves from competitors.

Montefiore-Einstein Center for the Aging Brain: Preliminary Data.

PubMed

Verghese, Joe; Malik, Rubina; Zwerling, Jessica

2016-11-01

Given the multifaceted nature of dementia care management, an interdisciplinary comprehensive clinical approach is necessary. We describe our one-year experience with outpatient based dementia care at the Montefiore-Einstein Center for the Aging Brain (CAB) involving an multispecialty team of geriatricians, neurologists, and neuropsychologists, supported by geriatric psychiatrists, physiatrists, and social services. The goals of the CAB is to maximize dementia outcomes, including regular monitoring of patient's health and cognition, education and support to patients, their families and caregivers; initiation of pharmacological and non-pharmacological treatments as appropriate, and the facilitation of access to clinical trials. The CAB follows a consultative model where patients referred to the center receive a comprehensive three step evaluation and management plan from Geriatric, Neuropsychology and Neurology specialists that is shared with patient, caregivers and primary care physicians. Of the 366 patients seen for cognitive complaints in our first year, 71% were women with a mean age of 74 years. Self-identified ethnicity of patients included Caucasian (26%), African-American (25%), Hispanic (18%) and multiracial (5%). Common final diagnoses assigned at the CAB included mild cognitive impairment syndromes (31%), Alzheimer's disease (20%), mixed dementia (11%), vascular dementia (9%), Frontotemporal dementia (4%) and dementia with Lewy bodies (4%). Our one-year progress report indicates that an interdisciplinary clinical dementia care model is feasible in the outpatient setting as well as highly accepted by patients, caregivers and referring physicians. © 2016, Copyright the Authors Journal compilation © 2016, The American Geriatrics Society.

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data.

PubMed

Tintle, Nathan L; Sitarik, Alexandra; Boerema, Benjamin; Young, Kylie; Best, Aaron A; Dejongh, Matthew

2012-08-08

Statistical analyses of whole genome expression data require functional information about genes in order to yield meaningful biological conclusions. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) are common sources of functionally grouped gene sets. For bacteria, the SEED and MicrobesOnline provide alternative, complementary sources of gene sets. To date, no comprehensive evaluation of the data obtained from these resources has been performed. We define a series of gene set consistency metrics directly related to the most common classes of statistical analyses for gene expression data, and then perform a comprehensive analysis of 3581 Affymetrix® gene expression arrays across 17 diverse bacteria. We find that gene sets obtained from GO and KEGG demonstrate lower consistency than those obtained from the SEED and MicrobesOnline, regardless of gene set size. Despite the widespread use of GO and KEGG gene sets in bacterial gene expression data analysis, the SEED and MicrobesOnline provide more consistent sets for a wide variety of statistical analyses. Increased use of the SEED and MicrobesOnline gene sets in the analysis of bacterial gene expression data may improve statistical power and utility of expression data.

Validation of housekeeping genes as an internal control for gene expression studies in Giardia lamblia using quantitative real-time PCR.

PubMed

Marcial-Quino, Jaime; Fierro, Francisco; De la Mora-De la Mora, Ignacio; Enríquez-Flores, Sergio; Gómez-Manzo, Saúl; Vanoye-Carlo, America; Garcia-Torres, Itzhel; Sierra-Palacios, Edgar; Reyes-Vivas, Horacio

2016-04-25

The analysis of transcript levels of specific genes is important for understanding transcriptional regulation and for the characterization of gene function. Real-time quantitative reverse transcriptase PCR (RT-qPCR) has become a powerful tool to quantify gene expression. The objective of this study was to identify reliable housekeeping genes in Giardia lamblia. Twelve genes were selected for this purpose, and their expression was analyzed in the wild type WB strain and in two strains with resistance to nitazoxanide (NTZ) and metronidazole (MTZ), respectively. RefFinder software analysis showed that the expression of the genes is different in the three strains. The integrated data from the four analyses showed that the NADH oxidase (NADH) and aldolase (ALD) genes were the most steadily expressed genes, whereas the glyceraldehyde-3-phosphate dehydrogenase gene was the most unstable. Additionally, the relative expression of seven genes were quantified in the NTZ- and MTZ-resistant strains by RT-qPCR, using the aldolase gene as the internal control, and the results showed a consistent differential pattern of expression in both strains. The housekeeping genes found in this work will facilitate the analysis of mRNA expression levels of other genes of interest in G. lamblia. Copyright © 2016 Elsevier B.V. All rights reserved.

Targeting gene expression selectively in cancer cells by using the progression-elevated gene-3 promoter.

PubMed

Su, Zhao-Zhong; Sarkar, Devanand; Emdad, Luni; Duigou, Gregory J; Young, Charles S H; Ware, Joy; Randolph, Aaron; Valerie, Kristoffer; Fisher, Paul B

2005-01-25

One impediment to effective cancer-specific gene therapy is the rarity of regulatory sequences targeting gene expression selectively in tumor cells. Although many tissue-specific promoters are recognized, few cancer-selective gene promoters are available. Progression-elevated gene-3 (PEG-3) is a rodent gene identified by subtraction hybridization that displays elevated expression as a function of transformation by diversely acting oncogenes, DNA damage, and cancer cell progression. The promoter of PEG-3, PEG-Prom, displays robust expression in a broad spectrum of human cancer cell lines with marginal expression in normal cellular counterparts. Whereas GFP expression, when under the control of a CMV promoter, is detected in both normal and cancer cells, when GFP is expressed under the control of the PEG-Prom, cancer-selective expression is evident. Mutational analysis identifies the AP-1 and PEA-3 transcription factors as primary mediators of selective, cancer-specific expression of the PEG-Prom. Synthesis of apoptosis-inducing genes, under the control of the CMV promoter, inhibits the growth of both normal and cancer cells, whereas PEG-Prom-mediated expression of these genes kills only cancer cells and spares normal cells. The efficacy of the PEG-Prom as part of a cancer gene therapeutic regimen is further documented by in vivo experiments in which PEG-Prom-controlled expression of an apoptosis-inducing gene completely inhibited prostate cancer xenograft growth in nude mice. These compelling observations indicate that the PEG-Prom, with its cancer-specific expression, provides a means of selectively delivering genes to cancer cells, thereby providing a crucial component in developing effective cancer gene therapies.

Evaluation of Allelic Expression of Imprinted Genes in Adult Human Blood

PubMed Central

Frost, Jennifer M.; Monk, Dave; Stojilkovic-Mikic, Taita; Woodfine, Kathryn; Chitty, Lyn S.; Murrell, Adele; Stanier, Philip; Moore, Gudrun E.

2010-01-01

Background Imprinted genes are expressed from only one allele in a parent-of-origin dependent manner. Loss of imprinted (LOI) expression can result in a variety of human disorders and is frequently reported in cancer. Biallelic expression of imprinted genes in adult blood has been suggested as a useful biomarker and is currently being investigated in colorectal cancer. In general, the expression profiles of imprinted genes are well characterised during human and mouse fetal development, but not in human adults. Methodology/Principal Findings We investigated quantitative expression of 36 imprinted genes in adult human peripheral blood leukocytes obtained from healthy individuals. Allelic expression was also investigated in B and T lymphocytes and myeloid cells. We found that 21 genes were essentially undetectable in adult blood. Only six genes were demonstrably monoallelic, and most importantly, we found that nine genes were either biallelic or showed variable expression in different individuals. Separated leukocyte populations showed the same expression patterns as whole blood. Differential methylation at each of the imprinting control loci analysed was maintained, including regions that contained biallelically expressed genes. This suggests in some cases methylation has become uncoupled from its role in regulating gene expression. Conclusions/Significance We conclude that only a limited set of imprinted genes, including IGF2 and SNRPN, may be useful for LOI cancer biomarker studies. In addition, blood is not a good tissue to use for the discovery of new imprinted genes. Finally, lymphocyte DNA methylation status in the adult may not always be a reliable indicator of monoallelic gene expression. PMID:21042416

Evaluation and selection of reliable reference genes for gene expression under abiotic stress in cotton (Gossypium hirsutum L.).

