Connections between Transcription Downstream of Genes and cis-SAGe Chimeric RNA.

PubMed

Chwalenia, Katarzyna; Qin, Fujun; Singh, Sandeep; Tangtrongstittikul, Panjapon; Li, Hui

2017-11-22

cis-Splicing between adjacent genes (cis-SAGe) is being recognized as one way to produce chimeric fusion RNAs. However, its detail mechanism is not clear. Recent study revealed induction of transcriptions downstream of genes (DoGs) under osmotic stress. Here, we investigated the influence of osmotic stress on cis-SAGe chimeric RNAs and their connection to DoGs. We found,the absence of induction of at least some cis-SAGe fusions and/or their corresponding DoGs at early time point(s). In fact, these DoGs and their cis-SAGe fusions are inversely correlated. This negative correlation was changed to positive at a later time point. These results suggest a direct competition between the two categories of transcripts when total pool of readthrough transcripts is limited at an early time point. At a later time point, DoGs and corresponding cis-SAGe fusions are both induced, indicating that total readthrough transcripts become more abundant. Finally, we observed overall enhancement of cis-SAGe chimeric RNAs in KCl-treated samples by RNA-Seq analysis.

3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information-rich hydropathic interaction environments described by maps.

PubMed

Ahmed, Mostafa H; Koparde, Vishal N; Safo, Martin K; Neel Scarsdale, J; Kellogg, Glen E

2015-06-01

Sidechain rotamer libraries are obtained through exhaustive statistical analysis of existing crystallographic structures of proteins and have been applied in multiple aspects of structural biology, for example, crystallography of relatively low-resolution structures, in homology model building and in biomolecular NMR. Little is known, however, about the driving forces that lead to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines reveals the environment around each, in terms of hydrophobic (π-π stacking, etc.) and polar (hydrogen bonding, etc.) interactions. After partitioning the tyrosines into backbone-dependent (ϕ, ψ) bins, a map similarity metric based on the correlation coefficient was applied to each map-map pair to build matrices suitable for clustering with k-means. The first bin (-200° ≤ ϕ < -155°; -205° ≤ ψ < -160°), representing 631 tyrosines, reduced to 14 unique hydropathic environments, with most diversity arising from favorable hydrophobic interactions with many different residue partner types. Polar interactions for tyrosine include surprisingly ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the tyrosine backbone. The memberships of all but one of the 14 environments are dominated (>50%) by a single χ(1)/χ(2) rotamer. The last environment has weak or no interactions with the tyrosine ring and its χ(1)/χ(2) rotamer is indeterminate, which is consistent with it being composed of mostly surface residues. Each tyrosine residue attempts to fulfill its hydropathic valence and thus, structural water molecules are seen in a variety of roles throughout protein structure. © 2015 Wiley Periodicals, Inc.

Identification of four rotamers of m-methoxystyrene by resonant two-photon ionization and mass analyzed threshold ionization spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Yanqi; Tzeng, Sheng Yuan; Shivatare, Vidya; Takahashi, Kaito; Zhang, Bing; Tzeng, Wen Bih

2015-03-01

We report the vibronic and cation spectra of four rotamers of m-methoxystyrene, recorded by using the two-color resonant two-photon ionization and mass-analyzed threshold ionization techniques. The excitation energies of the S1← S0 electronic transition are found to be 32 767, 32 907, 33 222, and 33 281 cm-1, and the corresponding adiabatic ionization energies are 65 391, 64 977, 65 114, and 64 525 cm-1 for these isomeric species. Most of the observed active vibrations in the electronically excited S1 and cationic ground D0 states involve in-plane ring deformation and substituent-sensitive bending motions. It is found that the relative orientation of the methoxyl with respect to the vinyl group does not influence the vibrational frequencies of the ring-substituent bending modes. The two dimensional potential energy surface calculations support our experimental finding that the isomerization is restricted in the S1 and D0 states.

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.

Biosynthesis of cis,cis-muconic acid and its aromatic precursors, catechol and protocatechuic acid, from renewable feedstocks by Saccharomyces cerevisiae.

PubMed

Weber, Christian; Brückner, Christine; Weinreb, Sheila; Lehr, Claudia; Essl, Christine; Boles, Eckhard

2012-12-01

Adipic acid is a high-value compound used primarily as a precursor for the synthesis of nylon, coatings, and plastics. Today it is produced mainly in chemical processes from petrochemicals like benzene. Because of the strong environmental impact of the production processes and the dependence on fossil resources, biotechnological production processes would provide an interesting alternative. Here we describe the first engineered Saccharomyces cerevisiae strain expressing a heterologous biosynthetic pathway converting the intermediate 3-dehydroshikimate of the aromatic amino acid biosynthesis pathway via protocatechuic acid and catechol into cis,cis-muconic acid, which can be chemically dehydrogenated to adipic acid. The pathway consists of three heterologous microbial enzymes, 3-dehydroshikimate dehydratase, protocatechuic acid decarboxylase composed of three different subunits, and catechol 1,2-dioxygenase. For each heterologous reaction step, we analyzed several potential candidates for their expression and activity in yeast to compose a functional cis,cis-muconic acid synthesis pathway. Carbon flow into the heterologous pathway was optimized by increasing the flux through selected steps of the common aromatic amino acid biosynthesis pathway and by blocking the conversion of 3-dehydroshikimate into shikimate. The recombinant yeast cells finally produced about 1.56 mg/liter cis,cis-muconic acid.

CisMiner: Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining

PubMed Central

Navarro, Carmen; Lopez, Francisco J.; Cano, Carlos; Garcia-Alcalde, Fernando; Blanco, Armando

2014-01-01

Eukaryotic gene control regions are known to be spread throughout non-coding DNA sequences which may appear distant from the gene promoter. Transcription factors are proteins that coordinately bind to these regions at transcription factor binding sites to regulate gene expression. Several tools allow to detect significant co-occurrences of closely located binding sites (cis-regulatory modules, CRMs). However, these tools present at least one of the following limitations: 1) scope limited to promoter or conserved regions of the genome; 2) do not allow to identify combinations involving more than two motifs; 3) require prior information about target motifs. In this work we present CisMiner, a novel methodology to detect putative CRMs by means of a fuzzy itemset mining approach able to operate at genome-wide scale. CisMiner allows to perform a blind search of CRMs without any prior information about target CRMs nor limitation in the number of motifs. CisMiner tackles the combinatorial complexity of genome-wide cis-regulatory module extraction using a natural representation of motif combinations as itemsets and applying the Top-Down Fuzzy Frequent- Pattern Tree algorithm to identify significant itemsets. Fuzzy technology allows CisMiner to better handle the imprecision and noise inherent to regulatory processes. Results obtained for a set of well-known binding sites in the S. cerevisiae genome show that our method yields highly reliable predictions. Furthermore, CisMiner was also applied to putative in-silico predicted transcription factor binding sites to identify significant combinations in S. cerevisiae and D. melanogaster, proving that our approach can be further applied genome-wide to more complex genomes. CisMiner is freely accesible at: http://genome2.ugr.es/cisminer. CisMiner can be queried for the results presented in this work and can also perform a customized cis-regulatory module prediction on a query set of transcription factor binding sites provided by

Synthesis, structural characterization and conversion of dinuclear iron-sulfur clusters containing the disulfide ligand: [Cp*Fe(μ-η2:η2-bdt)(cis-μ-η1:η1-S2)FeCp*], [Cp*Fe(μ-S(C6H4S2))(cis-μ-η1:η1-S2)FeCp*], and [{Cp*Fe(bdt)}2(trans-μ-η1:η1-S2)].

