A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements

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

Henry, Kelli F.; Kawashima, Tomokazu; Goldberg, Robert B.

Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean ( Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5'-GAAAAGCGAA-3'), the 10 bp-like motif (5'-GAAAAACGAA-3'), and Region 2 motif (partial sequence 5'-TTGGT-3'). Here, we usemore » site-directed mutagenesis experiments in transgenic tobacco globularstage embryos to identify two additional cis-regulatory elements within the 54-bp cis-regulatory module that are required for G564 suspensor transcription: the Fifth motif (5'-GAGTTA-3') and a third 10-bp-related sequence (5'-GAAAACCACA-3'). Further deletion of the 54-bp fragment revealed that a 47-bp fragment containing the five motifs (the 10-bp, 10-bp-like, 10-bp-related, Region 2 and Fifth motifs) is sufficient for suspensor transcription, and represents a cis-regulatory module. A consensus sequence for each type of motif was determined by comparing motif sequences shown to activate suspensor transcription. Phylogenetic analyses suggest that the regulation of G564 is evolutionarily conserved. Lastly, a homologous cis-regulatory module was found upstream of the G564 ortholog in the Common Bean (Phaseolus vulgaris), indicating that the regulation of G564 is evolutionarily conserved in closely related bean species.« less

A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements.

PubMed

Henry, Kelli F; Kawashima, Tomokazu; Goldberg, Robert B

2015-06-01

Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean (Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5'-GAAAAGCGAA-3'), the 10 bp-like motif (5'-GAAAAACGAA-3'), and Region 2 motif (partial sequence 5'-TTGGT-3'). Here, we use site-directed mutagenesis experiments in transgenic tobacco globular-stage embryos to identify two additional cis-regulatory elements within the 54-bp cis-regulatory module that are required for G564 suspensor transcription: the Fifth motif (5'-GAGTTA-3') and a third 10-bp-related sequence (5'-GAAAACCACA-3'). Further deletion of the 54-bp fragment revealed that a 47-bp fragment containing the five motifs (the 10-bp, 10-bp-like, 10-bp-related, Region 2 and Fifth motifs) is sufficient for suspensor transcription, and represents a cis-regulatory module. A consensus sequence for each type of motif was determined by comparing motif sequences shown to activate suspensor transcription. Phylogenetic analyses suggest that the regulation of G564 is evolutionarily conserved. A homologous cis-regulatory module was found upstream of the G564 ortholog in the Common Bean (Phaseolus vulgaris), indicating that the regulation of G564 is evolutionarily conserved in closely related bean species.

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers

PubMed Central

Kwon, Andrew T.; Chou, Alice Yi; Arenillas, David J.; Wasserman, Wyeth W.

2011-01-01

We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to differentiated C2C12 myotubes. A subset of 19 CRMs validated as functional in the assay. The rate of predictive success reveals striking limitations of computational regulatory sequence analysis methods for CRM discovery. Motif-based methods performed no better than predictions based only on sequence conservation. Analysis of the properties of the functional sequences relative to inactive sequences identifies nucleotide sequence composition can be an important characteristic to incorporate in future methods for improved predictive specificity. Muscle-related TFBSs predicted within the functional sequences display greater sequence conservation than non-TFBS flanking regions. Comparison with recent MyoD and histone modification ChIP-Seq data supports the validity of the functional regions. PMID:22144875

SNPs located at CpG sites modulate genome-epigenome interaction

USDA-ARS?s Scientific Manuscript database

DNA methylation is an important molecular-level phenotype that links genotypes and complex disease traits. Previous studies have found local correlation between genetic variants and DNA methylation levels (cis-meQTLs). However, general mechanisms underlying cis-meQTLs are unclear. We conducted a cis...

Photoinduced work function changes by isomerization of a densely packed azobenzene-based SAM on Au: a joint experimental and theoretical study.

PubMed

Crivillers, N; Liscio, A; Di Stasio, F; Van Dyck, C; Osella, S; Cornil, D; Mian, S; Lazzerini, G M; Fenwick, O; Orgiu, E; Reinders, F; Braun, S; Fahlman, M; Mayor, M; Cornil, J; Palermo, V; Cacialli, F; Samorì, P

2011-08-28

Responsive monolayers are key building blocks for future applications in organic and molecular electronics in particular because they hold potential for tuning the physico-chemical properties of interfaces, including their energetics. Here we study a photochromic SAM based on a conjugated azobenzene derivative and its influence on the gold work function (Φ(Au)) when chemisorbed on its surface. In particular we show that the Φ(Au) can be modulated with external stimuli by controlling the azobenzene trans/cis isomerization process. This phenomenon is characterized experimentally by four different techniques, kelvin probe, kelvin probe force microscopy, electroabsorption spectroscopy and ultraviolet photoelectron spectroscopy. The use of different techniques implies exposing the SAM to different measurement conditions and different preparation methods, which, remarkably, do not alter the observed work function change (Φ(trans)-Φ(cis)). Theoretical calculations provided a complementary insight crucial to attain a deeper knowledge on the origin of the work function photo-modulation.

Design of polarization imaging system based on CIS and FPGA

NASA Astrophysics Data System (ADS)

Zeng, Yan-an; Liu, Li-gang; Yang, Kun-tao; Chang, Da-ding

2008-02-01

As polarization is an important characteristic of light, polarization image detecting is a new image detecting technology of combining polarimetric and image processing technology. Contrasting traditional image detecting in ray radiation, polarization image detecting could acquire a lot of very important information which traditional image detecting couldn't. Polarization image detecting will be widely used in civilian field and military field. As polarization image detecting could resolve some problem which couldn't be resolved by traditional image detecting, it has been researched widely around the world. The paper introduces polarization image detecting in physical theory at first, then especially introduces image collecting and polarization image process based on CIS (CMOS image sensor) and FPGA. There are two parts including hardware and software for polarization imaging system. The part of hardware include drive module of CMOS image sensor, VGA display module, SRAM access module and the real-time image data collecting system based on FPGA. The circuit diagram and PCB was designed. Stokes vector and polarization angle computing method are analyzed in the part of software. The float multiply of Stokes vector is optimized into just shift and addition operation. The result of the experiment shows that real time image collecting system could collect and display image data from CMOS image sensor in real-time.

miRNA-Mediated Relationships between Cis-SNP Genotypes and Transcript Intensities in Lymphocyte Cell Lines

PubMed Central

Zhang, Wensheng; Edwards, Andrea; Zhu, Dongxiao; Flemington, Erik K.; Deininger, Prescott; Zhang, Kun

2012-01-01

In metazoans, miRNAs regulate gene expression primarily through binding to target sites in the 3′ UTRs (untranslated regions) of messenger RNAs (mRNAs). Cis-acting variants within, or close to, a gene are crucial in explaining the variability of gene expression measures. Single nucleotide polymorphisms (SNPs) in the 3′ UTRs of genes can affect the base-pairing between miRNAs and mRNAs, and hence disrupt existing target sites (in the reference sequence) or create novel target sites, suggesting a possible mechanism for cis regulation of gene expression. Moreover, because the alleles of different SNPs within a DNA sequence of limited length tend to be in strong linkage disequilibrium (LD), we hypothesize the variants of miRNA target sites caused by SNPs potentially function as bridges linking the documented cis-SNP markers to the expression of the associated genes. A large-scale analysis was herein performed to test this hypothesis. By systematically integrating multiple latest information sources, we found 21 significant gene-level SNP-involved miRNA-mediated post-transcriptional regulation modules (SNP-MPRMs) in the form of SNP-miRNA-mRNA triplets in lymphocyte cell lines for the CEU and YRI populations. Among the cognate genes, six including ALG8, DGKE, GNA12, KLF11, LRPAP1, and MMAB are related to multiple genetic diseases such as depressive disorder and Type-II diabetes. Furthermore, we found that ∼35% of the documented transcript intensity-related cis-SNPs (∼950) in a recent publication are identical to, or in significant linkage disequilibrium (LD) (p<0.01) with, one or multiple SNPs located in miRNA target sites. Based on these associations (or identities), 69 significant exon-level SNP-MPRMs and 12 disease genes were further determined for two populations. These results provide concrete in silico evidence for the proposed hypothesis. The discovered modules warrant additional follow-up in independent laboratory studies. PMID:22348086

In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression

PubMed Central

Zagrijchuk, Elizaveta A.; Sabirov, Marat A.; Holloway, David M.; Spirov, Alexander V.

2014-01-01

Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes. PMID:24712536

cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila

PubMed Central

2014-01-01

Background Cis-regulatory modules (CRMs), or the DNA sequences required for regulating gene expression, play the central role in biological researches on transcriptional regulation in metazoan species. Nowadays, the systematic understanding of CRMs still mainly resorts to computational methods due to the time-consuming and small-scale nature of experimental methods. But the accuracy and reliability of different CRM prediction tools are still unclear. Without comparative cross-analysis of the results and combinatorial consideration with extra experimental information, there is no easy way to assess the confidence of the predicted CRMs. This limits the genome-wide understanding of CRMs. Description It is known that transcription factor binding and epigenetic profiles tend to determine functions of CRMs in gene transcriptional regulation. Thus integration of the genome-wide epigenetic profiles with systematically predicted CRMs can greatly help researchers evaluate and decipher the prediction confidence and possible transcriptional regulatory functions of these potential CRMs. However, these data are still fragmentary in the literatures. Here we performed the computational genome-wide screening for potential CRMs using different prediction tools and constructed the pioneer database, cisMEP (cis-regulatory module epigenetic profile database), to integrate these computationally identified CRMs with genomic epigenetic profile data. cisMEP collects the literature-curated TFBS location data and nine genres of epigenetic data for assessing the confidence of these potential CRMs and deciphering the possible CRM functionality. Conclusions cisMEP aims to provide a user-friendly interface for researchers to assess the confidence of different potential CRMs and to understand the functions of CRMs through experimentally-identified epigenetic profiles. The deposited potential CRMs and experimental epigenetic profiles for confidence assessment provide experimentally testable hypotheses for the molecular mechanisms of metazoan gene regulation. We believe that the information deposited in cisMEP will greatly facilitate the comparative usage of different CRM prediction tools and will help biologists to study the modular regulatory mechanisms between different TFs and their target genes. PMID:25521507

Functional Evolution of a cis-Regulatory Module

PubMed Central

Palsson, Arnar; Alekseeva, Elena; Bergman, Casey M; Nathan, Janaki; Kreitman, Martin

2005-01-01

Lack of knowledge about how regulatory regions evolve in relation to their structure–function may limit the utility of comparative sequence analysis in deciphering cis-regulatory sequences. To address this we applied reverse genetics to carry out a functional genetic complementation analysis of a eukaryotic cis-regulatory module—the even-skipped stripe 2 enhancer—from four Drosophila species. The evolution of this enhancer is non-clock-like, with important functional differences between closely related species and functional convergence between distantly related species. Functional divergence is attributable to differences in activation levels rather than spatiotemporal control of gene expression. Our findings have implications for understanding enhancer structure–function, mechanisms of speciation and computational identification of regulatory modules. PMID:15757364

Retinoic Acid Isomers Facilitate Apolipoprotein E Production and Lipidation in Astrocytes through the Retinoid X Receptor/Retinoic Acid Receptor Pathway*

PubMed Central

Zhao, Jing; Fu, Yuan; Liu, Chia-Chen; Shinohara, Mitsuru; Nielsen, Henrietta M.; Dong, Qiang; Kanekiyo, Takahisa; Bu, Guojun

2014-01-01

Apolipoprotein E (apoE) is the major cholesterol transport protein in the brain. Among the three human APOE alleles (APOE2, APOE3, and APOE4), APOE4 is the strongest genetic risk factor for late-onset Alzheimer disease (AD). The accumulation of amyloid-β (Aβ) is a central event in AD pathogenesis. Increasing evidence demonstrates that apoE isoforms differentially regulate AD-related pathways through both Aβ-dependent and -independent mechanisms; therefore, modulating apoE secretion, lipidation, and function might be an attractive approach for AD therapy. We performed a drug screen for compounds that modulate apoE production in immortalized astrocytes derived from apoE3-targeted replacement mice. Here, we report that retinoic acid (RA) isomers, including all-trans-RA, 9-cis-RA, and 13-cis-RA, significantly increase apoE secretion to ∼4-fold of control through retinoid X receptor (RXR) and RA receptor. These effects on modulating apoE are comparable with the effects recently reported for the RXR agonist bexarotene. Furthermore, all of these compounds increased the expression of the cholesterol transporter ABCA1 and ABCG1 levels and decreased cellular uptake of Aβ in an apoE-dependent manner. Both bexarotene and 9-cis-RA promote the lipidation status of apoE, in which 9-cis-RA promotes a stronger effect and exhibits less cytotoxicity compared with bexarotene. Importantly, we showed that oral administration of bexarotene and 9-cis-RA significantly increases apoE, ABCA1, and ABCG1 levels in mouse brains. Taken together, our results demonstrate that RXR/RA receptor agonists, including several RA isomers, are effective modulators of apoE secretion and lipidation and may be explored as potential drugs for AD therapy. PMID:24599963

Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints

PubMed Central

2012-01-01

Background The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa) formed ten clusters of orthologous groups (COG) with genes from the monocot sorghum (Sorghum bicolor) and dicot Arabidopsis (Arabidopsis thaliana). The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns. Results The most apparent pattern observed was the occurrence of spatially conserved ‘core modules’ among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS) classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic) or organ-associated signals, which may be functioning as ‘regulatory fine-tuners’ and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis. Conclusions Patterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in conjunction with lineage-specific or species-specific regulatory fine-tuners. This synergy may be critical for finer-scale spatio-temporal regulation, hence unique expression profiles of homologous transcription factors from different species with distinct zones of ecological adaptation such as rice, sorghum and Arabidopsis. The patterns revealed from these comparisons set the stage for further empirical validation by functional genomics. PMID:22992304

Detection of eQTL modules mediated by activity levels of transcription factors.

PubMed

Sun, Wei; Yu, Tianwei; Li, Ker-Chau

2007-09-01

Studies of gene expression quantitative trait loci (eQTL) in different organisms have shown the existence of eQTL hot spots: each being a small segment of DNA sequence that harbors the eQTL of a large number of genes. Two questions of great interest about eQTL hot spots arise: (1) which gene within the hot spot is responsible for the linkages, i.e. which gene is the quantitative trait gene (QTG)? (2) How does a QTG affect the expression levels of many genes linked to it? Answers to the first question can be offered by available biological evidence or by statistical methods. The second question is harder to address. One simple situation is that the QTG encodes a transcription factor (TF), which regulates the expression of genes linked to it. However, previous results have shown that TFs are not overrepresented in the eQTL hot spots. In this article, we consider the scenario that the propagation of genetic perturbation from a QTG to other linked genes is mediated by the TF activity. We develop a procedure to detect the eQTL modules (eQTL hot spots together with linked genes) that are compatible with this scenario. We first detect 27 eQTL modules from a yeast eQTL data, and estimate TF activity profiles using the method of Yu and Li (2005). Then likelihood ratio tests (LRTs) are conducted to find 760 relationships supporting the scenario of TF activity mediation: (DNA polymorphism --> cis-linked gene --> TF activity --> downstream linked gene). They are organized into 4 eQTL modules: an amino acid synthesis module featuring a cis-linked gene LEU2 and the mediating TF Leu3; a pheromone response module featuring a cis-linked gene GPA1 and the mediating TF Ste12; an energy-source control module featuring two cis-linked genes, GSY2 and HAP1, and the mediating TF Hap1; a mitotic exit module featuring four cis-linked genes, AMN1, CSH1, DEM1 and TOS1, and the mediating TF complex Ace2/Swi5. Gene Ontology is utilized to reveal interesting functional groups of the downstream genes in each module. Our methods are implemented in an R package: eqtl.TF, which includes source codes and relevant data. It can be freely downloaded at http://www.stat.ucla.edu/~sunwei/software.htm. http://www.stat.ucla.edu/~sunwei/yeast_eQTL_TF/supplementary.pdf.

Rapid immuno-analytical system physically integrated with lens-free CMOS image sensor for food-borne pathogens.

PubMed

Jeon, Jin-Woo; Kim, Jee-Hyun; Lee, Jong-Mook; Lee, Won-Ho; Lee, Do-Young; Paek, Se-Hwan

2014-02-15

To realize an inexpensive, pocket-sized immunosensor system, a rapid test devise based on cross-flow immuno-chromatography was physically combined with a lens-free CMOS image sensor (CIS), which was then applied to the detection of the food-borne pathogen, Salmonella typhimurium (S. typhimurium). Two CISs, each retaining 1.3 mega pixel array, were mounted on a printed circuit board to fabricate a disposable sensing module, being connectable with a signal detection system. For the bacterial analysis, a cellulose membrane-based immunosensing platform, ELISA-on-a-chip (EOC), was employed, being integrated with the CIS module, and the antigen-antibody reaction sites were aligned with the respective sensor. In such sensor construction, the chemiluminescent signals produced from the EOC are transferred directly into the sensors and are converted to electric signals on the detector. The EOC-CIS integrated sensor was capable of detecting a traceable amount of the bacterium (4.22 × 10(3)CFU/mL), nearly comparable to that adopting a sophisticated detector such as cooled-charge-coupled device, while having greatly reduced dimensions and cost. Upon coupling with immuno-magnetic separation, the sensor showed an additional 67-fold enhancement in the detection limit. Furthermore, a real sample test was carried out for fish muscles inoculated with a sample of 3.3CFU S. typhimurium per 10 g, which was able to be detected earlier than 6h after the onset of pre-enrichment by culture. © 2013 Elsevier B.V. All rights reserved.

Pharmacotherapy of retinal disease with visual cycle modulators.

PubMed

Hussain, Rehan M; Gregori, Ninel Z; Ciulla, Thomas A; Lam, Byron L

2018-04-01

Pharmacotherapy with visual cycle modulators (VCMs) is under investigation for retinitis pigmentosa (RP), Leber congenital amaurosis (LCA), Stargardt macular dystrophy (SMD) and nonexudative age-related macular degeneration (AMD), all blinding diseases that lack effective treatment options. Areas covered: The authors review investigational VCMs, including oral retinoids, 9-cis-retinyl-acetate (zuretinol) and 9-cis-β-carotene, which restore 11-cis-retinal levels in RP and LCA caused by LRAT and RPE65 gene mutations, and may improve visual acuity and visual fields. Therapies for SMD aiming to decrease accumulation of toxic Vitamin A dimers and lipofuscin in the retina and retinal pigment epithelium (RPE) include C20-D3-vitamin A (ALK-001), isotretinoin, VM200, emixustat, and A1120. Mouse models of SMD show promising data for these treatments, though proof of efficacy in humans is currently lacking. Fenretinide and emixustat are investigational VCMs for dry AMD, though neither has been shown to reduce geographic atrophy or improve vision in human trials. A1120 prevents retinol transport into the RPE and may spare the side effects typically seen in VCMs (nyctalopia and chromatopsia) per mouse studies. Expert opinion: Oral VCMs may be feasible treatment options for degenerative retinal diseases based on pre-clinical and some early clinical studies. Further trials are warranted to assess their efficacy and safety in humans.

Pathogenic adaptation of intracellular bacteria by rewiring a cis-regulatory input function.

PubMed

Osborne, Suzanne E; Walthers, Don; Tomljenovic, Ana M; Mulder, David T; Silphaduang, Uma; Duong, Nancy; Lowden, Michael J; Wickham, Mark E; Waller, Ross F; Kenney, Linda J; Coombes, Brian K

2009-03-10

The acquisition of DNA by horizontal gene transfer enables bacteria to adapt to previously unexploited ecological niches. Although horizontal gene transfer and mutation of protein-coding sequences are well-recognized forms of pathogen evolution, the evolutionary significance of cis-regulatory mutations in creating phenotypic diversity through altered transcriptional outputs is not known. We show the significance of regulatory mutation for pathogen evolution by mapping and then rewiring a cis-regulatory module controlling a gene required for murine typhoid. Acquisition of a binding site for the Salmonella pathogenicity island-2 regulator, SsrB, enabled the srfN gene, ancestral to the Salmonella genus, to play a role in pathoadaptation of S. typhimurium to a host animal. We identified the evolved cis-regulatory module and quantified the fitness gain that this regulatory output accrues for the bacterium using competitive infections of host animals. Our findings highlight a mechanism of pathogen evolution involving regulatory mutation that is selected because of the fitness advantage the new regulatory output provides the incipient clones.

Pathogenic adaptation of intracellular bacteria by rewiring a cis-regulatory input function

PubMed Central

Osborne, Suzanne E.; Walthers, Don; Tomljenovic, Ana M.; Mulder, David T.; Silphaduang, Uma; Duong, Nancy; Lowden, Michael J.; Wickham, Mark E.; Waller, Ross F.; Kenney, Linda J.; Coombes, Brian K.

2009-01-01

The acquisition of DNA by horizontal gene transfer enables bacteria to adapt to previously unexploited ecological niches. Although horizontal gene transfer and mutation of protein-coding sequences are well-recognized forms of pathogen evolution, the evolutionary significance of cis-regulatory mutations in creating phenotypic diversity through altered transcriptional outputs is not known. We show the significance of regulatory mutation for pathogen evolution by mapping and then rewiring a cis-regulatory module controlling a gene required for murine typhoid. Acquisition of a binding site for the Salmonella pathogenicity island-2 regulator, SsrB, enabled the srfN gene, ancestral to the Salmonella genus, to play a role in pathoadaptation of S. typhimurium to a host animal. We identified the evolved cis-regulatory module and quantified the fitness gain that this regulatory output accrues for the bacterium using competitive infections of host animals. Our findings highlight a mechanism of pathogen evolution involving regulatory mutation that is selected because of the fitness advantage the new regulatory output provides the incipient clones. PMID:19234126

Theory on the mechanism of distal action of transcription factors: looping of DNA versus tracking along DNA

NASA Astrophysics Data System (ADS)

Murugan, R.

2010-10-01

In this paper, we develop a theory on the mechanism of distal action of the transcription factors, which are bound at their respective cis-regulatory enhancer modules on the promoter-RNA polymerase II (PR) complexes to initiate the transcription event in eukaryotes. We consider both the looping and tracking modes of their distal communication and calculate the mean first passage time that is required for the distal interactions of the complex of enhancer and transcription factor with the PR via both these modes. We further investigate how this mean first passage time is dependent on the length of the DNA segment (L, base-pairs) that connects the cis-regulatory binding site and the respective promoter. When the radius of curvature of this connecting segment of DNA is R that was induced upon binding of the transcription factor at the cis-acting element and RNAPII at the promoter in cis-positions, our calculations indicate that the looping mode of distal action will dominate when L is such that L > 2πR and the tracking mode of distal action will be favored when L < 2πR. The time required for the distal action will be minimum when L = 2πR where the typical value of R for the binding of histones will be R ~ 16 bps and L ~ 102 bps. It seems that the free energy associated with the binding of the transcription factor with its cis-acting element and the distance of this cis-acting element from the corresponding promoter of the gene of interest is negatively correlated. Our results suggest that the looping and tracking modes of distal action are concurrently operating on the transcription activation and the physics that determines the timescales associated with the looping/tracking in the mechanism of action of these transcription factors on the initiation of the transcription event must put a selection pressure on the distribution of the distances of cis-regulatory modules from their respective promoters of the genes. The computational analysis of the upstream sequences of promoters of various genes in the human and mouse genomes for the presence of putative cis-regulatory elements for a set of known transcription factors using the position weight matrices available with the JASPAR database indicates the presence of cis-acting elements with maximum probability at a distance of ~102 bps from the promoters which substantiates our theoretical predictions.

Proline N-oxides: modulators of the 3D conformation of linear peptides through "NO-turns".

PubMed

Farahani, Majid D; Honarparvar, Bahareh; Albericio, Fernando; Maguire, Glenn E M; Govender, Thavendran; Arvidsson, Per I; Kruger, Hendrik G

2014-07-07

Small peptides are essential mediators of numerous physiological processes. Consequently, there is huge interest in the de novo design of peptides with a predictable folding and related biological activity. In this study, we investigate the possibility of modulating the secondary structure of tetrapeptides through proline N-oxide moieties and N-methylation of the peptide backbone. A series of tetrapeptides were synthesised to investigate the combined effect of Pro N-oxide and N-methylation of the amide bond on the (n + 1) residue in terms of cis- and trans-isomerization, as well as how these modifications direct potential intramolecular hydrogen bonding interactions. The right combination of both these parameters led to a trans to cis-conformational interconversion and a change in the nature of the hydrogen bonding interactions, as demonstrated by NMR spectroscopic, molecular modeling analysis and thermal coefficient studies. Proline N-oxide residues were proposed to induce turns we named as NO-γ-turns and NO-β-turns based on their similarity to traditional γ- and β-turns.

Divergently overlapping cis-encoded antisense RNA regulating toxin-antitoxin systems from E. coli: hok/sok, ldr/rdl, symE/symR.

PubMed

Kawano, Mitsuoki

2012-12-01

Toxin-antitoxin (TA) systems are categorized into three classes based on the type of antitoxin. In type I TA systems, the antitoxin is a small antisense RNA that inhibits translation of small toxic proteins by binding to the corresponding mRNAs. Those type I TA systems were originally identified as plasmid stabilization modules rendering a post-segregational killing (PSK) effect on the host cells. The type I TA loci also exist on the Escherichia coli chromosome but their biological functions are less clear. Genetic organization and regulatory elements of hok/sok and ldr/rdl families are very similar and the toxins are predicted to contain a transmembrane domain, but otherwise share no detectable sequence similarity. This review will give an overview of the type I TA modules of E. coli K-12, especially hok/sok, ldr/rdl and SOS-inducible symE/symR systems, which are regulated by divergently overlapping cis-encoded antisense RNAs.

Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates

PubMed Central

Baudouin-Gonzalez, Luís; Santos, Marília A; Tempesta, Camille; Sucena, Élio; Roch, Fernando; Tanaka, Kohtaro

2017-01-01

Abstract Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. We have directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 Ma. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, we show that they diverged from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. Our analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. We argue that our findings will encourage studying cis-regulatory evolution at the whole-locus level to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression. PMID:28961967

Both the cis-trans equilibrium and isomerization dynamics of a single proline amide modulate β2-microglobulin amyloid assembly

PubMed Central

Torbeev, Vladimir Yu.; Hilvert, Donald

2013-01-01

The human protein β2-microglobulin (β2m) aggregates as amyloid fibrils in patients undergoing long-term hemodialysis. Isomerization of Pro32 from its native cis to a nonnative trans conformation is thought to trigger β2m misfolding and subsequent amyloid assembly. To examine this hypothesis, we systematically varied the free-energy profile of proline cis-trans isomerization by replacing Pro32 with a series of 4-fluoroprolines via total chemical synthesis. We show that β2m’s stability, (un)folding, and aggregation properties are all influenced by the rate and equilibrium of Pro32 cis-trans isomerization. As anticipated, the β2m monomer was either stabilized or destabilized by respective incorporation of (2S,4S)-fluoroproline, which favors the native cis amide bond, or the stereoisomeric (2S,4R)-fluoroproline, which disfavors this conformation. However, substitution of Pro32 with 4,4-difluoroproline, which has nearly the same cis-trans preference as proline but an enhanced isomerization rate, caused pronounced destabilization of the protein and increased oligomerization at neutral pH. More remarkably, these subtle alterations in chemical composition—incorporation of one or two fluorine atoms into a single proline residue in the 99 amino acid long protein—modulated the aggregation properties of β2m, inducing the formation of polymorphically distinct amyloid fibrils. These results highlight the importance of conformational dynamics for molecular assembly of an amyloid cross-β structure and provide insights into mechanistic aspects of Pro32 cis-trans isomerism in β2m aggregation. PMID:24262149

Both the cis-trans equilibrium and isomerization dynamics of a single proline amide modulate β2-microglobulin amyloid assembly.

PubMed

Torbeev, Vladimir Yu; Hilvert, Donald

2013-12-10

The human protein β2-microglobulin (β2m) aggregates as amyloid fibrils in patients undergoing long-term hemodialysis. Isomerization of Pro32 from its native cis to a nonnative trans conformation is thought to trigger β2m misfolding and subsequent amyloid assembly. To examine this hypothesis, we systematically varied the free-energy profile of proline cis-trans isomerization by replacing Pro32 with a series of 4-fluoroprolines via total chemical synthesis. We show that β2m's stability, (un)folding, and aggregation properties are all influenced by the rate and equilibrium of Pro32 cis-trans isomerization. As anticipated, the β2m monomer was either stabilized or destabilized by respective incorporation of (2S,4S)-fluoroproline, which favors the native cis amide bond, or the stereoisomeric (2S,4R)-fluoroproline, which disfavors this conformation. However, substitution of Pro32 with 4,4-difluoroproline, which has nearly the same cis-trans preference as proline but an enhanced isomerization rate, caused pronounced destabilization of the protein and increased oligomerization at neutral pH. More remarkably, these subtle alterations in chemical composition--incorporation of one or two fluorine atoms into a single proline residue in the 99 amino acid long protein--modulated the aggregation properties of β2m, inducing the formation of polymorphically distinct amyloid fibrils. These results highlight the importance of conformational dynamics for molecular assembly of an amyloid cross-β structure and provide insights into mechanistic aspects of Pro32 cis-trans isomerism in β2m aggregation.

A cis-regulatory logic simulator.

PubMed

Zeigler, Robert D; Gertz, Jason; Cohen, Barak A

2007-07-27

A major goal of computational studies of gene regulation is to accurately predict the expression of genes based on the cis-regulatory content of their promoters. The development of computational methods to decode the interactions among cis-regulatory elements has been slow, in part, because it is difficult to know, without extensive experimental validation, whether a particular method identifies the correct cis-regulatory interactions that underlie a given set of expression data. There is an urgent need for test expression data in which the interactions among cis-regulatory sites that produce the data are known. The ability to rapidly generate such data sets would facilitate the development and comparison of computational methods that predict gene expression patterns from promoter sequence. We developed a gene expression simulator which generates expression data using user-defined interactions between cis-regulatory sites. The simulator can incorporate additive, cooperative, competitive, and synergistic interactions between regulatory elements. Constraints on the spacing, distance, and orientation of regulatory elements and their interactions may also be defined and Gaussian noise can be added to the expression values. The simulator allows for a data transformation that simulates the sigmoid shape of expression levels from real promoters. We found good agreement between sets of simulated promoters and predicted regulatory modules from real expression data. We present several data sets that may be useful for testing new methodologies for predicting gene expression from promoter sequence. We developed a flexible gene expression simulator that rapidly generates large numbers of simulated promoters and their corresponding transcriptional output based on specified interactions between cis-regulatory sites. When appropriate rule sets are used, the data generated by our simulator faithfully reproduces experimentally derived data sets. We anticipate that using simulated gene expression data sets will facilitate the direct comparison of computational strategies to predict gene expression from promoter sequence. The source code is available online and as additional material. The test sets are available as additional material.

Design of low noise imaging system

NASA Astrophysics Data System (ADS)

Hu, Bo; Chen, Xiaolai

2017-10-01

In order to meet the needs of engineering applications for low noise imaging system under the mode of global shutter, a complete imaging system is designed based on the SCMOS (Scientific CMOS) image sensor CIS2521F. The paper introduces hardware circuit and software system design. Based on the analysis of key indexes and technologies about the imaging system, the paper makes chips selection and decides SCMOS + FPGA+ DDRII+ Camera Link as processing architecture. Then it introduces the entire system workflow and power supply and distribution unit design. As for the software system, which consists of the SCMOS control module, image acquisition module, data cache control module and transmission control module, the paper designs in Verilog language and drives it to work properly based on Xilinx FPGA. The imaging experimental results show that the imaging system exhibits a 2560*2160 pixel resolution, has a maximum frame frequency of 50 fps. The imaging quality of the system satisfies the requirement of the index.

Webinars on MyCDX Changes and New Defects and Recalls Reporting Module

EPA Pesticide Factsheets

This webinar focuses on MyCDX changes, overview of the new defects and recalls reporting module, the Engines and Vehicles Compliance Information System (EV-CIS) home page prototype and deployment information.

The potato amylase inhibitor gene SbAI regulates cold-induced sweetening in potato tubers by modulating amylase activity.

PubMed

Zhang, Huiling; Liu, Jun; Hou, Juan; Yao, Ying; Lin, Yuan; Ou, Yongbin; Song, Botao; Xie, Conghua

2014-09-01

Potato cold-induced sweetening (CIS) is critical for the postharvest quality of potato tubers. Starch degradation is considered to be one of the key pathways in the CIS process. However, the functions of the genes that encode enzymes related to starch degradation in CIS and the activity regulation of these enzymes have received less attention. A potato amylase inhibitor gene known as SbAI was cloned from the wild potato species Solanum berthaultii. This genetic transformation confirmed that in contrast to the SbAI suppression in CIS-resistant potatoes, overexpressing SbAI in CIS-sensitive potatoes resulted in less amylase activity and a lower rate of starch degradation accompanied by a lower reducing sugar (RS) content in cold-stored tubers. This finding suggested that the SbAI gene may play crucial roles in potato CIS by modulating the amylase activity. Further investigations indicated that pairwise protein-protein interactions occurred between SbAI and α-amylase StAmy23, β-amylases StBAM1 and StBAM9. SbAI could inhibit the activities of both α-amylase and β-amylase in potato tubers primarily by repressing StAmy23 and StBAM1, respectively. These findings provide the first evidence that SbAI is a key regulator of the amylases that confer starch degradation and RS accumulation in cold-stored potato tubers. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

PubMed Central

Sun, Hong; Guns, Tias; Fierro, Ana Carolina; Thorrez, Lieven; Nijssen, Siegfried; Marchal, Kathleen

2012-01-01

Computationally retrieving biologically relevant cis-regulatory modules (CRMs) is not straightforward. Because of the large number of candidates and the imperfection of the screening methods, many spurious CRMs are detected that are as high scoring as the biologically true ones. Using ChIP-information allows not only to reduce the regions in which the binding sites of the assayed transcription factor (TF) should be located, but also allows restricting the valid CRMs to those that contain the assayed TF (here referred to as applying CRM detection in a query-based mode). In this study, we show that exploiting ChIP-information in a query-based way makes in silico CRM detection a much more feasible endeavor. To be able to handle the large datasets, the query-based setting and other specificities proper to CRM detection on ChIP-Seq based data, we developed a novel powerful CRM detection method ‘CPModule’. By applying it on a well-studied ChIP-Seq data set involved in self-renewal of mouse embryonic stem cells, we demonstrate how our tool can recover combinatorial regulation of five known TFs that are key in the self-renewal of mouse embryonic stem cells. Additionally, we make a number of new predictions on combinatorial regulation of these five key TFs with other TFs documented in TRANSFAC. PMID:22422841

Improved perception of music with a harmonic based algorithm for cochlear implants.

PubMed

Li, Xing; Nie, Kaibao; Imennov, Nikita S; Rubinstein, Jay T; Atlas, Les E

2013-07-01

The lack of fine structure information in conventional cochlear implant (CI) encoding strategies presumably contributes to the generally poor music perception with CIs. To improve CI users' music perception, a harmonic-single-sideband-encoder (HSSE) strategy was developed , which explicitly tracks the harmonics of a single musical source and transforms them into modulators conveying both amplitude and temporal fine structure cues to electrodes. To investigate its effectiveness, vocoder simulations of HSSE and the conventional continuous-interleaved-sampling (CIS) strategy were implemented. Using these vocoders, five normal-hearing subjects' melody and timbre recognition performance were evaluated: a significant benefit of HSSE to both melody (p < 0.002) and timbre (p < 0.026) recognition was found. Additionally, HSSE was acutely tested in eight CI subjects. On timbre recognition, a significant advantage of HSSE over the subjects' clinical strategy was demonstrated: the largest improvement was 35% and the mean 17% (p < 0.013). On melody recognition, two subjects showed 20% improvement with HSSE; however, the mean improvement of 7% across subjects was not significant (p > 0.090). To quantify the temporal cues delivered to the auditory nerve, the neural spike patterns evoked by HSSE and CIS for one melody stimulus were simulated using an auditory nerve model. Quantitative analysis demonstrated that HSSE can convey temporal pitch cues better than CIS. The results suggest that HSSE is a promising strategy to enhance music perception with CIs.

Stereoselective modulatory actions of oleamide on GABAA receptors and voltage-gated Na+ channels in vitro: a putative endogenous ligand for depressant drug sites in CNS

PubMed Central

Verdon, Bernard; Zheng, Jian; Nicholson, Russell A; Ganelli, C Robin; Lees, George

2000-01-01

cis-9,10-octadecenoamide (‘oleamide') accumulates in CSF on sleep deprivation. It induces sleep in animals (the trans form is inactive) but its cellular actions are poorly characterized. We have used electrophysiology in cultures from embryonic rat cortex and biochemical studies in mouse nerve preparations to address these issues. Twenty μM cis-oleamide (but not trans) reversibly enhanced GABAA currents and depressed the frequency of spontaneous excitatory and inhibitory synaptic activity in cultured networks. cis-oleamide stereoselectively blocked veratridine-induced (but not K+-induced) depolarisation of mouse synaptoneurosomes (IC50, 13.9 μM). The cis isomer stereoselectively blocked veratridine-induced (but not K+-induced) [3H]-GABA release from mouse synaptosomes (IC50, 4.6 μM). At 20 μM cis-oleamide, but not trans, produced a marked inhibition of Na+ channel-dependent rises in intrasynaptosomal Ca2+. The physiological significance of these observations was examined by isolating Na+ spikes in cultured pyramidal neurones. Sixty-four μM cis-oleamide did not significantly alter the amplitude, rate of rise or duration of unitary action potentials (1 Hz). cis-Oleamide stereoselectively suppressed sustained repetitive firing (SRF) in these cells with an EC50 of 4.1 μM suggesting a frequency- or state-dependent block of voltage-gated Na+ channels. Oleamide is a stereoselective modulator of both postsynaptic GABAA receptors and presynaptic or somatic voltage-gated Na+ channels which are crucial for synaptic inhibition and conduction. The modulatory actions are strikingly similar to those displayed by sedative or anticonvulsant barbiturates and a variety of general anaesthetics. Oleamide may represent an endogenous modulator for drug receptors and an important regulator of arousal. PMID:10694234

Advances in polycrystalline thin-film photovoltaics for space applications

NASA Technical Reports Server (NTRS)

Lanning, Bruce R.; Armstrong, Joseph H.; Misra, Mohan S.

1994-01-01

Polycrystalline, thin-film photovoltaics represent one of the few (if not the only) renewable power sources which has the potential to satisfy the demanding technical requirements for future space applications. The demand in space is for deployable, flexible arrays with high power-to-weight ratios and long-term stability (15-20 years). In addition, there is also the demand that these arrays be produced by scalable, low-cost, high yield, processes. An approach to significantly reduce costs and increase reliability is to interconnect individual cells series via monolithic integration. Both CIS and CdTe semiconductor films are optimum absorber materials for thin-film n-p heterojunction solar cells, having band gaps between 0.9-1.5 ev and demonstrated small area efficiencies, with cadmium sulfide window layers, above 16.5 percent. Both CIS and CdTe polycrystalline thin-film cells have been produced on a laboratory scale by a variety of physical and chemical deposition methods, including evaporation, sputtering, and electrodeposition. Translating laboratory processes which yield these high efficiency, small area cells into the design of a manufacturing process capable of producing 1-sq ft modules, however, requires a quantitative understanding of each individual step in the process and its (each step) effect on overall module performance. With a proper quantification and understanding of material transport and reactivity for each individual step, manufacturing process can be designed that is not 'reactor-specific' and can be controlled intelligently with the design parameters of the process. The objective of this paper is to present an overview of the current efforts at MMC to develop large-scale manufacturing processes for both CIS and CdTe thin-film polycrystalline modules. CIS cells/modules are fabricated in a 'substrate configuration' by physical vapor deposition techniques and CdTe cells/modules are fabricated in a 'superstrate configuration' by wet chemical methods. Both laser and mechanical scribing operations are used to monolithically integrate (series interconnect) the individual cells into modules. Results will be presented at the cell and module development levels with a brief description of the test methods used to qualify these devices for space applications. The approach and development efforts are directed towards large-scale manufacturability of established thin-film, polycrystalline processing methods for large area modules with less emphasis on maximizing small area efficiencies.

Real-time detection of natural objects using AM-coded spectral matching imager

NASA Astrophysics Data System (ADS)

Kimachi, Akira

2004-12-01

This paper describes application of the amplitude-modulation (AM)-coded spectral matching imager (SMI) to real-time detection of natural objects such as human beings, animals, vegetables, or geological objects or phenomena, which are much more liable to change with time than artificial products while often exhibiting characteristic spectral functions associated with some specific activity states. The AM-SMI produces correlation between spectral functions of the object and a reference at each pixel of the correlation image sensor (CIS) in every frame, based on orthogonal amplitude modulation (AM) of each spectral channel and simultaneous demodulation of all channels on the CIS. This principle makes the SMI suitable to monitoring dynamic behavior of natural objects in real-time by looking at a particular spectral reflectance or transmittance function. A twelve-channel multispectral light source was developed with improved spatial uniformity of spectral irradiance compared to a previous one. Experimental results of spectral matching imaging of human skin and vegetable leaves are demonstrated, as well as a preliminary feasibility test of imaging a reflective object using a test color chart.

Real-time detection of natural objects using AM-coded spectral matching imager

NASA Astrophysics Data System (ADS)

Kimachi, Akira

2005-01-01

This paper describes application of the amplitude-modulation (AM)-coded spectral matching imager (SMI) to real-time detection of natural objects such as human beings, animals, vegetables, or geological objects or phenomena, which are much more liable to change with time than artificial products while often exhibiting characteristic spectral functions associated with some specific activity states. The AM-SMI produces correlation between spectral functions of the object and a reference at each pixel of the correlation image sensor (CIS) in every frame, based on orthogonal amplitude modulation (AM) of each spectral channel and simultaneous demodulation of all channels on the CIS. This principle makes the SMI suitable to monitoring dynamic behavior of natural objects in real-time by looking at a particular spectral reflectance or transmittance function. A twelve-channel multispectral light source was developed with improved spatial uniformity of spectral irradiance compared to a previous one. Experimental results of spectral matching imaging of human skin and vegetable leaves are demonstrated, as well as a preliminary feasibility test of imaging a reflective object using a test color chart.

Engineering Translational Activators with CRISPR-Cas System.

PubMed

Du, Pei; Miao, Chensi; Lou, Qiuli; Wang, Zefeng; Lou, Chunbo

2016-01-15

RNA parts often serve as critical components in genetic engineering. Here we report a design of translational activators which is composed of an RNA endoribonuclease (Csy4) and two exchangeable RNA modules. Csy4, a member of Cas endoribonuclease, cleaves at a specific recognition site; this cleavage releases a cis-repressive RNA module (crRNA) from the masked ribosome binding site (RBS), which subsequently allows the downstream translation initiation. Unlike small RNA as a translational activator, the endoribonuclease-based activator is able to efficiently unfold the perfect RBS-crRNA pairing. As an exchangeable module, the crRNA-RBS duplex was forwardly and reversely engineered to modulate the dynamic range of translational activity. We further showed that Csy4 and its recognition site, together as a module, can also be replaced by orthogonal endoribonuclease-recognition site homologues. These modularly structured, high-performance translational activators would endow the programming of gene expression in the translation level with higher feasibility.

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

PubMed Central

Sanges, Remo; Hadzhiev, Yavor; Gueroult-Bellone, Marion; Roure, Agnes; Ferg, Marco; Meola, Nicola; Amore, Gabriele; Basu, Swaraj; Brown, Euan R.; De Simone, Marco; Petrera, Francesca; Licastro, Danilo; Strähle, Uwe; Banfi, Sandro; Lemaire, Patrick; Birney, Ewan; Müller, Ferenc; Stupka, Elia

2013-01-01

Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as ‘Olfactores conserved non-coding elements’. PMID:23393190

Integrating mRNA and miRNA Weighted Gene Co-Expression Networks with eQTLs in the Nucleus Accumbens of Subjects with Alcohol Dependence

PubMed Central

Blevins, Tana; Aliev, Fazil; Adkins, Amy; Hack, Laura; Bigdeli, Tim; D. van der Vaart, Andrew; Web, Bradley Todd; Bacanu, Silviu-Alin; Kalsi, Gursharan; Kendler, Kenneth S.; Miles, Michael F.; Dick, Danielle; Riley, Brien P.; Dumur, Catherine; Vladimirov, Vladimir I.

2015-01-01

Alcohol consumption is known to lead to gene expression changes in the brain. After performing weighted gene co-expression network analyses (WGCNA) on genome-wide mRNA and microRNA (miRNA) expression in Nucleus Accumbens (NAc) of subjects with alcohol dependence (AD; N = 18) and of matched controls (N = 18), six mRNA and three miRNA modules significantly correlated with AD were identified (Bonferoni-adj. p≤ 0.05). Cell-type-specific transcriptome analyses revealed two of the mRNA modules to be enriched for neuronal specific marker genes and downregulated in AD, whereas the remaining four mRNA modules were enriched for astrocyte and microglial specific marker genes and upregulated in AD. Gene set enrichment analysis demonstrated that neuronal specific modules were enriched for genes involved in oxidative phosphorylation, mitochondrial dysfunction and MAPK signaling. Glial-specific modules were predominantly enriched for genes involved in processes related to immune functions, i.e. cytokine signaling (all adj. p≤ 0.05). In mRNA and miRNA modules, 461 and 25 candidate hub genes were identified, respectively. In contrast to the expected biological functions of miRNAs, correlation analyses between mRNA and miRNA hub genes revealed a higher number of positive than negative correlations (χ2 test p≤ 0.0001). Integration of hub gene expression with genome-wide genotypic data resulted in 591 mRNA cis-eQTLs and 62 miRNA cis-eQTLs. mRNA cis-eQTLs were significantly enriched for AD diagnosis and AD symptom counts (adj. p = 0.014 and p = 0.024, respectively) in AD GWAS signals in a large, independent genetic sample from the Collaborative Study on Genetics of Alcohol (COGA). In conclusion, our study identified putative gene network hubs coordinating mRNA and miRNA co-expression changes in the NAc of AD subjects, and our genetic (cis-eQTL) analysis provides novel insights into the etiological mechanisms of AD. PMID:26381263

13-cis-retinoic acid metabolism in vivo. The major tissue metabolites in the rat have the all-trans configuration.

PubMed

McCormick, A M; Kroll, K D; Napoli, J L

1983-08-02

The liver and intestinal metabolites of orally dosed 13-cis-[11-3H]retinoic acid were analyzed in normal and 13-cis-retinoic acid treated rats 3 h after administration of the radiolabeled retinoid. all-trans-Retinoic acid was identified as a liver and intestinal mucosa metabolite in normal rats given physiological doses of 13-cis-[3H]retinoic acid. all-trans-Retinoyl glucuronide was identified as the most abundant radiolabeled metabolite in mucosa and a prominent liver metabolite under the same conditions. Thus, the major 13-cis-retinoic acid metabolites retained in liver and mucosa, two retinoid target tissues, had the all-trans configuration. These data indicate that the isomerization of 13-cis-retinoic acid to all-trans-retinoic acid and the subsequent conversion to all-trans-retinoyl glucuronide are central events in the in vivo metabolism of 13-cis-retinoic acid in the rat. Moreover, the all-trans-retinoic acid detected in vivo could account for a significant fraction of the physiological activity of 13-cis-retinoic acid. The tissue disposition and metabolism of orally dosed 13-cis-[3H]retinoic acid are modulated by retinoid treatment. Chronic 13-cis-retinoic acid treatment apparently increased the intestinal accumulation of all-trans-retinoic acid, all-trans-retinoyl glucuronide, and 13-cis-retinoyl glucuronide. The liver concentrations of tritiated all-trans-retinoic acid and all-trans-retinoyl glucuronide were also elevated in 13-cis-retinoic acid treated rats.

Regulatory logic of pan-neuronal gene expression in C. elegans

PubMed Central

Stefanakis, Nikolaos; Carrera, Ines; Hobert, Oliver

2015-01-01

While neuronal cell types display an astounding degree of phenotypic diversity, most if not all neuron types share a core panel of terminal features. However, little is known about how pan-neuronal expression patterns are genetically programmed. Through an extensive analysis of the cis-regulatory control regions of a battery of pan-neuronal C.elegans genes, including genes involved in synaptic vesicle biology and neuropeptide signaling, we define a common organizational principle in the regulation of pan-neuronal genes in the form of a surprisingly complex array of seemingly redundant, parallel-acting cis-regulatory modules that direct expression to broad, overlapping domains throughout the nervous system. These parallel-acting cis-regulatory modules are responsive to a multitude of distinct trans-acting factors. Neuronal gene expression programs therefore fall into two fundamentally distinct classes. Neuron type-specific genes are generally controlled by discrete and non-redundantly acting regulatory inputs, while pan-neuronal gene expression is controlled by diverse, coincident and seemingly redundant regulatory inputs. PMID:26291158

cis-Regulatory control of the initial neurogenic pattern of onecut gene expression in the sea urchin embryo.

PubMed

Barsi, Julius C; Davidson, Eric H

2016-01-01

Specification of the ciliated band (CB) of echinoid embryos executes three spatial functions essential for postgastrular organization. These are establishment of a band about 5 cells wide which delimits and bounds other embryonic territories; definition of a neurogenic domain within this band; and generation within it of arrays of ciliary cells that bear the special long cilia from which the structure derives its name. In Strongylocentrotus purpuratus the spatial coordinates of the future ciliated band are initially and exactly determined by the disposition of a ring of cells that transcriptionally activate the onecut homeodomain regulatory gene, beginning in blastula stage, long before the appearance of the CB per se. Thus the cis-regulatory apparatus that governs onecut expression in the blastula directly reveals the genomic sequence code by which these aspects of the spatial organization of the embryo are initially determined. We screened the entire onecut locus and its flanking region for transcriptionally active cis-regulatory elements, and by means of BAC recombineered deletions identified three separated and required cis-regulatory modules that execute different functions. The operating logic of the crucial spatial control module accounting for the spectacularly precise and beautiful early onecut expression domain depends on spatial repression. Previously predicted oral ectoderm and aboral ectoderm repressors were identified by cis-regulatory mutation as the products of goosecoid and irxa genes respectively, while the pan-ectodermal activator SoxB1 supplies a transcriptional driver function. Copyright © 2015. Published by Elsevier Inc.

Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development

PubMed Central

Sehra, Bhupinder; Franks, Robert G.

2017-01-01

In the Arabidopsis thaliana seed pod, pod shatter and seed dispersal properties are in part determined by the development of a longitudinally orientated dehiscence zone (DZ) that derives from cells of the gynoecial valve margin (VM). Transcriptional regulation of the MADS protein encoding transcription factors genes SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2) are critical for proper VM identity specification and later on for DZ development. Current models of SHP1 and SHP2 regulation indicate that the transcription factors FRUITFULL (FUL) and REPLUMLESS (RPL) repress these SHP genes in the developing valve and replum domains, respectively. Thus the expression of the SHP genes is restricted to the VM. FUL encodes a MADS-box containing transcription factor that is predicted to act through CArG-box containing cis-regulatory motifs. Here we delimit functional modules within the SHP2 cis-regulatory region and examine the functional importance of CArG box motifs within these regulatory regions. We have characterized a 2.2kb region upstream of the SHP2 translation start site that drives early and late medial domain expression in the gynoecium, as well as expression within the VM and DZ. We identified two separable, independent cis-regulatory modules, a 1kb promoter region and a 700bp enhancer region, that are capable of giving VM and DZ expression. Our results argue for multiple independent cis-regulatory modules that support SHP2 expression during VM development and may contribute to the robustness of SHP2 expression in this tissue. Additionally, three closely positioned CArG box motifs located in the SHP2 upstream regulatory region were mutated in the context of the 2.2kb reporter construct. Mutating simultaneously all three CArG boxes caused a moderate de-repression of the SHP2 reporter that was detected within the valve domain, suggesting that these CArG boxes are involved in SHP2 repression in the valve. PMID:29085379

Cis-regulatory Evolution of Chalcone-Synthase Expression in the Genus Arabidopsis

PubMed Central

de Meaux, Juliette; Pop, A.; Mitchell-Olds, T.

2006-01-01

The contribution of cis-regulation to adaptive evolutionary change is believed to be essential, yet little is known about the evolutionary rules that govern regulatory sequences. Here, we characterize the short-term evolutionary dynamics of a cis-regulatory region within and among two closely related species, A. lyrata and A. halleri, and compare our findings to A. thaliana. We focused on the cis-regulatory region of chalcone synthase (CHS), a key enzyme involved in the synthesis of plant secondary metabolites. We observed patterns of nucleotide diversity that differ among species but do not depart from neutral expectations. Using intra- and interspecific F1 progeny, we have evaluated functional cis-regulatory variation in response to light and herbivory, environmental cues, which are known to induce CHS expression. We find that substantial cis-regulatory variation segregates within and among populations as well as between species, some of which results from interspecific genetic introgression. We further demonstrate that, in A. thaliana, CHS cis-regulation in response to herbivory is greater than in A. lyrata or A. halleri. Our work indicates that the evolutionary dynamics of a cis-regulatory region is characterized by pervasive functional variation, achieved mostly by modification of response modules to one but not all environmental cues. Our study did not detect the footprint of selection on this variation. PMID:17028316

Genome-wide computational analysis reveals cardiomyocyte-specific transcriptional Cis-regulatory motifs that enable efficient cardiac gene therapy.

PubMed

Rincon, Melvin Y; Sarcar, Shilpita; Danso-Abeam, Dina; Keyaerts, Marleen; Matrai, Janka; Samara-Kuko, Ermira; Acosta-Sanchez, Abel; Athanasopoulos, Takis; Dickson, George; Lahoutte, Tony; De Bleser, Pieter; VandenDriessche, Thierry; Chuah, Marinee K

2015-01-01

Gene therapy is a promising emerging therapeutic modality for the treatment of cardiovascular diseases and hereditary diseases that afflict the heart. Hence, there is a need to develop robust cardiac-specific expression modules that allow for stable expression of the gene of interest in cardiomyocytes. We therefore explored a new approach based on a genome-wide bioinformatics strategy that revealed novel cardiac-specific cis-acting regulatory modules (CS-CRMs). These transcriptional modules contained evolutionary-conserved clusters of putative transcription factor binding sites that correspond to a "molecular signature" associated with robust gene expression in the heart. We then validated these CS-CRMs in vivo using an adeno-associated viral vector serotype 9 that drives a reporter gene from a quintessential cardiac-specific α-myosin heavy chain promoter. Most de novo designed CS-CRMs resulted in a >10-fold increase in cardiac gene expression. The most robust CRMs enhanced cardiac-specific transcription 70- to 100-fold. Expression was sustained and restricted to cardiomyocytes. We then combined the most potent CS-CRM4 with a synthetic heart and muscle-specific promoter (SPc5-12) and obtained a significant 20-fold increase in cardiac gene expression compared to the cytomegalovirus promoter. This study underscores the potential of rational vector design to improve the robustness of cardiac gene therapy.

Overview Article: Identifying transcriptional cis-regulatory modules in animal genomes

PubMed Central

Suryamohan, Kushal; Halfon, Marc S.

2014-01-01

Gene expression is regulated through the activity of transcription factors and chromatin modifying proteins acting on specific DNA sequences, referred to as cis-regulatory elements. These include promoters, located at the transcription initiation sites of genes, and a variety of distal cis-regulatory modules (CRMs), the most common of which are transcriptional enhancers. Because regulated gene expression is fundamental to cell differentiation and acquisition of new cell fates, identifying, characterizing, and understanding the mechanisms of action of CRMs is critical for understanding development. CRM discovery has historically been challenging, as CRMs can be located far from the genes they regulate, have few readily-identifiable sequence characteristics, and for many years were not amenable to high-throughput discovery methods. However, the recent availability of complete genome sequences and the development of next-generation sequencing methods has led to an explosion of both computational and empirical methods for CRM discovery in model and non-model organisms alike. Experimentally, CRMs can be identified through chromatin immunoprecipitation directed against transcription factors or histone post-translational modifications, identification of nucleosome-depleted “open” chromatin regions, or sequencing-based high-throughput functional screening. Computational methods include comparative genomics, clustering of known or predicted transcription factor binding sites, and supervised machine-learning approaches trained on known CRMs. All of these methods have proven effective for CRM discovery, but each has its own considerations and limitations, and each is subject to a greater or lesser number of false-positive identifications. Experimental confirmation of predictions is essential, although shortcomings in current methods suggest that additional means of validation need to be developed. PMID:25704908

Using phosphine ligands with a biological role to modulate reactivity in novel platinum complexes

NASA Astrophysics Data System (ADS)

Echeverri, Marcelo; Alvarez-Valdés, Amparo; Navas, Francisco; Perles, Josefina; Sánchez-Pérez, Isabel; Quiroga, A. G.

2018-02-01

Three platinum complexes with cis and trans configuration cis-[Pt(TCEP)2Cl2], cis-[Pt(tmTCEP)2Cl2] and trans-[Pt(TCEP)2Cl2], where TCEP is tris(2-carboxyethyl)phosphine, have been synthesized and fully characterized by usual techniques including single-crystal X-ray diffraction for trans-[Pt(TCEP)2Cl2] and cis-[Pt(tmTCEP)2Cl2]. Here, we also report on an esterification process of TCEP, which takes place in the presence of alcohols, leading to a platinum complex coordinated to an ester tmTCEP (2-methoxycarbonylethyl phosphine) ligand. The stability in solution of the three compounds and their interaction with biological models such as DNA (pBR322 and calf thymus DNA) and proteins (lysozyme and RNase) have also been studied.

Pilot study on the use of data mining to identify cochlear implant candidates.

PubMed

Grisel, Jedidiah J; Schafer, Erin; Lam, Anne; Griffin, Terry

2018-05-01

The goal of this pilot study was to determine the clinical utility of data-mining software that screens for cochlear implant (CI) candidacy. The Auditory Implant Initiative developed a software module that screens for CI candidates via integration with a software system (Noah 4) that serves as a depository for hearing test data. To identify candidates, patient audiograms from one practice were exported into the screening module. Candidates were tracked to determine if any eventually underwent implantation. After loading 4836 audiograms from the Noah 4 system, the screening module identified 558 potential CI candidates. After reviewing the data for the potential candidates, 117 were targeted and invited to an educational event. Following the event, a total of six candidates were evaluated, and two were implanted. This objective approach to identifying candidates has the potential to address the gross underutilization of CIs by removing any bias or lack of knowledge regarding the management of severe to profound sensorineural hearing loss with CIs. The screening module was an effective tool for identifying potential CI candidates at one ENT practice. On a larger scale, the screening module has the potential to impact thousands of CI candidates worldwide.

Effects of proline cis-trans isomerization on TB domain secondary structure.

PubMed Central

Yuan, X.; Werner, J. M.; Knott, V.; Handford, P. A.; Campbell, I. D.; Downing, K.

1998-01-01

The transforming growth factor beta (TGF-beta) binding protein-like (TB) domain is found principally in proteins localized to extracellular matrix fibrils, including human fibrillin-1, the defective protein in the Marfan syndrome. Analysis of the nuclear magnetic resonance (NMR) data for the sixth TB module from human fibrillin-1 has revealed the existence of two stable conformers that differ in the isomerization states of two proline residues. Unusually, the two isoforms do not readily interconvert and are stable on the time scale of milliseconds. We have computed independent structures of the major and minor conformers of TB6 to assess how the domain fold adjusts to incorporate alternatively cis- or trans-prolines. Based on previous observations, it has been suggested that multiple conformers can only be accommodated in flexible regions of protein structure. In contrast, P22, which exists in trans in the major form and cis in the minor form of TB6, is in a rigid region of the domain, which is confirmed by backbone dynamics measurements. Overall, the structures of the major and minor conformers are similar. However, the secondary structure topologies of the two forms differ as a direct consequence of the changes in proline conformation. PMID:9792099

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.

PubMed

Schultheiss, Sebastian J; Busch, Wolfgang; Lohmann, Jan U; Kohlbacher, Oliver; Rätsch, Gunnar

2009-08-15

Understanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor (TF) binding sites in promoter regions of potential TF target genes. It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos. Such algorithms succeed in identifying single, relatively well-conserved binding sites, but tend to fail when it comes to the identification of combinations of several degenerate binding sites, as those often found in cis-regulatory modules. We propose a new algorithm that combines the benefits of existing motif finding with the ones of support vector machines (SVMs) to find degenerate motifs in order to improve the modeling of regulatory modules. In experiments on microarray data from Arabidopsis thaliana, we were able to show that the newly developed strategy significantly improves the recognition of TF targets. The python source code (open source-licensed under GPL), the data for the experiments and a Galaxy-based web service are available at http://www.fml.mpg.de/raetsch/suppl/kirmes/.

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

PubMed Central

Filichkin, Sergei A.; Breton, Ghislain; Priest, Henry D.; Dharmawardhana, Palitha; Jaiswal, Pankaj; Fox, Samuel E.; Michael, Todd P.; Chory, Joanne; Kay, Steve A.; Mockler, Todd C.

2011-01-01

Background Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized transcriptome cycling is driven through an extensive network of diurnal and clock-regulated transcription factors and their target cis-regulatory elements. Study of the cycling transcriptome in other plant species could thus help elucidate the similarities and differences and identify hubs of regulation common to monocot and dicot plants. Methodology/Principal Findings Using a combination of oligonucleotide microarrays and data mining pipelines, we examined daily rhythms in gene expression in one monocotyledonous and one dicotyledonous plant, rice and poplar, respectively. Cycling transcriptomes were interrogated under different diurnal (driven) and circadian (free running) light and temperature conditions. Collectively, photocycles and thermocycles regulated about 60% of the expressed nuclear genes in rice and poplar. Depending on the condition tested, up to one third of oscillating Arabidopsis-poplar-rice orthologs were phased within three hours of each other suggesting a high degree of conservation in terms of rhythmic gene expression. We identified clusters of rhythmically co-expressed genes and searched their promoter sequences to identify phase-specific cis-elements, including elements that were conserved in the promoters of Arabidopsis, poplar, and rice. Conclusions/Significance Our results show that the cycling patterns of many circadian clock genes are highly conserved across poplar, rice, and Arabidopsis. The expression of many orthologous genes in key metabolic and regulatory pathways is diurnal and/or circadian regulated and phased to similar times of day. Our results confirm previous findings in Arabidopsis of three major classes of cis-regulatory modules within the plant circadian network: the morning (ME, GBOX), evening (EE, GATA), and midnight (PBX/TBX/SBX) modules. Identification of identical overrepresented motifs in the promoters of cycling genes from different species suggests that the core diurnal/circadian cis-regulatory network is deeply conserved between mono- and dicotyledonous species. PMID:21694767

Infliximab Modulates Cisplatin-Induced Hepatotoxicity in Rats

PubMed Central

Cüre, Medine Cumhur; Cüre, Erkan; Kalkan, Yıldıray; Kırbaş, Aynur; Tümkaya, Levent; Yılmaz, Arif; Türkyılmaz, Ayşegül Küçükali; Şehitoğlu, İbrahim; Yüce, Süleyman

2016-01-01

Background: Cisplatin (Cis) is one of the most commonly used antineoplastic drugs. It is used as chemotherapy for many solid organ malignancies such as brain, neck, male and female urogenital, vesical and pulmonary cancers. Infliximab blocks tumor necrosis factor alpha (TNF-α). Several studies have reported that infliximab ameliorates cell damage by reducing cytokine levels. Aims: We aimed to investigate whether infliximab has a preventive effect against cisplatin-induced hepatotoxicity and whether it has a synergistic effect when combined with Cis. Study Design: Animal experimentation. Methods: Male Wistar albino rats were divided in three groups as follows: Cis group, infliximab + Cis (CIN) group and the control group. Each group comprised 10 animals. Animals in the Cis group received an intraperitoneal single-dose injection of Cis (7 mg/kg). In the CIN group, a single dose of infliximab (7 mg/kg) was administered 72 h prior to the Cis injection. After 72 h, a single dose of Cis (7 mg/kg) was administered. All rats were sacrificed five days after Cis injection. Results: TNF-α levels in the Cis group were significantly higher (345.5±40.0 pg/mg protein) than those of the control (278.7±62.1 pg/mg protein, p=0.003) and CIN groups (239.0±64.2 pg/mg protein, p=0.013). The Cis group was found to have high carbonic anhydrase (CA)-II and low carbamoyl phosphate synthetase-1 (CPS-1) levels. Aspartate transaminase (AST) and alanine transaminase (ALT) levels were lower in the CIN group as compared to the Cis group. Total histological damage was greater in the Cis group as compared to the control and CIN groups. Conclusion: Cis may lead to liver damage by increasing cytokine levels. It may increase oxidative stress-induced tissue damage by increasing carbonic anhydrase II (CA-II) enzyme levels and decreasing CPS-1 enzyme levels. Infliximab decreases Cis-induced hepatic damage by blocking TNF-α and it may also protect against liver damage by regulating CPS-1 and CA-II enzyme levels. PMID:27761277

Virtual Observatory and Colitec Software: Modules, Features, Methods

NASA Astrophysics Data System (ADS)

Pohorelov, A. V.; Khlamov, S. V.; Savanevych, V. E.; Briukhovetskyi, A. B.; Vlasenko, V. P.

In this article we described complex processing system created by the CoLiTec project. This system includes features, user-friendly tools for processing control, results reviewing, integration with online catalogs and a lot of different computational modules that are based on the developed methods. Some of them are described in the article.The main directions of the CoLiTec software development are the Virtual Observatory, software for automated asteroids and comets detection and software for brightness equalization.The CoLiTec software is widely used in a number of observatories in the CIS. It has been used in about 700 000 observations, during which 1560 asteroids, including 5 NEO, 21 Trojan asteroids of Jupiter, 1 Centaur and four comets were discovered.

A reversible conductivity modulation of azobenzene-based ionic liquids in aqueous solutions using UV/vis light.

PubMed

Li, Zhiyong; Yuan, Xiaoqing; Feng, Ying; Chen, Yongkui; Zhao, Yuling; Wang, Huiyong; Xu, Qingli; Wang, Jianji

2018-05-09

Photo-induced conductivity modulation of stimuli-responsive materials is of great importance from the viewpoint of fundamental research and technology. In this work, 5 new kinds of azobenzene-based photo-responsive ionic liquids were synthesized and characterized, and UV/vis light modulation of their conductivity was investigated in an aqueous solution. The factors affecting the conductivity modulation of the photo-responsive fluids, such as photo-isomerization efficiency, photo-regulation aggregation, concentration and chemical structure of the ionic liquids, were examined systematically. It was found that the conductivity of the ionic liquids in water exhibited a significant increase upon UV light irradiation and the ionic liquids with a shorter alkyl spacer in the cation showed a more remarkable photo-induced conductivity enhancement with a maximum increase of 150%. In addition, the solution conductivity was restored (or very close) to the initial value upon an alternative irradiation with visible light. Thus, the solution conductivity can be modulated using alternative irradiation with UV and visible light. Although the reversible photo-isomerization of the azobenzene group under UV/vis irradiation is the origin of the conductivity modulation, the photo-regulated aggregation of the ionic liquid in water is indispensable for the maximum degree of conductivity modulation because UV irradiation can weaken, even break the aggregated cis-isomers of the ionic liquids in an aqueous solution.

Impact of Chemotherapy on Normal Tissue Complication Probability Models of Acute Hematologic Toxicity in Patients Receiving Pelvic Intensity Modulated Radiation Therapy

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

Bazan, Jose G.; Luxton, Gary; Kozak, Margaret M.

Purpose: To determine how chemotherapy agents affect radiation dose parameters that correlate with acute hematologic toxicity (HT) in patients treated with pelvic intensity modulated radiation therapy (P-IMRT) and concurrent chemotherapy. Methods and Materials: We assessed HT in 141 patients who received P-IMRT for anal, gynecologic, rectal, or prostate cancers, 95 of whom received concurrent chemotherapy. Patients were separated into 4 groups: mitomycin (MMC) + 5-fluorouracil (5FU, 37 of 141), platinum ± 5FU (Cis, 32 of 141), 5FU (26 of 141), and P-IMRT alone (46 of 141). The pelvic bone was contoured as a surrogate for pelvic bone marrow (PBM) andmore » divided into subsites: ilium, lower pelvis, and lumbosacral spine (LSS). The volumes of each region receiving 5-40 Gy were calculated. The endpoint for HT was grade ≥3 (HT3+) leukopenia, neutropenia or thrombocytopenia. Normal tissue complication probability was calculated using the Lyman-Kutcher-Burman model. Logistic regression was used to analyze association between HT3+ and dosimetric parameters. Results: Twenty-six patients experienced HT3+: 10 of 37 (27%) MMC, 14 of 32 (44%) Cis, 2 of 26 (8%) 5FU, and 0 of 46 P-IMRT. PBM dosimetric parameters were correlated with HT3+ in the MMC group but not in the Cis group. LSS dosimetric parameters were well correlated with HT3+ in both the MMC and Cis groups. Constrained optimization (0« less

Bioinspired Orientation of β-Substituents on Porphyrin Antenna Ligands Switches Ytterbium(III) NIR Emission with Thermosensitivity.

PubMed

Ning, Yingying; Ke, Xian-Sheng; Hu, Ji-Yun; Liu, Yi-Wei; Ma, Fang; Sun, Hao-Ling; Zhang, Jun-Long

2017-02-20

"Configurational isomerism" is an important approach found in naturally occurring chlorophylls to modulate light harvesting function without significant structural changes; however, this feature has been seldom applied in design of antenna ligands for lanthanide (Ln) sensitization. In this work, we introduced a bioinspired approach by orientation of β-dilactone moieties on porphyrinates, namely cis-/trans-porphodilactones, to modulate the energy transfer process from the lowest triplet excited state of the ligand (T 1 ) to the emitting level of ytterbium(III) ( 2 F 5/2 , Yb*). Interestingly, near-infrared (NIR) emission of Yb(III) could be switched "on" by the cis-porphodilactone ligand, while the trans-isomer renders Yb(III) emission "off" and the ratio of quantum yields is ∼8. Analysis of the structure-photophysical properties relationship suggests that the significant emission difference is correlated to the energy gaps between T 1 and Yb* (1152 cm -1 in the cis- vs -25 cm -1 in the trans-isomer). More interestingly, due to back energy transfer (BEnT), the Yb(III) complex of cis-porphodilactone exhibits NIR emission with high thermosensitivity (4.0%°C -1 in solution and 4.9%°C -1 in solid state), comparable to previously reported terbium (Tb) and europium (Eu) visible emitters, in contrast to the trivial emission changes of the trans-isomer and porphyrin and porpholactone analogues. This work opens up new access to design NIR emissive Ln complexes by bioinspired modification of antenna ligands.

Conserved Non-Coding Regulatory Signatures in Arabidopsis Co-Expressed Gene Modules

PubMed Central

Spangler, Jacob B.; Ficklin, Stephen P.; Luo, Feng; Freeling, Michael; Feltus, F. Alex

2012-01-01

Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome. PMID:23024789

Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules.

PubMed

Spangler, Jacob B; Ficklin, Stephen P; Luo, Feng; Freeling, Michael; Feltus, F Alex

2012-01-01

Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome.

Organization and control of genes encoding catabolic enzymes in Rhizobiaceae. Progress report, March 1993

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

Parke, D.; Ornston, L.N.

1993-03-01

Rhizobiaceae, a diverse bacterial group comprising rhizobia and agrobacteria, symbiotic partnership with plants form nitrogen-fixing nodules on plant roots or are plant pathogens. Phenolic compounds produced by plants serve as inducers of rhizobial nodulation genes and agrobacterial virulence genes reflect their capacity to utilize numerous aromatics, including phenolics, as a source of carbon and energy. In many microbes the aerobic degradation of numerous aromatic compounds to tricarboxylic acid cycle intermediates is achieved by the {beta}-ketoadipate pathway. Our initial studies focused on the organization and regulation of the ketoadipate pathway in Agrobacterium tumefaciens. We have cloned, identified and characterized a novelmore » regulatory gene that modulates expression of an adjacent pca (protocatechuate) structural gene, pcaD. Regulation of pcaD is mediated by the regulatory gene, termed pcaQ, in concert with the intermediate {beta}-carboxy-cis,cis-muconate. {beta}-carboxy-cis,cismuconate is an unstable chemical, not marketed commercially, and it is unlikely to permeate Escherichia coli cells if supplied in media. Because of these factors, characterization of pcaQ in E. coli required an in vivo delivery system for {beta}-carboxycis,cis-muconate. This was accomplished by designing an E. coli strain that expressed an Acinetobacter calcoaceticus pcaA gene for conversion of protocatechuate to {beta}-carboxy-cis,cis-muconate.« less

Organization and control of genes encoding catabolic enzymes in Rhizobiaceae

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

Parke, D.; Ornston, L.N.

1993-03-01

Rhizobiaceae, a diverse bacterial group comprising rhizobia and agrobacteria, symbiotic partnership with plants form nitrogen-fixing nodules on plant roots or are plant pathogens. Phenolic compounds produced by plants serve as inducers of rhizobial nodulation genes and agrobacterial virulence genes reflect their capacity to utilize numerous aromatics, including phenolics, as a source of carbon and energy. In many microbes the aerobic degradation of numerous aromatic compounds to tricarboxylic acid cycle intermediates is achieved by the [beta]-ketoadipate pathway. Our initial studies focused on the organization and regulation of the ketoadipate pathway in Agrobacterium tumefaciens. We have cloned, identified and characterized a novelmore » regulatory gene that modulates expression of an adjacent pca (protocatechuate) structural gene, pcaD. Regulation of pcaD is mediated by the regulatory gene, termed pcaQ, in concert with the intermediate [beta]-carboxy-cis,cis-muconate. [beta]-carboxy-cis,cismuconate is an unstable chemical, not marketed commercially, and it is unlikely to permeate Escherichia coli cells if supplied in media. Because of these factors, characterization of pcaQ in E. coli required an in vivo delivery system for [beta]-carboxycis,cis-muconate. This was accomplished by designing an E. coli strain that expressed an Acinetobacter calcoaceticus pcaA gene for conversion of protocatechuate to [beta]-carboxy-cis,cis-muconate.« less

Switchable Photonic Crystals Using One-Dimensional Confined Liquid Crystals for Photonic Device Application.

PubMed

Ryu, Seong Ho; Gim, Min-Jun; Lee, Wonsuk; Choi, Suk-Won; Yoon, Dong Ki

2017-01-25

Photonic crystals (PCs) have recently attracted considerable attention, with much effort devoted to photonic bandgap (PBG) control for varying the reflected color. Here, fabrication of a modulated one-dimensional (1D) anodic aluminum oxide (AAO) PC with a periodic porous structure is reported. The PBG of the fabricated PC can be reversibly changed by switching the ultraviolet (UV) light on/off. The AAO nanopores contain a mixture of photoresponsive liquid crystals (LCs) with irradiation-activated cis/trans photoisomerizable azobenzene. The resultant mixture of LCs in the porous AAO film exhibits a reversible PBG, depending on the cis/trans configuration of azobenzene molecules. The PBG switching is reliable over many cycles, suggesting that the fabricated device can be used in optical and photonic applications such as light modulators, smart windows, and sensors.

Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer

PubMed Central

Drewell, Robert A.; Nevarez, Michael J.; Kurata, Jessica S.; Winkler, Lauren N.; Li, Lily; Dresch, Jacqueline M.

2013-01-01

Summary In Drosophila, the 330 kb bithorax complex regulates cellular differentiation along the anterio-posterior axis during development in the thorax and abdomen and is comprised of three homeotic genes: Ultrabithorax, abdominal-A, and Abdominal-B. The expression of each of these genes is in turn controlled through interactions between transcription factors and a number of cis-regulatory modules in the neighboring intergenic regions. In this study, we examine how the sequence architecture of transcription factor binding sites mediates the functional activity of one of these cis-regulatory modules. Using computational, mathematical modeling and experimental molecular genetic approaches we investigate the IAB7b enhancer, which regulates Abdominal-B expression specifically in the presumptive seventh and ninth abdominal segments of the early embryo. A cross-species comparison of the IAB7b enhancer reveals an evolutionarily conserved signature motif containing two FUSHI-TARAZU activator transcription factor binding sites. We find that the transcriptional repressors KNIRPS, KRUPPEL and GIANT are able to restrict reporter gene expression to the posterior abdominal segments, using different molecular mechanisms including short-range repression and competitive binding. Additionally, we show the functional importance of the spacing between the two FUSHI-TARAZU binding sites and discuss the potential importance of cooperativity for transcriptional activation. Our results demonstrate that the transcriptional output of the IAB7b cis-regulatory module relies on a complex set of combinatorial inputs mediated by specific transcription factor binding and that the sequence architecture at this enhancer is critical to maintain robust regulatory function. PMID:24514265

Cis- and trans-zeatin differentially modulate plant immunity.

PubMed

Großkinsky, Dominik K; Edelsbrunner, Kerstin; Pfeifhofer, Hartwig; van der Graaff, Eric; Roitsch, Thomas

2013-07-01

Phytohormones are essential regulators of various processes in plant growth and development. Several phytohormones are also known to regulate plant responses to environmental stress and pathogens. Only recently, cytokinins have been demonstrated to play an important role in plant immunity. Increased levels of cytokinins such as trans-zeatin, which are considered highly active, induced resistance against mainly (hemi)biotrophic pathogens in different plant species. In contrast, cis-zeatin is commonly regarded as a cytokinin exhibiting low or no activity. Here we comparatively study the impact of both zeatin isomers on the infection of Nicotiana tabacum by the (hemi)biotrophic microbial pathogen Pseudomonas syringae. We demonstrate a biological effect of cis-zeatin and a differential effect of the two zeatin isomers on symptom development, defense responses and bacterial multiplication.

Photocontrol of Voltage-Gated Ion Channel Activity by Azobenzene Trimethylammonium Bromide in Neonatal Rat Cardiomyocytes

PubMed Central

Frolova, Sheyda R.; Gaiko, Olga; Tsvelaya, Valeriya A.; Pimenov, Oleg Y.; Agladze, Konstantin I.

2016-01-01

The ability of azobenzene trimethylammonium bromide (azoTAB) to sensitize cardiac tissue excitability to light was recently reported. The dark, thermally relaxed trans- isomer of azoTAB suppressed spontaneous activity and excitation propagation speed, whereas the cis- isomer had no detectable effect on the electrical properties of cardiomyocyte monolayers. As the membrane potential of cardiac cells is mainly controlled by activity of voltage-gated ion channels, this study examined whether the sensitization effect of azoTAB was exerted primarily via the modulation of voltage-gated ion channel activity. The effects of trans- and cis- isomers of azoTAB on voltage-dependent sodium (INav), calcium (ICav), and potassium (IKv) currents in isolated neonatal rat cardiomyocytes were investigated using the whole-cell patch-clamp technique. The experiments showed that azoTAB modulated ion currents, causing suppression of sodium (Na+) and calcium (Ca2+) currents and potentiation of net potassium (K+) currents. This finding confirms that azoTAB-effect on cardiac tissue excitability do indeed result from modulation of voltage-gated ion channels responsible for action potential. PMID:27015602

Emerging photovoltaic technologies: Environmental and health issues update

NASA Astrophysics Data System (ADS)

Fthenakis, Vasilis M.; Moskowitz, Paul D.

1997-02-01

New photovoltaic (PV) technologies promise low-cost, reliable PV modules and have the potential for significant PV penetration into the energy market. These prospects for commercialization have attracted renewed interest in the advantageous environmental impact of using PV and also in the potential environmental, health and safety (EHS) burdens in PV manufacturing and decommissioning. In this paper, we highlight recent studies on EHS issues: a) An integrated energy-environmental-economic analysis which shows that large-scale use of PV can significantly contribute to alleviating the greenhouse effect; in the United States alone, it could displace 450 million tons of carbon emissions by the year 2030, b) Recycling of the spent modules and scarp is economically feasible; current research centers on improving the efficiency and economics of recycling CdTe and CIS modules, c) Toxicological studies conducted by the National Institute of Environmental Health Sciences (NIEHS) compared the acute toxicity of CdTe, CIS, and CGS; CdTe was the most toxic, and CGS the least toxic of the three. Additional studies are now comparing the systemic toxicity of these compounds with the toxicity of their precursors.

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

Wagner, Drew T.; Zeng, Jia; Bailey, Constance B.

In an effort to uncover the structural motifs and biosynthetic logic of the relatively uncharacterized trans-acyltransferase polyketide synthases, we have begun the dissection of the enigmatic dehydrating bimodules common in these enzymatic assembly lines. We report the 1.98 Å resolution structure of a ketoreductase (KR) from the first half of a type A dehydrating bimodule and the 2.22 Å resolution structure of a dehydratase (DH) from the second half of a type B dehydrating bimodule. The KR, from the third module of the bacillaene synthase, and the DH, from the tenth module of the difficidin synthase, possess features not observedmore » in structurally characterized homologs. The DH architecture provides clues for how it catalyzes a unique double dehydration. Correlations between the chemistries proposed for dehydrating bimodules and bioinformatic analysis indicate that type A dehydrating bimodules generally produce an α/β-cis alkene moiety, while type B dehydrating bimodules generally produce an α/β-trans, γ/δ-cis diene moiety.« less

Spectro-temporal cues enhance modulation sensitivity in cochlear implant users

PubMed Central

Zheng, Yi; Escabí, Monty; Litovsky, Ruth Y.

2018-01-01

Although speech understanding is highly variable amongst cochlear implants (CIs) subjects, the remarkably high speech recognition performance of many CI users is unexpected and not well understood. Numerous factors, including neural health and degradation of the spectral information in the speech signal of CIs, likely contribute to speech understanding. We studied the ability to use spectro-temporal modulations, which may be critical for speech understanding and discrimination, and hypothesize that CI users adopt a different perceptual strategy than normal-hearing (NH) individuals, whereby they rely more heavily on joint spectro-temporal cues to enhance detection of auditory cues. Modulation detection sensitivity was studied in CI users and NH subjects using broadband “ripple” stimuli that were modulated spectrally, temporally, or jointly, i.e., spectro-temporally. The spectro-temporal modulation transfer functions of CI users and NH subjects was decomposed into spectral and temporal dimensions and compared to those subjects’ spectral-only and temporal-only modulation transfer functions. In CI users, the joint spectro-temporal sensitivity was better than that predicted by spectral-only and temporal-only sensitivity, indicating a heightened spectro-temporal sensitivity. Such an enhancement through the combined integration of spectral and temporal cues was not observed in NH subjects. The unique use of spectro-temporal cues by CI patients can yield benefits for use of cues that are important for speech understanding. This finding has implications for developing sound processing strategies that may rely on joint spectro-temporal modulations to improve speech comprehension of CI users, and the findings of this study may be valuable for developing clinical assessment tools to optimize CI processor performance. PMID:28601530

A trans-acting enhancer modulates estrogen-mediated transcription of reporter genes in osteoblasts.