PubMed

Wang, Min; Wang, Qinglian; Zhang, Baohong

2013-11-01

Reference genes are critical for normalization of the gene expression level of target genes. The widely used housekeeping genes may change their expression levels at different tissue under different treatment or stress conditions. Therefore, systematical evaluation on the housekeeping genes is required for gene expression analysis. Up to date, no work was performed to evaluate the housekeeping genes in cotton under stress treatment. In this study, we chose 10 housekeeping genes to systematically assess their expression levels at two different tissues (leaves and roots) under two different abiotic stresses (salt and drought) with three different concentrations. Our results show that there is no best reference gene for all tissues at all stress conditions. The reliable reference gene should be selected based on a specific condition. For example, under salt stress, UBQ7, GAPDH and EF1A8 are better reference genes in leaves; TUA10, UBQ7, CYP1, GAPDH and EF1A8 were better in roots. Under drought stress, UBQ7, EF1A8, TUA10, and GAPDH showed less variety of expression level in leaves and roots. Thus, it is better to identify reliable reference genes first before performing any gene expression analysis. However, using a combination of housekeeping genes as reference gene may provide a new strategy for normalization of gene expression. In this study, we found that combination of four housekeeping genes worked well as reference genes under all the stress conditions. © 2013.

The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes.

PubMed

Gautier, Aude; Le Gac, Florence; Lareyre, Jean-Jacques

2011-02-01

The gonadal soma-derived factor (GSDF) belongs to the transforming growth factor-β superfamily and is conserved in teleostean fish species. Gsdf is specifically expressed in the gonads, and gene expression is restricted to the granulosa and Sertoli cells in trout and medaka. The gsdf gene expression is correlated to early testis differentiation in medaka and was shown to stimulate primordial germ cell and spermatogonia proliferation in trout. In the present study, we show that the gsdf gene localizes to a syntenic chromosomal fragment conserved among vertebrates although no gsdf-related gene is detected on the corresponding genomic region in tetrapods. We demonstrate using quantitative RT-PCR that most of the genes localized in the synteny are specifically expressed in medaka gonads. Gsdf is the only gene of the synteny with a much higher expression in the testis compared to the ovary. In contrast, gene expression pattern analysis of the gsdf surrounding genes (nup54, aff1, klhl8, sdad1, and ptpn13) indicates that these genes are preferentially expressed in the female gonads. The tissue distribution of these genes is highly similar in medaka and zebrafish, two teleostean species that have diverged more than 110 million years ago. The cellular localization of these genes was determined in medaka gonads using the whole-mount in situ hybridization technique. We confirm that gsdf gene expression is restricted to Sertoli and granulosa cells in contact with the premeiotic and meiotic cells. The nup54 gene is expressed in spermatocytes and previtellogenic oocytes. Transcripts corresponding to the ovary-specific genes (aff1, klhl8, and sdad1) are detected only in previtellogenic oocytes. No expression was detected in the gonocytes in 10 dpf embryos. In conclusion, we show that the gsdf gene localizes to a syntenic chromosomal fragment harboring evolutionary conserved genes in vertebrates. These genes are preferentially expressed in previtelloogenic oocytes, and thus, they display a different cellular localization compared to that of the gsdf gene indicating that the later gene is not co-regulated. Interestingly, our study identifies new clustered genes that are specifically expressed in previtellogenic oocytes (nup54, aff1, klhl8, sdad1). Copyright © 2010 Elsevier B.V. All rights reserved.

Single cell transcriptome analysis of MCF-7 reveals consistently and inconsistently expressed gene groups each associated with distinct cellular localization and functions

PubMed Central

Chen, Tzu-Han; Shiau, Hsin-Chieh

2018-01-01

Single cell transcriptome (SCT) analysis provides superior resolution to illustrate tumor cell heterogeneity for clinical implications. We characterized four SCTs of MCF-7 using 143 housekeeping genes (HKGs) as control, of which lactate dehydrogenase B (LDHB) expression is silenced. These SCT libraries mapped to 11,423, 11,486, 10,380, and 11,306 RefSeq genes (UCSC), respectively. High consistency in HKG expression levels across all four SCTs, along with transcriptional silencing of LDHB, was observed, suggesting a high sensitivity and reproducibility of the SCT analysis. Cross-library comparison on expression levels by scatter plotting revealed a linear correlation and an 83–94% overlap in transcript isoforms and expressed genes were also observed. To gain insight of transcriptional diversity among the SCTs, expressed genes were split into consistently expressed (CE) (expressed in all SCTs) and inconsistently expressed (IE) (expressed in some but not all SCTs) genes for further characterization, along with the 142 expressed HKGs as a reference. Distinct transcriptional strengths were found among these groups, with averages of 1,612.0, 88.0 and 1.2 FPKM for HKGs, CE and IE, respectively. Comparison between CE and IE groups further indicated that expressions of CE genes vary more significantly than that of IE genes. Gene Ontology analysis indicated that proteins encoded by CE genes are mainly involved in fundamental intracellular activities, while proteins encoded by IE genes are mainly for extracellular activities, especially acting as receptors or ion channels. The diversified gene expressions, especially for those encoded by IE genes, may contribute to cancer drug resistance. PMID:29920548

Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants.

PubMed

Kudo, Toru; Sasaki, Yohei; Terashima, Shin; Matsuda-Imai, Noriko; Takano, Tomoyuki; Saito, Misa; Kanno, Maasa; Ozaki, Soichi; Suwabe, Keita; Suzuki, Go; Watanabe, Masao; Matsuoka, Makoto; Takayama, Seiji; Yano, Kentaro

2016-10-13

In quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes. Recently emerging RNA sequencing (RNA-seq) provides an ideal resource for comprehensive exploration of reference genes since this method is capable of detecting all expressed genes, in principle including even unknown genes. We report the results of a comprehensive exploration of reference genes using public RNA-seq data from plants such as Arabidopsis thaliana (Arabidopsis), Glycine max (soybean), Solanum lycopersicum (tomato) and Oryza sativa (rice). To select reference genes suitable for the broadest experimental conditions possible, candidates were surveyed by the following four steps: (1) evaluation of the basal expression level of each gene in each experiment; (2) evaluation of the expression stability of each gene in each experiment; (3) evaluation of the expression stability of each gene across the experiments; and (4) selection of top-ranked genes, after ranking according to the number of experiments in which the gene was expressed stably. Employing this procedure, 13, 10, 12 and 21 top candidates for reference genes were proposed in Arabidopsis, soybean, tomato and rice, respectively. Microarray expression data confirmed that the expression of the proposed reference genes under broad experimental conditions was more stable than that of commonly used reference genes. These novel reference genes will be useful for analyzing gene expression profiles across experiments carried out under various experimental conditions.

Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling.

PubMed

Hinchliffe, Doug J; Meredith, William R; Yeater, Kathleen M; Kim, Hee Jin; Woodward, Andrew W; Chen, Z Jeffrey; Triplett, Barbara A

2010-05-01

Gene expression profiles of developing cotton (Gossypium hirsutum L.) fibers from two near-isogenic lines (NILs) that differ in fiber-bundle strength, short-fiber content, and in fewer than two genetic loci were compared using an oligonucleotide microarray. Fiber gene expression was compared at five time points spanning fiber elongation and secondary cell wall (SCW) biosynthesis. Fiber samples were collected from field plots in a randomized, complete block design, with three spatially distinct biological replications for each NIL at each time point. Microarray hybridizations were performed in a loop experimental design that allowed comparisons of fiber gene expression profiles as a function of time between the two NILs. Overall, developmental expression patterns revealed by the microarray experiment agreed with previously reported cotton fiber gene expression patterns for specific genes. Additionally, genes expressed coordinately with the onset of SCW biosynthesis in cotton fiber correlated with gene expression patterns of other SCW-producing plant tissues. Functional classification and enrichment analysis of differentially expressed genes between the two NILs revealed that genes associated with SCW biosynthesis were significantly up-regulated in fibers of the high-fiber quality line at the transition stage of cotton fiber development. For independent corroboration of the microarray results, 15 genes were selected for quantitative reverse transcription PCR analysis of fiber gene expression. These analyses, conducted over multiple field years, confirmed the temporal difference in fiber gene expression between the two NILs. We hypothesize that the loci conferring temporal differences in fiber gene expression between the NILs are important regulatory sequences that offer the potential for more targeted manipulation of cotton fiber quality.

Evolutionary conservation of vertebrate notochord genes in the ascidian Ciona intestinalis.