PubMed

Ji, Xiaoxiao; Tong, Peng; Yang, Dawei; Wang, Baomin; Zhao, Jinfeng; Li, Yang; Qu, Jingping

2017-03-21

The treatment of [Cp*Fe(μ-η 2 :η 4 -bdt)FeCp*] (1, Cp* = η 5 -C 5 Me 5 , bdt = benzene-1,2-dithiolate) with 1/4 equiv. of elemental sulfur (S 8 ) gave a dinuclear iron-sulfur cluster [Cp*Fe(μ-η 2 :η 2 -bdt)(cis-μ-η 1 :η 1 -S 2 )FeCp*] (2), which contains a cis-1,2-disulfide ligand. When complex 2 further interacted with 1/8 equiv. of S 8 , another sulfur atom inserted into an Fe-S bond to give a rare product [Cp*Fe(μ-S(C 6 H 4 S 2 ))(cis-μ-η 1 :η 1 -S 2 )FeCp*] (3). Unexpectedly, a trans-1,2 disulfide-bridged diiron complex [{Cp*Fe(bdt)} 2 (trans-μ-η 1 :η 1 -S 2 )] (4) was isolated from the reaction of complex 1 with 1/2 equiv. of S 8 , which represents a structural isomer of [2Fe-2S] ferredoxin-type clusters. In addition, cis-1,2-disulfide-bridged complex 3 can slowly convert into trans-1,2-disulfide-bridged complex 4 and the complex [Cp*Fe(μ-η 2 :η 2 -S 2 )(cis-μ-η 1 :η 1 -S 2 )FeCp*] (5) by self-assembly reaction at ambient temperature, which is evidenced by time-dependent 1 H NMR spectroscopy.

A rotamer energy level study of sulfuric acid.

PubMed

Partanen, Lauri; Pesonen, Janne; Sjöholm, Elina; Halonen, Lauri

2013-10-14

It is a common approach in quantum chemical calculations for polyatomic molecules to rigidly constrain some of the degrees of freedom in order to make the calculations computationally feasible. However, the presence of the rigid constraints also affects the kinetic energy operator resulting in the frozen mode correction, originally derived by Pesonen [J. Chem. Phys. 139, 144310 (2013)]. In this study, we compare the effects of this correction to several different approximations to the kinetic energy operator used in the literature, in the specific case of the rotamer energy levels of sulfuric acid. The two stable conformers of sulfuric acid are connected by the rotations of the O-S-O-H dihedral angles and possess C2 and Cs symmetry in the order of increasing energy. Our results show that of the models tested, the largest differences with the frozen mode corrected values were obtained by simply omitting the passive degrees of freedom. For the lowest 17 excited states, this inappropriate treatment introduces an increase of 9.6 cm(-1) on average, with an increase of 8.7 cm(-1) in the zero-point energies. With our two-dimensional potential energy surface calculated at the CCSD(T)-F12a/VDZ-F12 level, we observe a radical shift in the density of states compared to the harmonic picture, combined with an increase in zero point energy. Thus, we conclude that the quantum mechanical inclusion of the different conformers of sulfuric acid have a significant effect on its vibrational partition function, suggesting that it will also have an impact on the computational values of the thermodynamic properties of any reactions where sulfuric acid plays a role. Finally, we also considered the effect of the anharmonicities for the other vibrational degrees of freedom with a VSCF-calculation at the DF-MP2-F12/VTZ-F12 level of theory but found that the inclusion of the other conformer had the more important effect on the vibrational partition function.

Structure of the cyclic peptide [W8S]contryphan Vn: effect of the tryptophan/serine substitution on trans-cis proline isomerization.

PubMed

Nepravishta, Ridvan; Mandaliti, Walter; Melino, Sonia; Eliseo, Tommaso; Paci, Maurizio

2014-12-01

The structural characterization of [W8S]contryphan Vn, an analogue of Contryphan Vn with tryptophan 8 substituted with a serine residue (W8S), was performed by NMR spectroscopy, molecular dynamics simulations and fluorescence spectroscopy. Contryphan Vn, a bioactive cyclic peptide from the venom of the cone snail Conus ventricosus, contains an S-S bridge between two cysteines and a D-tryptophan. Like other Contryphans, [W8S]contryphan Vn has proline 7 isomerized trans, while the proline 4 has nearly equivalent populations of cis and trans configurations. The thermodynamic and kinetic parameters of the trans-cis isomerization of proline 4 were measured. The isomers of [W8S]contryphan Vn with proline 4 in cis and trans show structural differences. The absence of the salt bridge between the same Asp2 and Lys6, present in Contryphan Vn, may be attributed to the lack of the hydrophobic side chain of Trp8 where it likely protects the electrostatic interactions. These results may contribute to identifying, in these cyclic peptides, the structural determinants of the mechanism of proline trans-cis isomerization, this being also an important step in protein folding.

A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data

PubMed Central

Zeng, Jianyang; Roberts, Kyle E.; Zhou, Pei

2011-01-01

Abstract A major bottleneck in protein structure determination via nuclear magnetic resonance (NMR) is the lengthy and laborious process of assigning resonances and nuclear Overhauser effect (NOE) cross peaks. Recent studies have shown that accurate backbone folds can be determined using sparse NMR data, such as residual dipolar couplings (RDCs) or backbone chemical shifts. This opens a question of whether we can also determine the accurate protein side-chain conformations using sparse or unassigned NMR data. We attack this question by using unassigned nuclear Overhauser effect spectroscopy (NOESY) data, which records the through-space dipolar interactions between protons nearby in three-dimensional (3D) space. We propose a Bayesian approach with a Markov random field (MRF) model to integrate the likelihood function derived from observed experimental data, with prior information (i.e., empirical molecular mechanics energies) about the protein structures. We unify the side-chain structure prediction problem with the side-chain structure determination problem using unassigned NMR data, and apply the deterministic dead-end elimination (DEE) and A* search algorithms to provably find the global optimum solution that maximizes the posterior probability. We employ a Hausdorff-based measure to derive the likelihood of a rotamer or a pairwise rotamer interaction from unassigned NOESY data. In addition, we apply a systematic and rigorous approach to estimate the experimental noise in NMR data, which also determines the weighting factor of the data term in the scoring function derived from the Bayesian framework. We tested our approach on real NMR data of three proteins: the FF Domain 2 of human transcription elongation factor CA150 (FF2), the B1 domain of Protein G (GB1), and human ubiquitin. The promising results indicate that our algorithm can be applied in high-resolution protein structure determination. Since our approach does not require any NOE assignment, it can

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

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.