PubMed

Sasaki-Iwaoka, H; Maruyama, K; Endoh, H; Komori, T; Kato, S; Kawashima, H

1999-02-01

The presence of bone-specific estrogen agonists and discovery of the osteoblast-specific transcription factor (TF), Cbfa1, together with the discovery of synergism between a TF Pit-1 and estrogen receptor alpha (ERalpha) on rat prolactin gene, led to investigation of Cbfa1 in the modulation of osteoblast-specific actions of estrogen. Reverse transcribed-polymerase chain reaction demonstrated expression of Cbfa1 in the osteoblastic cell lines, MG63, ROS17/2.8, and MC3T3E1, but not in nonosteoblastic cell lines, MCF7, C3H10T1/2, and HeLa. An ER expression vector and a series of luciferase (Luc) reporter plasmids harboring the Cbfa1 binding site OSE2 (the osteoblast-specific cis element in the osteocalcin promoter) and palindromic estrogen response elements (EREs) were cotransfected into both osteoblastic and nonosteoblastic cells. OSE2 worked as a cis- acting element in osteoblastic cells but not nonosteoblastic cells, whereas EREs were cis- acting in all cell lines. Synergistic transactivation was observed in osteoblastic cells only when both ERE and OSE2 were placed in juxtaposition to the promoter. Forced expression of Cbfa1 in C3H10T1/2 cells also induced synergism. Tamoxifen, a partial agonist/antagonist of estrogen, acted as an osteoblast-specific agonist in cells transfected with a promoter containing ERE and acted synergistically with a promoter containing the ERE-OSE2 enhancer combination. These results support the idea that bone-specific TFs modulate the actions of estrogen in a tissue-specific manner.

Multiple alignment-free sequence comparison

PubMed Central

Ren, Jie; Song, Kai; Sun, Fengzhu; Deng, Minghua; Reinert, Gesine

2013-01-01

Motivation: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, and , extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequences, and second, , and , averages of sums of pairwise comparison statistics. The two tasks we consider are, first, to identify sequences that are similar to a set of target sequences, and, second, to measure the similarity within a set of sequences. Results: Our investigation uses both simulated data as well as cis-regulatory module data where the task is to identify cis-regulatory modules with similar transcription factor binding sites. We find that although for real data, all of our statistics show a similar performance, on simulated data the Shepp-type statistics are in some instances outperformed by star-type statistics. The multiple alignment-free statistics are more sensitive to contamination in the data than the pairwise average statistics. Availability: Our implementation of the five statistics is available as R package named ‘multiAlignFree’ at be http://www-rcf.usc.edu/∼fsun/Programs/multiAlignFree/multiAlignFreemain.html. Contact: reinert@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23990418

Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

PubMed Central

Dunipace, Leslie; Ozdemir, Anil; Stathopoulos, Angelike

2011-01-01

It has been shown in several organisms that multiple cis-regulatory modules (CRMs) of a gene locus can be active concurrently to support similar spatiotemporal expression. To understand the functional importance of such seemingly redundant CRMs, we examined two CRMs from the Drosophila snail gene locus, which are both active in the ventral region of pre-gastrulation embryos. By performing a deletion series in a ∼25 kb DNA rescue construct using BAC recombineering and site-directed transgenesis, we demonstrate that the two CRMs are not redundant. The distal CRM is absolutely required for viability, whereas the proximal CRM is required only under extreme conditions such as high temperature. Consistent with their distinct requirements, the CRMs support distinct expression patterns: the proximal CRM exhibits an expanded expression domain relative to endogenous snail, whereas the distal CRM exhibits almost complete overlap with snail except at the anterior-most pole. We further show that the distal CRM normally limits the increased expression domain of the proximal CRM and that the proximal CRM serves as a `damper' for the expression levels driven by the distal CRM. Thus, the two CRMs interact in cis in a non-additive fashion and these interactions may be important for fine-tuning the domains and levels of gene expression. PMID:21813571

A method to enhance the use of interaural time differences for cochlear implants in reverberant environments

PubMed Central

Monaghan, Jessica J. M.; Seeber, Bernhard U.

2017-01-01

The ability of normal-hearing (NH) listeners to exploit interaural time difference (ITD) cues conveyed in the modulated envelopes of high-frequency sounds is poor compared to ITD cues transmitted in the temporal fine structure at low frequencies. Sensitivity to envelope ITDs is further degraded when envelopes become less steep, when modulation depth is reduced, and when envelopes become less similar between the ears, common factors when listening in reverberant environments. The vulnerability of envelope ITDs is particularly problematic for cochlear implant (CI) users, as they rely on information conveyed by slowly varying amplitude envelopes. Here, an approach to improve access to envelope ITDs for CIs is described in which, rather than attempting to reduce reverberation, the perceptual saliency of cues relating to the source is increased by selectively sharpening peaks in the amplitude envelope judged to contain reliable ITDs. Performance of the algorithm with room reverberation was assessed through simulating listening with bilateral CIs in headphone experiments with NH listeners. Relative to simulated standard CI processing, stimuli processed with the algorithm generated lower ITD discrimination thresholds and increased extents of laterality. Depending on parameterization, intelligibility was unchanged or somewhat reduced. The algorithm has the potential to improve spatial listening with CIs. PMID:27586742

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

PubMed Central

Pardo-Diaz, Carolina; Hanly, Joseph J.; Martin, Simon H.; Mallet, James; Dasmahapatra, Kanchon K.; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W. Owen; Jiggins, Chris D.

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation. PMID:26771987

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling.

PubMed

Wallbank, Richard W R; Baxter, Simon W; Pardo-Diaz, Carolina; Hanly, Joseph J; Martin, Simon H; Mallet, James; Dasmahapatra, Kanchon K; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W Owen; Jiggins, Chris D

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation.

Association Between Carotid Bulb Diaphragm and Ischemic Stroke in Young Afro-Caribbean Patients: A Population-Based Case-Control Study.

PubMed

Joux, Julien; Boulanger, Marion; Jeannin, Severine; Chausson, Nicolas; Hennequin, Jean-Luc; Molinié, Vincent; Smadja, Didier; Touzé, Emmanuel; Olindo, Stephane

2016-10-01

Carotid bulb diaphragm (CBD) has been described in young carotid ischemic stroke (CIS) patients, especially in blacks. However, the prevalence of CBD in CIS patients is unknown, and whether CBD is a risk factor for CIS remains unclear. We assessed the association between CBD and incident CIS in a population-based study. We selected all young (<55 years) CIS patients from a 1-year population-based cohort study in the Afro-Caribbean population of Martinique in 2012. All patients had a comprehensive work-up including a computed tomographic angiography. We calculated CIS associated with ipsilateral CBD incidence with 95% confidence intervals using Poisson distribution. We then selected age- and sex-matched controls among young (<55 years) Afro-Caribbean stroke-free patients admitted for a road crash who routinely had computed tomographic angiography. Odds ratio (ORs) were calculated by conditional logistic regression adjusted for hypertension, dyslipidemia, diabetes and smoking. CIS associated with ipsilateral CBD incidence was 3.8 per 100 000 person-years (95% confidence interval, 1.4-6.1). Prevalence of ipsilateral CBD was 23% in all CIS and 37% in undetermined CIS patients. When restricted to undetermined CIS, CBD prevalence was 24 times higher than that in controls (adjusted OR, 24.1; 95% confidence interval, 1.8-325.6). CBD is associated with an increased risk of ipsilateral CIS in young Afro-Caribbean population. © 2016 American Heart Association, Inc.

Long Noncoding RNA-Associated Transcriptomic Changes in Resiliency or Susceptibility to Depression and Response to Antidepressant Treatment

PubMed Central

Roy, Bhaskar; Wang, Qingzhong; Dwivedi, Yogesh

2018-01-01

Abstract Background Recent emergence of long noncoding RNAs in regulating gene expression and thereby modulating physiological functions in brain has manifested their possible role in psychiatric disorders. In this study, the roles of long noncoding RNAs in susceptibility and resiliency to develop stress-induced depression and their response to antidepressant treatment were examined. Methods Microarray-based transcriptome-wide changes in long noncoding RNAs were determined in hippocampus of male Holtzman rats who showed susceptibility (learned helplessness) or resiliency (nonlearned helplessness) to develop depression. Changes in long noncoding RNA expression were also ascertained after subchronic administration of fluoxetine to learned helplessness rats. Bioinformatic and target prediction analyses (cis- and trans-acting) and qPCR-based assays were performed to decipher the functional role of altered long noncoding RNAs. Results Group-wise comparison showed an overrepresented class of long noncoding RNAs that were uniquely associated with nonlearned helplessness or learned helplessness behavior. Chromosomal mapping within the 5-kbp flank region of the top 20 dysregulated long noncoding RNAs in the learned helplessness group showed several target genes that were regulated through cis- or trans-actions, including Zbtb20 and Zfp385b from zinc finger binding protein family. Genomic context of differentially expressed long noncoding RNAs showed an overall blunted response in the learned helplessness group regardless of the long noncoding RNA classes analyzed. Gene ontology exhibited the functional clustering for anatomical structure development, cellular architecture modulation, protein metabolism, and cellular communications. Fluoxetine treatment reversed learned helplessness-induced changes in many long noncoding RNAs and target genes. Conclusions The involvement of specific classes of long noncoding RNAs with distinctive roles in modulating target gene expression could confer the role of long noncoding RNAs in resiliency or susceptibility to develop depression with a reciprocal response to antidepressant treatment. PMID:29390069

CisLunar Habitat Internal Architecture Design Criteria

NASA Technical Reports Server (NTRS)

Jones, R.; Kennedy, K.; Howard, R.; Whitmore, M.; Martin, C.; Garate, J.

2017-01-01

BACKGROUND: In preparation for human exploration to Mars, there is a need to define the development and test program that will validate deep space operations and systems. In that context, a Proving Grounds CisLunar habitat spacecraft is being defined as the next step towards this goal. This spacecraft will operate differently from the ISS or other spacecraft in human history. The performance envelope of this spacecraft (mass, volume, power, specifications, etc.) is being defined by the Future Capabilities Study Team. This team has recognized the need for a human-centered approach for the internal architecture of this spacecraft and has commissioned a CisLunar Phase-1 Habitat Internal Architecture Study Team to develop a NASA reference configuration, providing the Agency with a "smart buyer" approach for future acquisition. THE CISLUNAR HABITAT INTERNAL ARCHITECTURE STUDY: Overall, the CisLunar Habitat Internal Architecture study will address the most significant questions and risks in the current CisLunar architecture, habitation, and operations concept development. This effort is achieved through definition of design criteria, evaluation criteria and process, design of the CisLunar Habitat Phase-1 internal architecture, and the development and fabrication of internal architecture concepts combined with rigorous and methodical Human-in-the-Loop (HITL) evaluations and testing of the conceptual innovations in a controlled test environment. The vision of the CisLunar Habitat Internal Architecture Study is to design, build, and test a CisLunar Phase-1 Habitat Internal Architecture that will be used for habitation (e.g. habitability and human factors) evaluations. The evaluations will mature CisLunar habitat evaluation tools, guidelines, and standards, and will interface with other projects such as the Advanced Exploration Systems (AES) Program integrated Power, Avionics, Software (iPAS), and Logistics for integrated human-in-the-loop testing. The mission of the CisLunar Habitat Internal Architecture Study is to become a forcing function to establish a common understanding of CisLunar Phase-1 Habitation Internal Architecture design criteria, processes, and tools. The scope of the CisLunar Habitat Internal Architecture study is to design, develop, demonstrate, and evaluate a Phase-1 CisLunar Habitat common module internal architecture based on design criteria agreed to by NASA, the International Partners, and Commercial Exploration teams. This task is to define the CisLunar Phase-1 Internal Architecture Government Reference Design, assist NASA in becoming a "smart buyer" for Phase-1 Habitat Concepts, and ultimately to derive standards and requirements from the Internal Architecture Design Process. The first step was to define a Habitat Internal Architecture Design Criteria and create a structured philosophy to be used by design teams as a filter by which critical aspects of consideration would be identified for the purpose of organizing and utilizing interior spaces. With design criteria in place, the team will develop a series of iterative internal architecture concept designs which will be assessed by means of an evaluation criteria and process. These assessments will successively drive and refine the design, leading to the combination and down-selection of design concepts. A single refined reference design configuration will be developed into in a medium-to-high fidelity mockup. A multi-day human-in-the-loop mission test will fully evaluate the reference design and validate its configuration. Lessons learned from the design and evaluation will enable the team to identify appropriate standards for Phase-1 CisLunar Habitat Internal Architecture and will enable NASA to develop derived requirements in support of maturing CisLunar Habitation capabilities. This paper will describe the criteria definition process, workshop event, and resulting CisLunar Phase-1 Habitat Internal Architecture Design Criteria.

Development and initial evaluation of the Clinical Information Systems Success Model (CISSM).

PubMed

Garcia-Smith, Dianna; Effken, Judith A

2013-06-01

Most clinical information systems (CIS) today are technically sound, but the number of successful implementations of these systems is low. The purpose of this study was to develop and test a theoretically based integrated CIS Success Model (CISSM) from the nurse perspective. Model predictors of CIS success were taken from existing research on information systems acceptance, user satisfaction, use intention, user behavior and perceptions, as well as clinical research. Data collected online from 234 registered nurses in four hospitals were used to test the model. Each nurse had used the Cerner Power Chart Admission Health Profile for at least 3 months. Psychometric testing and factor analysis of the 23-item CISSM instrument established its construct validity and reliability. Initial analysis showed nurses' satisfaction with and dependency on CIS use predicted their perceived CIS use Net Benefit. Further analysis identified Social Influence and Facilitating Conditions as other predictors of CIS user Net Benefit. The level of hospital CIS integration may account for the role of CIS Use Dependency in the success of CIS. Based on our experience, CISSM provides a formative as well as summative tool for evaluating CIS success from the nurse's perspective. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Binding sites for abundant nuclear factors modulate RNA polymerase I-dependent enhancer function in Saccharomyces cerevisiae.

PubMed

Kang, J J; Yokoi, T J; Holland, M J

1995-12-01

The 190-base pair (bp) rDNA enhancer within the intergenic spacer sequences of Saccharomyces cerevisiae rRNA cistrons activates synthesis of the 35S-rRNA precursor about 20-fold in vivo (Mestel,, R., Yip, M., Holland, J. P., Wang, E., Kang, J., and Holland, M. J. (1989) Mol. Cell. Biol. 9, 1243-1254). We now report identification and analysis of transcriptional activities mediated by three cis-acting sites within a 90-bp portion of the rDNA enhancer designated the modulator region. In vivo, these sequences mediated termination of transcription by RNA polymerase I and potentiated the activity of the rDNA enhancer element. Two trans-acting factors, REB1 and REB2, bind independently to sites within the modulator region (Morrow, B. E., Johnson, S. P., and Warner, J. R. (1989) J. Biol. Chem. 264, 9061-9068). We show that REB2 is identical to the ABF1 protien. Site-directed mutagenesis of REB1 and ABF1 binding sites demonstrated uncoupling of RNA polymerase I-dependent termination from transcriptional activation in vivo. We conclude that REB1 and ABF1 are required for RNA polymerase I-dependent termination and enhancer function, respectively, Since REB1 and ABF1 proteins also regulate expression of class II genes and other nuclear functions, our results suggest further similarities between RNA polymerase I and II regulatory mechanisms. Two rDNA enhancers flanking a rDNA minigene stimulated RNA polymerase I transcription in a "multiplicative" fashion. Deletion mapping analysis showed that similar cis-acting sequences were required for enhancer function when positioned upstream or downstream from a rDNA minigene.

SPAD array based TOF SoC design for unmanned vehicle

NASA Astrophysics Data System (ADS)

Pan, An; Xu, Yuan; Xie, Gang; Huang, Zhiyu; Zheng, Yanghao; Shi, Weiwei

2018-03-01

As for the requirement of unmanned-vehicle mobile Lidar system, this paper presents a SoC design based on pulsed TOF depth image sensor. This SoC has a detection range of 300m and detecting resolution of 1.5cm. Pixels are made of SPAD. Meanwhile, SoC adopts a structure of multi-pixel sharing TDC, which significantly reduces chip area and improve the fill factor of light-sensing surface area. SoC integrates a TCSPC module to achieve the functionality of receiving each photon, measuring photon flight time and processing depth information in one chip. The SOC is designed in the SMIC 0.13μm CIS CMOS technology

Synthesis and Characterization of the First Liquid Single Source Precursors for the Deposition of Ternary Chalcopyrite (CuInS2) Thin Film Materials

NASA Technical Reports Server (NTRS)

Banger, Kulbinder K.; Cowen, Jonathan; Hepp, Aloysius

2002-01-01

Molecular engineering of ternary single source precursors based on the [{PBu3}2Cu(SR')2In(SR')2] architecture have afforded the first liquid CIS ternary single source precursors (when R = Et, n-Pr), which are suitable for low temperature deposition (< 350 C). Thermogravimetric analyses (TGA) and modulated-differential scanning calorimetry (DSC) confirm their liquid phase and reduced stability. X-ray diffraction studies, energy dispersive analyzer (EDS), and scanning electron microscopy (SEM) support the formation of the single-phase chalcopyrite CuInS2 at low temperatures.

Flavylium network of chemical reactions in confined media: modulation of 3',4',7-trihydroxyflavilium reactions by host-guest interactions with cucurbit[7]uril.

PubMed

Basílio, Nuno; Pina, Fernando

2014-08-04

In moderately acidic aqueous solutions, flavylium compounds undergo a pH-, and in some cases, light-dependent array of reversible chemical reactions. This network can be described as a single acid-base reaction involving a flavylium cation (acidic form) and a mixture of basic forms (quinoidal base, hemiketal and cis and trans chalcones). The apparent pK'a of the system and the relative mole fractions of the basic forms can be modulated by the interaction with cucurbit[7]uril. The system is studied by using (1) H NMR spectroscopy, UV/Vis spectroscopy, flash photolysis, and steady-state irradiation. Of all the network species, the flavylium cation possesses the highest affinity for cucurbit[7]uril. The rate of interconversion between flavylium cation and the basic species (where trans-chalcone is dominant) is approximately nine times lower inside the cucurbit[7]uril. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectro-temporal cues enhance modulation sensitivity in cochlear implant users.

PubMed

Zheng, Yi; Escabí, Monty; Litovsky, Ruth Y

2017-08-01

Although speech understanding is highly variable amongst cochlear implants (CIs) subjects, the remarkably high speech recognition performance of many CI users is unexpected and not well understood. Numerous factors, including neural health and degradation of the spectral information in the speech signal of CIs, likely contribute to speech understanding. We studied the ability to use spectro-temporal modulations, which may be critical for speech understanding and discrimination, and hypothesize that CI users adopt a different perceptual strategy than normal-hearing (NH) individuals, whereby they rely more heavily on joint spectro-temporal cues to enhance detection of auditory cues. Modulation detection sensitivity was studied in CI users and NH subjects using broadband "ripple" stimuli that were modulated spectrally, temporally, or jointly, i.e., spectro-temporally. The spectro-temporal modulation transfer functions of CI users and NH subjects was decomposed into spectral and temporal dimensions and compared to those subjects' spectral-only and temporal-only modulation transfer functions. In CI users, the joint spectro-temporal sensitivity was better than that predicted by spectral-only and temporal-only sensitivity, indicating a heightened spectro-temporal sensitivity. Such an enhancement through the combined integration of spectral and temporal cues was not observed in NH subjects. The unique use of spectro-temporal cues by CI patients can yield benefits for use of cues that are important for speech understanding. This finding has implications for developing sound processing strategies that may rely on joint spectro-temporal modulations to improve speech comprehension of CI users, and the findings of this study may be valuable for developing clinical assessment tools to optimize CI processor performance. Copyright © 2017 Elsevier B.V. All rights reserved.

Direct activation of a notochord cis-regulatory module by Brachyury and FoxA in the ascidian Ciona intestinalis.

PubMed

Passamaneck, Yale J; Katikala, Lavanya; Perrone, Lorena; Dunn, Matthew P; Oda-Ishii, Izumi; Di Gregorio, Anna

2009-11-01

The notochord is a defining feature of the chordate body plan. Experiments in ascidian, frog and mouse embryos have shown that co-expression of Brachyury and FoxA class transcription factors is required for notochord development. However, studies on the cis-regulatory sequences mediating the synergistic effects of these transcription factors are complicated by the limited knowledge of notochord genes and cis-regulatory modules (CRMs) that are directly targeted by both. We have identified an easily testable model for such investigations in a 155-bp notochord-specific CRM from the ascidian Ciona intestinalis. This CRM contains functional binding sites for both Ciona Brachyury (Ci-Bra) and FoxA (Ci-FoxA-a). By combining point mutation analysis and misexpression experiments, we demonstrate that binding of both transcription factors to this CRM is necessary and sufficient to activate transcription. To gain insights into the cis-regulatory criteria controlling its activity, we investigated the organization of the transcription factor binding sites within the 155-bp CRM. The 155-bp sequence contains two Ci-Bra binding sites with identical core sequences but opposite orientations, only one of which is required for enhancer activity. Changes in both orientation and spacing of these sites substantially affect the activity of the CRM, as clusters of identical sites found in the Ciona genome with different arrangements are unable to activate transcription in notochord cells. This work presents the first evidence of a synergistic interaction between Brachyury and FoxA in the activation of an individual notochord CRM, and highlights the importance of transcription factor binding site arrangement for its function.

Profile-likelihood Confidence Intervals in Item Response Theory Models.

PubMed

Chalmers, R Philip; Pek, Jolynn; Liu, Yang

2017-01-01

Confidence intervals (CIs) are fundamental inferential devices which quantify the sampling variability of parameter estimates. In item response theory, CIs have been primarily obtained from large-sample Wald-type approaches based on standard error estimates, derived from the observed or expected information matrix, after parameters have been estimated via maximum likelihood. An alternative approach to constructing CIs is to quantify sampling variability directly from the likelihood function with a technique known as profile-likelihood confidence intervals (PL CIs). In this article, we introduce PL CIs for item response theory models, compare PL CIs to classical large-sample Wald-type CIs, and demonstrate important distinctions among these CIs. CIs are then constructed for parameters directly estimated in the specified model and for transformed parameters which are often obtained post-estimation. Monte Carlo simulation results suggest that PL CIs perform consistently better than Wald-type CIs for both non-transformed and transformed parameters.

Renal Integrin-Linked Kinase Depletion Induces Kidney cGMP-Axis Upregulation: Consequences on Basal and Acutely Damaged Renal Function

PubMed Central

Cano-Peñalver, José Luis; Griera, Mercedes; García-Jerez, Andrea; Hatem-Vaquero, Marco; Ruiz-Torres, María Piedad; Rodríguez-Puyol, Diego; de Frutos, Sergio; Rodríguez-Puyol, Manuel

2015-01-01

Soluble guanylyl cyclase (sGC) is activated by nitric oxide (NO) and produces cGMP, which activates cGMP-dependent protein kinases (PKG) and is hydrolyzed by specific phosphodiesterases (PDE). The vasodilatory and cytoprotective capacity of cGMP-axis activation results in a therapeutic strategy for several pathologies. Integrin-linked kinase (ILK), a major scaffold protein between the extracellular matrix and intracellular signaling pathways, may modulate the expression and functionality of the cGMP-axis–related proteins. We introduce ILK as a novel modulator in renal homeostasis as well as a potential target for cisplatin (CIS)-induced acute kidney injury (AKI) improvement. We used an adult mice model of depletion of ILK (cKD-ILK), which showed basal increase of sGC and PKG expressions and activities in renal cortex when compared with wildtype (WT) littermates. Twenty-four h activation of sGC activation with NO enhanced the filtration rate in cKD-ILK. During AKI, cKD-ILK maintained the cGMP-axis upregulation with consequent filtration rates enhancement and ameliorated CIS-dependent tubular epithelial-to-mesenchymal transition and inflammation and markers. To emphasize the role of cGMP-axis upregulation due to ILK depletion, we modulated the cGMP axis under AKI in vivo and in renal cultured cells. A suboptimal dose of the PDE inhibitor ZAP enhanced the beneficial effects of the ILK depletion in AKI mice. On the other hand, CIS increased contractility-related events in cultured glomerular mesangial cells and necrosis rates in cultured tubular cells; ILK depletion protected the cells while sGC blockade with ODQ fully recovered the damage. PMID:26562149

N-Picolyl Derivatives of Kemp’s Triamine as Potential Antitumor Agents: A Preliminary Investigation

PubMed Central

Regino, Celeste Aida S.; Torti, Suzy V.; Ma, Rong; Yap, Glenn P.A.; Kreisel, Kevin A.; Torti, Frank M.; Planalp, Roy P.; Brechbiel, Martin W.

2008-01-01

Pre-organized tripodal ligands such as the N-picolyl derivatives of cis,cis-1,3,5-triamino-cis,cis-1,3,5-trimethylcyclohexane (Kemp’s triamine) were prepared as analogs to N,N’,N”- tris(2-pyridylmethyl)-cis,cis-1,3,5-triaminocyclohexane (tachpyr) in hopes of enhancing the rate of formation and stability of the metal complexes. A tricyclic bisaminal was formed via the reduction of the Schiff base while the tri(picolyl) derivative was synthesized via reductive amination of pyridine carboxaldehyde. Their cytotoxicities to the HeLa cell line were evaluated and directly compared to tachpyr and N,N’,N”- tris(2-pyridylmethyl)-tris(2-aminoethyl)amine (trenpyr). Results indicate that N,N’,N”-tris(2-pyridylmethyl)-cis,cis-1,3,5-triamino-cis,cis-1,3,5-trimethylcyclohexane (Kemp’s pyr) exhibits cytotoxic activity against the HeLa cancer cell line comparable to tachpyr (IC50 ~ 8.0 µM). Both Kemp’s pyr and tachpyr show higher cytotoxic activity over the aliphatic analogue of trenpyr (IC50 ~ 14 µM) suggesting that the major contributor to the activity is the ligand’s ability to form a stable and tight complex and that the equatorial/axial equilibrium impacting the complex formation for the cyclohexane-based ligands is not significant. PMID:16335923

Coordinated transcriptional regulation of two key genes in the lignin branch pathway - CAD and CCR - is mediated through MYB- binding sites

PubMed Central

2010-01-01

Background Cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the final steps in the biosynthesis of monolignols, the monomeric units of the phenolic lignin polymers which confer rigidity, imperviousness and resistance to biodegradation to cell walls. We have previously shown that the Eucalyptus gunnii CCR and CAD2 promoters direct similar expression patterns in vascular tissues suggesting that monolignol production is controlled, at least in part, by the coordinated transcriptional regulation of these two genes. Although consensus motifs for MYB transcription factors occur in most gene promoters of the whole phenylpropanoid pathway, functional evidence for their contribution to promoter activity has only been demonstrated for a few of them. Here, in the lignin-specific branch, we studied the functional role of MYB elements as well as other cis-elements identified in the regulatory regions of EgCAD2 and EgCCR promoters, in the transcriptional activity of these gene promoters. Results By using promoter deletion analysis and in vivo footprinting, we identified an 80 bp regulatory region in the Eucalyptus gunnii EgCAD2 promoter that contains two MYB elements, each arranged in a distinct module with newly identified cis-elements. A directed mutagenesis approach was used to introduce block mutations in all putative cis-elements of the EgCAD2 promoter and in those of the 50 bp regulatory region previously delineated in the EgCCR promoter. We showed that the conserved MYB elements in EgCAD2 and EgCCR promoters are crucial both for the formation of DNA-protein complexes in EMSA experiments and for the transcriptional activation of EgCAD2 and EgCCR promoters in vascular tissues in planta. In addition, a new regulatory cis-element that modulates the balance between two DNA-protein complexes in vitro was found to be important for EgCAD2 expression in the cambial zone. Conclusions Our assignment of functional roles to the identified cis-elements clearly demonstrates the importance of MYB cis-elements in the transcriptional regulation of two genes of the lignin-specific pathway and support the hypothesis that MYB elements serve as a common means for the coordinated regulation of genes in the entire lignin biosynthetic pathway. PMID:20584286

Evaluating cis-2,6-Dimethylpiperidide (cis-DMP) as a Base Component in Lithium-Mediated Zincation Chemistry

PubMed Central

Armstrong, David R; Garden, Jennifer A; Kennedy, Alan R; Leenhouts, Sarah M; Mulvey, Robert E; O'Keefe, Philip; O'Hara, Charles T; Steven, Alan

2013-01-01

Most recent advances in metallation chemistry have centred on the bulky secondary amide 2,2,6,6-tetramethylpiperidide (TMP) within mixed metal, often ate, compositions. However, the precursor amine TMP(H) is rather expensive so a cheaper substitute would be welcome. Thus this study was aimed towards developing cheaper non-TMP based mixed-metal bases and, as cis-2,6-dimethylpiperidide (cis-DMP) was chosen as the alternative amide, developing cis-DMP zincate chemistry which has received meagre attention compared to that of its methyl-rich counterpart TMP. A new lithium diethylzincate, [(TMEDA)LiZn(cis-DMP)Et2] (TMEDA=N,N,N′,N′-tetramethylethylenediamine) has been synthesised by co-complexation of Li(cis-DMP), Et2Zn and TMEDA, and characterised by NMR (including DOSY) spectroscopy and X-ray crystallography, which revealed a dinuclear contact ion pair arrangement. By using N,N-diisopropylbenzamide as a test aromatic substrate, the deprotonative reactivity of [(TMEDA)LiZn(cis-DMP)Et2] has been probed and contrasted with that of the known but previously uninvestigated di-tert-butylzincate, [(TMEDA)LiZn(cis-DMP)tBu2]. The former was found to be the superior base (for example, producing the ortho-deuteriated product in respective yields of 78 % and 48 % following D2O quenching of zincated benzamide intermediates). An 88 % yield of 2-iodo-N,N-diisopropylbenzamide was obtained on reaction of two equivalents of the diethylzincate with the benzamide followed by iodination. Comparisons are also drawn using 1,1,1,3,3,3-hexamethyldisilazide (HMDS), diisopropylamide and TMP as the amide component in the lithium amide, Et2Zn and TMEDA system. Under certain conditions, the cis-DMP base system was found to give improved results in comparison to HMDS and diisopropylamide (DA), and comparable results to a TMP system. Two novel complexes isolated from reactions of the di-tert-butylzincate and crystallographically characterised, namely the pre-metallation complex [{(iPr)2N(Ph)C=O}LiZn(cis-DMP)tBu2] and the post-metallation complex [(TMEDA)Li(cis-DMP){2-[1-C(=O)N(iPr)2]C6H4}Zn(tBu)], shed valuable light on the structures and mechanisms involved in these alkali-metal-mediated zincation reactions. Aspects of these reactions are also modelled by DFT calculations. PMID:23955639

Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.

PubMed

Yasuoka, Yuuri; Suzuki, Yutaka; Takahashi, Shuji; Someya, Haruka; Sudou, Norihiro; Haramoto, Yoshikazu; Cho, Ken W; Asashima, Makoto; Sugano, Sumio; Taira, Masanori

2014-07-09

Head specification by the head-selector gene, orthodenticle (otx), is highly conserved among bilaterian lineages. However, the molecular mechanisms by which Otx and other transcription factors (TFs) interact with the genome to direct head formation are largely unknown. Here we employ ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and find that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. On the basis of TLE binding and comprehensive CRM profiling, we define two distinct types of Otx2- and TLE-occupied CRMs. Using these devices, Otx2 and other head organizer TFs (for example, Lim1/Lhx1 (activator) or Goosecoid (repressor)) are able to upregulate or downregulate a large battery of target genes in the head organizer. An underlying principle is that Otx marks target genes for head specification to be regulated positively or negatively by partner TFs through specific types of CRMs.

Cytomegalovirus immune evasion of myeloid lineage cells.

PubMed

Brinkmann, Melanie M; Dağ, Franziska; Hengel, Hartmut; Messerle, Martin; Kalinke, Ulrich; Čičin-Šain, Luka

2015-06-01

Cytomegalovirus (CMV) evades the immune system in many different ways, allowing the virus to grow and its progeny to spread in the face of an adverse environment. Mounting evidence about the antiviral role of myeloid immune cells has prompted the research of CMV immune evasion mechanisms targeting these cells. Several cells of the myeloid lineage, such as monocytes, dendritic cells and macrophages, play a role in viral control, but are also permissive for CMV and are naturally infected by it. Therefore, CMV evasion of myeloid cells involves mechanisms that qualitatively differ from the evasion of non-CMV-permissive immune cells of the lymphoid lineage. The evasion of myeloid cells includes effects in cis, where the virus modulates the immune signaling pathways within the infected myeloid cell, and those in trans, where the virus affects somatic cells targeted by cytokines released from myeloid cells. This review presents an overview of CMV strategies to modulate and evade the antiviral activity of myeloid cells in cis and in trans.

Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13

DOE PAGES

Sheth, Rushikesh; Barozzi, Iros; Langlais, David; ...

2016-12-13

The combinatorial expression of Hox genes along the body axes is a major determinant of cell fate and plays a pivotal role in generating the animal body plan. Loss of HOXA13 and HOXD13 transcription factors (HOX13) leads to digit agenesis in mice, but how HOX13 proteins regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here, we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13–/–; Hoxd13–/– limbs. Ourmore » results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.« less

Ordered defect compounds in CuInSe{sub 2} for photovoltaic solar cell application

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

Sato, K.; Katayama-Yoshida, H.

2014-02-21

Due to the complete compensation, defect complex (2V{sub Cu}+In{sub Cu}), namely two Cu vacancies and In located at Cu site, is stable in CuInSe{sub 2} (CIS). It is known that the series of ordered defect compounds (ODC) are constracted by ordering the defect complex. Based on the total energy calcalation by using the Korringa-Kohn-Rostoker coherent potential approxiamtion (KKR-CPA) method, we discuss phase separation of the CIS with the defect complexes into ODC and CIS. Since the band alignment between ODC and CIS is calculated to be type 2, effective electron-hole separation at the interface between ODC and CIS can bemore » expected. This causes the enhancement of conversion efficiency of CIS-based solar cell materials.« less

A HLA class I cis-regulatory element whose activity can be modulated by hormones.

PubMed

Sim, B C; Hui, K M

1994-12-01

To elucidate the basis of the down-regulation in major histocompatibility complex (MHC) class I gene expression and to identify possible DNA-binding regulatory elements that have the potential to interact with class I MHC genes, we have studied the transcriptional regulation of class I HLA genes in human breast carcinoma cells. A 9 base pair (bp) negative cis-regulatory element (NRE) has been identified using band-shift assays employing DNA sequences derived from the 5'-flanking region of HLA class I genes. This 9-bp element, GTCATGGCG, located within exon I of the HLA class I gene, can potently inhibit the expression of a heterologous thymidine kinase (TK) gene promoter and the HLA enhancer element. Furthermore, this regulatory element can exert its suppressive function in either the sense or anti-sense orientation. More interestingly, NRE can suppress dexamethasone-mediated gene activation in the context of the reported glucocorticoid-responsive element (GRE) in MCF-7 cells but has no influence on the estrogen-mediated transcriptional activation of MCF-7 cells in the context of the reported estrogen-responsive element (ERE). Furthermore, the presence of such a regulatory element within the HLA class I gene whose activity can be modulated by hormones correlates well with our observation that the level of HLA class I gene expression can be down-regulated by hormones in human breast carcinoma cells. Such interactions between negative regulatory elements and specific hormone trans-activators are novel and suggest a versatile form of transcriptional control.

Co-regulation analysis of co-expressed modules under cold and pathogen stress conditions in tomato.

PubMed

Abedini, Davar; Rashidi Monfared, Sajad

2018-06-01

A primary mechanism for controlling the development of multicellular organisms is transcriptional regulation, which carried out by transcription factors (TFs) that recognize and bind to their binding sites on promoter region. The distance from translation start site, order, orientation, and spacing between cis elements are key factors in the concentration of active nuclear TFs and transcriptional regulation of target genes. In this study, overrepresented motifs in cold and pathogenesis responsive genes were scanned via Gibbs sampling method, this method is based on detection of overrepresented motifs by means of a stochastic optimization strategy that searches for all possible sets of short DNA segments. Then, identified motifs were checked by TRANSFAC, PLACE and Soft Berry databases in order to identify putative TFs which, interact to the motifs. Several cis/trans regulatory elements were found using these databases. Moreover, cross-talk between cold and pathogenesis responsive genes were confirmed. Statistical analysis was used to determine distribution of identified motifs on promoter region. In addition, co-regulation analysis results, illustrated genes in pathogenesis responsive module are divided into two main groups. Also, promoter region was crunched to six subareas in order to draw the pattern of distribution of motifs in promoter subareas. The result showed the majority of motifs are concentrated on 700 nucleotides upstream of the translational start site (ATG). In contrast, this result isn't true in another group. In other words, there was no difference between total and compartmentalized regions in cold responsive genes.

Comparison of parametric and bootstrap method in bioequivalence test.

PubMed

Ahn, Byung-Jin; Yim, Dong-Seok

2009-10-01

The estimation of 90% parametric confidence intervals (CIs) of mean AUC and Cmax ratios in bioequivalence (BE) tests are based upon the assumption that formulation effects in log-transformed data are normally distributed. To compare the parametric CIs with those obtained from nonparametric methods we performed repeated estimation of bootstrap-resampled datasets. The AUC and Cmax values from 3 archived datasets were used. BE tests on 1,000 resampled datasets from each archived dataset were performed using SAS (Enterprise Guide Ver.3). Bootstrap nonparametric 90% CIs of formulation effects were then compared with the parametric 90% CIs of the original datasets. The 90% CIs of formulation effects estimated from the 3 archived datasets were slightly different from nonparametric 90% CIs obtained from BE tests on resampled datasets. Histograms and density curves of formulation effects obtained from resampled datasets were similar to those of normal distribution. However, in 2 of 3 resampled log (AUC) datasets, the estimates of formulation effects did not follow the Gaussian distribution. Bias-corrected and accelerated (BCa) CIs, one of the nonparametric CIs of formulation effects, shifted outside the parametric 90% CIs of the archived datasets in these 2 non-normally distributed resampled log (AUC) datasets. Currently, the 80~125% rule based upon the parametric 90% CIs is widely accepted under the assumption of normally distributed formulation effects in log-transformed data. However, nonparametric CIs may be a better choice when data do not follow this assumption.

Comparison of Parametric and Bootstrap Method in Bioequivalence Test

PubMed Central

Ahn, Byung-Jin

2009-01-01

The estimation of 90% parametric confidence intervals (CIs) of mean AUC and Cmax ratios in bioequivalence (BE) tests are based upon the assumption that formulation effects in log-transformed data are normally distributed. To compare the parametric CIs with those obtained from nonparametric methods we performed repeated estimation of bootstrap-resampled datasets. The AUC and Cmax values from 3 archived datasets were used. BE tests on 1,000 resampled datasets from each archived dataset were performed using SAS (Enterprise Guide Ver.3). Bootstrap nonparametric 90% CIs of formulation effects were then compared with the parametric 90% CIs of the original datasets. The 90% CIs of formulation effects estimated from the 3 archived datasets were slightly different from nonparametric 90% CIs obtained from BE tests on resampled datasets. Histograms and density curves of formulation effects obtained from resampled datasets were similar to those of normal distribution. However, in 2 of 3 resampled log (AUC) datasets, the estimates of formulation effects did not follow the Gaussian distribution. Bias-corrected and accelerated (BCa) CIs, one of the nonparametric CIs of formulation effects, shifted outside the parametric 90% CIs of the archived datasets in these 2 non-normally distributed resampled log (AUC) datasets. Currently, the 80~125% rule based upon the parametric 90% CIs is widely accepted under the assumption of normally distributed formulation effects in log-transformed data. However, nonparametric CIs may be a better choice when data do not follow this assumption. PMID:19915699

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis.

PubMed

Hamelberg, Donald; Shen, Tongye; McCammon, J Andrew

2005-02-16

The presence of serine/threonine-proline motifs in proteins provides a conformational switching mechanism of the backbone through the cis/trans isomerization of the peptidyl-prolyl (omega) bond. The reversible phosphorylation of the serine/threonine modulates this switching in regulatory proteins to alter signaling and transcription. However, the mechanism is not well understood. This is partly because cis/trans isomerization is a very slow process and, hence, difficult to study. We have used our accelerated molecular dynamics method to study the cis/trans proline isomerization, preferred backbone conformation of a serine-proline motif, and the effects of phosphorylation of the serine residue. We demonstrate that, unlike normal molecular dynamics, the accelerated molecular dynamics allows for the system to escape very easily from the trans isomer to cis isomer, and vice versa. Moreover, for both the unphosphorylated and phosphorylated peptides, the statistical thermodynamic properties are recaptured, and the results are consistent with experimental values. Isomerization of the proline omega bond is shown to be asymmetric and strongly dependent on the psi backbone angle before and after phosphorylation. The rates of escape decrease after phosphorylation. Also, the alpha-helical backbone conformation is more favored after phosphorylation. This accelerated molecular dynamics approach provides a general approach for enhancing the conformational transitions of molecular systems without having prior knowledge of the location of the minima and barriers on the potential-energy landscape.

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

Cheng, Ke; Wang, Xiaoyun; Liu, Jingjing

Highlights: • Cu/In bilayer was fabricated by BMSMW deposition technique. • High quality CIS film was successfully fabricated. • A preferable ratio of Cu:In:S close to 1:1:2 was approached. • The SPV response as high as 6 mV was achieved. - Abstract: High-quality CuInS{sub 2} (CIS) thin films have been fabricated by sulfurization of electrodeposited copper–indium bilayer. A novel bell-like wave modulated square wave (BWMSW) electrodeposition technique is employed for the deposition of copper thin film. Three independent parameters (current or potential, frequency, duty cycle) are available for the BWMSW electrodeposition, which is different from the traditional electrodeposition technique withmore » only one adjustable parameter (current or potential). The influences of deposition parameters such as frequency, duty cycle and the concentration of complexing agent are investigated. Benefited from the high quality copper film obtained by the BWMSW technique, the indium film is electrodeposited successfully on the copper layer to form a compact copper–indium alloy bilayer. After sulfurized at 600 °C for 60 min, the phase pure CIS film is obtained with better crystallinity. The structures, morphologies and optoelectronic properties of the CIS film are also characterized.« less

Increasing the intracellular availability of all-trans retinoic acid in neuroblastoma cells.

PubMed

Armstrong, J L; Ruiz, M; Boddy, A V; Redfern, C P F; Pearson, A D J; Veal, G J

2005-02-28

Recent data indicate that isomerisation to all-trans retinoic acid (ATRA) is the key mechanism underlying the favourable clinical properties of 13-cis retinoic acid (13cisRA) in the treatment of neuroblastoma. Retinoic acid (RA) metabolism is thought to contribute to resistance, and strategies to modulate this may increase the clinical efficacy of 13cisRA. The aim of this study was to test the hypothesis that retinoids, such as acitretin, which bind preferentially to cellular retinoic acid binding proteins (CRABPs), or specific inhibitors of the RA hydroxylase CYP26, such as R116010, can increase the intracellular availability of ATRA. Incubation of SH-SY5Y cells with acitretin (50 microM) or R116010 (1 or 10 microM) in combination with either 10 microM ATRA or 13cisRA induced a selective increase in intracellular levels of ATRA, while 13cisRA levels were unaffected. CRABP was induced in SH-SY5Y cells in response to RA. In contrast, acitretin had no significant effect on intracellular retinoid concentrations in those neuroblastoma cell lines that showed little or no induction of CRABP after RA treatment. Both ATRA and 13cisRA dramatically induced the expression of CYP26A1 in SH-SY5Y cells, and treatment with R116010, but not acitretin, potentiated the RA-induced expression of a reporter gene and CYP26A1. The response of neuroblastoma cells to R116010 was consistent with inhibition of CYP26, indicating that inhibition of RA metabolism may further optimise retinoid treatment in neuroblastoma.

Increasing the intracellular availability of all-trans retinoic acid in neuroblastoma cells

PubMed Central

Armstrong, J L; Ruiz, M; Boddy, A V; Redfern, C P F; Pearson, A D J; Veal, G J

2005-01-01

Recent data indicate that isomerisation to all-trans retinoic acid (ATRA) is the key mechanism underlying the favourable clinical properties of 13-cis retinoic acid (13cisRA) in the treatment of neuroblastoma. Retinoic acid (RA) metabolism is thought to contribute to resistance, and strategies to modulate this may increase the clinical efficacy of 13cisRA. The aim of this study was to test the hypothesis that retinoids, such as acitretin, which bind preferentially to cellular retinoic acid binding proteins (CRABPs), or specific inhibitors of the RA hydroxylase CYP26, such as R116010, can increase the intracellular availability of ATRA. Incubation of SH-SY5Y cells with acitretin (50 μM) or R116010 (1 or 10 μM) in combination with either 10 μM ATRA or 13cisRA induced a selective increase in intracellular levels of ATRA, while 13cisRA levels were unaffected. CRABP was induced in SH-SY5Y cells in response to RA. In contrast, acitretin had no significant effect on intracellular retinoid concentrations in those neuroblastoma cell lines that showed little or no induction of CRABP after RA treatment. Both ATRA and 13cisRA dramatically induced the expression of CYP26A1 in SH-SY5Y cells, and treatment with R116010, but not acitretin, potentiated the RA-induced expression of a reporter gene and CYP26A1. The response of neuroblastoma cells to R116010 was consistent with inhibition of CYP26, indicating that inhibition of RA metabolism may further optimise retinoid treatment in neuroblastoma. PMID:15714209

Mechanical Stress Promotes Cisplatin-Induced Hepatocellular Carcinoma Cell Death

PubMed Central

Riad, Sandra; Bougherara, Habiba

2015-01-01

Cisplatin (CisPt) is a commonly used platinum-based chemotherapeutic agent. Its efficacy is limited due to drug resistance and multiple side effects, thereby warranting a new approach to improving the pharmacological effect of CisPt. A newly developed mathematical hypothesis suggested that mechanical loading, when coupled with a chemotherapeutic drug such as CisPt and immune cells, would boost tumor cell death. The current study investigated the aforementioned mathematical hypothesis by exposing human hepatocellular liver carcinoma (HepG2) cells to CisPt, peripheral blood mononuclear cells, and mechanical stress individually and in combination. HepG2 cells were also treated with a mixture of CisPt and carnosine with and without mechanical stress to examine one possible mechanism employed by mechanical stress to enhance CisPt effects. Carnosine is a dipeptide that reportedly sequesters platinum-based drugs away from their pharmacological target-site. Mechanical stress was achieved using an orbital shaker that produced 300 rpm with a horizontal circular motion. Our results demonstrated that mechanical stress promoted CisPt-induced death of HepG2 cells (~35% more cell death). Moreover, results showed that CisPt-induced death was compromised when CisPt was left to mix with carnosine 24 hours preceding treatment. Mechanical stress, however, ameliorated cell death (20% more cell death). PMID:25685789

Ultra-performance liquid chromatographic separation of geometric isomers of carotenoids and antioxidant activities of 20 tomato cultivars and breeding lines.

PubMed

Li, Hongyan; Deng, Zeyuan; Liu, Ronghua; Loewen, Steven; Tsao, Rong

2012-05-01

All-trans-lutein, lycopene, β-carotene and their 22 cis-isomers in 20 tomato breeding were separated and identified by a rapid and sensitive UPLC method using a 1.7μm C18 column and a new gradient mobile phase based on methanol-MTBE-water in 15 min. All-trans-carotenoids were predominant, but 9-cis, 13-cis-lutein, 5-cis, 9-cis, 13-cis, 15-cis, di-cis-lycopene, 9-cis, 13-cis, 15-cis and di-cis-β-carotene were also found. The cis-isomers were identified using absorption around 330nm and the Q-ratio. The total antioxidant activities as evaluated by PCL and DPPH assays were found to correlate well with the total carotenoid content, but not with the individual carotenoid or its different isomers. This paper provides an efficient analytical method for obtaining a complete picture of carotenoids in tomatoes. It can be a valuable tool for plant breeders, food processors and researchers in developing designer tomatoes and tomato-products with unique carotenoid compositions, and functional properties. Copyright © 2011 Elsevier Ltd. All rights reserved.

NF-Y Binding Site Architecture Defines a C-Fos Targeted Promoter Class

PubMed Central

Haubrock, Martin; Hartmann, Fabian; Wingender, Edgar

2016-01-01

ChIP-seq experiments detect the chromatin occupancy of known transcription factors in a genome-wide fashion. The comparisons of several species-specific ChIP-seq libraries done for different transcription factors have revealed a complex combinatorial and context-specific co-localization behavior for the identified binding regions. In this study we have investigated human derived ChIP-seq data to identify common cis-regulatory principles for the human transcription factor c-Fos. We found that in four different cell lines, c-Fos targeted proximal and distal genomic intervals show prevalences for either AP-1 motifs or CCAAT boxes as known binding motifs for the transcription factor NF-Y, and thereby act in a mutually exclusive manner. For proximal regions of co-localized c-Fos and NF-YB binding, we gathered evidence that a characteristic configuration of repeating CCAAT motifs may be responsible for attracting c-Fos, probably provided by a nearby AP-1 bound enhancer. Our results suggest a novel regulatory function of NF-Y in gene-proximal regions. Specific CCAAT dimer repeats bound by the transcription factor NF-Y define this novel cis-regulatory module. Based on this behavior we propose a new enhancer promoter interaction model based on AP-1 motif defined enhancers which interact with CCAAT-box characterized promoter regions. PMID:27517874

Stepwise encapsulation and controlled two-stage release system for cis-Diamminediiodoplatinum

PubMed Central

Chen, Yun; Li, Qian; Wu, Qingsheng

2014-01-01

cis-Diamminediiodoplatinum (cis-DIDP) is a cisplatin-like anticancer drug with higher anticancer activity, but lower stability and price than cisplatin. In this study, a cis-DIDP carrier system based on micro-sized stearic acid was prepared by an emulsion solvent evaporation method. The maximum drug loading capacity of cis-DIDP-loaded solid lipid nanoparticles was 22.03%, and their encapsulation efficiency was 97.24%. In vitro drug release in phosphate-buffered saline (pH =7.4) at 37.5°C exhibited a unique two-stage process, which could prove beneficial for patients with tumors and malignancies. MTT (3-[4,5-dimethylthiazol-2-yl]-2, 5-diphenyltetrazolium bromide) assay results showed that cis-DIDP released from cis-DIDP-loaded solid lipid nanoparticles had better inhibition activity than cis-DIDP that had not been loaded. PMID:25061294

Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation: A Genome-Wide Analysis among 1,800 South Asians

PubMed Central

Pierce, Brandon L.; Tong, Lin; Chen, Lin S.; Rahaman, Ronald; Argos, Maria; Jasmine, Farzana; Roy, Shantanu; Paul-Brutus, Rachelle; Westra, Harm-Jan; Franke, Lude; Esko, Tonu; Zaman, Rakibuz; Islam, Tariqul; Rahman, Mahfuzar; Baron, John A.; Kibriya, Muhammad G.; Ahsan, Habibul

2014-01-01

A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis- and trans-eQTLs and determine if observed trans-eQTL associations are mediated by expression of transcripts in cis with the SNPs showing trans-association, using Sobel tests of mediation. We observed 434 independent trans-eQTL associations at a false-discovery rate of 0.05, and 189 of these trans-eQTLs were also cis-eQTLs (enrichment P<0.0001). Among these 189 trans-eQTL associations, 39 were significantly attenuated after adjusting for a cis-mediator based on Sobel P<10-5. We attempted to replicate 21 of these mediation signals in two European cohorts, and while only 7 trans-eQTL associations were present in one or both cohorts, 6 showed evidence of cis-mediation. Analyses of simulated data show that complete mediation will be observed as partial mediation in the presence of mediator measurement error or imperfect LD between measured and causal variants. Our data demonstrates that trans-associations can become significantly stronger or switch directions after adjusting for a potential mediator. Using simulated data, we demonstrate that this phenomenon is expected in the presence of strong cis-trans confounding and when the measured cis-transcript is correlated with the true (unmeasured) mediator. In conclusion, by applying mediation analysis to eQTL data, we show that a substantial fraction of observed trans-eQTL associations can be explained by cis-mediation. Future studies should focus on understanding the mechanisms underlying widespread cis-mediation and their relevance to disease biology, as well as using mediation analysis to improve eQTL discovery. PMID:25474530

Superradiance of J-Aggregated 2,2'-Cyanine Absorbed onto a Vesicle Surface

NASA Technical Reports Server (NTRS)

Akins, Daniel L.; Ozcelik, Serdar

1995-01-01

Phospholipid vesicles are used as substrates to form adsorbed aggregates of 2,2'-cyanine, also referred to as pseudoisocyanine (PIC). In this paper, we report photophysical parameters of two putative adsorbed aggregates species (cis- and trans-aggregates, relating to their makeup from mono-cis and all-transstereoisomers, respectively). Phase modulation picosecond fluorescence decay measurements reveal that superradiance and energy transfer are dominant features controlling photophysical processes. Superradiance, coherence size, energy transfer and exciton-phonon coupling are discussed for the two types of aggregates; as regards photophysical parameters, the fluorescence lifetimes, fluorescence quantum yields, and nonradiative rate constants are determined. It is suggested that structure plays the crucial role in excited state dynamics.

A 7 ke-SD-FWC 1.2 e-RMS Temporal Random Noise 128×256 Time-Resolved CMOS Image Sensor With Two In-Pixel SDs for Biomedical Applications.

PubMed

Seo, Min-Woong; Kawahito, Shoji

2017-12-01

A large full well capacity (FWC) for wide signal detection range and low temporal random noise for high sensitivity lock-in pixel CMOS image sensor (CIS) embedded with two in-pixel storage diodes (SDs) has been developed and presented in this paper. For fast charge transfer from photodiode to SDs, a lateral electric field charge modulator (LEFM) is used for the developed lock-in pixel. As a result, the time-resolved CIS achieves a very large SD-FWC of approximately 7ke-, low temporal random noise of 1.2e-rms at 20 fps with true correlated double sampling operation and fast intrinsic response less than 500 ps at 635 nm. The proposed imager has an effective pixel array of and a pixel size of . The sensor chip is fabricated by Dongbu HiTek 1P4M 0.11 CIS process.

Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment.

PubMed

Exarchos, Konstantinos P; Exarchos, Themis P; Rigas, Georgios; Papaloukas, Costas; Fotiadis, Dimitrios I

2011-05-10

In peptides and proteins, only a small percentile of peptide bonds adopts the cis configuration. Especially in the case of amide peptide bonds, the amount of cis conformations is quite limited thus hampering systematic studies, until recently. However, lately the emerging population of databases with more 3D structures of proteins has produced a considerable number of sequences containing non-proline cis formations (cis-nonPro). In our work, we extract regular expression-type patterns that are descriptive of regions surrounding the cis-nonPro formations. For this purpose, three types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, and iii) pattern discovery using a structural equivalency set. Afterwards, using each pattern as predicate, we search the Eukaryotic Linear Motif (ELM) resource to identify potential functional implications of regions with cis-nonPro peptide bonds. The patterns extracted from each type of pattern discovery are further employed, in order to formulate a pattern-based classifier, which is used to discriminate between cis-nonPro and trans-nonPro formations. In terms of functional implications, we observe a significant association of cis-nonPro peptide bonds towards ligand/binding functionalities. As for the pattern-based classification scheme, the highest results were obtained using the structural equivalency set, which yielded 70% accuracy, 77% sensitivity and 63% specificity.

Effect of e-learning on quality of cervical-length measurements.

PubMed

van Os, M A; van der Ven, A J; Bloemendaal, P M; Pajkrt, E; de Groot, C J M; Mol, B W J; Haak, M C

2015-09-01

To assess the effect of implementation of a newly developed e-learning module on the quality of cervical-length measurements. With the introduction of cervical-length (CL) measurement in a research setting, a CL measurement e-learning module (CLEM) was developed with the purpose to enhance the knowledge and skills of experienced ultrasonographers. CLEM was designed specifically for ultrasonographers who perform ultrasound in a general obstetrical practice but who do not regularly perform CL measurements. CLEM consists of five theoretical questions and three caliper-placement tests to learn the CL measurement technique. The quality of the CL measurements of CLEM participants was compared with images of non-participants using a CL measurement image score (CIS), defined as the sum of six items which assess the quality of the image. Each CLEM participant submitted five CL images and the images of non-CLEM participants were selected randomly from an ultrasound database. The CIS of the CLEM participants (n = 61) were significantly higher than those of non-CLEM participants (n = 23) (164.9 vs 155.6, respectively; P = 0.03). Visualization of the internal os and positioning of the calipers on the internal and external ora were found to have significantly higher CIS among the CLEM participants than among the non-CLEM participants (P = 0.001 and P < 0.001, respectively). Introducing CLEM may improve the quality of CL measurements obtained by trained and untrained sonographers. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.

Computational exploration of cis-regulatory modules in rhythmic expression data using the "Exploration of Distinctive CREs and CRMs" (EDCC) and "CRM Network Generator" (CNG) programs.

PubMed

Bekiaris, Pavlos Stephanos; Tekath, Tobias; Staiger, Dorothee; Danisman, Selahattin

2018-01-01

Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, "Exploration of Distinctive CREs and CRMs" (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, "CRM Network Generator" (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression.

Computational exploration of cis-regulatory modules in rhythmic expression data using the “Exploration of Distinctive CREs and CRMs” (EDCC) and “CRM Network Generator” (CNG) programs

PubMed Central

Staiger, Dorothee

2018-01-01

Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, “Exploration of Distinctive CREs and CRMs” (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, “CRM Network Generator” (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression. PMID:29298348

Tissue-Specific and Genetic Regulation of Insulin Sensitivity-Associated Transcripts in African Americans

PubMed Central

Sharma, Neeraj K.; Sajuthi, Satria P.; Chou, Jeff W.; Calles-Escandon, Jorge; Demons, Jamehl; Rogers, Samantha; Ma, Lijun; Palmer, Nicholette D.; McWilliams, David R.; Beal, John; Comeau, Mary E.; Cherry, Kristina; Hawkins, Gregory A.; Menon, Lata; Kouba, Ethel; Davis, Donna; Burris, Marcie; Byerly, Sara J.; Easter, Linda; Bowden, Donald W.; Freedman, Barry I.; Langefeld, Carl D.

2016-01-01

Context: Compared with European Americans, African Americans (AAs) are more insulin resistant, have a higher insulin secretion response to glucose, and develop type 2 diabetes more often. Molecular processes and/or genetic variations contributing to altered glucose homeostasis in high-risk AAs remain uncharacterized. Objective: Adipose and muscle transcript expression profiling and genotyping were performed in 260 AAs to identify genetic regulatory mechanisms associated with insulin sensitivity (SI). We hypothesized that: 1) transcription profiles would reveal tissue-specific modulation of physiologic pathways with SI, and 2) a subset of SI-associated transcripts would be controlled by DNA sequence variants as expression quantitative traits, and these variants in turn would be associated with SI. Design and Settings: The cross-sectional research study was performed in a clinical research unit. Participants: Unrelated nondiabetic AAs were recruited for the study. Main Outcome Measures: SI was measured by frequently sampled iv glucose tolerance test. Results: The expression levels of 2212 transcripts in adipose and 145 transcripts in muscle were associated with SI. Genes involved in eIF2, eIF4-p70S6K, and mTOR signaling were modulated with SI in both tissues. Genes involved in leukocyte extravasation signaling showed adipose-specific regulation, and genes involved in oxidative phosphorylation had discordant regulation between tissues. Intersecting cis-expression quantitative trait loci results with data from transcript-SI association analysis identified cis-regulatory single nucleotide polymorphisms for 363 and 42 SI-associated transcripts in adipose and muscle, respectively. Cis-eSNPs for three SI-associated adipose transcripts, NINJ1, AGA, and CLEC10A were associated with SI. Abrogation of NINJ1 induction in THP1 macrophages modulated expression of genes in chemokine signaling, cell adhesion, and angiogenesis pathways. Conclusion: This study identified multiple pathways associated with SI; particularly discordant tissue-specific regulation of the oxidative phosphorylation pathway, and adipose-specific regulation of transcripts in the leukocyte extravasation signaling pathway that seem to be important in insulin resistance. Identification of single nucleotide polymorphisms associated with SI and with modulation of expression of SI-associated transcripts, including NINJ1, reveals novel genetic regulatory mechanisms of insulin resistance in AAs. PMID:26789776

Synthesis of 7-azabicyclo[2.2.1]heptane and 2-oxa-4-azabicyclo[3.3.1]non-3-ene derivatives by base-promoted heterocyclization of alkyl N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)carbamates and N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamides.

PubMed

Gómez-Sanchez, Elena; Soriano, Elena; Marco-Contelles, José

2007-11-09

We have studied the base-promoted heterocyclization of alkyl N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)carbamates and N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamides, investigating the effect of the nitrogen protecting group and the relative configuration of the leaving group at C3 and C4 on the outcome of this reaction. We have observed that the sodium hydride-promoted heterocyclization of alkyl N-(cis-3,trans-4-dibromocyclohex-1-yl)carbamates (10, 12, 14, 16, 18) is a convenient method for the synthesis of 7-azabicyclo[2.2.1]heptane derivatives. For instance, the reaction of tert-butyl N-(cis-3,trans-4-dibromocyclohex-1-yl)carbamate (10) with sodium hydride in DMF at room temperature provides 2-bromo-7-[(tert-butoxy)carbonyl]-7-azabicyclo[2.2.1]heptane (2) (52% yield), whose t-BuOK-promoted hydrogen bromide elimination affords 7-[(tert-butoxy)carbonyl]-7-azabicyclo[2.2.1]hept-2-ene (31) in 78% yield, an intermediate in the total synthesis of epibatidine (1). However, the NaH/DMF-mediated heterocyclization of alkyl N-(trans-3,cis-4-dibromocyclohex-1-yl)carbamates (11, 13) is a more structure dependent reaction, where the nucleophilic attack of the oxygen atom of the protecting group controls the outcome of the reaction, giving rise to benzooxazolone and 2-oxa-4-azabicyclo[3.3.1]non-3-ene derivatives, respectively, from low to moderate yields, in complex reaction mixtures. Conversely, the NaH/DMF heterocyclizations of N-(cis-3,trans-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamide (40) or N-(trans-3,cis-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamide (42) are very clean reactions giving 7-azabicyclo[2.2.1]heptane or 2-oxa-4-azabicyclo[3.3.1]non-3-ene derivatives, respectively, in good yields. Finally, a mechanistic investigation, based on DFT calculations, has been carried out to rationalize the formation of the different adducts.

Activation of the dopamine receptor type-2 (DRD2) promoter by 9-cis retinoic acid in a cellular model of Cushing's disease mediates the inhibition of cell proliferation and ACTH secretion without a complete corticotroph-to-melanotroph transdifferentiation.

PubMed

Occhi, Gianluca; Regazzo, Daniela; Albiger, Nora Maria; Ceccato, Filippo; Ferasin, Sergio; Scanarini, Massimo; Denaro, Luca; Cosma, Chiara; Plebani, Mario; Cassarino, Maria Francesca; Mantovani, Giovanna; Stalla, Günter K; Pecori Giraldi, Francesca; Paez-Pareda, Marcelo; Scaroni, Carla

2014-09-01

Cushing's disease (CD) is a rare condition in which hypercortisolemia is secondary to excessive ACTH release from a pituitary corticotroph adenoma. CD is associated with significant morbidity and mortality, and a safe therapy that effectively targets the pituitary tumor is still lacking. Retinoic acid (RA) and dopamine agonists (DAs) have recently been considered as monotherapy in CD patients, and satisfactory results have been reported, albeit in a limited number of patients. Given the permissive role of RA on the dopamine receptor type-2 (DRD2), the aim of the present study was to see whether a combination of 9-cis RA and the DA bromocriptine (Br) might represent a possible treatment for CD. Here we show that 9-cis RA induces a functional DRD2 in the pituitary corticotroph cell line AtT20, and increases cell sensitivity to Br via a mechanism only partially related to corticotroph-to-melanotroph transdifferentiation. In addition, 9-cis RA and Br act synergistically to modulate cell viability, with favorable implications for clinical use. In nearly 45% of corticotropinoma-derived primary cultures, the combined administration of 9-cis RA and Br lowered the steady-state level of the ACTH precursor proopiomelanocortin (POMC) more efficiently than either of the drugs alone. In conclusion, the effects of a combination of 9-cis RA and Br on ACTH synthesis/secretion and cell viability in AtT20, and on POMC transcriptional activity in human corticotropinomas might represent a suitable starting point for assessing the potential of this treatment regimen for ACTH-secreting pituitary adenomas. This study thus has potentially important implications for novel therapeutic approaches to CD.

Enhancement of antibody synthesis in rats by feeding cis-9,trans-11 conjugated linoleic acid during early life.

PubMed

Ramírez-Santana, Carolina; Castellote, Cristina; Castell, Margarida; Moltó-Puigmartí, Carolina; Rivero, Montserrat; Pérez-Cano, Francisco J; Franch, Angels

2011-05-01

Previous studies have demonstrated that the intake of a 1% conjugated linoleic acid (CLA) diet in an 80:20 mixture of cis-9,trans-11 and trans-10,cis-12 exerts age-specific effects on the immune system: immunoglobulin enhancement and proliferative down-modulation in neonatal and adult rats, respectively. The present study evaluates the influence of the same diet on antibody synthesis of early infant Wistar rats during suckling and/or after weaning. Dietary supplementation was performed during suckling and early infancy (4 weeks), only during suckling (3 weeks), or only in early infancy (1 week). CLA content in plasma and serum immunoglobulin (Ig) G, IgM and IgA concentration were determined. Proliferation, cytokines and Ig production were evaluated on isolated splenocytes. Cis-9,trans-11- and trans-10,cis-12-CLA isomers were detected in the plasma of all CLA-supplemented animals, and the highest content was quantified in those rats supplemented over the longest period. These rats also exhibited higher concentrations of serum IgG, IgM and IgA. Moreover, splenocytes from CLA-supplemented rats showed the highest IgM and IgG synthesis and interleukin (IL)-6 production, whereas their proliferative ability was lower. In summary, in infant rats, we observed both the enhance antibody synthesis previously reported in neonates, and the reduced lymphoproliferation previously reported in adults. Copyright © 2011 Elsevier Inc. All rights reserved.

Continuous-time ΣΔ ADC with implicit variable gain amplifier for CMOS image sensor.

PubMed

Tang, Fang; Bermak, Amine; Abbes, Amira; Benammar, Mohieddine Amor

2014-01-01

This paper presents a column-parallel continuous-time sigma delta (CTSD) ADC for mega-pixel resolution CMOS image sensor (CIS). The sigma delta modulator is implemented with a 2nd order resistor/capacitor-based loop filter. The first integrator uses a conventional operational transconductance amplifier (OTA), for the concern of a high power noise rejection. The second integrator is realized with a single-ended inverter-based amplifier, instead of a standard OTA. As a result, the power consumption is reduced, without sacrificing the noise performance. Moreover, the variable gain amplifier in the traditional column-parallel read-out circuit is merged into the front-end of the CTSD modulator. By programming the input resistance, the amplitude range of the input current can be tuned with 8 scales, which is equivalent to a traditional 2-bit preamplification function without consuming extra power and chip area. The test chip prototype is fabricated using 0.18 μm CMOS process and the measurement result shows an ADC power consumption lower than 63.5 μW under 1.4 V power supply and 50 MHz clock frequency.

Rational design of aptazyme riboswitches for efficient control of gene expression in mammalian cells

PubMed Central

Zhong, Guocai; Wang, Haimin; Bailey, Charles C; Gao, Guangping; Farzan, Michael

2016-01-01

Efforts to control mammalian gene expression with ligand-responsive riboswitches have been hindered by lack of a general method for generating efficient switches in mammalian systems. Here we describe a rational-design approach that enables rapid development of efficient cis-acting aptazyme riboswitches. We identified communication-module characteristics associated with aptazyme functionality through analysis of a 32-aptazyme test panel. We then developed a scoring system that predicts an aptazymes’s activity by integrating three characteristics of communication-module bases: hydrogen bonding, base stacking, and distance to the enzymatic core. We validated the power and generality of this approach by designing aptazymes responsive to three distinct ligands, each with markedly wider dynamic ranges than any previously reported. These aptayzmes efficiently regulated adeno-associated virus (AAV)-vectored transgene expression in cultured mammalian cells and mice, highlighting one application of these broadly usable regulatory switches. Our approach enables efficient, protein-independent control of gene expression by a range of small molecules. DOI: http://dx.doi.org/10.7554/eLife.18858.001 PMID:27805569

Mapping Adipose and Muscle Tissue Expression Quantitative Trait Loci in African Americans to Identify Genes for Type 2 Diabetes and Obesity

PubMed Central

Sajuthi, Satria P.; Sharma, Neeraj K.; Chou, Jeff W.; Palmer, Nicholette D.; McWilliams, David R.; Beal, John; Comeau, Mary E.; Ma, Lijun; Calles-Escandon, Jorge; Demons, Jamehl; Rogers, Samantha; Cherry, Kristina; Menon, Lata; Kouba, Ethel; Davis, Donna; Burris, Marcie; Byerly, Sara J.; Ng, Maggie C.Y.; Maruthur, Nisa M.; Patel, Sanjay R.; Bielak, Lawrence F.; Lange, Leslie; Guo, Xiuqing; Sale, Michèle M.; Chan, Kei Hang; Monda, Keri L.; Chen, Gary K.; Taylor, Kira; Palmer, Cameron; Edwards, Todd L; North, Kari E.; Haiman, Christopher A.; Bowden, Donald W.; Freedman, Barry I.; Langefeld, Carl D.; Das, Swapan K.

2016-01-01

Relative to European Americans, type 2 diabetes (T2D) is more prevalent in African Americans (AAs). Genetic variation may modulate transcript abundance in insulin-responsive tissues and contribute to risk; yet published studies identifying expression quantitative trait loci (eQTLs) in African ancestry populations are restricted to blood cells. This study aims to develop a map of genetically regulated transcripts expressed in tissues important for glucose homeostasis in AAs, critical for identifying the genetic etiology of T2D and related traits. Quantitative measures of adipose and muscle gene expression, and genotypic data were integrated in 260 non-diabetic AAs to identify expression regulatory variants. Their roles in genetic susceptibility to T2D, and related metabolic phenotypes were evaluated by mining GWAS datasets. eQTL analysis identified 1,971 and 2,078 cis-eGenes in adipose and muscle, respectively. Cis-eQTLs for 885 transcripts including top cis-eGenes CHURC1, USMG5, and ERAP2, were identified in both tissues. 62.1% of top cis-eSNPs were within ±50kb of transcription start sites and cis-eGenes were enriched for mitochondrial transcripts. Mining GWAS databases revealed association of cis-eSNPs for more than 50 genes with T2D (e.g. PIK3C2A, RBMS1, UFSP1), gluco-metabolic phenotypes, (e.g. INPP5E, SNX17, ERAP2, FN3KRP), and obesity (e.g. POMC, CPEB4). Integration of GWAS meta-analysis data from AA cohorts revealed the most significant association for cis-eSNPs of ATP5SL and MCCC1 genes, with T2D and BMI, respectively. This study developed the first comprehensive map of adipose and muscle tissue eQTLs in AAs (publically accessible at https://mdsetaa.phs.wakehealth.edu) and identified genetically-regulated transcripts for delineating genetic causes of T2D, and related metabolic phenotypes. PMID:27193597

Development of the Canadian Physiotherapy Assessment of Clinical Performance: A New Tool to Assess Physiotherapy Students' Performance in Clinical Education.

PubMed

Mori, Brenda; Brooks, Dina; Norman, Kathleen E; Herold, Jodi; Beaton, Dorcas E

2015-08-01

To develop the first draft of a Canadian tool to assess physiotherapy (PT) students' performance in clinical education (CE). Phase 1: to gain consensus on the items within the new tool, the number and placement of the comment boxes, and the rating scale; Phase 2: to explore the face and content validity of the draft tool. Phase 1 used the Delphi method; Phase 2 used cognitive interviewing methods with recent graduates and clinical instructors (CIs) and detailed interviews with clinical education and measurement experts. Consensus was reached on the first draft of the new tool by round 3 of the Delphi process, which was completed by 21 participants. Interviews were completed with 13 CIs, 6 recent graduates, and 7 experts. Recent graduates and CIs were able to interpret the tool accurately, felt they could apply it to a recent CE experience, and provided suggestions to improve the draft. Experts provided salient advice. The first draft of a new tool to assess PT students in CE, the Canadian Physiotherapy Assessment of Clinical Performance (ACP), was developed and will undergo further development and testing, including national consultation with stakeholders. Data from Phase 2 will contribute to developing an online education module for CIs and students.

Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins.

PubMed

Das, Sreetama; Bhadra, Pratiti; Ramakumar, Suryanarayanarao; Pal, Debnath

2017-08-04

cis-Peptide bonds, whose occurrence in proteins is rare but evolutionarily conserved, are implicated to play an important role in protein function. This has led to their previous use in a homology-independent, fragment-match-based protein function annotation method. However, proteins are not static molecules; dynamics is integral to their activity. This is nicely epitomized by the geometric isomerization of cis-peptide to trans form for molecular activity. Hence we have incorporated both static (cis-peptide) and dynamics information to improve the prediction of protein molecular function. Our results show that cis-peptide information alone cannot detect functional matches in cases where cis-trans isomerization exists but 3D coordinates have been obtained for only the trans isomer or when the cis-peptide bond is incorrectly assigned as trans. On the contrary, use of dynamics information alone includes false-positive matches for cases where fragments with similar secondary structure show similar dynamics, but the proteins do not share a common function. Combining the two methods reduces errors while detecting the true matches, thereby enhancing the utility of our method in function annotation. A combined approach, therefore, opens up new avenues of improving existing automated function annotation methodologies.

Integrating genome-wide genetic variations and monocyte expression data reveals trans-regulated gene modules in humans.

PubMed

Rotival, Maxime; Zeller, Tanja; Wild, Philipp S; Maouche, Seraya; Szymczak, Silke; Schillert, Arne; Castagné, Raphaele; Deiseroth, Arne; Proust, Carole; Brocheton, Jessy; Godefroy, Tiphaine; Perret, Claire; Germain, Marine; Eleftheriadis, Medea; Sinning, Christoph R; Schnabel, Renate B; Lubos, Edith; Lackner, Karl J; Rossmann, Heidi; Münzel, Thomas; Rendon, Augusto; Erdmann, Jeanette; Deloukas, Panos; Hengstenberg, Christian; Diemert, Patrick; Montalescot, Gilles; Ouwehand, Willem H; Samani, Nilesh J; Schunkert, Heribert; Tregouet, David-Alexandre; Ziegler, Andreas; Goodall, Alison H; Cambien, François; Tiret, Laurence; Blankenberg, Stefan

2011-12-01

One major expectation from the transcriptome in humans is to characterize the biological basis of associations identified by genome-wide association studies. So far, few cis expression quantitative trait loci (eQTLs) have been reliably related to disease susceptibility. Trans-regulating mechanisms may play a more prominent role in disease susceptibility. We analyzed 12,808 genes detected in at least 5% of circulating monocyte samples from a population-based sample of 1,490 European unrelated subjects. We applied a method of extraction of expression patterns-independent component analysis-to identify sets of co-regulated genes. These patterns were then related to 675,350 SNPs to identify major trans-acting regulators. We detected three genomic regions significantly associated with co-regulated gene modules. Association of these loci with multiple expression traits was replicated in Cardiogenics, an independent study in which expression profiles of monocytes were available in 758 subjects. The locus 12q13 (lead SNP rs11171739), previously identified as a type 1 diabetes locus, was associated with a pattern including two cis eQTLs, RPS26 and SUOX, and 5 trans eQTLs, one of which (MADCAM1) is a potential candidate for mediating T1D susceptibility. The locus 12q24 (lead SNP rs653178), which has demonstrated extensive disease pleiotropy, including type 1 diabetes, hypertension, and celiac disease, was associated to a pattern strongly correlating to blood pressure level. The strongest trans eQTL in this pattern was CRIP1, a known marker of cellular proliferation in cancer. The locus 12q15 (lead SNP rs11177644) was associated with a pattern driven by two cis eQTLs, LYZ and YEATS4, and including 34 trans eQTLs, several of them tumor-related genes. This study shows that a method exploiting the structure of co-expressions among genes can help identify genomic regions involved in trans regulation of sets of genes and can provide clues for understanding the mechanisms linking genome-wide association loci to disease.

Modulating lysosomal function through lysosome membrane permeabilization or autophagy suppression restores sensitivity to cisplatin in refractory non-small-cell lung cancer cells.

PubMed

Circu, Magdalena; Cardelli, James; Barr, Martin; O'Byrne, Kenneth; Mills, Glenn; El-Osta, Hazem

2017-01-01

Lung cancer is the leading cause of cancer-related deaths. Most patients develop resistance to platinum within several months of treatment. We investigated whether triggering lysosomal membrane permeabilization (LMP) or suppressing autophagy can restore cisplatin susceptibility in lung cancer with acquired chemoresistance. Cisplatin IC50 in A549Pt (parental) and A549cisR (cisplatin resistant) cells was 13 μM and 47 μM, respectively. Following cisplatin exposure, A549cisR cells failed to elicit an apoptotic response. This was manifested by diminished Annexin-V staining, caspase 3 and 9, BAX and BAK activation in resistant but not in parental cells. Chloroquine preferentially promoted LMP in A549cisR cells, revealed by leakage of FITC-dextran into the cytosol as detected by immunofluorescence microscopy. This was confirmed by increased cytosolic cathepsin D signal on Immunoblot. Cell viability of cisplatin-treated A549cisR cells was decreased when co-treated with chloroquine, corresponding to a combination index below 0.8, suggesting synergism between the two drugs. Notably, chloroquine activated the mitochondrial cell death pathway as indicated by increase in caspase 9 activity. Interestingly, inhibition of lysosomal proteases using E64 conferred cytoprotection against cisplatin and chloroquine co-treatment, suggesting that chloroquine-induced cell death occurred in a cathepsin-mediated mechanism. Likewise, blockage of caspases partially rescued A549cisR cells against the cytotoxicity of cisplatin and chloroquine combination. Cisplatin promoted a dose-dependent autophagic flux induction preferentially in A549cisR cells, as evidenced by a surge in LC3-II/α-tubulin following pre-treatment with E64 and increase in p62 degradation. Compared to untreated cells, cisplatin induced an increase in cyto-ID-loaded autophagosomes in A549cisR cells that was further amplified by chloroquine, pointing toward autophagic flux activation by cisplatin. Interestingly, this effect was less pronounced in A549Pt cells. Blocking autophagy by ATG5 depletion using siRNA markedly enhances susceptibility to cisplatin in A549cisR cells. Taken together, our results underscore the utility of targeting lysosomal function in overcoming acquired cisplatin refractoriness in lung cancer.

Intramolecular hydrogen bonding in malonaldehyde and its radical analogues.

PubMed

Lin, Chen; Kumar, Manoj; Finney, Brian A; Francisco, Joseph S

2017-09-28

High level Brueckner doubles with triples correction method-based ab initio calculations have been used to investigate the nature of intramolecular hydrogen bonding and intramolecular hydrogen atom transfer in cis-malonaldehyde (MA) and its radical analogues. The radicals considered here are the ones that correspond to the homolytic cleavage of C-H bonds in cis-MA. The results suggest that cis-MA and its radical analogues, cis-MA RS , and cis-MA RA , both exist in planar geometry. The calculated intramolecular O-H⋯O=C bond in cis-MA is shorter than that in the radical analogues. The intramolecular hydrogen bond in cis-MA is stronger than in its radicals by at least 3.0 kcal/mol. The stability of a cis-malonaldehyde radical correlates with the extent of electron spin delocalization; cis-MA RA , in which the radical spin is more delocalized, is the most stable MA radical, whereas cis-MA RS , in which the radical spin is strongly localized, is the least stable radical. The natural bond orbital analysis indicates that the intramolecular hydrogen bonding (O⋯H⋯O) in cis-malonaldehyde radicals is stabilized by the interaction between the lone pair orbitals of donor oxygen and the σ * orbital of acceptor O-H bond (n → σ * OH ). The calculated barriers indicate that the intramolecular proton transfer in cis-MA involves 2.2 kcal/mol lower barrier than that in cis-MA RS .

A novel measure and significance testing in data analysis of cell image segmentation.

PubMed

Wu, Jin Chu; Halter, Michael; Kacker, Raghu N; Elliott, John T; Plant, Anne L

2017-03-14

Cell image segmentation (CIS) is an essential part of quantitative imaging of biological cells. Designing a performance measure and conducting significance testing are critical for evaluating and comparing the CIS algorithms for image-based cell assays in cytometry. Many measures and methods have been proposed and implemented to evaluate segmentation methods. However, computing the standard errors (SE) of the measures and their correlation coefficient is not described, and thus the statistical significance of performance differences between CIS algorithms cannot be assessed. We propose the total error rate (TER), a novel performance measure for segmenting all cells in the supervised evaluation. The TER statistically aggregates all misclassification error rates (MER) by taking cell sizes as weights. The MERs are for segmenting each single cell in the population. The TER is fully supported by the pairwise comparisons of MERs using 106 manually segmented ground-truth cells with different sizes and seven CIS algorithms taken from ImageJ. Further, the SE and 95% confidence interval (CI) of TER are computed based on the SE of MER that is calculated using the bootstrap method. An algorithm for computing the correlation coefficient of TERs between two CIS algorithms is also provided. Hence, the 95% CI error bars can be used to classify CIS algorithms. The SEs of TERs and their correlation coefficient can be employed to conduct the hypothesis testing, while the CIs overlap, to determine the statistical significance of the performance differences between CIS algorithms. A novel measure TER of CIS is proposed. The TER's SEs and correlation coefficient are computed. Thereafter, CIS algorithms can be evaluated and compared statistically by conducting the significance testing.

Thin film lithium niobate electro-optic modulator with terahertz operating bandwidth.

PubMed

Mercante, Andrew J; Shi, Shouyuan; Yao, Peng; Xie, Linli; Weikle, Robert M; Prather, Dennis W

2018-05-28

We present a thin film crystal ion sliced (CIS) LiNbO 3 phase modulator that demonstrates an unprecedented measured electro-optic (EO) response up to 500 GHz. Shallow rib waveguides are utilized for guiding a single transverse electric (TE) optical mode, and Au coplanar waveguides (CPWs) support the modulating radio frequency (RF) mode. Precise index matching between the co-propagating RF and optical modes is responsible for the device's broadband response, which is estimated to extend even beyond 500 GHz. Matching the velocities of these co-propagating RF and optical modes is realized by cladding the modulator's interaction region in a thin UV15 polymer layer, which increases the RF modal index. The fabricated modulator possesses a tightly confined optical mode, which lends itself to a strong interaction between the modulating RF field and the guided optical carrier; resulting in a measured DC half-wave voltage of 3.8 V·cm -1 . The design, fabrication, and characterization of our broadband modulator is presented in this work.

Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord

PubMed Central

José-Edwards, Diana S.; Oda-Ishii, Izumi; Kugler, Jamie E.; Passamaneck, Yale J.; Katikala, Lavanya; Nibu, Yutaka; Di Gregorio, Anna

2015-01-01

A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs), and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC) microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs. PMID:26684323

Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.

PubMed

José-Edwards, Diana S; Oda-Ishii, Izumi; Kugler, Jamie E; Passamaneck, Yale J; Katikala, Lavanya; Nibu, Yutaka; Di Gregorio, Anna

2015-12-01

A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs), and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC) microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs.

Peptidyl-prolyl cis/trans-isomerase A1 (Pin1) is a target for modification by lipid electrophiles.