PubMed

Kugler, Jamie E; Passamaneck, Yale J; Feldman, Taya G; Beh, Jeni; Regnier, Todd W; Di Gregorio, Anna

2008-11-01

To reconstruct a minimum complement of notochord genes evolutionarily conserved across chordates, we scanned the Ciona intestinalis genome using the sequences of 182 genes reported to be expressed in the notochord of different vertebrates and identified 139 candidate notochord genes. For 66 of these Ciona genes expression data were already available, hence we analyzed the expression of the remaining 73 genes and found notochord expression for 20. The predicted products of the newly identified notochord genes range from the transcription factors Ci-XBPa and Ci-miER1 to extracellular matrix proteins. We examined the expression of the newly identified notochord genes in embryos ectopically expressing Ciona Brachyury (Ci-Bra) and in embryos expressing a repressor form of this transcription factor in the notochord, and we found that while a subset of the genes examined are clearly responsive to Ci-Bra, other genes are not affected by alterations in its levels. We provide a first description of notochord genes that are not evidently influenced by the ectopic expression of Ci-Bra and we propose alternative regulatory mechanisms that might control their transcription. Copyright 2008 Wiley-Liss, Inc.

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions.

PubMed

Versluis, Dennis; D'Andrea, Marco Maria; Ramiro Garcia, Javier; Leimena, Milkha M; Hugenholtz, Floor; Zhang, Jing; Öztürk, Başak; Nylund, Lotta; Sipkema, Detmer; van Schaik, Willem; de Vos, Willem M; Kleerebezem, Michiel; Smidt, Hauke; van Passel, Mark W J

2015-07-08

Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance.

Clustering cancer gene expression data by projective clustering ensemble

PubMed Central

Yu, Xianxue; Yu, Guoxian

2017-01-01

Gene expression data analysis has paramount implications for gene treatments, cancer diagnosis and other domains. Clustering is an important and promising tool to analyze gene expression data. Gene expression data is often characterized by a large amount of genes but with limited samples, thus various projective clustering techniques and ensemble techniques have been suggested to combat with these challenges. However, it is rather challenging to synergy these two kinds of techniques together to avoid the curse of dimensionality problem and to boost the performance of gene expression data clustering. In this paper, we employ a projective clustering ensemble (PCE) to integrate the advantages of projective clustering and ensemble clustering, and to avoid the dilemma of combining multiple projective clusterings. Our experimental results on publicly available cancer gene expression data show PCE can improve the quality of clustering gene expression data by at least 4.5% (on average) than other related techniques, including dimensionality reduction based single clustering and ensemble approaches. The empirical study demonstrates that, to further boost the performance of clustering cancer gene expression data, it is necessary and promising to synergy projective clustering with ensemble clustering. PCE can serve as an effective alternative technique for clustering gene expression data. PMID:28234920

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

NASA Astrophysics Data System (ADS)

Versluis, Dennis; D'Andrea, Marco Maria; Ramiro Garcia, Javier; Leimena, Milkha M.; Hugenholtz, Floor; Zhang, Jing; Öztürk, Başak; Nylund, Lotta; Sipkema, Detmer; Schaik, Willem Van; de Vos, Willem M.; Kleerebezem, Michiel; Smidt, Hauke; Passel, Mark W. J. Van

2015-07-01

Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance.

Involvement of Resveratrol and ω-3 Polyunsaturated Fatty Acids on Sirtuin 1 Gene Expression in THP1 Cells.

PubMed

Tsuchiya, Takafumi; Endo, Ayano; Tsujikado, Kyoko; Inukai, Toshihiko

2017-10-01

Resveratrol, a kind of polyphenol, has the potential to activate the longevity gene in several cells, in the same manner as calorie restriction. We investigated the effect of resveratrol and ω-3-line polyunsaturated fatty acid on surtuin 1 (SIRT1) gene expression in human monocytes (THP1) cells. We examined the gene expression of THP1 cells using real-time polymerase chain reaction and Western blotting analysis. Resveratol, eicosapentaenoic acid (EPA) and docosahexaeanoic acid (DHA) as n-3 polyunsaturated fatty acid were added on THP1 cells. We observed the changes in the SIRT1 gene expression in those cells, under various doses of agents and in time courses. Then, we examined the interaction of glucose and mannitol on those agents׳ effect of the gene expression. The concentration range of glucose and mannitol was from 5-20mM, respectively. The SIRT1 gene expression could be defined in 24 and 48 hours both in real-time polymerase chain reaction analysis and in Western blotting. Resveratrol showed SIRT1 gene expression in a dose-dependent manner in the range of 0-20μM in both analyses. Although EPA at 10μM showed marked increase in SIRT1 gene expression compared to control condition in Western blotting, this phenomenon was not in dose-dependent manner. DHA did not exhibit any augmentation of SIRT1 gene expression in a dose-dependent manner in the range of 0-20μM in both analyses. We refined the dose-dependent inhibition of the SIRT1 gene expression within 20mM glucose medium. Although 20mM did not exhibit any inhibition, 10μM resveratrol induced the gene expression compared to control medium. Both 5 and 15mM mannitol medium did not significantly alter basic gene expression and 10μM resveratrol-induced gene expression. The present results suggest that resveratrol and EPA, but not DHA, markedly activated the SIRT1 gene expression in THP1 cells, and that high glucose medium could inhibit the basic gene expression, but not powerful resveratrol-induced gene expression, in those cells. Copyright © 2017 Southern Society for Clinical Investigation. Published by Elsevier Inc. All rights reserved.

Influence of Genetic Variations in Selenoprotein Genes on the Pattern of Gene Expression after Supplementation with Brazil Nuts

PubMed Central

Rogero, Marcelo M.; Hesketh, John

2017-01-01

Selenium (Se) is an essential micronutrient for human health. Its beneficial effects are exerted by selenoproteins, which can be quantified in blood and used as molecular biomarkers of Se status. We hypothesize that the presence of genetic polymorphisms in selenoprotein genes may: (1) influence the gene expression of specific selenoproteins and (2) influence the pattern of global gene expression after Brazil nut supplementation. The study was conducted with 130 healthy volunteers in Sao Paulo, Brazil, who consumed one Brazil nut (300 μg/Se) a day for eight weeks. Gene expression of GPX1 and SELENOP and genotyping were measured by real-time PCR using TaqMan Assays. Global gene expression was assessed by microarray using Illumina HumanHT-12 v4 BeadChips. Brazil nut supplementation significantly increased GPX1 mRNA expression only in subjects with CC genotype at rs1050450 (p < 0.05). SELENOP mRNA expression was significantly higher in A-carriers at rs7579 either before or after supplementation (p < 0.05). Genotype for rs713041 in GPX4 affected the pattern of blood cell global gene expression. Genetic variations in selenoprotein genes modulated both GPX1 and SELENOP selenoprotein gene expression and global gene expression in response to Brazil nut supplementation. PMID:28696394

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction.

PubMed

Yu, Yao; Tu, Kang; Zheng, Siyuan; Li, Yun; Ding, Guohui; Ping, Jie; Hao, Pei; Li, Yixue

2009-08-25

In the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing and analyzing in scientific researches. In our work, we integrated gene expression information from Gene Expression Omnibus (GEO), biomedical ontology from Medical Subject Headings (MeSH) and signaling pathway knowledge from sigPathway entries to develop a context mining tool for gene expression analysis - GEOGLE. GEOGLE offers a rapid and convenient way for searching relevant experimental datasets, pathways and biological terms according to multiple types of queries: including biomedical vocabularies, GDS IDs, gene IDs, pathway names and signature list. Moreover, GEOGLE summarizes the signature genes from a subset of GDSes and estimates the correlation between gene expression and the phenotypic distinction with an integrated p value. This approach performing global searching of expression data may expand the traditional way of collecting heterogeneous gene expression experiment data. GEOGLE is a novel tool that provides researchers a quantitative way to understand the correlation between gene expression and phenotypic distinction through meta-analysis of gene expression datasets from different experiments, as well as the biological meaning behind. The web site and user guide of GEOGLE are available at: http://omics.biosino.org:14000/kweb/workflow.jsp?id=00020.

Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.)