Multi-phase back contacts for CIS solar cells

DOEpatents

Rockett, A.A.; Yang, L.C.

1995-12-19

Multi-phase, single layer, non-interdiffusing M-Mo back contact metallized films, where M is selected from Cu, Ga, or mixtures thereof, for CIS cells are deposited by a sputtering process on suitable substrates, preferably glass or alumina, to prevent delamination of the CIS from the back contact layer. Typical CIS compositions include CuXSe{sub 2} where X is In or/and Ga. The multi-phase mixture is deposited on the substrate in a manner to provide a columnar microstructure, with micro-vein Cu or/and Ga regions which partially or fully vertically penetrate the entire back contact layer. The CIS semiconductor layer is then deposited by hybrid sputtering and evaporation process. The Cu/Ga-Mo deposition is controlled to produce the single layer two-phase columnar morphology with controllable Cu or Ga vein size less than about 0.01 microns in width. During the subsequent deposition of the CIS layer, the columnar Cu/Ga regions within the molybdenum of the Cu/Ga-Mo back layer tend to partially leach out, and are replaced by columns of CIS. Narrower Cu and/or Ga regions, and those with fewer inner connections between regions, leach out more slowly during the subsequent CIS deposition. This gives a good mechanical and electrical interlock of the CIS layer into the Cu/Ga-Mo back layer. Solar cells employing In-rich CIS semiconductors bonded to the multi-phase columnar microstructure back layer of this invention exhibit vastly improved photo-electrical conversion on the order of 17% greater than Mo alone, improved uniformity of output across the face of the cell, and greater Fill Factor. 15 figs.

Multi-phase back contacts for CIS solar cells

DOEpatents

Rockett, Angus A.; Yang, Li-Chung

1995-01-01

Multi-phase, single layer, non-interdiffusing M-Mo back contact metallized films, where M is selected from Cu, Ga, or mixtures thereof, for CIS cells are deposited by a sputtering process on suitable substrates, preferably glass or alumina, to prevent delamination of the CIS from the back contact layer. Typical CIS compositions include CuXSe.sub.2 where X is In or/and Ga. The multi-phase mixture is deposited on the substrate in a manner to provide a columnar microstructure, with micro-vein Cu or/and Ga regions which partially or fully vertically penetrate the entire back contact layer. The CIS semiconductor layer is then deposited by hybrid sputtering and evaporation process. The Cu/Ga-Mo deposition is controlled to produce the single layer two-phase columnar morphology with controllable Cu or Ga vein size less than about 0.01 microns in width. During the subsequent deposition of the CIS layer, the columnar Cu/Ga regions within the molybdenum of the Cu/Ga-Mo back layer tend to partially leach out, and are replaced by columns of CIS. Narrower Cu and/or Ga regions, and those with fewer inner connections between regions, leach out more slowly during the subsequent CIS deposition. This gives a good mechanical and electrical interlock of the CIS layer into the Cu/Ga-Mo back layer. Solar cells employing In-rich CIS semiconductors bonded to the multi-phase columnar microstructure back layer of this invention exhibit vastly improved photo-electrical conversion on the order of 17% greater than Mo alone, improved uniformity of output across the face of the cell, and greater Fill Factor.

cis Retinol oxidation regulates photoreceptor access to the retina visual cycle and cone pigment regeneration

PubMed Central

Sato, Shinya

2016-01-01

Key points This study explores the nature of the cis retinol that Müller cells in the retina provide to cones for the regeneration of their visual pigment.We report that the retina visual cycle provides cones exclusively with 11‐cis chromophore in both salamander and mouse and show that this selectivity is dependent on the 11‐cis‐specific cellular retinaldehyde binding protein (CRALBP) present in Müller cells.Even though salamander blue cones and green rods share the same visual pigment, only blue cones but not green rods are able to dark‐adapt in the retina following a bleach and to use exogenous 9‐cis retinol for pigment regeneration, suggesting that access to the retina visual cycle is cone‐specific and pigment‐independent.Our results show that the retina produces 11‐cis retinol that can be oxidized and used for pigment regeneration and dark adaptation selectively in cones and not in rods. Abstract Chromophore supply by the retinal Müller cells (retina visual cycle) supports the efficient pigment regeneration required for cone photoreceptor function in bright light. Surprisingly, a large fraction of the chromophore produced by dihydroceramide desaturase‐1, the putative all‐trans retinol isomerase in Müller cells, appears to be 9‐cis retinol. In contrast, the canonical retinal pigment epithelium (RPE) visual cycle produces exclusively 11‐cis retinal. Here, we used the different absorption spectra of 9‐cis and 11‐cis pigments to identify the isoform of the chromophore produced by the visual cycle of the intact retina. We found that the spectral sensitivity of salamander and mouse cones dark‐adapted in the isolated retina (with only the retina visual cycle) was similar to that of cones dark‐adapted in the intact eye (with both the RPE and retina visual cycles) and consistent with pure 11‐cis pigment composition. However, in mice lacking the cellular retinaldehyde binding protein (CRALBP), cone spectral sensitivity contained a

In vitro antiprotozoal activity of (S)-cis-Verbenol against Leishmania spp. and Trypanosoma cruzi.

PubMed

Yaluff, Gloria; Vega, Celeste; Alvarenga, Nelson

2017-04-01

(S)-cis-Verbenol, a monoterpene frequently found as a component of essential oils, was assayed against Leishmania amazonensis, Leishmania infantum, Leishmania brasiliensis and against two strains of Trypanosoma cruzi. The cytotoxicity of the compound was also assayed against human fibroblast cells using a colorimetric method. Benznidazole was used as reference drug against T. cruzi and amphotericin B was used against Leishmania spp. The compound showed good activity against the trypanosomes, being more active against the CL Brenner strain, with an IC 50 value of 8.3μg/mL. Against Leishmania, the IC 50 values were between 2.1 and 3.8μg/mL. The compound showed no cytotoxicity against human fibroblasts at the concentrations assayed and was 100-500 times more toxic for the parasites than for the human cells, as indicated by the selectivity indexes. The results open interesting perspectives about the potential of (S)-cis-Verbenol and other individual components of essential oils for the treatment of these diseases. Copyright © 2016 Elsevier B.V. All rights reserved.

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

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.

Hyperproduction of sebaceous cis-6-hexadecenoic acid by esterase-reduced mutant of Rhodococcus sp. strain.