PubMed

Aluise, Christopher D; Rose, Kristie; Boiani, Mariana; Reyzer, Michelle L; Manna, Joseph D; Tallman, Keri; Porter, Ned A; Marnett, Lawrence J

2013-02-18

Oxidation of membrane phospholipids is associated with inflammation, neurodegenerative disease, and cancer. Oxyradical damage to phospholipids results in the production of reactive aldehydes that adduct proteins and modulate their function. 4-Hydroxynonenal (HNE), a common product of oxidative damage to lipids, adducts proteins at exposed Cys, His, or Lys residues. Here, we demonstrate that peptidyl-prolyl cis/trans-isomerase A1 (Pin1), an enzyme that catalyzes the conversion of the peptide bond of pSer/pThr-Pro moieties in signaling proteins from cis to trans, is highly susceptible to HNE modification. Incubation of purified Pin1 with HNE followed by MALDI-TOF/TOF mass spectrometry resulted in detection of Michael adducts at the active site residues His-157 and Cys-113. Time and concentration dependencies indicate that Cys-113 is the primary site of HNE modification. Pin1 was adducted in MDA-MB-231 breast cancer cells treated with 8-alkynyl-HNE as judged by click chemistry conjugation with biotin followed by streptavidin-based pulldown and Western blotting with anti-Pin1 antibody. Furthermore, orbitrap MS data support the adduction of Cys-113 in the Pin1 active site upon HNE treatment of MDA-MB-231 cells. siRNA knockdown of Pin1 in MDA-MB-231 cells partially protected the cells from HNE-induced toxicity. Recent studies indicate that Pin1 is an important molecular target for the chemopreventive effects of green tea polyphenols. The present study establishes that it is also a target for electrophilic modification by products of lipid peroxidation.

Structure of Zebrafish IRBP Reveals Fatty Acid Binding

PubMed Central

Ghosh, Debashis; Haswell, Karen M.; Sprada, Molly; Gonzalez-Fernandez, Federico

2015-01-01

Interphotoreceptor retinoid-binding protein (IRBP) has a remarkable role in targeting and protecting all-trans and 11-cis retinol, and 11-cis retinal during the rod and cone visual cycles. Little is known about how the correct retinoid is efficiently delivered and removed from the correct cell at the required time. It has been proposed that different fatty composition at that the outer-segments and retinal-pigmented epithelium could have an important role is regulating the delivery and uptake of the visual cycle retinoids at the cell-interphotoreceptor-matrix interface. Although this suggests intriguing mechanisms for the role of local fatty acids in visual-cycle retinoid trafficking, nothing is known about the structural basis of IRBP-fatty acid interactions. Such regulation may be mediated through IRBP’s unusual repeating homologous modules, each containing about 300 amino acids. We have been investigating structure-function relationships of Zebrafish IRBP (zIRBP), which has only two tandem modules (z1 and z2), as a model for the more complex four-module mammalian IRBP’s. Here we report the first X-ray crystal structure of a teleost IRBP, and the only structure with a bound ligand. The X-ray structure of z1, determined at 1.90Å resolution, reveals a two-domain organization of the module (domains A and B). A deep hydrophobic pocket was identified within the N-terminal domain A. In fluorescence titrations assays, oleic acid displaced all-trans retinol from zIRBP. Our study, which provides the first structure of an IRBP with bound ligand, supports a potential role for fatty acids in regulating retinoid binding. PMID:26344741

Screening for carcinoma in situ in the contralateral testicle in patients with testicular cancer: a population-based study.

PubMed

Kier, M G G; Lauritsen, J; Almstrup, K; Mortensen, M S; Toft, B G; Rajpert-De Meyts, E; Skakkebaek, N E; Rørth, M; von der Maase, H; Agerbaek, M; Holm, N V; Andersen, K K; Dalton, S O; Johansen, C; Daugaard, G

2015-04-01

Screening programmes for contralateral carcinoma in situ (CIS) testis in patients with unilateral germ-cell cancer (GCC) have never been evaluated. We investigated the effect of screening for contralateral CIS in a large nation-wide, population-based study. A contralateral single-site biopsy was offered to 4130 patients in whom GCC had been diagnosed in 1984-2007 (screened cohort); 462 patients in whom GCC was diagnosed in 1984-1988 comprised the unscreened cohort. Cases with CIS were offered radiotherapy. Initially CIS-negative biopsies in patients with metachronous GCC were revised according to today's standards. Risk for metachronous GCC was estimated using cumulative incidence and the Cox proportional hazards model. In the screened cohort, contralateral CIS was found in 181 (4.4%) patients. The cumulative incidence of metachronous GCC after 20 years was 1.9% in the screened cohort and 3.1% in the unscreened cohort (P = 0.097), hazard ratio (HR) for the unscreened cohort: 1.59 (P = 0.144). Expert revision with contemporary methodology of CIS-negative biopsy samples from patients with metachronous cancer revealed CIS in 17 out of 45 (38%) cases. Decreased risks for metachronous GCC were related to older age at diagnosis (HR 0.52 per 10 years, P < 0.001) and chemotherapy (HR 0.35, P = 0.002). Limitations include the small number of patients in the unscreened cohort and the retrospective study design. Our evaluation of a national population-based screening programme for contralateral CIS in patients with testicular cancer showed no significant difference in the risk for metachronous GCC between a screened and an unscreened cohort. Single-site biopsy including modern immunohistochemistry does not identify all cases of CIS. © The Author 2014. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Network perturbation by recurrent regulatory variants in cancer

PubMed Central

Cho, Ara; Lee, Insuk; Choi, Jung Kyoon

2017-01-01

Cancer driving genes have been identified as recurrently affected by variants that alter protein-coding sequences. However, a majority of cancer variants arise in noncoding regions, and some of them are thought to play a critical role through transcriptional perturbation. Here we identified putative transcriptional driver genes based on combinatorial variant recurrence in cis-regulatory regions. The identified genes showed high connectivity in the cancer type-specific transcription regulatory network, with high outdegree and many downstream genes, highlighting their causative role during tumorigenesis. In the protein interactome, the identified transcriptional drivers were not as highly connected as coding driver genes but appeared to form a network module centered on the coding drivers. The coding and regulatory variants associated via these interactions between the coding and transcriptional drivers showed exclusive and complementary occurrence patterns across tumor samples. Transcriptional cancer drivers may act through an extensive perturbation of the regulatory network and by altering protein network modules through interactions with coding driver genes. PMID:28333928

Single d(ApG)/cis-diamminedichloroplatinum(II) adduct-induced mutagenesis in Escherichia coli

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

Burnouf, D.; Fuchs, R.P.P.; Gauthier, C.

1990-08-01

The mutation spectrum induced by the widely used antitumor drug cis-diamminedichloroplatinum(II) (cis-DDP) showed that cisDDP(d(ApG)) adducts, although they account for only 25% of the lesions formed are {approx}5 times more mutagenic than the major GG adduct. The authors report the construction of vectors bearing a single cisDDP(d(ApG)) lesion and their use in mutagenesis experiments in Escherichia coli. The mutagenic processing of the lesion is found to depend strictly on induction of the SOS system of the bacterial host cells. In SOS-induced cells, mutation frequencies of 1-2% were detected. All these mutations are targeted to the 5{prime} base of the adduct.more » Single A {yields} T transversions are mainly observed (80%), whereas A {yields} G transitions account for 10% of the total mutations. Tandem base-pair substitutions involving the adenine residue and the thymine residue immediately 5{prime} to the adduct occur at a comparable frequency (10%). No selective loss of the strand bearing the platinum adduct was seen, suggesting that, in vivo, cisDDP(d(ApG)) adducts are not blocking lesions. The high mutation specificity of cisDDP-(d(ApG))-induced mutagenesis is discussed in relation to structural data.« less

Low aqueous solubility of 11-cis-retinal limits the rate of pigment formation and dark adaptation in salamander rods.

PubMed

Frederiksen, Rikard; Boyer, Nicholas P; Nickle, Benjamin; Chakrabarti, Kalyan S; Koutalos, Yiannis; Crouch, Rosalie K; Oprian, Daniel; Cornwall, M Carter

2012-06-01

We report experiments designed to test the hypothesis that the aqueous solubility of 11-cis-retinoids plays a significant role in the rate of visual pigment regeneration. Therefore, we have compared the aqueous solubility and the partition coefficients in photoreceptor membranes of native 11-cis-retinal and an analogue retinoid, 11-cis 4-OH retinal, which has a significantly higher solubility in aqueous medium. We have then correlated these parameters with the rates of pigment regeneration and sensitivity recovery that are observed when bleached intact salamander rod photoreceptors are treated with physiological solutions containing these retinoids. We report the following results: (a) 11-cis 4-OH retinal is more soluble in aqueous buffer than 11-cis-retinal. (b) Both 11-cis-retinal and 11-cis 4-OH retinal have extremely high partition coefficients in photoreceptor membranes, though the partition coefficient of 11-cis-retinal is roughly 50-fold greater than that of 11-cis 4-OH retinal. (c) Intact bleached isolated rods treated with solutions containing equimolar amounts of 11-cis-retinal or 11-cis 4-OH retinal form functional visual pigments that promote full recovery of dark current, sensitivity, and response kinetics. However, rods treated with 11-cis 4-OH retinal regenerated on average fivefold faster than rods treated with 11-cis-retinal. (d) Pigment regeneration from recombinant and wild-type opsin in solution is slower when treated with 11-cis 4-OH retinal than with 11-cis-retinal. Based on these observations, we propose a model in which aqueous solubility of cis-retinoids within the photoreceptor cytosol can place a limit on the rate of visual pigment regeneration in vertebrate photoreceptors. We conclude that the cytosolic gap between the plasma membrane and the disk membranes presents a bottleneck for retinoid flux that results in slowed pigment regeneration and dark adaptation in rod photoreceptors.

Effect of plasma membrane fluidity on serotonin transport by endothelial cells

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

Block, E.R.; Edwards, D.

1987-11-01

To evaluate the effect of plasma membrane fluidity of lung endothelial cells on serotonin transport, porcine pulmonary artery endothelial cells were incubated for 3 h with either 0.1 mM cholesterol hemisuccinate, 0.1 mM cis-vaccenic acid, or vehicle (control), after which plasma membrane fluidity and serotinin transport were measured. Fluorescence spectroscopy was used to measure fluidity in the plasma membrane. Serotonin uptake was calculated from the disappearance of ({sup 14}C)-serotonin from the culture medium. Cholesterol decreased fluidity in the subpolar head group and central and midacyl side-chain regions of the plasma membrane and decreased serotonin transport, whereas cis-vaccenic acid increased fluiditymore » in the central and midacyl side-chain regions of the plasma membrane and also increased serotonin transport. Cis-vaccenic acid had no effect of fluidity in the subpolar head group region of the plasma membrane. These results provide evidence that the physical state of the central and midacyl chains within the pulmonary artery endothelial cell plasma membrane lipid bilayer modulates transmembrane transport of serotonin by these cells.« less

Fast regional readout CMOS Image Sensor for dynamic MLC tracking

NASA Astrophysics Data System (ADS)

Zin, H.; Harris, E.; Osmond, J.; Evans, P.

2014-03-01

Advanced radiotherapy techniques such as volumetric modulated arc therapy (VMAT) require verification of the complex beam delivery including tracking of multileaf collimators (MLC) and monitoring the dose rate. This work explores the feasibility of a prototype Complementary metal-oxide semiconductor Image Sensor (CIS) for tracking these complex treatments by utilising fast, region of interest (ROI) read out functionality. An automatic edge tracking algorithm was used to locate the MLC leaves edges moving at various speeds (from a moving triangle field shape) and imaged with various sensor frame rates. The CIS demonstrates successful edge detection of the dynamic MLC motion within accuracy of 1.0 mm. This demonstrates the feasibility of the sensor to verify treatment delivery involving dynamic MLC up to ~400 frames per second (equivalent to the linac pulse rate), which is superior to any current techniques such as using electronic portal imaging devices (EPID). CIS provides the basis to an essential real-time verification tool, useful in accessing accurate delivery of complex high energy radiation to the tumour and ultimately to achieve better cure rates for cancer patients.

A Novel Feature Extraction Method with Feature Selection to Identify Golgi-Resident Protein Types from Imbalanced Data

PubMed Central

Yang, Runtao; Zhang, Chengjin; Gao, Rui; Zhang, Lina

2016-01-01

The Golgi Apparatus (GA) is a major collection and dispatch station for numerous proteins destined for secretion, plasma membranes and lysosomes. The dysfunction of GA proteins can result in neurodegenerative diseases. Therefore, accurate identification of protein subGolgi localizations may assist in drug development and understanding the mechanisms of the GA involved in various cellular processes. In this paper, a new computational method is proposed for identifying cis-Golgi proteins from trans-Golgi proteins. Based on the concept of Common Spatial Patterns (CSP), a novel feature extraction technique is developed to extract evolutionary information from protein sequences. To deal with the imbalanced benchmark dataset, the Synthetic Minority Over-sampling Technique (SMOTE) is adopted. A feature selection method called Random Forest-Recursive Feature Elimination (RF-RFE) is employed to search the optimal features from the CSP based features and g-gap dipeptide composition. Based on the optimal features, a Random Forest (RF) module is used to distinguish cis-Golgi proteins from trans-Golgi proteins. Through the jackknife cross-validation, the proposed method achieves a promising performance with a sensitivity of 0.889, a specificity of 0.880, an accuracy of 0.885, and a Matthew’s Correlation Coefficient (MCC) of 0.765, which remarkably outperforms previous methods. Moreover, when tested on a common independent dataset, our method also achieves a significantly improved performance. These results highlight the promising performance of the proposed method to identify Golgi-resident protein types. Furthermore, the CSP based feature extraction method may provide guidelines for protein function predictions. PMID:26861308

New probabilistic risk assessment of ethylhexyl methoxycinnamate: Comparing the genotoxic effects of trans- and cis-EHMC.

PubMed

Nečasová, Anežka; Bányiová, Katarína; Literák, Jaromír; Čupr, Pavel

2017-02-01

Ethylhexyl methoxycinnamate (EHMC) is a widely used UV filter present in a large number of personal care products (PCPs). Under normal conditions, EHMC occurs in a mixture of two isomers: trans-EHMC and cis-EHMC in a ratio of 99:1. When exposed to sunlight, the trans isomer is transformed to the less stable cis isomer and the efficiency of the UV filter is reduced. To date, the toxicological effects of the cis-EHMC isomer remain largely unknown. We developed a completely new method for preparing cis-EHMC. An EHMC technical mixture was irradiated using a UV lamp and 98% pure cis-EHMC was isolated from the irradiated solution using column chromatography. The genotoxic effects of the isolated cis-EHMC isomer and the nonirradiated trans-EHMC were subsequently measured using two bioassays (SOS chromotest and UmuC test). In the case of trans-EHMC, significant genotoxicity was observed using both bioassays at the highest concentrations (0.5 - 4 mg mL -1 ). In the case of cis-EHMC, significant genotoxicity was only detected using the UmuC test at concentrations of 0.25 - 1 mg mL -1 . Based on these results, the NOEC was calculated for both cis- and trans-EHMC, 0.038 and 0.064 mg mL -1 , respectively. Risk assessment of dermal, oral and inhalation exposure to PCPs containing EHMC was carried out for a female population using probabilistic simulation and by using Quantitative in vitro to in vivo extrapolation (QIVIVE). The risk of cis-EHMC was found to be ∼1.7 times greater than trans-EHMC. In the case of cis-EHMC, a hazard index of 1 was exceeded in the 92nd percentile. Based on the observed differences between the isomers, EHMC application in PCPs requires detailed reassessment. Further exploration of the toxicological effects and properties of cis-EHMC is needed in order to correctly predict risks posed to humans and the environment. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 569-580, 2017. © 2016 Wiley Periodicals, Inc.

WebCIS: large scale deployment of a Web-based clinical information system.

PubMed

Hripcsak, G; Cimino, J J; Sengupta, S

1999-01-01

WebCIS is a Web-based clinical information system. It sits atop the existing Columbia University clinical information system architecture, which includes a clinical repository, the Medical Entities Dictionary, an HL7 interface engine, and an Arden Syntax based clinical event monitor. WebCIS security features include authentication with secure tokens, authorization maintained in an LDAP server, SSL encryption, permanent audit logs, and application time outs. WebCIS is currently used by 810 physicians at the Columbia-Presbyterian center of New York Presbyterian Healthcare to review and enter data into the electronic medical record. Current deployment challenges include maintaining adequate database performance despite complex queries, replacing large numbers of computers that cannot run modern Web browsers, and training users that have never logged onto the Web. Although the raised expectations and higher goals have increased deployment costs, the end result is a far more functional, far more available system.

[Research on the range of motion measurement system for spine based on LabVIEW image processing technology].

PubMed

Li, Xiaofang; Deng, Linhong; Lu, Hu; He, Bin

2014-08-01

A measurement system based on the image processing technology and developed by LabVIEW was designed to quickly obtain the range of motion (ROM) of spine. NI-Vision module was used to pre-process the original images and calculate the angles of marked needles in order to get ROM data. Six human cadaveric thoracic spine segments T7-T10 were selected to carry out 6 kinds of loads, including left/right lateral bending, flexion, extension, cis/counterclockwise torsion. The system was used to measure the ROM of segment T8-T9 under the loads from 1 Nm to 5 Nm. The experimental results showed that the system is able to measure the ROM of the spine accurately and quickly, which provides a simple and reliable tool for spine biomechanics investigators.

Identification of cis-Acting Elements and Splicing Factors Involved in the Regulation of BIM Pre-mRNA Splicing

PubMed Central

Juan, Wen Chun; Roca, Xavier; Ong, S. Tiong

2014-01-01

Aberrant changes in the expression of the pro-apoptotic protein, BCL-2-like 11 (BIM), can result in either impaired or excessive apoptosis, which can contribute to tumorigenesis and degenerative disorders, respectively. Altering BIM pre-mRNA splicing is an attractive approach to modulate apoptosis because BIM activity is partly determined by the alternative splicing of exons 3 or 4, whereby exon 3-containing transcripts are not apoptotic. Here we identified several cis-acting elements and splicing factors involved in BIM alternative splicing, as a step to better understand the regulation of BIM expression. We analyzed a recently discovered 2,903-bp deletion polymorphism within BIM intron 2 that biased splicing towards exon 3, and which also impaired BIM-dependent apoptosis. We found that this region harbors multiple redundant cis-acting elements that repress exon 3 inclusion. Furthermore, we have isolated a 23-nt intronic splicing silencer at the 3′ end of the deletion that is important for excluding exon 3. We also show that PTBP1 and hnRNP C repress exon 3 inclusion, and that downregulation of PTBP1 inhibited BIM-mediated apoptosis. Collectively, these findings start building our understanding of the cis-acting elements and splicing factors that regulate BIM alternative splicing, and also suggest potential approaches to alter BIM splicing for therapeutic purposes. PMID:24743263

Identification of cis-acting elements and splicing factors involved in the regulation of BIM Pre-mRNA splicing.

PubMed

Juan, Wen Chun; Roca, Xavier; Ong, S Tiong

2014-01-01

Aberrant changes in the expression of the pro-apoptotic protein, BCL-2-like 11 (BIM), can result in either impaired or excessive apoptosis, which can contribute to tumorigenesis and degenerative disorders, respectively. Altering BIM pre-mRNA splicing is an attractive approach to modulate apoptosis because BIM activity is partly determined by the alternative splicing of exons 3 or 4, whereby exon 3-containing transcripts are not apoptotic. Here we identified several cis-acting elements and splicing factors involved in BIM alternative splicing, as a step to better understand the regulation of BIM expression. We analyzed a recently discovered 2,903-bp deletion polymorphism within BIM intron 2 that biased splicing towards exon 3, and which also impaired BIM-dependent apoptosis. We found that this region harbors multiple redundant cis-acting elements that repress exon 3 inclusion. Furthermore, we have isolated a 23-nt intronic splicing silencer at the 3' end of the deletion that is important for excluding exon 3. We also show that PTBP1 and hnRNP C repress exon 3 inclusion, and that downregulation of PTBP1 inhibited BIM-mediated apoptosis. Collectively, these findings start building our understanding of the cis-acting elements and splicing factors that regulate BIM alternative splicing, and also suggest potential approaches to alter BIM splicing for therapeutic purposes.

Interaction of formic acid with nitrogen: stabilization of the higher-energy conformer.

PubMed

Marushkevich, Kseniya; Räsänen, Markku; Khriachtchev, Leonid

2010-10-07

Conformational change is an important concept in chemistry and physics. In the present work, we study conformations of formic acid (HCOOH, FA) and report the preparation and identification of the complex of the higher-energy conformer cis-FA with N(2) in an argon matrix. The cis-FA···N(2) complex was synthesized by combining annealing and vibrational excitation of the ground-state trans-FA in a FA/N(2)/Ar matrix. The assignment is based on IR spectroscopic measurements and ab initio calculations. The cis-FA···N(2) complex decay in an argon matrix is much slower compared with the cis-FA monomer. In agreement with the experimental observations, the calculations predict a substantial increase in the stabilization barrier for the cis-FA···N(2) complex compared with the uncomplexed cis-FA monomer. A number of solvation effects in an argon matrix are computationally estimated and discussed. The present results on the cis-FA···N(2) complex show that intermolecular interaction can stabilize intrinsically unstable conformers, as previously found for some other cis-FA complexes.

Chemically Deposited Thin-Film Solar Cell Materials

NASA Technical Reports Server (NTRS)

Raffaelle, R.; Junek, W.; Gorse, J.; Thompson, T.; Harris, J.; Hehemann, D.; Hepp, A.; Rybicki, G.

2005-01-01

We have been working on the development of thin film photovoltaic solar cell materials that can be produced entirely by wet chemical methods on low-cost flexible substrates. P-type copper indium diselenide (CIS) absorber layers have been deposited via electrochemical deposition. Similar techniques have also allowed us to incorporate both Ga and S into the CIS structure, in order to increase its optical bandgap. The ability to deposit similar absorber layers with a variety of bandgaps is essential to our efforts to develop a multi-junction thin-film solar cell. Chemical bath deposition methods were used to deposit a cadmium sulfide (CdS) buffer layers on our CIS-based absorber layers. Window contacts were made to these CdS/CIS junctions by the electrodeposition of zinc oxide (ZnO). Structural and elemental determinations of the individual ZnO, CdS and CIS-based films via transmission spectroscopy, x-ray diffraction, x-ray photoelectron spectroscopy and energy dispersive spectroscopy will be presented. The electrical characterization of the resulting devices will be discussed.

Single Source Precursors for Thin Film Solar Cells

NASA Technical Reports Server (NTRS)

Banger, Kulbinder K.; Hollingsworth, Jennifer A.; Harris, Jerry D.; Cowen, Jonathan; Buhro, William E.; Hepp, Aloysius F.

2002-01-01

The development of thin film solar cells on flexible, lightweight, space-qualified substrates provides an attractive cost solution to fabricating solar arrays with high specific power, (W/kg). The use of a polycrystalline chalcopyrite absorber layer for thin film solar cells is considered as the next generation photovoltaic devices. At NASA GRC we have focused on the development of new single source precursors (SSP) and their utility to deposit the chalcopyrite semi-conducting layer (CIS) onto flexible substrates for solar cell fabrication. The syntheses and thermal modulation of SSPs via molecular engineering is described. Thin-film fabrication studies demonstrate the SSPs can be used in a spray CVD (chemical vapor deposition) process, for depositing CIS at reduced temperatures, which display good electrical properties, suitable for PV (photovoltaic) devices.

Effects of Infrared Laser Radiation on the In Vitro Isomerization of All-Trans Retinal to 11-Cis Retinal

PubMed Central

Liegner, J.; Taboada, J.; Tsin, A. T. C.

2015-01-01

The in vitro effect of infrared laser light on the isomerization of all-trans retinal dissolved in an ether/hexane and also an ethanol solvent was studied. Pulsed laser energy at 1064 nm was used to drive the molecular reconfiguration of all-trans retinal to 11-cis retinal. High pressure liquid chromatography (HPLC) was used to quantify the conversion. Overall isomerization was minimal (0.2 percent to 1.0 percent), yet, a significant difference in isomerization due to pulsed infrared laser energy over non-modulated monochromatic laser light was detected (up to 168 percent difference). Potentially, pulsed laser radiation tuned to the ethylenic stretch frequency of the C11=C12 bond of retinal may induce rotational changes to the chromophore. PMID:26321787

Discovery of functional non-coding conserved regions in the α-synuclein gene locus

PubMed Central

Sterling, Lori; Walter, Michael; Ting, Dennis; Schüle, Birgitt

2014-01-01

Several single nucleotide polymorphisms (SNPs) and the Rep-1 microsatellite marker of the α-synuclein ( SNCA) gene have consistently been shown to be associated with Parkinson’s disease, but the functional relevance is unclear. Based on these findings we hypothesized that conserved cis-regulatory elements in the SNCA genomic region regulate expression of SNCA, and that SNPs in these regions could be functionally modulating the expression of SNCA, thus contributing to neuronal demise and predisposing to Parkinson’s disease. In a pair-wise comparison of a 206kb genomic region encompassing the SNCA gene, we revealed 34 evolutionary conserved DNA sequences between human and mouse. All elements were cloned into reporter vectors and assessed for expression modulation in dual luciferase reporter assays.  We found that 12 out of 34 elements exhibited either an enhancement or reduction of the expression of the reporter gene. Three elements upstream of the SNCA gene displayed an approximately 1.5 fold (p<0.009) increase in expression. Of the intronic regions, three showed a 1.5 fold increase and two others indicated a 2 and 2.5 fold increase in expression (p<0.002). Three elements downstream of the SNCA gene showed 1.5 fold and 2.5 fold increase (p<0.0009). One element downstream of SNCA had a reduced expression of the reporter gene of 0.35 fold (p<0.0009) of normal activity. Our results demonstrate that the SNCA gene contains cis-regulatory regions that might regulate the transcription and expression of SNCA. Further studies in disease-relevant tissue types will be important to understand the functional impact of regulatory regions and specific Parkinson’s disease-associated SNPs and its function in the disease process. PMID:25566351

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann–Mangold organizer

PubMed Central

Sudou, Norihiro; Yamamoto, Shinji; Ogino, Hajime; Taira, Masanori

2012-01-01

How multiple developmental cues are integrated on cis-regulatory modules (CRMs) for cell fate decisions remains uncertain. The Spemann–Mangold organizer in Xenopus embryos expresses the transcription factors Lim1/Lhx1, Otx2, Mix1, Siamois (Sia) and VegT. Reporter analyses using sperm nuclear transplantation and DNA injection showed that cerberus (cer) and goosecoid (gsc) are activated by the aforementioned transcription factors through CRMs conserved between X. laevis and X. tropicalis. ChIP-qPCR analysis for the five transcription factors revealed that cer and gsc CRMs are initially bound by both Sia and VegT at the late blastula stage, and subsequently bound by all five factors at the gastrula stage. At the neurula stage, only binding of Lim1 and Otx2 to the gsc CRM, among others, persists, which corresponds to their co-expression in the prechordal plate. Based on these data, together with detailed expression pattern analysis, we propose a new model of stepwise formation of the organizer, in which (1) maternal VegT and Wnt-induced Sia first bind to CRMs at the blastula stage; then (2) Nodal-inducible Lim1, Otx2, Mix1 and zygotic VegT are bound to CRMs in the dorsal endodermal and mesodermal regions where all these genes are co-expressed; and (3) these two regions are combined at the gastrula stage to form the organizer. Thus, the in vivo dynamics of multiple transcription factors highlight their roles in the initiation and maintenance of gene expression, and also reveal the stepwise integration of maternal, Nodal and Wnt signaling on CRMs of organizer genes to generate the organizer. PMID:22492356

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann-Mangold organizer.

PubMed

Sudou, Norihiro; Yamamoto, Shinji; Ogino, Hajime; Taira, Masanori

2012-05-01

How multiple developmental cues are integrated on cis-regulatory modules (CRMs) for cell fate decisions remains uncertain. The Spemann-Mangold organizer in Xenopus embryos expresses the transcription factors Lim1/Lhx1, Otx2, Mix1, Siamois (Sia) and VegT. Reporter analyses using sperm nuclear transplantation and DNA injection showed that cerberus (cer) and goosecoid (gsc) are activated by the aforementioned transcription factors through CRMs conserved between X. laevis and X. tropicalis. ChIP-qPCR analysis for the five transcription factors revealed that cer and gsc CRMs are initially bound by both Sia and VegT at the late blastula stage, and subsequently bound by all five factors at the gastrula stage. At the neurula stage, only binding of Lim1 and Otx2 to the gsc CRM, among others, persists, which corresponds to their co-expression in the prechordal plate. Based on these data, together with detailed expression pattern analysis, we propose a new model of stepwise formation of the organizer, in which (1) maternal VegT and Wnt-induced Sia first bind to CRMs at the blastula stage; then (2) Nodal-inducible Lim1, Otx2, Mix1 and zygotic VegT are bound to CRMs in the dorsal endodermal and mesodermal regions where all these genes are co-expressed; and (3) these two regions are combined at the gastrula stage to form the organizer. Thus, the in vivo dynamics of multiple transcription factors highlight their roles in the initiation and maintenance of gene expression, and also reveal the stepwise integration of maternal, Nodal and Wnt signaling on CRMs of organizer genes to generate the organizer.

[Comparison of planning quality and delivery efficiency between volumetric modulated arc therapy and dynamic intensity modulated radiation therapy for nasopharyngeal carcinoma with more than 4 prescribed dose levels].

PubMed

Jia, Pengfei; Xu, Jun; Zhou, Xiaoxi; Chen, Jian; Tang, Lemin

2017-12-01

The aim of this study is to compare the planning quality and delivery efficiency between dynamic intensity modulated radiation therapy (d-IMRT) and dual arc volumetric modulated arc therapy (VMAT) systematically for nasopharyngeal carcinoma (NPC) patients with multi-prescribed dose levels, and to analyze the correlations between target volumes and plan qualities. A total of 20 patients of NPC with 4-5 prescribed dose levels to achieve simultaneous integrated boost (SIB) treated by sliding window d-IMRT in our department from 2014 to 2015 were re-planned with dual arc VMAT. All optimization objectives for each VMAT plan were as the same as the corresponding d-IMRT plan. The dose parameters for targets and organ at risk (OAR), the delivery time and monitor units (MU) in two sets of plans were compared respectively. The treatment accuracy was tested by three dimensional dose validation system. Finally, the correlations between the difference of planning quality and the volume of targets were discussed. The conform indexes (CIs) of planning target volumes (PTVs) in VMAT plans were obviously high than those in d-IMRT plans ( P < 0.05), but no significant correlations between the difference of CIs and the volume of targets were discovered ( P > 0.05). The target coverage and heterogeneity indexes (HIs) of PTV 1 and PGTV nd and PTV 3 in two sets of plans were consistent. The doses of PTV 2 decreased and HIs were worse in VMAT plans. VMAT could provide better spinal cord and brainstem sparing, but increase mean dose of parotids. The average number of MUs and delivery time for d-IMRT were 3.32 and 2.19 times of that for VMAT. The γ-index (3 mm, 3%) analysis for each plans was more than 97% in COMPASS ® measurement for quality assurance (QA). The results show that target dose coverages in d-IMRT and VMAT plans are similar for NPC with multi-prescribed dose levels. VMAT could improve the the CIs of targets, but reduce the dose to the target volume in neck except for PGTV nd . The biggest advantages of VMAT over d-IMRT are delivery efficiency and QA.

Modulating lysosomal function through lysosome membrane permeabilization or autophagy suppression restores sensitivity to cisplatin in refractory non-small-cell lung cancer cells

PubMed Central

Circu, Magdalena; Cardelli, James; Barr, Martin; O’Byrne, Kenneth; Mills, Glenn

2017-01-01

Lung cancer is the leading cause of cancer-related deaths. Most patients develop resistance to platinum within several months of treatment. We investigated whether triggering lysosomal membrane permeabilization (LMP) or suppressing autophagy can restore cisplatin susceptibility in lung cancer with acquired chemoresistance. Cisplatin IC50 in A549Pt (parental) and A549cisR (cisplatin resistant) cells was 13 μM and 47 μM, respectively. Following cisplatin exposure, A549cisR cells failed to elicit an apoptotic response. This was manifested by diminished Annexin–V staining, caspase 3 and 9, BAX and BAK activation in resistant but not in parental cells. Chloroquine preferentially promoted LMP in A549cisR cells, revealed by leakage of FITC-dextran into the cytosol as detected by immunofluorescence microscopy. This was confirmed by increased cytosolic cathepsin D signal on Immunoblot. Cell viability of cisplatin-treated A549cisR cells was decreased when co-treated with chloroquine, corresponding to a combination index below 0.8, suggesting synergism between the two drugs. Notably, chloroquine activated the mitochondrial cell death pathway as indicated by increase in caspase 9 activity. Interestingly, inhibition of lysosomal proteases using E64 conferred cytoprotection against cisplatin and chloroquine co-treatment, suggesting that chloroquine-induced cell death occurred in a cathepsin-mediated mechanism. Likewise, blockage of caspases partially rescued A549cisR cells against the cytotoxicity of cisplatin and chloroquine combination. Cisplatin promoted a dose-dependent autophagic flux induction preferentially in A549cisR cells, as evidenced by a surge in LC3-II/α-tubulin following pre-treatment with E64 and increase in p62 degradation. Compared to untreated cells, cisplatin induced an increase in cyto-ID-loaded autophagosomes in A549cisR cells that was further amplified by chloroquine, pointing toward autophagic flux activation by cisplatin. Interestingly, this effect was less pronounced in A549Pt cells. Blocking autophagy by ATG5 depletion using siRNA markedly enhances susceptibility to cisplatin in A549cisR cells. Taken together, our results underscore the utility of targeting lysosomal function in overcoming acquired cisplatin refractoriness in lung cancer. PMID:28945807

Cis-Lunar Base Camp

NASA Technical Reports Server (NTRS)

Merrill, Raymond G.; Goodliff, Kandyce E.; Mazanek, Daniel D.; Reeves, John D., Jr.

2012-01-01

Historically, when mounting expeditions into uncharted territories, explorers have established strategically positioned base camps to pre-position required equipment and consumables. These base camps are secure, safe positions from which expeditions can depart when conditions are favorable, at which technology and operations can be tested and validated, and facilitate timely access to more robust facilities in the event of an emergency. For human exploration missions into deep space, cis-lunar space is well suited to serve as such a base camp. The outer regions of cis-lunar space, such as the Earth-Moon Lagrange points, lie near the edge of Earth s gravity well, allowing equipment and consumables to be aggregated with easy access to deep space and to the lunar surface, as well as more distant destinations, such as near-Earth Asteroids (NEAs) and Mars and its moons. Several approaches to utilizing a cis-lunar base camp for sustainable human exploration, as well as some possible future applications are identified. The primary objective of the analysis presented in this paper is to identify options, show the macro trends, and provide information that can be used as a basis for more detailed mission development. Compared within are the high-level performance and cost of 15 preliminary cis-lunar exploration campaigns that establish the capability to conduct crewed missions of up to one year in duration, and then aggregate mass in cis-lunar space to facilitate an expedition from Cis-Lunar Base Camp. Launch vehicles, chemical propulsion stages, and electric propulsion stages are discussed and parametric sizing values are used to create architectures of in-space transportation elements that extend the existing in-space supply chain to cis-lunar space. The transportation options to cis-lunar space assessed vary in efficiency by almost 50%; from 0.16 to 0.68 kg of cargo in cis-lunar space for every kilogram of mass in Low Earth Orbit (LEO). For the 15 cases, 5-year campaign costs vary by only 15% from 0.36 to 0.51 on a normalized scale across all campaigns. Thus the development and first flight costs of assessed transportation options are similar. However, the cost of those options per flight beyond the initial operational capability varies by 70% from 0.3 to 1.0 on a normalized scale. The 10-year campaigns assessed begin to show the effect of this large range of cost beyond initial operational capability as they vary approximately 25% with values from 0.75 to 1.0 on the normalized campaign scale. Therefore, it is important to understand both the cost of implementation and first use as well as long term utilization. Finally, minimizing long term recurring costs is critical to the affordability of future human space exploration missions. Finally minimizing long term recurring costs is critical to the affordability of future human space exploration missions.

Sulforaphane, a natural constituent of broccoli, prevents cell death and inflammation in nephropathy.

PubMed

Guerrero-Beltrán, Carlos Enrique; Mukhopadhyay, Partha; Horváth, Béla; Rajesh, Mohanraj; Tapia, Edilia; García-Torres, Itzhel; Pedraza-Chaverri, José; Pacher, Pál

2012-05-01

Cisplatin (cis-diamminedichloroplatinum II, CIS) is a potent and widely used chemotherapeutic agent to treat various malignancies, but its therapeutic use is limited because of dose-dependent nephrotoxicity. Cell death and inflammation play a key role in the development and progression of CIS-induced nephropathy. Sulforaphane (SFN), a natural constituent of cruciferous vegetables such as broccoli, Brussels sprouts, etc., has been shown to exert various protective effects in models of tissue injury and cancer. In this study, we have investigated the role of prosurvival, cell death and inflammatory signaling pathways using a rodent model of CIS-induced nephropathy, and explored the effects of SFN on these processes. Cisplatin triggered marked activation of stress signaling pathways [p53, Jun N-terminal kinase (JNK), and p38-α mitogen-activated protein kinase (MAPK)] and promoted cell death in the kidneys (increased DNA fragmentation, caspases-3/7 activity, terminal deoxynucleotidyl transferase-mediated uridine triphosphate nick-end labeling), associated with attenuation of various prosurvival signaling pathways [e.g., extracellular signal-regulated kinase (ERK) and p38-β MAPK]. Cisplatin also markedly enhanced inflammation in the kidneys [promoted NF-κB activation, increased expression of adhesion molecules ICAM and VCAM, enhanced tumor necrosis factor-α (TNF-α) levels and inflammatory cell infiltration]. These effects were significantly attenuated by pretreatment of rodents with SFN. Thus, the cisplatin-induced nephropathy is associated with activation of various cell death and proinflammatory pathways (p53, JNK, p38-α, TNF-α and NF-κB) and impairments of key prosurvival signaling mechanisms (ERK and p38-β). SFN is able to prevent the CIS-induced renal injury by modulating these pathways, providing a novel approach for preventing this devastating complication of chemotherapy. Published by Elsevier Inc.

Sulforaphane, a natural constituent of broccoli, prevents cell death and inflammation in nephropathy

PubMed Central

Guerrero-Beltrán, Carlos Enrique; Mukhopadhyay, Partha; Horváth, Béla; Rajesh, Mohanraj; Tapia, Edilia; García-Torres, Itzhel; Pedraza-Chaverri, José; Pacher, Pál

2011-01-01

Cisplatin (cis-diamminedichloroplatinum II, CIS) is a potent and widely used chemotherapeutic agent to treat various malignancies, but its therapeutic use is limited because of the dose-dependent nephrotoxicity. Cell death and inflammation play key role in the development and progression of CIS-induced nephropathy. Sulforaphane (SFN), a natural constituent of cruciferous vegetables such as broccoli, Brussels sprouts, etc., has been shown to exert various protective effects in models of tissue injury and cancer. In this study, we have investigated the role of pro-survival, cell death and inflammatory signaling pathways using a rodent model of CIS-induced nephropathy, and explored the effects of SFN on these processes. Cisplatin triggered marked activation of stress signaling pathways (p53, Jun N-terminal kinase (JNK), and p38-α MAPK) and promoted cell death in the kidneys (increased DNA fragmentation, caspases-3/7 activity, TUNEL), associated with attenuation of various pro-survival signaling pathways (e.g. extracellular signal-regulated kinase (ERK) and p38-β MAPK). Cisplatin also markedly enhanced inflammation in the kidneys (promoted NF-κB activation, increased expression of adhesion molecules ICAM and VCAM, enhanced tumor necrosis factor-alpha (TNF-α) levels, and inflammatory cell infiltration). These effects were significantly attenuated by pre-treatment of rodents with SFN. Cisplatin-induced nephropathy is associated with activation of various cell death and pro-inflammatory pathways (p53, JNK, p38-α, TNF-α, and NF-κB) and impairments of key pro-survival signaling mechanisms (ERK and p38-β). SFN is able to prevent the CIS-induced renal injury by modulating these pathways, providing a novel approach for preventing this devastating complication of the chemotherapy. PMID:21684138

Type 2 diabetes (T2D) associated polymorphisms regulate expression of adjacent transcripts in transformed lymphocytes, adipose, and muscle from Caucasian and African-American subjects.

PubMed

Sharma, Neeraj K; Langberg, Kurt A; Mondal, Ashis K; Elbein, Steven C; Das, Swapan K

2011-02-01

Genome-wide association scans (GWAS) have identified novel single nucleotide polymorphisms (SNPs) that increase T2D susceptibility and indicated the role of nearby genes in T2D pathogenesis. We hypothesized that T2D-associated SNPs act as cis-regulators of nearby genes in human tissues and that expression of these transcripts may correlate with metabolic traits, including insulin sensitivity (S(I)). Association of SNPs with the expression of their nearest transcripts was tested in adipose and muscle from 168 healthy individuals who spanned a broad range of S(I) and body mass index (BMI) and in transformed lymphocytes (TLs). We tested correlations between the expression of these transcripts in adipose and muscle with metabolic traits. Utilizing allelic expression imbalance (AEI) analysis we examined the presence of other cis-regulators for those transcripts in TLs. SNP rs9472138 was significantly (P = 0.037) associated with the expression of VEGFA in TLs while rs6698181 was detected as a cis-regulator for the PKN2 in muscle (P = 0.00027) and adipose (P = 0.018). Significant association was also observed for rs17036101 (P = 0.001) with expression of SYN2 in adipose of Caucasians. Among 19 GWAS-implicated transcripts, expression of VEGFA in adipose was correlated with BMI (r = -0.305) and S(I) (r = 0.230). Although only a minority of the T2D-associated SNPs were validated as cis-eQTLs for nearby transcripts, AEI analysis indicated presence of other cis-regulatory polymorphisms in 54% of these transcripts. Our study suggests that a small subset of GWAS-identified SNPs may increase T2D susceptibility by modulating expression of nearby transcripts in adipose or muscle.

Genetic regulation of adipose tissue transcript expression is involved in modulating serum triglyceride and HDL-cholesterol.

PubMed

Sajuthi, Satria P; Sharma, Neeraj K; Comeau, Mary E; Chou, Jeff W; Bowden, Donald W; Freedman, Barry I; Langefeld, Carl D; Parks, John S; Das, Swapan K

2017-10-20

Dyslipidemia is a major contributor to the increased cardiovascular disease and mortality associated with obesity and type 2 diabetes. We hypothesized that variation in expression of adipose tissue transcripts is associated with serum lipid concentrations in African Americans (AAs), and common genetic variants regulate expression levels of these transcripts. Fasting serum lipid levels, genome-wide transcript expression profiles of subcutaneous adipose tissue, and genome-wide SNP genotypes were analyzed in a cohort of non-diabetic AAs (N=250). Serum triglyceride (TRIG) and high density lipoprotein-cholesterol (HDL-C) levels were associated (FDR<0.01) with expression level of 1021 and 1875 adipose tissue transcripts, respectively, but none associated with total cholesterol or LDL-C levels. Serum HDL-C-associated transcripts were enriched for salient biological pathways, including branched-chain amino acid degradation, and oxidative phosphorylation. Genes in immuno-inflammatory pathways were activated among individuals with higher serum TRIG levels. We identified significant cis-regulatory SNPs (cis-eSNPs) for 449 serum lipid-associated transcripts in adipose tissue. The cis-eSNPs of 12 genes were nominally associated (p<0.001) with serum lipid level in genome wide association studies in Global Lipids Genetics Consortium (GLGC) cohorts. Allelic effect direction of cis-eSNPs on expression of MARCH2, BEST1 and TMEM258 matched with effect direction of these SNP alleles on serum TRIG or HDL-C levels in GLGC cohorts. These data suggest that expressions of serum lipid-associated transcripts in adipose tissue are dependent on common cis-eSNPs in African Americans. Thus, genetically-mediated transcriptional regulation in adipose tissue may play a role in reducing HDL-C and increasing TRIG in serum. Copyright © 2017 Elsevier B.V. All rights reserved.

Low plasma levels of cholecalciferol and 13-cis-retinoic acid in tuberculosis: implications in host-based chemotherapy.

PubMed

Srinivasan, Anand; Syal, Kirtimaan; Banerjee, Dibyajyoti; Hota, Debasish; Gupta, Dheeraj; Kaul, Deepak; Chakrabarti, Amitava

2013-10-01

The aim of this study was to estimate the concentration of cholecalciferol and 13-cis-retinoic acid (RA) in the plasma and pleural fluid of patients with tuberculosis (TB) against controls. Plasma levels of cholecalciferol and 13-cis-RA were measured in 22 patients with TB and healthy controls and their pleural fluids levels were measured in 6 TB patients and diseased controls by established high-performance liquid chromatography-based procedure. Cholecalciferol levels in plasma and pleural fluid of patients with TB and healthy controls were 67.45 (10.71) nmol/L and 21.40 (8.58) nmol/L compared with 117.43 (18.40) nmol/L (P < 0.001) and 94.73 (33.34) nmol/L (P = 0.0049), respectively. 13-cis-RA level in the plasma of patients with TB and healthy controls were 1.51 (0.72) nmol/L and 6.67 (0.81) nmol/L (P < 0.001), respectively. 13-cis-RA was not detectable in pleural fluid. The levels of both the agents were lower in patients with TB than in controls. It was observed that in patients with TB there is a combined deficiency of cholecalciferol and 13-cis-RA compared with healthy volunteers. Because cholecalciferol and 13-cis-RA are in equilibrium with active ingredients of vitamins A and D, we feel that there is a combined deficiency of these vitamins in patients with TB. There is an evidence that concomitant vitamin A and D supplementation can kill intracellular Mycobacterium tuberculosis in vitro. Therefore, the observations made in this study can pave the path for a trial of combined supplementation of available formulations of vitamin A and D (cholecalciferol and 13-cis-RA) for novel anti-tubercular drug therapy. Because such an approach is host-based it has potential to treat even multidrug-resistant and extensively drug-resistant forms of TB. Copyright © 2013 Elsevier Inc. All rights reserved.

Effect of 11-Cis 13-Demethylretinal on Phototransduction in Bleach-Adapted Rod and Cone Photoreceptors

PubMed Central

Corson, D.Wesley; Kefalov, Vladimir J.; Cornwall, M. Carter; Crouch, Rosalie K.

2000-01-01

We used 11-cis 13-demethylretinal to examine the physiological consequences of retinal's noncovalent interaction with opsin in intact rod and cone photoreceptors during visual pigment regeneration. 11-Cis 13-demethylretinal is an analog of 11-cis retinal in which the 13 position methyl group has been removed. Biochemical experiments have shown that it is capable of binding in the chromophore pocket of opsin, forming a Schiff-base linkage with the protein to produce a pigment, but at a much slower rate than the native 11-cis retinal (Nelson, R., J. Kim deReil, and A. Kropf. 1970. Proc. Nat. Acad. Sci. USA. 66:531–538). Experimentally, this slow rate of pigment formation should allow separate physiological examination of the effects of the initial binding of retinal in the pocket and the subsequent formation of the protonated Schiff-base linkage. Currents from solitary rods and cones from the tiger salamander were recorded in darkness before and after bleaching and then after exposure to 11-cis 13-demethylretinal. In bleach-adapted rods, 11-cis 13-demethylretinal caused transient activation of phototransduction, as evidenced by a decrease of the dark current and sensitivity, acceleration of the dim flash responses, and activation of cGMP phosphodiesterase and guanylyl cyclase. The steady state of phototransduction activity was still higher than that of the bleach-adapted rod. In contrast, exposure of bleach-adapted cones to 11-cis 13-demethylretinal resulted in an immediate deactivation of transduction as measured by the same parameters. These results extend the validity of a model for the effects of the noncovalent binding of a retinoid in the chromophore pockets of rod and cone opsins to analogs capable of forming a Schiff-base and imply that the noncovalent binding by itself may play a role for the dark adaptation of photoreceptors. PMID:10919871

Modular multiple sensors information management for computer-integrated surgery.

PubMed

Vaccarella, Alberto; Enquobahrie, Andinet; Ferrigno, Giancarlo; Momi, Elena De

2012-09-01

In the past 20 years, technological advancements have modified the concept of modern operating rooms (ORs) with the introduction of computer-integrated surgery (CIS) systems, which promise to enhance the outcomes, safety and standardization of surgical procedures. With CIS, different types of sensor (mainly position-sensing devices, force sensors and intra-operative imaging devices) are widely used. Recently, the need for a combined use of different sensors raised issues related to synchronization and spatial consistency of data from different sources of information. In this study, we propose a centralized, multi-sensor management software architecture for a distributed CIS system, which addresses sensor information consistency in both space and time. The software was developed as a data server module in a client-server architecture, using two open-source software libraries: Image-Guided Surgery Toolkit (IGSTK) and OpenCV. The ROBOCAST project (FP7 ICT 215190), which aims at integrating robotic and navigation devices and technologies in order to improve the outcome of the surgical intervention, was used as the benchmark. An experimental protocol was designed in order to prove the feasibility of a centralized module for data acquisition and to test the application latency when dealing with optical and electromagnetic tracking systems and ultrasound (US) imaging devices. Our results show that a centralized approach is suitable for minimizing synchronization errors; latency in the client-server communication was estimated to be 2 ms (median value) for tracking systems and 40 ms (median value) for US images. The proposed centralized approach proved to be adequate for neurosurgery requirements. Latency introduced by the proposed architecture does not affect tracking system performance in terms of frame rate and limits US images frame rate at 25 fps, which is acceptable for providing visual feedback to the surgeon in the OR. Copyright © 2012 John Wiley & Sons, Ltd.

Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element.

PubMed

Lim, Chun Shen; Brown, Chris M

2016-09-01

Many viruses contain RNA elements that modulate splicing and/or promote nuclear export of their RNAs. The RNAs of the major human pathogen, hepatitis B virus (HBV) contain a large (~600 bases) composite cis-acting 'post-transcriptional regulatory element' (PRE). This element promotes expression from these naturally intronless transcripts. Indeed, the related woodchuck hepadnavirus PRE (WPRE) is used to enhance expression in gene therapy and other expression vectors. These PRE are likely to act through a combination of mechanisms, including promotion of RNA nuclear export. Functional components of both the HBV PRE and WPRE are 2 conserved RNA cis-acting stem-loop (SL) structures, SLα and SLβ. They are within the coding regions of polymerase (P) gene, and both P and X genes, respectively. Based on previous studies using mutagenesis and/or nuclear magnetic resonance (NMR), here we propose 2 covariance models for SLα and SLβ. The model for the 30-nucleotide SLα contains a G-bulge and a CNGG(U) apical loop of which the first and the fourth loop residues form a CG pair and the fifth loop residue is bulged out, as observed in the NMR structure. The model for the 23-nucleotide SLβ contains a 7-base-pair stem and a 9-nucleotide loop. Comparison of the models with other RNA structural elements, as well as similarity searches of human transcriptome and viral genomes demonstrate that SLα and SLβ are specific to HBV transcripts. However, they are well conserved among the hepadnaviruses of non-human primates, the woodchuck and ground squirrel.

Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element

PubMed Central

Lim, Chun Shen; Brown, Chris M.

2016-01-01

ABSTRACT Many viruses contain RNA elements that modulate splicing and/or promote nuclear export of their RNAs. The RNAs of the major human pathogen, hepatitis B virus (HBV) contain a large (~600 bases) composite cis-acting 'post-transcriptional regulatory element' (PRE). This element promotes expression from these naturally intronless transcripts. Indeed, the related woodchuck hepadnavirus PRE (WPRE) is used to enhance expression in gene therapy and other expression vectors. These PRE are likely to act through a combination of mechanisms, including promotion of RNA nuclear export. Functional components of both the HBV PRE and WPRE are 2 conserved RNA cis-acting stem-loop (SL) structures, SLα and SLβ. They are within the coding regions of polymerase (P) gene, and both P and X genes, respectively. Based on previous studies using mutagenesis and/or nuclear magnetic resonance (NMR), here we propose 2 covariance models for SLα and SLβ. The model for the 30-nucleotide SLα contains a G-bulge and a CNGG(U) apical loop of which the first and the fourth loop residues form a CG pair and the fifth loop residue is bulged out, as observed in the NMR structure. The model for the 23-nucleotide SLβ contains a 7-base-pair stem and a 9-nucleotide loop. Comparison of the models with other RNA structural elements, as well as similarity searches of human transcriptome and viral genomes demonstrate that SLα and SLβ are specific to HBV transcripts. However, they are well conserved among the hepadnaviruses of non-human primates, the woodchuck and ground squirrel. PMID:27031749

Synthesis of 1,2-cis-2-C-branched aryl-C-glucosides via desulfurization of carbohydrate based hemithioacetals

PubMed Central

Mebrahtu, Fanuel M; Manana, Mandlenkosi M; Madumo, Kagiso; Sokamisa, Mokela S

2015-01-01

Summary 1-C and 2-C-branched carbohydrates are present as substructures in a number of biologically important compounds. Although the synthesis of such carbohydrate derivatives is extensively studied, the synthesis of 1,2-cis-2-C-branched C-, S-, and N-glycosides is less explored. In this article a synthetic strategy for the synthesis of 1,2-cis-2-C-branched-aryl-C-glucosides is reported via a hydrogenolytic desulfurization of suitably orientated carbohydrate based hemithioacetals. 1,2-cis-2-Hydroxymethyl and 2-carbaldehyde of aryl-C-glucosides have been synthesized using the current strategy in very good yields. The 2-carbaldehyde-aryl-C-glucosides have been identified as suitable substrates for the stereospecific preparation of 2,3-unsaturated-aryl-C-glycosides (Ferrier products). PMID:26124859

The modules of trans-acyltransferase assembly lines redefined with a central acyl carrier protein.

PubMed

Vander Wood, Drew A; Keatinge-Clay, Adrian T

2018-06-01

Here, the term "module" is redefined for trans-acyltransferase (trans-AT) assembly lines to agree with how its domains cooperate and evolutionarily co-migrate. The key domain in both the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) modules of assembly lines is the acyl carrier protein (ACP). ACPs not only relay growing acyl chains through the assembly line but also collaborate with enzymes in modules, both in cis and in trans, to add a specific chemical moiety. A ketosynthase (KS) downstream of ACP often plays the role of gatekeeper, ensuring that only a single intermediate generated by the enzymes of a module is passed downstream. Bioinformatic analysis of 526 ACPs from 33 characterized trans-AT assembly lines reveals ACPs from the same module type generally clade together, reflective of the co-evolution of these domains with their cognate enzymes. While KSs downstream of ACPs from the same module type generally also clade together, KSs upstream of ACPs do not-in disagreement with the traditional definition of a module. Beyond nomenclature, the presented analysis impacts our understanding of module function, the evolution of assembly lines, pathway prediction, and assembly line engineering. © 2018 Wiley Periodicals, Inc.

Processing of CuInSe{sub 2}-based solar cells: Characterization of deposition processes in terms of chemical reaction analyses. Phase 2 Annual Report, 6 May 1996--5 May 1997

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

Anderson, T.

This report describes research performed by the University of Florida during Phase 2 of this subcontract. First, to study CIGS, researchers adapted a contactless, nondestructive technique previously developed for measuring photogenerated excess carrier lifetimes in SOI wafers. This dual-beam optical modulation (DBOM) technique was used to investigate the differences between three alternative methods of depositing CdS (conventional chemical-bath deposition [CBD], metal-organic chemical vapor deposition [MOCVD], and sputtering). Second, a critical assessment of the Cu-In-Se thermochemical and phase diagram data using standard CALPHAD procedures is being performed. The outcome of this research will produce useful information on equilibrium vapor compositions (requiredmore » annealing ambients, Sex fluxes from effusion cells), phase diagrams (conditions for melt-assisted growth), chemical potentials (driving forces for diffusion and chemical reactions), and consistent solution models (extents of solid solutions and extending phase diagrams). Third, an integrated facility to fabricate CIS PV devices was established that includes migration-enhanced epitaxy (MEE) for deposition of CIS, a rapid thermal processing furnace for absorber film formation, sputtering of ZnO, CBD or MOCVD of CdS, metallization, and pattern definition.« less

In situ trans ligands of CD22 identified by glycan-protein photocross-linking-enabled proteomics.

PubMed

Ramya, T N C; Weerapana, Eranthie; Liao, Lujian; Zeng, Ying; Tateno, Hiroaki; Liao, Liang; Yates, John R; Cravatt, Benjamin F; Paulson, James C

2010-06-01

CD22, a regulator of B-cell signaling, is a siglec that recognizes the sequence NeuAcalpha2-6Gal on glycoprotein glycans as ligands. CD22 interactions with glycoproteins on the same cell (in cis) and apposing cells (in trans) modulate its activity in B-cell receptor signaling. Although CD22 predominantly recognizes neighboring CD22 molecules as cis ligands on B-cells, little is known about the trans ligands on apposing cells. We conducted a proteomics scale study to identify candidate trans ligands of CD22 on B-cells by UV photocross-linking CD22-Fc chimera bound to B-cell glycoproteins engineered to carry sialic acids with a 9-aryl azide moiety. Using mass spectrometry-based quantitative proteomics to analyze the cross-linked products, 27 glycoproteins were identified as candidate trans ligands. Next, CD22 expressed on the surface of one cell was photocross-linked to glycoproteins on apposing B-cells followed by immunochemical analysis of the products with antibodies to the candidate ligands. Of the many candidate ligands, only the B-cell receptor IgM was found to be a major in situ trans ligand of CD22 that is selectively redistributed to the site of cell contact upon interaction with CD22 on the apposing cell.

Structural investigations of platinum anticancer drugs with DNA

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

Bellon, S.F.

The antitumor agent cis-diamminedichloroplatinum (II) (cis-DDP) can successfully treat testicular and ovarian cancers, presumably by binding to DNA and preventing replication. cis-DDP is less successful in treating lung and breast cancers and the trans isomer is inactive. It has been suggested that cellular recognition and repair processes may be responsible for the difference in activity between cis- and trans-DDP, the differential effectiveness against different types of cancers, as well as acquired resistance. The author reviews structural methods used to characterize several site-specific adducts. Structure-function relations that emerge may help clarify the mechanism of action. The extent of DNA bending causedmore » by several site-specific DNA adducts formed by cis- and trans-DDP has been determined using a gel electrophoresis assay. The adducts cis-GG, cis-AG, cis-GTG, and trans-GTG were incorporated into synthetic DNA oligonucleotides of varying lengths with two bp cohesive ends. Subtle DNA distortions were amplified by polymerizing these monomers and quantitated using polyacrylamide gel electrophoresis. The three adducts cis-GG, cis-AG, and cis-GTG were all found to bend the helix in a directed fashion by about 32-35[degrees]. The trans-GTG adduct gave a degree of flexibility to the double helix, allowing bending in more than one direction. The DNA unwinding caused by the platinum binding was measured by systematically varying the interplatinum distance in a series of synthetic DNA oligonucleotides. The cis-GG and cis-AG adducts both unwind the double helix by 13[degrees]C, while the cis-GTG adduct unwinds by 23[degrees]. To determine the complete structure of platinated duplex DNA< single crystals of a platinated 12 base pair duplex oligonucletide were obtained. Despite extreme temperature and radiation sensitivity problems, a complete set of data was collected. Several different approaches to solve the structure were attempted.« less

Role of UDP-glucuronosyltransferase isoforms in 13-cis retinoic acid metabolism in humans.

PubMed

Rowbotham, Sophie E; Illingworth, Nicola A; Daly, Ann K; Veal, Gareth J; Boddy, Alan V

2010-07-01

13-cis Retinoic acid (13cisRA, isotretinoin) is an important drug in both dermatology, and the treatment of high-risk neuroblastoma. 13cisRA is known to undergo cytochrome P450-mediated oxidation, mainly by CYP2C8, but phase II metabolic pathways have not been characterized. In the present study, the glucuronidation activities of human liver (HLM) and intestinal microsomes (HIM), as well as a panel of human UDP-glucuronosyltransferases (UGTs) toward both 13cisRA and the 4-oxo metabolite, 4-oxo 13cisRA, were compared using high-performance liquid chromatography. Both HLM and, to a greater extent, HIM catalyzed the glucuronidation of 13cisRA and 4-oxo 13cisRA. Based on the structures of 13cisRA and 4-oxo 13cisRA, the glucuronides formed are conjugated at the terminal carboxylic acid. Further analysis revealed that UGT1A1, UGT1A3, UGT1A7, UGT1A8, and UGT1A9 were the major isoforms responsible for the glucuronidation of both substrates. For 13cisRA, a pronounced substrate inhibition was observed with individual UGTs and with HIM. UGT1A3 exhibited the highest rate of activity toward both substrates, and a high rate of activity toward 13cisRA glucuronidation was also observed with UGT1A7. However, for both substrates, K(m) values were above concentrations reported in clinical studies. Therefore, UGT1A9 is likely to be the most important enzyme in the glucuronidation of both substrates as this enzyme had the lowest K(m) and is expressed in both the intestine and at high levels in the liver.

Regeneration of bovine and octopus opsins in situ with natural and artificial retinals

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

Koutalos, Y.; Ebrey, T.G.; Tsuda, M.

1989-03-21

The authors consider the problem of color regulation in visual pigments for both bovine rhodopsin and octopus rhodopsin. Both pigments have 11-cis-retinal as their chromophore. These rhodopsins were bleached in their native membranes, and the opsins were regenerated with natural and artificial chromophores. Both bovine and octopus opsins were regenerated with the 9-cis- and 11-cis-retinal isomers, but the octopus opsin was additionally regenerated with the 13-cis and all-trans isomers. Titration of the octopus opsin with 11-cis-retinal gave an extinction coefficient for octopus rhodopsin of 27,000 {plus minus} 3,000 M{sup {minus}1} cm{sup {minus}1} at 475 nm. The absorption maxima of bovinemore » artificial pigments formed by regenerating opsin with the 11-cis dihydro series of chromophores support a color regulation model for bovine rhodopsin in which the chromophore-binding site of the protein has two negative charges: one directly hydrogen bonded to the Schiff base nitrogen and another near carbon-13. Formation of octopus artificial pigments with both all-trans and 11-cis dihydro chromophores leads to a similar model for octopus rhodopsin and metarhodopsin: there are two negative charges in the chromophore-binding site, one directly hydrogen bonded to the Schiff base nitrogen and a second near carbon-13. The interaction of this second charge with the chromophore in octopus rhodopsin is weaker than in bovine, while in metarhodopsin it is as strong as in bovine.« less

Antimicrobial activity-specific to Gram-negative bacteria and immune modulation-mediated NF-kappaB and Sp1 of a medaka beta-defensin.

PubMed

Zhao, Jiu-Gang; Zhou, Li; Jin, Jun-Yan; Zhao, Zhe; Lan, Jing; Zhang, Yi-Bin; Zhang, Qi-Ya; Gui, Jian-Fang

2009-04-01

Defensins are a group of cationic antimicrobial peptides which play an important role in the innate immune system by exerting their antimicrobial activity against pathogens. In this study, we cloned a novel beta-defensin cDNA from medaka (Oryzias latipes) by rapid amplification of cDNA ends (RACE) technique. The full-length cDNA consists of 480 bp, and the open reading frame (ORF) of 189 bp encodes a polypeptide of 63 amino acids (aa) with a predicted molecular weight of 7.44 kDa. Its genomic organization was analyzed, and Southern blot detection confirmed that only one copy of beta-defensin exists in the medaka HNI strain. RT-PCR, Western blot and immunohistochemistry detections showed that the beta-defensin transcript and protein could be detected in eyes, liver, kidney, blood, spleen and gill, and obviously prevalent expression was found in eyes. Antimicrobial activity of the medaka beta-defensin was evaluated, and the antibacterial activity-specific to Gram-negative bacteria was revealed. Furthermore, the lipopolysaccharide (LPS), a major component of the outer membrane of Gram-negative bacteria, was demonstrated to be able to induce about 13-fold up-regulation of the beta-defensin within first 12h. In addition, promoter and promoter mutagenesis analysis were performed in the medaka beta-defensin. A proximal 100 base pair (bp) sequence (+26 to -73) and the next 1700 bp sequence (-73 to -1755) were demonstrated to be responsible for the basal promoter activity and for the transcription regulation. Three nuclear factor kappa B (NF-kappaB) cis-elements and a Sp1 cis-element were revealed by mutagenesis analysis to exist in the 5' flanking sequence, and they were confirmed to be responsible for the up-regulation of medaka beta-defensin stimulated by LPS. And, the Sp1 cis-element was further revealed to be related to the basal promoter activity, and transcriptional factor II D (TFIID) was found to be in charge of the gene transcription initiation. All the obtained data suggested that the novel medaka beta-defensin should have antimicrobial activity-specific to Gram-negative bacteria, and the antibacterial immune function should be modulated by NF-kappaB and Sp1.

cis-3,4-Methylene-heptanoylcarnitine: characterization and verification of the C8:1 acylcarnitine in human urine.

PubMed

Yang, Shuming; Minkler, Paul; Hoppel, Charles

2007-10-01

Acylcarnitine profiles have been used to diagnose specific inherited metabolic diseases. For some acylcarnitines, however, the detailed structure of their acyl group remains a question. One such incompletely characterized acylcarnitine is cis-3,4-methylene-heptanoylcarnitine. To investigate this problem, we isolated the "C8:1" acylcarnitine from human urine, transesterified it to form its acyl picolinyl ester, and characterized it by GC/EI-MS. These results were compared to GC/EI-MS results from authentic standards we synthesized (cis-3,4-methylene-heptanoylcarnitine, trans-2-octenoylcarnitine, 3-octenoylcarnitine, cis-4-octenoylcarnitine, and trans-4-octenoylcarnitine). Only cis-3,4-methylene-heptanoylcarnitine matched the urinary "C8:1" acylcarnitine. The standards were then spiked in human urine, converted to pentafluorophenacyl esters, and detected by HPLC/MS. cis-3,4-Methylene-heptanoylcarnitine exactly matched the "C8:1" acylcarnitine in urine, whereas none of the other C8:1 acylcarnitine standards matched. Based on the data from GC/EI-MS and HPLC/MS, the "C8:1" acylcarnitine in human urine is shown to be cis-3,4-methylene-heptanoylcarnitine.

A novel conformity index for intensity modulated radiation therapy plan evaluation

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

Cheung, Fion W. K.; Law, Maria Y. Y.; Medical Physics and Research Department, Hong Kong Sanatorium and Hospital, 999077 Hong Kong

2012-09-15

Purpose: Intensity modulated radiation therapy (IMRT) has gained popularity in the treatment of cancers. Manual evaluation of IMRT plans for head-and-neck cancers has been especially challenging necessitating efficient and objective assessment tools. In this work, the authors address this issue by developing a personalized conformity index (CI) for comparison of IMRT plans for head-and-neck cancers and evaluating its plan quality discerning power in comparison with other widely used CIs. Methods: A two-dimensional CI with dose and distance incorporated (CI{sub DD}) was developed using the MATLAB program language, to quantify the planning target volume (PTV) coverage. Valuable information contained in themore » digital imaging and communication in medicine (DICOM) RT objects were harvested for computation of each of the CI{sub DD} components. Apart from the dose penalty factor, a distance-based exponential function was employed by varying the penalty weight associated with the location of cold spots within the PTV. With the goal of deriving a customized penalty factor, the distances between individual pixel and its nearest PTV boundary was found. Using the exponential function, the impact of distance penalty was substantially larger for cold spots closer to the PTV centroid but petered out quickly wherever they were situated in the vicinity of PTV border. In order to evaluate the CI{sub DD} scoring system, three CT image data sets of nasopharyngeal carcinoma (NPC) patients were collected. Ten IMRT plans with degrading qualities were generated from each dataset and were ranked based on CI{sub DD} and other existing indices. The coefficient of variance was calculated for each dataset to compare the degree of variation. Results: The CI{sub DD} scoring system that considered spatial importance of each voxel within the PTV was successfully developed. The results demonstrated that the CI{sub DD} including four discrete factors could provide accurate rankings of plan quality by examining the relative importance of each cold spot within the PTVs. Apart from the dose penalty factor, a distance-based exponential function was employed taking the specific tumor geometry into account. Compared with other commonly used CIs, the CI{sub DD} resulted in the largest coefficient of variance among the ten IMRT plans for each dataset, indicating that its discerning power was the best among the CIs being compared. Conclusions: The CI{sub DD} scoring system was successfully developed to incorporate patient-specific spatial dose information and provide a geometry-based physical index for comparison of IMRT plans for head-and-neck cancers. By taking individual tumor geometry into account, the superiority of CI{sub DD} in plan discerning power was demonstrated. The use of CI{sub DD} could provide an effective means of benchmarking performance, reducing treatment plan variability, and advancing the quality of current IMRT planning.« less

ATP-binding cassette transporter ABCA4 and chemical isomerization protect photoreceptor cells from the toxic accumulation of excess 11-cis-retinal.

PubMed

Quazi, Faraz; Molday, Robert S

2014-04-01

The visual cycle is a series of enzyme-catalyzed reactions which converts all-trans-retinal to 11-cis-retinal for the regeneration of visual pigments in rod and cone photoreceptor cells. Although essential for vision, 11-cis-retinal like all-trans-retinal is highly toxic due to its highly reactive aldehyde group and has to be detoxified by either reduction to retinol or sequestration within retinal-binding proteins. Previous studies have focused on the role of the ATP-binding cassette transporter ABCA4 associated with Stargardt macular degeneration and retinol dehydrogenases (RDH) in the clearance of all-trans-retinal from photoreceptors following photoexcitation. How rod and cone cells prevent the accumulation of 11-cis-retinal in photoreceptor disk membranes in excess of what is required for visual pigment regeneration is not known. Here we show that ABCA4 can transport N-11-cis-retinylidene-phosphatidylethanolamine (PE), the Schiff-base conjugate of 11-cis-retinal and PE, from the lumen to the cytoplasmic leaflet of disk membranes. This transport function together with chemical isomerization to its all-trans isomer and reduction to all-trans-retinol by RDH can prevent the accumulation of excess 11-cis-retinal and its Schiff-base conjugate and the formation of toxic bisretinoid compounds as found in ABCA4-deficient mice and individuals with Stargardt macular degeneration. This segment of the visual cycle in which excess 11-cis-retinal is converted to all-trans-retinol provides a rationale for the unusually high content of PE and its long-chain unsaturated docosahexaenoyl group in photoreceptor membranes and adds insight into the molecular mechanisms responsible for Stargardt macular degeneration.

Non-syndromic hearing loss caused by the dominant cis mutation R75Q with the recessive mutation V37I of the GJB2 (Connexin 26) gene.

PubMed

Kim, Juwon; Jung, Jinsei; Lee, Min Goo; Choi, Jae Young; Lee, Kyung-A

2015-06-19

GJB2 alleles containing two cis mutations have been rarely found in non-syndromic hearing loss. Herein, we present a Korean patient with non-syndromic hearing loss caused by the R75Q cis mutation with V37I, which arose de novo in the father and was inherited by the patient. Biochemical coupling and hemichannel permeability assays were performed after molecular cloning and transfection of HEK293T cells. Student's t-tests or analysis of variance followed by Tukey's multiple comparison test was used as statistical analysis. Biochemical coupling was significantly reduced in connexin 26 (Cx26)-R75Q- and Cx26-V37I-transfected cells, with greater extent in Cx26-R75Q and Cx26-R75Q+V37I cells. Interestingly, our patient and his father with the mutations had more residual hearing compared with patients with the dominant mutation alone. Although the difference in hemichannel activity between R75Q alone and R75Q in combination with V37I failed to reach significance, it is of note that there is a possibility that V37I located upstream of R75Q might have the ability to ameliorate R75Q expression. Our study emphasizes the importance of cis mutations with R75Q, as the gene effect of R75Q can be modulated depending on the type of additional mutation.

Trans-cis isomerization of lipophilic dyes probing membrane microviscosity in biological membranes and in live cells.

PubMed

Chmyrov, Volodymyr; Spielmann, Thiemo; Hevekerl, Heike; Widengren, Jerker

2015-06-02

Membrane environment and fluidity can modulate the dynamics and interactions of membrane proteins and can thereby strongly influence the function of cells and organisms in general. In this work, we demonstrate that trans-cis isomerization of lipophilic dyes is a useful parameter to monitor packaging and fluidity of biomembranes. Fluorescence fluctuations, generated by trans-cis isomerization of the thiocarbocyanine dye Merocyanine 540 (MC540), were first analyzed by fluorescence correlation spectroscopy (FCS) in different alcohol solutions. Similar isomerization kinetics of MC540 in lipid vesicles could then also be monitored, and the influence of lipid polarity, membrane curvature, and cholesterol content was investigated. While no influence of membrane curvature and lipid polarity could be observed, a clear decrease in the isomerization rates could be observed with increasing cholesterol contents in the vesicle membranes. Finally, procedures to spatially map photoinduced and thermal isomerization rates on live cells by transient state (TRAST) imaging were established. On the basis of these procedures, MC540 isomerization was studied on live MCF7 cells, and TRAST images of the cells at different temperatures were found to reliably detect differences in the isomerization parameters. Our studies indicate that trans-cis isomerization is a useful parameter for probing membrane dynamics and that the TRAST imaging technique can provide spatial maps of photoinduced isomerization as well as both photoinduced and thermal back-isomerization, resolving differences in local membrane microviscosity in live cells.

Parallel evolution of chordate cis-regulatory code for development.

PubMed

Doglio, Laura; Goode, Debbie K; Pelleri, Maria C; Pauls, Stefan; Frabetti, Flavia; Shimeld, Sebastian M; Vavouri, Tanya; Elgar, Greg

2013-11-01

Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.

Rapid determination of retinoic acid and its main isomers in plasma by second-order high-performance liquid chromatography data modeling.

PubMed

Teglia, Carla M; Cámara, María S; Goicoechea, Héctor C

2014-12-01

This paper reports the development of a method based on high-performance liquid chromatography (HPLC) coupled to second-order data modeling with multivariate curve resolution-alternating least-squares (MCR-ALS) for quantification of retinoic acid and its main isomers in plasma in only 5.5 min. The compounds retinoic acid (RA), 13-cis-retinoic acid, 9-cis-retinoic acid, and 9,13-di-cis-retinoic acid were partially separated by use of a Poroshell 120 EC-C18 (3.0 mm × 30 mm, 2.7 μm particle size) column. Overlapping not only among the target analytes but also with the plasma interferents was resolved by exploiting the second-order advantage of the multi-way calibration. A validation study led to the following results: trueness with recoveries of 98.5-105.9 % for RA, 95.7-110.1 % for 13-cis-RA, 97.1-110.8 % for 9-cis-RA, and 99.5-110.9 % for 9,13-di-cis-RA; repeatability with RSD of 3.5-3.1 % for RA, 3.5-1.5 % for 13-cis-RA, 4.6-2.7 % for 9-cis-RA, and 5.2-2.7 % for 9,13-di-cis-RA (low and high levels); and intermediate precision (inter-day precision) with RSD of 3.8-3.0 % for RA, 2.9-2.4 % for 13-cis-RA, 3.6-3.2 % for 9,13-di-cis-RA, and 3.2-2.9 % for 9-cis-RA (low and high levels). In addition, a robustness study revealed the method was suitable for monitoring patients with dermatological diseases treated with pharmaceutical products containing RA and 13-cis-RA.

Asperger syndrome, violent thoughts and clinically isolated syndrome.

PubMed

Vanderbruggen, N; Van Geit, N; Bissay, V; Zeeuws, D; Santermans, L; Baeken, C

2010-12-01

A young man, 23 years old, with a clinically isolated syndrome (CIS), presented violent thoughts during a neurological consultation. He was diagnosed with Asperger Syndrome based on a psychiatric and (neuro)psychological examination. Possible risk factors for acting-out and the implications for treatment, if CIS would evolve to MS, are discussed based on a review of the literature.

Lateral cis-1,3,5,7-tetraazadecalin podands and their complexes: synthesis, structure, and strong binding with Pb(II) and other heavy metal ions.

PubMed

Reany, Ofer; Fuchs, Benzion

2013-02-18

The chemistry and complexation behavior of diaminal podands based on cis-1,3,5,7-tetraazadecalin (cis-TAD) were elaborated, reassessed, and extended. The synthesis of 2,6-bis(hydroxymethylene)-cis-TAD (9) and 2,6-bis(α,α'-dimethyl-β- hydroxyethyl)-cis-TAD (10) as well as of suitably substituted 2,6-diaryl-cis-TAD podands is laid out. For the latter, the effect of electron donating or withdrawing substituents on the benzaldehyde reagents was examined while 9 and 10 were probed and showed considerable propensity for heavy metal-ion chelation. The [Cd(II)·(9)] and [Pb(II)·(9)] complexes stood out indeed, and their structure and properties show a particularly interesting 5-amino-1,3-diazane chelation type and strong ligand-ion binding mode, with intramolecular donor exchange in solution, all strongly influenced by the anomeric effect in the ligand.

Structural characterization of cevimeline and its trans-impurity by single crystal XRD.

PubMed

Stepanovs, Dmitrijs; Tetere, Zenta; Rāviņa, Irisa; Kumpiņš, Viktors; Zicāne, Daina; Bizdēna, Ērika; Bogans, Jānis; Novosjolova, Irina; Grigaloviča, Agnese; Meri, Remo Merijs; Fotins, Juris; Čerkasovs, Maksims; Mishnev, Anatoly; Turks, Māris

2016-01-25

Cevimeline is muscarinic receptor agonist which increases secretion of exocrine glands. Cevimeline base is a liquid (m.p. 20-25 °C) at ambient conditions, therefore its pharmaceutical formulation as a solid hydrochloride hemihydrate has been developed. The synthesis of cevimeline yields its cis- and trans-isomers and only the cis-isomer is recognized as the API and used in the finished formulation. In this study structural and physicochemical investigations of hydrochloride hemihydrates of cis- and trans-cevimelines have been performed. Single crystal X-ray analyses of both cis- and trans-isomers of cevimeline are reported here for the first time. It was found that the cis-isomer, the API, has less dense crystal packing, lower melting point and higher solubility in comparison to the trans-isomer. Copyright © 2015 Elsevier B.V. All rights reserved.

Fabrication of nanocrystal ink based superstrate-type CuInS₂ thin film solar cells.

PubMed

Cho, Jin Woo; Park, Se Jin; Kim, Woong; Min, Byoung Koun

2012-07-05

A CuInS₂ (CIS) nanocrystal ink was applied to thin film solar cell devices with superstrate-type configuration. Monodispersed CIS nanocrystals were synthesized by a colloidal synthetic route and re-dispersed in toluene to form an ink. A spray method was used to coat CIS films onto conducting glass substrates. Prior to CIS film deposition, TiO₂ and CdS thin films were also prepared as a blocking layer and a buffer layer, respectively. We found that both a TiO₂ blocking layer and a CdS buffer layer are necessary to generate photoresponses in superstrate-type devices. The best power conversion efficiency (∼1.45%) was achieved by the CIS superstrate-type thin film solar cell device with 200 and 100 nm thick TiO₂ and CdS films, respectively.

Comparison of alternative beef production systems based on forage finishing or grain-forage diets with or without growth promotants: 2. Meat quality, fatty acid composition, and overall palatability.

PubMed

Faucitano, L; Chouinard, P Y; Fortin, J; Mandell, I B; Lafrenière, C; Girard, C L; Berthiaume, R

2008-07-01

Five beef cattle management regimens were evaluated for their effect on meat quality, fatty acid composition, and overall palatability of the longis-simus dorsi (LD) muscle in Angus cross steers. A 98-d growing phase was conducted using grass silage with or without supplementation of growth promotants (Revalor G and Rumensin) or soybean meal. Dietary treatments in the finishing phase were developed with or without supplementation of growth promotants based on exclusive feeding of forages with no grain supplementation, or the feeding of grain:forage (70:30) diets. Growth promotants increased (P < 0.01) shear force and tended (P = 0.06) to increase toughness of the LD muscle due to limited postmortem proteolytic activity (lower myofibrillar fragmentation index value; P = 0.02). Grain feeding increased DM and intramuscular fat content (P = 0.03 and P = 0.05, respectively) in the LD but decreased the sensory panel tenderness score (P = 0.01). Growth promotants increased (P

Neutral Guest Capture via Lewis Acid/Base Molecular Square Receptors. X-ray Crystal Structure of {Cyclobis[(cis-(dppp)Pt(4-ethynylpyridyl)(2))(cis- (PEt(3))(2)Pt)]Ag(2)}(+6)(phenazine)- ((-)OSO(2)CF(3))(6).

PubMed

Whiteford, Jeffery A.; Stang, Peter J.; Huang, Songping D.

1998-10-19

Interaction of {cyclobis[(cis-(dppp)Pt(4-ethynylpyridyl)(2))(cis-(L)M)]Ag(2)}(+6)((-)OSO(2)CF(3))(6), where M = Pt(II) or Pd(II) and L = dppp or 2PEt(3), with pyridine, pyrazine, phenazine, or 4,4'-dipyridyl ketone results in coordination Lewis acid/base host-guest assemblies via the "pi-tweezer effect" and mono or bis neutral guest coordination. All host-guest complexes are air stable microcrystalline solids with decomposition points greater than 170 degrees C. The homometallic Pt(II) receptors are more stable than the heteroaromatic Pt(II)-Pd(II) receptors toward heteratom-containing aromatic guests. The X-ray crystal structure of the host-guest complex {cyclobis[(cis-(dppp)Pt(4-ethynylpyridyl)(2))(cis-(PEt(3))(2)Pt)]Ag(2)}(+6)(phenazine)((-)OSO(2)CF(3))(6) is reported. The crystals with the empirical formula C(62)H(68)AgF(9)N(3)O(9)P(4)Pt(2)S(3) are triclinic P&onemacr; with a = 12.3919(8) Å, b = 17.160(1) Å, c = 18.932(1) Å, alpha = 90.892(1) degrees, beta = 97.127(1) degrees, gamma = 89.969(1) degrees, and Z = 2.

Distortions induced in double-stranded oligonucleotides by the binding of cis- or trans-diammine-dichloroplatinum(II) to the d(GTG) sequence.

PubMed Central

Anin, M F; Leng, M

1990-01-01

Conformational changes induced in double-stranded oligonucleotides by the binding of trans- or cis-diamminedichloro platinum(II) to the d(GTG) sequence have been characterized by means of melting temperatures, electrophoretic migrations in non-denaturing polyacrylamide gels, reactivities with the artificial nuclease Phenanthroline-copper and with chemical probes. The cis-platinum adduct behaves more as a centre of directed bend than as a hinge joint, the induced bend angle being of the order of 25-30 degrees. The double helix is locally denatured over 2 base pairs (corresponding to the platinated 5'G residue and the central T residue) and is distorted over 4-5 base pairs. The trans-platinum adduct behaves also more as a centre of directed bend than as a hinge joint, the induced bend angle being of the order of 60 degrees. The double helix is locally denatured over 4 base pairs (corresponding to the immediately 5'T residue adjacent to the adduct and to the three base residues of the adduct). Both the cis- and trans-platinum adducts decrease the thermal stability of the double helix. Images PMID:2388824

Long-lived and Well-resolved Mn2+ Ion Emissions in CuInS-ZnS Quantum Dots

PubMed Central

Cao, Sheng; Li, Chengming; Wang, Lin; Shang, Minghui; Wei, Guodong; Zheng, Jinju; Yang, Weiyou

2014-01-01

CuInS2 (CIS) quantum dots (QDs) have tunable photoluminescence (PL) behaviors in the visible and near infrared spectral range with markedly lower toxicity than the cadmium-based counterparts, making them very promising applications in light emitting and solar harvesting. However, there still remain material- and fabrication- related obstacles in realizing the high-performance CIS-based QDs with well-resolved Mn2+ d-d emission, long emission lifetimes as well as high efficiencies. Here, we demonstrate the growth of high-quality Mn2+-doped CuInS-ZnS (CIS-ZnS) QDs based on a multi-step hot-injection strategy. The resultant QDs exhibit a well-resolved Mn2+ d-d emission with a high PL quantum yield (QY) up to 66% and an extremely long excited state lifetime up to ~3.78 ms, which is nearly two times longer than the longest one of “green” QDs ever reported. It is promising that the synthesized Mn2+-doped CIS-ZnS QDs might open new doors for their practical applications in bioimaging and opto/electronic devices. PMID:25515207

URBAN-NET: A Network-based Infrastructure Monitoring and Analysis System for Emergency Management and Public Safety

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

Lee, Sangkeun; Chen, Liangzhe; Duan, Sisi

Abstract Critical Infrastructures (CIs) such as energy, water, and transportation are complex networks that are crucial for sustaining day-to-day commodity flows vital to national security, economic stability, and public safety. The nature of these CIs is such that failures caused by an extreme weather event or a man-made incident can trigger widespread cascading failures, sending ripple effects at regional or even national scales. To minimize such effects, it is critical for emergency responders to identify existing or potential vulnerabilities within CIs during such stressor events in a systematic and quantifiable manner and take appropriate mitigating actions. We present here amore » novel critical infrastructure monitoring and analysis system named URBAN-NET. The system includes a software stack and tools for monitoring CIs, pre-processing data, interconnecting multiple CI datasets as a heterogeneous network, identifying vulnerabilities through graph-based topological analysis, and predicting consequences based on what-if simulations along with visualization. As a proof-of-concept, we present several case studies to show the capabilities of our system. We also discuss remaining challenges and future work.« less

Assessment of composite motif discovery methods.