PubMed Central

2010-01-01

Background Perennial ryegrass (Lolium perenne L.) is an important pasture and turf crop. Biotechniques such as gene expression studies are being employed to improve traits in this temperate grass. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is among the best methods available for determining changes in gene expression. Before analysis of target gene expression, it is essential to select an appropriate normalisation strategy to control for non-specific variation between samples. Reference genes that have stable expression at different biological and physiological states can be effectively used for normalisation; however, their expression stability must be validated before use. Results Existing Serial Analysis of Gene Expression data were queried to identify six moderately expressed genes that had relatively stable gene expression throughout the year. These six candidate reference genes (eukaryotic elongation factor 1 alpha, eEF1A; TAT-binding protein homolog 1, TBP-1; eukaryotic translation initiation factor 4 alpha, eIF4A; YT521-B-like protein family protein, YT521-B; histone 3, H3; ubiquitin-conjugating enzyme, E2) were validated for qRT-PCR normalisation in 442 diverse perennial ryegrass (Lolium perenne L.) samples sourced from field- and laboratory-grown plants under a wide range of experimental conditions. Eukaryotic EF1A is encoded by members of a multigene family exhibiting differential expression and necessitated the expression analysis of different eEF1A encoding genes; a highly expressed eEF1A (h), a moderately, but stably expressed eEF1A (s), and combined expression of multigene eEF1A (m). NormFinder identified eEF1A (s) and YT521-B as the best combination of two genes for normalisation of gene expression data in perennial ryegrass following different defoliation management in the field. Conclusions This study is unique in the magnitude of samples tested with the inclusion of numerous field-grown samples, helping pave the way to conduct gene expression studies in perennial biomass crops under field-conditions. From our study several stably expressed reference genes have been validated. This provides useful candidates for reference gene selection in perennial ryegrass under conditions other than those tested here. PMID:20089196

DNMT3B modulates the expression of cancer-related genes and downregulates the expression of the gene VAV3 via methylation

PubMed Central

Peralta-Arrieta, Irlanda; Hernández-Sotelo, Daniel; Castro-Coronel, Yaneth; Leyva-Vázquez, Marco Antonio; Illades-Aguiar, Berenice

2017-01-01

Altered promoter DNA methylation is one of the most important epigenetic abnormalities in human cancer. DNMT3B, de novo methyltransferase, is clearly related to abnormal methylation of tumour suppressor genes, DNA repair genes and its overexpression contributes to oncogenic processes and tumorigenesis in vivo. The purpose of this study was to assess the effect of the overexpression of DNMT3B in HaCaT cells on global gene expression and on the methylation of selected genes to the identification of genes that can be target of DNMT3B. We found that the overexpression of DNMT3B in HaCaT cells, modulate the expression of genes related to cancer, downregulated the expression of 151 genes with CpG islands and downregulated the expression of the VAV3 gene via methylation of its promoter. These results highlight the importance of DNMT3B in gene expression and human cancer. PMID:28123849

DNMT3B modulates the expression of cancer-related genes and downregulates the expression of the gene VAV3 via methylation.

PubMed

Peralta-Arrieta, Irlanda; Hernández-Sotelo, Daniel; Castro-Coronel, Yaneth; Leyva-Vázquez, Marco Antonio; Illades-Aguiar, Berenice

2017-01-01

Altered promoter DNA methylation is one of the most important epigenetic abnormalities in human cancer. DNMT3B, de novo methyltransferase, is clearly related to abnormal methylation of tumour suppressor genes, DNA repair genes and its overexpression contributes to oncogenic processes and tumorigenesis in vivo . The purpose of this study was to assess the effect of the overexpression of DNMT3B in HaCaT cells on global gene expression and on the methylation of selected genes to the identification of genes that can be target of DNMT3B. We found that the overexpression of DNMT3B in HaCaT cells, modulate the expression of genes related to cancer, downregulated the expression of 151 genes with CpG islands and downregulated the expression of the VAV3 gene via methylation of its promoter. These results highlight the importance of DNMT3B in gene expression and human cancer.

Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks.

PubMed

Yeung, Enoch; Dy, Aaron J; Martin, Kyle B; Ng, Andrew H; Del Vecchio, Domitilla; Beck, James L; Collins, James J; Murray, Richard M

2017-07-26

Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks. We compare expression of induced genes arranged in convergent, divergent, or tandem orientations. Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem-oriented genes. Orientation affects gene expression whether one or both genes are induced. We postulate that transcriptional interference in divergent and tandem genes, mediated by supercoiling, can explain differences in expression and validate this hypothesis through modeling and in vitro supercoiling relaxation experiments. Treatment with gyrase abrogated intergenic context effects, bringing expression levels within 30% of each other. We rebuilt the toggle switch with convergent genes, taking advantage of supercoiling effects to improve threshold detection and switch stability. Copyright © 2017 Elsevier Inc. All rights reserved.

Differential gene expression in queen–worker caste determination in bumble-bees

PubMed Central

Pereboom, Jeffrey J. M; Jordan, William C; Sumner, Seirian; Hammond, Robert L; Bourke, Andrew F. G

2005-01-01

Investigating how differential gene expression underlies caste determination in the social Hymenoptera is central to understanding how variation in gene expression underlies adaptive phenotypic diversity. We investigated for the first time the association between differential gene expression and queen–worker caste determination in the bumble-bee Bombus terrestris. Using suppression subtractive hybridization we isolated 12 genes that were differentially expressed in queen- and worker-destined larvae. We found that the sets of genes underlying caste differences in larvae and adults failed to overlap greatly. We also found that B. terrestris shares some of the genes whose differential expression is associated with caste determination in the honeybee, Apis mellifera, but their expression patterns were not identical. Instead, we found B. terrestris to exhibit a novel pattern, whereby most genes upregulated (i.e. showing relatively higher levels of expression) in queen-destined larvae early in development were upregulated in worker-destined larvae late in development. Overall, our results suggest that caste determination in B. terrestris involves a difference not so much in the identity of genes expressed by queen- and worker-destined larvae, but primarily in the relative timing of their expression. This conclusion is of potential importance in the further study of phenotypic diversification via differential gene expression. PMID:16024376

Regulatory systems for hypoxia-inducible gene expression in ischemic heart disease gene therapy.

PubMed

Kim, Hyun Ah; Rhim, Taiyoun; Lee, Minhyung

2011-07-18

Ischemic heart diseases are caused by narrowed coronary arteries that decrease the blood supply to the myocardium. In the ischemic myocardium, hypoxia-responsive genes are up-regulated by hypoxia-inducible factor-1 (HIF-1). Gene therapy for ischemic heart diseases uses genes encoding angiogenic growth factors and anti-apoptotic proteins as therapeutic genes. These genes increase blood supply into the myocardium by angiogenesis and protect cardiomyocytes from cell death. However, non-specific expression of these genes in normal tissues may be harmful, since growth factors and anti-apoptotic proteins may induce tumor growth. Therefore, tight gene regulation is required to limit gene expression to ischemic tissues, to avoid unwanted side effects. For this purpose, various gene expression strategies have been developed for ischemic-specific gene expression. Transcriptional, post-transcriptional, and post-translational regulatory strategies have been developed and evaluated in ischemic heart disease animal models. The regulatory systems can limit therapeutic gene expression to ischemic tissues and increase the efficiency of gene therapy. In this review, recent progresses in ischemic-specific gene expression systems are presented, and their applications to ischemic heart diseases are discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

Expression patterns of WRKY genes in di-haploid Populus simonii × P. nigra in response to salinity stress revealed by quantitative real-time PCR and RNA sequencing.

PubMed

Wang, Shengji; Wang, Jiying; Yao, Wenjing; Zhou, Boru; Li, Renhua; Jiang, Tingbo

2014-10-01

Spatio-temporal expression patterns of 13 out of 119 poplar WRKY genes indicated dynamic and tissue-specific roles of WRKY family proteins in salinity stress tolerance. To understand the expression patterns of poplar WRKY genes under salinity stress, 51 of the 119 WRKY genes were selected from di-haploid Populus simonii × P. nigra by quantitative real-time PCR (qRT-PCR). We used qRT-PCR to profile the expression of the top 13 genes under salinity stress across seven time points, and employed RNA-Seq platforms to cross-validate it. Results demonstrated that all the 13 WRKY genes were expressed in root, stem, and leaf tissues, but their expression levels and overall patterns varied notably in these tissues. Regarding overall gene expression in roots, the 13 genes were significantly highly expressed at all six time points after the treatment, reaching the plateau of expression at hour 9. In leaves, the 13 genes were similarly up-regulated from 3 to 12 h in response to NaCl treatment. In stems, however, expression levels of the 13 genes did not show significant changes after the NaCl treatment. Regarding individual gene expression across the time points and the three tissues, the 13 genes can be classified into three clusters: the lowly expressed Cluster 1 containing PthWRKY28, 45 and 105; intermediately expressed Clusters 2 including PthWRKY56, 88 and 116; and highly expressed Cluster 3 consisting of PthWRKY41, 44, 51, 61, 62, 75 and 106. In general, genes in Cluster 2 and 3 displayed a dynamic pattern of "induced amplification-recovering", suggesting that these WRKY genes and corresponding pathways may play a critical role in mediating salt response and tolerance in a dynamic and tissue-specific manner.