PubMed

Araki, Hiroyuki; Hagihara, Hiroshi; Takigawa, Hirofumi; Kotani, Nobuharu; Tsujino, Yukiharu; Koike, Kenzo; Kawai, Shuji; Ozaki, Katsuya; Ito, Susumu

2007-10-01

cis-6-Hexadecenoic acid is a major component of human sebaceous lipids that is involved in skin self-sterilization and atopic dermatitis amelioration. It can be prepared by hydrolysis of isopropyl cis-6-hexadecenoate produced by resting cells of Rhodococcus sp. strain KSM-MT66. To devise an economical industrial-scale process for the production of this rare fatty acid, we optimized the conditions for growing rhodococcal cells. Mg(2+) and Fe(2+) ions are essential for the efficient production of isopropyl cis-6-hexadecenoate. To further increase the production of isopropyl cis-6-hexadecenoate, we created a mutant strain (T64) with reduced esterase activity by random mutagenesis using UV irradiation of MT66. Under an optimized condition, the mutant T64 produced more than 60 g l(-1) isopropyl cis-6-hexadecenoate in a 4-d cultivation, corresponding to about 52 g l(-1)cis-6-hexadecenoate.

Metabolomic fingerprinting of primed tobacco cells provide the first evidence for the biological origin of cis-chlorogenic acid.

PubMed

Mhlongo, M I; Piater, L A; Steenkamp, P A; Madala, N E; Dubery, I A

2015-01-01

Previous studies suggest that only trans-isomers of chlorogenic acid (CGA) are naturally produced. Cis-isomers have been noted in some plant tissues exposed to different mechanical processes as well as untreated tobacco leaves exposed to sunlight. Very little, however, is known about the biological significance and origin of cis-isomers. Here we show for the first time the accumulation of cis-5-caffeoylquinic acid in cultured tobacco cells treated with different inducers of plant defence (lipopolysaccharides, flagellin peptide-22, chitosan, acibenzolar-S-methyl and isonitrosoacetophenone), without exposure to UV light and with a 2-fold (on average) increase in the concentration of the pool in comparison to non-stimulated cells. Our UHPLC-Q-TOF-MS and multivariate statistical results suggest the presence of a possible biological pathway responsible for the production of cis-CGAs in tobacco plants.

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.

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.

Isolation and identification of flavonoids, including flavone rotamers, from the herbal drug 'Crataegi folium cum flore' (hawthorn).

PubMed

Rayyan, S; Fossen, T; Solheim Nateland, H; Andersen, O M

2005-01-01

Twelve flavonoids, including seven flavones, four flavonols and one flavanone, were isolated from methanolic extract of the herbal drug 'Crataegi folium cum flore' (hawthorn leaves and flowers) by a combination of CC (over Amberlite XAD-7 and Sephadex LH-20) and preparative HPLC. Their structures, including that of the novel flavonol 8-methoxykaempferol 3-O-(6"-malonyl-beta-glucopyranoside), were elucidated by homo- and heteronuclear NMR and electrospray/MS. The 1H- and 13C-NMR of all compounds, including rotameric pairs of five flavone C-glycosides, were assigned. The presence and relative proportion of each rotamer was shown by various NMR experiments, including two-dimensional nuclear Overhauser and exchange spectroscopy, to depend on solvent, linkage position and structure of the C-glycosyl substituent.

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

Inactivation of Cg10062, a cis-3-chloroacrylic acid dehalogenase homologue in Corynebacterium glutamicum, by (R)- and (S)-oxirane-2-carboxylate: analysis and implications.

PubMed

Robertson, Brooklyn A; Johnson, William H; Lo, Herng-Hsiang; Whitman, Christian P

2008-08-19

( R)- and ( S)-oxirane-2-carboxylate were determined to be active site-directed irreversible inhibitors of the cis-3-chloroacrylic acid dehalogenase ( cis-CaaD) homologue Cg10062 found in Corynebacterium glutamicum. Kinetic analysis indicates that the ( R) enantiomer binds more tightly and is the more potent inhibitor, likely reflecting more favorable interactions with active site residues. Pro-1 is the sole site of covalent modification by the ( R) and ( S) enantiomers. Pro-1, Arg-70, Arg-73, and Glu-114, previously identified as catalytic residues in Cg10062, have also been implicated in the inactivation mechanism. Pro-1, Arg-70, and Arg-73 are essential residues for the process as indicated by the observation that the enzymes with the corresponding alanine mutations are not covalently modified by either enantiomer. The E114Q mutant slows covalent modification of Cg10062 but does not prevent it. The results are comparable to those found for the irreversible inactivation of cis-CaaD by ( R)-oxirane-2-carboxylate with two important distinctions: the alkylation of cis-CaaD is stereospecific, and Glu-114 does not take part in the cis-CaaD inactivation mechanism. Cg10062 exhibits low-level cis-CaaD and trans-3-chloroacrylic acid dehalogenase (CaaD) activities, with the cis-CaaD activity predominating. Hence, the preference of Cg10062 for the cis isomer correlates with the observation that the ( R) enantiomer is the more potent inactivator. Moreover, the factors responsible for the relaxed substrate specificity of Cg10062 may account for the stereoselective inactivation by the enantiomeric epoxides. Delineation of these factors would provide a more complete picture of the substrate specificity determinants for cis-CaaD. This study represents an important step toward this goal by setting the stage for a crystallographic analysis of inactivated Cg10062.

Dipolarizing flux bundles in the cis-geosynchronous magnetosphere: Relationship between electric fields and energetic particle injections

NASA Astrophysics Data System (ADS)

Liu, Jiang; Angelopoulos, V.; Zhang, Xiao-Jia; Turner, D. L.; Gabrielse, C.; Runov, A.; Li, Jinxing; Funsten, H. O.; Spence, H. E.

2016-02-01

Dipolarizing flux bundles (DFBs) are small flux tubes (typically <3 RE in XGSM and YGSM) in the nightside magnetosphere that have magnetic field more dipolar than the background. Although DFBs are known to accelerate particles, creating energetic particle injections outside geosynchronous orbit (trans-GEO), the nature of the acceleration mechanism and the importance of DFBs in generating injections inside geosynchronous orbit (cis-GEO) are unclear. Our statistical study of cis-GEO DFBs using data from the Van Allen Probes reveals that just like trans-GEO DFBs, cis-GEO DFBs occur most often in the premidnight sector, but their occurrence rate is ~1/3 that of trans-GEO DFBs. Half the cis-GEO DFBs are accompanied by an energetic particle injection and have an electric field 3 times stronger than that of the injectionless half. All DFB injections are dispersionless within the temporal resolution considered (11 s). Our findings suggest that these injections are ushered or produced locally by the DFB, and the DFB's strong electric field is an important aspect of the injection generation mechanism.

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.

Photoinduced ICT vs. excited rotamer intercoversion in two quadrupolar polyaromatic N-methylpyridinium cations.