PubMed

Klepper, Kjetil; Sandve, Geir K; Abul, Osman; Johansen, Jostein; Drablos, Finn

2008-02-26

Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery - discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual datasets also shows that the new benchmark datasets represents a suitable variety of challenges to most methods for module discovery.

Specifications of a Mechanized Center for Information Services for a Public Library Reference Center. Final Report. Part 1, Preliminary Specification: Mechanized Information Services in Public Library Reference Centers.

ERIC Educational Resources Information Center

California Univ., Los Angeles. Inst. of Library Research.

This document presents preliminary specifications for a library-based Center for Information Services (CIS). Four sets of issues are covered: (1) data base inventory, providing a listing of magnetic tape data bases now available from national sources or soon to be so; (2) administrative issues, including the organization of the CIS within the…

Saturn Apollo Program

NASA Image and Video Library

1968-12-17

Apollo 8 crew members paused before the mission simulator during training for the first manned lunar orbital mission. Frank Borman, commander; James Lovell, Command Module (CM) pilot; and William Anders, Lunar Module (LM) pilot , were also the first humans to launch aboard the massive Saturn V space vehicle. Lift off occurred on December 21, 1968 and returned safely to Earth on December 27, 1968. The mission achieved operational experience and tested the Apollo command module systems, including communications, tracking, and life-support, in cis-lunar space and lunar orbit, and allowed evaluation of crew performance on a lunar orbiting mission. The crew photographed the lunar surface, both far side and near side, obtaining information on topography and landmarks as well as other scientific information necessary for future Apollo landings. All systems operated within allowable parameters and all objectives of the mission were achieved.

StInvInh2 as an inhibitor of StvacINV1 regulates the cold-induced sweetening of potato tubers by specifically capping vacuolar invertase activity.

PubMed

Liu, Xun; Lin, Yuan; Liu, Jun; Song, Botao; Ou, Yongbin; Zhang, Huiling; Li, Meng; Xie, Conghua

2013-06-01

Reducing sugar (RS) accumulation in cold-stored potato tubers, known as cold-induced sweetening (CIS), is a crucial factor causing unacceptable colour changes and acrylamide formation of fried products. The activity of vacuolar invertase (StvacINV1) is proved important for the CIS process, and invertase inhibitors are speculated to play roles in the post-translational regulation of StvacINV1 activity. In our previous research, two putative inhibitors (StInvInh2A and StInvInh2B) of StvacINV1 were implied to be involved in potato CIS. Here, we further reported that StInvInh2A and StInvInh2B had similar function that specifically inhibited StvacINV1 activity in potatoes. The genetic transformation of these inhibitor genes in potatoes by overexpression in CIS-sensitive and RNAi-silenced in CIS-resistant genotypes showed that StvacINV1 activity was strongly regulated by alteration of the transcripts of the inhibitors without impacting on the expression of StvacINV1. A negative power relationship was found between the transcripts of the inhibitors and StvacINV1 activity, suggesting 1) a transcriptional determination of the inhibitory capacity of StInvInh2A and StInvInh2B and 2) a significant inhibitory role of these inhibitors in post-translational modulation of StvacINV1. The results also demonstrated that depression of StvacINV1 activity through overexpression of StInvInh2A and StInvInh2B weakened accumulation of RS and acrylamide in cold-stored tubers and consequently improved the chip quality. The present research strongly suggest that both StInvInh2A and StInvInh2B function as inhibitors of StvacINV1 and play similar roles in regulating potato CIS by capping StvacINV1 activity. These inhibitors could be novel genetic resources applicable for improving quality of potato processing products. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.

PubMed

Turatsinze, Jean-Valery; Thomas-Chollier, Morgane; Defrance, Matthieu; van Helden, Jacques

2008-01-01

This protocol shows how to detect putative cis-regulatory elements and regions enriched in such elements with the regulatory sequence analysis tools (RSAT) web server (http://rsat.ulb.ac.be/rsat/). The approach applies to known transcription factors, whose binding specificity is represented by position-specific scoring matrices, using the program matrix-scan. The detection of individual binding sites is known to return many false predictions. However, results can be strongly improved by estimating P value, and by searching for combinations of sites (homotypic and heterotypic models). We illustrate the detection of sites and enriched regions with a study case, the upstream sequence of the Drosophila melanogaster gene even-skipped. This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour.

Chemical Vapor Deposition for Ultra-lightweight Thin-film Solar Arrays for Space

NASA Technical Reports Server (NTRS)

Hepp, Aloysius F.; Raffaelle, Ryne P.; Banger, Kulbinder K.; Jin, Michael H.; Lau, Janice E.; Harris, Jerry D.; Cowen, Jonathan E.; Duraj, Stan A.

2002-01-01

The development of thin-film solar cells on flexible, lightweight, space-qualified substrates provides an attractive cost solution to fabricating solar arrays with high specific power, (W/kg). The use of a polycrystalline chalcopyrite absorber layer for thin film solar cells is considered as the next generation photovoltaic devices. A key technical issues outlined in the 2001 U.S. Photovoltaic Roadmap, is the need to develop low cost, high throughput manufacturing for high-efficiency thin film solar cells. At NASA GRC we have focused on the development of new single-source-precursors (SSPs) and their utility to deposit the chalcopyrite semi-conducting layer (CIS) onto flexible substrates for solar cell fabrication. The syntheses and thermal modulation of SSPs via molecular engineering is described. Thin-film fabrication studies demonstrate the SSPs can be used in a spray CVD process, for depositing CIS at reduced temperatures, which display good electrical properties, suitable for PV devices.

Sugar regulation of SUGAR TRANSPORTER PROTEIN 1 (STP1) expression in Arabidopsis thaliana

PubMed Central

Cordoba, Elizabeth; Aceves-Zamudio, Denise Lizeth; Hernández-Bernal, Alma Fabiola; Ramos-Vega, Maricela; León, Patricia

2015-01-01

Sugars regulate the expression of many genes at the transcriptional level. In Arabidopsis thaliana, sugars induce or repress the expression of >1800 genes, including the STP1 (SUGAR TRANSPORTER PROTEIN 1) gene, which encodes an H+/monosaccharide cotransporter. STP1 transcript levels decrease more rapidly after the addition of low concentrations of sugars than the levels of other repressed genes, such as DIN6 (DARK-INDUCED 6). We found that this regulation is exerted at the transcriptional level and is initiated by phosphorylatable sugars. Interestingly, the sugar signal that modulates STP1 expression is transmitted through a HEXOKINASE 1-independent signalling pathway. Finally, analysis of the STP1 5′ regulatory region allowed us to delimit a region of 309bp that contains the cis elements implicated in the glucose regulation of STP1 expression. Putative cis-acting elements involved in this response were identified. PMID:25281700

Z-Selective Ruthenium Metathesis Catalysts: Comparison of Nitrate and Nitrite X-type Ligands

PubMed Central

Pribisko, Melanie A.; Ahmed, Tonia S.; Grubbs, Robert H.

2014-01-01

Two new Ru-based metathesis catalysts, 3 and 4, have been synthesized for the purpose of comparing their catalytic properties to those of their cis-selective nitrate analogues, 1 and 2. Although catalysts 3 and 4 exhibited slower initiation rates than 1 and 2, they maintained high cis-selectivity in homodimerization and ring-opening metathesis polymerization reactions. Furthermore, the nitrite catalysts displayed higher cis-selectivity than 2 for ring-opening metathesis polymerizations, and 4 delivered higher yields of polymer. PMID:25484484

Z-Selective Ruthenium Metathesis Catalysts: Comparison of Nitrate and Nitrite X-type Ligands.

PubMed

Pribisko, Melanie A; Ahmed, Tonia S; Grubbs, Robert H

2014-12-14

Two new Ru-based metathesis catalysts, 3 and 4 , have been synthesized for the purpose of comparing their catalytic properties to those of their cis -selective nitrate analogues, 1 and 2 . Although catalysts 3 and 4 exhibited slower initiation rates than 1 and 2 , they maintained high cis -selectivity in homodimerization and ring-opening metathesis polymerization reactions. Furthermore, the nitrite catalysts displayed higher cis -selectivity than 2 for ring-opening metathesis polymerizations, and 4 delivered higher yields of polymer.

Pulse-spreading harmonic complex as an alternative carrier for vocoder simulations of cochlear implants.

PubMed

Mesnildrey, Quentin; Hilkhuysen, Gaston; Macherey, Olivier

2016-02-01

Noise- and sine-carrier vocoders are often used to acoustically simulate the information transmitted by a cochlear implant (CI). However, sine-waves fail to mimic the broad spread of excitation produced by a CI and noise-bands contain intrinsic modulations that are absent in CIs. The present study proposes pulse-spreading harmonic complexes (PSHCs) as an alternative acoustic carrier in vocoders. Sentence-in-noise recognition was measured in 12 normal-hearing subjects for noise-, sine-, and PSHC-vocoders. Consistent with the amount of intrinsic modulations present in each vocoder condition, the average speech reception threshold obtained with the PSHC-vocoder was higher than with sine-vocoding but lower than with noise-vocoding.

Glucose Sensing with Phenylboronic Acid Functionalized Hydrogel-Based Optical Diffusers

PubMed Central

2018-01-01

Phenylboronic acids have emerged as synthetic receptors that can reversibly bind to cis-diols of glucose molecules. The incorporation of phenylboronic acids in hydrogels offers exclusive attributes; for example, the binding process with glucose induces Donnan osmotic pressure resulting in volumetric changes in the matrix. However, their practical applications are hindered because of complex readout approaches and their time-consuming fabrication processes. Here, we demonstrate a microimprinting method to fabricate densely packed concavities in phenylboronic acid functionalized hydrogel films. A microengineered optical diffuser structure was imprinted on a phenylboronic acid based cis-diol recognizing motif prepositioned in a hydrogel film. The diffuser structure engineered on the hydrogel was based on laser-inscribed arrays of imperfect microlenses that focused the incoming light at different focal lengths and direction resulting in a diffused profile of light in transmission and reflection readout modes. The signature of the dimensional modulation was detected in terms of changing focal lengths of the microlenses due to the volumetric expansion of the hydrogel that altered the diffusion spectra and transmitted beam profile. The transmitted optical light spread and intensity through the sensor was measured to determine variation in glucose concentrations at physiological conditions. The sensor was integrated in a contact lens and placed over an artificial eye. Artificial stimulation of variation in glucose concentration allowed quantitative measurements using a smartphone’s photodiode. A smartphone app was utilized to convert the received light intensity to quantitative glucose concentration values. The developed sensing platform offers low cost, rapid fabrication, and easy detection scheme as compared to other optical sensing counterparts. The presented detection scheme may have applications in wearable real-time biomarker monitoring devices at point-of-care settings. PMID:29529366

PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.

PubMed

Elati, Mohamed; Nicolle, Rémy; Junier, Ivan; Fernández, David; Fekih, Rim; Font, Julio; Képès, François

2013-02-01

Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices, which may match large numbers of sites and produce an unreliable list of target genes. To improve the prediction of binding sites, we propose to additionally use the unrelated knowledge of the genome layout. Indeed, it has been shown that co-regulated genes tend to be either neighbors or periodically spaced along the whole chromosome. This study demonstrates that respective gene positioning carries significant information. This novel type of information is combined with traditional sequence information by a machine learning algorithm called PreCisIon. To optimize this combination, PreCisIon builds a strong gene target classifier by adaptively combining weak classifiers based on either local binding sequence or global gene position. This strategy generically paves the way to the optimized incorporation of any future advances in gene target prediction based on local sequence, genome layout or on novel criteria. With the current state of the art, PreCisIon consistently improves methods based on sequence information only. This is shown by implementing a cross-validation analysis of the 20 major TFs from two phylogenetically remote model organisms. For Bacillus subtilis and Escherichia coli, respectively, PreCisIon achieves on average an area under the receiver operating characteristic curve of 70 and 60%, a sensitivity of 80 and 70% and a specificity of 60 and 56%. The newly predicted gene targets are demonstrated to be functionally consistent with previously known targets, as assessed by analysis of Gene Ontology enrichment or of the relevant literature and databases.

Facile access to unnatural dipeptide-alcohols based on cis-2,5-disubstituted pyrrolidines.

PubMed

Jia, Yan-Yan; Li, Xiao-Ye; Wang, Ping-An; Wen, Ai-Dong

2015-02-11

Well-defined unnatural dipeptide-alcohols based on a cis-2,5-disubstitued pyrrolidine backbone were synthesized from commercially available starting materials meso-diethyl-2,5-dibromoadipate, (S)-(-)-1-phenylethylamine, and phenylalaninol. The structures of these unnatural dipeptide-alcohols are supported by HRMS, 1H- and 13C-NMR spectroscopy. These unnatural dipeptide-alcohols can act as building blocks for peptidomimetics.

Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

PubMed Central

Genshaft, Alexander; Moser, Joe-Ann S.; D'Antonio, Edward L.; Bowman, Christine M.; Christianson, David W.

2013-01-01

The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations. PMID:23401043

Interaction proteins of invertase and invertase inhibitor in cold-stored potato tubers suggested a protein complex underlying post-translational regulation of invertase.

PubMed

Lin, Yuan; Liu, Jun; Liu, Xun; Ou, Yongbin; Li, Meng; Zhang, Huiling; Song, Botao; Xie, Conghua

2013-12-01

The activity of vacuolar invertase (VI) is vital to potato cold-induced sweetening (CIS). A post-translational regulation of VI activity has been proposed which involves invertase inhibitor (VIH), but the mechanism for the interaction between VI and VIH has not been fully understood. To identify the potential partners of VI and VIH, two cDNA libraries were respectively constructed from CIS-resistant wild potato species Solanum berthaultii and CIS-sensitive potato cultivar AC035-01 for the yeast two-hybrid analysis. The StvacINV1 (one of the potato VIs) and StInvInh2B (one of the potato VIHs), previously identified to be associated with potato CIS, were used as baits to screen the two libraries. Through positive selection and sequencing, 27 potential target proteins of StvacINV1 and eight of StInvInh2B were clarified. The Kunitz-type protein inhibitors were captured by StvacINV1 in both libraries and the interaction between them was confirmed by bimolecular fluorescence complementation assay in tobacco cells, reinforcing a fundamental interaction between VI and VIH. Notably, a sucrose non-fermenting-1-related protein kinase 1 was captured by both the baits, suggesting that a protein complex could be necessary for fine turning of the invertase activity. The target proteins clarified in present research provide a route to elucidate the mechanism by which the VI activity can be subtly modulated. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Isolation of Persicaria minor sesquiterpene synthase promoter and its deletions for transgenic Arabidopsis thaliana

NASA Astrophysics Data System (ADS)

Omar, Aimi Farehah; Ismail, Ismanizan

2016-11-01

Sesquiterpene synthase (SS) catalyzes the formation of sesquiterpenes from farnesyl diphosphate (FDP) via carbocation intermediates. In this study, the promoter region of sesquiterpene synthase was isolated from Persicaria minor to identify possible cis-acting elements in the promoter. The full-length PmSS promoter of P. minor is 1824-bp sequences. The sequence was analyzed and several putative cis-acting regulatory elements were identified. Three cis-acting regulatory elements were selected for deletion analysis which are cis-acting element involved in wound responsiveness (WUN), cis - acting element involved in defense and stress responsiveness (TC) and cis-acting element involved in ABA responsiveness (ABRE). Series of deletions were conducted to assess the promoter activity producing three truncated fragments promoter; Prom 2 1606-bp, Prom 3 1144- bp, and Prom 4 921-bp. The full-length promoter and its deletion series were cloned into the pBGWFS7 vector which contain β-glucuronidase (GUS) gene and green fluorescent protein (GFP) as the reporter gene. All constructs were successfully transformed into Arabidopsis thaliana based on PCR of positive BASTA resistance plants.

Mechanistic analysis of water oxidation catalyst cis-[Ru(bpy) 2(H 2O) 2] 2+: Effect of dimerization

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

Erdman, Darren; Pineda-Galvan, Yuliana; Pushkar, Yulia

While the catalytic activity of some Ru-based polypyridine complexes in water oxidation is well established, the relationship between their chemical structure and activity is less known. In this work, the single site Ru complex [Ru(bpy) 2(H 2O) 2] 2+ (bpy = 2,20-bipyridine)—which can exist as either a cis isomer or a trans isomer—is investigated. While a difference in the catalytic activity of these two isomers is well established, with cis-[Ru(bpy) 2(H 2O) 2] 2+ being much more active, no mechanistic explanation of this fact has been presented. The oxygen evolving capability of both isomers at multiple concentrations has been investigated,more » with cis-[Ru(bpy) 2(H 2O) 2] 2+ showing a second-order dependence of O2 evolution activity with increased catalyst concentration. Measurement of the electron paramagnetic resonance (EPR) spectrum of cis-[Ru(bpy) 2(H 2O) 2] 2+, shortly after oxidation with CeIV, showed the presence of a signal matching that of cis,cis-[Ru III(bpy) 2(H 2O)ORu IV(bpy) 2(OH)] 4+, also known as “blue dimer”. The formation of dimers is a concentration-dependent process, which could serve to explain the greater than first order increase in catalytic activity. The trans isomer showed a first-order dependence of O 2 evolution on catalyst concentration. As a result, behavior of [Ru(bpy) 2(H 2O) 2] 2+ isomers is compared with other Ru-based catalysts, in particular [Ru(tpy)(bpy)(H 2O)] 2+ (tpy = 2,20;6,20 0-terpyridine).« less

Do socioeconomic disparities affect accessing and keeping antihypertensive drug therapy? Evidence from an Italian population-based study.

PubMed

Corrao, G; Zambon, A; Parodi, A; Mezzanzanica, M; Merlino, L; Cesana, G; Mancia, G

2009-04-01

We conducted this population-based cohort study by linking several databases to explore the role of socioeconomic position for accessing and keeping antihypertensive drug therapy. A total of 71 469 patients, residents in the city of Milan (Italy) aged 40-80 years, who received an antihypertensive drug during 1999-2002 were followed for 1 year starting from the first dispensation. Socioeconomic position and drug prescriptions were respectively obtained from tax registry and outpatient prescription database. The effect of socioeconomic characteristics on standardized incidence rate (SIR) of new users of antihypertensive agents, odds ratio (OR) of using combined antihypertensive agents and non-antihypertensive drugs and hazard ratio (HR) of discontinuing antihypertensive therapy were estimated after adjustment for potential confounders. SIRs were 3.7 and 4.2 per 1000 person-months among persons at the lowest and intermediate income, respectively, and 2.4 and 3.0 among immigrants and Italians, respectively. Compared to persons at the highest income, those at the lowest income had increased chances of starting with combined antihypertensive drugs (OR: 1.1; 95% confidence intervals (CIs): 1.0, 1.2), and of using drugs for heart failure (OR:1.5; CIs:1.3, 1.6) and diabetes (OR: 1.7; CIs: 1.6, 1.9). Compared with Italians, non-western immigrants had increased chances of starting with combined antihypertensive agents (OR: 1.2; CIs: 1.0, 1.3), of using drugs for heart failure (OR: 1.2; CIs: 1.0, 1.4) and for diabetes (OR: 1.8; CIs: 1.6, 2.1), and of interrupting antihypertensive therapy (HR: 1.1; 95% CIs: 1.0, 1.2). Despite the universal health coverage of the Italian National Health Service (NHS), social disparities affect accessing and keeping antihypertensive therapy.

Mechanistic analysis of water oxidation catalyst cis-[Ru(bpy) 2(H 2O) 2] 2+: Effect of dimerization

DOE PAGES

Erdman, Darren; Pineda-Galvan, Yuliana; Pushkar, Yulia

2017-01-25

While the catalytic activity of some Ru-based polypyridine complexes in water oxidation is well established, the relationship between their chemical structure and activity is less known. In this work, the single site Ru complex [Ru(bpy) 2(H 2O) 2] 2+ (bpy = 2,20-bipyridine)—which can exist as either a cis isomer or a trans isomer—is investigated. While a difference in the catalytic activity of these two isomers is well established, with cis-[Ru(bpy) 2(H 2O) 2] 2+ being much more active, no mechanistic explanation of this fact has been presented. The oxygen evolving capability of both isomers at multiple concentrations has been investigated,more » with cis-[Ru(bpy) 2(H 2O) 2] 2+ showing a second-order dependence of O2 evolution activity with increased catalyst concentration. Measurement of the electron paramagnetic resonance (EPR) spectrum of cis-[Ru(bpy) 2(H 2O) 2] 2+, shortly after oxidation with CeIV, showed the presence of a signal matching that of cis,cis-[Ru III(bpy) 2(H 2O)ORu IV(bpy) 2(OH)] 4+, also known as “blue dimer”. The formation of dimers is a concentration-dependent process, which could serve to explain the greater than first order increase in catalytic activity. The trans isomer showed a first-order dependence of O 2 evolution on catalyst concentration. As a result, behavior of [Ru(bpy) 2(H 2O) 2] 2+ isomers is compared with other Ru-based catalysts, in particular [Ru(tpy)(bpy)(H 2O)] 2+ (tpy = 2,20;6,20 0-terpyridine).« less

Interconnectedness and interdependencies of critical infrastructures in the US economy: Implications for resilience

NASA Astrophysics Data System (ADS)

Chopra, Shauhrat S.; Khanna, Vikas

2015-10-01

Natural disasters in 2011 yielded close to 55 billion in economic damages alone in the United States (US), which highlights the need to reduce impacts of such disasters or other deliberate attacks. The US Department of Homeland Security (DHS) identifies a list of 16 Critical Infrastructure Sectors (CIS) whose incapacity due to disruptions would have a debilitating impact on the nation's economy. The goal of this work is to understand the implications of interdependencies among CIS on the resilience of the US economic system as a whole. We develop a framework that combines the empirical economic input-output (EIO) model with graph theory based techniques for understanding interdependencies, interconnectedness and resilience in the US economic system. By representing the US economy as a network, we are able to analyze its topology by separately looking at its unweighted and weighted forms. Topological analysis of the US EIO network suggests that it exhibits small world properties for the unweighted case, and in the weighted case, the throughput of industry sectors follows a power-law with an exponential cutoff. Implications of these topological properties are discussed in the paper. We also simulate hypothetical disruptions on CIS in order to identify industrial sectors that experience the largest economic impacts, and to quantify systemic vulnerability in economic terms. In addition, insights from community detection and hypothetical disruption scenarios help assess vulnerability of individual industrial communities to disruptions on individual CIS. These methodologies also provide insights regarding the extent of coupling between each CIS in the US EIO network. Based on our analysis, we observe that excessive interconnectedness and interdependencies of CIS results in high systemic vulnerability. This information can guide policymakers to design policies that improve resilience of economic networks, and evaluate policies that might indirectly increase coupling between CIS.

What can paper-based clinical information systems tell us about the design of computerized clinical information systems (CIS) in the ICU?

PubMed

Miller, A; Pilcher, D; Mercaldo, N; Leong, T; Scheinkestel, C; Schildcrout, J

2010-08-01

Screen designs in computerized clinical information systems (CIS) have been modeled on their paper predecessors. However, limited understanding about how paper forms support clinical work means that we risk repeating old mistakes and creating new opportunities for error and inefficiency as illustrated by problems associated with computerized provider order entry systems. This study was designed to elucidate principles underlying a successful ICU paper-based CIS. The research was guided by two exploratory hypotheses: (1) paper-based artefacts (charts, notes, equipment, order forms) are used differently by nurses, doctors and other healthcare professionals in different (formal and informal) conversation contexts and (2) different artefacts support different decision processes that are distributed across role-based conversations. All conversations undertaken at the bedsides of five patients were recorded with any supporting artefacts for five days per patient. Data was coded according to conversational role-holders, clinical decision process, conversational context and artefacts. 2133 data points were analyzed using Poisson logistic regression analyses. Results show significant interactions between artefacts used during different professional conversations in different contexts (chi(2)((df=16))=55.8, p<0.0001). The interaction between artefacts used during different professional conversations for different clinical decision processes was not statistically significant although all two-way interactions were statistically significant. Paper-based CIS have evolved to support complex interdisciplinary decision processes. The translation of two design principles - support interdisciplinary perspectives and integrate decision processes - from paper to computerized CIS may minimize the risks associated with computerization. 2010 Australian College of Critical Care Nurses Ltd. Published by Elsevier Ltd. All rights reserved.

Understanding critical barriers to implementing a clinical information system in a nursing home through the lens of a socio-technical perspective.

PubMed

Or, Calvin; Dohan, Michael; Tan, Joseph

2014-09-01

This paper addresses key barriers to implementing a clinical information system (CIS) in a Hong Kong nursing home setting, from a healthcare specific socio-technical perspective. Data was collected through field observations (n = 12) and semi-structured individual interviews (n = 18) of CIS stakeholders in a Hong Kong nursing home, and analyzed using the immersion/crystallization approach. Complex interactions relevant to our case were contextualized and interpreted within the perspective of the Sittig-Singh Healthcare Socio-Technical Framework (HSTF). Three broad clusters of implementation barriers from the eight HSTF dimensions were identified: (a) Infrastructure-based barriers, which relate to conflict between government regulations and system functional needs of users; lack of financial support; inconsistency between workflow, work policy, and procedures; and inadequacy of hardware-software infrastructural and technical support; (b) Process-based barriers, which relate to mismatch between the technology, existing work practice and workflow, and communication; low system speed, accessibility, and stability; deficient computer literacy; more experience in health care profession; clinical content inadequacy and unavailability; as well as poor system usefulness and user interface design; and (c) Outcome-based barriers, which relate to the lack of measurement and monitoring of system effectiveness. Two additional dimensions underlining the importance of the ability of a CIS to change are proposed to extend the Sittig-Singh HSTF. First, advocacy would promote the articulation and influence of changes in the system and subsequent outcomes by CIS stakeholders, and second, adaptability would ensure the ability of the system to adjust to emerging needs. The broad set of discovered implementation shortcomings expands prior research on why CIS can fail in nursing home settings. Moreover, our investigation offers a knowledge base and recommendations that can serve as a guide for future implementation strategies and policies in CIS initiatives.

The biosynthetic origin of irregular monoterpenes in Lavandula: isolation and biochemical characterization of a novel cis-prenyl diphosphate synthase gene, lavandulyl diphosphate synthase.

PubMed

Demissie, Zerihun A; Erland, Lauren A E; Rheault, Mark R; Mahmoud, Soheil S

2013-03-01

Lavender essential oils are constituted predominantly of regular monoterpenes, for example linalool, 1,8-cineole, and camphor. However, they also contain irregular monoterpenes including lavandulol and lavandulyl acetate. Although the majority of genes responsible for the production of regular monoterpenes in lavenders are now known, enzymes (including lavandulyl diphosphate synthase (LPPS)) catalyzing the biosynthesis of irregular monoterpenes in these plants have not been described. Here, we report the isolation and functional characterization of a novel cis-prenyl diphosphate synthase cDNA, termed Lavandula x intermedia lavandulyl diphosphate synthase (LiLPPS), through a homology-based cloning strategy. The LiLPPS ORF, encoding for a 305-amino acid long protein, was expressed in Escherichia coli, and the recombinant protein was purified by nickel-nitrilotriacetic acid affinity chromatography. The approximately 34.5-kDa bacterially produced protein specifically catalyzed the head-to-middle condensation of two dimethylallyl diphosphate units to LPP in vitro with apparent Km and kcat values of 208 ± 12 μm and 0.1 s(-1), respectively. LiLPPS is a homodimeric enzyme with a sigmoidal saturation curve and Hill coefficient of 2.7, suggesting a positive co-operative interaction among its catalytic sites. LiLPPS could be used to modulate the production of lavandulol and its derivatives in plants through metabolic engineering.

Deficits in the pitch sensitivity of cochlear-implanted children speaking English or Mandarin

PubMed Central

Deroche, Mickael L. D.; Lu, Hui-Ping; Limb, Charles J.; Lin, Yung-Song; Chatterjee, Monita

2014-01-01

Sensitivity to complex pitch is notoriously poor in adults with cochlear implants (CIs), but it is unclear whether this is true for children with CIs. Many are implanted today at a very young age, and factors related to brain plasticity (age at implantation, duration of CI experience, and speaking a tonal language) might have strong influences on pitch sensitivity. School-aged children participated, speaking English or Mandarin, having normal hearing (NH) or wearing a CI, using their clinically assigned settings with envelope-based coding strategies. Percent correct was measured in three-interval three-alternative forced choice tasks, for the discrimination of fundamental frequency (F0) of broadband harmonic complexes, and for the discrimination of sinusoidal amplitude modulation rate (AMR) of broadband noise, with reference frequencies at 100 and 200 Hz to focus on voice pitch processing. Data were fitted using a maximum-likelihood technique. CI children displayed higher thresholds and shallower slopes than NH children in F0 discrimination, regardless of linguistic background. Thresholds and slopes were more similar between NH and CI children in AMR discrimination. Once the effect of chronological age was extracted from the variance, the aforementioned factors related to brain plasticity did not contribute significantly to the CI children's sensitivity to pitch. Unless different strategies attempt to encode fine structure information, potential benefits of plasticity may be missed. PMID:25249932

CisSERS: Customizable in silico sequence evaluation for restriction sites

DOE PAGES

Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus; ...

2016-04-12

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated tomore » enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.« less

CisSERS: Customizable in silico sequence evaluation for restriction sites

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

Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated tomore » enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.« less

Diagnosis and management of urothelial carcinoma in situ of the lower urinary tract: a systematic review.

PubMed

Casey, Rowan G; Catto, James W F; Cheng, Liang; Cookson, Michael S; Herr, Harry; Shariat, Sharokh; Witjes, J Alfred; Black, Peter C

2015-05-01

Urothelial carcinoma in situ (CIS) has a high propensity for progression. It is usually reported within the heterogeneous context of non-muscle-invasive bladder cancer (NMIBC) but warrants special consideration. To review the contemporary literature on the diagnosis and management of CIS. A systematic search using broad terms to capture the diagnosis and treatment of CIS was performed according to Preferred Reporting Items for Systematic Reviews and Meta-analysis criteria. Full-text original articles, reviews, and editorials from 1966 to 2014 in English were included. References from selected articles, relevant guidelines, and conference abstracts were searched. Abstracts were excluded. A total of 1887 articles were identified, of which 120 were used in this review. Most reports were retrospective and heterogeneous in caseload. There is a lack of standardised classification of CIS. Many studies consider CIS in the context of NMIBC without a clear separation of the subset with CIS. Recent prospective phase 2 and 3 studies have improved the evidence base. We are beginning to understand that CIS has a spectrum of biologic potential. Bacillus Calmette-Guérin immunotherapy appears superior to other intravesical agents and may alter the natural history of CIS. New imaging modalities, agents, and treatment strategies have emerged in recent years with the aim of better identification of CIS, more bladder-preserving treatments, and prevention of surgical overtreatment. Improvements in imaging techniques combined with new bladder-preserving treatments will continue to have an impact on the outcomes of bladder carcinoma in situ. Copyright © 2014 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Incidence of invasive cancers following carcinoma in situ of the cervix.

PubMed Central

Levi, F.; Randimbison, L.; La Vecchia, C.; Franceschi, S.

1996-01-01

Women with carcinoma in situ (CIS) of the cervix uteri, notified to the population-based Cancer Registry of the Swiss Canton of Vaud between 1974 and 1993, were actively followed up to 31 December 1993 for the occurrence of subsequent invasive neoplasms. Among 2190 incident cases of CIS, followed for a total of 22,225 person-years, 95 metachronous cancers were observed vs 77.9 expected, corresponding to a significant standardised incidence ratio (SIR) of 1.2. Ten cases of invasive cervical cancer were observed vs 3.0 expected (SIR = 3.4, P < 0.01), the excess being larger in the first 10 years since CIS diagnosis. A total of 11 cases of four major tobacco-related sites (lung, mouth or pharynx, oesophagus and urinary bladder) were observed vs 5.1 expected, corresponding to a significant SIR of 2.2. The excess was observed > or = 10 years after CIS diagnosis. There was also an excess of non-melanomatous skin cancers (29 observed, 16.9 expected, SIR = 1.7; P < 0.01), but not of skin melanoma and of any of the other neoplasms considered, including breast and corpus uteri. This population-based study, therefore, finds an excess of invasive cervical cancer in the short term after CIS diagnosis, and a medium- to long-term excess risk of tobacco-related and non-melanomatous skin neoplasms. These findings are discussed in terms of increased surveillance and case ascertainment after CIS, and of potential shared risk factors (tobacco and/or viral infections). PMID:8883426

White matter microstructural alterations in clinically isolated syndrome and multiple sclerosis.

PubMed

Huang, Jing; Liu, Yaou; Zhao, Tengda; Shu, Ni; Duan, Yunyun; Ren, Zhuoqiong; Sun, Zheng; Liu, Zheng; Chen, Hai; Dong, Huiqing; Li, Kuncheng

2018-07-01

This study aims to determine whether and how diffusion alteration occurs in the earliest stage of multiple sclerosis (MS) and the differences in diffusion metrics between CIS and MS by using the tract-based spatial statistics (TBSS) method based on diffusion tensor imaging (DTI). Thirty-six CIS patients (mean age ± SD: 34.0 years ± 12.6), 36 relapsing-remitting multiple sclerosis (RRMS) patients (mean age ± SD: 35.0 years ± 9.4) and 36 age- and gender-matched normal controls (NCs) were included in this study. Voxel-wise analyses were performed with TBSS using multiple diffusion metrics, including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (λ 1 ) and radial diffusivity (λ 23 ). In the CIS patients, TBSS analyses revealed diffusion alterations in a few white matter (WM) regions including the anterior thalamic radiation, corticospinal tract, inferior fronto-occipital fasciculus, superior longitudinal fasciculus, body and splenium of the corpus callosum, internal capsule, external capsule, and cerebral peduncle. MS patients showed more widespread diffusion changes (decreased FA, increased λ 1 , λ 23 and MD) than CIS. Exploratory analyses also revealed the possible associations between WM diffusion metrics and clinical variables (Expanded Disability Status Scale and disease duration) in the patients. This study provided imaging evidence for DTI abnormalities in CIS and MS and suggested that DTI can improve our knowledge of the path physiology of CIS and MS and clinical progression. Copyright © 2018 Elsevier Ltd. All rights reserved.

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

PubMed

Curtis, Christina; Shah, Sohrab P; Chin, Suet-Feung; Turashvili, Gulisa; Rueda, Oscar M; Dunning, Mark J; Speed, Doug; Lynch, Andy G; Samarajiwa, Shamith; Yuan, Yinyin; Gräf, Stefan; Ha, Gavin; Haffari, Gholamreza; Bashashati, Ali; Russell, Roslin; McKinney, Steven; Langerød, Anita; Green, Andrew; Provenzano, Elena; Wishart, Gordon; Pinder, Sarah; Watson, Peter; Markowetz, Florian; Murphy, Leigh; Ellis, Ian; Purushotham, Arnie; Børresen-Dale, Anne-Lise; Brenton, James D; Tavaré, Simon; Caldas, Carlos; Aparicio, Samuel

2012-04-18

The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome.

Supplementation of increasing amounts of linseed oil to dairy cows fed total mixed rations: effects on digestion, ruminal fermentation characteristics, protozoal populations, and milk fatty acid composition.

PubMed

Benchaar, C; Romero-Pérez, G A; Chouinard, P Y; Hassanat, F; Eugene, M; Petit, H V; Côrtes, C

2012-08-01

The effect of linseed oil (LO) supplementation on nutrient digestibility, forage (i.e., timothy hay) in sacco ruminal degradation, ruminal fermentation characteristics, protozoal populations, milk production, and milk fatty acid (FA) profile in dairy cows was investigated. Four ruminally cannulated, primiparous lactating cows were used in a 4 × 4 Latin square design (28-d periods). They were fed a total mixed ration (50:50 forage:concentrate (F:C) ratio [dry matter (DM) basis] without supplementation (control, CTL), or supplemented (wt/wt; DM basis) with LO at 2, 3, or 4%. Supplementation with LO had no effect on DM intake (19 kg/d) and apparent total-tract digestibility of nutrients (organic matter, neutral detergent fiber, acid detergent fiber, starch, and gross energy). Ruminal pH, ammonia, and total volatile FA concentrations were not changed by LO supplementation to diets. Extent of changes in volatile FA pattern and effective ruminal degradability of DM of timothy hay were minor. Neither the total numbers nor the genera distribution of protozoa was changed by the addition of increasing amounts of LO to the diet. Milk yield increased linearly (26.1, 27.3, 27.4, and 28.4 kg/d for CTL to LO4, respectively) as the amount of LO added to the diet increased. Milk fat content was not affected by LO supplementation, whereas milk protein content decreased linearly with increasing amounts of LO in the diet. Milk fat proportions of several intermediates of ruminal biohydrogenation of polyunsaturated FA (i.e., trans-10 18:1, trans-11 18:1, cis-9,trans-11 18:2, trans-11,cis-15 18:2, and cis-9,trans-11,cis-15 18:3) increased linearly with LO addition to the diet. The proportion of cis-9,cis-12 18:2 decreased linearly (2.06, 1.99, 1.91, and 1.83% for CTL to LO4, respectively) as the amount of LO in the diet increased. Milk fat content of cis-9,cis-12,cis-15 18:3 increased as the level of LO in the diet increased up to 3% but no further increase was observed when 4% of LO was fed (0.33, 0.79, 0.86, and 0.86% for CTL to LO4, respectively). A similar quadratic response to LO supplementation was also observed for cis-5,cis-8,cis-11,cis-14,cis-17 20:5 and cis-5,cis-7,cis-10,cis-13,cis-16 22:5. The results of the present study show that LO can be safely supplemented up to 4% in forage-based diets of dairy cows to enrich milk with potential health beneficial FA (i.e., n-3 FA) without causing any detrimental effects on rumen function, digestion, and milk production. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

DNA unwinding produced by site-specific intrastrand cross-links of the antitumor drug cis-diamminedichloroplatinum(II)

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

Bellon, S.F.; Coleman, J.H.; Lippard, S.J.

The DNA unwinding produced by specific adducts of the antitumor drug cis-diamminedi-chloroplatinum(II) has been quantitatively determined. Synthetic DNA duplex oligonucleotides of varying lengths with two base pair cohesive ends were synthesized and characterized that contained site-specific intrastrand N7-purine/N7-purine cross-links. Included are cis-(Pt(NH{sub 3}){sub 2}(d(GpG))), cis-(Pt(NH){sub 3}{sub 2}(d(ApG))), and cis-(Pt(NH{sub 3}){sub 2}(d(GpTpG))) adducts, respectively referred to as cis-GG, cis-AG, and cis-GTG. Local DNA distortions at the site of platination were amplified by polymerization of these monomers and quantitatively evaluated by using polyacrylamide gel electrophoresis. The extent of DNA unwinding was determined by systematically varying the interplatinum distance, or phasing, in polymersmore » containing the adducts. The multimer that migrates most slowly gives the optimal phasing for cooperative bending, from which the degree of unwinding can be obtained. The authors find that the cis-GG and cis-AG adducts both unwind DNA by 13{degrees}, while the cis-GTG adduct unwinds DNA by 23{degrees}. In addition, experiments are presented that support previous studies revealing that a hinge joint forms at the sites of platination in DNA molecules containing trans-GTG adducts. On the basis of an analysis of the present and other published studies of site-specifically modified DNA. The authors propose that local duplex unwinding is a major determinant in the recognition of DNA damage by the Escherichia coli (A)BC excinuclease. In addition, local duplex unwinding of 13{degrees} and bending by 35{degrees} are shown to correlate well with the recognition of platinated DNA by a previously identified damage recognition protein (DRP) in human cells.« less

Novel green tissue-specific synthetic promoters and cis-regulatory elements in rice.

PubMed

Wang, Rui; Zhu, Menglin; Ye, Rongjian; Liu, Zuoxiong; Zhou, Fei; Chen, Hao; Lin, Yongjun

2015-12-11

As an important part of synthetic biology, synthetic promoter has gradually become a hotspot in current biology. The purposes of the present study were to synthesize green tissue-specific promoters and to discover green tissue-specific cis-elements. We first assembled several regulatory sequences related to tissue-specific expression in different combinations, aiming to obtain novel green tissue-specific synthetic promoters. GUS assays of the transgenic plants indicated 5 synthetic promoters showed green tissue-specific expression patterns and different expression efficiencies in various tissues. Subsequently, we scanned and counted the cis-elements in different tissue-specific promoters based on the plant cis-elements database PLACE and the rice cDNA microarray database CREP for green tissue-specific cis-element discovery, resulting in 10 potential cis-elements. The flanking sequence of one potential core element (GEAT) was predicted by bioinformatics. Then, the combination of GEAT and its flanking sequence was functionally identified with synthetic promoter. GUS assays of the transgenic plants proved its green tissue-specificity. Furthermore, the function of GEAT flanking sequence was analyzed in detail with site-directed mutagenesis. Our study provides an example for the synthesis of rice tissue-specific promoters and develops a feasible method for screening and functional identification of tissue-specific cis-elements with their flanking sequences at the genome-wide level in rice.

Flexible copper-indium-diselenide films and devices for space applications

NASA Technical Reports Server (NTRS)

Armstrong, J. H.; Pistole, C. O.; Misra, M. S.; Kapur, V. K.; Basol, B. M.

1991-01-01

With the ever increasing demands on space power systems, it is imperative that low cost, lightweight, reliable photovoltaics be developed. One avenue of pursuit for future space power applications is the use of low cost, lightweight flexible PV cells and arrays. Most work in this area assumes the use of flexible amorphous silicon (a-Si), despite its inherent instability and low efficiencies. However, polycrystalline thin film PV such as copper-indium-diselenide (CIS) are inherently more stable and exhibit better performance than a-Si. Furthermore, preliminary data indicate that CIS also offers exciting properties with respect to space applications. However, CIS has only heretofore only produced on rigid substrates. The implications of flexible CIS upon present and future space power platforms was explored. Results indicate that space qualified CIS can dramatically reduce the cost of PV, and in most cases, can be substituted for silicon (Si) based on end-of-life (EOL) estimations. Furthermore, where cost is a prime consideration, CIS can become cost effective than gallium arsenide (GaAs) in some applications. Second, investigations into thin film deposition on flexible substrates were made, and data from these tests indicate that fabrication of flexible CIS devices is feasible. Finally, data is also presented on preliminary TCO/CdS/CuInSe2/Mo devices.

Trust and Reputation Management for Critical Infrastructure Protection

NASA Astrophysics Data System (ADS)

Caldeira, Filipe; Monteiro, Edmundo; Simões, Paulo

Today's Critical Infrastructures (CI) depend of Information and Communication Technologies (ICT) to deliver their services with the required level of quality and availability. ICT security plays a major role in CI protection and risk prevention for single and also for interconnected CIs were cascading effects might occur because of the interdependencies that exist among different CIs. This paper addresses the problem of ICT security in interconnected CIs. Trust and reputation management using the Policy Based Management paradigm is the proposed solution to be applied at the CI interconnection points for information exchange. The proposed solution is being applied to the Security Mediation Gateway being developed in the European FP7 MICIE project, to allow for information exchange among interconnected CIs.

Designing CIS to improve decisions in depression disease management: a discourse analysis of front line practice.

PubMed

Mirel, Barbara; Ackerman, Mark S; Kerber, Kevin; Klinkman, Michael

2006-01-01

Clinical care management promises to help diminish the major health problem of depression. To realize this promise, front line clinicians must know which care management interventions are best for which patients and act accordingly. Unfortunately, the detailed intervention data required for such differentiated assessments are missing in most clinical information systems (CIS). To determine frontline clinicians' needs for these data and to identify the data that CIS should keep, we conducted an 18 month ethnographic study and discourse analysis of telehealth depression care management. Results show care managers need data-based evidence to choose best options, and discourse analysis suggests some personalized interventions that CIS should and can feasibly capture for evidence.

Influence of Hofmeister ions on the structure of proline-based peptide models: A combined experimental and molecular modeling study

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

Brohl, Andreas; Albrecht, Benjamin; Zhang, Yong

Here, the influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The anions preferentially interact with the cis conformers of the peptide models, which is rationalized by the respective electrostatic potential surfaces. These preferred interactions have a strong impact on the thermodynamics of the cis/trans equilibria, leading to a higher population of the cis conformers. In distinct cases, these equilibria are nearly independent of temperature, showing that the salts are alsomore » able to stabilize the conformers over wide temperature ranges.« less

Influence of Hofmeister Ions on the Structure of Proline-Based Peptide Models: A Combined Experimental and Molecular Modeling Study.

PubMed

Bröhl, Andreas; Albrecht, Benjamin; Zhang, Yong; Maginn, Edward; Giernoth, Ralf

2017-03-09

The influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The anions preferentially interact with the cis conformers of the peptide models, which is rationalized by the respective electrostatic potential surfaces. These preferred interactions have a strong impact on the thermodynamics of the cis/trans equilibria, leading to a higher population of the cis conformers. In distinct cases, these equilibria are nearly independent of temperature, showing that the salts are also able to stabilize the conformers over wide temperature ranges.

Influence of Hofmeister ions on the structure of proline-based peptide models: A combined experimental and molecular modeling study

DOE PAGES

Brohl, Andreas; Albrecht, Benjamin; Zhang, Yong; ...

2017-02-13

Here, the influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The anions preferentially interact with the cis conformers of the peptide models, which is rationalized by the respective electrostatic potential surfaces. These preferred interactions have a strong impact on the thermodynamics of the cis/trans equilibria, leading to a higher population of the cis conformers. In distinct cases, these equilibria are nearly independent of temperature, showing that the salts are alsomore » able to stabilize the conformers over wide temperature ranges.« less

Cis-regulatory Elements and Human Evolution

PubMed Central

Siepel, Adam

2014-01-01

Modification of gene regulation has long been considered an important force in human evolution, particularly through changes to cis-regulatory elements (CREs) that function in transcriptional regulation. For decades, however, the study of cis-regulatory evolution was severely limited by the available data. New data sets describing the locations of CREs and genetic variation within and between species have now made it possible to study CRE evolution much more directly on a genome-wide scale. Here, we review recent research on the evolution of CREs in humans based on large-scale genomic data sets. We consider inferences based on primate divergence, human polymorphism, and combinations of divergence and polymorphism. We then consider “new frontiers” in this field stemming from recent research on transcriptional regulation. PMID:25218861

CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data

PubMed Central

O'Connor, Timothy; Bodén, Mikael

2017-01-01

Abstract Identifying the genomic regions and regulatory factors that control the transcription of genes is an important, unsolved problem. The current method of choice predicts transcription factor (TF) binding sites using chromatin immunoprecipitation followed by sequencing (ChIP-seq), and then links the binding sites to putative target genes solely on the basis of the genomic distance between them. Evidence from chromatin conformation capture experiments shows that this approach is inadequate due to long-distance regulation via chromatin looping. We present CisMapper, which predicts the regulatory targets of a TF using the correlation between a histone mark at the TF's bound sites and the expression of each gene across a panel of tissues. Using both chromatin conformation capture and differential expression data, we show that CisMapper is more accurate at predicting the target genes of a TF than the distance-based approaches currently used, and is particularly advantageous for predicting the long-range regulatory interactions typical of tissue-specific gene expression. CisMapper also predicts which TF binding sites regulate a given gene more accurately than using genomic distance. Unlike distance-based methods, CisMapper can predict which transcription start site of a gene is regulated by a particular binding site of the TF. PMID:28204599

A CMOS-based large-area high-resolution imaging system for high-energy x-ray applications

NASA Astrophysics Data System (ADS)

Rodricks, Brian; Fowler, Boyd; Liu, Chiao; Lowes, John; Haeffner, Dean; Lienert, Ulrich; Almer, John

2008-08-01

CCDs have been the primary sensor in imaging systems for x-ray diffraction and imaging applications in recent years. CCDs have met the fundamental requirements of low noise, high-sensitivity, high dynamic range and spatial resolution necessary for these scientific applications. State-of-the-art CMOS image sensor (CIS) technology has experienced dramatic improvements recently and their performance is rivaling or surpassing that of most CCDs. The advancement of CIS technology is at an ever-accelerating pace and is driven by the multi-billion dollar consumer market. There are several advantages of CIS over traditional CCDs and other solid-state imaging devices; they include low power, high-speed operation, system-on-chip integration and lower manufacturing costs. The combination of superior imaging performance and system advantages makes CIS a good candidate for high-sensitivity imaging system development. This paper will describe a 1344 x 1212 CIS imaging system with a 19.5μm pitch optimized for x-ray scattering studies at high-energies. Fundamental metrics of linearity, dynamic range, spatial resolution, conversion gain, sensitivity are estimated. The Detective Quantum Efficiency (DQE) is also estimated. Representative x-ray diffraction images are presented. Diffraction images are compared against a CCD-based imaging system.

The human oxytocin gene promoter is regulated by estrogens.

PubMed

Richard, S; Zingg, H H

1990-04-15

Gonadal steroids affect brain function primarily by altering the expression of specific genes, yet the specific mechanisms by which neuronal target genes undergo such regulation are unknown. Recent evidence suggests that the expression of the neuropeptide gene for oxytocin (OT) is modulated by estrogens. We therefore examined the possibility that this regulation occurred via a direct interaction of the estrogen-receptor complex with cis-acting elements flanking the OT gene. DNA-mediated gene transfer experiments were performed using Neuro-2a neuroblastoma cells and chimeric plasmids containing portions of the human OT gene 5'-glanking region linked to the chloramphenicol acetyltransferase gene. We identified a 19-base pair region located at -164 to -146 upstream of the transcription start site which is capable of conferring estrogen responsiveness to the homologous as well as to a heterologous promoter. The hormonal response is strictly dependent on the presence of intracellular estrogen receptors, since estrogen induced stimulation occurred only in Neuro-2a cells co-transfected with an expression vector for the human estrogen receptor. The identified region contains a novel imperfect palindrome (GGTGACCTTGACC) with sequence similarity to other estrogen response elements (EREs). To define cis-acting elements that function in synergism with the ERE, sequences 3' to the ERE were deleted, including the CCAAT box, two additional motifs corresponding to the right half of the ERE palindrome (TGACC), as well as a CTGCTAA heptamer similar to the "elegans box" found in Caenorhabditis elegans. Interestingly, optimal function of the identified ERE was fully independent of these elements and only required a short promoter region (-49 to +36). Our studies define a molecular mechanism by which estrogens can directly modulate OT gene expression. However, only a subset of OT neurons are capable of binding estrogens, therefore, direct action of estrogens on the OT gene may be restricted to a subpopulation of OT neurons.

Apollo 8 Commander Frank Borman Receives Presidential Call

NASA Technical Reports Server (NTRS)

1968-01-01

Apollo 8 Astronaut Frank Borman, commander of the first manned Saturn V space flight into Lunar orbit, accepted a phone call from the U.S. President Lyndon B. Johnson prior to launch. Borman, along with astronauts William Anders, Lunar Module (LM) pilot, and James Lovell, Command Module (CM) pilot, launched aboard the Apollo 8 mission on December 21, 1968 and returned safely to Earth on December 27, 1968. The mission achieved operational experience and tested the Apollo command module systems, including communications, tracking, and life-support, in cis-lunar space and lunar orbit, and allowed evaluation of crew performance on a lunar orbiting mission. The crew photographed the lunar surface, both far side and near side, obtaining information on topography and landmarks as well as other scientific information necessary for future Apollo landings. All systems operated within allowable parameters and all objectives of the mission were achieved.

Apollo 8 Astronaut Anders Suits Up For Countdown Demonstration Test

NASA Technical Reports Server (NTRS)

1968-01-01

Apollo 8 astronaut William Anders, Lunar Module (LM) pilot, is suited up for the Apollo 8 mission countdown demonstration test. The first manned Apollo mission launched aboard the Saturn V and first manned Apollo craft to enter lunar orbit, the SA-503, Apollo 8 mission lift off occurred on December 21, 1968 and returned safely to Earth on December 27, 1968. Aboard were Anders and fellow astronauts James Lovell, Command Module (CM) pilot; and Frank Borman, commander. The mission achieved operational experience and tested the Apollo command module systems, including communications, tracking, and life-support, in cis-lunar space and lunar orbit, and allowed evaluation of crew performance on a lunar orbiting mission. The crew photographed the lunar surface, both far side and near side, obtaining information on topography and landmarks as well as other scientific information necessary for future Apollo landings. All systems operated within allowable parameters and all objectives of the mission were achieved.

Apollo 8 Astronaut James Lovell On Phone With President Johnson

NASA Technical Reports Server (NTRS)

1968-01-01

Apollo 8 Astronaut James Lovell, Command Module (CM) pilot of the first manned Saturn V space flight into Lunar orbit, accepted a phone call from the U.S. President Lyndon B. Johnson prior to launch. Lovell, along with astronauts William Anders, Lunar Module (LM) pilot, and Frank Borman, commander, launched aboard the Apollo 8 mission on December 21, 1968 and returned safely to Earth on December 27, 1968. The mission achieved operational experience and tested the Apollo command module systems, including communications, tracking, and life-support, in cis-lunar space and lunar orbit, and allowed evaluation of crew performance on a lunar orbiting mission. The crew photographed the lunar surface, both far side and near side, obtaining information on topography and landmarks as well as other scientific information necessary for future Apollo landings. All systems operated within allowable parameters and all objectives of the mission were achieved.

Apollo 8 Astronaut William Anders On Phone With President Johnson

NASA Technical Reports Server (NTRS)

1968-01-01

Apollo 8 Astronaut William Anders, Lunar Module (LM) pilot of the first manned Saturn V space flight into Lunar orbit, accepted a phone call from the U.S. President Lyndon B. Johnson prior to launch. Anders, along with astronauts James Lovell, Command Module (CM) pilot, and Frank Borman, commander, launched aboard the Apollo 8 mission on December 21, 1968 and returned safely to Earth on December 27, 1968. The mission achieved operational experience and tested the Apollo command module systems, including communications, tracking, and life-support, in cis-lunar space and lunar orbit, and allowed evaluation of crew performance on a lunar orbiting mission. The crew photographed the lunar surface, both far side and near side, obtaining information on topography and landmarks as well as other scientific information necessary for future Apollo landings. All systems operated within allowable parameters and all objectives of the mission were achieved.

Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin

PubMed Central

Rognoni, Lorenz; Möst, Tobias; Žoldák, Gabriel; Rief, Matthias

2014-01-01

Proline switches, controlled by cis–trans isomerization, have emerged as a particularly effective regulatory mechanism in a wide range of biological processes. In this study, we use single-molecule mechanical measurements to develop a full kinetic and energetic description of a highly conserved proline switch in the force-sensing domain 20 of human filamin and how prolyl isomerization modulates the force-sensing mechanism. Proline isomerization toggles domain 20 between two conformations. A stable cis conformation with slow unfolding, favoring the autoinhibited closed conformation of filamin’s force-sensing domain pair 20–21, and a less stable, uninhibited conformation promoted by the trans form. The data provide detailed insight into the folding mechanisms that underpin the functionality of this binary switch and elucidate its remarkable efficiency in modulating force-sensing, thus combining two previously unconnected regulatory mechanisms, proline switches and mechanosensing. PMID:24706888

A combination strategy for enhancing linkage to and retention in HIV care among adults newly diagnosed with HIV in Mozambique: study protocol for a site-randomized implementation science study.

PubMed

Elul, Batya; Lahuerta, Maria; Abacassamo, Fatima; Lamb, Matthew R; Ahoua, Laurence; McNairy, Margaret L; Tomo, Maria; Horowitz, Deborah; Sutton, Roberta; Mussa, Antonio; Gurr, Danielle; Jani, Ilesh

2014-10-15

Despite the extraordinary scale up of HIV prevention, care and treatment services in sub-Saharan Africa (SSA) over the past decade, the overall effectiveness of HIV programs has been significantly hindered by high levels of attrition across the HIV care continuum. Data from "real-life" settings are needed on the effectiveness of an easy to deliver package of services that can improve overall performance of the HIV care continuum. We are conducting an implementation science study using a two-arm cluster site-randomized design to determine the effectiveness of a combination intervention strategy (CIS) using feasible, evidence-based, and practical interventions-including (1) point-of-care (POC) CD4 count testing, (2) accelerated antiretroviral therapy initiation for eligible individuals, and (3) SMS reminders for linkage to and retention in care-as compared to the standard of care (SOC) in Mozambique in improving linkage and retention among adults following HIV diagnosis. A pre-post intervention two-sample design is nested within the CIS arm to assess the incremental effectiveness of the CIS plus financial incentives (CIS + FI) compared to the CIS without FI on study outcomes. Randomization is done at the level of the study site, defined as a primary health facility. Five sites are included from the City of Maputo and five from Inhambane Province. Target enrollment is a total of 2,250 adults: 750 in the SOC arm, 750 in the CIS cohort of the intervention arm and 750 in the CIS + FI cohort of the intervention arm (average of 150 participants per site). Participants are followed for 12 months from time of HIV testing to ascertain a combined endpoint of linkage to care within 1 month after testing and retention in care 12 months from HIV test. Cost-effectiveness analyses of CIS compared to SOC and CIS + FI compared to CIS will also be conducted. Study findings will provide evidence on the effectiveness of a CIS and the incremental effectiveness of a CIS + FI in a "real-life" service delivery system in a SSA country severely impacted by HIV. Clinicaltrials.gov, NCT01930084.

Lovastatin prevents cisplatin-induced activation of pro-apoptotic DNA damage response (DDR) of renal tubular epithelial cells

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

Krüger, Katharina; Ziegler, Verena; Hartmann, Christina

The platinating agent cisplatin (CisPt) is commonly used in the therapy of various types of solid tumors. The anticancer efficacy of CisPt largely depends on the formation of bivalent DNA intrastrand crosslinks, which stimulate mechanisms of the DNA damage response (DDR), thereby triggering checkpoint activation, gene expression and cell death. The clinically most relevant adverse effect associated with CisPt treatment is nephrotoxicity that results from damage to renal tubular epithelial cells. Here, we addressed the question whether the HMG-CoA-reductase inhibitor lovastatin affects the DDR of renal cells by employing rat renal proximal tubular epithelial (NRK-52E) cells as in vitro model.more » The data show that lovastatin has extensive inhibitory effects on CisPt-stimulated DDR of NRK-52E cells as reflected on the levels of phosphorylated ATM, Chk1, Chk2, p53 and Kap1. Mitigation of CisPt-induced DDR by lovastatin was independent of the formation of DNA damage as demonstrated by (i) the analysis of Pt-(GpG) intrastrand crosslink formation by Southwestern blot analyses and (ii) the generation of DNA strand breaks as analyzed on the level of nuclear γH2AX foci and employing the alkaline comet assay. Lovastatin protected NRK-52E cells from the cytotoxicity of high CisPt doses as shown by measuring cell viability, cellular impedance and flow cytometry-based analyses of cell death. Importantly, the statin also reduced the level of kidney DNA damage and apoptosis triggered by CisPt treatment of mice. The data show that the lipid-lowering drug lovastatin extensively counteracts pro-apoptotic signal mechanisms of the DDR of tubular epithelial cells following CisPt injury. - Highlights: • Lovastatin blocks ATM/ATR-regulated DDR of tubular cells following CisPt treatment. • Lovastatin attenuates CisPt-induced activation of protein kinase ATM in vitro. • Statin-mediated DDR inhibition is independent of initial DNA damage formation. • Statin-mediated blockage of CisPt-triggered DDR leads to cytoprotection. • Lovastatin attenuates CisPt-induced kidney DNA damage and apoptosis in vivo.« less

Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework.

PubMed

Maeso, Ignacio; Tena, Juan J

2016-09-01

Cis-regulatory changes are arguably the primary evolutionary source of animal morphological diversity. With the recent explosion of genome-wide comparisons of the cis-regulatory content in different animal species is now possible to infer general principles underlying enhancer evolution. However, these studies have also revealed numerous discrepancies and paradoxes, suggesting that the mechanistic causes and modes of cis-regulatory evolution are still not well understood and are probably much more complex than generally appreciated. Here, we argue that the mutational mechanisms and genomic regions generating new regulatory activities must comply with the constraints imposed by the molecular properties of cis-regulatory elements (CREs) and the organizational features of long-range chromatin interactions. Accordingly, we propose a new integrative evolutionary framework for cis-regulatory evolution based on two major premises for the origin of novel enhancer activity: (i) an accessible chromatin environment and (ii) compatibility with the 3D structure and interactions of pre-existing CREs. Mechanisms and DNA sequences not fulfilling these premises, will be less likely to have a measurable impact on gene expression and as such, will have a minor contribution to the evolution of gene regulation. Finally, we discuss current comparative cis-regulatory data under the light of this new evolutionary model, and propose that the two most prominent mechanisms for the evolution of cis-regulatory changes are the overprinting of ancestral CREs and the exaptation of transposable elements. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sad and happy emotion discrimination in music by children with cochlear implants.

PubMed

Hopyan, Talar; Manno, Francis A M; Papsin, Blake C; Gordon, Karen A

2016-01-01

Children using cochlear implants (CIs) develop speech perception but have difficulty perceiving complex acoustic signals. Mode and tempo are the two components used to recognize emotion in music. Based on CI limitations, we hypothesized children using CIs would have impaired perception of mode cues relative to their normal hearing peers and would rely more heavily on tempo cues to distinguish happy from sad music. Study participants were children with 13 right CIs and 3 left CIs (M = 12.7, SD = 2.6 years) and 16 normal hearing peers. Participants judged 96 brief piano excerpts from the classical genre as happy or sad in a forced-choice task. Music was randomly presented with alterations of transposed mode, tempo, or both. When music was presented in original form, children using CIs discriminated between happy and sad music with accuracy well above chance levels (87.5%) but significantly below those with normal hearing (98%). The CI group primarily used tempo cues, whereas normal hearing children relied more on mode cues. Transposing both mode and tempo cues in the same musical excerpt obliterated cues to emotion for both groups. Children using CIs showed significantly slower response times across all conditions. Children using CIs use tempo cues to discriminate happy versus sad music reflecting a very different hearing strategy than their normal hearing peers. Slower reaction times by children using CIs indicate that they found the task more difficult and support the possibility that they require different strategies to process emotion in music than normal.

Dropout Risk Factors and Exemplary Programs: A Technical Report

ERIC Educational Resources Information Center

Hammond, Cathy; Linton, Dan; Smink, Jay; Drew, Sam

2007-01-01

Communities In Schools (CIS) is the nation's fifth-largest youth-serving organization and the leading dropout prevention organization, delivering resources to nearly one million students in 3,250 schools across the country. To further their network-wide commitment to evidence-based practice, CIS collaborated with the National Dropout Prevention…

Lmx1b-targeted cis-regulatory modules involved in limb dorsalization.

PubMed

Haro, Endika; Watson, Billy A; Feenstra, Jennifer M; Tegeler, Luke; Pira, Charmaine U; Mohan, Subburaman; Oberg, Kerby C

2017-06-01

Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct gene targets in the limb have been confirmed. To determine direct targets, we performed a chromatin immunoprecipitation against Lmx1b in mouse limbs at embryonic day 12.5 followed by next-generation sequencing (ChIP-seq). Nearly 84% ( n =617) of the Lmx1b-bound genomic intervals (LBIs) identified overlap with chromatin regulatory marks indicative of potential cis -regulatory modules (PCRMs). In addition, 73 LBIs mapped to CRMs that are known to be active during limb development. We compared Lmx1b-bound PCRMs with genes regulated by Lmx1b and found 292 PCRMs within 1 Mb of 254 Lmx1b-regulated genes. Gene ontological analysis suggests that Lmx1b targets extracellular matrix production, bone/joint formation, axonal guidance, vascular development, cell proliferation and cell movement. We validated the functional activity of a PCRM associated with joint-related Gdf5 that provides a mechanism for Lmx1b-mediated joint modification and a PCRM associated with Lmx1b that suggests a role in autoregulation. This is the first report to describe genome-wide Lmx1b binding during limb development, directly linking Lmx1b to targets that accomplish limb dorsalization. © 2017. Published by The Company of Biologists Ltd.

Mapping cis- and trans-regulatory effects across multiple tissues in twins

PubMed Central

Grundberg, Elin; Small, Kerrin S.; Hedman, Åsa K.; Nica, Alexandra C.; Buil, Alfonso; Keildson, Sarah; Bell, Jordana T.; Yang, Tsun-Po; Meduri, Eshwar; Barrett, Amy; Nisbett, James; Sekowska, Magdalena; Wilk, Alicja; Shin, So-Youn; Glass, Daniel; Travers, Mary; Min, Josine L.; Ring, Sue; Ho, Karen; Thorleifsson, Gudmar; Kong, Augustine; Thorsteindottir, Unnur; Ainali, Chrysanthi; Dimas, Antigone S.; Hassanali, Neelam; Ingle, Catherine; Knowles, David; Krestyaninova, Maria; Lowe, Christopher E.; Di Meglio, Paola; Montgomery, Stephen B.; Parts, Leopold; Potter, Simon; Surdulescu, Gabriela; Tsaprouni, Loukia; Tsoka, Sophia; Bataille, Veronique; Durbin, Richard; Nestle, Frank O.; O’Rahilly, Stephen; Soranzo, Nicole; Lindgren, Cecilia M.; Zondervan, Krina T.; Ahmadi, Kourosh R.; Schadt, Eric E.; Stefansson, Kari; Smith, George Davey; McCarthy, Mark I.; Deloukas, Panos; Dermitzakis, Emmanouil T.; Spector, Tim D.

2013-01-01

Sequence-based variation in gene expression is a key driver of disease risk. Common variants regulating expression in cis have been mapped in many eQTL studies typically in single tissues from unrelated individuals. Here, we present a comprehensive analysis of gene expression across multiple tissues conducted in a large set of mono- and dizygotic twins that allows systematic dissection of genetic (cis and trans) and non-genetic effects on gene expression. Using identity-by-descent estimates, we show that at least 40% of the total heritable cis-effect on expression cannot be accounted for by common cis-variants, a finding which exposes the contribution of low frequency and rare regulatory variants with respect to both transcriptional regulation and complex trait susceptibility. We show that a substantial proportion of gene expression heritability is trans to the structural gene and identify several replicating trans-variants which act predominantly in a tissue-restricted manner and may regulate the transcription of many genes. PMID:22941192

NASA Human Spaceflight Architecture Team Cis-Lunar Analysis

NASA Technical Reports Server (NTRS)

Lupisella, M.; Bobskill, M. R.

2012-01-01

The Cis-Lunar Destination Team of NASA's Human Spaceflight Architecture Teait1 (HAT) has been perfom1ing analyses of a number of cis-lunar locations to infom1 architecture development, transportation and destination elements definition, and operations. The cis-lunar domain is defined as that area of deep space under the gravitation influence of the earth-moon system, including a set of orbital locations (low earth orbit (LEO]. geosynchronous earth orbit [GEO]. highly elliptical orbits [HEO]); earth-moon libration or "Lagrange·· points (EMLl through EMLS, and in particular, EMLI and EML2), and low lunar orbit (LLO). We developed a set of cis-lunar mission concepts defined by mission duration, pre-deployment, type of mission, and location, to develop mission concepts and the associated activities, capabilities, and architecture implications. To date, we have produced two destination operations J concepts based on present human space exploration architectural considerations. We have recently begun defining mission activities that could be conducted within an EM LI or EM L2 facility.

NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

PubMed

Wiedemann, Christoph; Ohlenschläger, Oliver; Mrestani-Klaus, Carmen; Bordusa, Frank

2017-09-13

NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual 1 H and 13 C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.

Utilization of surface differences to improve dyeing properties of poly( m-phenylene isophthalamide) membranes

NASA Astrophysics Data System (ADS)

Ouyang, Shenshen; Wang, Tao; Zhong, Longgang; Wang, Shunli; Wang, Sheng

2018-06-01

Bulk poly( m-phenylene isophthalamide) (PMIA) can achieve flexibility upon dissolution by a LiCl/dimethylacetamide co-solvent, but remains hydrophobic despite the occasional emergence of cis amide groups providing a weak negative charge. In this study, based on the significant surface differences between PMIA membranes processed by nanofiber electrospinning and casting, a series of chemical analyses, in-situ Au nanoparticle depositions, and dye-adsorption experiments revealed that more cis-configuration amide groups appeared on the surface of the electrospun PMIA membrane than on that of the cast membrane. Based on this surface difference, a strategy was proposed to improve the dyeing properties of PMIA by reversibly changing the cis/trans configurations of electrospun and cast membranes. The reversible chain-segment switch mechanism is a novel method for tuning the macroscale properties of polymer materials based on inherent molecular characteristics.

Utilization of surface differences to improve dyeing properties of poly(m-phenylene isophthalamide) membranes

NASA Astrophysics Data System (ADS)

Ouyang, Shenshen; Wang, Tao; Zhong, Longgang; Wang, Shunli; Wang, Sheng

2018-05-01

Bulk poly(m-phenylene isophthalamide) (PMIA) can achieve flexibility upon dissolution by a LiCl/dimethylacetamide co-solvent, but remains hydrophobic despite the occasional emergence of cis amide groups providing a weak negative charge. In this study, based on the significant surface differences between PMIA membranes processed by nanofiber electrospinning and casting, a series of chemical analyses, in-situ Au nanoparticle depositions, and dye-adsorption experiments revealed that more cis-configuration amide groups appeared on the surface of the electrospun PMIA membrane than on that of the cast membrane. Based on this surface difference, a strategy was proposed to improve the dyeing properties of PMIA by reversibly changing the cis/trans configurations of electrospun and cast membranes. The reversible chain-segment switch mechanism is a novel method for tuning the macroscale properties of polymer materials based on inherent molecular characteristics.

Retinoid Binding Properties of Nucleotide Binding Domain 1 of the Stargardt Disease-associated ATP Binding Cassette (ABC) Transporter, ABCA4*

PubMed Central

Biswas-Fiss, Esther E.; Affet, Stephanie; Ha, Malissa; Biswas, Subhasis B.

2012-01-01

The retina-specific ATP binding cassette transporter, ABCA4 protein, is associated with a broad range of inherited macular degenerations, including Stargardt disease, autosomal recessive cone rod dystrophy, and fundus flavimaculatus. In order to understand its role in retinal transport in rod out segment discs, we have investigated the interactions of the soluble domains of ABCA4 with both 11-cis- and all-trans-retinal. Using fluorescence anisotropy-based binding analysis and recombinant polypeptides derived from the amino acid sequences of the four soluble domains of ABCA4, we demonstrated that the nucleotide binding domain 1 (NBD1) specifically bound 11-cis-retinal. Its affinity for all-trans-retinal was markedly reduced. Stargardt disease-associated mutations in this domain resulted in attenuation of 11-cis-retinal binding. Significant differences in 11-cis-retinal binding affinities were observed between NBD1 and other cytoplasmic and lumenal domains of ABCA4. The results suggest a possible role of ABCA4 and, in particular, the NBD1 domain in 11-cis-retinal binding. These results also correlate well with a recent report on the in vivo role of ABCA4 in 11-cis-retinal transport. PMID:23144455

Detection of trans–cis flips and peptide-plane flips in protein structures

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

Touw, Wouter G., E-mail: wouter.touw@radboudumc.nl; Joosten, Robbie P.; Vriend, Gert, E-mail: wouter.touw@radboudumc.nl

A method is presented to detect peptide bonds that need either a trans–cis flip or a peptide-plane flip. A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans–cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans–cis flips and many thousands of hitherto unknown peptide-plane flips. A few examples are highlighted for which a correction of the peptide-plane geometry leads to a correction of the understanding of the structure–function relation. All data, including 1088 manually validated cases, are freely availablemore » and the method is available from a web server, a web-service interface and through WHAT-CHECK.« less

Laboratory and scaled up evaluation of cis-permethrin applied as a new ultra low volume formulation against Aedes aegypti (Diptera: Culicidae).

PubMed

Seccacini, Emilia; Masuh, Héctor; Licastro, Susana A; Zerba, Eduardo Nicolás

2006-01-01

Ultra low volume (ULV) aerial spraying is a common methodology for spatial treatments for Aedes aegypti (L.) control. Previous studies from our laboratory indicated that the cis isomer of permethrin has an excellent efficacy for vector control, in particular for Triatoma infestans. It was of interest to determine the efficacy of this pure isomer in a ULV water-based formulation for adult A. aegypti control, since both vectors usually are found together in South America. A method is presented to make a quick measure at laboratory level of the knock down effect (KT50) of a new EC water-based formulation of cis-permethrin, in a small Peet Grady chamber of 0.34 m3, with a specially designed glass sprayer. A deltamethrin standard ULV formulation "CISLIN" was used for comparison. cis-Permethrin showed a significantly lower KT50 value than deltamethrin (7.50 and 9.65 min, respectively). When the mosquitoes were introduced into the chamber 10 min after spraying KT50 values were almost equal (15.59 and 15.88 min, respectively). In scaled up bioassays the ULV formulation of cis-permethrin showed 100% mortality of A. aegypti adult mosquitoes at the beginning of the treatment (t=0) and some mortality at 1h post treatment of freshly introduced mosquitoes. It was concluded that cis-permethrin could be an excellent tool for control of A. aegypti and other vectors of medical importance, with fewer side effects and better cost-effectiveness than with the cyanopyrethroids.

Major histocompatibility complex class I molecules modulate embryonic neuritogenesis and neuronal polarization

PubMed Central

Bilousova, Tina; Dang, Hoa; Xu, Willem; Gustafson, Sarah; Jin, Yingli; Wickramasinghe, Lalinda; Won, Tony; Bobarnac, Gabriela; Middleton, Blake; Tian, Jide; Kaufman, Daniel L.

2012-01-01

We studied cultured hippocampal neurons from embryonic wildtype, major histocompatibility complex class I (MHCI) heavy chain-deficient (KbDb−/−) and NSE-Db (which have elevated neuronal MHCI expression) C57BL/6 mice. KbDb−/− neurons displayed slower neuritogenesis and establishment of polarity, while NSE-Db neurons had faster neurite outgrowth, more primary neurites, and tended to have accelerated polarization. Additional studies with ϐ2M−/− neurons, exogenous ϐ2M, and a self-MHCI monomer suggest that free heavy chain cis interactions with other surface molecules can promote neuritogenesis while tripartite MHCI interactions with classical MHCI receptors can inhibit axon outgrowth. Together with the results of others, MHCI appears to differentially modulate neuritogenesis and synaptogenesis. PMID:22503373

Enhanced Photovoltaic Performances of Dye-Sensitized Solar Cells by Co-Sensitization of Benzothiadiazole and Squaraine-Based Dyes.

PubMed

Islam, Ashraful; Akhtaruzzaman, Md; Chowdhury, Towhid H; Qin, Chuanjiang; Han, Liyuan; Bedja, Idriss M; Stalder, Romain; Schanze, Kirk S; Reynolds, John R

2016-02-01

Dye-sensitized solar cells (DSSCs) based on a donor-acceptor-donor oligothienylene dye containing benzothiadiazole (T4BTD-A) were cosensitized with dyes containing cis-configured squaraine rings (HSQ3 and HSQ4). The cosensitized dyes showed incident monochromatic photon-to-current conversion efficiency (IPCE) greater than 70% in the 300-850 nm wavelength region. The individual overall conversion efficiencies of the sensitizers T4BTD-A, HSQ3, and HSQ4 were 6.4%, 4.8%, and 5.8%, respectively. Improved power conversion efficiencies of 7.0% and 7.7% were observed when T4BTD-A was cosensitized with HSQ3 and HSQ4, respectively, thanks to a significant increase in current density (JSC) for the cosensitized DSSCs. Intensity-modulated photovoltage spectroscopy results showed a longer lifetime for cosensitized T4BTD-A+HSQ3 and T4BTD-A+HSQ4 compared to that of HSQ3 and HSQ4, respectively.

Cloning and characterization of two 9-cis-epoxycarotenoid dioxygenase genes, differentially regulated during fruit maturation and under stress conditions, from orange (Citrus sinensis L. Osbeck).

PubMed

Rodrigo, María-Jesús; Alquezar, Berta; Zacarías, Lorenzo

2006-01-01

There is now biochemical and genetic evidence that oxidative cleavage of cis-epoxycarotenoids by 9-cis-epoxycarotenoid dioxygenase (NCED) is the critical step in the regulation of abscisic acid (ABA) synthesis in higher plants. The peel of Citrus fruit accumulates large amounts of ABA during maturation. To understand the regulation of ABA biosynthesis in Citrus, two full-length cDNAs (CsNCED1 and CsNCED2) encoding NCEDs were isolated and characterized from the epicarp of orange fruits (Citrus sinensis L. Osbeck). Expression of the CsNCED1 gene increased in the epicarp during natural and ethylene-induced fruit maturation, and in water-stressed leaves, in a pattern consistent with the accumulation of ABA. The second gene, CsNCED2, was not detected in dehydrated leaves and, in fruits, exhibited a differential expression to that of CsNCED1. Taken together, these results suggests that CsNCED1 is likely to play a primary role in the biosynthesis of ABA in both leaves and fruits, while CsNCED2 appears to play a subsidiary role restricted to chromoplast-containing tissue. Furthermore, analysis of 9-cis-violaxanthin and 9'-cis-neoxanthin, as the two possible substrates for NCEDs, revealed that the former was the main carotenoid in the outer coloured part of the fruit peel as the fruit ripened or after ethylene treatment, whereas 9'-cis-neoxanthin was not detected or was in trace amounts. By contrast, turgid and dehydrated leaves contained 9'-cis-neoxanthin but 9-cis-violaxanthin was absent. Based on these results, it is suggested that 9-cis-violaxanthin may be the predominant substrate for NCED in the peel of Citrus fruits, whereas 9'-cis-neoxanthin would be the precursor of ABA in photosynthetic tissues.

Potential for Microbial Degradation of cis-Dichloroethene and Vinyl Chloride in Streambed Sediment at the U.S. Department of Energy, Kansas City Plant, Missouri, 2008

USGS Publications Warehouse

Bradley, Paul M.

2009-01-01

A series of carbon-14 (14C) radiotracer-based microcosm experiments was conducted to assess the mechanisms and products of degradation of cis-dichloroethene (cis-DCE) and vinyl chloride (VC) in streambed sediments at the U.S. Department of Energy, Kansas City Plant in Kansas City, Missouri. The focus of the investigation was the potential for biotic and abiotic cis-DCE and VC degradation in surficial and underlying hyporheic sediment from the Blue River and its tributaries, Indian Creek and Boone Creek. Substantial degradation of [1,2-14C] cis-DCE and [1,2-14C] VC to 14C-carbon dioxide (14CO2) was observed in all viable surficial sediment microcosms prepared under oxic conditions. No significant accumulation of reductive dechlorination products was observed under these oxic incubation conditions. The results indicate that microbial mineralization processes involving direct oxidation or co-metabolic oxidation are the primary mechanisms of cis-DCE and VC biodegradation in oxic stream sediment at the Kansas City Plant. Substantial mineralization of [1,2-14C] VC also was observed in all viable surficial sediment microcosms incubated in the absence of detectable oxygen (dissolved oxygen concentrations less than 25 micrograms per liter). In general, the accumulation of mineralization products (14CO2 and 14C-methane [14CH4]) predominated with only trace-level detection of the reductive dechlorination product, 14C-ethene. In contrast, microbial degradation of [1,2-14C] cis-DCE by reductive dechlorination or mineralization was not significant in the absence of detectable oxygen. The potential for [1,2-14C] VC biodegradation also was significant in sediments from the deeper hyporheic zones under oxic conditions and in the absence of detectable oxygen. In this study, microbial degradation of [1,2-14C] cis-DCE was not significant in hyporheic sediment treatments under either oxygen condition. Taken together, the results indicate that microbial mineralization processes in streambed sediments at the Kansas City Plant can be an important component of cis-DCE and VC degradation under oxic conditions and of VC degradation even in the absence of detectable oxygen. These results demonstrate that an evaluation of the efficiency of in situ cis-DCE and VC biodegradation in streambed sediments, based solely on observed accumulations of reduced daughter products, may underestimate substantially the total extent of contaminant biodegradation and, thus, the potential importance of the hyporheic zone and streambed sediments as barriers to the discharge of contaminated groundwater.

RNA-mediated regulation in Gram-positive pathogens: an overview punctuated with examples from the group A Streptococcus

PubMed Central

Miller, Eric W.; Cao, Tram N.; Pflughoeft, Kathryn J.; Sumby, Paul

2014-01-01

RNA-based mechanisms of regulation represent a ubiquitous class of regulators that are associated with diverse processes including nutrient sensing, stress response, modulation of horizontal gene transfer, and virulence factor expression. While better studied in Gram-negative bacteria, the literature is replete with examples of the importance of RNA-mediated regulatory mechanisms to the virulence and fitness of Gram-positives. Regulatory RNAs are classified as cis-acting, e.g. riboswitches, which modulate the transcription, translation, or stability of co-transcribed RNA, or trans-acting, e.g. small regulatory RNAs, which target separate mRNAs or proteins. The group A Streptococcus (GAS, Streptococcus pyogenes) is a Gram-positive bacterial pathogen from which several regulatory RNA mechanisms have been characterized. The study of RNA-mediated regulation in GAS has uncovered novel concepts with respect to how small regulatory RNAs may positively regulate target mRNA stability, and to how CRISPR RNAs are processed from longer precursors. This review provides an overview of RNA-mediated regulation in Gram-positive bacteria, and is highlighted with specific examples from GAS research. The key roles that these systems play in regulating bacterial virulence are discussed and future perspectives outlined. PMID:25091277

Patterns of usage for a Web-based clinical information system.

PubMed

Chen, Elizabeth S; Cimino, James J

2004-01-01

Understanding how clinicians are using clinical information systems to assist with their everyday tasks is valuable to the system design and development process. Developers of such systems are interested in monitoring usage in order to make enhancements. System log files are rich resources for gaining knowledge about how the system is being used. We have analyzed the log files of our Web-based clinical information system (WebCIS) to obtain various usage statistics including which WebCIS features are frequently being used. We have also identified usage patterns, which convey how the user is traversing the system. We present our method and these results as well as describe how the results can be used to customize menus, shortcut lists, and patient reports in WebCIS and similar systems.

A human induced pluripotent stem cell-based in vitro assay predicts developmental toxicity through a retinoic acid receptor-mediated pathway for a series of related retinoid analogues.