Hox gene expression during postlarval development of the polychaete Alitta virens.

PubMed

Bakalenko, Nadezhda I; Novikova, Elena L; Nesterenko, Alexander Y; Kulakova, Milana A

2013-05-01

Hox genes are the family of transcription factors that play a key role in the patterning of the anterior-posterior axis of all bilaterian animals. These genes display clustered organization and colinear expression. Expression boundaries of individual Hox genes usually correspond with morphological boundaries of the body. Previously, we studied Hox gene expression during larval development of the polychaete Alitta virens (formerly Nereis virens) and discovered that Hox genes are expressed in nereid larva according to the spatial colinearity principle. Adult Alitta virens consist of multiple morphologically similar segments, which are formed sequentially in the growth zone. Since the worm grows for most of its life, postlarval segments constantly change their position along the anterior-posterior axis. We studied the expression dynamics of the Hox cluster during postlarval development of the nereid Alitta virens and found that 8 out of 11 Hox genes are transcribed as wide gene-specific gradients in the ventral nerve cord, ectoderm, and mesoderm. The expression domains constantly shift in accordance with the changing proportions of the growing worm, so expression domains of most Hox genes do not have stable anterior or/and posterior boundaries.In the course of our study, we revealed long antisense RNA (asRNA) for some Hox genes. Expression patterns of two of these genes were analyzed using whole-mount in-situ hybridization. This is the first discovery of antisense RNA for Hox genes in Lophotrochozoa. Hox gene expression in juvenile A. virens differs significantly from Hox gene expression patterns both in A. virens larva and in other Bilateria.We suppose that the postlarval function of the Hox genes in this polychaete is to establish and maintain positional coordinates in a constantly growing body, as opposed to creating morphological difference between segments.

Genomic DNA-based absolute quantification of gene expression in Vitis

USDA-ARS?s Scientific Manuscript database

Many studies in which gene expression is quantified by polymerase chain reaction represent the expression of a gene of interest (GOI) relative to that of a reference gene (RG). Relative expression is founded on the assumptions that RG expression is stable across samples, treatments, organs, etc., an...

Co-regulation of the atrial natriuretic factor and cardiac myosin light chain-2 genes during alpha-adrenergic stimulation of neonatal rat ventricular cells. Identification of cis sequences within an embryonic and a constitutive contractile protein gene which mediate inducible expression.

PubMed

Knowlton, K U; Baracchini, E; Ross, R S; Harris, A N; Henderson, S A; Evans, S M; Glembotski, C C; Chien, K R

1991-04-25

To study the mechanisms which mediate the transcriptional activation of cardiac genes during alpha adrenergic stimulation, the present study examined the regulated expression of three cardiac genes, a ventricular embryonic gene (atrial natriuretic factor, ANF), a constitutively expressed contractile protein gene (cardiac MLC-2), and a cardiac sodium channel gene. alpha 1-Adrenergic stimulation activates the expression and release of ANF from neonatal ventricular cells. As assessed by RNase protection analyses, treatment with alpha-adrenergic agonists increases the steady-state levels of ANF mRNA by greater than 15-fold. However, a rat cardiac sodium channel gene mRNA is not induced, indicating that alpha-adrenergic stimulation does not lead to an increase in the expression of all cardiac genes. Studies employing a series of rat ANF luciferase and rat MLC-2 luciferase fusion genes identify 315- and 92-base pair cis regulatory sequences within an embryonic gene (ANF) and a constitutively expressed contractile protein gene (MLC-2), respectively, which mediate alpha-adrenergic-inducible gene expression. Transfection of various ANF luciferase reporters into neonatal rat ventricular cells demonstrated that upstream sequences which mediate tissue-specific expression (-3003 to -638) can be segregated from those responsible for inducibility. The lack of inducibility of a cardiac Na+ channel gene, and the segregation of ANF gene sequences which mediate cardiac specific from those which mediate inducible expression, provides further insight into the relationship between muscle-specific and inducible expression during cardiac myocyte hypertrophy. Based on these results, a testable model is proposed for the induction of embryonic cardiac genes and constitutively expressed contractile protein genes and the noninducibility of a subset of cardiac genes during alpha-adrenergic stimulation of neonatal rat ventricular cells.

A framework for analyzing the relationship between gene expression and morphological, topological, and dynamical patterns in neuronal networks.

PubMed

de Arruda, Henrique Ferraz; Comin, Cesar Henrique; Miazaki, Mauro; Viana, Matheus Palhares; Costa, Luciano da Fontoura

2015-04-30

A key point in developmental biology is to understand how gene expression influences the morphological and dynamical patterns that are observed in living beings. In this work we propose a methodology capable of addressing this problem that is based on estimating the mutual information and Pearson correlation between the intensity of gene expression and measurements of several morphological properties of the cells. A similar approach is applied in order to identify effects of gene expression over the system dynamics. Neuronal networks were artificially grown over a lattice by considering a reference model used to generate artificial neurons. The input parameters of the artificial neurons were determined according to two distinct patterns of gene expression and the dynamical response was assessed by considering the integrate-and-fire model. As far as single gene dependence is concerned, we found that the interaction between the gene expression and the network topology, as well as between the former and the dynamics response, is strongly affected by the gene expression pattern. In addition, we observed a high correlation between the gene expression and some topological measurements of the neuronal network for particular patterns of gene expression. To our best understanding, there are no similar analyses to compare with. A proper understanding of gene expression influence requires jointly studying the morphology, topology, and dynamics of neurons. The proposed framework represents a first step towards predicting gene expression patterns from morphology and connectivity. Copyright © 2015. Published by Elsevier B.V.

HOX gene expression in phenotypic and genotypic subgroups and low HOXA gene expression as an adverse prognostic factor in pediatric ALL.

PubMed

Starkova, Julia; Zamostna, Blanka; Mejstrikova, Ester; Krejci, Roman; Drabkin, Harry A; Trka, Jan

2010-12-01

HOX genes play an important role in both normal lymphopoiesis and leukemogenesis. However, HOX expression patterns in leukemia cells compared to normal lymphoid progenitors have not been systematically studied in acute lymphoblastic leukemia (ALL) subtypes. The RNA expression levels of HOXA, HOXB, and CDX1/2 genes were analyzed by qRT-PCR in a cohort of 61 diagnostic pediatric ALL samples and FACS-sorted subpopulations of normal lymphoid progenitors. The RNA expression of HOXA7-10, HOXA13, and HOXB2-4 genes was exclusively detected in leukemic cells and immature progenitors. The RNA expression of HOXB6 and CDX2 genes was exclusively detected in leukemic cells but not in B-lineage cells at any of the studied developmental stages. HOXA3-4, HOXA7, and HOXB3-4 genes were differentially expressed between BCP-ALL and T-ALL subgroups, and among genotypically defined MLL/AF4, TEL/AML1, BCR/ABL, hyperdiploid and normal karyotype subgroups. However, this differential expression did not define specific clusters in hierarchical cluster analysis. HOXA7 gene was low expressed at the RNA level in patients with hyperdiploid leukemia, whereas HOXB7 and CDX2 genes were low expressed in TEL/AML1-positive and BCR/ABL-positive cases, respectively. In contrast to previous findings in acute myeloid leukemia, high HOXA RNA expression was associated with an excellent prognosis in Cox's regression model (P = 0.03). In MLL/AF4-positive ALL, lower HOXA RNA expression correlated with the methylation status of their promoters. HOX gene RNA expression cannot discriminate leukemia subgroups or relative maturity of leukemic cells. However, HOXA RNA expression correlates with prognosis, and particular HOX genes are expressed in specific genotypically characterized subgroups.

Evolution of AGL6-like MADS Box Genes in Grasses (Poaceae): Ovule Expression Is Ancient and Palea Expression Is New[W][OA

PubMed Central

Reinheimer, Renata; Kellogg, Elizabeth A.