PubMed

Cesaretti, A; Carlotti, B; Elisei, F; Fortuna, C G; Spalletti, A

2018-01-24

The excited state dynamics of two quadrupolar polyaromatic N-methylpyridinium cations have been fully investigated in order to acquire detailed information on their photo-induced behavior. The two molecules are symmetric push-pull compounds having a D-π-A + -π-D motif, with the same electron-acceptor central unit (A = N-methylpyridinium) and two distinctive electron-donor polyaromatic side groups (D), namely naphthyl and pyrenyl substituents. Both molecules undergo charge transfer during the absorption, as revealed by a significant solvatochromism exhibited with solvent polarity, but the fate of their excited state was found to be markedly different. The careful analysis of the data gathered from femtosecond-resolved fluorescence up-conversion and transient absorption experiments, supported by DFT quantum mechanical calculations and temperature-dependent stationary measurements, shows the leading role of intramolecular charge transfer, assisted by symmetry breaking, in the pyrenyl derivative and that of rotamer interconversion in the naphthtyl one. Both excited state processes are controlled by the viscosity rather than polarity of the solvent, and they occur during inertial solvation in low-viscous media and lengthening up to tens of picoseconds in highly viscous solvents.

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

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

Advances in methods to characterize ligand-induced ionic lock and rotamer toggle molecular switch in G protein-coupled receptors.

PubMed

Xie, Xiang-Qun; Chowdhury, Ananda

2013-01-01

Structural biology of GPCRs has made significant progress upon recently developed technologies for GPCRs expression/purification and elucidation of GPCRs crystal structures. The crystal structures provide a snapshot of the receptor structural disposition of GPCRs itself or with cocrystallized ligands, and the results are congruent with biophysical and computer modeling studies reported about GPCRs conformational and dynamics flexibility, regulated activation, and the various stabilizing interactions, such as "molecular switches." The molecular switches generally constitute the most conserved domains within a particular GPCR superfamily. Often agonist-induced receptor activation proceeds by the disruption of majority of these interactions, while antagonist and inverse agonist act as blockers and structural stabilizers, respectively. Several elegant studies, particularly for the β2AR, have demonstrated the relationship between ligand structure, receptor conformational changes, and corresponding pharmacological outcomes. Thus, it is of great importance to understand GPCRs activation related to cell signaling pathways. Herein, we summarize the steps to produce functional GPCRs, generate suitably fluorescent labeled GPCRs and the procedure to use that to understand if ligand-induced activation can proceed by activation of the GPCRs via ionic lock switch and/or rotamer toggle switch mechanisms. Such understanding of ligand structure and mechanism of receptor activation will provide great insight toward uncovering newer pathways of GPCR activation and aid in structure-based drug design. Copyright © 2013 Elsevier Inc. All rights reserved.

Information Spreadsheet for Engines and Vehicles Compliance Information System (EV-CIS) User Registration

EPA Pesticide Factsheets

In this spreadsheet, user(s) provide their company’s manufacturer code, user contact information for EV-CIS, and user roles. This spreadsheet is used for the Company Authorizing Official (CAO), CROMERR Signer, and EV-CIS Submitters.

PAA, WSH, and CIS Overview Self-Study #47656

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

Schroeder, Rachel Anne

This course presents an overview of the Department of Energy’s (DOE’s) regulatory requirements relevant to the Price-Anderson Amendments Act (PAAA, also referred to as nuclear safety), worker safety and health (WSH), and classified information security (CIS) that are enforceable under the DOE enforcement program; describes the DOE enforcement process; and provides an overview of Los Alamos National Laboratory’s (LANL’s) internal compliance program relative to these DOE regulatory requirements. The LANL PAAA Program is responsible for maintaining LANL’s internal compliance program, which ensures the prompt identification, screening, and reporting of noncompliances to DOE regulatory requirements pertaining to nuclear safety, WSH, andmore » CIS to build the strongest mitigation position for the Laboratory with respect to civil or other penalties.« less

Attraction of New Zealand flower thrips, Thrips obscuratus, to cis-jasmone, a volatile identified from Japanese honeysuckle flowers.

PubMed

El-Sayed, A M; Mitchell, V J; McLaren, G F; Manning, L M; Bunn, B; Suckling, D M

2009-06-01

This work was undertaken to identify floral compound(s) produced by honeysuckle flowers, Lonicera japonica (Thunberg), that mediate the attraction of New Zealand flower thrips Thrips obscuratus (Crawford). Volatiles were collected during the day and night and analyzed by gas chromatography-mass spectrometry (GC-MS) to determine their emission over these two periods. Nine compounds were identified in the headspace; the main compound was linalool, and the other compounds were germacrene D, E,E-alpha-farnesene, nerolidol, cis-jasmone, cis-3-hexenyl acetate, hexyl acetate, cis-hexenyl tiglate, and indole. There was a quantitative difference between day and night volatiles, with cis-3-hexenyl acetate, hexyl acetate, cis-hexenyl tiglate, and cis-jasmone emitted in higher amounts during the day compared to the night. When the compounds were tested individually in field trapping experiments, only cis-jasmone attracted New Zealand flower thrips in a significant number. In another field trapping experiment, cis-jasmone caught similar numbers of New Zealand flower thrips compared to a floral blend formulated to mimic the ratios of the compounds emitted during the day, while catch with the night-emitted floral blend was not significantly different from the control. Subsequently, two field trapping experiments were conducted to determine the optimal attraction dose for cis-jasmone, a range of 1-100 mg loaded onto a red rubber stopper was tested, and the highest catches were in traps baited with 100 mg loading. A higher range of 100-1000 mg loaded into polyethylene vials was tested, and the highest catch was in traps baited with 500 mg. In another experiment aimed at comparing the attraction efficacy of cis-jasmone with the two other known thrips attractants (ethyl nicotinate and p-anisaldehyde), ethyl nicotinate showed the highest trap catch followed by cis-jasmone. A smaller number of Thrips tabaci (Lindeman) was attracted to traps baited with cis-jasmone. These results

Thermal processing differentially affects lycopene and other carotenoids in cis-lycopene containing, tangerine tomatoes.

PubMed

Cooperstone, Jessica L; Francis, David M; Schwartz, Steven J

2016-11-01

Tangerine tomatoes, unlike red tomatoes, accumulate cis-lycopenes instead of the all-trans isomer. cis-Lycopene is the predominating isomeric form of lycopene found in blood and tissues. Our objective was to understand how thermal processing and lipid concentration affect carotenoid isomerisation and degradation in tangerine tomatoes. We conducted duplicated factorial designed experiments producing tangerine tomato juice and sauce, varying both processing time and lipid concentration. Carotenoids were extracted and analysed using high-performance liquid chromatography with photodiode array detection. Phytoene, phytofluene, ζ-carotene, neurosporene, tetra-cis-lycopene, all-trans-lycopene and other-cis-lycopenes were quantified. Tetra-cis-lycopene decreased with increasing heating time and reached 80% of the original level in sauce after processing times of 180min. All-trans-lycopene and other-cis-lycopenes increased with longer processing times. Total carotenoids and total lycopene decreased with increased heating times while phytoene and phytofluene were unchanged. These data suggest limiting thermal processing of tangerine tomato products if delivery of tetra-cis-lycopene is desirable. Copyright © 2016 Elsevier Ltd. All rights reserved.

cis,cis-Muconic acid: separation and catalysis to bio-adipic acid for nylon-6,6 polymerization