PubMed

Palmer, Jessica A; Smith, Alan M; Egnash, Laura A; Colwell, Michael R; Donley, Elizabeth L R; Kirchner, Fred R; Burrier, Robert E

2017-10-01

The relative developmental toxicity potency of a series of retinoid analogues was evaluated using a human induced pluripotent stem (iPS) cell assay that measures changes in the biomarkers ornithine and cystine. Analogue potency was predicted, based on the assay endpoint of the ornithine/cystine (o/c) ratio, to be all-trans-retinoic acid>TTNPB>13-cis-retinoic acid≈9-cis-retinoic acid>acitretin>etretinate>retinol. These rankings correlate with in vivo data and demonstrate successful application of the assay to rank a series of related toxic and non-toxic compounds. The retinoic acid receptor α (RARα)-selective antagonist Ro 41-5253 inhibited the cystine perturbation caused by all-trans-retinoic acid, TTNPB, 13-cis-retinoic acid, 9-cis-retinoic acid, and acitretin. Ornithine was altered independent of RARα in all retinoids except acitretin. These results suggest a role for an RARα-mediated mechanism in retinoid-induced developmental toxicity through altered cystine metabolism. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis.

PubMed

Hwang, Sun-Goo; Kim, Dong Sub; Hwang, Jung Eun; Han, A-Reum; Jang, Cheol Seong

2014-05-15

In order to better understand the biological systems that are affected in response to cosmic ray (CR), we conducted weighted gene co-expression network analysis using the module detection method. By using the Pearson's correlation coefficient (PCC) value, we evaluated complex gene-gene functional interactions between 680 CR-responsive probes from integrated microarray data sets, which included large-scale transcriptional profiling of 1000 microarray samples. These probes were divided into 6 distinct modules that contained 20 enriched gene ontology (GO) functions, such as oxidoreductase activity, hydrolase activity, and response to stimulus and stress. In particular, modules 1 and 2 commonly showed enriched annotation categories such as oxidoreductase activity, including enriched cis-regulatory elements known as ROS-specific regulators. These results suggest that the ROS-mediated irradiation response pathway is affected by CR in modules 1 and 2. We found 243 ionizing radiation (IR)-responsive probes that exhibited similarities in expression patterns in various irradiation microarray data sets. The expression patterns of 6 randomly selected IR-responsive genes were evaluated by quantitative reverse transcription polymerase chain reaction following treatment with CR, gamma rays (GR), and ion beam (IB); similar patterns were observed among these genes under these 3 treatments. Moreover, we constructed subnetworks of IR-responsive genes and evaluated the expression levels of their neighboring genes following GR treatment; similar patterns were observed among them. These results of network-based analyses might provide a clue to understanding the complex biological system related to the CR response in plants. Copyright © 2014 Elsevier B.V. All rights reserved.

Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system

PubMed Central

Hutton, John J; Jegga, Anil G; Kong, Sue; Gupta, Ashima; Ebert, Catherine; Williams, Sarah; Katz, Jonathan D; Aronow, Bruce J

2004-01-01

Background In this study we have built and mined a gene expression database composed of 65 diverse mouse tissues for genes preferentially expressed in immune tissues and cell types. Using expression pattern criteria, we identified 360 genes with preferential expression in thymus, spleen, peripheral blood mononuclear cells, lymph nodes (unstimulated or stimulated), or in vitro activated T-cells. Results Gene clusters, formed based on similarity of expression-pattern across either all tissues or the immune tissues only, had highly significant associations both with immunological processes such as chemokine-mediated response, antigen processing, receptor-related signal transduction, and transcriptional regulation, and also with more general processes such as replication and cell cycle control. Within-cluster gene correlations implicated known associations of known genes, as well as immune process-related roles for poorly described genes. To characterize regulatory mechanisms and cis-elements of genes with similar patterns of expression, we used a new version of a comparative genomics-based cis-element analysis tool to identify clusters of cis-elements with compositional similarity among multiple genes. Several clusters contained genes that shared 5–6 cis-elements that included ETS and zinc-finger binding sites. cis-Elements AP2 EGRF ETSF MAZF SP1F ZF5F and AREB ETSF MZF1 PAX5 STAT were shared in a thymus-expressed set; AP4R E2FF EBOX ETSF MAZF SP1F ZF5F and CREB E2FF MAZF PCAT SP1F STAT cis-clusters occurred in activated T-cells; CEBP CREB NFKB SORY and GATA NKXH OCT1 RBIT occurred in stimulated lymph nodes. Conclusion This study demonstrates a series of analytic approaches that have allowed the implication of genes and regulatory elements that participate in the differentiation, maintenance, and function of the immune system. Polymorphism or mutation of these could adversely impact immune system functions. PMID:15504237

Impact of a Multifaceted and Clinically Integrated Training Program in Evidence-Based Practice on Knowledge, Skills, Beliefs and Behaviour among Clinical Instructors in Physiotherapy: A Non-Randomized Controlled Study.

PubMed

Olsen, Nina Rydland; Bradley, Peter; Espehaug, Birgitte; Nortvedt, Monica Wammen; Lygren, Hildegunn; Frisk, Bente; Bjordal, Jan Magnus

2015-01-01

Physiotherapists practicing at clinical placement sites assigned the role as clinical instructors (CIs), are responsible for supervising physiotherapy students. For CIs to role model evidence-based practice (EBP) they need EBP competence. The aim of this study was to assess the short and long term impact of a six-month multifaceted and clinically integrated training program in EBP on the knowledge, skills, beliefs and behaviour of CIs supervising physiotherapy students. We invited 37 CIs to participate in this non-randomized controlled study. Three self-administered questionnaires were used pre- and post-intervention, and at six-month follow-up: 1) The Adapted Fresno test (AFT), 2) the EBP Belief Scale and 3) the EBP Implementation Scale. The analysis approach was linear regression modeling using Generalized Estimating Equations. In total, 29 CIs agreed to participate in the study: 14 were invited to participate in the intervention group and 15 were invited to participate in the control group. One in the intervention group and five in the control group were lost to follow-up. At follow-up, the group difference was statistically significant for the AFT (mean difference = 37, 95% CI (15.9 -58.1), p < 0.001) and the EBP Beliefs scale (mean difference = 8.1, 95% CI (3.1 -13.2), p = 0.002), but not for the EBP Implementation scale (mean difference = 1.8. 95% CI (-4.5-8.1), p = 0.574). Comparing measurements over time, we found a statistically significant increase in mean scores related to all outcome measures for the intervention group only. A multifaceted and clinically integrated training program in EBP was successful in improving EBP knowledge, skills and beliefs among CIs. Future studies need to ensure long-term EBP behaviour change, in addition to assessing CIs' abilities to apply EBP knowledge and skills when supervising students.

Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9-cis-retinoic acid at the base of metazoan evolution

PubMed Central

Novotný, Jan Philipp; Chughtai, Ahmed Ali; Kostrouchová, Markéta; Kostrouchová, Veronika; Kostrouch, David; Kaššák, Filip; Kaňa, Radek; Schierwater, Bernd; Kostrouchová, Marta

2017-01-01

Trichoplax adhaerens, the only known species of Placozoa is likely to be closely related to an early metazoan that preceded branching of Cnidaria and Bilateria. This animal species is surprisingly well adapted to free life in the World Ocean inhabiting tidal costal zones of oceans and seas with warm to moderate temperatures and shallow waters. The genome of T. adhaerens (sp. Grell) includes four nuclear receptors, namely orthologue of RXR (NR2B), HNF4 (NR2A), COUP-TF (NR2F) and ERR (NR3B) that show a high degree of similarity with human orthologues. In the case of RXR, the sequence identity to human RXR alpha reaches 81% in the DNA binding domain and 70% in the ligand binding domain. We show that T. adhaerens RXR (TaRXR) binds 9-cis retinoic acid (9-cis-RA) with high affinity, as well as high specificity and that exposure of T. adhaerens to 9-cis-RA regulates the expression of the putative T. adhaerens orthologue of vertebrate L-malate-NADP+ oxidoreductase (EC 1.1.1.40) which in vertebrates is regulated by a heterodimer of RXR and thyroid hormone receptor. Treatment by 9-cis-RA alters the relative expression profile of T. adhaerens nuclear receptors, suggesting the existence of natural ligands. Keeping with this, algal food composition has a profound effect on T. adhaerens growth and appearance. We show that nanomolar concentrations of 9-cis-RA interfere with T. adhaerens growth response to specific algal food and causes growth arrest. Our results uncover an endocrine-like network of nuclear receptors sensitive to 9-cis-RA in T. adhaerens and support the existence of a ligand-sensitive network of nuclear receptors at the base of metazoan evolution. PMID:28975052

New evidence on the validity of the Arnett Caregiver Interaction Scale: Results from the Early Childhood Longitudinal Study-Birth Cohort

PubMed Central

Colwell, Nicole; Gordon, Rachel A.; Fujimoto, Ken; Kaestner, Robert; Korenman, Sanders

2013-01-01

The Arnett Caregiver Interaction Scale (CIS) has been widely used in research studies to measure the quality of caregiver–child interactions. The scale was modeled on a well-established theory of parenting, but there are few psychometric studies of its validity. We applied factor analyses and item response theory methods to assess the psychometric properties of the Arnett CIS in a national sample of toddlers in home-based care and preschoolers in center-based care from the Early Childhood Longitudinal Study-Birth Cohort. We found that a bifactor structure (one common factor and a second set of specific factors) best fits the data. In the Arnett CIS, the bifactor model distinguishes a common substantive dimension from two methodological dimensions (for positively and negatively oriented items). Despite the good fit of this model, the items are skewed (most teachers/caregivers display positive interactions with children) and, as a result, the Arnett CIS is not well suited to distinguish between caregivers who are “highly” versus “moderately” positive in their interactions with children, according to the items on the scale. Regression-adjusted associations between the Arnett CIS and child outcomes are small, especially for preschoolers in centers. We encourage future scale development work on measures of child care quality by early childhood scholars. PMID:24058264

Nonadiabatic dynamics simulation of photoisomerization mechanism of the second stablest isomer of N-salicilydenemethylfurylamine

NASA Astrophysics Data System (ADS)

Gao, Aihua; Li, Jianpeng; Wang, Dehua; Ma, Xiaoguang; Wang, Meishan

2018-02-01

The photoisomerization processes of the second stablest isomer in the aromatic Schiff base, N-salicilydenemethylfurylamine, in the gas phase have been studied by static electronic structure calculations and surface-hopping dynamics simulations based on the Zhu-Nakamura theory. Various stable structures are obtained in the optimization because of different orientations of methyl-furyl part with respect to the salicylaldimine part and different orientations of hydroxy group with respect to the benzene ring. Upon photoexcitation into the first excited state, bond isomerization in the salicylaldimine part is completely suppressed until the strong excited-state hydrogen bond is broken. The decay pathway involves two excited-state minima, one in cis-enol form and the other in cis-keto form. After the excited-state proton transfer, twists of bonds lead to a conical intersection between the ground and excited states. After internal conversion around a conical intersection, the molecule is stabilized in cis- or trans-keto form. If the reverse hydrogen transfer process occurs in the ground state, the molecule will finally end up in the cis-enol region. The cis-keto and trans-keto isomers are observed as photoproducts. According to our full-dimensional nonadiabatic dynamics simulations, we find the excited-state intramolecular proton transfer and torsions of three single bonds in the chain to be responsible for photoisomerization of the second stablest isomer of N-salicilydenemethylfurylamine.

Molecular pharmacodynamics of emixustat in protection against retinal degeneration

PubMed Central

Zhang, Jianye; Kiser, Philip D.; Badiee, Mohsen; Palczewska, Grazyna; Dong, Zhiqian; Golczak, Marcin; Tochtrop, Gregory P.; Palczewski, Krzysztof

2015-01-01

Emixustat is a visual cycle modulator that has entered clinical trials as a treatment for age-related macular degeneration (AMD). This molecule has been proposed to inhibit the visual cycle isomerase RPE65, thereby slowing regeneration of 11-cis-retinal and reducing production of retinaldehyde condensation byproducts that may be involved in AMD pathology. Previously, we reported that all-trans-retinal (atRAL) is directly cytotoxic and that certain primary amine compounds that transiently sequester atRAL via Schiff base formation ameliorate retinal degeneration. Here, we have shown that emixustat stereoselectively inhibits RPE65 by direct active site binding. However, we detected the presence of emixustat-atRAL Schiff base conjugates, indicating that emixustat also acts as a retinal scavenger, which may contribute to its therapeutic effects. Using agents that lack either RPE65 inhibitory activity or the capacity to sequester atRAL, we assessed the relative importance of these 2 modes of action in protection against retinal phototoxicity in mice. The atRAL sequestrant QEA-B-001-NH2 conferred protection against phototoxicity without inhibiting RPE65, whereas an emixustat derivative incapable of atRAL sequestration was minimally protective, despite direct inhibition of RPE65. These data indicate that atRAL sequestration is an essential mechanism underlying the protective effects of emixustat and related compounds against retinal phototoxicity. Moreover, atRAL sequestration should be considered in the design of next-generation visual cycle modulators. PMID:26075817

Hydrated electrons react with high specificity with cisplatin bound to single-stranded DNA.

PubMed

Behmand, B; Cloutier, P; Girouard, S; Wagner, J R; Sanche, L; Hunting, D J

2013-12-19

Short oligonucleotides TTTTTGTGTTT and TTTTTTTGTTT in solution with and without cisplatin (cisPt) bound to the guanine bases were irradiated with γ-rays at doses varying from 0 to 2500 Gy. To determine the effect of hydrated electrons from water radiolysis on the oligonucleotides, we quenched (•)OH radicals with ethylenediaminetetraacetic acid (EDTA) and displaced oxygen, which reacts with hydrated electrons, by bubbling the solution with wet nitrogen. DNA strand breaks and platinum detachment were quantified by gel electrophoresis. Our results demonstrate that hydrated electrons react almost exclusively at the position of the cisPt adduct, where they induce cisPt detachment from one or both guanines in the oligonucleotide. Given the high yield of hydrated electrons in irradiated tissues, this reaction may be an important step in the mechanism of radiosensitization of DNA by cisPt.

A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.

PubMed

Gustafson, Chelsea L; Parsley, Nicole C; Asimgil, Hande; Lee, Hsiau-Wei; Ahlbach, Christopher; Michael, Alicia K; Xu, Haiyan; Williams, Owen L; Davis, Tara L; Liu, Andrew C; Partch, Carrie L

2017-05-18

The C-terminal transactivation domain (TAD) of BMAL1 (brain and muscle ARNT-like 1) is a regulatory hub for transcriptional coactivators and repressors that compete for binding and, consequently, contributes to period determination of the mammalian circadian clock. Here, we report the discovery of two distinct conformational states that slowly exchange within the dynamic TAD to control timing. This binary switch results from cis/trans isomerization about a highly conserved Trp-Pro imide bond in a region of the TAD that is required for normal circadian timekeeping. Both cis and trans isomers interact with transcriptional regulators, suggesting that isomerization could serve a role in assembling regulatory complexes in vivo. Toward this end, we show that locking the switch into the trans isomer leads to shortened circadian periods. Furthermore, isomerization is regulated by the cyclophilin family of peptidyl-prolyl isomerases, highlighting the potential for regulation of BMAL1 protein dynamics in period determination. Copyright © 2017 Elsevier Inc. All rights reserved.

Conjugated Linoleic Acid: Potential Health Benefits as a Functional Food Ingredient.

PubMed

Kim, Jun Ho; Kim, Yoo; Kim, Young Jun; Park, Yeonhwa

2016-01-01

Conjugated linoleic acid (CLA) has drawn significant attention since the 1980s for its various biological activities. CLA consists mainly of two isomers, cis-9,trans-11 and trans-10,cis-12, and the mixture of these two (CLA mix or 50:50) has been approved for food as GRAS (generally recognized as safe) in the United States since 2008. Along with its original discovery as an anticancer component, CLA has been shown to prevent the development of atherosclerosis, reduce body fat while improving lean body mass, and modulate immune and/or inflammatory responses. This review summarizes the clinical trials involving CLA since 2012; additional uses of CLA for age-associated health issues are discussed; and CLA's potential health concerns, including glucose homeostasis, oxidative stress, hepatic steatosis, and milk-fat depression, are examined. With ongoing applications to food products, CLA consumption is expected to rise and close monitoring of not only its efficacy but also its known and unknown consequences are required to ensure proper applications of CLA.

Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs.

PubMed

Lopez-Rios, Javier; Duchesne, Amandine; Speziale, Dario; Andrey, Guillaume; Peterson, Kevin A; Germann, Philipp; Unal, Erkan; Liu, Jing; Floriot, Sandrine; Barbey, Sarah; Gallard, Yves; Müller-Gerbl, Magdalena; Courtney, Andrew D; Klopp, Christophe; Rodriguez, Sabrina; Ivanek, Robert; Beisel, Christian; Wicking, Carol; Iber, Dagmar; Robert, Benoit; McMahon, Andrew P; Duboule, Denis; Zeller, Rolf

2014-07-03

The large spectrum of limb morphologies reflects the wide evolutionary diversification of the basic pentadactyl pattern in tetrapods. In even-toed ungulates (artiodactyls, including cattle), limbs are adapted for running as a consequence of progressive reduction of their distal skeleton to symmetrical and elongated middle digits with hoofed phalanges. Here we analyse bovine embryos to establish that polarized gene expression is progressively lost during limb development in comparison to the mouse. Notably, the transcriptional upregulation of the Ptch1 gene, which encodes a Sonic hedgehog (SHH) receptor, is disrupted specifically in the bovine limb bud mesenchyme. This is due to evolutionary alteration of a Ptch1 cis-regulatory module, which no longer responds to graded SHH signalling during bovine handplate development. Our study provides a molecular explanation for the loss of digit asymmetry in bovine limb buds and suggests that modifications affecting the Ptch1 cis-regulatory landscape have contributed to evolutionary diversification of artiodactyl limbs.

Conformational Preferences of α-Substituted Proline Analogues

PubMed Central

Flores-Ortega, Alejandra; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Alemán, Carlos; Casanovas, Jordi

2009-01-01

DFT calculations at the B3LYP/6-31+G(d,p) level have been used to investigate how the replacement of the α hydrogen by a more sterically demanding group affects the conformational preferences of proline. Specifically, the N-acetyl-N’-methylamide derivatives of L-proline, L-α-methylproline and L-α-phenylproline have been calculated, with both the cis/trans isomerism of the peptide bonds and the puckering of the pyrrolidine ring being considered. The effects of solvation have been evaluated using a Self Consistent Reaction Field model. As expected, tetrasubstitution at the α carbon destabilizes the conformers with one or more peptide bonds arranged in cis. The lowest energy minimum has been found to be identical for the three compounds investigated, but important differences are observed regarding other energetically accessible backbone conformations. The results obtained provide evidence that the distinct steric requirements of the substituent at Cα may play a significant role in modulating the conformational preferences of proline. PMID:18351745

Xiao Yao San Improves Depressive-Like Behaviors in Rats with Chronic Immobilization Stress through Modulation of Locus Coeruleus-Norepinephrine System.

PubMed

Ding, Xiu-Fang; Zhao, Xiao-Hua; Tao, Yang; Zhong, Wei-Chao; Fan, Qin; Diao, Jian-Xin; Liu, Yuan-Liang; Chen, Yu-Yao; Chen, Jia-Xu; Lv, Zhi-Ping

2014-01-01

Most research focuses on the hypothalamic-pituitary-adrenal (HPA) axis, hypothalamus-pituitary-thyroid (HPT) axis, and hypothalamus-pituitary-gonadal (HPGA) axis systems of abnormalities of emotions and behaviors induced by stress, while no studies of Chinese herbal medicine such as Xiao Yao San (XYS) on the mechanisms of locus coeruleus-norepinephrine (LC-NE) system have been reported. Therefore, experiments were carried out to observe mechanism of LC-NE system in response to chronic immobilization stress (CIS) and explore the antidepressant effect of XYS. Rat model was established by CIS. LC morphology in rat was conducted. The serum norepinephrine (NE) concentrations and NE biosynthesis such as tyrosine hydroxylase (TH), dopamine-β-hydroxylase (DBH), and corticotrophin-releasing-factor (CRF) in LC were determined. Results showed that there were no discernible alterations in LC in rats. The serum NE concentrations, positive neurons, mean optical density (MOD), and protein levels of TH, DBH, and CRF in model group were significantly increased compared to the control group. But XYS-treated group displayed a significantly decreased in NE levels and expressions of TH, DBH, and CRF compared to the model group. In conclusion, CIS can activate LC-NE system to release NE and then result in a significant decrease in rats. XYS treatment can effectively improve depressive-like behaviors in rats through inhibition of LC-NE neurons activity.

Xiao Yao San Improves Depressive-Like Behaviors in Rats with Chronic Immobilization Stress through Modulation of Locus Coeruleus-Norepinephrine System

PubMed Central

Ding, Xiu-Fang; Zhao, Xiao-Hua; Tao, Yang; Zhong, Wei-Chao; Fan, Qin; Diao, Jian-Xin; Liu, Yuan-Liang; Chen, Yu-Yao; Chen, Jia-Xu; Lv, Zhi-Ping

2014-01-01

Most research focuses on the hypothalamic-pituitary-adrenal (HPA) axis, hypothalamus-pituitary-thyroid (HPT) axis, and hypothalamus-pituitary-gonadal (HPGA) axis systems of abnormalities of emotions and behaviors induced by stress, while no studies of Chinese herbal medicine such as Xiao Yao San (XYS) on the mechanisms of locus coeruleus-norepinephrine (LC-NE) system have been reported. Therefore, experiments were carried out to observe mechanism of LC-NE system in response to chronic immobilization stress (CIS) and explore the antidepressant effect of XYS. Rat model was established by CIS. LC morphology in rat was conducted. The serum norepinephrine (NE) concentrations and NE biosynthesis such as tyrosine hydroxylase (TH), dopamine-β-hydroxylase (DBH), and corticotrophin-releasing-factor (CRF) in LC were determined. Results showed that there were no discernible alterations in LC in rats. The serum NE concentrations, positive neurons, mean optical density (MOD), and protein levels of TH, DBH, and CRF in model group were significantly increased compared to the control group. But XYS-treated group displayed a significantly decreased in NE levels and expressions of TH, DBH, and CRF compared to the model group. In conclusion, CIS can activate LC-NE system to release NE and then result in a significant decrease in rats. XYS treatment can effectively improve depressive-like behaviors in rats through inhibition of LC-NE neurons activity. PMID:25610478

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

PubMed Central

Curtis, Christina; Shah, Sohrab P.; Chin, Suet-Feung; Turashvili, Gulisa; Rueda, Oscar M.; Dunning, Mark J.; Speed, Doug; Lynch, Andy G.; Samarajiwa, Shamith; Yuan, Yinyin; Gräf, Stefan; Ha, Gavin; Haffari, Gholamreza; Bashashati, Ali; Russell, Roslin; McKinney, Steven; Langerød, Anita; Green, Andrew; Provenzano, Elena; Wishart, Gordon; Pinder, Sarah; Watson, Peter; Markowetz, Florian; Murphy, Leigh; Ellis, Ian; Purushotham, Arnie; Børresen-Dale, Anne-Lise; Brenton, James D.; Tavaré, Simon; Caldas, Carlos; Aparicio, Samuel

2012-01-01

The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome. PMID:22522925

Ephrin-B3 regulates glutamate receptor signaling at hippocampal synapses

PubMed Central

Antion, Marcia D.; Christie, Louisa A.; Bond, Allison M.; Dalva, Matthew B.; Contractor, Anis

2010-01-01

B-ephrin - EphB receptor signaling modulates NMDA receptors by inducing tyrosine phosphorylation of NR2 subunits. Ephrins and EphB RTKs are localized to postsynaptic compartments in the CA1, and therefore potentially interact in a non-canonical cis-configuration. However, it is not known whether cis- configured receptor-ligand signaling is utilized by this class of RTKs, and whether this might influence excitatory synapses. We found that ablation of ephrin-B3 results in an enhancement of the NMDA receptor component of synaptic transmission relative to the AMPA receptor component in CA1 synapses. Synaptic AMPA receptor expression is reduced in ephrin-B3 knockout mice, and there is a marked enhancement of tyrosine phosphorylation of the NR2B receptor subunit. In a reduced system co-expression of ephrin-B3 attenuated EphB2-mediated NR2B tyrosine phosphorylation. Moreover, phosphorylation of EphB2 was elevated in the hippocampus of ephrin-B3 knockout mice, suggesting that regulation of EphB2 activity is lost in these mice. Direct activation of EphB RTKs resulted in phosphorylation of NR2B and a potential signaling partner, the non-receptor tyrosine kinase Pyk2. Our data suggests that ephrin-B3 limits EphB RTK-mediated phosphorylation of the NR2B subunit through an inhibitory cis- interaction which is required for the correct function of glutamatergic CA1 synapses. PMID:20678574

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information.

PubMed

Song, Jiangning; Burrage, Kevin; Yuan, Zheng; Huber, Thomas

2006-03-09

The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Chinese International Students' and Faculty Members' Views of Plagiarism in Higher Education

ERIC Educational Resources Information Center

Grigg, Alan

2016-01-01

As the enrollment of Chinese international students (CIS) increased at a private institution in the Midwest, so did suspected cases of plagiarism. This study addressed the problem of how faculty members grappled with CIS' interpretation and application of Western-based views of plagiarism. The purpose of the study was to identify similarities and…

COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets

PubMed Central

Lohmann, Ingrid

2012-01-01

In multi-cellular organisms, spatiotemporal activity of cis-regulatory DNA elements depends on their occupancy by different transcription factors (TFs). In recent years, genome-wide ChIP-on-Chip, ChIP-Seq and DamID assays have been extensively used to unravel the combinatorial interaction of TFs with cis-regulatory modules (CRMs) in the genome. Even though genome-wide binding profiles are increasingly becoming available for different TFs, single TF binding profiles are in most cases not sufficient for dissecting complex regulatory networks. Thus, potent computational tools detecting statistically significant and biologically relevant TF-motif co-occurrences in genome-wide datasets are essential for analyzing context-dependent transcriptional regulation. We have developed COPS (Co-Occurrence Pattern Search), a new bioinformatics tool based on a combination of association rules and Markov chain models, which detects co-occurring TF binding sites (BSs) on genomic regions of interest. COPS scans DNA sequences for frequent motif patterns using a Frequent-Pattern tree based data mining approach, which allows efficient performance of the software with respect to both data structure and implementation speed, in particular when mining large datasets. Since transcriptional gene regulation very often relies on the formation of regulatory protein complexes mediated by closely adjoining TF binding sites on CRMs, COPS additionally detects preferred short distance between co-occurring TF motifs. The performance of our software with respect to biological significance was evaluated using three published datasets containing genomic regions that are independently bound by several TFs involved in a defined biological process. In sum, COPS is a fast, efficient and user-friendly tool mining statistically and biologically significant TFBS co-occurrences and therefore allows the identification of TFs that combinatorially regulate gene expression. PMID:23272209

Interaction of cis- and trans-RuCl2(DMSO)4 with the nucleotides GpA, d(GpA), ApG, d(ApG) and d(CCTGGTCC): high-field NMR characterization of the reaction products.

PubMed

Anagnostopoulou, A; Moldrheim, E; Katsaros, N; Sletten, E

1999-04-01

Both cis- and trans-RuCl2(DMSO)4 (cis-Ru and trans-Ru) react with ApG, GpA, d(ApG) and d(GpA) to yield products with bifunctional metal coordination of the bases. For each dinucleotide one major product and several minor species are formed. This is in contrast to previous results on analogous reactions between trans-Ru and d(GpG) where a substantial amount of an intermediate species was found. The rates of reaction between dinucleotides and cis-Ru are approximately 20-fold slower than for trans-Ru. The compounds formed with the two isomers exhibit identical proton NMR spectra, suggesting the same coordination mode for ruthenium in the final product. The two purine bases are coordinated to ruthenium through N7 in a head-to-head conformation with the glycosidic angles being in the anti range. Coupling constants indicate a relatively pure 3'-endo conformation for the 5'-sugar and mainly 2'-endo for the 3'-sugar. The similar bifunctional binding mode of cis- and trans-Ru(II) with dinucleotides as evident from the NMR spectra are in contrast to the different mode of interaction suggested earlier for cis- and trans-Ru complexes with DNA. trans-Ru interacts with the deoxyoctanucleotide d(CCTGGTCC), giving two main products during the first 2 h of incubation time. Four H8 guanine resonances are shifted downfield, characteristic of N7 metal coordination. The products are not analyzed in detail, but it is suggested that the structures may be described as two chiral G(N7/N7) chelates.

Etiology and early pathogenesis of malignant testicular germ cell tumors: towards possibilities for preinvasive diagnosis

PubMed Central

Elzinga-Tinke, Jenny E; Dohle, Gert R; Looijenga, Leendert HJ

2015-01-01

Malignant testicular germ cell tumors (TGCT) are the most frequent cancers in Caucasian males (20–40 years) with an 70% increasing incidence the last 20 years, probably due to combined action of (epi)genetic and (micro)environmental factors. It is expected that TGCT have carcinoma in situ (CIS) as their common precursor, originating from an embryonic germ cell blocked in its maturation process. The overall cure rate of TGCT is more than 90%, however, men surviving TGCT can present long-term side effects of systemic cancer treatment. In contrast, men diagnosed and treated for CIS only continue to live without these long-term side effects. Therefore, early detection of CIS has great health benefits, which will require an informative screening method. This review described the etiology and early pathogenesis of TGCT, as well as the possibilities of early detection and future potential of screening men at risk for TGCT. For screening, a well-defined risk profile based on both genetic and environmental risk factors is needed. Since 2009, several genome wide association studies (GWAS) have been published, reporting on single-nucleotide polymorphisms (SNPs) with significant associations in or near the genes KITLG, SPRY4, BAK1, DMRT1, TERT, ATF7IP, HPGDS, MAD1L1, RFWD3, TEX14, and PPM1E, likely to be related to TGCT development. Prenatal, perinatal, and postnatal environmental factors also influence the onset of CIS. A noninvasive early detection method for CIS would be highly beneficial in a clinical setting, for which specific miRNA detection in semen seems to be very promising. Further research is needed to develop a well-defined TGCT risk profile, based on gene-environment interactions, combined with noninvasive detection method for CIS. PMID:25791729

Parental Expectation from Children with Cochlear Implants in Indian Context: a Questionnaire Based Study.

PubMed

Kumar, Prawin; Sanju, Himanshu Kumar; Mishra, Rajkishor; Singh, Varun; Mohan, Priyanka

2017-04-01

Introduction  Parental support is important in the habilitation/rehabilitation of children using cochlear implant devices. Hence, it is important for families to know the realistic expectations regarding outcomes from CIs. Objective  The objective of the present study is to know the parents' expectation from children using CIs. Methods  For this study, we recruited 23 parents of children using CIs. We administered 15 questions translated in to Hindi related to communication abilities, social skills, academic achievement, change in future life, rehabilitation demand, and stress due to hearing impairment. Results  The response of the questions (5-point rating scale) related to communication abilities showed that parents were expecting children using CIs to use the telephone (95%), to be able to detect soft sounds (99%), to listen in crowds (86%), to be able to easily understand others (76%), and to show improvement in communication skills (78%). Similarly, for questions related to social skills showed 90% of the parents expecting that their children with CIs should be able to easily make friends with normal hearing peers, and 80% of the parents were expecting the children to achieve high standards in their reading and writing skills. Questions related to change in future life showed 86% of the parents expecting their children with CIs to act like normal hearing children. Further, 78% parents showed positive response regarding importance of intensive training. However, 70% of the parents reported stress in the family due to the existence of the hearing impaired child. Conclusion  Overall, the existing questionnaire-based study showed that parents have high expectations from their children with cochlear implant.

Genome-wide prediction of cis-regulatory regions using supervised deep learning methods.

PubMed

Li, Yifeng; Shi, Wenqiang; Wasserman, Wyeth W

2018-05-31

In the human genome, 98% of DNA sequences are non-protein-coding regions that were previously disregarded as junk DNA. In fact, non-coding regions host a variety of cis-regulatory regions which precisely control the expression of genes. Thus, Identifying active cis-regulatory regions in the human genome is critical for understanding gene regulation and assessing the impact of genetic variation on phenotype. The developments of high-throughput sequencing and machine learning technologies make it possible to predict cis-regulatory regions genome wide. Based on rich data resources such as the Encyclopedia of DNA Elements (ENCODE) and the Functional Annotation of the Mammalian Genome (FANTOM) projects, we introduce DECRES based on supervised deep learning approaches for the identification of enhancer and promoter regions in the human genome. Due to their ability to discover patterns in large and complex data, the introduction of deep learning methods enables a significant advance in our knowledge of the genomic locations of cis-regulatory regions. Using models for well-characterized cell lines, we identify key experimental features that contribute to the predictive performance. Applying DECRES, we delineate locations of 300,000 candidate enhancers genome wide (6.8% of the genome, of which 40,000 are supported by bidirectional transcription data), and 26,000 candidate promoters (0.6% of the genome). The predicted annotations of cis-regulatory regions will provide broad utility for genome interpretation from functional genomics to clinical applications. The DECRES model demonstrates potentials of deep learning technologies when combined with high-throughput sequencing data, and inspires the development of other advanced neural network models for further improvement of genome annotations.

Water-stable helical structure of tertiary amides of bicyclic β-amino acid bearing 7-azabicyclo[2.2.1]heptane. Full control of amide cis-trans equilibrium by bridgehead substitution.

PubMed

Hosoya, Masahiro; Otani, Yuko; Kawahata, Masatoshi; Yamaguchi, Kentaro; Ohwada, Tomohiko

2010-10-27

Helical structures of oligomers of non-natural β-amino acids are significantly stabilized by intramolecular hydrogen bonding between main-chain amide moieties in many cases, but the structures are generally susceptible to the environment; that is, helices may unfold in protic solvents such as water. For the generation of non-hydrogen-bonded ordered structures of amides (tertiary amides in most cases), control of cis-trans isomerization is crucial, even though there is only a small sterical difference with respect to cis and trans orientations. We have established methods for synthesis of conformationally constrained β-proline mimics, that is, bridgehead-substituted 7-azabicyclo[2.2.1]heptane-2-endo-carboxylic acids. Our crystallographic, 1D- and 2D-NMR, and CD spectroscopic studies in solution revealed that a bridgehead methoxymethyl substituent completely biased the cis-trans equilibrium to the cis-amide structure along the main chain, and helical structures based on the cis-amide linkage were generated independently of the number of residues, from the minimalist dimer through the tetramer, hexamer, and up to the octamer, and irrespective of the solvent (e.g., water, alcohol, halogenated solvents, and cyclohexane). Generality of the control of the amide equilibrium by bridgehead substitution was also examined.

Real-Time and Accurate Identification of Single Oligonucleotide Photoisomers via an Aerolysin Nanopore.

PubMed

Hu, Zheng-Li; Li, Zi-Yuan; Ying, Yi-Lun; Zhang, Junji; Cao, Chan; Long, Yi-Tao; Tian, He

2018-04-03

Identification of the configuration for the photoresponsive oligonucleotide plays an important role in the ingenious design of DNA nanomolecules and nanodevices. Due to the limited resolution and sensitivity of present methods, it remains a challenge to determine the accurate configuration of photoresponsive oligonucleotides, much less a precise description of their photoconversion process. Here, we used an aerolysin (AeL) nanopore-based confined space for real-time determination and quantification of the absolute cis/ trans configuration of each azobenzene-modified oligonucleotide (Azo-ODN) with a single molecule resolution. The two completely separated current distributions with narrow peak widths at half height (<0.62 pA) are assigned to cis/ trans-Azo-ODN isomers, respectively. Due to the high current sensitivity, each isomer of Azo-ODN could be undoubtedly identified, which gives the accurate photostationary conversion values of 82.7% for trans-to- cis under UV irradiation and 82.5% for cis-to- trans under vis irradiation. Further real-time kinetic evaluation reveals that the photoresponsive rate constants of Azo-ODN from trans-to- cis and cis-to -trans are 0.43 and 0.20 min -1 , respectively. This study will promote the sophisticated design of photoresponsive ODN to achieve an efficient and applicable photocontrollable process.

A Catalogue of Putative cis-Regulatory Interactions Between Long Non-coding RNAs and Proximal Coding Genes Based on Correlative Analysis Across Diverse Human Tumors.

PubMed

Basu, Swaraj; Larsson, Erik

2018-05-31

Antisense transcripts and other long non-coding RNAs are pervasive in mammalian cells, and some of these molecules have been proposed to regulate proximal protein-coding genes in cis For example, non-coding transcription can contribute to inactivation of tumor suppressor genes in cancer, and antisense transcripts have been implicated in the epigenetic inactivation of imprinted genes. However, our knowledge is still limited and more such regulatory interactions likely await discovery. Here, we make use of available gene expression data from a large compendium of human tumors to generate hypotheses regarding non-coding-to-coding cis -regulatory relationships with emphasis on negative associations, as these are less likely to arise for reasons other than cis -regulation. We document a large number of possible regulatory interactions, including 193 coding/non-coding pairs that show expression patterns compatible with negative cis -regulation. Importantly, by this approach we capture several known cases, and many of the involved coding genes have known roles in cancer. Our study provides a large catalog of putative non-coding/coding cis -regulatory pairs that may serve as a basis for further experimental validation and characterization. Copyright © 2018 Basu and Larsson.

Synthesis and structural characterisation of Pd(II) and Pt(II) complexes with a flexible, ferrocene-based P,S-donor amidophosphine ligand.

PubMed

Tauchman, Jiří; Císařová, Ivana; Stěpnička, Petr

2014-01-28

1'-Diphenylphosphino-1-{[(2-(methylthio)ethyl)amino]carbonyl}ferrocene (1), accessible via amidation of 1'-(diphenylphosphino)ferrocene-1-carboxylic acid (Hdpf) with 2-(methylthio)ethylamine, reacts with [PdCl2(cod)] (cod = cycloocta-1,5-diene) at a 1 : 1 metal-to-ligand ratio to give trans-[PdCl2(1-κ(2)P,S)] (trans-2) as the sole product. A similar reaction with [PtCl2(cod)] affords a mixture of cis- and trans-[PtCl2(1-κ(2)P,S)] (cis- and trans-3), which can be separated by fractional crystallisation. Complexation reactions performed with 2 equiv. of the ligand are less selective, yielding mixtures of the expected bis-phosphine complexes (i.e., trans-[PdCl2(1-κP)2], or a mixture of cis- and trans-[PtCl2(-κP)2]) with the respective monophosphine complexes. The structures of 1, trans-2, cis-3 and trans-3 determined by X-ray diffraction demonstrate the ability of the title ligand to act as a flexible cis- or trans-P,S-chelate donor (the ligand bite angles are 174.03(2)/173.05(2)° for trans-2/3 and 92.86(2)° for cis-3).

TALEN-Based Mutagenesis of Lipoxygenase LOX3 Enhances the Storage Tolerance of Rice (Oryza sativa) Seeds.

PubMed

Ma, Lei; Zhu, Fugui; Li, Zhenwei; Zhang, Jianfu; Li, Xin; Dong, Jiangli; Wang, Tao

2015-01-01

The deterioration of rice grain reduces the quality of rice, resulting in serious economic losses for farmers. Lipoxygenases (LOXs) catalyze the dioxygenation of polyunsaturated fatty acids with at least one cis,cis-1,4-pentadiene to form hydroperoxide, which is a major factor influencing seed longevity and viability. Recently, genome editing, an essential tool employed in reverse genetics, has been used experimentally to investigate basic plant biology or to modify crop plants for the improvement of important agricultural traits. In this study, we performed targeted mutagenesis in rice using transcription activator-like effector nucleases (TALENs) to improve seed storability. A modified ligation-independent cloning method (LIC) was employed to allow for the quick and efficient directional insertion of TALEN monomer modules into destination vectors used in plants. We demonstrated the feasibility and flexibility of the technology by developing a set of modular vectors for genome editing. After construction and validation, the TALEN pairs were used to create stable transgenic rice lines via Agrobacterium-mediated transformation. One heterozygous mutant (4%) was recovered from 25 transgenic NPTII-resistant lines, and the mutation was transmitted to the next generation. Further molecular and protein level experiments verified LOX3 deficiency and demonstrated the improvement of seed storability. Our work provides a flexible genome editing tool for improving important agronomic traits, as well as direct evidence that Lox3 has only a limited impact on seed longevity.

TALEN-Based Mutagenesis of Lipoxygenase LOX3 Enhances the Storage Tolerance of Rice (Oryza sativa) Seeds

PubMed Central

Li, Zhenwei; Zhang, Jianfu; Li, Xin; Dong, Jiangli; Wang, Tao

2015-01-01

The deterioration of rice grain reduces the quality of rice, resulting in serious economic losses for farmers. Lipoxygenases (LOXs) catalyze the dioxygenation of polyunsaturated fatty acids with at least one cis,cis-1,4-pentadiene to form hydroperoxide, which is a major factor influencing seed longevity and viability. Recently, genome editing, an essential tool employed in reverse genetics, has been used experimentally to investigate basic plant biology or to modify crop plants for the improvement of important agricultural traits. In this study, we performed targeted mutagenesis in rice using transcription activator-like effector nucleases (TALENs) to improve seed storability. A modified ligation-independent cloning method (LIC) was employed to allow for the quick and efficient directional insertion of TALEN monomer modules into destination vectors used in plants. We demonstrated the feasibility and flexibility of the technology by developing a set of modular vectors for genome editing. After construction and validation, the TALEN pairs were used to create stable transgenic rice lines via Agrobacterium-mediated transformation. One heterozygous mutant (4%) was recovered from 25 transgenic NPTII-resistant lines, and the mutation was transmitted to the next generation. Further molecular and protein level experiments verified LOX3 deficiency and demonstrated the improvement of seed storability. Our work provides a flexible genome editing tool for improving important agronomic traits, as well as direct evidence that Lox3 has only a limited impact on seed longevity. PMID:26641666

Construction of RGO/CdIn2S4/g-C3N4 ternary hybrid with enhanced photocatalytic activity for the degradation of tetracycline hydrochloride

NASA Astrophysics Data System (ADS)

Xiao, Peng; Jiang, Deli; Ju, Lixin; Jing, Junjie; Chen, Min

2018-03-01

Although RGO shows great advantage in promoting charge separation and transfer of semiconductor, construction of an efficient RGO-incorporated photocatalyst is still challenging. Herein, RGO was employed to construct novel RGO/CdIn2S4/g-C3N4 (donated as RGO/CIS/CN) ternary photocatalyst by a facile hydrothermal method for the degradation of tetracycline hydrochloride (TC). The RGO/CIS/CN ternary photocatalyst showed significantly enhanced photocatalytic activity towards the degradation of TC as compared to the binary CIS/CN, CIS/CN, and CN/RGO. The photoluminescence and photocurrent response results indicate that this enhanced photocatalytic activity can be mainly ascribed to the improved charge separation and transfer efficiency. Based on the radical trapping and electron spin resonance results, the superoxide radicals and holes are proposed to play an important role in the degradation of TC over RGO/CIS/CN ternary photocatalyst. This work paves new opportunities for the synthesis of RGO-incorporated ternary photocatalyst as an efficient photocatalyst for the degradation of organic contaminant.

Enhanced Photocarrier Separation in Hierarchical Graphitic-C3N4-Supported CuInS2 for Noble-Metal-Free Z-Scheme Photocatalytic Water Splitting.

PubMed

Li, Xiaoxue; Xie, Keyu; Song, Long; Zhao, Mengjia; Zhang, Zhipan

2017-07-26

The effective separation of photogenerated electrons and holes in photocatalysts is a prerequisite for efficient photocatalytic water splitting. CuInS 2 (CIS) is a widely used light absorber that works properly in photovoltaics but only shows limited performance in solar-driven hydrogen evolution due to its intrinsically severe charge recombination. Here, we prepare hierarchical graphitic C 3 N 4 -supported CuInS 2 (denoted as GsC) by an in situ growth of CIS directly on exfoliated thin graphitic C 3 N 4 nanosheets (g-C 3 N 4 NS) and demonstrate efficient separation of photoinduced charge carriers in the GsC by forming the Z-scheme system for the first time in CIS-catalyzed water splitting. Under visible light illumination, the GsC features an enhanced hydrogen evolution rate up to 1290 μmol g -1 h -1 , which is 3.3 and 6.1 times higher than that of g-C 3 N 4 NS and bare-CIS, respectively, thus setting a new performance benchmark for CIS-based water-splitting photocatalysts.

Optical control of GPR40 signalling in pancreatic β-cells.

PubMed

Frank, James Allen; Yushchenko, Dmytro A; Fine, Nicholas H F; Duca, Margherita; Citir, Mevlut; Broichhagen, Johannes; Hodson, David J; Schultz, Carsten; Trauner, Dirk

2017-11-01

Fatty acids activate GPR40 and K + channels to modulate β-cell function. Herein, we describe the design and synthesis of FAAzo-10 , a light-controllable GPR40 agonist based on Gw-9508. FAAzo-10 is a potent GPR40 agonist in the trans -configuration and can be inactivated on isomerization to cis with UV-A light. Irradiation with blue light reverses this effect, allowing FAAzo-10 activity to be cycled ON and OFF with a high degree of spatiotemporal precision. In dissociated primary mouse β-cells, FAAzo-10 also inactivates voltage-activated and ATP-sensitive K + channels, and allows us to control glucose-stimulated Ca 2+ oscillations in whole islets with light. As such, FAAzo-10 is a useful tool to study the complex effects, with high specificity, which FA-derivatives such as Gw-9508 exert at multiple targets in mouse β-cells.

Toward understanding the evolution of vertebrate gene regulatory networks: comparative genomics and epigenomic approaches.

PubMed

Martinez-Morales, Juan R

2016-07-01

Vertebrates, as most animal phyla, originated >500 million years ago during the Cambrian explosion, and progressively radiated into the extant classes. Inferring the evolutionary history of the group requires understanding the architecture of the developmental programs that constrain the vertebrate anatomy. Here, I review recent comparative genomic and epigenomic studies, based on ChIP-seq and chromatin accessibility, which focus on the identification of functionally equivalent cis-regulatory modules among species. This pioneer work, primarily centered in the mammalian lineage, has set the groundwork for further studies in representative vertebrate and chordate species. Mapping of active regulatory regions across lineages will shed new light on the evolutionary forces stabilizing ancestral developmental programs, as well as allowing their variation to sustain morphological adaptations on the inherited vertebrate body plan. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Treatment Patterns for Cervical Carcinoma In Situ in Michigan, 1998-2003

PubMed Central

Patel, Divya A.; Saraiya, Mona; Copeland, Glenn; Cote, Michele L.; Datta, S. Deblina; Sawaya, George F.

2015-01-01

Objective To characterize population-level surgical treatment patterns for cervical carcinoma in situ (CIS) reported to the Michigan Cancer Surveillance Program (MCSP), and to inform data collection strategies. Methods All cases of cervical carcinoma in situ (CIS) (including cervical intraepithelial neoplasia grade 3 and adenocarcinoma in situ [AIS]) reported to the MCSP during 1998–2003 were identified. First course of treatment (ablative procedure, cone biopsy, loop electrosurgical excisional procedure [LEEP], hysterectomy, unspecified surgical treatment, no surgical treatment, unknown if surgically treated) was described by histology, race, and age at diagnosis. Results Of 17,022 cases of cervical CIS, 82.8% were squamous CIS, 3% AIS/adenosquamous CIS, and 14.2% unspecified/other CIS. Over half (54.7%) of cases were diagnosed in women under age 30. Excisional treatments (LEEP, 32.3% and cone biopsy, 17.3%) were most common, though substantial proportions had no reported treatment (17.8%) or unknown treatment (21.1%). Less common were hysterectomy (7.2%) and ablative procedures (2.6%). LEEP was the most common treatment for squamous cases, while hysterectomy was the most treatment for AIS/adenosquamous CIS cases. Across histologic types, a sizeable proportion of women diagnosed ≤30 years of age underwent excision, either LEEP (20%–38.7%) or cone biopsy (13.7%–44%). Conclusion Despite evidence suggesting it may be safer and equally effective as excision, ablation was rarely used for treating cervical squamous CIS. These population-based data indicate some notable differences in treatment by histology and age at diagnosis, with observed patterns appearing consistent with consensus guidelines in place at the time of study, but favoring more aggressive procedures. Future data collection strategies may need to validate treatment information, including the large proportion of no or unknown treatment. PMID:24002133

Hazard identification of cis/trans-zearalenone through the looking-glass.

PubMed

Dellafiora, Luca; Galaverna, Gianni; Dall'Asta, Chiara; Cozzini, Pietro

2015-12-01

Among the food-related health issues, the presence of contaminants has a prominent role, due to the wide range of exogenous compounds that can occur in food commodities and to their large differences in structure and biological activity. A comprehensive assessment of the related risk is thus actually demanding in terms of time and facilities involved. In this context, the use of computational strategies can be an effective choice for supporting the hazard identification procedure at the early stage. In this work, we focused on the food contaminant zearalenone by comparing the trans and cis isomers, respectively the well-known mycoestrogen and its still largely understudied isomer. We estimated the possible effects exerted by human metabolism on the xenoestrogenicity of cis-ZEN by using a validated in silico strategy based on docking simulations and rescoring procedures. Similarly, the exploitation of the most promising enzymatic detoxifying routes designed for trans-ZEN - which relies on the enzyme lactono hydrolase from Clonostachys rosea - has been assessed for the cis-isomer as well. Our results showed that both isomers can act as functional analogues with respect to xenoestrogenic activity, and several cis-ZEN metabolites with high biological potential have been identified. On the contrary, in spite of the high degree of structural analogy, the cis isomer showed a pattern of interaction with the degrading enzyme in stark contrast with that observed for trans-ZEN. For these reasons, the outcomes presented herein strongly support the inclusion of cis-ZEN in further studies of occurrence, metabolism and bioactivity assessment, and suggest the need for a dedicated handling for the cis isomer in risk assessment studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Muscarinic subtypes profile modulation within a series of new antagonists, bridged bicyclic derivatives of 2,2-diphenyl-[1,3]-dioxolan-4-ylmethyl-dimethylamine.

PubMed

Piergentili, Alessandro; Gentili, Francesco; Ghelfi, Francesca; Marucci, Gabriella; Pigini, Maria; Quaglia, Wilma; Giannella, Mario

2003-09-01

A set of new muscarinic antagonists, bridged bicyclic derivatives of 2,2-diphenyl-[1,3]-dioxolan-4-ylmethyl-dimethylamine (1), was synthesized and tested to evaluate their affinity and selectivity for M(1), M(2), M(3) and M(4) receptor subtypes. The conformational constraint of 1 in a bicyclic structure, and the variation in distance and stereochemistry of the active functions allowed us to modulate the selectivity of interaction with the M(1)-M(3) receptor subtypes. The most interesting compound was (cis,trans)-2-(2,2-diphenylethyl)-5-methyl-tetrahydro-[1,3]dioxolo[4,5-c]pyrrole oxalate (6), which is equipotent with Pirenzepine on rabbit vas deferens (M(1)-putative) but shows a better selectivity profile.

Parental 'affectionless control' in adolescent depressive disorder.

PubMed

Patton, G C; Coffey, C; Posterino, M; Carlin, J B; Wolfe, R

2001-10-01

Adults with depressive disorder report high rates of sub-optimal maternal care in childhood. Despite the greater salience of relationships with parents earlier in life, associations with parenting style have not yet been systematically studied in adolescent onset disorder. A six-wave, 3-year study of adolescent health in 2032 Australian secondary school students provided an opportunity to undertake a two-phase study of early onset depression. Between waves 2 to 6, a self-administered computerised form of the revised Clinical Interview Schedule (CIS-R) was used to generate a first phase diagnosis of ICD-10 depressive episode. Each subject with a CIS-R-defined depressive episode was selected for second phase assessment together with two subjects from the CIS-R non-cases in each school. Second phase assessment included a second diagnostic assessment using the depression and hypomania modules of the Composite International Diagnostic Interview (CIDI) and assessment of paternal and maternal style using the Parental Bonding Instrument. A total of 1947 out of 2032 subjects in the sampling frame (95.8%) participated in the cohort study (phase 1) at least once; 406 (94%) of the 435 selected subjects completed second phase assessment. One hundred and nineteen subjects fulfilled criteria for depressive episode on the CIS-R at one or more waves. Over the 30-month study period, 69 subjects (10 male, 59 female) fulfilled both CIS-R and CIDI definitions of depression at the same wave and were classified as 'definite depressive disorder'. Low maternal and paternal care held independent associations with both definitions of depression, with the effects clearest in those in the lowest quartile of reported care. After adjusting for low parental care, the associations between high parental control and depression were small. Sub-optimal parenting is associated with depressive disorder in adolescents. Low maternal and paternal care are each associated with a two- to three-fold higher rate of depressive disorder. These findings are consistent with an effect of sub-optimal parenting on the onset rather than course of disorder. Whether sub-optimal parenting is associated with a risk for the onset of depression outside the adolescent years has yet to be clarified.

Improvements of reinforced silica aerogel nanocomposites thermal properties for architecture applications.

PubMed

Saboktakin, Amin; Saboktakin, Mohammad Reza

2015-01-01

An 1,4-cis polybutadiene rubber/carboxymethyl starch (CMS)-based silica aerogel nanocomposites as a insulation material was developed that will provide superior thermal insulation properties, flexibility, toughness, durability of the parent polymer, yet with the low density and superior insulation properties associated with the aerogels. In this study, reinforced 1,4-cis polybutadiene-CMS-silica aerogel nanocomposites were prepared from a silica aerogel with a surface area 710 m(2) g(-1), a pore size of 25.3 nm and a pore volume of 4.7 cm(3) g(-1). The tensile properties and dynamic mechanical properties of 1,4-cis polybutadiene/CMS nanocomposites were systematically enhanced at low silica loading. Similar improvements in tensile modulus and strength have been observed for 1,4-cis polybutadiene/CMS mesoporous silica aerogel nanocomposites. Copyright © 2014 Elsevier B.V. All rights reserved.

Herpesvirus papio contains a plasmid origin of replication that acts in cis interspecies with an Epstein-Barr virus trans-acting function.

PubMed Central

Pesano, R L; Pagano, J S

1986-01-01

Herpesvirus papio (HVP) and Epstein-Barr virus (EBV) are closely related biologically and biochemically; lymphoblastoid cells infected with either virus contain episomal viral DNA. The putative origin of replication for EBV plasmids (oriP) has been assigned to a 1,790-base-pair fragment (cis) in the short unique region of the genome which requires a viral function supplied in trans from elsewhere in the genome (J. Yates, N. Warren, D. Reisman, and B. Sugden, Proc. Natl. Acad. Sci. USA 81:3806-3810, 1984). We report here the identification of the putative origin of replication (cis) in HVP; we assigned it to the HVP EcoRI K fragment. The results indicate that the HVP replication process requires both a cis and a trans-acting function, analogous to that found in EBV. Images PMID:3023667

Hydrated Electrons React with High Specificity with Cisplatin Bound to Single-Stranded DNA

PubMed Central

Behmand, B.; Cloutier, P.; Girouard, S.; Wagner, J. R.; Sanche, L.; Hunting, D. J.

2015-01-01

Short oligonucleotides TTTTTGTGTTT and TTTTTTTGTTT in solution with and without cisplatin (cisPt) bound to the guanine bases were irradiated with γ-rays at doses varying from 0 to 2500 Gy. To determine the effect of hydrated electrons from water radiolysis on the oligonucleotides, we quenched •OH radicals with ethylenediaminetetraacetic acid (EDTA) and displaced oxygen, which reacts with hydrated electrons, by bubbling the solution with wet nitrogen. DNA strand breaks and platinum detachment were quantified by gel electrophoresis. Our results demonstrate that hydrated electrons react almost exclusively at the position of the cisPt adduct, where they induce cisPt detachment from one or both guanines in the oligonucleotide. Given the high yield of hydrated electrons in irradiated tissues, this reaction may be an important step in the mechanism of radiosensitization of DNA by cisPt. PMID:24205952

Effect of incremental levels of sunflower-seed oil in the diet on ruminal lipid metabolism in lactating cows.

PubMed

Shingfield, K J; Ahvenjärvi, S; Toivonen, V; Vanhatalo, A; Huhtanen, P; Griinari, J M

2008-05-01

Based on the potential benefits of cis-9, trans-11-conjugated linoleic acid (CLA) for human health there is interest in developing sustainable nutritional strategies for enhancing the concentration of this fatty acid in ruminant-derived foods. Most evidence to date suggests that endogenous synthesis is the major source of cis-9, trans-11 in milk fat and ruminal outflow is limited and largely independent of dietary 18 : 2n-6 supply. Four lactating cows fitted with a rumen cannula were used in a 4 x 4 Latin square with 14 d experimental periods to examine the effects of sunflower-seed oil (SFO) as a source of 18 : 2n-6 on ruminal lipid metabolism. Cows were offered grass silage-based diets supplemented with 0, 250, 500 or 750 g SFO/d. Supplements of SFO had no effect on DM intake, milk fat or protein secretion, but increased linearly (P < 0.01) milk yield and milk lactose output and shifted (P < 0.001) rumen fermentation towards propionate at the expense of acetate. SFO supplements increased linearly (P < 0.05) the flow of 18 : 0, 18 : 1, 18 : 2n-6 and total CLA at the omasum and enhanced ruminal cis-9-18 : 1, 18 : 2n-6 and 18 : 3n-3 metabolism. Flows of all-trans- (Delta4-16) and cis- (Delta9-16) 18 : 1 isomers were elevated, while increases in ruminal CLA outflow were confined to trans-8, trans-10 and geometric 9,11 and 10,12 isomers. It is concluded that supplementing grass silage-based diets with plant oils rich in 18 : 2n-6 enhances ruminal outflow of trans-11-18 : 1 and cis-9, trans-11-CLA in lactating cows.

Chemical probes of the conformation of DNA modified by cis-diamminedichloroplatinum(II)

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

Marrot, L.; Leng, M.

The purpose of this work was to analyze at the nucleotide level the distortions induced by the binding of cis-diamminedichloroplatinum(II) (cis-DDP) to DNA by means of chemical probes. In order to test the chemical probes, experiments were first carried out on two platinated oligonucleotides. It has been verified by circular dichroism and gel electrophoresis that the binding of cis-DDP to an AG or to a GTG site within a double-stranded oligonucleotide distorts the double helix. The reactivity of the oligonucleotide platinated at the GTG site with chloroacetaldehyde, diethyl pyrocarbonate, and osmium tetraoxide, respectively, suggests a local denaturation of the doublemore » helix. The 5'G residue and the T residue within the adduct are no longer paired, while the 3'G residue is paired. The double helix is more distorted (but not denatured) at the 5' side of the adduct than at the 3' side. The reactivities of the chemical probes with six platinated DNA restriction fragments show that even at a relatively high level of platination only a few base pairs are unpaired but the double helix is largely distorted. No local denaturation has been detected at the GG sites separated from the nearest GG or AG sites by at least three base pairs. The AG sites separated from the nearest AG or GG sites by at least three base pairs do not denature the double helix locally when they are in the sequences puAG/pyTC. It is suggested that the distortion within these sequences is induced by adducts located further away along the DNA fragments, these sequences not being the major sites for the binding of cis-DDP.« less

Photoregeneration of bovine rhodopsin from its signaling state.

PubMed

Arnis, S; Hofmann, K P

1995-07-25

In rhodopsin, 11-cis-retinal is bound by a protonated Schiff base and acts as a strong antagonist, which holds the receptor in its inactive ground state conformation. Light induces cis-/trans-retinal isomerization and a sequence of thermal transitions through intermediates. The active conformation that catalyzes GDP/GTP exchange in the G-protein (Gt) is generated from the metarhodopsin II intermediate (MII) and mediated by Schiff base proton translocation and proton uptake from the aqueous phase. In the stable nucleotide-free MII-Gt complex, any thermal transition of MII into other forms of rhodopsin is blocked. We have now studied how Gt affects flash-induced photochemical conversions of MII. Difference spectra from measured absorption changes show that MII photolyzes through two parallel pathways, with fast (1 ms) and slow (50 ms) kinetics (12 degrees C, pH 6). The slow pathway regenerates rhodopsin (9- or 11-cis) via Schiff base reprotonation and proton release. We infer a cis-isomerized early photoproduct (reverted meta, RM) preceding these thermal transitions. When MII is photolyzed in the MII-Gt complex, the slow absorption change is abolished, indicating that Gt blocks the completion of the regeneration process. This is due to the formation of a stable RM-Gt complex, as shown by successive photolysis of MII, RM, and ground state rhodopsin, and the application of GTP gamma S at different stages. The complex dissociates with GTP gamma S, and rhodopsin relaxes to the ground state. The results indicate that cis-retinal and Gt can bind to the receptor at the same time. We discuss the result that the protonations in the meta II state uncouple retinal geometry from Gt interaction.

A novel speech-processing strategy incorporating tonal information for cochlear implants.

PubMed

Lan, N; Nie, K B; Gao, S K; Zeng, F G

2004-05-01

Good performance in cochlear implant users depends in large part on the ability of a speech processor to effectively decompose speech signals into multiple channels of narrow-band electrical pulses for stimulation of the auditory nerve. Speech processors that extract only envelopes of the narrow-band signals (e.g., the continuous interleaved sampling (CIS) processor) may not provide sufficient information to encode the tonal cues in languages such as Chinese. To improve the performance in cochlear implant users who speak tonal language, we proposed and developed a novel speech-processing strategy, which extracted both the envelopes of the narrow-band signals and the fundamental frequency (F0) of the speech signal, and used them to modulate both the amplitude and the frequency of the electrical pulses delivered to stimulation electrodes. We developed an algorithm to extract the fundatmental frequency and identified the general patterns of pitch variations of four typical tones in Chinese speech. The effectiveness of the extraction algorithm was verified with an artificial neural network that recognized the tonal patterns from the extracted F0 information. We then compared the novel strategy with the envelope-extraction CIS strategy in human subjects with normal hearing. The novel strategy produced significant improvement in perception of Chinese tones, phrases, and sentences. This novel processor with dynamic modulation of both frequency and amplitude is encouraging for the design of a cochlear implant device for sensorineurally deaf patients who speak tonal languages.

The DSF Family of Cell–Cell Signals: An Expanding Class of Bacterial Virulence Regulators

PubMed Central

Ryan, Robert P.; An, Shi-qi; Allan, John H.; McCarthy, Yvonne; Dow, J. Maxwell

2015-01-01

Many pathogenic bacteria use cell–cell signaling systems involving the synthesis and perception of diffusible signal molecules to control virulence as a response to cell density or confinement to niches. Bacteria produce signals of diverse structural classes. Signal molecules of the diffusible signal factor (DSF) family are cis-2-unsaturated fatty acids. The paradigm is cis-11-methyl-2-dodecenoic acid from Xanthomonas campestris pv. campestris (Xcc), which controls virulence in this plant pathogen. Although DSF synthesis was thought to be restricted to the xanthomonads, it is now known that structurally related molecules are produced by the unrelated bacteria Burkholderia cenocepacia and Pseudomonas aeruginosa. Furthermore, signaling involving these DSF family members contributes to bacterial virulence, formation of biofilms and antibiotic tolerance in these important human pathogens. Here we review the recent advances in understanding DSF signaling and its regulatory role in different bacteria. These advances include the description of the pathway/mechanism of DSF biosynthesis, identification of novel DSF synthases and new members of the DSF family, the demonstration of a diversity of DSF sensors to include proteins with a Per-Arnt-Sim (PAS) domain and the description of some of the signal transduction mechanisms that impinge on virulence factor expression. In addition, we address the role of DSF family signals in interspecies signaling that modulates the behavior of other microorganisms. Finally, we consider a number of recently reported approaches for the control of bacterial virulence through the modulation of DSF signaling. PMID:26181439

Transient-Absorption Spectroscopy of Cis-Trans Isomerization of N,N-dimethyl-4,4'-Azodianiline with 3D-Printed Temperature-Controlled Sample Holder

ERIC Educational Resources Information Center

Kosenkov, Dmytro; Shaw, James; Zuczek, Jennifer; Kholod, Yana

2016-01-01

The laboratory unit demonstrates a project based approach to teaching physical chemistry laboratory where upper-division undergraduates carry out a transient-absorption experiment investigating the kinetics of cis-trans isomerization of N,N-dimethyl-4,4'-azodianiline. Students participate in modification of a standard flash-photolysis spectrometer…

Getting It Going--Keeping It Running: A Handbook for Career Information Systems.

ERIC Educational Resources Information Center

Clyde, John S.

This handbook was designed as a tool to assist school and agency staff in management and in-service training needed in implementing a comprehensive Career Information System (CIS). The background, goals, and organization of CIS are given briefly. An explanation of the System which is computer-based yet also employs a manual needle-sort system is…

Multiple polysaccharide-drug complex-loaded liposomes: A unique strategy in drug loading and cancer targeting.

PubMed

Ruttala, Hima Bindu; Ramasamy, Thiruganesh; Gupta, Biki; Choi, Han-Gon; Yong, Chul Soon; Kim, Jong Oh

2017-10-01

In the present study, a unique strategy was developed to develop nanocarriers containing multiple therapeutics with controlled release characteristics. In this study, we demonstrated the synthesis of dextran sulfate-doxorubicin (DS-DOX) and alginate-cisplatin (AL-CIS) polymer-drug complexes to produce a transferrin ligand-conjugated liposome. The targeted nanoparticles (TL-DDAC) were nano-sized and spherical. The targeted liposome exhibited a specific receptor-mediated endocytic uptake in cancer cells. The enhanced cellular uptake of TL-DDAC resulted in a significantly better anticancer effect in resistant and sensitive breast cancer cells compared to that of the free drugs. Specifically, DOX and CIS at a molar ratio of 1:1 exhibited better therapeutic performance compared to that of other combinations. The combination of an anthracycline-based topoisomerase II inhibitor (DOX) and a platinum compound (CIS) resulted in significantly higher cell apoptosis (early and late) in both types of cancer cells. In conclusion, treatment with DS-DOX and AL-CIS based combination liposomes modified with transferrin (TL-DDAC) was an effective cancer treatment strategy. Further investigation in clinically relevant animal models is warranted to prove the therapeutic efficacy of this unique strategy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cisplatin impairs rat liver mitochondrial functions by inducing changes on membrane ion permeability: prevention by thiol group protecting agents.

PubMed

Custódio, José B A; Cardoso, Carla M P; Santos, Maria S; Almeida, Leonor M; Vicente, Joaquim A F; Fernandes, Maria A S

2009-05-02

Cisplatin (CisPt) is the most important platinum anticancer drug widely used in the treatment of head, neck, ovarian and testicular cancers. However, the mechanisms by which CisPt induces cytotoxicity, namely hepatotoxicity, are not completely understood. The goal of this study was to investigate the influence of CisPt on rat liver mitochondrial functions (Ca(2+)-induced mitochondrial permeability transition (MPT), mitochondrial bioenergetics, and mitochondrial oxidative stress) to better understand the mechanism underlying its hepatotoxicity. The effect of thiol group protecting agents and some antioxidants against CisPt-induced mitochondrial damage was also investigated. Treatment of rat liver mitochondria with CisPt (20nmol/mg protein) induced Ca(2+)-dependent mitochondrial swelling, depolarization of membrane potential (DeltaPsi), Ca(2+) release, and NAD(P)H fluorescence intensity decay. These effects were prevented by cyclosporine A (CyA), a potent and specific inhibitor of the MPT. In the concentration range of up to 40nmol/mg protein, CisPt slightly inhibited state 3 and stimulated state 2 and state 4 respiration rates using succinate as respiratory substrate. The respiratory indexes, respiratory control ratio (RCR) and ADP/O ratios, the DeltaPsi, and the ADP phosphorylation rate were also depressed. CisPt induced mitochondrial inner membrane permeabilization to protons (proton leak) but did not induce significant changes on mitochondrial H(2)O(2) generation. All the effects induced by CisPt on rat liver mitochondria were prevented by thiol group protecting agents namely, glutathione (GSH), dithiothreitol (DTT), N-acetyl-L-cysteine (NAC) and cysteine (CYS), whereas superoxide-dismutase (SOD), catalase (CAT) and ascorbate (ASC) were without effect. In conclusion, the anticancer drug CisPt: (1) increases the sensitivity of mitochondria to Ca(2+)-induced MPT; (2) interferes with mitochondrial bioenergetics by increasing mitochondrial inner membrane permeabilization to H(+); (3) does not significantly affect H(2)O(2) generation by mitochondria; (4) its mitochondrial damaging effects are protected by thiol group protecting agents. Based on these conclusions, it is possible to hypothesise that small changes on the redox-status of thiol groups, affecting membrane permeability to cations (Ca(2+) and H(+)) underlie CisPt-induced liver mitochondrial damage, putatively responsible for its hepatotoxicity. Therefore, we propose that CisPt-induced mitochondrial damage and consequent hepatotoxicity could be prevented by using thiol group protecting agents as therapeutic adjuvants.

Facile Synthesis of Novel Redox-Mediator-free Direct Z-Scheme CaIn2S4 Marigold-Flower-like/TiO2 Photocatalysts with Superior Photocatalytic Efficiency.

PubMed

Jo, Wan-Kuen; Sivakumar Natarajan, Thillai

2015-08-12

Novel redox-mediator-free direct Z-scheme CaIn2S4 marigold-flower-like/TiO2 (CIS/TNP) photocatalysts with different CaIn2S4 weight percentages were synthesized using a facile wet-impregnation method. Uniform hierarchical marigold-flower-like CaIn2S4 (CIS) microspheres were synthesized using a hydrothermal method. Field-emission scanning electron microscopy and transmission electron microscopy analyses suggested that the formation and aggregation of nanoparticles, followed by the growth of petals or sheets and their subsequent self-assembly, led to the formation of the uniform hierarchical marigold-flower-like CIS structures. The photocatalytic degradation efficiency of the direct Z-scheme CIS/TNP photocatalysts was evaluated through the degradation of the pharmaceutical compounds isoniazid (ISN) and metronidazole (MTZ). The direct Z-scheme CaIn2S4 marigold-flower-like/TiO2 (1%-CIS/TNP) photocatalyst showed enhanced performance in the ISN (71.9%) and MTZ (86.5%) photocatalytic degradations as compared to composites with different CaIn2S4 contents or the individual TiO2 and CaIn2S4. A possible enhancement mechanism based on the Z-scheme formed between the CIS and TNP for the improved photocatalytic efficiency was also proposed. The recombination rate of the photoinduced charge carriers was significantly suppressed for the direct Z-scheme CIS/TNP photocatalyst, which was confirmed by photoluminescence analysis. Radical-trapping studies revealed that photogenerated holes (h+), •OH, and O2•- are the primary active species, and suggested that the enhanced photocatalytic efficiency of the 1%-CIS/TNP follows the Z-scheme mechanism for transferring the charge carriers. It was further confirmed by hydroxyl (•OH) radical determination via fluorescence techniques revealed that higher concentration of •OH radical were formed over 1%-CIS/TNP than over bare CIS and TNP. The separation of the charge carriers was further confirmed using photocurrent and electron spin resonance measurements. Kinetic and chemical oxygen demand analyses were performed to confirm the ISN and MTZ degradation. The results demonstrated that the direct Z-scheme CIS/TNP photocatalyst shows superior decomposition efficiency for the degradation of these pharmaceuticals under the given reaction conditions.

Engineering a hyper-catalytic enzyme by photo-activated conformation modulation

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

Agarwal, Pratul K

2012-01-01

Enzyme engineering for improved catalysis has wide implications. We describe a novel chemical modification of Candida antarctica lipase B that allows modulation of the enzyme conformation to promote catalysis. Computational modeling was used to identify dynamical enzyme regions that impact the catalytic mechanism. Surface loop regions located distal to active site but showing dynamical coupling to the reaction were connected by a chemical bridge between Lys136 and Pro192, containing a derivative of azobenzene. The conformational modulation of the enzyme was achieved using two sources of light that alternated the azobenzene moiety in cis and trans conformations. Computational model predicted thatmore » mechanical energy from the conformational fluctuations facilitate the reaction in the active-site. The results were consistent with predictions as the activity of the engineered enzyme was found to be enhanced with photoactivation. Preliminary estimations indicate that the engineered enzyme achieved 8-52 fold better catalytic activity than the unmodulated enzyme.« less

An integrative systems genetics approach reveals potential causal genes and pathways related to obesity.

PubMed

Kogelman, Lisette J A; Zhernakova, Daria V; Westra, Harm-Jan; Cirera, Susanna; Fredholm, Merete; Franke, Lude; Kadarmideen, Haja N

2015-10-20

Obesity is a multi-factorial health problem in which genetic factors play an important role. Limited results have been obtained in single-gene studies using either genomic or transcriptomic data. RNA sequencing technology has shown its potential in gaining accurate knowledge about the transcriptome, and may reveal novel genes affecting complex diseases. Integration of genomic and transcriptomic variation (expression quantitative trait loci [eQTL] mapping) has identified causal variants that affect complex diseases. We integrated transcriptomic data from adipose tissue and genomic data from a porcine model to investigate the mechanisms involved in obesity using a systems genetics approach. Using a selective gene expression profiling approach, we selected 36 animals based on a previously created genomic Obesity Index for RNA sequencing of subcutaneous adipose tissue. Differential expression analysis was performed using the Obesity Index as a continuous variable in a linear model. eQTL mapping was then performed to integrate 60 K porcine SNP chip data with the RNA sequencing data. Results were restricted based on genome-wide significant single nucleotide polymorphisms, detected differentially expressed genes, and previously detected co-expressed gene modules. Further data integration was performed by detecting co-expression patterns among eQTLs and integration with protein data. Differential expression analysis of RNA sequencing data revealed 458 differentially expressed genes. The eQTL mapping resulted in 987 cis-eQTLs and 73 trans-eQTLs (false discovery rate < 0.05), of which the cis-eQTLs were associated with metabolic pathways. We reduced the eQTL search space by focusing on differentially expressed and co-expressed genes and disease-associated single nucleotide polymorphisms to detect obesity-related genes and pathways. Building a co-expression network using eQTLs resulted in the detection of a module strongly associated with lipid pathways. Furthermore, we detected several obesity candidate genes, for example, ENPP1, CTSL, and ABHD12B. To our knowledge, this is the first study to perform an integrated genomics and transcriptomics (eQTL) study using, and modeling, genomic and subcutaneous adipose tissue RNA sequencing data on obesity in a porcine model. We detected several pathways and potential causal genes for obesity. Further validation and investigation may reveal their exact function and association with obesity.

Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

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

Suh, Myungkoo

1995-12-06

Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7β, 8α-dihydoxy-9α, l0α-epoxy-7,8,9, 10-tetrahydrobenzo[α]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, (-)-trans-, (+)-cis- and (-)-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( ~25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant π-π stacking interactions between the pyrenyl residues and the bases.more » Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G 2 or G 3 (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N 2-dG in DNA isolated from the skin of mice treated topically with benzo[α]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N 2-dG.« less

Collision tectonics of the Central Indian Suture zone as inferred from a deep seismic sounding study

USGS Publications Warehouse

Mall, D.M.; Reddy, P.R.; Mooney, W.D.

2008-01-01

The Central Indian Suture (CIS) is a mega-shear zone extending for hundreds of kilometers across central India. Reprocessing of deep seismic reflection data acquired across the CIS was carried out using workstation-based commercial software. The data distinctly indicate different reflectivity characteristics northwest and southeast of the CIS. Reflections northwest of the CIS predominantly dip southward, while the reflection horizons southeast of the CIS dip northward. We interpret these two adjacent seismic fabric domains, dipping towards each other, to represent a suture between two crustal blocks. The CIS itself is not imaged as a sharp boundary, probably due to the disturbed character of the crust in a 20 to 30-km-wide zone. The time sections also show the presence of strong bands of reflectors covering the entire crustal column in the first 65??km of the northwestern portion of the profile. These reflections predominantly dip northward creating a domal structure with the apex around 30??km northwest of the CIS. There are a very few reflections in the upper 2-2.5??s two-way time (TWT), but the reflectivity is good below 2.5??s TWT. The reflection Moho, taken as the depth to the deepest set of reflections, varies in depth from 41 to 46??km and is imaged sporadically across the profile with the largest amplitude occurring in the northwest. We interpret these data as recording the presence of a mid-Proterozoic collision between two micro-continents, with the Satpura Mobile Belt being thrust over the Bastar craton. ?? 2008.

Photoisomerization and photochemistry of matrix-isolated 3-furaldehyde.

PubMed

Kuş, Nihal; Reva, Igor; Fausto, Rui

2010-12-02

3-Furaldehyde (3FA) was isolated in an argon matrix at 12 K and studied using FTIR spectroscopy and quantum chemistry. The molecule has two conformers, with trans and cis orientation of the O=C-C=C dihedral angle. At the B3LYP/6-311++G(d,p) level of theory, the trans form was computed to be ca. 4 kJ mol(-1) more stable than the cis form. The relative stability of the two conformers was explained using the natural bond orbital (NBO) method. In fair agreement with their calculated relative energies and the high barrier of rotamerization (ca. 34 kJ mol(-1) from trans to cis), the trans and cis conformers were trapped in an argon matrix from the compound room temperature gas phase in proportion ~7:1. The experimentally observed vibrational signatures of the two forms are in a good agreement with the theoretically calculated spectra. Broad-band UV-irradiation (λ > 234 nm) of the matrix-isolated compound resulted in partial trans → cis isomerization, which ended at a photostationary state with the trans/cis ratio being ca. 1.85:1. This result was interpreted based on results of time-dependent DFT calculations. Irradiation at higher energies (λ > 200 nm) led to decarbonylation of the compound, yielding furan, cyclopropene-3-carbaldehyde, and two C(3)H(4) isomers: cyclopropene and propadiene.

Fabrication of a white electroluminescent device based on bilayered yellow and blue quantum dots

NASA Astrophysics Data System (ADS)

Kim, Jong-Hoon; Lee, Ki-Heon; Kang, Hee-Don; Park, Byoungnam; Hwang, Jun Yeon; Jang, Ho Seong; Do, Young Rag; Yang, Heesun

2015-03-01

Until now most work on colloidal quantum dot-light-emitting diodes (QLEDs) has been focused on the improvement of the electroluminescent (EL) performance of monochromatic devices, and multi-colored white QLEDs comprising more than one type of QD emitter have been rarely investigated. To demonstrate a white EL as a result of color mixing between blue and yellow, herein a unique combination of two dissimilar QDs of blue- CdZnS/ZnS plus a yellow-emitting Cu-In-S (CIS)/ZnS is used for the formation of the emitting layer (EML) of a multilayered QLED. First, the QLED consisting of a single EML randomly mixed with two QDs is fabricated, however, its EL is dominated by blue emission with the contribution of yellow emission substantially weaker. Thus, another EML configuration is devised in the form of a QD bilayer with two stacking sequences of CdZnS/ZnS//CIS/ZnS QD and vice versa. The QLED with the former stacking sequence shows an overwhelming contribution of blue EL, similar to the mixed QD EML-based device. Upon applying the oppositely stacked QD bilayer of CIS/ZnS//CdZnS/ZnS, however, a bicolored white EL can be successfully achieved by means of the effective extension of the radiative excitonic recombination zone throughout both QD EML regions. Such QD EML configuration-dependent EL results, which are discussed primarily using the proposed device energy level diagram, strongly suggest that the positional design of individual QD emitters is a critical factor for the realization of multicolored, white emissive devices.Until now most work on colloidal quantum dot-light-emitting diodes (QLEDs) has been focused on the improvement of the electroluminescent (EL) performance of monochromatic devices, and multi-colored white QLEDs comprising more than one type of QD emitter have been rarely investigated. To demonstrate a white EL as a result of color mixing between blue and yellow, herein a unique combination of two dissimilar QDs of blue- CdZnS/ZnS plus a yellow-emitting Cu-In-S (CIS)/ZnS is used for the formation of the emitting layer (EML) of a multilayered QLED. First, the QLED consisting of a single EML randomly mixed with two QDs is fabricated, however, its EL is dominated by blue emission with the contribution of yellow emission substantially weaker. Thus, another EML configuration is devised in the form of a QD bilayer with two stacking sequences of CdZnS/ZnS//CIS/ZnS QD and vice versa. The QLED with the former stacking sequence shows an overwhelming contribution of blue EL, similar to the mixed QD EML-based device. Upon applying the oppositely stacked QD bilayer of CIS/ZnS//CdZnS/ZnS, however, a bicolored white EL can be successfully achieved by means of the effective extension of the radiative excitonic recombination zone throughout both QD EML regions. Such QD EML configuration-dependent EL results, which are discussed primarily using the proposed device energy level diagram, strongly suggest that the positional design of individual QD emitters is a critical factor for the realization of multicolored, white emissive devices. Electronic supplementary information (ESI) available: Detailed description of synthesis of CdZnS/ZnS, CIS/ZnS QDs and ZnO NPs; TEM images of CdZnS/ZnS and CIS/ZnS QDs; voltage-dependent luminance (CE variations of blue CdZnS/ZnS and yellow CIS/ZnS monochromatic QLEDs; EL spectra and energy band diagram of bilayered QD EML-based QLED with a stacking sequence of CdZnS/ZnS//CIS/ZnS QD; normalized EL spectra of CIS/ZnS//CdZnS/ZnS QD-bilayered QLEDs; comparison of current density of monochromatic QLEDs and bicolored white QLEDs; and voltage-dependent luminance (CE variations of CIS/ZnS QLED fabricated through 150 °C-EML baking. See DOI: 10.1039/c5nr00426h

Cost-effectiveness of pemetrexed in combination with cisplatin as first line treatment for patients with advanced non-squamous non-small-cell lung cancer in Spain.

PubMed

González García, Jonathan; Gutiérrez Nicolás, Fernando; Nazco Casariego, Gloria Julia; Valcárcel Nazco, Cristina; Batista López, Jose Norberto; Oramas Rodríguez, Juana

2017-01-01

Lung cancer is the third most frequent neoplastic tumour in Spain, with around 27 000 new cases diagnosed per year; 80-95% of these are non-small-cell cancer (NSCLC), and the majority of cases are diagnosed in advanced stages of the disease, and for this reason it is one of the oncologic conditions with higher mortality rates (21.4% mean survival at 5 years). The main treatment regimens used for first-line treatment of NSCLC are: cisplatin/pemetrexed (cis/pem), cisplatin/gemcitabine/ bevacizumab (cis/gem/bev), and carboplatin/paclitaxel/ bevacizumab (carb/pac/bev). The objective of this study was to evaluate the cost-effectiveness ratio of antineoplastic 1st line NSCLC treatment regimens, from the point of view of hospital management. A cost-efficacy mathematical model was prepared, based on a decision tree. The efficacy variable was Progression Free Survival, obtained from the PARAMOUNT, AVAIL and SAIL Phase III clinical trials. The study was conducted from the perspective of the hospital management, considering only the direct costs of drug acquisition. A deterministic sensitivity analysis was conducted to confirm the robustness of outcomes. The PFS obtained in clinical trials with cis/pem, cis/ gem/bev and carb/pac/bev was: 6.9, 6.7 and 6.2 months, respectively. Based on our model, the mean cost of treatment per patient for these regimens was: 19 942 €, 15 594 € and 36 095 €, respectively. The incremental cost-effectiveness ratio per month of additional PFS between cis/pem and cis/gem/bev was 19 303 €. Estimating a 30% reduction in acquisition costs for pemetrexed (Alimta®Eli Lilly Nederland B.V.), due to the forthcoming launch of generic medications, the cis/pem treatment would become the predominant alternative for 1st line treatment of NSCLC patients, by offering the best health results at a lower cost. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Defining adolescent common mental disorders using electronic primary care data: a comparison with outcomes measured using the CIS-R.