2009-01-01

AGAMOUS-like6 (AGL6) genes encode MIKC-type MADS box transcription factors and are closely related to SEPALLATA and AP1/FUL-like genes. Here, we focus on the molecular evolution and expression of the AGL6-like genes in grasses. We have found that AGL6-like genes are expressed in ovules, lodicules (second whorl floral organs), paleas (putative first whorl floral organs), and floral meristems. Each of these expression domains was acquired at a different time in evolution, indicating that each represents a distinct function of the gene product and that the AGL6-like genes are pleiotropic. Expression in the inner integument of the ovule appears to be an ancient expression pattern corresponding to the expression of the gene in the megasporangium and integument in gymnosperms. Expression in floral meristems appears to have been acquired in the angiosperms and expression in second whorl organs in monocots. Early in grass evolution, AGL6-like orthologs acquired a new expression domain in the palea. Stamen expression is variable. Most grasses have a single AGL6-like gene (orthologous to the rice [Oryza sativa] gene MADS6). However, rice and other species of Oryza have a second copy (orthologous to rice MADS17) that appears to be the result of an ancient duplication. PMID:19749151

Untangling the Contributions of Sex-Specific Gene Regulation and X-Chromosome Dosage to Sex-Biased Gene Expression in Caenorhabditis elegans

PubMed Central

Kramer, Maxwell; Rao, Prashant; Ercan, Sevinc

2016-01-01

Dosage compensation mechanisms equalize the level of X chromosome expression between sexes. Yet the X chromosome is often enriched for genes exhibiting sex-biased, i.e., imbalanced expression. The relationship between X chromosome dosage compensation and sex-biased gene expression remains largely unexplored. Most studies determine sex-biased gene expression without distinguishing between contributions from X chromosome copy number (dose) and the animal’s sex. Here, we uncoupled X chromosome dose from sex-specific gene regulation in Caenorhabditis elegans to determine the effect of each on X expression. In early embryogenesis, when dosage compensation is not yet fully active, X chromosome dose drives the hermaphrodite-biased expression of many X-linked genes, including several genes that were shown to be responsible for hermaphrodite fate. A similar effect is seen in the C. elegans germline, where X chromosome dose contributes to higher hermaphrodite X expression, suggesting that lack of dosage compensation in the germline may have a role in supporting higher expression of X chromosomal genes with female-biased functions in the gonad. In the soma, dosage compensation effectively balances X expression between the sexes. As a result, somatic sex-biased expression is almost entirely due to sex-specific gene regulation. These results suggest that lack of dosage compensation in different tissues and developmental stages allow X chromosome copy number to contribute to sex-biased gene expression and function. PMID:27356611

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs.

PubMed

Gálvez, José Héctor; Tai, Helen H; Lagüe, Martin; Zebarth, Bernie J; Strömvik, Martina V

2016-05-19

Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha(-1) was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency.

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs

PubMed Central

Gálvez, José Héctor; Tai, Helen H.; Lagüe, Martin; Zebarth, Bernie J.; Strömvik, Martina V.

2016-01-01

Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha−1 was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency. PMID:27193058

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations

PubMed Central

Peng, Cheng; Shiu, Shin-Han

2016-01-01

Gene co-expression has been widely used to hypothesize gene function through guilt-by association. However, it is not clear to what degree co-expression is informative, whether it can be applied to genes involved in different biological processes, and how the type of dataset impacts inferences about gene functions. Here our goal is to assess the utility and limitations of using co-expression as a criterion to recover functional associations between genes. By determining the percentage of gene pairs in a metabolic pathway with significant expression correlation, we found that many genes in the same pathway do not have similar transcript profiles and the choice of dataset, annotation quality, gene function, expression similarity measure, and clustering approach significantly impacts the ability to recover functional associations between genes using Arabidopsis thaliana as an example. Some datasets are more informative in capturing coordinated expression profiles and larger data sets are not always better. In addition, to recover the maximum number of known pathways and identify candidate genes with similar functions, it is important to explore rather exhaustively multiple dataset combinations, similarity measures, clustering algorithms and parameters. Finally, we validated the biological relevance of co-expression cluster memberships with an independent phenomics dataset and found that genes that consistently cluster with leucine degradation genes tend to have similar leucine levels in mutants. This study provides a framework for obtaining gene functional associations by maximizing the information that can be obtained from gene expression datasets. PMID:27935950

Skin transcriptome profiles associated with coat color in sheep

PubMed Central

2013-01-01

Background Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color. Results There were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category. Conclusion The white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep. PMID:23758853

GEsture: an online hand-drawing tool for gene expression pattern search.

PubMed

Wang, Chunyan; Xu, Yiqing; Wang, Xuelin; Zhang, Li; Wei, Suyun; Ye, Qiaolin; Zhu, Youxiang; Yin, Hengfu; Nainwal, Manoj; Tanon-Reyes, Luis; Cheng, Feng; Yin, Tongming; Ye, Ning

2018-01-01

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a 'desirable' or 'user-defined' pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users' requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.

Juxtaposed genes in 7q21-22 amplicon contribute for two major gastric cancer sub-Types by mutual exclusive expression.

PubMed

Tamilzhalagan, Sembulingam; Muthuswami, Muthulakshmi; Ganesan, Kumaresan

2017-04-01

Genomic Copy Number Variations (CNV) and the associated gene signatures are useful for cancer prognosis, diagnosis, and targeted therapeutics. Earlier, 7q21-22 region was reported for frequent amplification in gastric cancer and potential candidate genes were identified. An analysis of the expression pattern of the 159 genes located in this amplicon revealed the consistent elevated expression of 21 genes in gastric tumors. These genes are closely arranged within the 20 Mb region, and they showed a bimodal expression pattern. SHFM1 and 14 other genes are expressed in intestinal type gastric tumors. COL1A2 and PCOLCE genes of this region are expressed in diffuse type gastric tumors. Similarly, genome-wide expression neighbors of SHFM1 and COL1A2 also showed mutually exclusive expression pattern, and stratify intestinal and diffuse type gastric tumors. The expression of COL1A2 gene-set is associated with poor prognosis, whereas the SHFM1 gene-set is associated with better prognosis among the gastric cancer patients. Despite being physical neighbors, the SHFM1 and COL1A2 genes express differentially in the two major clinical sub-types of gastric cancer in a mutually exclusive manner. The tight gene regulations operating between these juxtaposed genes deserve investigation to understand the molecular regulatory switch defining the determinants of the gastric cancer sub-types. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

[Application of dhfr gene negative Chinese hamster ovary cell line to express hepatitis B virus surface antigen].

PubMed

Yi, Y; Zhang, M; Liu, C

2001-06-01

To set up an efficient expressing system for recombinant hepatitis B virus surface antigen (HBsAg) in dhfr gene negative CHO cell line. HBsAg gene expressing plasmid pCI-dhfr-S was constructed by integrating HBsAg gene into plasmid pCI which carries dhfr gene. The HBsAg expressing cell line was set up by transfection of plasmid pCI-dhfr-S into dhfr gene negative CHO cell line in the way of lipofectin. Under the selective pressure of MTX, 18 of 28 clonized cell lines expressed HBsAg, 4 of them reached a high titer of 1:32 and protein content 1-3 micrograms/ml. In this study, the high level expression of HBsAg demonstrated that the dhfr negative mammalian cell line when recombined with plasmid harboring the corresponding deleted gene can efficiently express the foreign gene. The further steps toward building optimum conditions of the expressing system and the increase of expressed product are under study.

Gene expression inference with deep learning.

PubMed

Chen, Yifei; Li, Yi; Narayan, Rajiv; Subramanian, Aravind; Xie, Xiaohui

2016-06-15

Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes. We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes. D-GEX is available at https://github.com/uci-cbcl/D-GEX CONTACT: xhx@ics.uci.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Gene expression inference with deep learning

PubMed Central

Chen, Yifei; Li, Yi; Narayan, Rajiv; Subramanian, Aravind; Xie, Xiaohui

2016-01-01

Motivation: Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes. Results: We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes. Availability and implementation: D-GEX is available at https://github.com/uci-cbcl/D-GEX. Contact: xhx@ics.uci.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26873929

An atlas of gene expression and gene co-regulation in the human retina.