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

Vardon, Derek R.; Rorrer, Nicholas A.; Salvachúa, Davinia

cis,cis-Muconic acid is a polyunsaturated dicarboxylic acid that can be produced renewably via the biological conversion of sugars and lignin-derived aromatic compounds. Subsequently, muconic acid can be catalytically converted to adipic acid -- the most commercially significant dicarboxylic acid manufactured from petroleum. Nylon-6,6 is the major industrial application for adipic acid, consuming 85% of market demand; however, high purity adipic acid (99.8%) is required for polymer synthesis. As such, process technologies are needed to effectively separate and catalytically transform biologically derived muconic acid to adipic acid in high purity over stable catalytic materials. To that end, this study: (1) demonstratesmore » bioreactor production of muconate at 34.5 g L-1 in an engineered strain of Pseudomonas putida KT2440, (2) examines the staged recovery of muconic acid from culture media, (3) screens platinum group metals (e.g., Pd, Pt, Rh, Ru) for activity and leaching stability on activated carbon (AC) and silica supports, (4) evaluates the time-on-stream performance of Rh/AC in a trickle bed reactor, and (5) demonstrates the polymerization of bio-adipic acid to nylon-6,6. Separation experiments confirmed AC effectively removed broth color compounds, but subsequent pH/temperature shift crystallization resulted in significant levels of Na, P, K, S and N in the crystallized product. Ethanol dissolution of muconic acid precipitated bulk salts, achieving a purity of 99.8%. Batch catalysis screening reactions determined that Rh and Pd were both highly active compared to Pt and Ru, but Pd leached significantly (1-9%) from both AC and silica supports. Testing of Rh/AC in a continuous trickle bed reactor for 100 h confirmed stable performance after 24 h, although organic adsorption resulted in reduced steady-state activity. Lastly, polymerization of bio-adipic acid with hexamethyldiamine produced nylon-6,6 with comparable properties to its petrochemical

The CIS Database: Occupational Health and Safety Information Online.

ERIC Educational Resources Information Center

Siegel, Herbert; Scurr, Erica

1985-01-01

Describes document acquisition, selection, indexing, and abstracting and discusses online searching of the CIS database, an online system produced by the International Occupational Safety and Health Information Centre. This database comprehensively covers information in the field of occupational health and safety. Sample searches and search…

A review of recent analyses of the Canadian Incidence Study of Reported Child Abuse and Neglect (CIS)

PubMed Central

Potter, D.; Nasserie, T.; Tonmyr, L.

2015-01-01

Abstract Introduction: The objective of this analysis is to identify, assess the quality and summarize the findings of peer-reviewed articles that used data from the Canadian Incidence Study of Reported Child Abuse and Neglect (CIS) published since November 2011 and data from provincial oversamples of the CIS as well as to illustrate evolving uses of these datasets. Methods: Articles were identified from the Public Health Agency of Canada’s data request records tracking access to CIS data and publications produced from that data. At least two raters independently reviewed and appraised the quality of each article. Results: A total of 32 articles were included. Common strengths of articles included clearly stated research aims, appropriate control variables and analyses, sufficient sample sizes, appropriate conclusions and relevance to practice or policy. Common problem areas of articles included unclear definitions for variables and inclusion criteria of cases. Articles frequently measured the associations between maltreatment, child, caregiver, household and agency/referral characteristics and investigative outcomes such as opening cases for ongoing services and placement. Conclusion: Articles using CIS data were rated positively on most quality indicators. Researchers have recently focussed on inadequately studied categories of maltreatment (exposure to intimate partner violence [IPV]), neglect and emotional maltreatment) and examined factors specific to First Nations children. Data from the CIS oversamples have been underutilized. The use of multivariate analysis techniques has increased. PMID:26605559

Two negative cis-regulatory regions involved in fruit-specific promoter activity from watermelon (Citrullus vulgaris S.).

PubMed

Yin, Tao; Wu, Hanying; Zhang, Shanglong; Lu, Hongyu; Zhang, Lingxiao; Xu, Yong; Chen, Daming; Liu, Jingmei

2009-01-01

A 1.8 kb 5'-flanking region of the large subunit of ADP-glucose pyrophosphorylase, isolated from watermelon (Citrullus vulgaris S.), has fruit-specific promoter activity in transgenic tomato plants. Two negative regulatory regions, from -986 to -959 and from -472 to -424, were identified in this promoter region by fine deletion analyses. Removal of both regions led to constitutive expression in epidermal cells. Gain-of-function experiments showed that these two regions were sufficient to inhibit RFP (red fluorescent protein) expression in transformed epidermal cells when fused to the cauliflower mosaic virus (CaMV) 35S minimal promoter. Gel mobility shift experiments demonstrated the presence of leaf nuclear factors that interact with these two elements. A TCCAAAA motif was identified in these two regions, as well as one in the reverse orientation, which was confirmed to be a novel specific cis-element. A quantitative beta-glucuronidase (GUS) activity assay of stable transgenic tomato plants showed that the activities of chimeric promoters harbouring only one of the two cis-elements, or both, were approximately 10-fold higher in fruits than in leaves. These data confirm that the TCCAAAA motif functions as a fruit-specific element by inhibiting gene expression in leaves.

Two negative cis-regulatory regions involved in fruit-specific promoter activity from watermelon (Citrullus vulgaris S.)

PubMed Central

Yin, Tao; Wu, Hanying; Zhang, Shanglong; Liu, Jingmei; Lu, Hongyu; Zhang, Lingxiao; Xu, Yong; Chen, Daming

2009-01-01

A 1.8 kb 5′-flanking region of the large subunit of ADP-glucose pyrophosphorylase, isolated from watermelon (Citrullus vulgaris S.), has fruit-specific promoter activity in transgenic tomato plants. Two negative regulatory regions, from –986 to –959 and from –472 to –424, were identified in this promoter region by fine deletion analyses. Removal of both regions led to constitutive expression in epidermal cells. Gain-of-function experiments showed that these two regions were sufficient to inhibit RFP (red fluorescent protein) expression in transformed epidermal cells when fused to the cauliflower mosaic virus (CaMV) 35S minimal promoter. Gel mobility shift experiments demonstrated the presence of leaf nuclear factors that interact with these two elements. A TCCAAAA motif was identified in these two regions, as well as one in the reverse orientation, which was confirmed to be a novel specific cis-element. A quantitative β-glucuronidase (GUS) activity assay of stable transgenic tomato plants showed that the activities of chimeric promoters harbouring only one of the two cis-elements, or both, were ∼10-fold higher in fruits than in leaves. These data confirm that the TCCAAAA motif functions as a fruit-specific element by inhibiting gene expression in leaves. PMID:19073962

Synthesis of cis-4-trifluoromethyl- and cis-4-difluoromethyl-l-pyroglutamic acids.