PubMed

Cornish, Rosie P; John, Ann; Boyd, Andy; Tilling, Kate; Macleod, John

2016-12-01

To compare the prevalence of common mental disorders (CMDs) derived from data held in primary care records with that measured using the revised Clinical Interview Schedule (CIS-R) in order to assess the potential robustness of findings based only on routinely collected data. Comparison study using linkage between the Avon Longitudinal Study of Parents and Children (ALSPAC) and electronic primary care records. We studied 1562 adolescents who had completed the CIS-R in ALSPAC at age 17-18 years and had linkage established to their primary care records. Outcome measures from ALSPAC were whether or not an individual met International Classification of Diseases-10 criteria for a diagnosis of (1) a CMD or, specifically, (2) depression. Lists of Read codes corresponding to diagnoses, symptoms and treatments were used to create 12 definitions of CMD and depression alone using the primary care data. We calculated sensitivities and specificities of these, using CIS-R definitions as the reference standard. Sensitivities ranged from 5.2% to 24.3% for depression and from 3.8% to 19.2% for CMD. The specificities of all definitions were above 98% for depression and above 96% for CMD.For both outcomes, the definition that included current diagnosis, treatment or symptoms identified the highest proportion of CIS-R cases. Most individuals meeting case definitions for CMD based on primary care data also met CIS-R case definitions. Conversely many individuals identified as cases using the CIS-R had no evidence of CMD in their clinical records. This suggests that clinical databases are likely to yield underestimates of the burden of CMD in the population. However, clinical records appear to yield valid diagnoses which may be useful for studying risk factors and consequences of CMD. The greatest epidemiological value may be obtained when information is available from survey and clinical records. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Formic acid dimers in a nitrogen matrix

NASA Astrophysics Data System (ADS)

Lopes, Susy; Fausto, Rui; Khriachtchev, Leonid

2018-01-01

Formic acid (HCOOH) dimers are studied by infrared spectroscopy in a nitrogen matrix and by ab initio calculations. We benefit from the use of a nitrogen matrix where the lifetime of the higher-energy (cis) conformer is very long (˜11 h vs. 7 min in an argon matrix). As a result, in a nitrogen matrix, a large proportion of the cis conformer can be produced by vibrational excitation of the lower-energy (trans) conformer. Three trans-trans, four trans-cis, and three cis-cis dimers are found in the experiments. The spectroscopic information on most of these dimers is enriched compared to the previous studies in an argon matrix. The cis-cis dimers of ordinary formic acid (without deuteration) are reported here for the first time. Several conformational processes are obtained using selective excitation by infrared light, some of them also for the first time. In particular, we report on the formation of cis-cis dimers upon vibrational excitation of trans-cis dimers. Tunneling decays of several dimers have been detected in the dark. The tunneling decay of cis-cis dimers of formic acid as well as the stabilization of cis units in cis-cis dimers is also observed for the first time.

Formic acid dimers in a nitrogen matrix.

PubMed

Lopes, Susy; Fausto, Rui; Khriachtchev, Leonid

2018-01-21

Formic acid (HCOOH) dimers are studied by infrared spectroscopy in a nitrogen matrix and by ab initio calculations. We benefit from the use of a nitrogen matrix where the lifetime of the higher-energy (cis) conformer is very long (∼11 h vs. 7 min in an argon matrix). As a result, in a nitrogen matrix, a large proportion of the cis conformer can be produced by vibrational excitation of the lower-energy (trans) conformer. Three trans-trans, four trans-cis, and three cis-cis dimers are found in the experiments. The spectroscopic information on most of these dimers is enriched compared to the previous studies in an argon matrix. The cis-cis dimers of ordinary formic acid (without deuteration) are reported here for the first time. Several conformational processes are obtained using selective excitation by infrared light, some of them also for the first time. In particular, we report on the formation of cis-cis dimers upon vibrational excitation of trans-cis dimers. Tunneling decays of several dimers have been detected in the dark. The tunneling decay of cis-cis dimers of formic acid as well as the stabilization of cis units in cis-cis dimers is also observed for the first time.

cis-Proline-mediated Ser(P)[superscript 5] Dephosphorylation by the RNA Polymerase II C-terminal Domain Phosphatase Ssu72

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

Werner-Allen, Jon W.; Lee, Chul-Jin; Liu, Pengda

2012-05-16

RNA polymerase II coordinates co-transcriptional events by recruiting distinct sets of nuclear factors to specific stages of transcription via changes of phosphorylation patterns along its C-terminal domain (CTD). Although it has become increasingly clear that proline isomerization also helps regulate CTD-associated processes, the molecular basis of its role is unknown. Here, we report the structure of the Ser(P){sup 5} CTD phosphatase Ssu72 in complex with substrate, revealing a remarkable CTD conformation with the Ser(P){sup 5}-Pro{sup 6} motif in the cis configuration. We show that the cis-Ser(P){sup 5}-Pro{sup 6} isomer is the minor population in solution and that Ess1-catalyzed cis-trans-proline isomerizationmore » facilitates rapid dephosphorylation by Ssu72, providing an explanation for recently discovered in vivo connections between these enzymes and a revised model for CTD-mediated small nuclear RNA termination. This work presents the first structural evidence of a cis-proline-specific enzyme and an unexpected mechanism of isomer-based regulation of phosphorylation, with broad implications for CTD biology« less

Fabrication and Cytotoxicity of Fucoidan-Cisplatin Nanoparticles for Macrophage and Tumor Cells.

PubMed

Hwang, Pai-An; Lin, Xiao-Zhen; Kuo, Ko-Liang; Hsu, Fu-Yin

2017-03-14

Fucoidan, an anionic, sulfated polysaccharide from brown seaweed, is known to exhibit antitumor and immunomodulatory functions. To develop an immune protection and chemotherapeutic agent, fucoidan-cisplatin nanoparticles (FCNPs) were designed. FCNPs were prepared by mixing cisplatin with fucoidan solution or fucoidan with cisplatin solution, followed by dialysis to remove trace elements. The nanoparticles, comprising 10 mg of fucoidan and 2 mg of cisplatin, which exhibited the highest cisplatin content and loading efficiency during the production process, were named as Fu100Cis20. The cisplatin content, cisplatin loading efficiency, nanoparticle size, and zeta potential of Fu100Cis20 were 18.9% ± 2.7%, 93.3% ± 7.8%, 181.2 ± 21.0 nm, and -67.4 ± 2.3 mV, respectively. Immune protection assay revealed that Fu100Cis20-treated RAW264.7 cells were protected from the cytotoxicity of cisplatin. Furthermore, antitumor assay indicated that Fu100Cis20-treated HCT-8 cells showed stronger cytotoxicity than those treated with cisplatin alone. These results suggested that fucoidan-based nanoparticles exhibited suitable particle size and high drug encapsulation, and that Fu100Cis20 has potential application in both immunotherapy and chemotherapy.

Comparative effects of conjugated linoleic acid (CLA) and linoleic acid (LA) on the oxidoreduction status in THP-1 macrophages.

PubMed

Rybicka, Marta; Stachowska, Ewa; Gutowska, Izabela; Parczewski, Miłosz; Baśkiewicz, Magdalena; Machaliński, Bogusław; Boroń-Kaczmarska, Anna; Chlubek, Dariusz

2011-04-27

The aim of this study was to investigate the effect of conjugated linoleic acids (CLAs) on macrophage reactive oxygen species synthesis and the activity and expression of antioxidant enzymes, catalase (Cat), glutathione peroxidase (GPx), and superoxide dismutase (SOD). The macrophages were obtained from the THP-1 monocytic cell line. Cells were incubated with the addition of cis-9,trans-11 CLA or trans-10,cis-12 CLA or linoleic acid. Reactive oxygen species (ROS) formation was estimated by flow cytometry. Enzymes activity was measured spectrophotometrically. The antioxidant enzyme mRNA expression was estimated by real-time reverse transcriptase polymerase chain reaction (RT-PCR). Statistical analysis was based on nonparametric statistical tests [Friedman analysis of variation (ANOVA) and Wilcoxon signed-rank test]. cis-9,trans-11 CLA significantly increased the activity of Cat, while trans-10,cis-12 CLA notably influenced GPx activity. Both isomers significantly decreased mRNA expression for Cat. Only trans-10,cis-12 significantly influenced mRNA for SOD-2 expression. The CLAs activate processes of the ROS formation in macrophages. Adverse metabolic effects of each isomer action were observed.

Status of flexible CIS research at ISET

NASA Technical Reports Server (NTRS)

Basol, B. M.; Kapur, V. K.; Minnick, A.; Halani, A.; Leidholm, C. R.

1994-01-01

Polycrystalline thin film solar cells fabricated on light-weight, flexible substrates are very attractive for space applications. In this work CulnSe2 (CIS) based thin film devices were processed on metallic foil substrates using the selenization technique. CIS deposition method involved reaction of electron-bean evaporated Cu-In precursor layers with a selenizing atmosphere at around 400 C. Several metallic foils such as Mo, Ti, Al, Ni, and Cu were evaluated as possible substrates for these devices. Solar cells with AM1.5 efficiencies of 9.0-9.34 percent and good mechanical integrity were demonstrated on Mo and Ti foils. Monolithic integration of these devices was also demonstrated up to 4 in x 4 in size.

Synthesis of highly functionalized macrocycles by the peripheral functionalization of macrocyclic diimines.

PubMed

Sierra, Miguel A; Pellico, Daniel; Gómez-Gallego, Mar; Mancheño, María José; Torres, Rosario

2006-11-10

The easily available macrocyclic diimines 4-7 can be stereoselectively transformed to macrocyclic bis-beta-amino acids 13-17, macrocyclic bisazetidines 18-20, and macrocyclic bisamides 21 and 22 by means of the corresponding bis-beta-lactam scaffolds 8-12. These key intermediates are available through standard Staudinger reaction and obtained as the cis-cis diastereomers, exclusively. An interesting relation between the proximity of the reactive C=N bonds and the selectivity in the formation of the bis-beta-lactams 8-12 is observed. Thus, diimine 4 leads to low selectivities, producing a 1:1 mixture of cis-syn-cis and cis-anti-cis diastereomers, while diimines 5-7 having the diimine sites more separated lead almost exclusively to the cis-anti-cis diastereomers. The stereochemistry of all the products was unambiguously assigned by X-ray diffraction analysis of compounds cis-syn-cis 8 and cis-anti-cis 12-Co2CO6 complex.

Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome

PubMed Central

Sztuba-Solinska, Joanna; Teramoto, Tadahisa; Rausch, Jason W.; Shapiro, Bruce A.; Padmanabhan, Radhakrishnan; Le Grice, Stuart F. J.

2013-01-01

The Dengue virus (DENV) genome contains multiple cis-acting elements required for translation and replication. Previous studies indicated that a 719-nt subgenomic minigenome (DENV-MINI) is an efficient template for translation and (−) strand RNA synthesis in vitro. We performed a detailed structural analysis of DENV-MINI RNA, combining chemical acylation techniques, Pb2+ ion-induced hydrolysis and site-directed mutagenesis. Our results highlight protein-independent 5′–3′ terminal interactions involving hybridization between recognized cis-acting motifs. Probing analyses identified tandem dumbbell structures (DBs) within the 3′ terminus spaced by single-stranded regions, internal loops and hairpins with embedded GNRA-like motifs. Analysis of conserved motifs and top loops (TLs) of these dumbbells, and their proposed interactions with downstream pseudoknot (PK) regions, predicted an H-type pseudoknot involving TL1 of the 5′ DB and the complementary region, PK2. As disrupting the TL1/PK2 interaction, via ‘flipping’ mutations of PK2, previously attenuated DENV replication, this pseudoknot may participate in regulation of RNA synthesis. Computer modeling implied that this motif might function as autonomous structural/regulatory element. In addition, our studies targeting elements of the 3′ DB and its complementary region PK1 indicated that communication between 5′–3′ terminal regions strongly depends on structure and sequence composition of the 5′ cyclization region. PMID:23531545

Retinoic acid and nitric oxide promote cell proliferation and differentially induce neuronal differentiation in vitro in the cnidarian Renilla koellikeri.

PubMed

Estephane, Djoyce; Anctil, Michel

2010-10-01

Retinoic acid (RA) and nitric oxide (NO) are known to promote neuronal development in both vertebrates and invertebrates. Retinoic acid receptors appear to be present in cnidarians and NO plays various physiological roles in several cnidarians, but there is as yet no evidence that these agents have a role in neural development in this basal metazoan phylum. We used primary cultures of cells from the sea pansy Renilla koellikeri to investigate the involvement of these signaling molecules in cnidarian cell differentiation. We found that 9-cis RA induce cell proliferation in dose- and time-dependent manners in dishes coated with polylysine from the onset of culture. Cells in cultures exposed to RA in dishes devoid of polylysine were observed to differentiate into epithelium-associated cells, including sensory cells, without net gain in cell density. NO donors also induce cell proliferation in polylysine-coated dishes, but induce neuronal differentiation and neurite outgrowth in uncoated dishes. No other cell type undergoes differentiation in the presence of NO. These observations suggest that in the sea pansy (1) cell adhesion promotes proliferation without morphogenesis and this proliferation is modulated positively by 9-cis RA and NO, (2) 9-cis RA and NO differentially induce neuronal differentiation in nonadherent cells while repressing proliferation, and (3) the involvement of RA and NO in neuronal differentiation appeared early during the evolutionary emergence of nervous systems. 2010 Wiley Periodicals, Inc.

Excited stilbene: intramolecular vibrational redistribution and solvation studied by femtosecond stimulated Raman spectroscopy.

PubMed

Weigel, A; Ernsting, N P

2010-06-17

Excited-state relaxation of cis- and trans-stilbene is traced with femtosecond stimulated Raman spectroscopy, exploiting S(n) <-- S(1) resonance conditions. For both isomers, decay in Raman intensity, shift of spectral positions, and broadening of the bands indicate intramolecular vibrational redistribution (IVR). In n-hexane this process effectively takes 0.5-0.7 ps. Analysis of the intensity decay allows us to further distinguish two phases for trans-stilbene: fast IVR within a subset of modes (approximately 0.3 ps) followed by slower equilibration over the full vibrational manifold (approximately 0.9 ps). In acetonitrile IVR completes with 0.15 ps; this acceleration may originate from symmetry breakage induced by the polar solvent. Another process, dynamic solvation by acetonitrile, is seen as spectral narrowing and characteristic band shifts of the C=C stretch and phenyl bending modes with 0.69 ps. Wavepacket motion is observed in both isomers as oscillation of low-frequency bands with their pertinent mode frequency (90 or 195 cm(-1) in trans-stilbene; 250 cm(-1) in cis-stilbene). Anharmonic coupling shows up as a modulation of high-frequency peak positions by phenyl/ethylene torsion modes of 57 and 90 cm(-1). Decay and shift of the 90 cm(-1) inverse Raman band within the first 0.3 ps suggests a gradual involvement of phenyl/ethylene torsion in relaxation. In cis- and trans-stilbene, low-frequency spectral changes are found within 0.15 ps, indicating an additional ultrafast process.

Unsaturated fatty acyl recognition by Frizzled receptors mediates dimerization upon Wnt ligand binding

PubMed Central

Nile, Aaron H.; Mukund, Susmith; Stanger, Karen; Wang, Weiru; Hannoush, Rami N.

2017-01-01

Frizzled (FZD) receptors mediate Wnt signaling in diverse processes ranging from bone growth to stem cell activity. Moreover, high FZD receptor expression at the cell surface contributes to overactive Wnt signaling in subsets of pancreatic, ovarian, gastric, and colorectal tumors. Despite the progress in biochemical understanding of Wnt–FZD receptor interactions, the molecular basis for recognition of Wnt cis-unsaturated fatty acyl groups by the cysteine-rich domain (CRD) of FZD receptors remains elusive. Here, we determined a crystal structure of human FZD7 CRD unexpectedly bound to a 24-carbon fatty acid. We also report a crystal structure of human FZD5 CRD bound to C16:1 cis-Δ9 unsaturated fatty acid. Both structures reveal a dimeric arrangement of the CRD. The lipid-binding groove exhibits flexibility and spans both monomers, adopting a U-shaped geometry that accommodates the fatty acid. Re-evaluation of the published mouse FZD8 CRD structure reveals that it also shares the same architecture as FZD5 and FZD7 CRDs. Our results define a common molecular mechanism for recognition of the cis-unsaturated fatty acyl group, a necessary posttranslational modification of Wnts, by multiple FZD receptors. The fatty acid bridges two CRD monomers, implying that Wnt binding mediates FZD receptor dimerization. Our data uncover possibilities for the arrangement of Wnt–FZD CRD complexes and shed structural insights that could aide in the identification of pharmacological strategies to modulate FZD receptor function. PMID:28377511

Cis-acting elements in its 3′ UTR mediate post-transcriptional regulation of KRAS

PubMed Central

Kim, Minlee; Kogan, Nicole; Slack, Frank J.

2016-01-01

Multiple RNA-binding proteins and non-coding RNAs, such as microRNAs (miRNAs), are involved in post-transcriptional gene regulation through recognition motifs in the 3′ untranslated region (UTR) of their target genes. The KRAS gene encodes a key signaling protein, and its messenger RNA (mRNA) contains an exceptionally long 3′ UTR; this suggests that it may be subject to a highly complex set of regulatory processes. However, 3′ UTR-dependent regulation of KRAS expression has not been explored in detail. Using extensive deletion and mutational analyses combined with luciferase reporter assays, we have identified inhibitory and stabilizing cis-acting regions within the KRAS 3′ UTR that may interact with miRNAs and RNA-binding proteins, such as HuR. Particularly, we have identified an AU-rich 49-nt fragment in the KRAS 3′ UTR that is required for KRAS 3′ UTR reporter repression. This element contains a miR-185 complementary element, and we show that overexpression of miR-185 represses endogenous KRAS mRNA and protein in vitro. In addition, we have identified another 49-nt fragment that is required to promote KRAS 3′ UTR reporter expression. These findings indicate that multiple cis-regulatory motifs in the 3′ UTR of KRAS finely modulate its expression, and sequence alterations within a binding motif may disrupt the precise functions of trans-regulatory factors, potentially leading to aberrant KRAS expression. PMID:26930719

Metabolism of oral 9-cis-retinoic acid in the human. Identification of 9-cis-retinoyl-beta-glucuronide and 9-cis-4-oxo-retinoyl-beta-glucuronide as urinary metabolites.

PubMed

Sass, J O; Masgrau, E; Saurat, J H; Nau, H

1995-09-01

Data from a number of investigators suggest that the 9-cis-isomer of RA1 (9-cis-RA) may be a promising agent in chemoprevention and treatment of certain types of cancer. Therefore, clinical studies on this retinoid have been initiated. However, up to now, no information has been published on the metabolism of 9-cis-RA in the human. Herein, we report the first data on retinoid metabolism after multiple administration of 9-cis-RA (20 mg/day po) to human volunteers. After 2 and 12-13 hr, plasma concentrations of 9-cis-RA and its metabolites 9,13-dicis-RA, 13-cis-RA, and all-trans-RA were low. In contrast, dosing with 13-cis-RA yielded much higher plasma retinoid levels. Effects on plasma retinol concentrations did not become obvious after any drug treatment. Several retinoid metabolites were found in the urine of 9-cis-RA-treated individuals, and 9-cis-RAG, as well as 9-cis-4-oxo-RAG, could be identified. After treatment with 9-cis-RA, high concentrations of the administered drug were found in the feces, along with comparably low concentrations of 13-cis-RA, 9,13-dicis-RA, and all-trans-RA. Our report indicates that 9-cis-RA is either eliminated much more rapidly than 13-cis-RA, or it is poorly absorbed, and presents the characterization of two urinary glucuronides.

Using bioinformatics and systems genetics to dissect HDL-cholesterol genetics in an MRL/MpJ x SM/J intercross.

PubMed

Leduc, Magalie S; Blair, Rachael Hageman; Verdugo, Ricardo A; Tsaih, Shirng-Wern; Walsh, Kenneth; Churchill, Gary A; Paigen, Beverly

2012-06-01

A higher incidence of coronary artery disease is associated with a lower level of HDL-cholesterol. We searched for genetic loci influencing HDL-cholesterol in F2 mice from a cross between MRL/MpJ and SM/J mice. Quantitative trait loci (QTL) mapping revealed one significant HDL QTL (Apoa2 locus), four suggestive QTL on chromosomes 10, 11, 13, and 18 and four additional QTL on chromosomes 1 proximal, 3, 4, and 7 after adjusting HDL for the strong Apoa2 locus. A novel nonsynonymous polymorphism supports Lipg as the QTL gene for the chromosome 18 QTL, and a difference in Abca1 expression in liver tissue supports it as the QTL gene for the chromosome 4 QTL. Using weighted gene co-expression network analysis, we identified a module that after adjustment for Apoa2, correlated with HDL, was genetically determined by a QTL on chromosome 11, and overlapped with the HDL QTL. A combination of bioinformatics tools and systems genetics helped identify several candidate genes for both the chromosome 11 HDL and module QTL based on differential expression between the parental strains, cis regulation of expression, and causality modeling. We conclude that integrating systems genetics to a more-traditional genetics approach improves the power of complex trait gene identification.

Thermal cis-trans isomerization of cis,cis-3,7-decadiene - A model for cis-1,4-polybutadiene

NASA Technical Reports Server (NTRS)

Golub, M. A.; Lee, W. M.

1983-01-01

The thermal cis-trans isomerization of cis,cis-3,7-decadiene (DD), a model compound for cis-PBD, is reported. It is demonstrated that the rather low E for the polyalkenamer isomerizations compared with that for the 2-olefins is not an artifact of the solid polymer structures, but rather is characteristic of both small and large molecules possessing pairs of nonconjugated vinylene double bonds in a suitable arrangement.

Systematic review and meta-analysis of serious infections with tofacitinib and biologic disease-modifying antirheumatic drug treatment in rheumatoid arthritis clinical trials.

PubMed

Strand, Vibeke; Ahadieh, Sima; French, Jonathan; Geier, Jamie; Krishnaswami, Sriram; Menon, Sujatha; Checchio, Tina; Tensfeldt, Thomas G; Hoffman, Elaine; Riese, Richard; Boy, Mary; Gómez-Reino, Juan J

2015-12-15

Tofacitinib is an oral Janus kinase inhibitor for the treatment of rheumatoid arthritis (RA). Tofacitinib modulates the signaling of cytokines that are integral to lymphocyte activation, proliferation, and function. Thus, tofacitinib therapy may result in suppression of multiple elements of the immune response. Serious infections have been reported in tofacitinib RA trials. However, limited head-to-head comparator data were available within the tofacitinib RA development program to directly compare rates of serious infections with tofacitinib relative to biologic agents, and specifically adalimumab (employed as an active control agent in two randomized controlled trials of tofacitinib). A systematic literature search of data from interventional randomized controlled trials and long-term extension studies with biologics in RA was carried out. Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) consensus was followed for reporting results of the review and meta-analysis. Incidence rates (unique patients with events/100 patient-years) for each therapy were estimated based on data from randomized controlled trials and long-term extension studies using a random-effects model. Relative and absolute risk comparisons versus placebo used Mantel-Haenszel methods. The search produced 657 hits. In total, 66 randomized controlled trials and 22 long-term extension studies met the selection criteria. Estimated incidence rates (95% confidence intervals [CIs]) for abatacept, rituximab, tocilizumab, and tumor necrosis factor inhibitors were 3.04 (2.49, 3.72), 3.72 (2.99, 4.62), 5.45 (4.26, 6.96), and 4.90 (4.41, 5.44), respectively. Incidence rates (95% CIs) for tofacitinib 5 and 10 mg twice daily (BID) in phase 3 trials were 3.02 (2.25, 4.05) and 3.00 (2.24, 4.02), respectively. Corresponding incidence rates in long-term extension studies were 2.50 (2.05, 3.04) and 3.19 (2.74, 3.72). The risk ratios (95% CIs) versus placebo for tofacitinib 5 and 10 mg BID were 2.21 (0.60, 8.14) and 2.02 (0.56, 7.28), respectively. Risk differences (95% CIs) versus placebo for tofacitinib 5 and 10 mg BID were 0.38% (-0.24%, 0.99%) and 0.40% (-0.22%, 1.02%), respectively. In interventional studies, the risk of serious infections with tofacitinib is comparable to published rates for biologic disease-modifying antirheumatic drugs in patients with moderate to severely active RA.

Fabrication of CuInS2/ZnS quantum dots-based white light-emitting diodes with high color rendering index

NASA Astrophysics Data System (ADS)

Hsiao, Chih-Chun; Su, Yu-Sheng; Chung, Shu-Ru

2017-09-01

Among solid-state lighting technology, phosphor-converted white light-emitting diodes (pc-WLEDs) are excellent candidates to replace incandescent lamps for their merit of high energy conservation, long lifetime, high luminous efficiency as well as polarized emissions. Semiconductor quantum dots (QDs) are emerging color tunable emissive light converters. They have shown significant promise as light emitters, as solar cells, and in biological imaging. It has been demonstrated that the pc-WLED devices integrated with red emissive ZnCdSe QDs show improved color rendering index of device. However, cadmium-based QDs have limited future owing to the well-known toxicity. Recently, non-cadmium luminescence materials, i.e. CuInS2-based QDs, are investigated as desirable low toxic alternatives. Particularly, CuInS2-based QDs exhibit very broad emissions spectra with full width at half maximum (FWHM) of 100-120 nm, large Stokes shifts of 200 300 meV and finely-tunable emissions. In order to adjust emission wavelengths and improved quantum yield (QY), CuInS2/ZnS (CIS/ZnS) core/shell structure was introduced. Therefore, CIS/ZnS QDs have been extensively investigated and be used as color converter in solid-state lighting. Synthesis and application of CuInS2/ZnS core/shell QDs are conducted using a hot injection route. CIS/ZnS core/shell QDs with molar ratio of Cu:In equal to 1:4 are prepared. For WLED fabrication, the CIS/ZnS QD is dispersed in toluene first, and then it is blended with transparent acrylic-based UV resin. Subsequently, the commercial green-emitting Lu3Al5O12: Ce3+ (LuAG) phosphors are mixed with QDs-resin mixture. After that, the QDs-phosphors-resin mixtures are put in the oven at 140 °C for 1 h to evaporate the toluene. Subsequently, the homogeneous QDs-phosphors-resin mixture is dropped on the top of a blue LED chip (InGaN). Then, the device is cured by 400 W UV light to form WLED. The emission wavelength of CIS/ZnS QD exhibits yellow region of 552 nm with QY of 76 %, and with relatively broad bandwidth of 86 nm. The structure of CIS/ZnS belongs to chalcopyrite phase and its average particle size is 3.2 nm. The luminous efficacy, color rendering index (CRI), correlated color temperature (CCT), and CIE chromaticity coordinate of WLED is 47 lm/W, 89, 5661 K, and (0.33, 0.29), respectively.

cis-chlorobenzene dihydrodiol dehydrogenase (TcbB) from Pseudomonas sp. strain P51, expressed in Escherichia coli DH5alpha(pTCB149), catalyzes enantioselective dehydrogenase reactions.

PubMed

Raschke, H; Fleischmann, T; Van Der Meer, J R; Kohler, H P

1999-12-01

cis-Chlorobenzene dihydrodiol dehydrogenase (CDD) from Pseudomonas sp. strain P51, cloned into Escherichia coli DH5alpha(pTCB149) was able to oxidize cis-dihydrodihydroxy derivatives (cis-dihydrodiols) of dihydronaphthalene, indene, and four para-substituted toluenes to the corresponding catechols. During the incubation of a nonracemic mixture of cis-1,2-indandiol, only the (+)-cis-(1R,2S) enantiomer was oxidized; the (-)-cis-(S,2R) enantiomer remained unchanged. CDD oxidized both enantiomers of cis-1,2-dihydroxy-1,2,3, 4-tetrahydronaphthalene, but oxidation of the (+)-cis-(1S,2R) enantiomer was delayed until the (-)-cis-(1R,2S) enantiomer was completely depleted. When incubated with nonracemic mixtures of para-substituted cis-toluene dihydrodiols, CDD always oxidized the major enantiomer at a higher rate than the minor enantiomer. When incubated with racemic 1-indanol, CDD enantioselectively transformed the (+)-(1S) enantiomer to 1-indanone. This stereoselective transformation shows that CDD also acted as an alcohol dehydrogenase. Additionally, CDD was able to oxidize (+)-cis-(1R,2S)-dihydroxy-1, 2-dihydronaphthalene, (+)-cis-monochlorobiphenyl dihydrodiols, and (+)-cis-toluene dihydrodiol to the corresponding catechols.

Thermal decay of rhodopsin: role of hydrogen bonds in thermal isomerization of 11-cis retinal in the binding site and hydrolysis of protonated Schiff base.

PubMed

Liu, Jian; Liu, Monica Yun; Nguyen, Jennifer B; Bhagat, Aditi; Mooney, Victoria; Yan, Elsa C Y

2009-07-01

Although thermal stability of the G protein-coupled receptor rhodopsin is directly related to its extremely low dark noise level and has recently generated considerable interest, the chemistry behind the thermal decay process of rhodopsin has remained unclear. Using UV-vis spectroscopy and HPLC analysis, we have demonstrated that the thermal decay of rhodopsin involves both hydrolysis of the protonated Schiff base and thermal isomerization of 11-cis to all-trans retinal. Examining the unfolding of rhodopsin by circular dichroism spectroscopy and measuring the rate of thermal isomerization of 11-cis retinal in solution, we conclude that the observed thermal isomerization of 11-cis to all-trans retinal happens when 11-cis retinal is in the binding pocket of rhodopsin. Furthermore, we demonstrate that solvent deuterium isotope effects are involved in the thermal decay process by decreasing the rates of thermal isomerization and hydrolysis, suggesting that the rate-determining step of these processes involves breaking hydrogen bonds. These results provide insight into understanding the critical role of an extensive hydrogen-bonding network on stabilizing the inactive state of rhodopsin and contribute to our current understanding of the low dark noise level of rhodopsin, which enables this specialized protein to function as an extremely sensitive biological light detector. Because similar hydrogen-bonding networks have also been suggested by structural analysis of two other GPCRs, beta1 and beta2 adrenergic receptors, our results could reveal a general role of hydrogen bonds in facilitating GPCR function.

CRISPR/Cas9 and active genetics-based trans-species replacement of the endogenous Drosophila kni-L2 CRM reveals unexpected complexity.

PubMed

Xu, Xiang-Ru Shannon; Gantz, Valentino Matteo; Siomava, Natalia; Bier, Ethan

2017-12-23

The knirps ( kni ) locus encodes transcription factors required for induction of the L2 wing vein in Drosophila . Here, we employ diverse CRISPR/Cas9 genome editing tools to generate a series of targeted lesions within the endogenous cis-regulatory module (CRM) required for kni expression in the L2 vein primordium. Phenotypic analysis of these ' in locus ' mutations based on both expression of Kni protein and adult wing phenotypes, reveals novel unexpected features of L2-CRM function including evidence for a chromosome pairing-dependent process that promotes transcription. We also demonstrate that self-propagating active genetic elements (CopyCat elements) can efficiently delete and replace the L2-CRM with orthologous sequences from other divergent fly species. Wing vein phenotypes resulting from these trans-species enhancer replacements parallel features of the respective donor fly species. This highly sensitive phenotypic readout of enhancer function in a native genomic context reveals novel features of CRM function undetected by traditional reporter gene analysis. © 2017, Xu et al.

CRISPR/Cas9 and active genetics-based trans-species replacement of the endogenous Drosophila kni-L2 CRM reveals unexpected complexity

PubMed Central

Siomava, Natalia

2017-01-01

The knirps (kni) locus encodes transcription factors required for induction of the L2 wing vein in Drosophila. Here, we employ diverse CRISPR/Cas9 genome editing tools to generate a series of targeted lesions within the endogenous cis-regulatory module (CRM) required for kni expression in the L2 vein primordium. Phenotypic analysis of these ‘in locus’ mutations based on both expression of Kni protein and adult wing phenotypes, reveals novel unexpected features of L2-CRM function including evidence for a chromosome pairing-dependent process that promotes transcription. We also demonstrate that self-propagating active genetic elements (CopyCat elements) can efficiently delete and replace the L2-CRM with orthologous sequences from other divergent fly species. Wing vein phenotypes resulting from these trans-species enhancer replacements parallel features of the respective donor fly species. This highly sensitive phenotypic readout of enhancer function in a native genomic context reveals novel features of CRM function undetected by traditional reporter gene analysis. PMID:29274230

Differential diagnosis of urothelial carcinoma in situ from non-neoplastic urothelia: Analysis of CK20, CD44, P53 and Ki67

PubMed Central

Asgari, Mojgan; Nabi Maybodi, Mahtab; Abolhasani, Maryam

2016-01-01

Background: Flat urothelial lesions comprise a spectrum of morphologic changes ranging from reactive atypia to carcinoma in situ (CIS). Urothelial dysplasia and CIS are associated with the recurrence and progression of urothelial carcinoma. Distinguishing CIS and dysplasia from reactive atypia based on histolopathogical features alone is often difficult. Using different immunohistochemical markers such as Cytokeratin 20 (CK20), CD44, p53, and Ki-67 is recommended for differential diagnosis. The aim of this study was to evaluate the immunohistochemical pattern of these antibodies to differentiate different flat urothelial lesions. Methods: In this cross- sectional study, three groups of bladder biopsy specimens were evaluated: 20 samples with reactive urothelial lesions, 20 histologically diagnosed as CIS, and 20 morphologically normal samples. Immunohistochemical staining of CK20, p53, CD44 and Ki-67 markers was performed on paraffin-embedded blocks. The groups were compared using chi square test, and the diagnostic value of the markers were evaluated with sensitivity, specificity, positive and negative predictive values. Results: CK20 was full thickness positive in 15 (75%) CIS samples and negative in all samples of the normal and reactive groups (p<0.001); CD44 was positive in 2 (10%) cases of the CIS group and in 17 (85%) of the reactive group; this marker was negative in all the normal samples (p<0.001). P53 was positive in 12 (60%) samples of the CIS group and negative in all samples of the normal and reactive groups (p<0.001). Ki67 was positive in 13 (65%) samples of the CIS group and 1 (5%) sample of the reactive group. This marker was negative in all samples of the normal group (p<0.001). Conclusion: The results of this study revealed that CK20, CD44, P53 and Ki67 are useful in distinguishing CIS from reactive and normal samples. However, they should be used in a panel including at least three markers. Correlation with the morphologic features is necessary. PMID:27579290

Nuclear size measurement for distinguishing urothelial carcinomas from reactive urothelium on tissue sections.

PubMed

Poropatich, Kate; Yang, Jason C; Goyal, Rajen; Parini, Vamsi; Yang, Ximing J

2016-06-30

Pathological diagnosis of urothelial carcinoma (UC) is primarily based on cytological atypia. It has previously been shown that high-grade (HG) UC, particularly UC in situ cells (CIS), can be over five times the size of a lymphocyte. However, this has not been demonstrated in comparison to reactive urothelium. The objective of this study was to empirically compare the difference in nuclear size of UC cells with reactive urothelial cells. Using CellSens imaging software, we measured urothelial nuclear length (l) and width (w) on digital images of H&E sections. The area (a) of a nucleus was calculated based on the oval shape of most urothelial cells. Lymphocytes were measured to calculate normalized urothelial linear and area ratios. A total of 1085 urothelial cell nuclei from 60 cases were measured from reactive urothelium, low grade (LG) UC, HG UC and CIS. CIS nuclei were found to have an a 2.75 times larger than reactive nuclei (p < 0.001). A nuclear size cut-off of 11 um for l and 7 um for w was found to be sensitive [98.09 % (95 % CI: 95.60-99.38 %) and 89.31 % (95 % CI: 83.6-91.82 %) for l and w, respectively] and specific [92.60 % (95 % CI: 87.13-95.82 %) and 85.71 % (95 % CI: 79.49-90.63 %) for l and w, respectively] for distinguishing CIS from reactive atypia. Nuclear morphometry can be used to differentiate CIS from reactive atypia. A l over 11 um and a w over 7 um and is highly sensitive and specific for CIS compared to reactive urothelium. This difference in nuclear size may be used as a tool for differentiating the flat urothelial lesions from reactive urothelium in daily practice.

Staff Training Reduces the Use of Physical Restraint in Mental Health Service, Evidence-based Reflection for China.

PubMed

Ye, Junrong; Xiao, Aixiang; Yu, Lin; Guo, Jianxiong; Lei, Huawei; Wei, Hongmei; Luo, Wei

2018-06-01

The purpose of this article was to synthesize the evidence regarding the reduction of physical restraint, and to seek some practical recommendations based on the current situation in China. Nine databases were retrieved; these were PubMed, CINAHL, MEDLINE, Trip Database, PsysINFO, Cochrane Library, CNKI (Chinese database), Wanfang (Chinese database) and CBM (Chinese database) respectively. The selected articles were screened manually, and the identified researches were appraised through Review manager 5.3. Eight studies (four randomized controlled trials and four quasi-experimental studies) published between June 2013 and May 2017 were selected. Risk ratios (RRs) with 95% confidence intervals (CIs) were used as the effect index for dichotomous variables. The standardized mean differences (SMDs) with 95% CIs were calculated as the pooled continuous effect. The outcome of meta-analysis suggested staff training reduced the duration (IV=-0.88; 95% CIs=-1.65 to -0.10; Z=2.22; p=0.03) and adverse effect (RR, 0.16; 95% CIs=0.09 to 0.30; Z=5.96; p<0.00001) of physical restraint, but there were no statistical change in the frequency of physical restraint (RR, 0.74; 95% CIs=0.43 to 1.28; Z=1.07; p=0.28). Noticeably, the result of pooled estimates from 3 RCTs suggested staff training had no effects on the incidence of physical restraint. (RR, 1.01; 95% CIs=0.45 to 2.24; Z=0.02; p=0.99) CONCLUSION: Staff training was an effective measure to minimize the duration and adverse effects of physical restraint. More studies are needed to examine the effectiveness of staff training in relation to reduce the prevalence of physical restraint. Furthermore, considering the nurse's education background in China, it is recommended to conduct a compulsory training program to reduce the unnecessary restraint. Copyright © 2017 Elsevier Inc. All rights reserved.

Impact of a Multifaceted and Clinically Integrated Training Program in Evidence-Based Practice on Knowledge, Skills, Beliefs and Behaviour among Clinical Instructors in Physiotherapy: A Non-Randomized Controlled Study

PubMed Central

Olsen, Nina Rydland; Bradley, Peter; Espehaug, Birgitte; Nortvedt, Monica Wammen; Lygren, Hildegunn; Frisk, Bente; Bjordal, Jan Magnus

2015-01-01

Background and Purpose Physiotherapists practicing at clinical placement sites assigned the role as clinical instructors (CIs), are responsible for supervising physiotherapy students. For CIs to role model evidence-based practice (EBP) they need EBP competence. The aim of this study was to assess the short and long term impact of a six-month multifaceted and clinically integrated training program in EBP on the knowledge, skills, beliefs and behaviour of CIs supervising physiotherapy students. Methods We invited 37 CIs to participate in this non-randomized controlled study. Three self-administered questionnaires were used pre- and post-intervention, and at six-month follow-up: 1) The Adapted Fresno test (AFT), 2) the EBP Belief Scale and 3) the EBP Implementation Scale. The analysis approach was linear regression modeling using Generalized Estimating Equations. Results In total, 29 CIs agreed to participate in the study: 14 were invited to participate in the intervention group and 15 were invited to participate in the control group. One in the intervention group and five in the control group were lost to follow-up. At follow-up, the group difference was statistically significant for the AFT (mean difference = 37, 95% CI (15.9 -58.1), p<0.001) and the EBP Beliefs scale (mean difference = 8.1, 95% CI (3.1 -13.2), p = 0.002), but not for the EBP Implementation scale (mean difference = 1.8. 95% CI (-4.5-8.1), p = 0.574). Comparing measurements over time, we found a statistically significant increase in mean scores related to all outcome measures for the intervention group only. Conclusions A multifaceted and clinically integrated training program in EBP was successful in improving EBP knowledge, skills and beliefs among CIs. Future studies need to ensure long-term EBP behaviour change, in addition to assessing CIs’ abilities to apply EBP knowledge and skills when supervising students. PMID:25894559

Ruthenium indenylidene “1st generation” olefin metathesis catalysts containing triisopropyl phosphite

PubMed Central

Guidone, Stefano; Nahra, Fady; Slawin, Alexandra M Z

2015-01-01

Summary The reaction of triisopropyl phosphite with phosphine-based indenylidene pre-catalysts affords “1st generation” cis-complexes. These have been used in olefin metathesis reactions. The cis-Ru species exhibit noticeable differences with the trans-Ru parent complexes in terms of structure, thermal stability and reactivity. Experimental data underline the importance of synergistic effects between phosphites and L-type ligands. PMID:26425210

Novel Rhenium(III, IV, and V) Tetradentate N2O2 Schiff Base Mononuclear and Dinuclear Complexes

PubMed Central

Rotsch, David A.; Reinig, Kimberly M.; Weis, Eric M.; Taylor, Anna B.; Barnes, Charles L.

2013-01-01

Reaction of (Bu4N)[ReOCl4] with the tetradentate Schiff base ligand α, α’-[(1,1-dimethylethylene)dinitrilo]di-o-cresol (sal2ibnH2) yields cis-[ReVOCl(sal2ibn)], which quickly forms trans-[μ-O(ReVO(sal2ibn))2] in solution. The dinuclear complex can also be isolated by the addition of base (Et3N) to the reaction mixture. Conversely, the mononuclear complex can be trapped as cis-[ReVO(NCS)(sal2ibn)] by addition of (Bu4N)SCN to the reaction mixture. Reduction of cis-[ReVO(NCS)sal2ibn] with triphenylphosphine gives the unique trans-[ReIII(NCS)(PPh3)(sal2ibn)] and rare μ-oxo Re(IV) dimer trans-[μ-O(ReIV(NCS)(sal2ibn))2]. All of the complexes were characterized by 1H and 13C NMR, FT-IR spectroscopy, electrospray ionization mass spectrometry (ESI-MS), cyclic voltammetry and single crystal X-ray diffraction. PMID:23824208

Theoretical Studies of Possible Synthetic Routes for the High Energy Density Material Td N4: Excited Electronic States

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

2001-01-01

Vertical electronic excitation energies for single states have been computed for the high energy density material (HEDM) Td N4 in order to assess possible synthetic routes that originate from excited electronic states of N2 molecules. Several ab initio theoretical approaches have been used, including complete active space self-consistent field (CASSCF), state averaged CASSCF (SA-CASSCF), singles configuration interaction (CIS), CIS with second-order and third-order correlation corrections [CIS(D)) and CIS(3)], and linear response singles and doubles coupled-cluster (LRCCSD), which is the highest level of theory employed. Standard double zeta polarized (DZP) and triple zeta double polarized (TZ2P) one-particle basis sets were used. The CASSCF calculations are found to overestimate the excitation energies, while the SA-CASSCF approach rectifies this error to some extent, but not completely. The accuracy of the CIS calculations varied depending on the particular state, while the CIS(D), CIS(3), and LRCCSD results are in generally good agreement. Based on the LRCCSD calculations, the lowest six excited singlet states are 9.35(l(sup)T1), 10.01(l(sup)T2), 10.04(1(sup)A2), 10.07(1(sup)E), 10.12(2(sup)T1), and 10.42(2(sup)T2) eV above the ground state, respectively. Comparison of these excited state energies with the energies of possible excited states of N2+N2 fragments, leads us to propose that the most likely synthetic route for Td N4 involving this mechanism arises from combination of two bound quintet states of N2.

A Mechanistic and Structural Analysis of the Inhibition of the 90-kDa Heat Shock Protein by the Benzoquinone and Hydroquinone AnsamycinsS⃞

PubMed Central

Reigan, Philip; Siegel, David; Guo, Wenchang

2011-01-01

The benzoquinone ansamycins inhibit the ATPase activity of the 90-kDa heat shock protein (Hsp90), disrupting the function of numerous client proteins involved in oncogenesis. In this study, we examine the role of NAD(P)H:quinone oxidoreductase 1 (NQO1) in the metabolism of trans- and cis-amide isomers of the benzoquinone ansamycins and their mechanism of Hsp90 inhibition. Inhibition of purified human Hsp90 by a series of benzoquinone ansamycins was examined in the presence and absence of NQO1, and their relative rate of NQO1-mediated reduction was determined. Computational-based molecular docking simulations indicated that the trans- but not the cis-amide isomers of the benzoquinone ansamycins could be accommodated by the NQO1 active site, and the ranking order of binding energies correlated with the relative reduction rate using purified human NQO1. The trans-cis isomerization of the benzoquinone ansamycins in Hsp90 inhibition has been disputed in recent reports. Previous computational studies have used the closed or cocrystallized Hsp90 structures in an attempt to explore this isomerization step; however, we have successfully docked both the trans- and cis-amide isomers of the benzoquinone ansamycins into the open Hsp90 structure. The results of these studies indicate that both trans- and cis-amide isomers of the hydroquinone ansamycins exhibited increased binding affinity for Hsp90 relative to their parent quinones. Our data support a mechanism in which trans- rather than cis-amide forms of benzoquinone ansamycins are metabolized by NQO1 to hydroquinone ansamycins and that Hsp90-mediated trans-cis isomerization via tautomerization plays an important role in subsequent Hsp90 inhibition. PMID:21285336

Is ovarian reserve associated with body mass index and obesity in reproductive aged women? A meta-analysis.

PubMed

Moslehi, Nazanin; Shab-Bidar, Sakineh; Ramezani Tehrani, Fahimeh; Mirmiran, Parvin; Azizi, Fereidoun

2018-05-07

The associations of body mass index (BMI) and obesity with ovarian reserve are controversial. This systematic review and meta-analysis was conducted to investigate the associations in reproductive-aged women. PubMed and Scopus were searched up to December, 2016. Original studies on the association of BMI with ovarian reserve markers, anti-Mullerian hormone (AMH), follicle-stimulating hormone (FSH), inhibin β, and antral follicle count (AFC), either according to BMI categories or a continuous variable, were selected. Analyses were stratified into three groups based on polycystic ovary syndrome (PCOS) and fertility status of women. Of 4,055 records identified, 45 studies were eligible for inclusion. Comparing the obese with nonobese, the pooled mean differences (MDs) and 95% confidence intervals (CIs) were -1.08 (95% CIs -1.52, -0.63) ng/mL for AMH, -0.22 (95% CIs -0.39, -0.06) mIU/mL for FSH, -0.09 (95% CIs -0.60, 0.42) for AFC, and -21.06 (95% CIs -41.18, -0.85) pg/mL for inhibin β in overall populations. The MDs were significant for AMH in fertile non-PCOS and PCOS women, and for FSH only in PCOS women. Fisher's Z showed significant correlations of BMI with AMH in the overall populations (-0.15 [95% CIs -0.20, -0.11]) and in all subgroups, and with FSH in the fertile non-PCOS women (-0.16 [95% CIs -0.28, -0.04]). Ovarian reserve markers of AMH and FSH are significantly lower in obese than in nonobese women, and BMI is negatively correlated with AMH in all study populations, and with FSH in fertile non-PCOS subgroups. PCOS and fertility status do not appear to affect the associations.

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

R Vasquez-Del Carpio; T Silverstein; S Lone

Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase {Kappa} (Pol{Kappa}), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Pol{Kappa} in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure revealsmore » a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Pol{Kappa} in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.« less

cisTEM, user-friendly software for single-particle image processing.

PubMed

Grant, Timothy; Rohou, Alexis; Grigorieff, Nikolaus

2018-03-07

We have developed new open-source software called cis TEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cis TEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k - 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cis TEM is available for download from cistem.org. © 2018, Grant et al.

cisTEM, user-friendly software for single-particle image processing

PubMed Central

2018-01-01

We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org. PMID:29513216

Osteoarthritis in Siberia's Cis-Baikal: Skeletal indicators of hunter-gatherer adaptation and cultural change.

PubMed

Lieverse, Angela R; Weber, Andrzej W; Bazaliiskiy, Vladimir Ivanovich; Goriunova, Olga Ivanovna; Savel'ev, Nikolai Aleksandrovich

2007-01-01

This examination of osteoarthritis in Siberia's Cis-Baikal region focuses on the reconstruction of mid-Holocene mobility and activity patterns with particular interest in an alleged fifth millennium BC biocultural hiatus. Five cemetery populations--two representing the pre-hiatus Kitoi culture (6800-4900 BC) and three the post-hiatus Serovo-Glaskovo (4200-1000 BC)-are considered. The objective is to investigate osteoarthritic prevalence and distribution (patterning) within and among these populations in order to reconstruct mobility and activity patterns among the Cis-Baikal foragers, and to test for possible disparities that may reflect differing adaptive strategies. The data reveal that levels of activity remained relatively constant throughout the mid-Holocene but that mobility and specific activity patterns did not. Although results are consistent with the current understanding of distinct Kitoi and Serovo-Glaskovo subsistence regimes, specifically the lower residential mobility and narrower resource base of the former, they also draw attention to adaptive characteristics shared by all occupants of the Cis-Baikal. (c) 2006 Wiley-Liss, Inc

A new genetic variant in the Sp1 binding cis-element of cholecystokinin gene promoter region and relationship to alcoholism.

PubMed

Harada, S; Okubo, T; Tsutsumi, M; Takase, S; Muramatsu, T

1998-05-01

Neuropeptide cholecystokinin (CCK) and the CCK receptors in the central nervous system mediate actions on increasing firings, anxiety, and nociceptions. Furthermore, CCK modulates the release of dopamine and dopamine-related behaviors in the mesolimbic pathway. In our study, genetic variation in the promoter and coding regions of the prepro-CCK gene were analyzed among 66 Japanese, 66 American Whites, 54 Chinese, and 41 Colombian natives. Two nucleotide sequence variants were found: a frequent mutation at nucleotide position -45 C to T involved in core sequence of Sp1 binding cis-element of the promoter region, and a C to T substitution at the 1662 position in intron 2. Analysis for the segregation study in 10 families of twins confirmed codominant heredity of two alleles. Distribution of genotypes and gene frequencies of 66 controls and 108 alcoholics in Japan presented that allelic variant T type in alcoholics was found in higher frequencies than that of controls, and distribution of these genotypes was significantly different between the both groups.

Supplemental feeding of a gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, alleviates spontaneous atopic dermatitis and modulates intestinal microbiota in NC/nga mice.

PubMed

Kaikiri, Hiroko; Miyamoto, Junki; Kawakami, Takahiro; Park, Si-Bum; Kitamura, Nahoko; Kishino, Shigenobu; Yonejima, Yasunori; Hisa, Keiko; Watanabe, Jun; Ogita, Tasuku; Ogawa, Jun; Tanabe, Soichi; Suzuki, Takuya

2017-12-01

The present study investigated the antiallergic and anti-inflammatory effects of 10-hydroxy-cis-12-octadecenoic acid (HYA), a novel gut microbial metabolite of linoleic acid, in NC/Nga mice, a model of atopic dermatitis (AD). Feeding HYA decreased the plasma immunoglobulin E level and skin infiltration of mast cells with a concomitant decrease in dermatitis score. HYA feeding decreased TNF-α and increased claudin-1, a tight junction protein, levels in the mouse skin. Cytokine expression levels in the skin and intestinal Peyer's patches cells suggested that HYA improved the Th1/Th2 balance in mice. Immunoglobulin A concentration in the feces of the HYA-fed mice was approximately four times higher than that in the control mice. Finally, denaturing gradient gel electrophoresis of the PCR-amplified 16 S rRNA gene of fecal microbes indicated the modification of microbiota by HYA. Taken together, the alterations in the intestinal microbiota might be, at least in part, associated with the antiallergic effect of HYA.

All-trans-retinoic acid and 13-cis-retinoic acid: pharmacokinetics and biological activity in different cell culture models of human keratinocytes.

PubMed

Schroeder, M; Zouboulis, C C

2007-02-01

Despite its known biological effect on epithelial cells, 13- CIS-retinoic acid shows low binding affinity to either cellular retinoic acid-binding proteins or nuclear retinoid receptors compared to its isomer all- TRANS-retinoic acid. We have postulated a prodrug-drug relation with 13- CIS-retinoic acid which isomerizes to all- TRANS-retinoic acid. On the other hand, the biological effects of these two compounds can differ in the widely used cell culture models of HaCaT and normal primary keratinocytes. In this study, we seeded HaCaT and normal keratinocytes at high densities leading to early confluence in order to imitate high keratinocyte proliferation, such as in acne and psoriasis, while to model decreased keratinocyte proliferation, as in aged and steroid-damaged skin, cells were seeded at a low density. High performance liquid chromatography was administered to examine retinoid uptake and metabolism in monolayer HaCaT and normal keratinocyte cultures and the 4-methylumbelliferyl heptanoate assay to estimate cell growth at different cell densities. Major qualitative and quantitative differences were detected in the two cell types regarding intracellular 13- CIS-retinoic acid isomerization to all- TRANS-retinoic acid. On the other hand, the two retinoic acid isomers showed similar effects on cell growth of both cell types tested with increasing proliferation at low cell densities, but being rather inactive at high ones in normal keratinocytes and exhibiting an antiproliferative effect in HaCaT keratinocytes. The missing effect of retinoids on cell proliferation in high seeding densities of normal keratinocytes may indicate that the normalizing activity of retinoids on hyperkeratotic diseases, such as acne or psoriasis, is likely to be carried out by modulation of cell differentiation than cell growth. On the other hand, induced keratinocyte proliferation in low seeding densities may provide an explanation for the acanthosis induced by topical retinoids in aged and steroid-damaged skin.

A Fixed-Pattern Noise Correction Method Based on Gray Value Compensation for TDI CMOS Image Sensor.

PubMed

Liu, Zhenwang; Xu, Jiangtao; Wang, Xinlei; Nie, Kaiming; Jin, Weimin

2015-09-16

In order to eliminate the fixed-pattern noise (FPN) in the output image of time-delay-integration CMOS image sensor (TDI-CIS), a FPN correction method based on gray value compensation is proposed. One hundred images are first captured under uniform illumination. Then, row FPN (RFPN) and column FPN (CFPN) are estimated based on the row-mean vector and column-mean vector of all collected images, respectively. Finally, RFPN are corrected by adding the estimated RFPN gray value to the original gray values of pixels in the corresponding row, and CFPN are corrected by subtracting the estimated CFPN gray value from the original gray values of pixels in the corresponding column. Experimental results based on a 128-stage TDI-CIS show that, after correcting the FPN in the image captured under uniform illumination with the proposed method, the standard-deviation of row-mean vector decreases from 5.6798 to 0.4214 LSB, and the standard-deviation of column-mean vector decreases from 15.2080 to 13.4623 LSB. Both kinds of FPN in the real images captured by TDI-CIS are eliminated effectively with the proposed method.

Acoustic properties of vocal singing in prelingually-deafened children with cochlear implants or hearing aids.

PubMed

Mao, Yitao; Zhang, Mengchao; Nutter, Heather; Zhang, Yijing; Zhou, Qixin; Liu, Qiaoyun; Wu, Weijing; Xie, Dinghua; Xu, Li

2013-11-01

The purpose of the present study was to investigate vocal singing performance of hearing-impaired children with cochlear implants (CI) and hearing aids (HA) as well as to evaluate the relationship between demographic factors of those hearing-impaired children and their singing ability. Thirty-seven prelingually-deafened children with CIs and 31 prelingually-deafened children with HAs, and 37 normal-hearing (NH) children participated in the study. The fundamental frequencies (F0) of each note in the recorded songs were extracted and the duration of each sung note was measured. Five metrics were used to evaluate the pitch-related and rhythm-based aspects of singing accuracy. Children with CIs and HAs showed significantly poorer performance in either the pitch-based assessments or the rhythm-based measure than the NH children. No significant differences were seen between the CI and HA groups in all of these measures except for the mean deviation of the pitch intervals. For both hearing-impaired groups, length of device use was significantly correlated with singing accuracy. There is a marked deficit in vocal singing ability either in pitch or rhythm accuracy in a majority of prelingually-deafened children who have received CIs or fitted with HAs. Although an increased length of device use might facilitate singing performance to some extent, the chance for the hearing-impaired children fitted with either HAs or CIs to reach high proficiency in singing is quite slim. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Effect of the inclusion of quebracho tannins in a diet rich in linoleic acid on milk fatty acid composition in dairy ewes.

PubMed

Toral, P G; Hervás, G; Belenguer, A; Bichi, E; Frutos, P

2013-01-01

Despite controversy surrounding the ability of tannins to modulate the fatty acid (FA) profile of ruminant-derived products, reports on this issue are still very limited for dairy sheep. This study was conducted to examine the effect of the inclusion of quebracho tannins in a diet rich in linoleic acid on ewe performance and milk FA composition. Thirty-six lactating ewes were distributed into 6 lots and allocated to 2 treatments (3 lots/treatment): control or quebracho. All sheep received a total mixed ration based on alfalfa hay and a concentrate (forage:concentrate ratio of 40:60) supplemented with 20 g of sunflower oil/kg of dry matter plus 0 (control diet) or 20 g of an extract of quebracho tannins/kg of dry matter (QUE diet). Milk production and composition were analyzed on d 0, 3, 6, 9, 12, 15, 18, 21, 24, and 27 on treatments, and milk FA profile on d 0, 3, 6, 12, 18, and 27. On d 27, samples of rumen fluid were collected for pH, and lactate, ammonia, and volatile FA concentration analysis. Feeding the QUE diet had no apparent effect on animal performance and hardly modified ruminal fermentation characteristics, except for a reduction in the molar proportions of minor volatile FA. Dietary tannins increased the milk concentration of several 18:1 and 18:2 isomers and decreased that of branched-chain FA. Some of these changes were relatively constant throughout the experiment (e.g., cis-12 18:1 and trans-9,cis-12 18:2), whereas others varied over time (e.g., trans-10 18:1, which increased gradually with the QUE diet). Significant differences between treatments in trans-11 18:1 and cis-9,trans-11 conjugated linoleic acid were only observed on d 3. Overall, addition of quebracho tannins to a diet rich in linoleic acid did not prove useful to beneficially modify milk FA composition, especially over the long term. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Development and utilization of complementary communication channels for treatment decision making and survivorship issues among cancer patients: The CIS Research Consortium Experience.

PubMed

Fleisher, Linda; Wen, Kuang Yi; Miller, Suzanne M; Diefenbach, Michael; Stanton, Annette L; Ropka, Mary; Morra, Marion; Raich, Peter C

2015-11-01

Cancer patients and survivors are assuming active roles in decision-making and digital patient support tools are widely used to facilitate patient engagement. As part of Cancer Information Service Research Consortium's randomized controlled trials focused on the efficacy of eHealth interventions to promote informed treatment decision-making for newly diagnosed prostate and breast cancer patients, and post-treatment breast cancer, we conducted a rigorous process evaluation to examine the actual use of and perceived benefits of two complementary communication channels -- print and eHealth interventions. The three Virtual Cancer Information Service (V-CIS) interventions were developed through a rigorous developmental process, guided by self-regulatory theory, informed decision-making frameworks, and health communications best practices. Control arm participants received NCI print materials; experimental arm participants received the additional V-CIS patient support tool. Actual usage data from the web-based V-CIS was also obtained and reported. Print materials were highly used by all groups. About 60% of the experimental group reported using the V-CIS. Those who did use the V-CIS rated it highly on improvements in knowledge, patient-provider communication and decision-making. The findings show that how patients actually use eHealth interventions either singularly or within the context of other communication channels is complex. Integrating rigorous best practices and theoretical foundations is essential and multiple communication approaches should be considered to support patient preferences.

Uneven distribution of human papillomavirus 16 in cervical carcinoma in situ and squamous cell carcinoma in older females: A retrospective database study

PubMed Central

ANDERSSON, SONIA; MINTS, MIRIAM; GYLLENSTEN, ULF; LINDELL, MONICA; GUSTAVSSON, INGER; LAMBE, MATS; WILANDER, ERIK

2014-01-01

Human papillomavirus (HPV) 16 is the dominant cofactor in cervical cancer development. The present report investigated the age-specific prevalence of HPV16 in cervical carcinoma in situ (CIS) in females attending organised cervical cancer screening. A retrospective observational study was performed based on individual data from two databases. A total of 162 females aged between 20 and 65 years from Uppsala County, Sweden with CIS and an HPV test conducted between 2010 and 2011, preceding or concomitant to CIS diagnosis, were included. Females with cervical squamous cell carcinoma (SCC; n=35) were used for comparison. In total, 96% (n=156) of females with CIS were positive for high-risk HPV; HPV16 was the most prevalent (44.5%), followed by HPV33/52/58 (19.5%), HPV31 (13.1%) and HPV18/45 (9.5%). HPV16 was most frequently detected in females with CIS aged between 20 and 29 years (73.6%) and least frequently detected in those aged between 50 and 65 years (33.3%), with a statistically significant age-specific difference (P=0.001). Among the HPV16-positive females, multiple infections were most frequent in the younger age groups. The prevalence of HPV16 in females with CIS decreased with age, whereas a high prevalence of HPV16 remained in females with SCC. These results may indicate that HPV16 has increased oncogenic potential in older females. PMID:25202362

Female athlete triad screening in Canadian Interuniversity Sport universities: analysis of the pre-participation evaluation form.

PubMed

Cuddington, Erin; Shin, Jason J; Frank, Rachel M

2016-03-01

Our aim was to examine inclusion of screening questions related to female athlete triad in the Canadian Interuniversity Sport (CIS) pre-participation evaluation (PPE) forms. We hypothesized that the current CIS PPE forms are not comprehensive screening tools for identifying athletes at risk for the female athlete triad. All 48 English-speaking CIS universities were invited to participate in the study. Via e-mail, a copy of the PPE form was requested from team physicians and certified athletic trainers. Two reviewers evaluated the PPE forms for inclusion of the 12 items recommended by the Female Athlete Triad Coalition for primary screening for the triad. Thirty-nine of 48 CIS universities responded (81%). The majority of the universities (97%), required a PPE for incoming athletes. Only 9 universities (24%) had 6 or more of the 12 recommended screening items included in their forms, whereas 26 universities (70%) included 4 or less items. Three universities (8%) did not address any of the recommended questions. Questions related to disordered eating were often absent in the collected PPEs. In 10 universities (27%), PPE forms were completed by the athlete alone. The remaining 27 (73%) universities required the form to be completed by the athlete in conjunction with a therapist, physician, or both. PPE forms used by CIS universities have limited ability to identify athletes at risk of the triad-based on the recommendations of the Coalition. Furthermore, there is a lack of uniformity of the PPE forms within the CIS.

A novel speech processing algorithm based on harmonicity cues in cochlear implant

NASA Astrophysics Data System (ADS)

Wang, Jian; Chen, Yousheng; Zhang, Zongping; Chen, Yan; Zhang, Weifeng

2017-08-01

This paper proposed a novel speech processing algorithm in cochlear implant, which used harmonicity cues to enhance tonal information in Mandarin Chinese speech recognition. The input speech was filtered by a 4-channel band-pass filter bank. The frequency ranges for the four bands were: 300-621, 621-1285, 1285-2657, and 2657-5499 Hz. In each pass band, temporal envelope and periodicity cues (TEPCs) below 400 Hz were extracted by full wave rectification and low-pass filtering. The TEPCs were modulated by a sinusoidal carrier, the frequency of which was fundamental frequency (F0) and its harmonics most close to the center frequency of each band. Signals from each band were combined together to obtain an output speech. Mandarin tone, word, and sentence recognition in quiet listening conditions were tested for the extensively used continuous interleaved sampling (CIS) strategy and the novel F0-harmonic algorithm. Results found that the F0-harmonic algorithm performed consistently better than CIS strategy in Mandarin tone, word, and sentence recognition. In addition, sentence recognition rate was higher than word recognition rate, as a result of contextual information in the sentence. Moreover, tone 3 and 4 performed better than tone 1 and tone 2, due to the easily identified features of the former. In conclusion, the F0-harmonic algorithm could enhance tonal information in cochlear implant speech processing due to the use of harmonicity cues, thereby improving Mandarin tone, word, and sentence recognition. Further study will focus on the test of the F0-harmonic algorithm in noisy listening conditions.

Behavioral genomics of honeybee foraging and nest defense

NASA Astrophysics Data System (ADS)

Hunt, Greg J.; Amdam, Gro V.; Schlipalius, David; Emore, Christine; Sardesai, Nagesh; Williams, Christie E.; Rueppell, Olav; Guzmán-Novoa, Ernesto; Arechavaleta-Velasco, Miguel; Chandra, Sathees; Fondrk, M. Kim; Beye, Martin; Page, Robert E.

2007-04-01

The honeybee has been the most important insect species for study of social behavior. The recently released draft genomic sequence for the bee will accelerate honeybee behavioral genetics. Although we lack sufficient tools to manipulate this genome easily, quantitative trait loci (QTLs) that influence natural variation in behavior have been identified and tested for their effects on correlated behavioral traits. We review what is known about the genetics and physiology of two behavioral traits in honeybees, foraging specialization (pollen versus nectar), and defensive behavior, and present evidence that map-based cloning of genes is more feasible in the bee than in other metazoans. We also present bioinformatic analyses of candidate genes within QTL confidence intervals (CIs). The high recombination rate of the bee made it possible to narrow the search to regions containing only 17-61 predicted peptides for each QTL, although CIs covered large genetic distances. Knowledge of correlated behavioral traits, comparative bioinformatics, and expression assays facilitated evaluation of candidate genes. An overrepresentation of genes involved in ovarian development and insulin-like signaling components within pollen foraging QTL regions suggests that an ancestral reproductive gene network was co-opted during the evolution of foraging specialization. The major QTL influencing defensive/aggressive behavior contains orthologs of genes involved in central nervous system activity and neurogenesis. Candidates at the other two defensive-behavior QTLs include modulators of sensory signaling ( Am5HT 7 serotonin receptor, AmArr4 arrestin, and GABA-B-R1 receptor). These studies are the first step in linking natural variation in honeybee social behavior to the identification of underlying genes.

Tetrahydrophthalic Anhydrides as Addition Curing Polyimide End Caps: Thermal Isomerization of Methylendianiline 3,6-Diphenyltetrahydrophthalic Bisimides

NASA Technical Reports Server (NTRS)

Frimer, Aryeh A.; Gilinsky-Sharon, Pessia; Gottlieb, Hugo E.; Meador, Mary Ann B.; Johnston, J. Christopher

2005-01-01

In depth NMR studies confirm that heating a 1:2 mixture of cis, cis, cis 3,6-diphenyltetrahydrophthalic anhydride (end cap 9c) with methylenedianiline at 316 C initially yields the corresponding highly congested cis, cis, cis 3,6-diphenyltetrahydrophthalic bisimide 11, which is converted at this temperature to the observed product, the less hindered trans, cis, trans isomer 12.

cis-Chlorobenzene Dihydrodiol Dehydrogenase (TcbB) from Pseudomonas sp. Strain P51, Expressed in Escherichia coli DH5α(pTCB149), Catalyzes Enantioselective Dehydrogenase Reactions

PubMed Central

Raschke, Henning; Fleischmann, Thomas; Van Der Meer, Jan Roelof; Kohler, Hans-Peter E.

1999-01-01

cis-Chlorobenzene dihydrodiol dehydrogenase (CDD) from Pseudomonas sp. strain P51, cloned into Escherichia coli DH5α(pTCB149) was able to oxidize cis-dihydrodihydroxy derivatives (cis-dihydrodiols) of dihydronaphthalene, indene, and four para-substituted toluenes to the corresponding catechols. During the incubation of a nonracemic mixture of cis-1,2-indandiol, only the (+)-cis-(1R,2S) enantiomer was oxidized; the (−)-cis-(S,2R) enantiomer remained unchanged. CDD oxidized both enantiomers of cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, but oxidation of the (+)-cis-(1S,2R) enantiomer was delayed until the (−)-cis-(1R,2S) enantiomer was completely depleted. When incubated with nonracemic mixtures of para-substituted cis-toluene dihydrodiols, CDD always oxidized the major enantiomer at a higher rate than the minor enantiomer. When incubated with racemic 1-indanol, CDD enantioselectively transformed the (+)-(1S) enantiomer to 1-indanone. This stereoselective transformation shows that CDD also acted as an alcohol dehydrogenase. Additionally, CDD was able to oxidize (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene, (+)-cis-monochlorobiphenyl dihydrodiols, and (+)-cis-toluene dihydrodiol to the corresponding catechols. PMID:10583971

Metabolism of 13-cis-retinoic acid by a rat liver 9000g supernatant preparation.

PubMed

Vane, F M; Buggé, C J; Williams, T H

1982-01-01

The in vitro metabolites formed on incubation of 13-cis-retinoic acid (13-cis-RA, isotretinoin) with a 9000g rat liver supernatant system were isolated by HPLC and identified by their mass and NMR spectra. The major metabolic pathway was hydroxylation at C4 to give 4-hydroxy-13-cis-RA, which was rapidly oxidized to 4-oxo-13-cis-RA, the major isolated metabolite. Further metabolism of this 4-oxo metabolite led to two novel compounds, 2-hydroxy-4-oxo-13-cis-RA and 3-hydroxy-4-oxo-13-cis-RA. In addition, small amounts of 13-cis-RA and 4-oxo-13-cis-RA were enzymatically converted to their all-trans isomers. Support for these pathways was obtained by the metabolism of reference samples of 4-hydroxy-13-cis-RA, 4-oxo-13-cis-RA, all-trans-RA, and 4-oxo-all-trans-RA. The predominant formation of 4-oxo metabolites of 13-cis-RA in this in vitro rat system and the results from previously reported in vivo metabolism studies suggest that oxidation at C4 is a major metabolic pathway of 13-cis-RA in both rats and humans.

Implication of fermentable carbohydrates targeting the gut microbiota on conjugated linoleic acid production in high-fat-fed mice.

PubMed

Druart, Céline; Neyrinck, Audrey M; Dewulf, Evelyne M; De Backer, Fabienne C; Possemiers, Sam; Van de Wiele, Tom; Moens, Frédéric; De Vuyst, Luc; Cani, Patrice D; Larondelle, Yvan; Delzenne, Nathalie M

2013-09-28

In vitro experiments have shown that isolated human gut bacteria are able to metabolise PUFA into conjugated PUFA like conjugated linoleic acids (CLA). The hypothesis of the present paper was that high-fat (HF) diet feeding and supplementation with fermentable carbohydrates that have prebiotic properties modulate the in vivo production of CLA by the mouse gut microbiota. Mice were treated for 4 weeks as follows: control (CT) groups were fed a standard diet; HF groups were fed a HF diet rich in linoleic acid (18 : 2n-6); the third groups were fed with the HF diet supplemented with either inulin-type fructans (HF-ITF) or arabinoxylans (HF-Ax). HF diet feeding increased rumenic acid (cis-9,trans-11-18 : 2 CLA) content both in the caecal and liver tissues compared with the CT groups. ITF supplementation had no major effect compared with the HF diet whereas Ax supplementation increased further rumenic acid (cis-9,trans-11-18 : 2 CLA) in the caecal tissue. These differences between both prebiotics may be linked to the high fat-binding capacity of Ax that provides more substrates for bacterial metabolism and to differential modulation of the gut microbiota (specific increase in Roseburia spp. in HF-Ax v. HF). In conclusion, these experiments supply the proof of concept that the mouse gut microbiota produces CLA in vivo, with consequences on the level of CLA in the caecal and liver tissues. We postulate that the CLA-producing bacteria could be a mediator to consider in the metabolic effects of both HF diet feeding and prebiotic supplementation.

Estrogen receptor β (ERβ1) transactivation is differentially modulated by the transcriptional coregulator Tip60 in a cis-acting element-dependent manner.

PubMed

Lee, Ming-Tsung; Leung, Yuet-Kin; Chung, Irving; Tarapore, Pheruza; Ho, Shuk-Mei

2013-08-30

Estrogen receptor (ER) β1 and ERα have overlapping and distinct functions despite their common use of estradiol as the physiological ligand. These attributes are explained in part by their differential utilization of coregulators and ligands. Although Tip60 has been shown to interact with both receptors, its regulatory role in ERβ1 transactivation has not been defined. In this study, we found that Tip60 enhances transactivation of ERβ1 at the AP-1 site but suppresses its transcriptional activity at the estrogen-response element (ERE) site in an estradiol-independent manner. However, different estrogenic compounds can modify the Tip60 action. The corepressor activity of Tip60 at the ERE site is abolished by diarylpropionitrile, genistein, equol, and bisphenol A, whereas its coactivation at the AP-1 site is augmented by fulvestrant (ICI 182,780). GRIP1 is an important tethering mediator for ERs at the AP-1 site. We found that coexpression of GRIP1 synergizes the action of Tip60. Although Tip60 is a known acetyltransferase, it is unable to acetylate ERβ1, and its coregulatory functions are independent of its acetylation activity. In addition, we showed the co-occupancy of ERβ1 and Tip60 at ERE and AP-1 sites of ERβ1 target genes. Tip60 differentially regulates the endogenous expression of the target genes by modulating the binding of ERβ1 to the cis-regulatory regions. Thus, we have identified Tip60 as the first dual-function coregulator of ERβ1.

Estrogen Receptor β (ERβ1) Transactivation Is Differentially Modulated by the Transcriptional Coregulator Tip60 in a cis-Acting Element-dependent Manner*

PubMed Central

Lee, Ming-Tsung; Leung, Yuet-Kin; Chung, Irving; Tarapore, Pheruza; Ho, Shuk-Mei

2013-01-01

Estrogen receptor (ER) β1 and ERα have overlapping and distinct functions despite their common use of estradiol as the physiological ligand. These attributes are explained in part by their differential utilization of coregulators and ligands. Although Tip60 has been shown to interact with both receptors, its regulatory role in ERβ1 transactivation has not been defined. In this study, we found that Tip60 enhances transactivation of ERβ1 at the AP-1 site but suppresses its transcriptional activity at the estrogen-response element (ERE) site in an estradiol-independent manner. However, different estrogenic compounds can modify the Tip60 action. The corepressor activity of Tip60 at the ERE site is abolished by diarylpropionitrile, genistein, equol, and bisphenol A, whereas its coactivation at the AP-1 site is augmented by fulvestrant (ICI 182,780). GRIP1 is an important tethering mediator for ERs at the AP-1 site. We found that coexpression of GRIP1 synergizes the action of Tip60. Although Tip60 is a known acetyltransferase, it is unable to acetylate ERβ1, and its coregulatory functions are independent of its acetylation activity. In addition, we showed the co-occupancy of ERβ1 and Tip60 at ERE and AP-1 sites of ERβ1 target genes. Tip60 differentially regulates the endogenous expression of the target genes by modulating the binding of ERβ1 to the cis-regulatory regions. Thus, we have identified Tip60 as the first dual-function coregulator of ERβ1. PMID:23857583

Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation

NASA Technical Reports Server (NTRS)

Romano, Laura A.; Wray, Gregory A.

2003-01-01

Evolutionary changes in transcriptional regulation undoubtedly play an important role in creating morphological diversity. However, there is little information about the evolutionary dynamics of cis-regulatory sequences. This study examines the functional consequence of evolutionary changes in the Endo16 promoter of sea urchins. The Endo16 gene encodes a large extracellular protein that is expressed in the endoderm and may play a role in cell adhesion. Its promoter has been characterized in exceptional detail in the purple sea urchin, Strongylocentrotus purpuratus. We have characterized the structure and function of the Endo16 promoter from a second sea urchin species, Lytechinus variegatus. The Endo16 promoter sequences have evolved in a strongly mosaic manner since these species diverged approximately 35 million years ago: the most proximal region (module A) is conserved, but the remaining modules (B-G) are unalignable. Despite extensive divergence in promoter sequences, the pattern of Endo16 transcription is largely conserved during embryonic and larval development. Transient expression assays demonstrate that 2.2 kb of upstream sequence in either species is sufficient to drive GFP reporter expression that correctly mimics this pattern of Endo16 transcription. Reciprocal cross-species transient expression assays imply that changes have also evolved in the set of transcription factors that interact with the Endo16 promoter. Taken together, these results suggest that stabilizing selection on the transcriptional output may have operated to maintain a similar pattern of Endo16 expression in S. purpuratus and L. variegatus, despite dramatic divergence in promoter sequence and mechanisms of transcriptional regulation.

Biohydrogenation of C20 polyunsaturated fatty acids by anaerobic bacteria.

PubMed

Sakurama, Haruko; Kishino, Shigenobu; Mihara, Kousuke; Ando, Akinori; Kita, Keiko; Takahashi, Satomi; Shimizu, Sakayu; Ogawa, Jun

2014-09-01

The PUFAs include many bioactive lipids. The microbial metabolism of C18 PUFAs is known to produce their bioactive isomers, such as conjugated FAs and hydroxy FAs, but there is little information on that of C20 PUFAs. In this study, we aimed to obtain anaerobic bacteria with the ability to produce novel PUFAs from C20 PUFAs. Through the screening of ∼100 strains of anaerobic bacteria, Clostridium bifermentans JCM 1386 was selected as a strain with the ability to saturate PUFAs during anaerobic cultivation. This strain converted arachidonic acid (cis-5,cis-8,cis-11,cis-14-eicosatetraenoic acid) and EPA (cis-5,cis-8,cis-11,cis-14,cis-17-EPA) into cis-5,cis-8,trans-13-eicosatrienoic acid and cis-5,cis-8,trans-13,cis-17-eicosatetraenoic acid, giving yields of 57% and 67% against the added PUFAs, respectively. This is the first report of the isolation of a bacterium transforming C20 PUFAs into corresponding non-methylene-interrupted FAs. We further investigated the substrate specificity of the biohydrogenation by this strain and revealed that it can convert two cis double bonds at the ω6 and ω9 positions in various C18 and C20 PUFAs into a trans double bond at the ω7 position. This study should serve to open up the development of novel potentially bioactive PUFAs. Copyright © 2014 by the American Society for Biochemistry and Molecular Biology, Inc.

Technological innovations in the development of cardiovascular clinical information systems.

PubMed

Hsieh, Nan-Chen; Chang, Chung-Yi; Lee, Kuo-Chen; Chen, Jeen-Chen; Chan, Chien-Hui

2012-04-01

Recent studies have shown that computerized clinical case management and decision support systems can be used to assist surgeons in the diagnosis of disease, optimize surgical operation, aid in drug therapy and decrease the cost of medical treatment. Therefore, medical informatics has become an extensive field of research and many of these approaches have demonstrated potential value for improving medical quality. The aim of this study was to develop a web-based cardiovascular clinical information system (CIS) based on innovative techniques, such as electronic medical records, electronic registries and automatic feature surveillance schemes, to provide effective tools and support for clinical care, decision-making, biomedical research and training activities. The CIS developed for this study contained monitoring, surveillance and model construction functions. The monitoring layer function provided a visual user interface. At the surveillance and model construction layers, we explored the application of model construction and intelligent prognosis to aid in making preoperative and postoperative predictions. With the use of the CIS, surgeons can provide reasonable conclusions and explanations in uncertain environments.

Ameliorative effect of selenium in cisplatin-induced testicular damage in rats.

PubMed

Simsek, Nejdet; Koc, Akif; Karadeniz, Ali; Yildirim, Mehmet Erol; Celik, Hüseyin Tuğrul; Sari, Erhan; Kara, Adem

2016-04-01

In this study, we investigated the protective effect of selenium (Se) on cisplatin (Cis) induced testicular damage using histopathological, immunohistochemical and biochemical approaches. Twenty-one male Wistar rats were equally divided into three groups of seven rats each: control (C), Cis, and Cis+Se. Cis and Cis+Se group rats received Cis at a dose of 12mg/kg b.w./day, intraperitoneally for 3 consecutive days. Cis+Se group rats received selenium via oral gavage 3mg/kg/day (twice-a day as 1.5mg/kg) until 11th consecutive days starting at 5 days before cisplatin injection. C group received only 0.9% NaCl intraperitoneally and orally at same time and at equal volume. After the treatment, the histopathological, immunohistochemical and biochemical examinations were performed. In seminiferous tubules of Cis treated rats were observed the most consistent findings characterized with vacuolization, desquamation, disorganization, and also was a considerable reduction in elongated spermatids, however the Cis+Se group exhibited improved histopathologic changes. In the immunohistochemical examinations, caspase-3 immunopositive cells displayed higher in the Cis group according to C and Cis+Se groups. Bcl-2 and NF-κB staining revealed a moderate number in the C group and significantly fewer in the Cis group compared to the Cis+Se groups. Additionally, MDA levels were also significantly increased in the Cis group in comparison to Control group, but pretreatment with selenium prevented elevation of MDA levels significantly in Cis+Se group rats. This study indicates that Cis-treatment induced testicular apoptosis and lipid peroxidation, and combined treatment with selenium prevented severity of the toxicity in rats. Copyright © 2016 Elsevier GmbH. All rights reserved.

Photoswitching a Molecular Catalyst to Regulate CO 2 Hydrogenation

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

Priyadarshani, Nilusha; Ginovska-Pangovska, Bojana; Bays, J. Timothy

2015-07-24

Inspired by nature’s ability to regulate catalysis using physiological stimuli, azobenzene was incorporated into Rh(bis)diphosphine CO 2 hydrogenation catalysts to photoinitiate structural changes to modulate the resulting catalytic activity. The rhodium bound diphosphine ligands (P(Ph 2)-CH 2-N(R) CH 2-P(Ph2)) contain the terminal amine of a non-natural amino acid, either β-alanine (β-Ala) or γ-aminobutyric acid (GABA). For both β-ala and GABA containing complexes, the carboxylic acids of the amino acids were coupled to the amines of diaminoazobenzene, creating a rhodium bound trans-spanning tetraphosphine complex. The photo-induced cis-trans isomerization of the azobenzene-containing complexes imposes structural changes on these complexes, as evidenced bymore » 1H NMR. We found that the CO 2 hydrogenation activity for the β-ala bound Rh complex is 40% faster with azobenzene in the cis configuration (16 s -1) than in the trans conformation (11 s -1), while the γ-aminobutyric acid containing Rh complex has the same rate (~17 s -1) in either the cis or the trans configuration at 27 °C. The corresponding complexes without the attached azobenzene were also prepared, characterized, and catalytically tested for comparison, and have rates of 30 s -1. Computational studies were undertaken to evaluate the difference in rate between the cis and trans isomers for the β-Ala bound Rh complex, and revealed major structural changes between all cis and trans structures, but only minor structural changes that would be unique to the β-Ala bound Rh complex. We postulate that the slower rate of the azobenzene-containing β-Ala bound Rh complex is due to subtle changes in the bite angle arising from steric strain due to the trans-spanning azobenzene, altering hydricity and consequently rate. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for the DOE by Battelle. A portion of this research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.« less

Enantioselective disruption of the endocrine system by Cis-Bifenthrin in the male mice.

PubMed

Jin, Yuanxiang; Wang, Jiangcong; Pan, Xiuhong; Miao, Wenyu; Lin, Xiaojian; Wang, Linggang; Fu, Zhengwei

2015-07-01

Bifenthrin (BF), as a chiral pyrethroid, is widely used to control field and household pests in China. At present, the commercial BF is a mixed compound containing cis isomers (cis-BF) including two enantiomers of 1R-cis-BF and 1S-cis-BF. In the present study, the two individual cis-BF enantiomers were separated by a preparative supercritical fluid chromatography. Then, four week-old adolescent male ICR mice were orally administered 1R-cis-BF and 1S-cis-BF separately daily for 3 weeks at doses of 0, 7.5 and 15 mg/kg/day, respectively. Results showed that the transcription status of some genes involved in cholesterol synthesis and transport as well as testosterone (T) synthesis in the testes were influenced by cis-BF enantiomers. Especially, we observed that the transcription status of key genes on the pathway of T synthesis including cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc) and cytochrome P450 17α-hydroxysteroid dehydrogenase (P45017α)) were selectively altered in the testis of mice when treated with 1S-cis-BF, suggesting that it is the possible reason to explain why the lower serum T concentration in 1S-cis-BF treated group. Taken together, it concluded that both of the cis-BF enantiomers have the endocrine disruption activities, while 1S-cis-BF was higher than 1R-cis-BF in mice when exposed during the puberty. The data was helpful to understand the toxicity of cis-BF in mammals under enantiomeric level. © 2014 Wiley Periodicals, Inc.