PubMed

Pinelli, Michele; Carissimo, Annamaria; Cutillo, Luisa; Lai, Ching-Hung; Mutarelli, Margherita; Moretti, Maria Nicoletta; Singh, Marwah Veer; Karali, Marianthi; Carrella, Diego; Pizzo, Mariateresa; Russo, Francesco; Ferrari, Stefano; Ponzin, Diego; Angelini, Claudia; Banfi, Sandro; di Bernardo, Diego

2016-07-08

The human retina is a specialized tissue involved in light stimulus transduction. Despite its unique biology, an accurate reference transcriptome is still missing. Here, we performed gene expression analysis (RNA-seq) of 50 retinal samples from non-visually impaired post-mortem donors. We identified novel transcripts with high confidence (Observed Transcriptome (ObsT)) and quantified the expression level of known transcripts (Reference Transcriptome (RefT)). The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. The RefT included 13 792 genes across 94 521 known transcripts. Mitochondrial genes were among the most highly expressed, accounting for about 10% of the reads. Of all the protein-coding genes in Gencode, 65% are expressed in the retina. We exploited inter-individual variability in gene expression to infer a gene co-expression network and to identify genes specifically expressed in photoreceptor cells. We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. RNA-seq data and the gene co-expression network are available online (http://retina.tigem.it). © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Selection and validation of reference genes for gene expression analysis in apomictic and sexual Cenchrus ciliaris

PubMed Central

2013-01-01

Background Apomixis is a naturally occurring asexual mode of seed reproduction resulting in offspring genetically identical to the maternal plant. Identifying differential gene expression patterns between apomictic and sexual plants is valuable to help deconstruct the trait. Quantitative RT-PCR (qRT-PCR) is a popular method for analyzing gene expression. Normalizing gene expression data using proper reference genes which show stable expression under investigated conditions is critical in qRT-PCR analysis. We used qRT-PCR to validate expression and stability of six potential reference genes (EF1alpha, EIF4A, UBCE, GAPDH, ACT2 and TUBA) in vegetative and reproductive tissues of B-2S and B-12-9 accessions of C. ciliaris. Findings Among tissue types evaluated, EF1alpha showed the highest level of expression while TUBA showed the lowest. When all tissue types were evaluated and compared between genotypes, EIF4A was the most stable reference gene. Gene expression stability for specific ovary stages of B-2S and B-12-9 was also determined. Except for TUBA, all other tested reference genes could be used for any stage-specific ovary tissue normalization, irrespective of the mode of reproduction. Conclusion Our gene expression stability assay using six reference genes, in sexual and apomictic accessions of C. ciliaris, suggests that EIF4A is the most stable gene across all tissue types analyzed. All other tested reference genes, with the exception of TUBA, could be used for gene expression comparison studies between sexual and apomictic ovaries over multiple developmental stages. This reference gene validation data in C. ciliaris will serve as an important base for future apomixis-related transcriptome data validation. PMID:24083672

Object-location training elicits an overlapping but temporally distinct transcriptional profile from contextual fear conditioning.

PubMed

Poplawski, Shane G; Schoch, Hannah; Wimmer, Mathieu; Hawk, Joshua D; Walsh, Jennifer L; Giese, Karl P; Abel, Ted

2014-12-01

Hippocampus-dependent learning is known to induce changes in gene expression, but information on gene expression differences between different learning paradigms that require the hippocampus is limited. The bulk of studies investigating RNA expression after learning use the contextual fear conditioning task, which couples a novel environment with a footshock. Although contextual fear conditioning has been useful in discovering gene targets, gene expression after spatial memory tasks has received less attention. In this study, we used the object-location memory task and studied gene expression at two time points after learning in a high-throughput manner using a microfluidic qPCR approach. We found that expression of the classic immediate-early genes changes after object-location training in a fashion similar to that observed after contextual fear conditioning. However, the temporal dynamics of gene expression are different between the two tasks, with object-location memory producing gene expression changes that last at least 2 hours. Our findings indicate that different training paradigms may give rise to distinct temporal dynamics of gene expression after learning. Copyright © 2014 Elsevier Inc. All rights reserved.

Object-Location Training Elicits an Overlapping but Temporally Distinct Transcriptional Profile from Contextual Fear Conditioning

PubMed Central

Wimmer, Mathieu; Hawk, Joshua D.; Walsh, Jennifer L.; Giese, Karl P.; Abel, Ted

2014-01-01

Hippocampus-dependent learning is known to induce changes in gene expression, but information on gene expression differences between different learning paradigms that require the hippocampus is limited. The bulk of studies investigating RNA expression after learning use the contextual fear conditioning task, which couples a novel environment with a footshock. Although contextual fear conditioning has been useful in discovering gene targets, gene expression after spatial memory tasks has received less attention. In this study, we used the object-location memory task and studied gene expression at two time points after learning in a high-throughput manner using a microfluidic qPCR approach. We found that expression of the classic immediate-early genes changes after object-location training in a fashion similar to that observed after contextual fear conditioning. However, the temporal dynamics of gene expression are different between the two tasks, with object-location memory producing gene expression changes that last at least 2 hours. Our findings indicate that different training paradigms may give rise to distinct temporal dynamics of gene expression after learning. PMID:25242102

Using RNA-seq data to select reference genes for normalizing gene expression in apple roots.

PubMed

Zhou, Zhe; Cong, Peihua; Tian, Yi; Zhu, Yanmin

2017-01-01

Gene expression in apple roots in response to various stress conditions is a less-explored research subject. Reliable reference genes for normalizing quantitative gene expression data have not been carefully investigated. In this study, the suitability of a set of 15 apple genes were evaluated for their potential use as reliable reference genes. These genes were selected based on their low variance of gene expression in apple root tissues from a recent RNA-seq data set, and a few previously reported apple reference genes for other tissue types. Four methods, Delta Ct, geNorm, NormFinder and BestKeeper, were used to evaluate their stability in apple root tissues of various genotypes and under different experimental conditions. A small panel of stably expressed genes, MDP0000095375, MDP0000147424, MDP0000233640, MDP0000326399 and MDP0000173025 were recommended for normalizing quantitative gene expression data in apple roots under various abiotic or biotic stresses. When the most stable and least stable reference genes were used for data normalization, significant differences were observed on the expression patterns of two target genes, MdLecRLK5 (MDP0000228426, a gene encoding a lectin receptor like kinase) and MdMAPK3 (MDP0000187103, a gene encoding a mitogen-activated protein kinase). Our data also indicated that for those carefully validated reference genes, a single reference gene is sufficient for reliable normalization of the quantitative gene expression. Depending on the experimental conditions, the most suitable reference genes can be specific to the sample of interest for more reliable RT-qPCR data normalization.

Using RNA-seq data to select reference genes for normalizing gene expression in apple roots

PubMed Central

Zhou, Zhe; Cong, Peihua; Tian, Yi

2017-01-01

Gene expression in apple roots in response to various stress conditions is a less-explored research subject. Reliable reference genes for normalizing quantitative gene expression data have not been carefully investigated. In this study, the suitability of a set of 15 apple genes were evaluated for their potential use as reliable reference genes. These genes were selected based on their low variance of gene expression in apple root tissues from a recent RNA-seq data set, and a few previously reported apple reference genes for other tissue types. Four methods, Delta Ct, geNorm, NormFinder and BestKeeper, were used to evaluate their stability in apple root tissues of various genotypes and under different experimental conditions. A small panel of stably expressed genes, MDP0000095375, MDP0000147424, MDP0000233640, MDP0000326399 and MDP0000173025 were recommended for normalizing quantitative gene expression data in apple roots under various abiotic or biotic stresses. When the most stable and least stable reference genes were used for data normalization, significant differences were observed on the expression patterns of two target genes, MdLecRLK5 (MDP0000228426, a gene encoding a lectin receptor like kinase) and MdMAPK3 (MDP0000187103, a gene encoding a mitogen-activated protein kinase). Our data also indicated that for those carefully validated reference genes, a single reference gene is sufficient for reliable normalization of the quantitative gene expression. Depending on the experimental conditions, the most suitable reference genes can be specific to the sample of interest for more reliable RT-qPCR data normalization. PMID:28934340

Stepwise evolution of corolla symmetry in CYCLOIDEA2-like and RADIALIS-like gene expression patterns in Lamiales.

PubMed

Zhong, Jinshun; Kellogg, Elizabeth A

2015-08-01

• CYCLOIDEA2 (CYC2)-like and RADIALIS (RAD)-like genes are needed for the normal development of corolla bilateral symmetry in Antirrhinum majus L. (snapdragon, Plantaginaceae, Lamiales). However, if and how changes in expression of CYC2-like and RAD-like genes correlate with the origin of corolla bilateral symmetry early in Lamiales remains largely unknown. The asymmetrical expression of CYC2-like and/or RAD-like genes during floral meristem development could be ancestral or derived in Plantaginaceae.• We used in situ RNA localization to examine the expression of CYC2-like and RAD-like genes in two early-diverging Lamiales.• CYC2-like and RAD-like genes are expressed broadly in the floral meristems in early-diverging Lamiales with radially symmetrical corollas, in contrast to their restricted expression in adaxial/lateral regions in core Lamiales. The expression pattern of CYC2-like genes has evolved in stepwise fashion, in that CYC2-like genes are likely expressed briefly in the floral meristem during flower development in sampled Oleaceae; prolonged expression of CYC2-like genes in petals originated in the common ancestor of Tetrachondraceae and core Lamiales, and asymmetrical expression in adaxial/lateral petals appeared later, in the common ancestor of the core Lamiales. Likewise, expression of RAD-like genes in petals appeared in early-diverging Lamiales or earlier; asymmetrical expression in adaxial/lateral petals then appeared in core Lamiales.• These data plus published reports of CYC2-like and RAD-like genes show that asymmetrical expression of these two genes is likely derived and correlates with the origins of corolla bilateral symmetry. © 2015 Botanical Society of America, Inc.