PubMed

Qiu, Xiao-Long; Qing, Feng-Ling

2003-05-02

Efforts to synthesize 4-trifluoromethyl- and 4-difluoromethyl-l-pyroglutamic acids are described. After many arduous efforts, we successfully synthesized our target molecules cis-4-trifluoromethyl-l-pyroglutamic acid 25 and cis-4-difluoromethyl-l-pyroglutamic acid 26 from trans-4-hydroxy-l-proline through oxidation of fluorinated prolinates with RuO(4).

cis p-tau: early driver of brain injury and tauopathy blocked by antibody

PubMed Central

Mannix, Rebekah; Qiu, Jianhua; Moncaster, Juliet; Chen, Chun-Hau; Yao, Yandan; Lin, Yu-Min; Driver, Jane A; Sun, Yan; Wei, Shuo; Luo, Man-Li; Albayram, Onder; Huang, Pengyu; Rotenberg, Alexander; Ryo, Akihide; Goldstein, Lee E; Pascual-Leone, Alvaro; McKee, Ann C.; Meehan, William; Zhou, Xiao Zhen; Lu, Kun Ping

2015-01-01

Traumatic brain injury (TBI), characterized by acute neurological dysfunction, is one of the best known environmental risk factors for chronic traumatic encephalopathy (CTE) and Alzheimer's disease (AD), whose defining pathologic features include tauopathy made of phosphorylated tau (p-tau). However, tauopathy has not been detected in early stages after TBI and how TBI leads to tauopathy is unknown. Here we find robust cis p-tau pathology after sport- and military-related TBI in humans and mice. Acutely after TBI in mice and stress in vitro, neurons prominently produce cis p-tau, which disrupts axonal microtubule network and mitochondrial transport, spreads to other neurons, and leads to apoptosis. This process, termed “cistauosis”, appears long before other tauopathy. Treating TBI mice with cis antibody blocks cistauosis, prevents tauopathy development and spread, and restores many TBI-related structural and functional sequelae. Thus, cis p-tau is a major early driver after TBI and leads to tauopathy in CTE and AD, and cis antibody may be further developed to detect and treat TBI, and prevent progressive neurodegeneration after injury. PMID:26176913

cis-1,2-Dichloroethylene

Integrated Risk Information System (IRIS)

EPA / 635 / R - 09 / 006 F www.epa.gov / iris TOXICOLOGICAL REVIEW OF cis - 1,2 - DICHLOROETHYLENE and trans - 1,2 - DICHLOROETHYLENE ( CAS Nos . cis : 156 - 59 - 2 ; trans : 156 - 60 - 5 ; mixture : 540 - 59 - 0 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS )

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

Effects of metals on enantioselective toxicity and biotransformation of cis-bifenthrin in zebrafish.

PubMed

Yang, Ye; Ji, Dapeng; Huang, Xin; Zhang, Jianyun; Liu, Jing

2017-08-01

Co-occurrence of pyrethroids and metals in watersheds previously has been reported to pose great risk to aquatic species. Pyrethroids are a class of chiral insecticides that have been shown to have enantioselective toxicity and biotransformation. However, the influence of metals on enantioselectivity of pyrethroids has not yet been evaluated. In the present study, the effects of cadmium (Cd), copper (Cu), and lead (Pb) on the enantioselective toxicity and metabolism of cis-bifenthrin (cis-BF) were investigated in zebrafish at environmentally relevant concentrations. The addition of Cd, Cu, or Pb significantly increased the mortality of zebrafish in racemate and R-enantiomer of cis-BF-treated groups. In rac-cis-BF- or 1R-cis-BF-treated groups, the addition of Cd, Cu, or Pb caused a decrease in enantiomeric fraction (EF) and an increased ratio of R-enantiomer residues in zebrafish. In 1S-cis-BF-treated groups, coexposure to Cd led to a lower EF and decreased residue levels of S-enantiomer. In addition, coexposure to the 3 metals resulted in different biodegradation characteristics of each enantiomer accompanied with differential changes in the expression of cytochrome P450 (CYP)1, CYP2, and CYP3 genes, which might be responsible for the enantioselective biodegradation of cis-BF in zebrafish. These results suggest that the influence of coexistent metals should be considered in the ecological risk assessment of chiral pyrethroids in aquatic environments. Environ Toxicol Chem 2017;36:2139-2146. © 2017 SETAC. © 2017 SETAC.

Synthesis of Conjugated Polymers Containing cis-Phenylenevinylenes by Titanium Mediated Reductions

PubMed Central

Moslin, Ryan M.; Espino, Christine G.; Swager, Timothy M.

2009-01-01

The utility of Sato's titanium-mediated reduction of alkynes towards the synthesis of all cis-poly(phenylenevinylene)s (PPVs) is demonstrated by the syn-selective reduction of a variety of model diynes as well as a tetrayne. This technique was then applied to the reduction of a poly(phenyleneethynylene) (PPE) to provide the corresponding all-cis PPV polymer. PMID:20827441

REMPI and MATI spectroscopy of cis and trans 4-chloro-3-fluoroanisole

NASA Astrophysics Data System (ADS)

Liu, Sheng; Dai, Wenshuai; Lin, Dan; Cheng, Min; Du, YiKui; Zhu, Qihe

2017-08-01

The Resonance-enhanced two-photon ionization (R2PI) and Mass-analyzed threshold ionization (MATI) spectra of 4-chloro-3-fluoroanisole (4Cl3FA) were recorded in detail. The experimental and calculated results revealed that cis and trans 4Cl3FA are the only two stable conformers in each of the S0, S1 and D0 states. The first electronic excitation energies (E1's) of cis and trans35Cl-4Cl3FA were measured to be 35,326 ± 3 and 35,443 ± 3 cm-1 by the R2PI spectroscopy and the corresponding adiabatic ionization energies (IEs) were determined to be 67,330 ± 5 and 67,591 ± 5 cm-1 by the MATI spectroscopy. The E1's and IEs of cis and trans37Cl-4Cl3FA were also obtained and found to be identical to that of the 35Cl-4Cl3FA conformers. Compared with the trans 4Cl3FA, the cis 4Cl3FA is more stable in the S0, S1 and D0 states. The vibrational bands observed in the R2PI and MATI spectra are related to the vibrations involving the in-plane deformation of the benzene ring, the CH3 torsion and the OCH3 inversion. The substituent effects on the molecular structures, transition energies and vibrations of 4Cl3FA are discussed.

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)

cis-fumagillin, a new methionine aminopeptidase (type 2) inhibitor produced by Penicillium sp. F2757.

PubMed

Kwon, J Y; Jeong, H W; Kim, H K; Kang, K H; Chang, Y H; Bae, K S; Choi, J D; Lee, U C; Son, K H; Kwon, B M

2000-08-01

Selective inhibition against the yeast MetAP2 (methionine aminopeptidase type 2) was detected in the fermentation broth of a fungus F2757 that was later identified as Penicillium janczewskii. A new compound cis-fumagillin methyl ester (1) was isolated from the diazomethane treated fermentation extracts together with the known compound fumagillin methyl ester (2). The cis-fumagillin methyl ester, a stereoisomer of fumagillin methyl ester at the C2'-C3' position of the aliphatic side chain, selectively inhibited growth of the map1 mutant yeast strain (MetAP1 deletion strain) at a concentration as low as 1 ng. However, the wild type yeast w303 and the mutant map2 (MetAP2 deleted) strains were resistant up to 10 microg of the compound. In enzyme experiments, compound 1 inhibited the MetAP2 with an IC50 value of 6.3 nM, but it did not inhibit the MetAP1 (IC50 >200 microM). Compound 2 also inhibited the MetAP2 with an IC50 value of 9.2 nM and 105 microM against MetAP1.