Zero- vs. one-dimensional, parametric vs. non-parametric, and confidence interval vs. hypothesis testing procedures in one-dimensional biomechanical trajectory analysis.

PubMed

Pataky, Todd C; Vanrenterghem, Jos; Robinson, Mark A

2015-05-01

Biomechanical processes are often manifested as one-dimensional (1D) trajectories. It has been shown that 1D confidence intervals (CIs) are biased when based on 0D statistical procedures, and the non-parametric 1D bootstrap CI has emerged in the Biomechanics literature as a viable solution. The primary purpose of this paper was to clarify that, for 1D biomechanics datasets, the distinction between 0D and 1D methods is much more important than the distinction between parametric and non-parametric procedures. A secondary purpose was to demonstrate that a parametric equivalent to the 1D bootstrap exists in the form of a random field theory (RFT) correction for multiple comparisons. To emphasize these points we analyzed six datasets consisting of force and kinematic trajectories in one-sample, paired, two-sample and regression designs. Results showed, first, that the 1D bootstrap and other 1D non-parametric CIs were qualitatively identical to RFT CIs, and all were very different from 0D CIs. Second, 1D parametric and 1D non-parametric hypothesis testing results were qualitatively identical for all six datasets. Last, we highlight the limitations of 1D CIs by demonstrating that they are complex, design-dependent, and thus non-generalizable. These results suggest that (i) analyses of 1D data based on 0D models of randomness are generally biased unless one explicitly identifies 0D variables before the experiment, and (ii) parametric and non-parametric 1D hypothesis testing provide an unambiguous framework for analysis when one׳s hypothesis explicitly or implicitly pertains to whole 1D trajectories. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Virtuous Circles of Clinical Information Systems: a Modern Utopia.

PubMed

Degoulet, P

2016-11-10

Clinical information systems (CIS) are developed with the aim of improving both the efficiency and the quality of care. This position paper is based on the hypothesis that such vision is partly a utopian view of the emerging eSociety. Examples are drawn from 15 years of experience with the fully integrated Georges Pompidou University Hospital (HEGP) CIS and temporal data series extracted from the data warehouses of Assistance Publique - Hôpitaux de Paris (AP-HP) acute care hospitals which share the same administrative organization as HEGP. Three main virtuous circles are considered: user satisfaction vs. system use, system use vs. cost efficiency, and system use vs quality of care. In structural equation models (SEM), the positive bidirectional relationship between user satisfaction and use was only observed in the early HEGP CIS deployment phase (first four years) but disappeared in late post-adoption (≥8 years). From 2009 to 2013, financial efficiency of 20 AP-HP hospitals evaluated with stochastic frontier analysis (SFA) models diminished by 0.5% per year. The lower decrease of efficiency observed between the three hospitals equipped with a more mature CIS and the 17 other hospitals was of the same order of magnitude than the difference observed between pediatric and non-pediatric hospitals. Outcome quality benefits that would bring evidence to the system use vs. quality loop are unlikely to be obtained in a near future since they require integration with population-based outcome measures including mortality, morbidity, and quality of life that may not be easily available. Barriers to making the transformation of the utopian part of the CIS virtuous circles happen should be overcome to actually benefit the emerging eSociety.

Identification of the 11-cis-specific retinyl-ester synthase in retinal Müller cells as multifunctional O-acyltransferase (MFAT)

PubMed Central

Kaylor, Joanna J.; Cook, Jeremy D.; Makshanoff, Jacob; Bischoff, Nicholas; Yong, Jennifer; Travis, Gabriel H.

2014-01-01

Absorption of a photon by a rhodopsin or cone-opsin pigment isomerizes its 11-cis-retinaldehyde (11-cis-RAL) chromophore to all-trans-retinaldehyde (all-trans-RAL), which dissociates after a brief period of activation. Light sensitivity is restored to the resulting apo-opsin when it recombines with another 11-cis-RAL. Conversion of all-trans-RAL to 11-cis-RAL is carried out by an enzyme pathway called the visual cycle in cells of the retinal pigment epithelium. A second visual cycle is present in Müller cells of the retina. The retinol isomerase for this noncanonical pathway is dihydroceramide desaturase (DES1), which catalyzes equilibrium isomerization of retinol. Because 11-cis-retinol (11-cis-ROL) constitutes only a small fraction of total retinols in an equilibrium mixture, a subsequent step involving selective removal of 11-cis-ROL is required to drive synthesis of 11-cis-retinoids for production of visual chromophore. Selective esterification of 11-cis-ROL is one possibility. Crude homogenates of chicken retinas rapidly convert all-trans-ROL to 11-cis-retinyl esters (11-cis-REs) with minimal formation of other retinyl-ester isomers. This enzymatic activity implies the existence of an 11-cis-specific retinyl-ester synthase in Müller cells. Here, we evaluated multifunctional O-acyltransferase (MFAT) as a candidate for this 11-cis-RE-synthase. MFAT exhibited much higher catalytic efficiency as a synthase of 11-cis-REs versus other retinyl-ester isomers. Further, we show that MFAT is expressed in Müller cells. Finally, homogenates of cells coexpressing DES1 and MFAT catalyzed the conversion of all-trans-ROL to 11-cis-RP, similar to what we observed with chicken-retina homogenates. MFAT is therefore an excellent candidate for the retinyl-ester synthase that cooperates with DES1 to drive synthesis of 11-cis-retinoids by mass action. PMID:24799687

PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs

PubMed Central

Cheng, Zhongshan; Chu, Hin; Fan, Yanhui; Li, Cun; Song, You-Qiang; Zhou, Jie; Yuen, Kwok-Yung

2015-01-01

Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets. PMID:26612672

Synthesis and structural and photoswitchable properties of novel chiral host molecules: axis chiral 2,2'-dihydroxy-1,1'-binaphthyl-appended stiff-stilbene.

PubMed

Shimasaki, Toshiaki; Kato, Shin-ichiro; Ideta, Keiko; Goto, Kenta; Shinmyozu, Teruo

2007-02-16

Novel photoswitchable chiral hosts having an axis chiral 2,2'-dihydroxy-1,1'-binaphthyl (BINOL)-appended stiff-stilbene, trans-(R,R)- and -(S,S)-1, were synthesized by palladium-catalyzed Suzuki-Miyaura coupling and low-valence titanium-catalyzed McMurry coupling as key steps, and they were fully characterized by various NMR spectral techniques. The enantiomers of trans-1 showed almost complete mirror images in the CD spectra, where two split Cotton effects (exciton coupling) were observed in the beta-transitions of the naphthyl chromophore at 222 and 235 nm, but no Cotton effect was observed in the stiff-stilbene chromophore at 365 nm. The structures of (R)-10 and trans-(R,R)-1 were confirmed by X-ray structural analysis. The optimized structure of cis-1 by MO calculations has a wide chiral cavity of 7-8 A in diameter, whereas trans-1 cannot form an intramolecular cavity based on the X-ray data. Irradiation of (R,R)-trans-1 with black light (lambda = 365 nm) in CH3CN or benzene at 23 degrees C led to the conversion to the corresponding cis-isomer, as was monitored by 1H NMR, UV-vis, and CD spectra. At the photostationary state, the cis-1/trans-1 ratio was 86/14 in benzene or 75/25 in CH3CN. On the other hand, irradiation of the cis-1/trans-1 (75/25) mixture in CH3CN with an ultra-high-pressure Hg lamp at 23 degrees C (lambda = 410 nm) led to the photostationary state, where the cis-1/trans-1 ratio was estimated to be 9/91 on the basis of the 1H NMR spectra. The cis-trans and trans-cis interconversions could be repeated 10 times without decomposition of the C=C double bond. Thus, a new type of photoswitchable molecule has been developed, and trans-1 and cis-1 were quite durable under irradiation conditions. The guest binding properties of the BINOL moieties of trans- and cis-(R,R)-1 with F-, Cl-, and H2PO4- were examined by 1H NMR titration in CDCl3. Similar interaction with F- and Cl- was observed in trans-1 (host/guest = 1/1, Kassoc = (1.0 +/- 0.13) x 103 for F- and (4.6 +/- 0.72) x 102 M-1 for Cl-) and cis-1 (host/guest = 1/1, Kassoc = (1.0 +/- 0.13) x 103 for F- and (5.9 +/- 0.69) x 10 M-1 for Cl-), but H2PO4- interacted differently: the cis-isomer formed the 1/1 complex (Kassoc = (9.38 +/- 2.67) x 10 M-1), whereas multistep equilibrium was expected for the trans-isomer.

CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.

PubMed

Nikulova, Anna A; Favorov, Alexander V; Sutormin, Roman A; Makeev, Vsevolod J; Mironov, Andrey A

2012-07-01

Identification of transcriptional regulatory regions and tracing their internal organization are important for understanding the eukaryotic cell machinery. Cis-regulatory modules (CRMs) of higher eukaryotes are believed to possess a regulatory 'grammar', or preferred arrangement of binding sites, that is crucial for proper regulation and thus tends to be evolutionarily conserved. Here, we present a method CORECLUST (COnservative REgulatory CLUster STructure) that predicts CRMs based on a set of positional weight matrices. Given regulatory regions of orthologous and/or co-regulated genes, CORECLUST constructs a CRM model by revealing the conserved rules that describe the relative location of binding sites. The constructed model may be consequently used for the genome-wide prediction of similar CRMs, and thus detection of co-regulated genes, and for the investigation of the regulatory grammar of the system. Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila.

Green tea flavour determinants and their changes over manufacturing processes.

PubMed

Han, Zhuo-Xiao; Rana, Mohammad M; Liu, Guo-Feng; Gao, Ming-Jun; Li, Da-Xiang; Wu, Fu-Guang; Li, Xin-Bao; Wan, Xiao-Chun; Wei, Shu

2016-12-01

Flavour determinants in tea infusions and their changes during manufacturing processes were studied using Camellia sinensis cultivars 'Bai-Sang Cha' ('BAS') possessing significant floral scents and 'Fuding-Dabai Cha' ('FUD') with common green tea odour. Metabolite profiling based on odour activity threshold revealed that 'BAS' contained higher levels of the active odorants β-ionone, linalool and its two oxides, geraniol, epoxylinalool, decanal and taste determinant catechins than 'FUD' (p<0.05). Enhanced transcription of some terpenoid and catechin biosynthetic genes in 'BAS' suggested genetically enhanced production of those flavour compounds. Due to manufacturing processes, the levels of linalool and geraniol decreased whereas those of β-ionone, linalool oxides, indole and cis-jasmone increased. Compared with pan-fire treatment, steam treatment reduced the levels of catechins and proportion of geraniol, linalool and its derivatives, consequently, reducing catechin-related astringency and monoterpenol-related floral scent. Our study suggests that flavour determinant targeted modulation could be made through genotype and manufacturing improvements. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nematode sperm maturation triggered by protease involves sperm-secreted serine protease inhibitor (Serpin)

PubMed Central

Zhao, Yanmei; Sun, Wei; Zhang, Pan; Chi, Hao; Zhang, Mei-Jun; Song, Chun-Qing; Ma, Xuan; Shang, Yunlong; Wang, Bin; Hu, Youqiao; Hao, Zhiqi; Hühmer, Andreas F.; Meng, Fanxia; L'Hernault, Steven W.; He, Si-Min; Dong, Meng-Qiu; Miao, Long

2012-01-01

Spermiogenesis is a series of poorly understood morphological, physiological and biochemical processes that occur during the transition of immotile spermatids into motile, fertilization-competent spermatozoa. Here, we identified a Serpin (serine protease inhibitor) family protein (As_SRP-1) that is secreted from spermatids during nematode Ascaris suum spermiogenesis (also called sperm activation) and we showed that As_SRP-1 has two major functions. First, As_SRP-1 functions in cis to support major sperm protein (MSP)-based cytoskeletal assembly in the spermatid that releases it, thereby facilitating sperm motility acquisition. Second, As_SRP-1 released from an activated sperm inhibits, in trans, the activation of surrounding spermatids by inhibiting vas deferens-derived As_TRY-5, a trypsin-like serine protease necessary for sperm activation. Because vesicular exocytosis is necessary to create fertilization-competent sperm in many animal species, components released during this process might be more important modulators of the physiology and behavior of surrounding sperm than was previously appreciated. PMID:22307610

Perspectives on Teaching the International Classification of Functioning, Disability, and Health Model to Physical Therapy Students.

PubMed

Peters-Brinkerhoff, Cheryl

2016-01-01

During a reaccreditation visit, deficiencies were discovered in the clinical education curriculum regarding patient-centered care in a Doctorate of Physical Therapy program. To understand the problem and address those deficiencies, the clinical internship experience was examined using the International Classification of Functioning, Disability, and Health (ICF) model as a conceptual framework for clinical reasoning. This qualitative case study aimed to study (1) perceptions of physical therapy (PT) students regarding their knowledge and learning experiences during clinical affiliations and what knowledge they acquired of the ICF as applied to patient-centered care during their internship, and (2) the perceptions of clinical instructors (CIs) of their knowledge of the ICF model, its integration into their practice, barriers to its use, and the learning experiences the CIs provided to students regarding the ICF model. Data were collected using questionnaires sent to 42 CIs and at focus groups of 22 PT students conducted at the study site. Data were also collected from student evaluations on the Clinical Performance Instrument. Data were analyzed using coding techniques and themes based on the use of the ICF model in the clinical setting by students and CIs. Most CIs reported a poor understanding of the ICF model or how it relates to patient-centered care; both CIs and students reported none to minimal learning experience related to the ICF model. Document analysis of the student evaluations revealed no assessment of the ICF model was mentioned. Learning experiences of all domains of the ICF model are generally not being presented to PT students during their clinical affiliations.

Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

PubMed Central

Brody, Thomas; Yavatkar, Amarendra S; Kuzin, Alexander; Kundu, Mukta; Tyson, Leonard J; Ross, Jermaine; Lin, Tzu-Yang; Lee, Chi-Hon; Awasaki, Takeshi; Lee, Tzumin; Odenwald, Ward F

2012-01-01

Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc. Key findings A genome-wide catalog of Drosophila conserved DNA sequence clusters. cis-Decoder discovers functionally related enhancers. Functionally related enhancers share balanced sequence element copy numbers. Many enhancers function during multiple phases of development. PMID:22174086

In vitro human metabolism of permethrin isomers alone or as a mixture and the formation of the major metabolites in cryopreserved primary hepatocytes.

PubMed

Willemin, M-E; Kadar, A; de Sousa, G; Leclerc, E; Rahmani, R; Brochot, C

2015-06-01

In vitro metabolism of permethrin, a pyrethroid insecticide, was assessed in primary human hepatocytes. In vitro kinetic experiments were performed to estimate the Michaelis-Menten parameters and the clearances or formation rates of the permethrin isomers (cis- and trans-) and three metabolites, cis- and trans-3-(2,2 dichlorovinyl)-2,2-dimethyl-(1-cyclopropane) carboxylic acid (cis- and trans-DCCA) and 3-phenoxybenzoic acid (3-PBA). Non-specific binding and the activity of the enzymes involved in permethrin's metabolism (cytochromes P450 and carboxylesterases) were quantified. Trans-permethrin was cleared more rapidly than cis-permethrin with a 2.6-factor (25.7±0.6 and 10.1±0.3 μL/min/10(6) cells respectively). A 3-factor was observed between the formation rates of DCCA and 3-PBA obtained from trans- and cis-permethrin. For both isomers, the rate of formation of DCCA was higher than the one of 3-PBA. The metabolism of the isomers in mixture was also quantified. The co-incubation of isomers at different ratios showed the low inhibitory potential of cis- and trans-permethrin on each other. The estimates of the clearances and the formation rates in the co-incubation condition did not differ from the estimates obtained with a separate incubation. These metabolic parameters may be integrated in physiologically based pharmacokinetic (PBPK) models to predict the fate of permethrin and metabolites in the human body. Copyright © 2015 Elsevier Ltd. All rights reserved.

Carotenoids and β-carotene in orange fleshed sweet potato: A possible solution to vitamin A deficiency.

PubMed

Islam, Sheikh Nazrul; Nusrat, Tania; Begum, Parveen; Ahsan, Monira

2016-05-15

The present study, in line with a plant-food-based approach to address vitamin A deficiency, reports the analysis of total carotenoids, and trans- and cis-β-carotenes, in different varieties of raw and boiled orange-fleshed sweet potatoes (OFSP). Carotenoids were isolated using acetone-petroleum ether extraction followed by spectrophotometric determination. trans- and cis-β-Carotenes were analyzed by reversed-phase HPLC method using a mobile phase containing acetonitrile:methanol:2-propanol in the ratio of 85:15:33 with 0.01% ammonium acetate. Intra-varietal difference in carotenoids as well as trans- and cis-β-carotenes were noted in both the raw and boiled potatoes. Carotenoid content was found to be higher in the raw potatoes compared to the boiled samples from the same variety. Amongst the OFSP varieties, Kamalasundari (BARI SP-2) was found to contain the most carotenoids in both the raw and boiled samples. β-Carotene was significantly higher in the Kamalsundari and BARI SP-5 varieties. trans-β-Carotene was found to be the major carotenoid in all of the raw potatoes, but boiling was associated with an increase in cis-β-carotene and a decrease in the trans isomer. Kamalsundari and BARI SP-5 orange-fleshed sweet potatoes have the potential to be used as food-based supplements to reduce vitamin A deficiency. Copyright © 2015 Elsevier Ltd. All rights reserved.

An electro-optical and electron injection study of benzothiazole-based squaraine dyes as efficient dye-sensitized solar cell materials: a first principles study.

PubMed

Al-Fahdan, Najat Saeed; Asiri, Abdullah M; Irfan, Ahmad; Basaif, Salem A; El-Shishtawy, Reda M

2014-12-01

Squaraine dyes have attracted significant attention in many areas of daily life from biomedical imaging to semiconducting materials. Moreover, these dyes are used as photoactive materials in the field of solar cells. In the present study, we investigated the structural, electronic, photophysical, and charge transport properties of six benzothiazole-based squaraine dyes (Cis-SQ1-Cis-SQ3 and Trans-SQ1-Trans-SQ3). The effect of electron donating (-OCH3) and electron withdrawing (-COOH) groups was investigated intensively. Ground state geometry and frequency calculations were performed by applying density functional theory (DFT) at B3LYP/6-31G** level of theory. Absorption spectra were computed in chloroform at the time-dependent DFT/B3LYP/6-31G** level of theory. The driving force of electron injection (ΔG (inject)), relative driving force of electron injection (ΔG r (inject)), electronic coupling constants (|VRP|) and light harvesting efficiency (LHE) of all six compounds were calculated and compared with previously studied sensitizers. The ΔG (inject), ΔG r (inject) and |VRP| of all six compounds revealed that these sensitizers would be efficient dye-sensitized solar cell materials. Cis/Trans-SQ3 exhibited superior LHE as compared to other derivatives. The Cis/Trans geometric effect was studied and discussed with regard to electro-optical and charge transport properties.

Computational studies of molecular charge transfer complexes of heterocyclic 4-methylepyridine-2-azomethine-p-benzene derivatives with picric acid and m-dinitrobenzene.

PubMed

Al-Harbi, L M; El-Mossalamy, E H; Obaid, A Y; Al-Jedaani, A H

2014-01-01

Charge transfer complexes of substituted aryl Schiff bases as donors with picric acid and m-dinitrobenzene as acceptors were investigated by using computational analysis calculated by Configuration Interaction Singles Hartree-Fock (CIS-HF) at standard 6-31G∗ basis set and Time-Dependent Density-Functional Theory (TD-DFT) levels of theory at standard 6-31G∗∗ basis set, infrared spectra, visible and nuclear magnetic resonance spectra are investigated. The optimized geometries and vibrational frequencies were evaluated. The energy and oscillator strength were calculated by Configuration Interaction Singles Hartree-Fock method (CIS-HF) and the Time-Dependent Density-Functional Theory (TD-DFT) results. Electronic properties, such as HOMO and LUMO energies and band gaps of CTCs set, were studied by the Time-Dependent density functional theory with Becke-Lee-Young-Parr (B3LYP) composite exchange correlation functional and by Configuration Interaction Singles Hartree-Fock method (CIS-HF). The ionization potential Ip and electron affinity EA were calculated by PM3, HF and DFT methods. The columbic force was calculated theoretically by using (CIS-HF and TD-DFT) methods. This study confirms that the theoretical calculation of vibrational frequencies for (aryl Schiff bases--(m-dinitrobenzene and picric acid)) complexes are quite useful for the vibrational assignment and for predicting new vibrational frequencies. Copyright © 2013 Elsevier B.V. All rights reserved.

Iodine-Catalyzed Isomerization of Dimethyl Muconate.

PubMed

Settle, Amy E; Berstis, Laura; Zhang, Shuting; Rorrer, Nicholas A; Hu, Haiming; Richards, Ryan M; Beckham, Gregg T; Crowley, Michael F; Vardon, Derek R

2018-06-11

cis,cis-Muconic acid is a platform bio-based chemical that can be upgraded to drop-in commodity and novel monomers. Among the possible drop-in products, dimethyl terephthalate can be synthesized via esterification, isomerization, Diels-Alder cycloaddition, and dehydrogenation. The isomerization of cis,cis-dimethyl muconate (ccDMM) to the trans,trans-form (ttDMM) can be catalyzed by iodine; however, studies have yet to address (i) the mechanism and reaction barriers unique to DMM, and (ii) the influence of solvent, potential for catalyst recycle, and recovery of high-purity ttDMM. To address this gap, we apply a joint computational and experimental approach to investigate iodine-catalyzed isomerization of DMM. Density functional theory calculations identified unique regiochemical considerations owing to the large number of halogen-diene coordination schemes. Both transition state theory and experiments estimate significant barrier reductions with photodissociated iodine. Solvent selection was critical for rapid kinetics, likely because of solvent complexation with iodine. Under select conditions, ttDMM yields of 95 % were achieved in <1 h with methanol, followed by high purity recovery (>98 %) with crystallization. Lastly, post-reaction iodine can be recovered and recycled with minimal loss of activity. Overall, these findings provide new insight into the mechanism and conditions necessary for DMM isomerization with iodine to advance the state-of-the-art for bio-based chemicals. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comprehensive analysis of mycolic acid subclass and molecular species composition of Mycobacterium bovis BCG Tokyo 172 cell wall skeleton (SMP-105).

PubMed

Uenishi, Yuko; Fujita, Yukiko; Kusunose, Naoto; Yano, Ikuya; Sunagawa, Makoto

2008-02-01

The mycobacterial cell envelope consists of a characteristic cell wall skeleton (CWS), a mycoloyl arabinogalactan peptidoglycan complex, and related hydrophobic components that contribute to the cell surface properties. Since mycolic acids have recently been reported to play crucial roles in host immune response, detailed molecular characterization of mycolic acid subclasses and sub-subclasses of CWS from Mycobacterium bovis BCG Tokyo 172 (SMP-105) was performed. Mycolic acids were liberated by alkali hydrolysis from SMP-105, and their methyl esters were separated by silica gel TLC into three subclasses: alpha-, methoxy-, and keto-mycolates. Each mycolate subclass was further separated by silver nitrate (AgNO(3))-coated silica gel TLC into sub-subclasses. Molecular weights of individual mycolic acid were determined by MALDI-TOF mass spectrometry. alpha-Mycolates were sub-grouped into cis, cis-dicyclopropanoic (alpha1), and cis-monocyclopropanoic-cis-monoenoic (alpha2) series; methoxy-mycolates were sub-grouped into cis-monocyclopropanoic (m1), trans-monocyclopropanoic (m2), trans-monoenoic (m3), cis-monocyclopropanoic-trans-monoenoic (m4), cis-monoenoic (m5), and cis-monocyclopropanoic-cis-monoenoic (m6) series; and keto-mycolates were sub-grouped into cis-monocyclopropanoic (k1), trans-monocyclopropanoic (k2), trans-monoenoic (k3), cis-monoenoic (k4), and cis-monocyclopropanoic-cis-monoenoic (k5) series. The position of each functional group, including cyclopropane rings and methoxy and keto groups, was determined by analysis of the meromycolates with fast atom bombardment (FAB) mass spectrometry and FAB mass-mass spectrometry, and the cis/trans ratio of cyclopropane rings and double bonds were determined by NMR analysis of methyl mycolates. Mycolic acid subclass and molecular species composition of SMP-105 showed characteristic features including newly-identified cis-monocyclopropanoic-trans-monoenoic mycolic acid (m4).

Teratogenicity and transplacental pharmacokinetics of 13-cis-retinoic acid in rabbits.

PubMed

Eckhoff, C; Chari, S; Kromka, M; Staudner, H; Juhasz, L; Rudiger, H; Agnish, N

1994-03-01

No embryotoxic or teratogenic effects, considered to be treatment related, were observed in rabbits after daily oral doses of 3 mg/kg of 13-cis-retinoic acid (13-cis-RA) from Day 8 to Day 11 of gestation. In contrast, treatment with 15 mg/kg/day significantly increased the rate of fetal resorptions (22%) and 13 out of 68 surviving fetuses (16%) were malformed. Pharmacokinetic studies with both dosing regimens of 13-cis-RA in pregnant rabbits showed that on Day 11 of gestation, high concentrations of parent compound, 13-cis-RA, and its major metabolite, 13-cis-4-oxoRA, existed in maternal plasma. Much lower concentrations were found for all-trans-4-oxoRA and all-trans-RA. The area under the concentration-time curve (AUC) of all-trans-RA following the 15 mg/kg/day dosing regimen of 13-cis-RA was only 1.2% that of parent compound 13-cis-RA. At this dose, embryo levels of 13-cis-RA, 13-cis-4-oxoRA, and all-trans-4-oxoRA were 2.5-, 4.7-, and 3.6-fold higher by AUC comparison (24-hr period of Day 11) compared with the dose of 3 mg/kg. However, embryo levels of all-trans-RA were virtually identical at both doses and were, in fact, somewhat lower than endogenous concentrations measured in untreated rabbit embryos. In contrast to mice, where isomerization from 13-cis- to all-trans-RA was suggested to be crucial for the teratogenic action of 13-cis-RA, we found that the teratogenic action of 13-cis-RA (15 mg/kg/day) in rabbits is characterized by increased whole embryo concentrations of 13-cis-RA, 13-cis-4-oxoRA, and all-trans-4-oxoRA, but not of all-trans-RA.

In tight junctions, claudins regulate the interactions between occludin, tricellulin and marvelD3, which, inversely, modulate claudin oligomerization.

PubMed

Cording, Jimmi; Berg, Johanna; Käding, Nadja; Bellmann, Christian; Tscheik, Christian; Westphal, Julie K; Milatz, Susanne; Günzel, Dorothee; Wolburg, Hartwig; Piontek, Jörg; Huber, Otmar; Blasig, Ingolf Ernst

2013-01-15

Tight junctions seal the paracellular cleft of epithelia and endothelia, form vital barriers between tissue compartments and consist of tight-junction-associated marvel proteins (TAMPs) and claudins. The function of TAMPs and the interaction with claudins are not understood. We therefore investigated the binding between the TAMPs occludin, tricellulin, and marvelD3 and their interaction with claudins in living tight-junction-free human embryonic kidney-293 cells. In contrast to claudins and occludin, tricellulin and marvelD3 showed no enrichment at cell-cell contacts indicating lack of homophilic trans-interaction between two opposing cell membranes. However, occludin, marvelD3 and tricellulin exhibited homophilic cis-interactions, along one plasma membrane, as measured by fluorescence resonance energy transfer. MarvelD3 also cis-interacted with occludin and tricellulin heterophilically. Classic claudins, such as claudin-1 to -5 may show cis-oligomerization with TAMPs, whereas the non-classic claudin-11 did not. Claudin-1 and -5 improved enrichment of occludin and tricellulin at cell-cell contacts. The low mobile claudin-1 reduced the membrane mobility of the highly mobile occludin and tricellulin, as studied by fluorescence recovery after photobleaching. Co-transfection of claudin-1 with TAMPs led to changes of the tight junction strand network of this claudin to a more physiological morphology, depicted by freeze-fracture electron microscopy. The results demonstrate multilateral interactions between the tight junction proteins, in which claudins determine the function of TAMPs and vice versa, and provide deeper insights into the tight junction assembly.

Massively parallel cis-regulatory analysis in the mammalian central nervous system

PubMed Central

Shen, Susan Q.; Myers, Connie A.; Hughes, Andrew E.O.; Byrne, Leah C.; Flannery, John G.; Corbo, Joseph C.

2016-01-01

Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery to target organs in vivo. As a proof of concept, we introduce a capture library of about 46,000 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as nonhuman primates and human stem cell–derived organoids. PMID:26576614

Overlapping local and long-range RNA-RNA interactions modulate dengue virus genome cyclization and replication.

PubMed

de Borba, Luana; Villordo, Sergio M; Iglesias, Nestor G; Filomatori, Claudia V; Gebhard, Leopoldo G; Gamarnik, Andrea V

2015-03-01

The dengue virus genome is a dynamic molecule that adopts different conformations in the infected cell. Here, using RNA folding predictions, chemical probing analysis, RNA binding assays, and functional studies, we identified new cis-acting elements present in the capsid coding sequence that facilitate cyclization of the viral RNA by hybridization with a sequence involved in a local dumbbell structure at the viral 3' untranslated region (UTR). The identified interaction differentially enhances viral replication in mosquito and mammalian cells. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Innovation in pediatric clinical education: application of the essential competencies.

PubMed

Kenyon, Lisa K; Birkmeier, Marisa; Anderson, Deborah K; Martin, Kathy

2015-01-01

At the Section on Pediatrics Education Summit in July 2012, consensus was achieved on 5 essential core competencies (ECCs) that represent a knowledge base essential to all graduates of professional physical therapist education programs. This article offers suggestions for how clinical instructors (CIs) might use the ECCs to identify student needs and guide student learning during a pediatric clinical education experience. Pediatric CIs potentially might choose to use the ECCs as a reference tool in clinical education to help (1) organize and develop general, clinic-specific clinical education objectives, (2) develop and plan individualized student learning experiences, (3) identify student needs, and (4) show progression of student learning from beginner to intermediate to entry level. The ECCs may offer CIs insights into the role of pediatric clinical education in professional physical therapist education.

Genomic Identification and Analysis of Shared Cis-regulator Elements in a Developmentally Critical homeobox Cluster

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

Chris Amemiya

2003-04-01

The goals of this project were to isolate, characterize, and sequence the Dlx3/Dlx7 bigene cluster from twelve different species of mammals. The Dlx3 and Dlx7 genes are known to encode homeobox transcription factors involved in patterning of structures in the vertebrate jaw as well as vertebrate limbs. Genomic sequences from the respective taxa will subsequently be compared in order to identify conserved non-coding sequences that are potential cis-regulatory elements. Based on the comparisons they will fashion transgenic mouse experiments to functionally test the strength of the potential cis-regulatory elements. A goal of the project is to attempt to identify thosemore » elements that may function in coordinately regulating both Dlx3 and Dlx7 functions.« less

The Role of Cis-Lunar Space in Future Global Space Exploration

NASA Technical Reports Server (NTRS)

Bobskill, Marianne R.; Lupisella, Mark L.

2012-01-01

Cis-lunar space offers affordable near-term opportunities to help pave the way for future global human exploration of deep space, acting as a bridge between present missions and future deep space missions. While missions in cis-lunar space have value unto themselves, they can also play an important role in enabling and reducing risk for future human missions to the Moon, Near-Earth Asteroids (NEAs), Mars, and other deep space destinations. The Cis-Lunar Destination Team of NASA's Human Spaceflight Architecture Team (HAT) has been analyzing cis-lunar destination activities and developing notional missions (or "destination Design Reference Missions" [DRMs]) for cis-lunar locations to inform roadmap and architecture development, transportation and destination elements definition, operations, and strategic knowledge gaps. The cis-lunar domain is defined as that area of deep space under the gravitational influence of the earth-moon system. This includes a set of earth-centered orbital locations in low earth orbit (LEO), geosynchronous earth orbit (GEO), highly elliptical and high earth orbits (HEO), earth-moon libration or "Lagrange" points (E-ML1 through E-ML5, and in particular, E-ML1 and E-ML2), and low lunar orbit (LLO). To help explore this large possibility space, we developed a set of high level cis-lunar mission concepts in the form of a large mission tree, defined primarily by mission duration, pre-deployment, type of mission, and location. The mission tree has provided an overall analytical context and has helped in developing more detailed design reference missions that are then intended to inform capabilities, operations, and architectures. With the mission tree as context, we will describe two destination DRMs to LEO and GEO, based on present human space exploration architectural considerations, as well as our recent work on defining mission activities that could be conducted with an EML1 or EML2 facility, the latter of which will be an emphasis of this paper, motivated in part by recent interest expressed at the Global Exploration Roadmap Stakeholder meeting. This paper will also explore the links between this HAT Cis-Lunar Destination Team analysis and the recently released ISECG Global Exploration Roadmap and other potential international considerations, such as preventing harmful interference to radio astronomy observations in the shielded zone of the moon.

Examination of the persistency of milk fatty acid composition responses to fish oil and sunflower oil in the diet of dairy cows.

PubMed

Shingfield, K J; Reynolds, C K; Hervás, G; Griinari, J M; Grandison, A S; Beever, D E

2006-02-01

Based on the potential benefits of cis-9, trans-11 conjugated linoleic acid (CLA) for human health, there is a need to develop effective strategies for enhancing milk fat CLA concentrations. Levels of cis-9, trans-11 CLA in milk can be increased by supplements of fish oil (FO) and sunflower oil (SO), but there is considerable variation in the response. Part of this variance may reflect time-dependent ruminal adaptations to high levels of lipid in the diet, which lead to alterations in the formation of specific biohydrogenation intermediates. To test this hypothesis, 16 late lactation Holstein-British Friesian cows were used in a repeated measures randomized block design to examine milk fatty acid composition responses to FO and SO in the diet over a 28-d period. Cows were allocated at random to corn silage-based rations (8 per treatment) containing 0 (control) or 45 g of oil supplement/kg of dry matter consisting (1:2; wt/wt) of FO and SO (FSO), and milk composition was determined on alternate days from d 1. Compared with the control, the FSO diet decreased mean dry matter intake (21.1 vs. 17.9 kg/d), milk fat (47.7 vs. 32.6 g/kg), and protein content (36.1 vs. 33.3 g/kg), but had no effect on milk yield (27.1 vs. 26.4 kg/d). Reductions in milk fat content relative to the FSO diet were associated with increases in milk trans-10 18:1, trans-10, cis-12 CLA, and trans-9, cis-11 CLA concentrations (r(2) = 0.74, 0.57, and 0.80, respectively). Compared with the control, the FSO diet reduced milk 4:0 to 18:0 and cis 18:1 content and increased trans 18:1, trans 18:2, cis-9, trans-11 CLA, 20:5 n-3, and 22:6 n-3 concentrations. The FSO diet caused a rapid elevation in milk cis-9, trans-11 CLA content, reaching a maximum of 5.37 g/100 g of fatty acids on d 5, but these increases were transient, declining to 2.35 g/100 g of fatty acids by d 15. They remained relatively constant thereafter. Even though concentrations of trans-11 18:1 followed the same pattern of temporal changes as cis-9, trans-11 CLA, the total trans 18:1 content of FSO milk was unchanged because of the concomitant increases in the concentration of other isomers (Delta(4-10) and Delta(12-15)), predominantely trans-10 18:1. In conclusion, supplementing diets with FSO enhances milk fat cis-9, trans-11 CLA content, but the high level of enrichment declines because of changes in ruminal biohydrogenation that result in trans-10 replacing trans-11 as the major 18:1 biohydrogenation intermediate formed in the rumen.

Decoding a Signature-Based Model of Transcription Cofactor Recruitment Dictated by Cardinal Cis-Regulatory Elements in Proximal Promoter Regions

PubMed Central

Benner, Christopher; Hutt, Kasey R.; Stunnenberg, Rieka; Garcia-Bassets, Ivan

2013-01-01

Genome-wide maps of DNase I hypersensitive sites (DHSs) reveal that most human promoters contain perpetually active cis-regulatory elements between −150 bp and +50 bp (−150/+50 bp) relative to the transcription start site (TSS). Transcription factors (TFs) recruit cofactors (chromatin remodelers, histone/protein-modifying enzymes, and scaffold proteins) to these elements in order to organize the local chromatin structure and coordinate the balance of post-translational modifications nearby, contributing to the overall regulation of transcription. However, the rules of TF-mediated cofactor recruitment to the −150/+50 bp promoter regions remain poorly understood. Here, we provide evidence for a general model in which a series of cis-regulatory elements (here termed ‘cardinal’ motifs) prefer acting individually, rather than in fixed combinations, within the −150/+50 bp regions to recruit TFs that dictate cofactor signatures distinctive of specific promoter subsets. Subsequently, human promoters can be subclassified based on the presence of cardinal elements and their associated cofactor signatures. In this study, furthermore, we have focused on promoters containing the nuclear respiratory factor 1 (NRF1) motif as the cardinal cis-regulatory element and have identified the pervasive association of NRF1 with the cofactor lysine-specific demethylase 1 (LSD1/KDM1A). This signature might be distinctive of promoters regulating nuclear-encoded mitochondrial and other particular genes in at least some cells. Together, we propose that decoding a signature-based, expanded model of control at proximal promoter regions should lead to a better understanding of coordinated regulation of gene transcription. PMID:24244184

Protective Effect of Selenium Against Cisplatin-Induced Ototoxicity in an Experimental Design.

PubMed

Doğan, Sedat; Yazici, Hasmet; Yalçinkaya, Esin; Erdoğdu, Halil Ibrahim; Tokgöz, Sibel Alicura; Sarici, Furkan; Namuslu, Mehmet; Sarikaya, Yasin

2016-10-01

Cisplatin is an effective chemotherapeutic agent in the treatment of several types of malignant solid tumors but its clinical use is associated with ototoxicity. In the present study, we investigated the effect of selenium administration on lipid peroxidation (malondialdehyde [MDA]) and cisplatin-induced ototoxicity in rats. Healthy wistar albino rats (n = 21) were randomly divided into 3 groups: control (C), cisplatin (Cis), cisplatin and selenium (Cis+Se). Cisplatin was administered for 3 days to Cis and Cis+Se groups. Cis+Se group received selenium 5 days before cisplatin injection and continued for 11 consecutive days. Hearing thresholds and lipid peroxidation (MDA) levels of the rats were recorded before injections and at the end of experimental protocol. The cochleas of animals were harvested for histologic and immunuhistochemical examinations. In biochemichal analyses, pretreatment with selenium prevented the elevation of MDA levels in Cis+Se group rats. Moreover, animals in Cis+Se group had better hearing threshold levels than animals in cis group. Samples obtained from the animals in Cis group revealed extensive loss of the normal microarchitecture of the organ of Corti. On the other hand, animals in Cis+Se group exhibited a preservation of the morphology of the organ of Corti and outer hair cells. In the immunohistochemical examinations of cochlear tissues stained with anti-caspase-3, a higher degree of immunopositivity was found in the Cis group. When Cis+Se group and Cis group were compared, significantly less immunopositivity occurred in the Cis+Se group (P < 0.05). Thus, it appears that pretreatment with selenium may reduce cisplatin-induced ototoxicity in rats.

SAR and X-ray Structures of Enantiopure 1,2-cis-(1R,2S)-cyclopentyldiamine and Cyclohexyldiamine Derivativies as Inhibitors of Coagulation Factor Xa

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

Qiao,J.; Chang, C.; Cheney, D.

In the search of Factor Xa (FXa) inhibitors structurally different from the pyrazole-based series, we identified a viable series of enantiopure cis-(1R,2S)-cycloalkyldiamine derivatives as potent and selective inhibitors of FXa. Among them, cyclohexyldiamide 7 and cyclopentyldiamide 9 were the most potent neutral compounds, and had good anticoagulant activity comparable to the pyrazole-based analogs. Crystal structures of 7-FXa and 9-FXa illustrate binding similarities and differences between the five- and the six-membered core systems, and provide rationales for the observed SAR of P1 and linker moieties.

Methods for estimating confidence intervals in interrupted time series analyses of health interventions.

PubMed

Zhang, Fang; Wagner, Anita K; Soumerai, Stephen B; Ross-Degnan, Dennis

2009-02-01

Interrupted time series (ITS) is a strong quasi-experimental research design, which is increasingly applied to estimate the effects of health services and policy interventions. We describe and illustrate two methods for estimating confidence intervals (CIs) around absolute and relative changes in outcomes calculated from segmented regression parameter estimates. We used multivariate delta and bootstrapping methods (BMs) to construct CIs around relative changes in level and trend, and around absolute changes in outcome based on segmented linear regression analyses of time series data corrected for autocorrelated errors. Using previously published time series data, we estimated CIs around the effect of prescription alerts for interacting medications with warfarin on the rate of prescriptions per 10,000 warfarin users per month. Both the multivariate delta method (MDM) and the BM produced similar results. BM is preferred for calculating CIs of relative changes in outcomes of time series studies, because it does not require large sample sizes when parameter estimates are obtained correctly from the model. Caution is needed when sample size is small.

Real time radiation dosimeters based on vertically aligned multiwall carbon nanotubes and graphene.

PubMed

Funaro, Maria; Sarno, Maria; Ciambelli, Paolo; Altavilla, Claudia; Proto, Antonio

2013-02-22

Measurements of the absorbed dose and quality assurance programs play an important role in radiotherapy. Ionization chambers (CIs) are considered the most important dosimeters for their high accuracy, practicality and reliability, allowing absolute dose measurements. However, they have a relative large physical size, which limits their spatial resolution, and require a high bias voltage to achieve an acceptable collection of charges, excluding their use for in vivo dosimetry. In this paper, we propose new real time radiation detectors with electrodes based on graphene or vertically aligned multiwall carbon nanotubes (MWCNTs). We have investigated their charge collection efficiency and compared their performance with electrodes made of a conventional material. Moreover, in order to highlight the effect of nanocarbons, reference radiation detectors were also tested. The proposed dosimeters display an excellent linear response to dose and collect more charge than reference ones at a standard bias voltage, permitting the construction of miniaturized CIs. Moreover, an MWCNT based CI gives the best charge collection efficiency and it enables working also to lower bias voltages and zero volts, allowing in vivo applications. Graphene based CIs show better performance with respect to reference dosimeters at a standard bias voltage. However, at decreasing bias voltage the charge collection efficiency becomes worse if compared to a reference detector, likely due to graphene's semiconducting behavior.

Comparing the landcapes of common retroviral insertion sites across tumor models

NASA Astrophysics Data System (ADS)

Weishaupt, Holger; Čančer, Matko; Engström, Cristopher; Silvestrov, Sergei; Swartling, Fredrik J.

2017-01-01

Retroviral tagging represents an important technique, which allows researchers to screen for candidate cancer genes. The technique is based on the integration of retroviral sequences into the genome of a host organism, which might then lead to the artificial inhibition or expression of proximal genetic elements. The identification of potential cancer genes in this framework involves the detection of genomic regions (common insertion sites; CIS) which contain a number of such viral integration sites that is greater than expected by chance. During the last two decades, a number of different methods have been discussed for the identification of such loci and the respective techniques have been applied to a variety of different retroviruses and/or tumor models. We have previously established a retrovirus driven brain tumor model and reported the CISs which were found based on a Monte Carlo statistics derived detection paradigm. In this study, we consider a recently proposed alternative graph theory based method for identifying CISs and compare the resulting CIS landscape in our brain tumor dataset to those obtained when using the Monte Carlo approach. Finally, we also employ the graph-based method to compare the CIS landscape in our brain tumor model with those of other published retroviral tumor models.

Controlled Attenuation Parameter and Liver Stiffness Measurements for Steatosis Assessment in the Liver Transplant of Brain Dead Donors.

PubMed

Mancia, Claire; Loustaud-Ratti, Véronique; Carrier, Paul; Naudet, Florian; Bellissant, Eric; Labrousse, François; Pichon, Nicolas

2015-08-01

One of the main selection criteria of the quality of a liver graft is the degree of steatosis, which will determine the success of the transplantation. The aim of this study was to evaluate the ability of FibroScan and its related methods Controlled Attenuation Parameter and Liver Stiffness to assess objectively steatosis and fibrosis in livers from brain-dead donors to be potentially used for transplantation. Over a period of 10 months, 23 consecutive brain dead donors screened for liver procurement underwent a FibroScan and a liver biopsy. The different predictive models of liver retrievability using liver biopsy as the gold standard have led to the following area under receiver operating characteristic curve: 76.6% (95% confidence intervals [95% CIs], 48.2%-100%) when based solely on controlled attenuation parameter, 75.0% (95% CIs, 34.3%-100%) when based solely on liver stiffness, and 96.7% (95% CIs, 88.7%-100%) when based on combined indices. Our study suggests that a preoperative selection of brain-dead donors based on a combination of both Controlled Attenuation Parameter and Liver Stiffness obtained with FibroScan could result in a good preoperative prediction of the histological status and degree of steatosis of a potential liver graft.

Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules

PubMed Central

McEntee, Connor; Byer, Amanda; Trout, Jonathan D; Hazen, Samuel P; Shen, Rongkun; Priest, Henry D; Sullivan, Christopher M; Givan, Scott A; Yanovsky, Marcelo; Hong, Fangxin; Kay, Steve A; Chory, Joanne

2008-01-01

Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation. PMID:18248097

Determination of 13-cis-retinoic acid and its major metabolite, 4-oxo-13-cis-retinoic acid, in human blood by reversed-phase high-performance liquid chromatography.

PubMed

Vane, F M; Stoltenborg, J K; Buggé, C J

1982-02-12

A high-performance liquid chromatography (HPLC) method for the quantitation of 13-cis-retinoic acid (13-cis-RA) and its major metabolite, 4-oxo-13-cis-RA, in human blood has been developed. The method includes extraction of 1 ml of blood with diethyl ether at pH 6 and the analysis of the extract by reversed-phase HPLC with solvent programming and detection at 365 nm. The quantitation ranges for 13-cis-RA and 4-oxo-13-cis-RA are 10--2000 and 50--2000 ng/ml of blood, respectively. The method also provides estimates of the concentrations of all-trans-RA and 4-oxo-all-trans-RA. The mean intra- and inter-assay variabilities for all four compounds were 6% or less. The method separates 13-cis-RA and 4-oxo-13-cis-RA from 9-cis-RA, all-trans-RA, 4-oxo-all-trans-RA, and some other possible metabolites, such as hydroxy and epoxy retinoic acids. The method has been successfully applied to the analyses of over 1200 blood samples from four 13-cis-RA clinical studies.

Cis-Natural Antisense Transcripts Are Mainly Co-expressed with Their Sense Transcripts and Primarily Related to Energy Metabolic Pathways during Muscle Development.

PubMed

Zhao, Yunxia; Hou, Ye; Zhao, Changzhi; Liu, Fei; Luan, Yu; Jing, Lu; Li, Xinyun; Zhu, Mengjin; Zhao, Shuhong

2016-01-01

Cis-natural antisense transcripts (cis-NATs) are a new class of RNAs identified in various species. However, the biological functions of cis-NATs are largely unknown. In this study, we investigated the transcriptional characteristics and functions of cis-NATs in the muscle tissue of lean Landrace and indigenous fatty Lantang pigs. In total, 3,306 cis-NATs of 2,469 annotated genes were identified in the muscle tissue of pigs. More than 1,300 cis-NATs correlated with their sense genes at the transcriptional level, and approximately 80% of them were co-expressed in the two breeds. Furthermore, over 1,200 differentially expressed cis-NATs were identified during muscle development. Function annotation showed that the cis-NATs participated in muscle development mainly by co-expressing with genes involved in energy metabolic pathways, including citrate cycle (TCA cycle), glycolysis or gluconeogenesis, mitochondrial activation and so on. Moreover, these cis-NATs and their sense genes abruptly increased at the transition from the late fetal stages to the early postnatal stages and then decreased along with muscle development. In conclusion, the cis-NATs in the muscle tissue of pigs were identified and determined to be mainly co-expressed with their sense genes. The co-expressed cis-NATs and their sense gene were primarily related to energy metabolic pathways during muscle development in pigs. Our results offered novel evidence on the roles of cis-NATs during the muscle development of pigs.

TP53-based interaction analysis identifies cis-eQTL variants for TP53BP2, FBXO28, and FAM53A that associate with survival and treatment outcome in breast cancer

PubMed Central

Fagerholm, Rainer; Khan, Sofia; Schmidt, Marjanka K.; GarcClosas, Montserrat; Heikkilä, Päivi; Saarela, Jani; Beesley, Jonathan; Jamshidi, Maral; Aittomäki, Kristiina; Liu, Jianjun; Raza Ali, H.; Andrulis, Irene L.; Beckmann, Matthias W.; Behrens, Sabine; Blows, Fiona M.; Brenner, Hermann; Chang-Claude, Jenny; Couch, Fergus J.; Czene, Kamila; Fasching, Peter A.; Figueroa, Jonine; Floris, Giuseppe; Glendon, Gord; Guo, Qi; Hall, Per; Hallberg, Emily; Hamann, Ute; Holleczek, Bernd; Hooning, Maartje J.; Hopper, John L.; Jager, Agnes; Kabisch, Maria; Investigators, kConFab/AOCS; Keeman, Renske; Kosma, Veli-Matti; Lambrechts, Diether; Lindblom, Annika; Mannermaa, Arto; Margolin, Sara; Provenzano, Elena; Shah, Mitul; Southey, Melissa C.; Dennis, Joe; Lush, Michael; Michailidou, Kyriaki; Wang, Qin; Bolla, Manjeet K.; Dunning, Alison M.; Easton, Douglas F.; Pharoah, Paul D.P .; Chenevix-Trench, Georgia; Blomqvist, Carl; Nevanlinna, Heli

2017-01-01

TP53 overexpression is indicative of somatic TP53 mutations and associates with aggressive tumors and poor prognosis in breast cancer. We utilized a two-stage SNP association study to detect variants associated with breast cancer survival in a TP53-dependent manner. Initially, a genome-wide study (n = 575 cases) was conducted to discover candidate SNPs for genotyping and validation in the Breast Cancer Association Consortium (BCAC). The SNPs were then tested for interaction with tumor TP53 status (n = 4,610) and anthracycline treatment (n = 17,828). For SNPs interacting with anthracycline treatment, siRNA knockdown experiments were carried out to validate candidate genes. In the test for interaction between SNP genotype and TP53 status, we identified one locus, represented by rs10916264 (p(interaction) = 3.44 05E010-5; FDR-adjusted p = 0.0011) in estrogen receptor (ER) positive cases. The rs10916264 AA genotype associated with worse survival among cases with ER-positive, TP53-positive tumors (hazard ratio [HR] 2.36, 95% confidence interval [C.I] 1.45 - 3.82). This is a cis-eQTL locus for FBXO28 and TP53BP2; expression levels of these genes were associated with patient survival specifically in ER-positive, TP53-mutated tumors. Additionally, the SNP rs798755 was associated with survival in interaction with anthracycline treatment (p(interaction) = 9.57 05E010-5, FDR-adjusted p = 0.0130). RNAi-based depletion of a predicted regulatory target gene, FAM53A, indicated that this gene can modulate doxorubicin sensitivity in breast cancer cell lines. If confirmed in independent data sets, these results may be of clinical relevance in the development of prognostic and predictive marker panels for breast cancer. PMID:28179588

P-MAPA immunotherapy potentiates the effect of cisplatin on serous ovarian carcinoma through targeting TLR4 signaling.

PubMed

de Almeida Chuffa, Luiz Gustavo; de Moura Ferreira, Grazielle; Lupi, Luiz Antonio; da Silva Nunes, Iseu; Fávaro, Wagner José

2018-01-17

Toll-like receptors (TLRs) are transmembrane proteins expressed on the surface of ovarian cancer (OC) and immune cells. Identifying the specific roles of the TLR-mediated signaling pathways in OC cells is important to guide new treatments. Because immunotherapies have emerged as the adjuvant treatment for patients with OC, we investigated the effect of a promising immunotherapeutic strategy based on protein aggregate magnesium-ammonium phospholinoleate-palmitoleate anhydride (P-MAPA) combined with cisplatin (CIS) on the TLR2 and TLR4 signaling pathways via myeloid differentiation factor 88 (MyD88) and TLR-associated activator of interferon (TRIF) in an in vivo model of OC. Tumors were chemically induced by a single injection of 100 μg of 7,12-dimethylbenz(a)anthracene (DMBA) directly under the left ovarian bursa in Fischer 344 rats. After the rats developed serous papillary OC, they were given P-MAPA, CIS or the combination P-MAPA+CIS as therapies. To understand the effects of the treatments, we assessed the tumor size, histopathology, and the TLR2- and TLR4-mediated inflammatory responses. Although CIS therapy was more effective than P-MAPA in reducing the tumor size, P-MAPA immunotherapy significantly increased the expressions of TLR2 and TLR4. More importantly, the combination of P-MAPA with CIS showed a greater survival rate compared to CIS alone, and exhibited a significant reduction in tumor volume compared to P-MAPA alone. The combination therapy also promoted the increase in the levels of the following OC-related proteins: TLR4, MyD88, TRIF, inhibitor of phosphorylated NF-kB alpha (p-IkBα), and nuclear factor kappa B (NF-kB p65) in both cytoplasmic and nuclear sites. While P-MAPA had no apparent effect on tumor necrosis factor alpha (TNF-α) and interleukin (IL)-6, it seems to increase interferon-γ (IFN-γ), which may induce the Thelper (Th1)-mediated immune response. Collectively, our results suggest that P-MAPA immunotherapy combined with cisplatin could be considered an important therapeutic strategy against OC cells based on signaling pathways activated by TLR4.

Clinical Information Systems as the Backbone of a Complex Information Logistics Process: Findings from the Clinical Information Systems Perspective for 2016.

PubMed

Hackl, W O; Ganslandt, T

2017-08-01

Objective: To summarize recent research and to propose a selection of best papers published in 2016 in the field of Clinical Information Systems (CIS). Method: The query used to retrieve the articles for the CIS section of the 2016 edition of the IMIA Yearbook of Medical Informatics was reused. It again aimed at identifying relevant publications in the field of CIS from PubMed and Web of Science and comprised search terms from the Medical Subject Headings (MeSH) catalog as well as additional free text search terms. The retrieved articles were categorized in a multi-pass review carried out by the two section editors. The final selection of candidate papers was then peer-reviewed by Yearbook editors and external reviewers. Based on the review results, the best papers were then chosen at the selection meeting with the IMIA Yearbook editorial board. Text mining, term co-occurrence mapping, and topic modelling techniques were used to get an overview on the content of the retrieved articles. Results: The query was carried out in mid-January 2017, yielding a consolidated result set of 2,190 articles published in 921 different journals. Out of them, 14 papers were nominated as candidate best papers and three of them were finally selected as the best papers of the CIS field. The content analysis of the articles revealed the broad spectrum of topics covered by CIS research. Conclusions: The CIS field is multi-dimensional and complex. It is hard to draw a well-defined outline between CIS and other domains or other sections of the IMIA Yearbook. The trends observed in the previous years are progressing. Clinical information systems are more than just sociotechnical systems for data collection, processing, exchange, presentation, and archiving. They are the backbone of a complex, trans-institutional information logistics process. Georg Thieme Verlag KG Stuttgart.

Purification and characterization of 9-hexadecenoic acid cis-trans isomerase from pseudomonas sp. strain E-3

PubMed

Okuyama; Ueno; Enari; Morita; Kusano

1998-01-01

A 9-hexadecenoic acid cis-trans isomerase (9-isomerase) that catalyzed the cis-to-trans isomerization of the double bond of free 9-cis-hexadecenoic acid [16:1(9c)] was purified to homogeneity from an extract of Pseudomonas sp. strain E-3 and characterized. Electrophoresis of the purified enzyme on both incompletely denaturing and denaturing polyacrylamide gels yielded a single band of a protein with a molecular mass of 80 kDa, suggesting that the isomerase is a monomeric protein of 80 kDa. The 9-isomerase, assayed with 16:1(9c) as a substrate, had a specific activity of 22.8 &mgr;mol h-1 (mg protein)-1 and a Km of 117.6 mM. The optimal pH and temperature for catalysis were approximately pH 7-8 and 30 degrees C, respectively. The 9-isomerase catalyzed the cis-to-trans conversion of a double bond at positions 9, 10, or 11, but not that of a double bond at position 6 or 7 of cis-mono-unsaturated fatty acids with carbon chain lengths of 14, 15, 16, and 17. Octadecenoic acids with a double bond at position 9 or 11 were not susceptible to isomerization. These results suggest that 9-isomerase has a strict specificity for both the position of the double bond and the chain length of the fatty acid. The enzyme catalyzed the cis-to-trans isomerization of fatty acids in a free form, and in the presence of a membrane fraction it was also able to isomerize 16:1(9c) esterified to phosphatidylethanolamine. The 9-isomerase was strongly inhibited by catecholic antioxidants such as alpha-tocopherol and nordihydroguaiaretic acid, but was not inhibited by 1, 10-phenanthroline or EDTA or under anoxic conditions. Based on these results, the possible mechanism of catalysis by this enzyme is discussed.

Adverse lipid profile elevates risk for subarachnoid hemorrhage: A prospective population-based cohort study.

PubMed

Lindbohm, Joni; Korja, Miikka; Jousilahti, Pekka; Salomaa, Veikko; Kaprio, Jaakko

2018-05-05

Studies report that both high and low total cholesterol (TC) elevates SAH risk. There are few prospective studies on high-density lipoproteins (HDL-C) and low-density lipoproteins (LDL-C), and apparently none concerns apolipoproteins A and B. We aimed to clarify the association between lipid profile and SAH risk. The National FINRISK study provided risk-factor data recorded at enrolment between 1972 and 2007. During 1.52 million person-years of follow-up until 2014, 543 individuals suffered from incident hospitalized SAH or outside-hospital-fatal SAH. Cox proportional hazards model was used to calculate the hazard ratios and multiple imputation predicted ApoA1, ApoB, and LDL-C values for cohorts from a time before apolipoprotein-measurement methods were available. One SD elevation (1.28 mmol/l) in TC elevated SAH risk in men (hazard ratio (HR) 1.15 (95% CIs 1.00-1.32)). Low HDL-C levels increased SAH risk, as each SD decrease (0.37 mmol/l) in HDL-C raised the risk in women (HR 1.29 (95% CIs 1.07-1.55)) and men (HR 1.20 (95% CIs 1.14-1.27)). Each SD increase (0.29 g/l) in ApoA1 decreased SAH risk in women (HR 0.85 (95% CIs 0.74-0.97)) and men (HR 0.88 (95% CIs 0.76-1.02)). LDL-C (SD 1.07 mmol/l) and ApoB (SD 0.28 g/l) elevated SAH risk in men with HR 1.15 (95% CIs 1.01-1.31) and HR 1.26 (95% CIs 1.10-1.44) per one SD increase. Age did not change these findings. An adverse lipid profile seems to elevate SAH risk similar to its effect in other cardiovascular diseases, especially in men. Whether SAH incidence diminishes with increasing statin use remains to be studied. Copyright © 2018 Elsevier B.V. All rights reserved.

Plasma pharmacokinetics and metabolism of 13-cis- and all-trans-retinoic acid in the cynomolgus monkey and the identification of 13-cis- and all-trans-retinoyl-beta-glucuronides. A comparison to one human case study with isotretinoin.

PubMed

Kraft, J C; Slikker, W; Bailey, J R; Roberts, L G; Fischer, B; Wittfoht, W; Nau, H

1991-01-01

In order to compare the disposition and metabolism of 13-cis-retinoic acid (13-cis-RA) and all-trans-retinoic acid (all-trans-RA) in the nonpregnant female cynomolgus monkey, the plasma concentrations of the parent compound, the oxidized metabolites 4-oxo-13-cis-retinoic acid and 4-oxo-all-trans-retinoic acid, and the conjugate metabolites 13-cis-retinoyl-beta-glucuronide (13-cis-RAG) and all trans-retinoyl-beta-glucuronide (all-trans-RAG), were determined on day 1 and day 10 after oral dosing of 2 and 10 mg 13-cis- and all-trans-RA/kg/day. Both 13-cis-RAG and all-trans-RAG have been identified as major plasma metabolites in these studies using thermospray/HPLC/mass-spectrometry of the intact conjugates. AUC comparisons from 0-24 hr after administration indicated that 13-cis-RA treatment resulted in primarily cis metabolites and all-trans-RA treatment resulted in primarily trans metabolites, although low levels of isomerization products were observed. Comparison of the two doses (2 and 10 mg/kg, po) revealed that the AUCs were proportional to the dose administered. Although qualitatively similar, elimination of 13-cis-RA in the monkey was more rapid than in the human, and approximately a 10-fold greater dose of 13-cis-RA was required in the monkey to produce the AUC values comparable to the human. The elimination of all-trans-RA in monkey was faster than that of 13-cis-RA and tended to increase with repeated dosing.(ABSTRACT TRUNCATED AT 250 WORDS)

Novel cis-acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization.

PubMed

Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao; Deng, Yong-Qiang; Zhao, Hui; Wang, Hong-Jiang; Ye, Qing; Zhu, Shun-Ya; Qiu, Yang; Zhou, Xi; Qin, E-De; Qin, Cheng-Feng

2013-06-01

cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5' cyclization sequence (5'CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5'CS, and the presence of DCS-PK facilitates the formation of 5'-3' RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution.

Novel cis-Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

PubMed Central

Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao; Deng, Yong-Qiang; Zhao, Hui; Wang, Hong-Jiang; Ye, Qing; Zhu, Shun-Ya; Qiu, Yang; Zhou, Xi; Qin, E-De

2013-01-01

cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5′ cyclization sequence (5′CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5′CS, and the presence of DCS-PK facilitates the formation of 5′-3′ RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution. PMID:23576500

Study of the UV Light Conversion of Feruloyl Amides from Portulaca oleracea and Their Inhibitory Effect on IL-6-Induced STAT3 Activation.

PubMed

Hwang, Joo Tae; Kim, Yesol; Jang, Hyun-Jae; Oh, Hyun-Mee; Lim, Chi-Hwan; Lee, Seung Woong; Rho, Mun-Chual

2016-06-30

Two new feruloyl amides, N-cis-hibiscusamide (5) and (7'S)-N-cis-feruloylnormetanephrine (9), and eight known feruloyl amides were isolated from Portulaca oleracea L. and the geometric conversion of the ten isolated feruloyl amides by UV light was verified. The structures of the feruloyl amides were determined based on spectroscopic data and comparison with literature data. The NMR data revealed that the structures of the isolated compounds showed cis/trans-isomerization under normal laboratory light conditions. Therefore, cis and trans-isomers of feruloyl amides were evaluated for their convertibility and stability by UV light of a wavelength of 254 nm. After 96 h of UV light exposure, 23.2%-35.0% of the cis and trans-isomers were converted to trans-isomers. Long-term stability tests did not show any significant changes. Among all compounds and conversion mixtures collected, compound 6 exhibited the strongest inhibition of IL-6-induced STAT3 activation in Hep3B cells, with an IC50 value of 0.2 μM. This study is the first verification of the conversion rates and an equilibrium ratio of feruloyl amides. These results indicate that this natural material might provide useful information for the treatment of various diseases involving IL-6 and STAT3.

Complexes of cis-dioxomolybdenum(VI) and oxovanadium(IV) with a tridentate ONS donor ligand: Synthesis, spectroscopic properties, X-ray crystal structure and catalytic activity

NASA Astrophysics Data System (ADS)

Fayed, Ahmed M.; Elsayed, Shadia A.; El-Hendawy, Ahmed M.; Mostafa, Mohamed R.

2014-08-01

New cis-dioxomolybdenum(VI) and oxovanadium(IV) complexes of the Schiff base, derived from S-methyl dithiocarbazate and 2,3-dihydroxybenzaldehyde (H2dhsm), have been synthesized. The complexes of the type cis-[MoO2(dhsm)] (1a), cis-[MoO2(dhsm)(D)] (1b-1d) [D = neutral monodentate ligand; EtOH, pyridine (py) or imidazole (imz)], [VO(dhsm)(Nsbnd N)] (2a, 2b) [Nsbnd N = 2,2‧-bipyridine (bipy) or 1,10-phenanthroline (phen)] and [VO(dhsm)] (2c) have been isolated, characterized by 1H NMR, IR, UV-Vis and EPR spectral studies and investigated by cyclic voltammetry. The X-ray crystal structure of cis-[MoO2(dhsm)(EtOH)] (1b) has been determined and shows that the complex has a distorted octahedral geometry in which the H2dhsm behaves as a dianionic ONS tridentate ligand coordinating via phenoxide oxygen, hydrazinic nitrogen and thiolate sulfur. The oxomolybdenum(IV) complex [MoO(dhsm)] (1e) has obtained from dioxomolybdenum(VI) complex (1b) by oxo abstraction with PPh3. The reactivity of the complexes toward catalytic oxidation of alcohols in the presence of H2O2 and t-BuOOH as co-oxidants under solvent free conditions is reported.

Analytical and semipreparative chiral separation of cis-itraconazole on cellulose stationary phases by high-performance liquid chromatography.

PubMed

Kurka, Ondřej; Kučera, Lukáš; Bednář, Petr

2016-07-01

cis-Itraconazole is a chiral antifungal drug administered as a racemate. The knowledge of properties of individual cis-itraconazole stereoisomers is vital information for medicine and biosciences as different stereoisomers of cis-itraconazole may possess different affinity to certain biological pathways in the human body. For this purpose, either chiral synthesis of enantiomers or chiral separation of racemate can be used. This paper presents a two-step high-performance liquid chromatography approach for the semipreparative isolation of four stereoisomers (two enantiomeric pairs) of itraconazole using polysaccharide stationary phases and volatile organic mobile phases without additives in isocratic mode. The approach used involves the separation of the racemate into three fractions (i.e. two pure stereoisomers and one mixed fraction containing the remaining two stereoisomers) in the first run and consequent separation of the collected mixed fraction in the second one. For this purpose, combination of cellulose tris-(4-methylbenzoate) and cellulose tris-(3,5-dimehylphenylcarbamate) columns with complementary selectivity for cis-itraconazole provided full separation of all four stereoisomers (with purity of each isomer > 97%). The stereoisomers were collected, their optical rotation determined and their identity confirmed based on the results of a previously published study. Pure separated stereoisomers are subjected to further biological studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of pyrethroid-like fluorescent substrates for glutathione S-transferase

PubMed Central

Huang, Huazhang; Yao, Hongwei; Liu, Jun-Yan; Samra, Aman I.; Kamita, Shizuo G.; Cornel, Anthony J.; Hammock, Bruce D.

2012-01-01

The availability of highly sensitive substrates is critical for the development of precise and rapid assays for detecting changes in glutathione S-transferase (GST) activity that are associated with GST-mediated metabolism of insecticides. In this study, six pyrethroid-like compounds were synthesized and characterized as substrates for insect and mammalian GSTs. All of the substrates were esters composed of the same alcohol moiety, 7-hydroxy-4-methylcoumarin, and acid moieties that structurally mimic some commonly used pyrethroid insecticides including cypermethrin and cyhalothrin. CpGSTD1, a recombinant Delta class GST from the mosquito Culex pipiens, metabolized our pyrethroid-like substrates with both chemical and geometric (i.e., the cis-isomers were metabolized at 2- to 5-fold higher rates than the corresponding trans-isomers) preference. A GST preparation from mouse liver also metabolized most of our pyrethroid-like substrates with both chemical and geometric preference but at 10- to 170-fold lower rates. CpGSTD1 and mouse GSTs metabolized CDNB, a general GST substrate, at more than 200-fold higher rates than our novel pyrethroid-like substrates. There was a 10-fold difference in the specificity constant (kcat/KM ratio) of CpGSTD1 for CDNB and those of CpGSTD1 for cis-DCVC and cis-TFMCVC suggesting that cis-DCVC and cis-TFMCVC may be useful for the detection of GST-based metabolism of pyrethroids in mosquitoes. PMID:23000005

Different HER2 protein expression profiles aid in the histologic differential diagnosis between urothelial carcinoma in situ (CIS) and non-CIS conditions (dysplasia and reactive atypia) of the urinary bladder mucosa.

PubMed

Gunia, Sven; Koch, Stefan; Hakenberg, Oliver W; May, Matthias; Kakies, Christoph; Erbersdobler, Andreas

2011-12-01

We evaluated HER2 expression profiles in 32 carcinoma in situ (CIS) and 31 non-CIS conditions (5 dysplasia and 26 reactive atypia) of the urinary bladder mucosa by applying breast cancer scoring rules. In situ hybridization was performed on tissue microarrays to assess HER2 gene amplification status. Our immunoprofiling data disclosed moderate to strong HER2 expression in CIS, including the basal layer of the urothelium, and absent to weak HER2 expression in non-CIS conditions. From the histologic differential diagnostic standpoint, immunostaining for HER2 protein represents a useful adjunct to aid in the delineation between CIS and non-CIS conditions of the bladder mucosa. Pathogenically, aberrant HER2 protein expression in CIS seems to be more commonly associated with polysomy than with gene amplification. From a therapeutic viewpoint, prospective clinical studies should investigate the potential benefit of HER2-targeted therapies in CIS, particularly in cases unresponsive to conventional therapeutic regimens.

Three-Fold Intramolecular Ring Closing Alkene Metatheses of Square Planar Complexes with cis Phosphorus Donor Ligands P(X(CH2) mCH═CH2)3 (X = -, m = 5-10; X = O, m = 3-5): Syntheses, Structures, and Thermal Properties of Macrocyclic Dibridgehead Diphosphorus Complexes.

PubMed

Joshi, Hemant; Kharel, Sugam; Ehnbom, Andreas; Skopek, Katrin; Hess, Gisela D; Fiedler, Tobias; Hampel, Frank; Bhuvanesh, Nattamai; Gladysz, John A

2018-05-17

Reactions of cis-PtCl 2 (P((CH 2 ) m CH═CH 2 ) 3 ) 2 and Grubbs' first generation catalyst and then hydrogenations afford cis- PtCl 2 (P((CH 2 ) n ) 3 P) ( cis-2; n = 2 m + 2 = 12 (b), 14 (c), 16 (d), 18 (e), 20 (f), 22 (g); 6-40%), derived from 3-fold interligand metatheses. The phosphite complexes cis-PtCl 2 (P(O(CH 2 ) m* CH═CH 2 ) 3 ) 2 are similarly converted to cis- PtCl 2 (P(O(CH 2 ) n* O) 3 P) ( cis-5; n* = 8 (a), 10 (b), 12 (c), 10-20%). The substitution products cis- PtPh 2 (P((CH 2 ) n ) 3 P) ( cis-6c,d) and cis- PtI 2 (P(O(CH 2 ) 10 O) 3 P) are prepared using Ph 2 Zn and NaI, respectively. Crystal structures of cis-2c,d,f, cis-5a,b, and cis-6c show one methylene bridge that roughly lies in the platinum coordination plane and two that are perpendicular. The thermal behavior of the complexes is examined. When the bridges are sufficiently long, they rapidly exchange via an unusual "triple jump rope" motion over the PtX 2 moieties. NMR data establish Δ H ⧧ , Δ S ⧧ , and Δ G 298K ⧧ /Δ G 393K ⧧ values of 7.8 kcal/mol, -27.9 eu, and 16.1/18.8 kcal/mol for cis-2d, and a Δ G 393K ⧧ of ≥19.6 kcal/mol for the shorter bridged cis-2c. While cis-2c,g gradually convert to trans-2c,g at 150-185 °C in haloarenes, trans-2c,g give little reaction under analogous conditions, establishing the stability order trans > cis. Similar metathesis/hydrogenation sequences with octahedral complexes containing two cis phosphine ligands, fac-ReX(CO) 3 (P((CH 2 ) 6 CH═CH 2 ) 3 ) 2 (X = Cl, Br), give fac- ReX(CO) 3 ( P(CH 2 ) 13 CH 2 )((CH 2 ) 14 )( P(CH 2 ) 13 CH 2 ) (19-50%), which are derived from a combination of interligand and intraligand metathesis. The relative stabilities of cis/ trans and other types of isomers are probed by combinations of molecular dynamics and DFT calculations.

Promiscuous Diffusible Signal Factor Production and Responsiveness of the Xylella fastidiosa Rpf System.

PubMed

Ionescu, Michael; Yokota, Kenji; Antonova, Elena; Garcia, Angelica; Beaulieu, Ellen; Hayes, Terry; Iavarone, Anthony T; Lindow, Steven E

2016-07-19

Cell density-dependent regulation of gene expression in Xylella fastidiosa that is crucial to its switching between plant hosts and insect vectors is dependent on RpfF and its production of 2-enoic acids known as diffusible signal factor (DSF). We show that X. fastidiosa produces a particularly large variety of similar, relatively long-chain-length 2-enoic acids that are active in modulating gene expression. Both X. fastidiosa itself and a Pantoea agglomerans surrogate host harboring X. fastidiosa RpfF (XfRpfF) is capable of producing a variety of both saturated and unsaturated free fatty acids. However, only 2-cis unsaturated acids were found to be biologically active in X. fastidiosa X. fastidiosa produces, and is particularly responsive to, a novel DSF species, 2-cis-hexadecanoic acid that we term XfDSF2. It is also responsive to other, even longer 2-enoic acids to which other taxa such as Xanthomonas campestris are unresponsive. The 2-enoic acids that are produced by X. fastidiosa are strongly affected by the cellular growth environment, with XfDSF2 not detected in culture media in which 2-tetradecenoic acid (XfDSF1) had previously been found. X. fastidiosa is responsive to much lower concentrations of XfDSF2 than XfDSF1. Apparently competitive interactions can occur between various saturated and unsaturated fatty acids that block the function of those agonistic 2-enoic fatty acids. By altering the particular 2-enoic acids produced and the relative balance of free enoic and saturated fatty acids, X. fastidiosa might modulate the extent of DSF-mediated quorum sensing. X. fastidiosa, having a complicated lifestyle in which it moves and multiplies within plants but also must be vectored by insects, utilizes DSF-based quorum sensing to partition the expression of traits needed for these two processes within different cells in this population based on local cellular density. The finding that it can produce a variety of DSF species in a strongly environmentally context-dependent manner provides insight into how it coordinates the many genes under the control of DSF signaling to successfully associate with its two hosts. Since the new DSF variant XfDSF2 described here is much more active than the previously recognized DSF species, it should contribute to plant disease control, given that the susceptibility of plants can be greatly reduced by artificially elevating the levels of DSF in plants, creating "pathogen confusion," resulting in lower virulence. Copyright © 2016 Ionescu et al.

Using bioinformatics and systems genetics to dissect HDL-cholesterol genetics in an MRL/MpJ × SM/J intercross[S

PubMed Central

Leduc, Magalie S.; Blair, Rachael Hageman; Verdugo, Ricardo A.; Tsaih, Shirng-Wern; Walsh, Kenneth; Churchill, Gary A.; Paigen, Beverly

2012-01-01

A higher incidence of coronary artery disease is associated with a lower level of HDL-cholesterol. We searched for genetic loci influencing HDL-cholesterol in F2 mice from a cross between MRL/MpJ and SM/J mice. Quantitative trait loci (QTL) mapping revealed one significant HDL QTL (Apoa2 locus), four suggestive QTL on chromosomes 10, 11, 13, and 18 and four additional QTL on chromosomes 1 proximal, 3, 4, and 7 after adjusting HDL for the strong Apoa2 locus. A novel nonsynonymous polymorphism supports Lipg as the QTL gene for the chromosome 18 QTL, and a difference in Abca1 expression in liver tissue supports it as the QTL gene for the chromosome 4 QTL. Using weighted gene co-expression network analysis, we identified a module that after adjustment for Apoa2, correlated with HDL, was genetically determined by a QTL on chromosome 11, and overlapped with the HDL QTL. A combination of bioinformatics tools and systems genetics helped identify several candidate genes for both the chromosome 11 HDL and module QTL based on differential expression between the parental strains, cis regulation of expression, and causality modeling. We conclude that integrating systems genetics to a more-traditional genetics approach improves the power of complex trait gene identification. PMID:22498810

Conjugated linolenic acid (CLnA), conjugated linoleic acid (CLA) and other biohydrogenation intermediates in plasma and milk fat of cows fed raw or extruded linseed.

PubMed

Akraim, F; Nicot, M C; Juaneda, P; Enjalbert, F

2007-07-01

Thirty lactating dairy cows were used in a 3 × 3 Latin-square design to investigate the effects of a raw or extruded blend of linseed and wheat bran (70:30) on plasma and milk fatty-acids (FA). Linseed diets, containing 16.6% linseed blend on a dry-matter basis, decreased milk yield and protein percentage. They decreased the proportions of FA with less than 18 carbons in plasma and milk and resulted in cis-9, cis-12, cis-15 18:3 proportions that were more than three and four times higher in plasma and milk, respectively, whereas cis-9, cis-12 18:2 proportions were decreased by 10-15%. The cis-9, trans-11, cis-15 18:3 isomer of conjugated linolenic acid was not detected in the milk of control cows, but was over 0.15% of total FA in the milk fat of linseed-supplemented cows. Similarly, linseed increased plasma and milk proportions of all biohydrogenation (BH) intermediates in plasma and milk, including the main isomer of conjugated linoleic acid cis-9, trans-11 18:2, except trans-4 18:1 and cis-11, trans-15 18:2 in plasma lipids. In milk fat, compared with raw linseed, extruded linseed further reduced 6:0-16:0 even-chain FA, did not significantly affect the proportions of 18:0, cis-9 18:1 and cis-9, cis-12 18:2, tended to increase cis-9, cis-12, cis-15 18:3, and resulted in an additional increase in the proportions of most BH intermediates. It was concluded that linseed addition can improve the proportion of conjugated linoleic and linolenic acids, and that extrusion further increases the proportions of intermediates of ruminal BH in milk fat.

Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation

PubMed Central

Li, Wencheng; You, Bei; Hoque, Mainul; Zheng, Dinghai; Luo, Wenting; Ji, Zhe; Park, Ji Yeon; Gunderson, Samuel I.; Kalsotra, Auinash; Manley, James L.; Tian, Bin

2015-01-01

Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage/polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1 and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI-25/68 or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly inhibiting C/P events in introns near the 5’ end of gene and U2 suppressing those in introns with features for efficient splicing. Furthermore, PABPN1 inhibits expression of transcripts with pAs near the transcription start site (TSS), a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results support an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the TSS, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core C/P factors. PMID:25906188

Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules

PubMed Central

2013-01-01

Background Cytokine-activated transcription factors from the STAT (Signal Transducers and Activators of Transcription) family control common and context-specific genetic programs. It is not clear to what extent cell-specific features determine the binding capacity of seven STAT members and to what degree they share genetic targets. Molecular insight into the biology of STATs was gained from a meta-analysis of 29 available ChIP-seq data sets covering genome-wide occupancy of STATs 1, 3, 4, 5A, 5B and 6 in several cell types. Results We determined that the genomic binding capacity of STATs is primarily defined by the cell type and to a lesser extent by individual family members. For example, the overlap of shared binding sites between STATs 3 and 5 in T cells is greater than that between STAT5 in T cells and non-T cells. Even for the top 1,000 highly enriched STAT binding sites, ~15% of STAT5 binding sites in mouse female liver are shared by other STATs in different cell types while in T cells ~90% of STAT5 binding sites are co-occupied by STAT3, STAT4 and STAT6. In addition, we identified 116 cis-regulatory modules (CRM), which are recognized by all STAT members across cell types defining a common JAK-STAT signature. Lastly, in liver STAT5 binding significantly coincides with binding of the cell-specific transcription factors HNF4A, FOXA1 and FOXA2 and is associated with cell-type specific gene transcription. Conclusions Our results suggest that genomic binding of STATs is primarily determined by the cell type and further specificity is achieved in part by juxtaposed binding of cell-specific transcription factors. PMID:23324445

ERalpha and AP-1 interact in vivo with a specific sequence of the F promoter of the human ERalpha gene in osteoblasts.

PubMed

Lambertini, Elisabetta; Tavanti, Elisa; Torreggiani, Elena; Penolazzi, Letizia; Gambari, Roberto; Piva, Roberta

2008-07-01

Estrogen-responsive genes often have an estrogen response element (ERE) positioned next to activator protein-1 (AP-1) binding sites. Considering that the interaction between ERE and AP-1 elements has been described for the modulation of bone-specific genes, we investigated the 17-beta-estradiol responsiveness and the role of these cis-elements present in the F promoter of the human estrogen receptor alpha (ERalpha) gene. The F promoter, containing the sequence analyzed here, is one of the multiple promoters of the human ERalpha gene and is the only active promoter in bone tissue. Through electrophoretic mobility shift (EMSA), chromatin immunoprecipitation (ChIP), and re-ChIP assays, we investigated the binding of ERalpha and four members of the AP-1 family (c-Jun, c-fos, Fra-2, and ATF2) to a region located approximately 800 bp upstream of the transcriptional start site of exon F of the human ERalpha gene in SaOS-2 osteoblast-like cells. Reporter gene assay experiments in combination with DNA binding assays demonstrated that F promoter activity is under the control of upstream cis-acting elements which are recognized by specific combinations of ERalpha, c-Jun, c-fos, and ATF2 homo- and heterodimers. Moreover, ChIP and re-ChIP experiments showed that these nuclear factors bind the F promoter in vivo with a simultaneous occupancy stimulated by 17-beta-estradiol. Taken together, our findings support a model in which ERalpha/AP-1 complexes modulate F promoter activity under conditions of 17-beta-estradiol stimulation. (c) 2008 Wiley-Liss, Inc.

Retinoid X receptor and peroxisome proliferator-activated receptor activate an estrogen responsive gene independent of the estrogen receptor.

PubMed

Nuñez, S B; Medin, J A; Braissant, O; Kemp, L; Wahli, W; Ozato, K; Segars, J H

1997-03-14

Estrogen receptors regulate transcription of genes essential for sexual development and reproductive function. Since the retinoid X receptor (RXR) is able to modulate estrogen responsive genes and both 9-cis RA and fatty acids influenced development of estrogen responsive tumors, we hypothesized that estrogen responsive genes might be modulated by RXR and the fatty acid receptor (peroxisome proliferator-activated receptor, PPAR). To test this hypothesis, transfection assays in CV-1 cells were performed with an estrogen response element (ERE) coupled to a luciferase reporter construct. Addition of expression vectors for RXR and PPAR resulted in an 11-fold increase in luciferase activity in the presence of 9-cis RA. Furthermore, mobility shift assays demonstrated binding of RXR and PPAR to the vitellogenin A2-ERE and an ERE in the oxytocin promoter. Methylation interference assays demonstrated that specific guanine residues required for RXR/PPAR binding to the ERE were similar to residues required for ER binding. Moreover, RXR domain-deleted constructs in transfection assays showed that activation required RXR since an RXR delta AF-2 mutant completely abrogated reporter activity. Oligoprecipitation binding studies with biotinylated ERE and (35)S-labeled in vitro translated RXR constructs confirmed binding of delta AF-2 RXR mutant to the ERE in the presence of baculovirus-expressed PPAR. Finally, in situ hybridization confirmed RXR and PPAR mRNA expression in estrogen responsive tissues. Collectively, these data suggest that RXR and PPAR are present in reproductive tissues, are capable of activating estrogen responsive genes and suggest that the mechanism of activation may involve direct binding of the receptors to estrogen response elements.

pH-modulation of chloride channels from the sarcoplasmic reticulum of skeletal muscle.