Transient, Inducible, Placenta-Specific Gene Expression in Mice

PubMed Central

Fan, Xiujun; Petitt, Matthew; Gamboa, Matthew; Huang, Mei; Dhal, Sabita; Druzin, Maurice L.; Wu, Joseph C.

2012-01-01

Molecular understanding of placental functions and pregnancy disorders is limited by the absence of methods for placenta-specific gene manipulation. Although persistent placenta-specific gene expression has been achieved by lentivirus-based gene delivery methods, developmentally and physiologically important placental genes have highly stage-specific functions, requiring controllable, transient expression systems for functional analysis. Here, we describe an inducible, placenta-specific gene expression system that enables high-level, transient transgene expression and monitoring of gene expression by live bioluminescence imaging in mouse placenta at different stages of pregnancy. We used the third generation tetracycline-responsive tranactivator protein Tet-On 3G, with 10- to 100-fold increased sensitivity to doxycycline (Dox) compared with previous versions, enabling unusually sensitive on-off control of gene expression in vivo. Transgenic mice expressing Tet-On 3G were created using a new integrase-based, site-specific approach, yielding high-level transgene expression driven by a ubiquitous promoter. Blastocysts from these mice were transduced with the Tet-On 3G-response element promoter-driving firefly luciferase using lentivirus-mediated placenta-specific gene delivery and transferred into wild-type pseudopregnant recipients for placenta-specific, Dox-inducible gene expression. Systemic Dox administration at various time points during pregnancy led to transient, placenta-specific firefly luciferase expression as early as d 5 of pregnancy in a Dox dose-dependent manner. This system enables, for the first time, reliable pregnancy stage-specific induction of gene expression in the placenta and live monitoring of gene expression during pregnancy. It will be widely applicable to studies of both placental development and pregnancy, and the site-specific Tet-On G3 mouse will be valuable for studies in a broad range of tissues. PMID:23011919

Analyzing gene expression time-courses based on multi-resolution shape mixture model.

PubMed

Li, Ying; He, Ye; Zhang, Yu

2016-11-01

Biological processes actually are a dynamic molecular process over time. Time course gene expression experiments provide opportunities to explore patterns of gene expression change over a time and understand the dynamic behavior of gene expression, which is crucial for study on development and progression of biology and disease. Analysis of the gene expression time-course profiles has not been fully exploited so far. It is still a challenge problem. We propose a novel shape-based mixture model clustering method for gene expression time-course profiles to explore the significant gene groups. Based on multi-resolution fractal features and mixture clustering model, we proposed a multi-resolution shape mixture model algorithm. Multi-resolution fractal features is computed by wavelet decomposition, which explore patterns of change over time of gene expression at different resolution. Our proposed multi-resolution shape mixture model algorithm is a probabilistic framework which offers a more natural and robust way of clustering time-course gene expression. We assessed the performance of our proposed algorithm using yeast time-course gene expression profiles compared with several popular clustering methods for gene expression profiles. The grouped genes identified by different methods are evaluated by enrichment analysis of biological pathways and known protein-protein interactions from experiment evidence. The grouped genes identified by our proposed algorithm have more strong biological significance. A novel multi-resolution shape mixture model algorithm based on multi-resolution fractal features is proposed. Our proposed model provides a novel horizons and an alternative tool for visualization and analysis of time-course gene expression profiles. The R and Matlab program is available upon the request. Copyright © 2016 Elsevier Inc. All rights reserved.

Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution

PubMed Central

Moretti, Stefano; van Leeuwen, Danitsja; Gmuender, Hans; Bonassi, Stefano; van Delft, Joost; Kleinjans, Jos; Patrone, Fioravante; Merlo, Domenico Franco

2008-01-01

Background In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, game theory has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions. Results In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called Comparative Analysis of Shapley value (shortly, CASh), is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability. Conclusion CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a synergistic effect between coalitional games and statistics that resulted in a selection of genes with a potential impact in the regulation of complex pathways. PMID:18764936

Variation-preserving normalization unveils blind spots in gene expression profiling

PubMed Central

Roca, Carlos P.; Gomes, Susana I. L.; Amorim, Mónica J. B.; Scott-Fordsmand, Janeck J.

2017-01-01

RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much larger than currently believed, and that it can be measured with available assays. Our results also explain, at least partially, the reproducibility problems encountered in transcriptomics studies. We expect that this improvement in detection will help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression. PMID:28276435

The CNET Automated Budget System (CABS) IV.

DTIC Science & Technology

1982-12-01

r RD-A124 173 THE CNET RUTOMATED BUDGET SYSTEM (CABS) IV(U) TRAINING 1/ ANALYSIS AND EVALUATION GROUP (NAVY) ORLANDO FL G N HODAK ET AL. DEC 82 TREG ...Ix ,A Ix A to 0 A a u H o••# •N U~~dl1 0-4 IL : IL N• €: . of, 4A "’ u j ilC x: 11-. ofl 11. 0 14 l of •joft -9 I C)l 0l 1 V) 0-0 r t 0 . Vl L-0C

Wheat differential gene expression induced by different races of Puccinia triticina.

PubMed

Neugebauer, Kerri A; Bruce, Myron; Todd, Tim; Trick, Harold N; Fellers, John P

2018-01-01

Puccinia triticina, the causal agent of wheat leaf rust, causes significant losses in wheat yield and quality each year worldwide. During leaf rust infection, the host plant recognizes numerous molecules, some of which trigger host defenses. Although P. triticina reproduces clonally, there is still variation within the population due to a high mutation frequency, host specificity, and environmental adaptation. This study explores how wheat responds on a gene expression level to different P. triticina races. Six P. triticina races were inoculated onto a susceptible wheat variety and samples were taken at six days post inoculation, just prior to pustule eruption. RNA sequence data identified 63 wheat genes differentially expressed between the six races. A time course, conducted over the first seven days post inoculation, was used to examine the expression pattern of 63 genes during infection. Forty-seven wheat genes were verified to have differential expression. Three common expression patterns were identified. In addition, two genes were associated with race specific gene expression. Differential expression of an ER molecular chaperone gene was associated with races from two different P. triticina lineages. Also, differential expression in an alanine glyoxylate aminotransferase gene was associated with races with virulence shifts for leaf rust resistance genes.

Genome-Wide Identification, Characterization and Expression Analysis of the Solute Carrier 6 Gene Family in Silkworm (Bombyx mori)

PubMed Central

Tang, Xin; Liu, Huawei; Chen, Quanmei; Wang, Xin; Xiong, Ying; Zhao, Ping

2016-01-01

The solute carrier 6 (SLC6) gene family, initially known as the neurotransmitter transporters, plays vital roles in the regulation of neurotransmitter signaling, nutrient absorption and motor behavior. In this study, a total of 16 candidate genes were identified as SLC6 family gene homologs in the silkworm (Bombyx mori) genome. Spatio-temporal expression patterns of silkworm SLC6 gene transcripts indicated that these genes were highly and specifically expressed in midgut, brain and gonads; moreover, these genes were expressed primarily at the feeding stage or adult stage. Levels of expression for most midgut-specific and midgut-enriched gene transcripts were down-regulated after starvation but up-regulated after re-feeding. In addition, we observed that expression levels of these genes except for BmSLC6-15 and BmGT1 were markedly up-regulated by a juvenile hormone analog. Moreover, brain-enriched genes showed differential expression patterns during wandering and mating processes, suggesting that these genes may be involved in modulating wandering and mating behaviors. Our results improve our understanding of the expression patterns and potential physiological functions of the SLC6 gene family, and provide valuable information for the comprehensive functional analysis of the SLC6 gene family. PMID:27706106