PubMed

Kourie, J I

1999-01-01

The understanding of the role of cytoplasmic pH in modulating sarcoplasmic reticulum (SR) ion channels involved in Ca2+ regulation is important for the understanding of the function of normal and adversely affected muscles. The dependency of the SR small chloride (SCl) channel from rabbit skeletal muscle on cytoplasmic pH (pHcis) and luminal pH (pHtrans) was investigated using the lipid bilayer-vesicle fusion technique. Low pHcis 6.75-4.28 modifies the operational mode of this multiconductance channel (conductance levels between 5 and 75 pS). At pHcis 7.26-7.37 the channel mode is dominated by the conductance and kinetics of the main conductance state (65-75 pS) whereas at low pHcis 6.75-4.28 the channel mode is dominated by the conductance and kinetics of subconductance states (5-40 pS). Similarly, low pHtrans 4.07, but not pHtrans 6.28, modified the activity of SCl channels. The effects of low pHcis are pronounced at 10(-3) and 10(-4) M [Ca2+]cis but are not apparent at 10(-5) M [Ca2+]cis, where the subconductances of the channel are already prominent. Low pHcis-induced mode shift in the SCl channel activity is due to modification of the channel proteins that cause the uncoupling of the subconductance states. The results in this study suggest that low pHcis can modify the functional properties of the skeletal SR ion channels and hence contribute, at least partly, to the malfunction in the contraction-relaxation mechanism in skeletal muscle under low cytoplasmic pH levels.

Promiscuous Diffusible Signal Factor Production and Responsiveness of the Xylella fastidiosa Rpf System

PubMed Central

Ionescu, Michael; Yokota, Kenji; Antonova, Elena; Garcia, Angelica; Beaulieu, Ellen; Hayes, Terry; Iavarone, Anthony T.

2016-01-01

ABSTRACT Cell density-dependent regulation of gene expression in Xylella fastidiosa that is crucial to its switching between plant hosts and insect vectors is dependent on RpfF and its production of 2-enoic acids known as diffusible signal factor (DSF). We show that X. fastidiosa produces a particularly large variety of similar, relatively long-chain-length 2-enoic acids that are active in modulating gene expression. Both X. fastidiosa itself and a Pantoea agglomerans surrogate host harboring X. fastidiosa RpfF (XfRpfF) is capable of producing a variety of both saturated and unsaturated free fatty acids. However, only 2-cis unsaturated acids were found to be biologically active in X. fastidiosa. X. fastidiosa produces, and is particularly responsive to, a novel DSF species, 2-cis-hexadecanoic acid that we term XfDSF2. It is also responsive to other, even longer 2-enoic acids to which other taxa such as Xanthomonas campestris are unresponsive. The 2-enoic acids that are produced by X. fastidiosa are strongly affected by the cellular growth environment, with XfDSF2 not detected in culture media in which 2-tetradecenoic acid (XfDSF1) had previously been found. X. fastidiosa is responsive to much lower concentrations of XfDSF2 than XfDSF1. Apparently competitive interactions can occur between various saturated and unsaturated fatty acids that block the function of those agonistic 2-enoic fatty acids. By altering the particular 2-enoic acids produced and the relative balance of free enoic and saturated fatty acids, X. fastidiosa might modulate the extent of DSF-mediated quorum sensing. PMID:27435463

Comparison of the Spectral-Temporally Modulated Ripple Test With the Arizona Biomedical Institute Sentence Test in Cochlear Implant Users.

PubMed

Lawler, Marshall; Yu, Jeffrey; Aronoff, Justin M

Although speech perception is the gold standard for measuring cochlear implant (CI) users' performance, speech perception tests often require extensive adaptation to obtain accurate results, particularly after large changes in maps. Spectral ripple tests, which measure spectral resolution, are an alternate measure that has been shown to correlate with speech perception. A modified spectral ripple test, the spectral-temporally modulated ripple test (SMRT) has recently been developed, and the objective of this study was to compare speech perception and performance on the SMRT for a heterogeneous population of unilateral CI users, bilateral CI users, and bimodal users. Twenty-five CI users (eight using unilateral CIs, nine using bilateral CIs, and eight using a CI and a hearing aid) were tested on the Arizona Biomedical Institute Sentence Test (AzBio) with a +8 dB signal to noise ratio, and on the SMRT. All participants were tested with their clinical programs. There was a significant correlation between SMRT and AzBio performance. After a practice block, an improvement of one ripple per octave for SMRT corresponded to an improvement of 12.1% for AzBio. Additionally, there was no significant difference in slope or intercept between any of the CI populations. The results indicate that performance on the SMRT correlates with speech recognition in noise when measured across unilateral, bilateral, and bimodal CI populations. These results suggest that SMRT scores are strongly associated with speech recognition in noise ability in experienced CI users. Further studies should focus on increasing both the size and diversity of the tested participants, and on determining whether the SMRT technique can be used for early predictions of long-term speech scores, or for evaluating differences among different stimulation strategies or parameter settings.

RAD51 potentiates synergistic effects of chemotherapy with PCI-24781 and cis-diamminedichloroplatinum on gastric cancer

PubMed Central

He, Wei-Ling; Li, Yu-Huang; Hou, Wei-Jian; Ke, Zun-Fu; Chen, Xin-Lin; Lu, Li-Ya; Cai, Shi-Rong; Song, Wu; Zhang, Chang-Hua; He, Yu-Long

2014-01-01

AIM: To explore the efficacy of PCI-24781, a broad-spectrum, hydroxamic acid-derived histone deacetylase inhibitor, in the treatment of gastric cancer (GC). METHODS: With or without treatment of PCI-24781 and/or cis-diamminedichloroplatinum (CDDP), GC cell lines were subjected to functional analysis, including cell growth, apoptosis and clonogenic assays. Chromatin immunoprecipitation and luciferase reporter assays were used to determine the interacting molecules and the activity of the enzyme. An in vivo study was carried out in GC xenograft mice. Cell culture-based assays were represented as mean ± SD. ANOVA tests were used to assess differences across groups. All pairwise comparisons between tumor weights among treatment groups were made using the Tukey-Kramer method for multiple comparison adjustment to control experimental-wise type I error rates. Significance was set at P < 0.05. RESULTS: PCI-24781 significantly reduced the growth of the GC cells, enhanced cell apoptosis and suppressed clonogenicity, and these effects synergized with the effects of CDDP. PCI-24781 modulated the cell cycle and significantly reduced the expression of RAD51, which is related to homologous recombination. Depletion of RAD51 augmented the biological functions of PCI-24781, CDDP and the combination treatment, whereas overexpressing RAD51 had the opposite effects. Increased binding of the transcription suppressor E2F4 on the RAD51 promoter appeared to play a major role in these processes. Furthermore, significant suppression of tumor growth and weight in vivo was obtained following PCI-24781 treatment, which synergized with the anticancer effect of CDDP. CONCLUSION: These data suggest that RAD51 potentiates the synergistic effects of chemotherapy with PCI-24781 and CDDP on GC. PMID:25110436

Cis-encoded non-coding antisense RNAs in streptococci and other low GC Gram (+) bacterial pathogens

PubMed Central

Cho, Kyu Hong; Kim, Jeong-Ho

2015-01-01

Due to recent advances of bioinformatics and high throughput sequencing technology, discovery of regulatory non-coding RNAs in bacteria has been increased to a great extent. Based on this bandwagon, many studies searching for trans-acting small non-coding RNAs in streptococci have been performed intensively, especially in the important human pathogen, group A and B streptococci. However, studies for cis-encoded non-coding antisense RNAs in streptococci have been scarce. A recent study shows antisense RNAs are involved in virulence gene regulation in group B streptococcus, S. agalactiae. This suggests antisense RNAs could have important roles in the pathogenesis of streptococcal pathogens. In this review, we describe recent discoveries of chromosomal cis-encoded antisense RNAs in streptococcal pathogens and other low GC Gram (+) bacteria to provide a guide for future studies. PMID:25859258

Different as night and day: Patterns of isolated seizures, clusters, and status epilepticus.

PubMed

Goldenholz, Daniel M; Rakesh, Kshitiz; Kapur, Kush; Gaínza-Lein, Marina; Hodgeman, Ryan; Moss, Robert; Theodore, William H; Loddenkemper, Tobias

2018-05-01

Using approximations based on presumed U.S. time zones, we characterized day and nighttime seizure patterns in a patient-reported database, Seizure Tracker. A total of 632 995 seizures (9698 patients) were classified into 4 categories: isolated seizure event (ISE), cluster without status epilepticus (CWOS), cluster including status epilepticus (CIS), and status epilepticus (SE). We used a multinomial mixed-effects logistic regression model to calculate odds ratios (ORs) to determine night/day ratios for the difference between seizure patterns: ISE versus SE, ISE versus CWOS, ISE versus CIS, and CWOS versus CIS. Ranges of OR values were reported across cluster definitions. In adults, ISE was more likely at night compared to CWOS (OR = 1.49, 95% adjusted confidence interval [CI] = 1.36-1.63) and to CIS (OR = 1.61, 95% adjusted CI = 1.34-1.88). The ORs for ISE versus SE and CWOS versus SE were not significantly different regardless of cluster definition. In children, ISE was less likely at night compared to SE (OR = 0.85, 95% adjusted CI = 0.79-0.91). ISE was more likely at night compared to CWOS (OR = 1.35, 95% adjusted CI = 1.26-1.44) and CIS (OR = 1.65, 95% adjusted CI = 1.44-1.86). CWOS was more likely during the night compared to CIS (OR = 1.22, 95% adjusted CI = 1.05-1.39). With the exception of SE in children, our data suggest that more severe patterns favor daytime. This suggests distinct day/night preferences for different seizure patterns in children and adults. Wiley Periodicals, Inc. © 2018 International League Against Epilepsy.

Evolution of Enzymatic Activities in the Enolase Superfamily: Stereochemically Distinct Mechanisms in Two Families of cis,cis-Muconate Lactonizing Enzymes

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

Sakai, A.; Fedorov, A; Fedorov, E

2009-01-01

The mechanistically diverse enolase superfamily is a paradigm for elucidating Nature's strategies for divergent evolution of enzyme function. Each of the different reactions catalyzed by members of the superfamily is initiated by abstraction of the a-proton of a carboxylate substrate that is coordinated to an essential Mg2+. The muconate lactonizing enzyme (MLE) from Pseudomonas putida, a member of a family that catalyzes the syn-cycloisomerization of cis,cis-muconate to (4S)-muconolactone in the e-ketoadipate pathway, has provided critical insights into the structural bases for evolution of function within the superfamily. A second, divergent family of homologous MLEs that catalyzes anti-cycloisomerization has been identified.more » Structures of members of both families liganded with the common (4S)-muconolactone product (syn, Pseudomonas fluorescens, gi 70731221; anti, Mycobacterium smegmatis, gi 118470554) document that the conserved Lys at the end of the second e-strand in the (e/a)7e-barrel domain serves as the acid catalyst in both reactions. The different stereochemical courses (syn and anti) result from different structural strategies for determining substrate specificity: although the distal carboxylate group of the cis,cis-muconate substrate attacks the same face of the proximal double bond, opposite faces of the resulting enolate anion intermediate are presented to the conserved Lys acid catalyst. The discovery of two families of homologous, but stereochemically distinct, MLEs likely provides an example of 'pseudoconvergent' evolution of the same function from different homologous progenitors within the enolase superfamily, in which different spatial arrangements of active site functional groups and substrate specificity determinants support catalysis of the same reaction.« less

Comparing apples and oranges: the Community Intercomparison Suite

NASA Astrophysics Data System (ADS)

Schutgens, Nick; Stier, Philip; Kershaw, Philip; Pascoe, Stephen

2015-04-01

Visual representation and comparison of geoscientific datasets presents a huge challenge due to the large variety of file formats and spatio-temporal sampling of data (be they observations or simulations). The Community Intercomparison Suite attempts to greatly simplify these tasks for users by offering an intelligent but simple command line tool for visualisation and colocation of diverse datasets. In addition, CIS can subset and aggregate large datasets into smaller more manageable datasets. Our philosophy is to remove as much as possible the need for specialist knowledge by the user of the structure of a dataset. The colocation of observations with model data is as simple as: "cis col ::" which will resample the simulation data to the spatio-temporal sampling of the observations, contingent on a few user-defined options that specify a resampling kernel. As an example, we apply CIS to a case study of biomass burning aerosol from the Congo. Remote sensing observations, in-situe observations and model data are shown in various plots, with the purpose of either comparing different datasets or integrating them into a single comprehensive picture. CIS can deal with both gridded and ungridded datasets of 2, 3 or 4 spatio-temporal dimensions. It can handle different spatial coordinates (e.g. longitude or distance, altitude or pressure level). CIS supports both HDF, netCDF and ASCII file formats. The suite is written in Python with entirely publicly available open source dependencies. Plug-ins allow a high degree of user-moddability. A web-based developer hub includes a manual and simple examples. CIS is developed as open source code by a specialist IT company under supervision of scientists from the University of Oxford and the Centre of Environmental Data Archival as part of investment in the JASMIN superdatacluster facility.

Oligo(cis-1,4-isoprene) aldehyde-oxidizing dehydrogenases of the rubber-degrading bacterium Gordonia polyisoprenivorans VH2.

PubMed

Vivod, Robin; Oetermann, Sylvia; Hiessl, Sebastian; Gutsche, Stefanie; Remmers, Naomi; Meinert, Christina; Voigt, Birgit; Riedel, Katharina; Steinbüchel, Alexander

2017-11-01

The actinomycete Gordonia polyisoprenivorans strain VH2 is well-known for its ability to efficiently degrade and catabolize natural rubber [poly(cis-1,4-isoprene)]. Recently, a pathway for the catabolism of rubber by strain VH2 was postulated based on genomic data and the analysis of mutants (Hiessl et al. in Appl Environ Microbiol 78:2874-2887, 2012). To further elucidate the degradation pathway of poly(cis-1,4-isoprene), 2-dimensional-polyacrylamide gel electrophoresis was performed. The analysis of the identified protein spots by matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry confirmed the postulated intracellular pathway suggesting a degradation of rubber via β-oxidation. In addition, other valuable information on rubber catabolism of G. polyisoprenivorans strain VH2 (e.g. oxidative stress response) was provided. Identified proteins, which were more abundant in cells grown with rubber than in cells grown with propionate, implied a putative long-chain acyl-CoA-dehydrogenase, a 3-ketoacyl-CoA-thiolase, and an aldehyde dehydrogenase. The amino acid sequence of the latter showed a high similarity towards geranial dehydrogenases. The expression of the corresponding gene was upregulated > 10-fold under poly(cis-1,4-isoprene)-degrading conditions. The putative geranial dehydrogenase and a homolog were purified and used for enzyme assays. Deletion mutants for five aldehyde dehydrogenases were generated, and growth with poly(cis-1,4-isoprene) was investigated. While none of the mutants had an altered phenotype regarding growth with poly(cis-1,4-isoprene) as sole carbon and energy source, purified aldehyde dehydrogenases were able to catalyze the oxidation of oligoisoprene aldehydes indicating an involvement in rubber degradation.

Identification of trans-acting factors regulating SamDC expression in Oryza sativa

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

Basu, Supratim, E-mail: supratim_genetics@yahoo.co.in; Division of Plant Biology, Bose Institute, Kolkata; Roychoudhury, Aryadeep

2014-03-07

Highlights: • Identification of cis elements responsible for SamDC expression by in silico analysis. • qPCR analysis of SamDC expression to abiotic and biotic stress treatments. • Detection of SamDC regulators using identified cis-elements as probe by EMSA. • Southwestern Blot analysis to predict the size of the trans-acting factors. - Abstract: Abiotic stress affects the growth and productivity of crop plants; to cope with the adverse environmental conditions, plants have developed efficient defense machinery comprising of antioxidants like phenolics and flavonoids, and osmolytes like polyamines. SamDC is a key enzyme in the polyamine biosynthesis pathway in plants. In ourmore » present communication we have done in silico analysis of the promoter region of SamDC to look for the presence of different cis-regulatory elements contributing to its expression. Based on the presence of different cis-regulatory elements we completed comparative analysis of SamDC gene expression in rice lamina of IR-29 and Nonabokra by qPCR in response to the abiotic stress treatments of salinity, drought, cold and the biotic stress treatments of ABA and light. Additionally, to explore the role of the cis-regulatory elements in regulating the expression of SamDC gene in plants we comparatively analyzed the binding of rice nuclear proteins prepared from IR-29 and Nonabokra undergoing various stress treatments. The intensity of the complex formed was low and inducible in IR-29 in contrast to Nonabokra. Southwestern blot analysis helped in predicting the size of the trans-acting factors binding to these cis-elements. To our knowledge this is the first report on the comprehensive analysis of SamDC gene expression in rice and identification of the trans-acting factors regulating its expression.« less

Identification of 4-oxo-13-cis-retinoic acid as the major metabolite of 13-cis-retinoic acid in human blood.

PubMed

Vane, F M; Buggé, C J

1981-01-01

The metabolites of 13-cis-retinoic acid (Accutane) were investigated in blood samples from human volunteers on chronic treatment for dermatological disorders. The major metabolite was isolated by reverse-phase high-pressure liquid chromatography and identified as 4-oxo-13-cis-retinoic acid by comparison of its mass and NMR spectra to the spectra of the reference compound. 4-Oxo-all-trans-retinoic acid was also identified, but the extent to which this compound was a metabolite of 13-cis-retinoic acid or an artifactual isomerization product of the major metabolite is unknown. Chromatographic data suggested that small amounts of 13-cis-retinoic acid, 4-hydroxy-13-cis-retinoic acid, and dioxygenated metabolites of 13-cis-retinoic acid may also be present in the blood. This study indicates that a major metabolic pathway of 13-cis-retinoic acid in humans is oxidation at C4 of the cyclohexenyl group.

Lateral assembly of the immunoglobulin protein SynCAM 1 controls its adhesive function and instructs synapse formation.

PubMed

Fogel, Adam I; Stagi, Massimiliano; Perez de Arce, Karen; Biederer, Thomas

2011-09-16

Synapses are specialized adhesion sites between neurons that are connected by protein complexes spanning the synaptic cleft. These trans-synaptic interactions can organize synapse formation, but their macromolecular properties and effects on synaptic morphology remain incompletely understood. Here, we demonstrate that the synaptic cell adhesion molecule SynCAM 1 self-assembles laterally via its extracellular, membrane-proximal immunoglobulin (Ig) domains 2 and 3. This cis oligomerization generates SynCAM oligomers with increased adhesive capacity and instructs the interactions of this molecule across the nascent and mature synaptic cleft. In immature neurons, cis assembly promotes the adhesive clustering of SynCAM 1 at new axo-dendritic contacts. Interfering with the lateral self-assembly of SynCAM 1 in differentiating neurons strongly impairs its synaptogenic activity. At later stages, the lateral oligomerization of SynCAM 1 restricts synaptic size, indicating that this adhesion molecule contributes to the structural organization of synapses. These results support that lateral interactions assemble SynCAM complexes within the synaptic cleft to promote synapse induction and modulate their structure. These findings provide novel insights into synapse development and the adhesive mechanisms of Ig superfamily members.

Natural sequence variants of yeast environmental sensors confer cell-to-cell expression variability

PubMed Central

Fehrmann, Steffen; Bottin-Duplus, Hélène; Leonidou, Andri; Mollereau, Esther; Barthelaix, Audrey; Wei, Wu; Steinmetz, Lars M; Yvert, Gaël

2013-01-01

Living systems may have evolved probabilistic bet hedging strategies that generate cell-to-cell phenotypic diversity in anticipation of environmental catastrophes, as opposed to adaptation via a deterministic response to environmental changes. Evolution of bet hedging assumes that genotypes segregating in natural populations modulate the level of intraclonal diversity, which so far has largely remained hypothetical. Using a fluorescent Pmet17-GFP reporter, we mapped four genetic loci conferring to a wild yeast strain an elevated cell-to-cell variability in the expression of MET17, a gene regulated by the methionine pathway. A frameshift mutation in the Erc1p transmembrane transporter, probably resulting from a release of laboratory strains from negative selection, reduced Pmet17-GFP expression variability. At a second locus, cis-regulatory polymorphisms increased mean expression of the Mup1p methionine permease, causing increased expression variability in trans. These results demonstrate that an expression quantitative trait locus (eQTL) can simultaneously have a deterministic effect in cis and a probabilistic effect in trans. Our observations indicate that the evolution of transmembrane transporter genes can tune intraclonal variation and may therefore be implicated in both reactive and anticipatory strategies of adaptation. PMID:24104478

Simultaneous targeting of ATM and Mcl-1 increases cisplatin sensitivity of cisplatin-resistant non-small cell lung cancer.

PubMed

Zhang, Fuquan; Shen, Mingjing; Yang, Li; Yang, Xiaodong; Tsai, Ying; Keng, Peter C; Chen, Yongbing; Lee, Soo Ok; Chen, Yuhchyau

2017-08-03

Development of cisplatin-resistance is an obstacle in non-small cell lung cancer (NSCLC) therapeutics. To investigate which molecules are associated with cisplatin-resistance, we analyzed expression profiles of several DNA repair and anti-apoptosis associated molecules in parental (A549P and H157P) and cisplatin-resistant (A549CisR and H157CisR) NSCLC cells. We detected constitutively upregulated nuclear ATM and cytosolic Mcl-1 molcules in cisplatin-resistant cells compared with parental cells. Increased levels of phosphorylated ATM (p-ATM) and its downstream molecules, CHK2, p-CHK2, p-53, and p-p53 were also detected in cisplatin-resistant cells, suggesting an activation of ATM signaling in these cells. Upon inhibition of ATM and Mcl-1 expression/activity using specific inhibitors of ATM and/or Mcl-1, we found significantly enhanced cisplatin-cytotoxicity and increased apoptosis of A549CisR cells after cisplatin treatment. Several A549CisR-derived cell lines, including ATM knocked down (A549CisR-siATM), Mcl-1 knocked down (A549CisR-shMcl1), ATM/Mcl-1 double knocked down (A549CisR-siATM/shMcl1) as well as scramble control (A549CisR-sc), were then developed. Higher cisplatin-cytotoxicity and increased apoptosis were observed in A549CisR-siATM, A549CisR-shMcl1, and A549CisR-siATM/shMcl1 cells compared with A549CisR-sc cells, and the most significant effect was shown in A549CisR-siATM/shMcl1 cells. In in vivo mice studies using subcutaneous xenograft mouse models developed with A549CisR-sc and A549CisR-siATM/shMcl1 cells, significant tumor regression in A549CisR-siATM/shMcl1 cells-derived xenografts was observed after cisplatin injection, but not in A549CisR-sc cells-derived xenografts. Finally, inhibitor studies revealed activation of Erk signaling pathway was most important in upregulation of ATM and Mcl-1 molcules in cisplatin-resistant cells. These studies suggest that simultaneous blocking of ATM/Mcl-1 molcules or downstream Erk signaling may recover the cisplatin-resistance of lung cancer.

Febuxostat exerts dose-dependent renoprotection in rats with cisplatin-induced acute renal injury.

PubMed

Fahmi, Alaa N A; Shehatou, George S G; Shebl, Abdelhadi M; Salem, Hatem A

2016-08-01

The aim of the present study was to investigate possible renoprotective effects of febuxostat, a highly potent xanthine oxidase inhibitor, against cisplatin (CIS)-induced acute kidney injury in rats. Male Sprague Dawley rats were randomly assigned into four groups of six rats each, as follows: normal control; CIS, received a single intraperitoneal injection of CIS (7.5 mg/kg); [febuxostat 10 + CIS] and [febuxostat 15 + CIS], received febuxostat (10 and 15 mg/kg/day, respectively, orally) for 14 days, starting 7 days before CIS injection. At the end of experiment, 24-h urine output was collected and serum was separated for biochemical assessments. Kidney tissue homogenate was prepared for determination of oxidative stress-related parameters, nitric oxide (NO), and tumor necrosis factor-α (TNF-α). Moreover, histological alterations of kidney tissues were evaluated. Serum creatinine, blood urea, and urinary total protein were significantly elevated, while serum albumin and creatinine clearance were significantly reduced, in CIS-intoxicated rats, indicating depressed renal function. CIS administration also elicited renal oxidative stress, evidenced by increased malondialdehyde content and depleted levels of reduced glutathione and superoxide dismutase activity. Moreover, enhancement of renal levels of the pro-inflammatory TNF-α indicated renal inflammation. CIS-administered rats also showed increased serum lactate dehydrogenase activity and reduced renal NO bioavailability. Febuxostat dose-dependently improved or restored these changes to near-normal (e.g., mean ± SD of serum creatinine levels in control, CIS, [febuxostat 10 + CIS] and [febuxostat 15 + CIS] groups were 0.78 ± 0.19, 3.28 ± 2.0 (P < 0.01 versus control group), 1.03 ± 0.36 (P < 0.01 versus CIS group), and 0.93 ± 0.21 (P < 0.01 versus CIS group) mg/dl, respectively, and blood urea levels for the different groups were 36.80 ± 4.36, 236.10 ± 89.19 (P < 0.0001 versus control group), 114.50 ± 78.63 (P < 0.05 versus CIS group), and 60.91 ± 14.30 (P < 0.001 versus CIS group) mg/dl, respectively). Histological analysis of renal tissues also demonstrated that febuxostat offered a dose-dependent renoprotection. The present study suggests that antioxidant, anti-inflammatory, and cytoprotective mechanisms potentially mediate the renoprotective effects of febuxostat in CIS-administered rats, presenting febuxostat as a promising combinatorial strategy for cancer patients undergoing CIS chemotherapy.

Graph Theory-Based Brain Connectivity for Automatic Classification of Multiple Sclerosis Clinical Courses.

PubMed

Kocevar, Gabriel; Stamile, Claudio; Hannoun, Salem; Cotton, François; Vukusic, Sandra; Durand-Dubief, Françoise; Sappey-Marinier, Dominique

2016-01-01

Purpose: In this work, we introduce a method to classify Multiple Sclerosis (MS) patients into four clinical profiles using structural connectivity information. For the first time, we try to solve this question in a fully automated way using a computer-based method. The main goal is to show how the combination of graph-derived metrics with machine learning techniques constitutes a powerful tool for a better characterization and classification of MS clinical profiles. Materials and Methods: Sixty-four MS patients [12 Clinical Isolated Syndrome (CIS), 24 Relapsing Remitting (RR), 24 Secondary Progressive (SP), and 17 Primary Progressive (PP)] along with 26 healthy controls (HC) underwent MR examination. T1 and diffusion tensor imaging (DTI) were used to obtain structural connectivity matrices for each subject. Global graph metrics, such as density and modularity, were estimated and compared between subjects' groups. These metrics were further used to classify patients using tuned Support Vector Machine (SVM) combined with Radial Basic Function (RBF) kernel. Results: When comparing MS patients to HC subjects, a greater assortativity, transitivity, and characteristic path length as well as a lower global efficiency were found. Using all graph metrics, the best F -Measures (91.8, 91.8, 75.6, and 70.6%) were obtained for binary (HC-CIS, CIS-RR, RR-PP) and multi-class (CIS-RR-SP) classification tasks, respectively. When using only one graph metric, the best F -Measures (83.6, 88.9, and 70.7%) were achieved for modularity with previous binary classification tasks. Conclusion: Based on a simple DTI acquisition associated with structural brain connectivity analysis, this automatic method allowed an accurate classification of different MS patients' clinical profiles.

SYNTHESIS OF NOVEL CROWN ETHERS BEARING THE exo-cis-2,3-NORBORNYL GROUP AS POTENTIAL Na+ AND K+ EXTRACTANTS

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

Robeson, R.M.; Bonnesen, P.

2007-01-01

The synthesis of a series of novel dinorbornyl-16-crown-5 and dinorbornyl-18-crown-6 ethers that incorporate the exo-cis-2,3-norbornyl moiety within the macrocycle framework is described. The key starting material for the crown ethers, exo-cis-2,3-norbornanediol, was successfully prepared on a large (>30g) scale in 88% yield from norbornylene by osmium tetroxide-catalyzed hydroxylation. The syn and anti isomers of the dinorbornyl-16-crown-5 ether family were prepared using diethylene glycol with ring closure achieved using a methallyl linkage. The isomers cis-syn-cis and cis-anti-cis di-norbornano-15-methyleno-16-crown-5 (6A and 6B) could be separated using column chromatography, and a single crystal of the syn isomer 6A suitable for X-ray crystal structuremore » analysis was obtained, thereby confi rming the syn orientation. The syn and anti isomers of the dinorbornyl-18-crown-6 ether family were successfully prepared employing a different synthetic strategy, involving the potassium–templated cyclization of two bis-hydroxyethoxy-substituted exo-cis-2,3-norbornyl groups under high dilution conditions. Attempts to fully separate cis-syn-cis di-norbornano-18-crown-6 (10A) and cis-anti-cis di-norbornano-18-crown-6 (10B) from one another using column chromatography were unsuccessful. All intermediates and products were checked for purity using either thin layer chromatography or gas chromatography, and characterized by proton and carbon NMR. Crown ethers 6AB and 10AB are to our knowledge the fi rst crown ethers to incorporate the exo-cis-2,3-norbornyl moiety into the crown ring to be successfully synthesized and characterized.« less

Prevalence of BRCA1 and BRCA2 mutations in women with carcinoma in situ of the breast referred for genetic testing

PubMed Central

Hall, Michael J.; Reid, Julia E.; Wenstrup, Richard J.

2010-01-01

Background Carcinoma in situ (CIS) of the breast will account for 62,280 (24.5%) of new breast cancer diagnoses in 2009. Management guidelines for BRCA1/2 mutation carriers advise close follow-up, intensive screening, and consideration of prophylactic surgeries to lower cancer risk. The prevalence of BRCA1/2 mutations in women with a history of CIS using comprehensive DNA sequencing and rearrangement testing has not been definitively documented. Methods The prevalence of mutations in non-Ashkenazi Jewish women with CIS was assessed by way of a cross-sectional analysis of the Myriad Genetic Laboratories, Inc. BRCA1/2 database. Women reporting any diagnosis of CIS were included. All statistical tests are two-sided, and confidence intervals are reported at the 95% level (α =0.05). Results Among the test population (N=64717), 11.3%(n=7295) reported a history of CIS (any reported CIS). For women without personal history of invasive cancer (CIS alone+CIS and any family history subgroups), those with early-onset CIS had a significantly increased risk of a BRCA1/2 mutation compared to women with late-onset disease (≥50 years)(OR 1.5, 95% CI 1.1–2.1). Among women reporting only a history of CIS and no personal or family history (CIS alone), mutation prevalence was 2.3% (17/738). Conclusions In patients referred for genetic testing, early-onset CIS is associated with BRCA1/2. When a family history of breast and/or ovarian cancer are also present, testing women with early-onset CIS may increase the likelihood of BRCA1/2 mutation detection, and the opportunity for carriers to consider additional cancer prevention strategies. PMID:21149333

Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora

PubMed Central

Steige, Kim A.; Laenen, Benjamin; Reimegård, Johan; Slotte, Tanja

2017-01-01

Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species. PMID:28096395

Advanced Cancer and End-of-Life Preferences: Curative Intent Surgery Versus Noncurative Intent Treatment.

PubMed

Schubart, Jane R; Green, Michael J; Van Scoy, Lauren J; Lehman, Erik; Farace, Elana; Gusani, Niraj J; Levi, Benjamin H

2015-12-01

People with cancer face complex medical decisions, including whether to receive life-sustaining treatments at the end of life. It is not unusual for clinicians to make assumptions about patients' wishes based on whether they had previously chosen to pursue curative treatment. We hypothesized that cancer patients who initially underwent curative intent surgery (CIS) would prefer more aggressive end-of-life treatments compared to patients whose treatment was noncurative intent (non-CIT). This study was a retrospective review of data from a large, randomized controlled trial examining the use of an online decision aid for advance care planning, "Making Your Wishes Known" (MYWK), with patients who had advanced cancer. We reviewed patients' medical records to determine which patients underwent CIS versus non-CIT. In the parent trial, conducted at an academic medical center (2007-2012), 200 patients were enrolled with stage IV malignancy or other poor prognosis cancer. Patients' preferences for aggressive treatment were measured in two ways: using patient-selected General Wishes statements generated by the decision aid and patient-selected wishes for specific treatments under various hypothetical clinical scenarios (Specific Wishes). We evaluated 79 patients. Of these, 48 had undergone initial CIS and 31 had non-CIT. Cancer patients who initially underwent CIS did not prefer more aggressive end-of-life treatments compared to patients whose treatment was non-CIT. Clinicians should avoid assumptions about patients' preferences for life-sustaining treatment based on their prior choices for aggressive treatment.

ABO Mistyping of cis-AB Blood Group by the Automated Microplate Technique.

PubMed

Chun, Sejong; Ryu, Mi Ra; Cha, Seung-Yeon; Seo, Ji-Young; Cho, Duck

2018-01-01

The cis -AB phenotype, although rare, is the relatively most frequent of ABO subgroups in Koreans. To prevent ABO mistyping of cis -AB samples, our hospital has applied a combination of the manual tile method with automated devices. Herein, we report cases of ABO mistyping detected by the combination testing system. Cases that showed discrepant results by automated devices and the manual tile method were evaluated. These samples were also tested by the standard tube method. The automated devices used in this study were a QWALYS-3 and Galileo NEO. Exons 6 and 7 of the ABO gene were sequenced. 13 cases that had the cis -AB allele showed results suggestive of the cis -AB subgroup by manual methods, but were interpreted as AB by either automated device. This happened in 87.5% of these cases by QWALYS-3 and 70.0% by Galileo NEO. Genotyping results showed that 12 cases were ABO*cis-AB01/ABO*O01 or ABO*cis-AB01/ABO*O02 , and one case was ABO*cis-AB01/ ABO*A102. Cis -AB samples were mistyped as AB by the automated microplate technique in some cases. We suggest that the manual tile method can be a simple supplemental test for the detection of the cis -AB phenotype, especially in countries with relatively high cis- AB prevalence.

13-cis Retinoic acid induces apoptosis and cell cycle arrest in human SEB-1 sebocytes.

PubMed

Nelson, Amanda M; Gilliland, Kathryn L; Cong, Zhaoyuan; Thiboutot, Diane M

2006-10-01

Isotretinoin (13-cis retinoic acid (13-cis RA)) is the most potent inhibitor of sebum production, a key component in the pathophysiology of acne, yet its mechanism of action remains largely unknown. The effects of 13-cis RA, 9-cis retinoic acid (9-cis RA), and all-trans retinoic acid (ATRA) on cell proliferation, apoptosis, and cell cycle proteins were examined in SEB-1 sebocytes and keratinocytes. 13-cis RA causes significant dose-dependent and time-dependent decreases in viable SEB-1 sebocytes. A portion of this decrease can be attributed to cell cycle arrest as evidenced by decreased DNA synthesis, increased p21 protein expression, and decreased cyclin D1. Although not previously demonstrated in sebocytes, we report that 13-cis RA induces apoptosis in SEB-1 sebocytes as shown by increased Annexin V-FITC staining, increased TUNEL staining, and increased cleaved caspase 3 protein. Furthermore, the ability of 13-cis RA to induce apoptosis cannot be recapitulated by 9-cis RA or ATRA, and it is not inhibited by the presence of a retinoid acid receptor (RAR) pan-antagonist AGN 193109. Taken together these data indicate that 13-cis RA causes cell cycle arrest and induces apoptosis in SEB-1 sebocytes by a RAR-independent mechanism, which contributes to its sebosuppressive effect and the resolution of acne.

Cooxidation of 13-cis-retinoic acid by prostaglandin H synthase.

PubMed

Samokyszyn, V M; Sloane, B F; Honn, K V; Marnett, L J

1984-10-30

Cooxidative metabolism of 13-cis-retinoic acid (13-CIS) via prostaglandin H synthase was investigated employing ram seminal vesicle microsomes. Oxidation of 13-CIS utilizing H2O2, 13-hydroperoxy-9-cis-11-trans-octadecadienoic acid (13-OOH-18:2), or 1-hydroperoxy-5-phenyl-4-pentene was detected by measurement of O2 incorporation. UV spectroscopy and HPLC of extracted incubation mixtures demonstrated that 13-CIS was metabolized to oxidized derivatives. Similar spectral changes and HPLC profiles were obtained with H2O2, 13-OOH-18:2, or arachidonic acid as substrates. 4-Hydroxy-13-cis-retinoic acid and all trans-retinoic acid were products of cooxidation as well as other polar metabolites. Oxidation was inhibited by the antioxidant butylated hydroxyanisole and the spin trap, nitrosobenzene. These results indicate that 13-cis-retinoic acid is cooxidized by prostaglandin H synthase and suggest a free radical mechanism resembling that of lipid peroxidation.

Synthetic Biology of Proteins: Tuning GFPs Folding and Stability with Fluoroproline

PubMed Central

Steiner, Thomas; Hess, Petra; Bae, Jae Hyun; Wiltschi, Birgit; Moroder, Luis; Budisa, Nediljko

2008-01-01

Background Proline residues affect protein folding and stability via cis/trans isomerization of peptide bonds and by the Cγ-exo or -endo puckering of their pyrrolidine rings. Peptide bond conformation as well as puckering propensity can be manipulated by proper choice of ring substituents, e.g. Cγ-fluorination. Synthetic chemistry has routinely exploited ring-substituted proline analogs in order to change, modulate or control folding and stability of peptides. Methodology/Principal Findings In order to transmit this synthetic strategy to complex proteins, the ten proline residues of enhanced green fluorescent protein (EGFP) were globally replaced by (4R)- and (4S)-fluoroprolines (FPro). By this approach, we expected to affect the cis/trans peptidyl-proline bond isomerization and pyrrolidine ring puckering, which are responsible for the slow folding of this protein. Expression of both protein variants occurred at levels comparable to the parent protein, but the (4R)-FPro-EGFP resulted in irreversibly unfolded inclusion bodies, whereas the (4S)-FPro-EGFP led to a soluble fluorescent protein. Upon thermal denaturation, refolding of this variant occurs at significantly higher rates than the parent EGFP. Comparative inspection of the X-ray structures of EGFP and (4S)-FPro-EGFP allowed to correlate the significantly improved refolding with the Cγ-endo puckering of the pyrrolidine rings, which is favored by 4S-fluorination, and to lesser extents with the cis/trans isomerization of the prolines. Conclusions/Significance We discovered that the folding rates and stability of GFP are affected to a lesser extent by cis/trans isomerization of the proline bonds than by the puckering of pyrrolidine rings. In the Cγ-endo conformation the fluorine atoms are positioned in the structural context of the GFP such that a network of favorable local interactions is established. From these results the combined use of synthetic amino acids along with detailed structural knowledge and existing protein engineering methods can be envisioned as a promising strategy for the design of complex tailor-made proteins and even cellular structures of superior properties compared to the native forms. PMID:18301757

Placental transfer and developmental effects of 9-cis retinoic acid in mice.

PubMed

Kochhar, D M; Jiang, H; Penner, J D; Heyman, R A

1995-04-01

9-cis retinoic acid (RA) is a naturally occurring isomer of all-trans RA. While both isomers can bind with high affinity and activate RA receptors, only 9-cis RA is the specific ligand for the retinoid X receptors. 9-cis RA has also been shown to be much more potent than all-trans RA in inducing digit duplication in the chick embryo wing bud. To gain further insight into its mechanisms, here we investigated the teratogenic activity in pregnant mice of 9-cis RA and compared it with those of all-trans RA and 13-cis RA. Using frequency and severity of limb reduction defects as well as palatal clefts in the resultant fetuses as indicators, we found that orally administered 9-cis RA was one-half as potent a teratogen as all-trans RA. That 9-cis RA was intrinsically less active than all-trans RA was deduced by comparing the inhibitory activities of the two retinoids in the limb bud mesenchymal cell micromass cultures using chondrogenesis as an end-point. Since placental transfer of cis isomers of RA is generally poor, we monitored the identities and amounts of retinoids in the embryo after administration of 9-cis RA to the mother. We found that 9-cis RA undergoes extensive metabolism and isomerization during absorption resulting in a number of metabolites in the maternal circulation within 30 min after administration. Although some of these metabolites remain to be identified, the most abundant RA isomers in the plasma coeluted with 13-cis RA.(ABSTRACT TRUNCATED AT 250 WORDS)

Generation of Chimeric RNAs by cis-splicing of adjacent genes (cis-SAGe) in mammals.

PubMed

Zhuo, Jian-Shu; Jing, Xiao-Yan; Du, Xin; Yang, Xiu-Qin

2018-02-20

Chimeric RNA molecules, possessing exons from two or more independent genes, are traditionally believed to be produced by chromosome rearrangement. However, recent studies revealed that cis-splicing of adjacent genes (cis- SAGe) is one of the major mechanisms underlying the formation of chimeric RNAs. cis-SAGe refers to intergenic splicing of directly adjacent genes with the same transcriptional orientation, resulting in read-through transcripts, termed chimeric RNAs, which contain sequences from two or more parental genes. cis-SAGe was first identified in tumor cells, since then its potential in carcinogenesis has attracted extensive attention. More and more scientists are focusing on it. With the development of research, cis-SAGe was found to be ubiquitous in various normal tissues, and might make a crucial contribution to the formation of novel genes in the evolution of genomes. In this review, we summarize the splicing pattern, expression characteristics, possible mechanisms, and significance of cis-SAGe in mammals. This review will be helpful for general understanding of the current status and development tendency of cis-SAGe.

cis-Prenyltransferase: New Insights into Protein Glycosylation, Rubber Synthesis, and Human Diseases.

PubMed

Grabińska, Kariona A; Park, Eon Joo; Sessa, William C

2016-08-26

cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. cis-PTs catalyze consecutive condensation reactions of allylic diphosphate acceptor with isopentenyl diphosphate (IPP) in the cis (Z) configuration to generate linear polyprenyl diphosphate. The chain lengths of isoprenoid carbon skeletons vary widely from neryl pyrophosphate (C10) to natural rubber (C>10,000). The homo-dimeric bacterial enzyme, undecaprenyl diphosphate synthase (UPPS), has been structurally and mechanistically characterized in great detail and serves as a model for understanding the mode of action of eukaryotic cis-PTs. However, recent experiments have revealed that mammals, fungal, and long-chain plant cis-PTs are heteromeric enzymes composed of two distantly related subunits. In this review, the classification, function, and evolution of cis-PTs will be discussed with a special emphasis on the role of the newly described NgBR/Nus1 subunit and its plants' orthologs as essential, structural components of the cis-PTs activity. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

S- Cis Diene Conformation: A New Bathochromic Shift Strategy for Near-Infrared Fluorescence Switchable Dye and the Imaging Applications.

PubMed

Chen, Hsiang-Jung; Chew, Chee Ying; Chang, En-Hao; Tu, Yu-Wei; Wei, Li-Yu; Wu, Bo-Han; Chen, Chien-Hung; Yang, Ya-Ting; Huang, Su-Chin; Chen, Jen-Kun; Chen, I-Chia; Tan, Kui-Thong

2018-04-18

In this paper, we present a novel charge-free fluorescence-switchable near-infrared (IR) dye based on merocyanine for target specific imaging. In contrast to the typical bathochromic shift approach by extending π-conjugation, the bathochromic shift of our merocyanine dye to the near-IR region is due to an unusual S- cis diene conformer. This is the first example where a fluorescent dye adopts the stable S- cis conformation. In addition to the novel bathochromic shift mechanism, the dye exhibits fluorescence-switchable properties in response to polarity and viscosity. By incorporating a protein-specific ligand to the dye, the probes (for SNAP-tag and hCAII proteins) exhibited dramatic fluorescence increase (up to 300-fold) upon binding with its target protein. The large fluorescence enhancement, near-IR absorption/emission, and charge-free scaffold enabled no-wash and site-specific imaging of target proteins in living cells and in vivo with minimum background fluorescence. We believe that our unconventional approach for a near-IR dye with the S- cis diene conformation can lead to new strategies for the design of near-IR dyes.

Serum adipokine profile and fatty acid composition of adipose tissues are affected by conjugated linoleic acid and saturated fat diets in obese Zucker rats.

PubMed

Martins, Susana V; Lopes, Paula A; Alfaia, Cristina M; Rodrigues, Pedro O; Alves, Susana P; Pinto, Rui M A; Castro, Matilde F; Bessa, Rui J B; Prates, José A M

2010-03-01

Conjugated linoleic acid (CLA) has been reported as having body fat lowering properties and the ability to modulate the inflammatory system in several models. In the present study, the effects of CLA added to saturated fat diets, from vegetable and animal origins, on the serum adipokine profile of obese Zucker rats were assessed. In addition, the fatty acid composition of epididymal and retroperitoneal adipose tissues was determined and a principal component analysis (PCA) was used to assess possible relationships between fatty acids and serum metabolites. Atherogenic diets (2 % cholesterol) were formulated with palm oil and ovine fat and supplemented or not with 1 % of a mixture (1:1) of cis-9, trans-11 and trans-10, cis-12-CLA isomers. CLA-fed animals exhibited lower daily feed intake, final body and liver weights, and hepatic lipids content. Total and LDL-cholesterol levels were increased in CLA-supplemented groups. CLA also promoted higher adiponectin and lower plasminogen activator inhibitor-1 (PAI-1) serum concentrations. In contrast to palm oil diets, ovine fat increased insulin resistance and serum levels of leptin, TNF-alpha and IL-1beta. Epididymal and retroperitoneal adipose tissues had similar deposition of individual fatty acids. The PCA analysis showed that the trans-10, cis-12-CLA isomer was highly associated with adiponectin and PAI-1 levels. Summing up, CLA added to vegetable saturated enriched diets, relative to those from animal origin, seems to improve the serum profile of adipokines and inflammatory markers in obese Zucker rats due to a more favourable fatty acid composition.

Development of a dual-pulse RF driver for an S-band (= 2856 MHz) RF electron linear accelerator

NASA Astrophysics Data System (ADS)

Cha, Sungsu; Kim, Yujong; Lee, Byeong-No; Lee, Byung Cheol; Cha, Hyungki; Ha, Jang Ho; Park, Hyung Dal; Lee, Seung Hyun; Kim, Hui Su; Buaphad, Pikad

2016-04-01

The radiation equipment research division of Korea Atomic Energy Research Institute has developed a Container Inspection System (CIS) using a Radio Frequency (RF) electron linear accelerator for port security. The primary purpose of the CIS is to detect nuclear materials and explosives, as well country-specific prohibited substances, e.g., smuggled. The CIS consists of a 9/6 MeV dualenergy electron linear accelerator for distinguishing between organic and inorganic materials. The accelerator consists of an electron gun, an RF accelerating structure, an RF driver, a modulator, electromagnets, a cooling system, a X-ray generating target, X-ray collimator, a detector, and a container moving system. The RF driver is an important part of the configuration because it is the RF power source: it supplies the RF power to the accelerating structure. A unique aspect of the RF driver is that it generates dual RF power to generate dual energy (9/6 MeV). The advantage of this RF driver is that it can allow the pulse width to vary and can be used to obtain a wide range of energy output, and pulse repetition rates up to 300 Hz. For this reason, 140 W (5 MW - 9 MeV) and 37 W (3.4 MW - 6 MeV) power outputs are available independently. A high power test for 20 minutes demonstrate that stable dual output powers can be generated. Moreover, the dual power can be applied to the accelerator which has stable accelerator operation. In this paper, the design, fabrication and high power test of the RF driver for the RF electron linear accelerator (linac) are presented.

Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy.

PubMed

Tong, Pin; Monahan, Jack; Prendergast, James G D

2017-03-01

Large-scale gene expression datasets are providing an increasing understanding of the location of cis-eQTLs in the human genome and their role in disease. However, little is currently known regarding the extent of regulatory site-sharing between genes. This is despite it having potentially wide-ranging implications, from the determination of the way in which genetic variants may shape multiple phenotypes to the understanding of the evolution of human gene order. By first identifying the location of non-redundant cis-eQTLs, we show that regulatory site-sharing is a relatively common phenomenon in the human genome, with over 10% of non-redundant regulatory variants linked to the expression of multiple nearby genes. We show that these shared, local regulatory sites are linked to high levels of chromatin looping between the regulatory sites and their associated genes. In addition, these co-regulated gene modules are found to be strongly conserved across mammalian species, suggesting that shared regulatory sites have played an important role in shaping human gene order. The association of these shared cis-eQTLs with multiple genes means they also appear to be unusually important in understanding the genetics of human phenotypes and pleiotropy, with shared regulatory sites more often linked to multiple human phenotypes than other regulatory variants. This study shows that regulatory site-sharing is likely an underappreciated aspect of gene regulation and has important implications for the understanding of various biological phenomena, including how the two and three dimensional structures of the genome have been shaped and the potential causes of disease pleiotropy outside coding regions.

In silico modeling of epigenetic-induced changes in photoreceptor cis-regulatory elements.

PubMed

Hossain, Reafa A; Dunham, Nicholas R; Enke, Raymond A; Berndsen, Christopher E

2018-01-01

DNA methylation is a well-characterized epigenetic repressor of mRNA transcription in many plant and vertebrate systems. However, the mechanism of this repression is not fully understood. The process of transcription is controlled by proteins that regulate recruitment and activity of RNA polymerase by binding to specific cis-regulatory sequences. Cone-rod homeobox (CRX) is a well-characterized mammalian transcription factor that controls photoreceptor cell-specific gene expression. Although much is known about the functions and DNA binding specificity of CRX, little is known about how DNA methylation modulates CRX binding affinity to genomic cis-regulatory elements. We used bisulfite pyrosequencing of human ocular tissues to measure DNA methylation levels of the regulatory regions of RHO , PDE6B, PAX6 , and LINE1 retrotransposon repeats. To describe the molecular mechanism of repression, we used molecular modeling to illustrate the effect of DNA methylation on human RHO regulatory sequences. In this study, we demonstrate an inverse correlation between DNA methylation in regulatory regions adjacent to the human RHO and PDE6B genes and their subsequent transcription in human ocular tissues. Docking of CRX to the DNA models shows that CRX interacts with the grooves of these sequences, suggesting changes in groove structure could regulate binding. Molecular dynamics simulations of the RHO promoter and enhancer regions show changes in the flexibility and groove width upon epigenetic modification. Models also demonstrate changes in the local dynamics of CRX binding sites within RHO regulatory sequences which may account for the repression of CRX-dependent transcription. Collectively, these data demonstrate epigenetic regulation of CRX binding sites in human retinal tissue and provide insight into the mechanism of this mode of epigenetic regulation to be tested in future experiments.

Role of cis-trans proline isomerization in the function of pathogenic enterobacterial Periplasmic Binding Proteins

PubMed Central

Cortes-Hernandez, Paulina

2017-01-01

Periplasmic Binding Proteins (PBPs) trap nutrients for their internalization into bacteria by ABC transporters. Ligand binding triggers PBP closure by bringing its two domains together like a Venus flytrap. The atomic determinants that control PBP opening and closure for nutrient capture and release are not known, although it is proposed that opening and ligand release occur while in contact with the ABC transporter for concurrent substrate translocation. In this paper we evaluated the effect of the isomerization of a conserved proline, located near the binding site, on the propensity of PBPs to open and close. ArgT/LAO from Salmonella typhimurium and HisJ from Escherichia coli were studied through molecular mechanics at two different temperatures: 300 and 323 K. Eight microseconds were simulated per protein to analyze protein opening and closure in the absence of the ABC transporter. We show that when the studied proline is in trans, closed empty LAO and HisJ can open. In contrast, with the proline in cis, opening transitions were much less frequent and characterized by smaller changes. The proline in trans also renders the open trap prone to close over a ligand. Our data suggest that the isomerization of this conserved proline modulates the PBP mechanism: the proline in trans allows the exploration of conformational space to produce trap opening and closure, while in cis it restricts PBP movement and could limit ligand release until in productive contact with the ABC transporter. This is the first time that a proline isomerization has been related to the control of a large conformational change like the PBP flytrap mechanism. PMID:29190818

Accurate millimetre and submillimetre rest frequencies for cis- and trans-dithioformic acid, HCSSH

NASA Astrophysics Data System (ADS)

Prudenzano, D.; Laas, J.; Bizzocchi, L.; Lattanzi, V.; Endres, C.; Giuliano, B. M.; Spezzano, S.; Palumbo, M. E.; Caselli, P.

2018-04-01

Context. A better understanding of sulphur chemistry is needed to solve the interstellar sulphur depletion problem. A way to achieve this goal is to study new S-bearing molecules in the laboratory, obtaining accurate rest frequencies for an astronomical search. We focus on dithioformic acid, HCSSH, which is the sulphur analogue of formic acid. Aims: The aim of this study is to provide an accurate line list of the two HCSSH trans and cis isomers in their electronic ground state and a comprehensive centrifugal distortion analysis with an extension of measurements in the millimetre and submillimetre range. Methods: We studied the two isomers in the laboratory using an absorption spectrometer employing the frequency-modulation technique. The molecules were produced directly within a free-space cell by glow discharge of a gas mixture. We measured lines belonging to the electronic ground state up to 478 GHz, with a total number of 204 and 139 new rotational transitions, respectively, for trans and cis isomers. The final dataset also includes lines in the centimetre range available from literature. Results: The extension of the measurements in the mm and submm range lead to an accurate set of rotational and centrifugal distortion parameters. This allows us to predict frequencies with estimated uncertainties as low as 5 kHz at 1 mm wavelength. Hence, the new dataset provided by this study can be used for astronomical search. Frequency lists are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/612/A56

Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique

PubMed Central

Rahmani-Badi, Azadeh; Sepehr, Shayesteh; Fallahi, Hossein; Heidari-Keshel, Saeed

2015-01-01

Many bacterial pathogens use quorum-sensing (QS) signaling to regulate the expression of factors contributing to virulence and persistence. Bacteria produce signals of different chemical classes. The signal molecule, known as diffusible signal factor (DSF), is a cis-unsaturated fatty acid that was first described in the plant pathogen Xanthomonas campestris. Previous works have shown that human pathogen, Pseudomonas aeruginosa, also synthesizes a structurally related molecule, characterized as cis-2-decenoic acid (C10: Δ2, CDA) that induces biofilm dispersal by multiple types of bacteria. Furthermore, CDA has been shown to be involved in inter-kingdom signaling that modulates fungal behavior. Therefore, an understanding of its signaling mechanism could suggest strategies for interference, with consequences for disease control. To identify the components of CDA signaling pathway in this pathogen, a comparative transcritpome analysis was conducted, in the presence and absence of CDA. A protein-protein interaction (PPI) network for differentially expressed (DE) genes with known function was then constructed by STRING and Cytoscape. In addition, the effects of CDA in combination with antimicrobial agents on the biofilm surface area and bacteria viability were evaluated using fluorescence microscopy and digital image analysis. Microarray analysis identified 666 differentially expressed genes in the presence of CDA and gene ontology (GO) analysis revealed that in P. aeruginosa, CDA mediates dispersion of biofilms through signaling pathways, including enhanced motility, metabolic activity, virulence as well as persistence at different temperatures. PPI data suggested that a cluster of five genes (PA4978, PA4979, PA4980, PA4982, PA4983) is involved in the CDA synthesis and perception. Combined treatments using both CDA and antimicrobial agents showed that following exposure of the biofilms to CDA, remaining cells on the surface were easily removed and killed by antimicrobials. PMID:25972860

The Visual Cycle in the Inner Retina of Chicken and the Involvement of Retinal G-Protein-Coupled Receptor (RGR).

PubMed

Díaz, Nicolás M; Morera, Luis P; Tempesti, Tomas; Guido, Mario E

2017-05-01

The vertebrate retina contains typical photoreceptor (PR) cones and rods responsible for day/night vision, respectively, and intrinsically photosensitive retinal ganglion cells (ipRGCs) involved in the regulation of non-image-forming tasks. Rhodopsin/cone opsin photopigments in visual PRs or melanopsin (Opn4) in ipRGCs utilizes retinaldehyde as a chromophore. The retinoid regeneration process denominated as "visual cycle" involves the retinal pigment epithelium (RPE) or Müller glial cells. Opn4, on the contrary, has been characterized as a bi/tristable photopigment, in which a photon of one wavelength isomerizes 11-cis to all-trans retinal (Ral), with a second photon re-isomerizing it back. However, it is unknown how the chromophore is further metabolized in the inner retina. Nor is it yet clear whether an alternative secondary cycle occurs involving players such as the retinal G-protein-coupled receptor (RGR), a putative photoisomerase of unidentified inner retinal activity. Here, we investigated the role of RGR in retinoid photoisomerization in Opn4x (Xenopus ortholog) (+) RGC primary cultures free of RPE and other cells from chicken embryonic retinas. Opn4x (+) RGCs display significant photic responses by calcium fluorescent imaging and photoisomerize exogenous all-trans to 11-cis Ral and other retinoids. RGR was found to be expressed in developing retina and in primary cultures; when its expression was knocked down, the levels of 11-cis, all-trans Ral, and all-trans retinol in cultures exposed to light were significantly higher and those in all-trans retinyl esters lower than in dark controls. The results support a novel role for RGR in ipRGCs to modulate retinaldehyde levels in light, keeping the balance of inner retinal retinoid pools.

Exploring international clinical education in US-based programs: identifying common practices and modifying an existing conceptual model of international service-learning.

PubMed

Pechak, Celia M; Black, Jill D

2014-02-01

Increasingly physical therapist students complete part of their clinical training outside of their home country. This trend is understudied. The purposes of this study were to: (1) explore, in depth, various international clinical education (ICE) programs; and (2) determine whether the Conceptual Model of Optimal International Service-Learning (ISL) could be applied or adapted to represent ICE. Qualitative content analysis was used to analyze ICE programs and consider modification of an existing ISL conceptual model for ICE. Fifteen faculty in the United States currently involved in ICE were interviewed. The interview transcriptions were systematically analyzed by two researchers. Three models of ICE practices emerged: (1) a traditional clinical education model where local clinical instructors (CIs) focus on the development of clinical skills; (2) a global health model where US-based CIs provide the supervision in the international setting, and learning outcomes emphasized global health and cultural competency; and (3) an ICE/ISL hybrid where US-based CIs supervise the students, and the foci includes community service. Additionally the data supported revising the ISL model's essential core conditions, components and consequence for ICE. The ICE conceptual model may provide a useful framework for future ICE program development and research.

Regulation of cytoplasmic mRNA decay

PubMed Central

Schoenberg, Daniel R.; Maquat, Lynne E.

2012-01-01

Discoveries made over the past 20 years highlight the importance of mRNA decay as a means to modulate gene expression and thereby protein production. Up until recently, studies focused largely on identifying cis-acting sequences that serve as mRNA stability or instability elements, the proteins that bind these elements, how the process of translation influences mRNA decay, and the ribonucleases that catalyze decay. Now, current studies have begun to elucidate how the decay process is regulated. This review examines our current understanding of how mammalian-cell mRNA decay is controlled by different signaling pathways and lays out a framework for future research. PMID:22392217

Replication timing and nuclear structure.

PubMed

Fu, Haiqing; Baris, Adrian; Aladjem, Mirit I

2018-06-01

DNA replication proceeds along spatially and temporally coordinated patterns within the nucleus, thus protecting the genome during the synthesis of new genetic material. While we have been able to visualize replication patterns on DNA fibers for 50 years, recent developments and discoveries have provided a greater insight into how DNA replication is controlled. In this review, we highlight many of these discoveries. Of great interest are the physiological role of the replication timing program, cis and trans-acting factors that modulate replication timing and the effects of chromatin structure on the replication timing program. We also discuss future directions in the study of replication timing. Published by Elsevier Ltd.

Development and Testing of the Contaminant Insensitive Sublimator

NASA Technical Reports Server (NTRS)

Leimkuehler, Thomas O.; Stephan, Ryan A.; Westheimer, David T.

2006-01-01

Sublimators have been used for heat rejection for a variety of space applications including the Apollo Lunar Module and the Extravehicular Mobility Unit (EMU). Some of the attractive features of sublimators are that they are compact, lightweight, and self-regulating. One of the drawbacks of previous designs has been sensitivity to non-volatile contamination in the feedwater, which can clog relatively small pores (approx.3-6 microns) in the porous plates where ice forms and sublimates. A new design that is less sensitive to contaminants is being developed at the Johnson Space Center. This paper describes the design, fabrication, and testing of the Contaminant Insensitive Sublimator (CIS) Engineering Development Unit (EDU).

Research-grade CMOS image sensors for demanding space applications

NASA Astrophysics Data System (ADS)

Saint-Pé, Olivier; Tulet, Michel; Davancens, Robert; Larnaudie, Franck; Magnan, Pierre; Corbière, Franck; Martin-Gonthier, Philippe; Belliot, Pierre

2004-06-01

Imaging detectors are key elements for optical instruments and sensors on board space missions dedicated to Earth observation (high resolution imaging, atmosphere spectroscopy...), Solar System exploration (micro cameras, guidance for autonomous vehicle...) and Universe observation (space telescope focal planes, guiding sensors...). This market has been dominated by CCD technology for long. Since the mid-90s, CMOS Image Sensors (CIS) have been competing with CCDs for more and more consumer domains (webcams, cell phones, digital cameras...). Featuring significant advantages over CCD sensors for space applications (lower power consumption, smaller system size, better radiations behaviour...), CMOS technology is also expanding in this field, justifying specific R&D and development programs funded by national and European space agencies (mainly CNES, DGA, and ESA). All along the 90s and thanks to their increasingly improving performances, CIS have started to be successfully used for more and more demanding applications, from vision and control functions requiring low-level performances to guidance applications requiring medium-level performances. Recent technology improvements have made possible the manufacturing of research-grade CIS that are able to compete with CCDs in the high-performances arena. After an introduction outlining the growing interest of optical instruments designers for CMOS image sensors, this talk will present the existing and foreseen ways to reach high-level electro-optics performances for CIS. The developments of CIS prototypes built using an imaging CMOS process and of devices based on improved designs will be presented.

The effects of mental fatigue on cricket-relevant performance among elite players.

PubMed

Veness, Darren; Patterson, Stephen David; Jeffries, Owen; Waldron, Mark

2017-12-01

This study investigated the effects of a mentally fatiguing test on physical tasks among elite cricketers. In a cross-over design, 10 elite male cricket players from a professional club performed a cricket run-two test, a Batak Lite reaction time test and a Yo-Yo-Intermittent Recovery Level 1 (Yo-Yo-IR1) test, providing a rating of perceived exertion (RPE) after completing a 30-min Stroop test (mental fatigue condition) or 30-min control condition. Perceived fatigue was assessed before and after the two conditions and motivation was measured before testing. There were post-treatment differences in the perception of mental fatigue (P < 0.001; d = -7.82, 95% CIs = -9.05-6.66; most likely). Cricket run-two (P = 0.002; d = -0.51, 95% CIs = -0.72-0.30; very likely), Yo-Yo-IR1 distance (P = 0.023; d = 0.39, 95% CIs = 0.14-0.64; likely) and RPE (P = 0.001; d = -1.82, 95% CIs = -2.49-1.14; most likely) were negatively affected by mental fatigue. The Batak Lite test was not affected (P = 0.137), yet a moderate (d = 0.41, 95% CIs = -0.05-0.87) change was likely. Mental fatigue, induced by an app-based Stroop test, negatively affected cricket-relevant performance.

Research-grade CMOS image sensors for demanding space applications

NASA Astrophysics Data System (ADS)

Saint-Pé, Olivier; Tulet, Michel; Davancens, Robert; Larnaudie, Franck; Magnan, Pierre; Corbière, Franck; Martin-Gonthier, Philippe; Belliot, Pierre

2017-11-01

Imaging detectors are key elements for optical instruments and sensors on board space missions dedicated to Earth observation (high resolution imaging, atmosphere spectroscopy...), Solar System exploration (micro cameras, guidance for autonomous vehicle...) and Universe observation (space telescope focal planes, guiding sensors...). This market has been dominated by CCD technology for long. Since the mid- 90s, CMOS Image Sensors (CIS) have been competing with CCDs for more and more consumer domains (webcams, cell phones, digital cameras...). Featuring significant advantages over CCD sensors for space applications (lower power consumption, smaller system size, better radiations behaviour...), CMOS technology is also expanding in this field, justifying specific R&D and development programs funded by national and European space agencies (mainly CNES, DGA, and ESA). All along the 90s and thanks to their increasingly improving performances, CIS have started to be successfully used for more and more demanding applications, from vision and control functions requiring low-level performances to guidance applications requiring medium-level performances. Recent technology improvements have made possible the manufacturing of research-grade CIS that are able to compete with CCDs in the high-performances arena. After an introduction outlining the growing interest of optical instruments designers for CMOS image sensors, this talk will present the existing and foreseen ways to reach high-level electro-optics performances for CIS. The developments of CIS prototypes built using an imaging CMOS process and of devices based on improved designs will be presented.

Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability.

PubMed

Schweiger, Regev; Fisher, Eyal; Rahmani, Elior; Shenhav, Liat; Rosset, Saharon; Halperin, Eran

2018-06-22

Estimation of heritability is an important task in genetics. The use of linear mixed models (LMMs) to determine narrow-sense single-nucleotide polymorphism (SNP)-heritability and related quantities has received much recent attention, due of its ability to account for variants with small effect sizes. Typically, heritability estimation under LMMs uses the restricted maximum likelihood (REML) approach. The common way to report the uncertainty in REML estimation uses standard errors (SEs), which rely on asymptotic properties. However, these assumptions are often violated because of the bounded parameter space, statistical dependencies, and limited sample size, leading to biased estimates and inflated or deflated confidence intervals (CIs). In addition, for larger data sets (e.g., tens of thousands of individuals), the construction of SEs itself may require considerable time, as it requires expensive matrix inversions and multiplications. Here, we present FIESTA (Fast confidence IntErvals using STochastic Approximation), a method for constructing accurate CIs. FIESTA is based on parametric bootstrap sampling, and, therefore, avoids unjustified assumptions on the distribution of the heritability estimator. FIESTA uses stochastic approximation techniques, which accelerate the construction of CIs by several orders of magnitude, compared with previous approaches as well as to the analytical approximation used by SEs. FIESTA builds accurate CIs rapidly, for example, requiring only several seconds for data sets of tens of thousands of individuals, making FIESTA a very fast solution to the problem of building accurate CIs for heritability for all data set sizes.

Dissection of expression-quantitative trait locus and allele specificity using a haploid/diploid plant system - insights into compensatory evolution of transcriptional regulation within populations.

PubMed

Verta, Jukka-Pekka; Landry, Christian R; MacKay, John

2016-07-01

Regulation of gene expression plays a central role in translating genotypic variation into phenotypic variation. Dissection of the genetic basis of expression variation is key to understanding how expression regulation evolves. Such analyses remain challenging in contexts where organisms are outbreeding, highly heterozygous and long-lived such as in the case of conifer trees. We developed an RNA sequencing (RNA-seq)-based approach for both expression-quantitative trait locus (eQTL) mapping and the detection of cis-acting (allele-specific) vs trans-acting (non-allele-specific) eQTLs. This method can be potentially applied to many conifers. We used haploid and diploid meiotic seed tissues of a single self-fertilized white spruce (Picea glauca) individual to dissect eQTLs according to linkage and allele specificity. The genetic architecture of local eQTLs linked to the expressed genes was particularly complex, consisting of cis-acting, trans-acting and, surprisingly, compensatory cis-trans effects. These compensatory effects influence expression in opposite directions and are neutral when combined in homozygotes. Nearly half of local eQTLs were under compensation, indicating that close linkage between compensatory cis-trans factors is common in spruce. Compensated genes were overrepresented in developmental and cell organization functions. Our haploid-diploid eQTL analysis in spruce revealed that compensatory cis-trans eQTLs segregate within populations and evolve in close genetic linkage. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Comparing apples and oranges: the Community Intercomparison Suite

NASA Astrophysics Data System (ADS)

Schutgens, Nick; Stier, Philip; Pascoe, Stephen

2014-05-01

Visual representation and comparison of geoscientific datasets presents a huge challenge due to the large variety of file formats and spatio-temporal sampling of data (be they observations or simulations). The Community Intercomparison Suite attempts to greatly simplify these tasks for users by offering an intelligent but simple command line tool for visualisation and colocation of diverse datasets. In addition, CIS can subset and aggregate large datasets into smaller more manageable datasets. Our philosophy is to remove as much as possible the need for specialist knowledge by the user of the structure of a dataset. The colocation of observations with model data is as simple as: "cis col ::" which will resample the simulation data to the spatio-temporal sampling of the observations, contingent on a few user-defined options that specify a resampling kernel. CIS can deal with both gridded and ungridded datasets of 2, 3 or 4 spatio-temporal dimensions. It can handle different spatial coordinates (e.g. longitude or distance, altitude or pressure level). CIS supports both HDF, netCDF and ASCII file formats. The suite is written in Python with entirely publicly available open source dependencies. Plug-ins allow a high degree of user-moddability. A web-based developer hub includes a manual and simple examples. CIS is developed as open source code by a specialist IT company under supervision of scientists from the University of Oxford as part of investment in the JASMIN superdatacluster facility at the Centre of Environmental Data Archival.

Therans-3-enoic acids ofAster alpinus andArctium minus seed oils.

PubMed

Morris, L J; Marshall, M O; Hammond, E W

1968-01-01

Thetrans-3-enoic acids ofAster alpinus (dwarf aster, rock aster) andArctium minus (burdock) seed oils have been isolated and characterized.Arctium seed oil containstrans-3,cis-9,cis-12-octadecatrienoic acid (9.9%), andAster oil containstrans-3-hexadecenoic (7.1%),rans-3-octadecenoic (1.9%),trans-3,cis-9-octadecadienoic (3.0%),a ndtrans-3,cis-9,cis-12-octadecatrienoic (13.7%) acids.Aster oil also has an epoxy acid as a minor constituent (ca. 2.0%), which has been identified ascis-9,10-epoxy-cis-12-octadecenoic acid.

The efficacy of 9-cis retinoic acid in experimental models of cancer.

PubMed

Gottardis, M M; Lamph, W W; Shalinsky, D R; Wellstein, A; Heyman, R A

1996-01-01

9-cis retinoic acid (9-cis RA) is a retinoid receptor pan-agonist that binds with high affinity to both retinoic acid receptors (RARs) and retinoid X receptors (RXRs). Using a variety of in vivo and in vitro cancer models, we present experimental data that 9-cis RA has activity as a potential chemotherapeutic agent. Treatment of the human promyelocytic leukemia cell line HL-60 with 9-cis RA decreases cell proliferation, increases cell differentiation, and increases apoptosis. Induction of apoptosis correlates with an increase in tissue transglutaminase (type II) activity. In vivo, 9-cis RA induces complete tumor regression of an early passage human lip squamous cell carcinoma xenograft. Finally, 9-cis RA inhibits the anchorage-independent growth of the human breast cancer cell lines MCF-7 and LY2 (an antiestrogen-resistant MCF-7 variant). Transient co-transfection assays indicate that 9-cis RA inhibits estrogen receptor transcription of an ERE-tk-LUC reporter through RAR or RXR receptors. These data suggest that retinoid receptors can antagonize estrogen-dependent transcription and provides one possible mechanism for the inhibition of cell growth by 9-cis RA in breast cancer cell lines. In summary, these findings present evidence that 9-cis RA has a wide range of activities in human cancer models.

PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches

PubMed Central

Fujibuchi, Wataru; Anderson, John S. J.; Landsman, David

2001-01-01

Consensus pattern and matrix-based searches designed to predict cis-acting transcriptional regulatory sequences have historically been subject to large numbers of false positives. We sought to decrease false positives by incorporating expression profile data into a consensus pattern-based search method. We have systematically analyzed the expression phenotypes of over 6000 yeast genes, across 121 expression profile experiments, and correlated them with the distribution of 14 known regulatory elements over sequences upstream of the genes. Our method is based on a metric we term probabilistic element assessment (PEA), which is a ranking of potential sites based on sequence similarity in the upstream regions of genes with similar expression phenotypes. For eight of the 14 known elements that we examined, our method had a much higher selectivity than a naïve consensus pattern search. Based on our analysis, we have developed a web-based tool called PROSPECT, which allows consensus pattern-based searching of gene clusters obtained from microarray data. PMID:11574681

The EU-project United4Health: User-Centred Design and Evaluation of a Collaborative Information System for a Norwegian Telehealth Service.

PubMed

Smaradottir, Berglind; Gerdes, Martin; Martinez, Santiago; Fensli, Rune

2015-01-01

This study presents the user-centred design and evaluation process of a Collaborative Information System (CIS), developed for a new telehealth service for remote monitoring of chronic obstructive pulmonary disease patients after hospital discharge. The CIS was designed based on the information gathered in a workshop, where target end-users described the context of use, a telehealth workflow and their preferred ways of interaction with the solution. Evaluation of the iterative refinements were made through user tests, semi-structured interviews and a questionnaire. A field trial reported results on the ease of use and user satisfaction during the interaction with the fully developed system. The implemented CIS was successfully deployed within the secured Norwegian Health Network. The research was a result of cooperation between international partners within the EU FP7 project United4Health.

Demonstration of an efficient cooling approach for SBIRS-Low

NASA Astrophysics Data System (ADS)

Nieczkoski, S. J.; Myers, E. A.

2002-05-01

The Space Based Infrared System-Low (SBIRS-Low) segment is a near-term Air Force program for developing and deploying a constellation of low-earth orbiting observation satellites with gimbaled optics cooled to cryogenic temperatures. The optical system design and requirements present unique challenges that make conventional cooling approaches both complicated and risky. The Cryocooler Interface System (CIS) provides a remote, efficient, and interference-free means of cooling the SBIRS-Low optics. Technology Applications Inc. (TAI), through a two-phase Small Business Innovative Research (SBIR) program with Air Force Research Laboratory (AFRL), has taken the CIS from initial concept feasibility through the design, build, and test of a prototype system. This paper presents the development and demonstration testing of the prototype CIS. Prototype system testing has demonstrated the high efficiency of this cooling approach, making it an attractive option for SBIRS-Low and other sensitive optical and detector systems that require low-impact cryogenic cooling.

Electrostatics of polymer translocation events in electrolyte solutions.

PubMed

Buyukdagli, Sahin; Ala-Nissila, T

2016-07-07

We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based membranes are driven by a competition between the repulsive DNA-image-charge interactions and the attractive coupling between the DNA segments on the trans and the cis sides of the membrane. The latter effect is induced by the reduction of the coupling by the dielectric membrane. In strong salt solutions where the repulsive image-charge effects dominate the attractive trans-cis coupling, the DNA molecule encounters a translocation barrier of ≈10 kBT. In dilute electrolytes, the trans-cis coupling takes over image-charge forces and the membrane becomes a metastable attraction point that can trap translocating polymers over long time intervals. This mechanism can be used in translocation experiments in order to control DNA motion by tuning the salt concentration of the solution.

A Veterinary Comparative Counseling Elective Featuring Web-based, Student-created, Client Information Sheets.

PubMed

Miller, Jennifer C; Sehgal, Inder

2016-02-25

To design and implement a course in Companion Animal Comparative Counseling that would expose students (N=38) to essential elements of veterinary therapeutics and provide them with the opportunity to apply their knowledge by writing and posting client information sheets (CIS) on an open web site. The elective course was limited to companion animals. Nine different topics were covered over the semester. Class sessions included a didactic component, trivia questions, and field trips. There were 4 major graded assessments: an examination on foundation knowledge, followed by two comparative counseling assessments and evaluation of group-composed CIS. Attendance and participation were also considered. The class learned comparative disease states, how to counsel on common pet prescriptions, where to access informatics about specific veterinary drugs, and how to create their own CIS. As pharmacists, these students may have improved their training in veterinary comparative pharmacy.

A Veterinary Comparative Counseling Elective Featuring Web-based, Student-created, Client Information Sheets

PubMed Central

Miller, Jennifer C.

2016-01-01

Objective. To design and implement a course in Companion Animal Comparative Counseling that would expose students (N=38) to essential elements of veterinary therapeutics and provide them with the opportunity to apply their knowledge by writing and posting client information sheets (CIS) on an open web site. Design. The elective course was limited to companion animals. Nine different topics were covered over the semester. Class sessions included a didactic component, trivia questions, and field trips. There were 4 major graded assessments: an examination on foundation knowledge, followed by two comparative counseling assessments and evaluation of group-composed CIS. Attendance and participation were also considered. Assessment. The class learned comparative disease states, how to counsel on common pet prescriptions, where to access informatics about specific veterinary drugs, and how to create their own CIS. Conclusion. As pharmacists, these students may have improved their training in veterinary comparative pharmacy. PMID:26941441

PalmCIS: A Wireless Handheld Application for Satisfying Clinician Information Needs

PubMed Central

Chen, Elizabeth S.; Mendonça, Eneida A.; McKnight, Lawrence K.; Stetson, Peter D.; Lei, Jianbo; Cimino, James J.

2004-01-01

Wireless handheld technology provides new ways to deliver and present information. As with any technology, its unique features must be taken into consideration and its applications designed accordingly. In the clinical setting, availability of needed information can be crucial during the decision-making process. Preliminary studies performed at New York Presbyterian Hospital (NYPH) determined that there are inadequate access to information and ineffective communication among clinicians (potential proximal causes of medical errors). In response to these findings, the authors have been developing extensions to their Web-based clinical information system including PalmCIS, an application that provides access to needed patient information via a wireless personal digital assistant (PDA). The focus was on achieving end-to-end security and developing a highly usable system. This report discusses the motivation behind PalmCIS, design and development of the system, and future directions. PMID:14527976

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

PubMed

Vierstra, Jeff; Rynes, Eric; Sandstrom, Richard; Zhang, Miaohua; Canfield, Theresa; Hansen, R Scott; Stehling-Sun, Sandra; Sabo, Peter J; Byron, Rachel; Humbert, Richard; Thurman, Robert E; Johnson, Audra K; Vong, Shinny; Lee, Kristen; Bates, Daniel; Neri, Fidencio; Diegel, Morgan; Giste, Erika; Haugen, Eric; Dunn, Douglas; Wilken, Matthew S; Josefowicz, Steven; Samstein, Robert; Chang, Kai-Hsin; Eichler, Evan E; De Bruijn, Marella; Reh, Thomas A; Skoultchi, Arthur; Rudensky, Alexander; Orkin, Stuart H; Papayannopoulou, Thalia; Treuting, Piper M; Selleri, Licia; Kaul, Rajinder; Groudine, Mark; Bender, M A; Stamatoyannopoulos, John A

2014-11-21

To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes. Copyright © 2014, American Association for the Advancement of Science.

Utilizing Semantic Big Data for realizing a National-scale Infrastructure Vulnerability Analysis System

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

Chinthavali, Supriya; Shankar, Mallikarjun

Critical Infrastructure systems(CIs) such as energy, water, transportation and communication are highly interconnected and mutually dependent in complex ways. Robust modeling of CIs interconnections is crucial to identify vulnerabilities in the CIs. We present here a national-scale Infrastructure Vulnerability Analysis System (IVAS) vision leveraging Se- mantic Big Data (SBD) tools, Big Data, and Geographical Information Systems (GIS) tools. We survey existing ap- proaches on vulnerability analysis of critical infrastructures and discuss relevant systems and tools aligned with our vi- sion. Next, we present a generic system architecture and discuss challenges including: (1) Constructing and manag- ing a CI network-of-networks graph,more » (2) Performing analytic operations at scale, and (3) Interactive visualization of ana- lytic output to generate meaningful insights. We argue that this architecture acts as a baseline to realize a national-scale network based vulnerability analysis system.« less

Short communication: Genetic study of methane production predicted from milk fat composition in dairy cows.

PubMed

van Engelen, S; Bovenhuis, H; Dijkstra, J; van Arendonk, J A M; Visker, M H P W

2015-11-01

Dairy cows produce enteric methane, a greenhouse gas with 25 times the global warming potential of CO2. Breeding could make a permanent, cumulative, and long-term contribution to methane reduction. Due to a lack of accurate, repeatable, individual methane measurements needed for breeding, indicators of methane production based on milk fatty acids have been proposed. The aim of the present study was to quantify the genetic variation for predicted methane yields. The milk fat composition of 1,905 first-lactation Dutch Holstein-Friesian cows was used to investigate 3 different predicted methane yields (g/kg of DMI): Methane1, Methane2, and Methane3. Methane1 was based on the milk fat proportions of C17:0anteiso, C18:1 rans-10+11, C18:1 cis-11, and C18:1 cis-13 (R(2)=0.73). Methane2 was based on C4:0, C18:0, C18:1 trans-10+11, and C18:1 cis-11 (R(2)=0.70). Methane3 was based on C4:0, C6:0, and C18:1 trans-10+11 (R(2)=0.63). Predicted methane yields were demonstrated to be heritable traits, with heritabilities between 0.12 and 0.44. Breeding can, thus, be used to decrease methane production predicted based on milk fatty acids. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT

PubMed Central

Cheung, Tom Hiu; Kwan, Yin Lam; Hamady, Micah; Liu, Xuedong

2006-01-01

Deciphering gene regulatory networks requires the systematic identification of functional cis-acting regulatory elements. We present a suite of web-based bioinformatics tools, called GeneACT , that can rapidly detect evolutionarily conserved transcription factor binding sites or microRNA target sites that are either unique or over-represented in differentially expressed genes from DNA microarray data. GeneACT provides graphic visualization and extraction of common regulatory sequence elements in the promoters and 3'-untranslated regions that are conserved across multiple mammalian species. PMID:17064417

Abnormally high levels of anti-collagen type IV IgG antibodies in the serum of patients with a clinically isolated syndrome correlate with an increased risk of conversion to MS.

PubMed

Sadarzanska-Terzieva, Behidhe; Tzvetanov, Plamen; Hegde, Vishwajit; Al-Hashel, Jasem Y; Rousseff, Rossen Т; Haralanov, Lubomir; Stamenov, Boyko; Atanassova, Milena; Marinova, Iveta; Marinova, Anna; Rousseva, Adelaida

2015-06-01

To investigate anti-collagen-type-IV serum antibodies (ACIVAbs) levels in patients with clinically isolated syndrome (CIS), and to determine their predictive value for conversion into multiple sclerosis (MS). Serum levels of IgM and IgG ACIVAbs in 40 untreated patients with CIS (13 male, mean age 34.85±11.4 years, range 16-58 years) were compared to those of 27 gender- and age-matched healthy controls. ACIVAbs were quantified using ELISA. Patients were followed for 5 years by clinical examination and MRI studies. Thirty two patients (80%) converted to MS (converted CIS, C-CIS group) while the rest 8 (20%) did not (non-converted CIS, NC-CIS). The C-CIS patients had significantly higher levels of IgG ACIVAb compared to NC-CIS while the IgM levels did not differ between C-CIS and NC-CIS. Conversion to MS occurred in 66% of patients with IgG ACIVAbs levels exceeding the 95th percentile found in controls. IgG ACIVAbs levels correlated positively with the serum levels of matrix metalloproteinases type 9 (r = 0.37; p = 0.003) and inversely with those of tissue inhibitor of metalloproteinases type 1 (r = -0.43; p = 0.0008). High serum levels of IgG ACIVAbs in patients with CIS correlate strongly with increased risk of conversion to MS. Copyright © 2015 Elsevier B.V. All rights reserved.