Infrared laser Stark spectroscopy of hydroxymethoxycarbene in 4He nanodroplets

DOE PAGES

Broderick, Bernadette M.; Moradi, Christopher P.; Douberly, Gary E.

2015-09-07

Hydroxymethoxycarbene, CH 3OCOH, was produced via pyrolysis of monomethyl oxalate and subsequently isolated in 4He nanodroplets. Infrared laser spectroscopy reveals two rotationally resolved a,b-hybrid bands in the OH-stretch region, which are assigned to trans, trans- and cis, trans-rotamers. Stark spectroscopy of the trans, trans-OH stretch band provides the a-axis inertial component of the dipole moment, namely μ a = 0.62(7) D. Here, the computed equilibrium dipole moment agrees well with the expectation value determined from experiment, consistent with a semi-rigid CH 3OCOH backbone computed via a potential energy scan at the B3LYP/cc-pVTZ level of theory, which reveals substantial conformer interconversionmore » barriers of ≈17 kcal/mol.« less

Photoinduced Trans-to-cis Phase Transition of Polycrystalline Azobenzene at Low Irradiance Occurs in the Solid State

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

Bhattacharjee, Ujjal; Freppon, Daniel; Men, Long

2017-07-09

The ability to produce large-scale, reversible structural changes in a variety of materials by photoexcitation of a wide variety of azobenzene derivatives has been recognized for almost two decades. Because photoexcitation of trans-azobenzene produces the cis-isomer in solution, it has generally been inferred that the macroscopic structural changes occurring in materials are also initiated by a similar large-amplitude trans-to-cis isomerization. This paper provides the first demonstration that a trans-to-cis photoisomerization occurs in polycrystalline azobenzene, and is consistent with the previously hypothesized nature of the trigger in the photoactuated mechanisms of the materials in question. It is also demonstrated that undermore » low irradiance, trans-to-cis isomerization occurs in the solid (not via a pre-melted phase); and the presence of the cis-isomer thus lowers the melting point of the sample, providing a liquid phase. A variety of experimental techniques were employed, including X-ray diffraction measurements of polycrystalline azobenzene during exposure to laser irradiation and fluorescence measurements of the solid sample. Finally, a practical consequence of this work is that it establishes trans-azobenzene as an easily obtainable and well-defined control for monitoring photoinduced structural changes in X-ray diffraction experiments, using easily accessible laser wavelengths.« less

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

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.

Molecular mechanism of 9-cis-retinoic acid inhibition of adipogenesis in 3T3-L1 cells

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

Sagara, Chiaki; Takahashi, Katsuhiko; Kagechika, Hiroyuki

2013-03-29

Highlights: ► We examined the effects of 9-cis-RA on adipogenesis in mouse preadipocyte 3T3-L1. ► 9-cis-RA inhibited lipid accumulation in adipogenetically-induced 3T3-L1 cells. ► A RXR pan-antagonist suppressed the inhibitory effects of 9-cis-RA on adipogenesis. ► This antagonist had no effects on RXRα and PPARγ levels in 9-cis-RA-treated cells. ► 9-cis-RA-induced decrease in both RXRα and PPARγ was independent of RXR activation. -- Abstract: Retinoic acid (RA) signaling is mediated by specific nuclear hormone receptors. Here we examined the effects of 9-cis-RA on adipogenesis in mouse preadipocyte 3T3-L1 cells. 9-cis-RA inhibits the lipid accumulation of adipogenetically induced 3T3-L1 cells. Themore » complex of retinoid X receptor α (RXRα) with peroxisome proliferator-activated receptor γ (PPARγ) is a major transcription factor in the process of adipogenesis, and the levels of these molecules were decreased by 9-cis-RA treatment. A RXR pan-antagonist suppressed 9-cis-RA’s inhibitory effects on adipogenesis, but not on the intracellular levels of both RXRα and PPARγ. These results suggest that 9-cis-RA could inhibit adipogenesis by activating RXR, and decrease both RXR and PPARγs levels in a RXR activation-independent manner.« 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.

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

Stimulation of Phospholipid Scrambling of the Erythrocyte Membrane by 9-Cis-Retinoic Acid.

PubMed

Abed, Majed; Alzoubi, Kousi; Lang, Florian; Al Mamun Bhuayn, Abdulla

2017-01-01

The endogenous retinoid 9-cis-retinoic acid has previously been shown to trigger apoptosis in a wide variety of cells including several tumor cells and has thus been suggested for the treatment of malignancy. Similar to apoptosis of nucleated cells, erythrocytes may enter suicidal erythrocyte death or eryptosis, which is characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine translocation to the erythrocyte surface. Cellular mechanisms participating in the accomplishment of eryptosis include increase of cytosolic Ca2+ activity ([Ca2+]i) and formation of ceramide. The present study explored, whether 9-cis-retinoic acid induces eryptosis and whether the effect involves Ca2+ and/or ceramide. Flow cytometry was employed to estimate erythrocyte volume from forward scatter, phosphatidylserine exposure at the cell surface from annexin-V-binding, [Ca2+]i from Fluo3-fluorescence, and ceramide abundance utilizing specific antibodies. Hemolysis was quantified from hemoglobin concentration in the supernatant. A 48 hours exposure of human erythrocytes to 9-cis-retinoic acid (≥ 0.5 µg/ml) significantly increased the percentage of annexin-V-binding cells and significantly decreased forward scatter. Exposure to 9-cis-retinoic acid (≥ 0.5 µg/ml) significantly increased Fluo3-fluorescence, and the effect of 9-cis-retinoic acid on annexin-V-binding was significantly blunted by removal of extracellular Ca2+. Exposure to 9-cis-retinoic acid (1 µg/ml) further significantly increased the ceramide abundance at the erythrocyte surface and significantly increased hemolysis. 9-cis-retinoic acid triggers phospholipid scrambling of the erythrocyte cell membrane, an effect at least in part downstream of Ca2+ and ceramide. © 2017 The Author(s)Published by S. Karger AG, Basel.

The Molecular Structure of cis-FONO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.; Rice, Julia E.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

The molecular structure of cis-FONO has been determined with the CCSD(T) correlation method using an spdf quality basis set. In agreement with previous coupled-cluster calculations but in disagreement with density functional theory, cis-FONO is found to exhibit normal bond distances. The quadratic and cubic force fields of cis-FONO have also been determined in order to evaluate the effect of vibrational averaging on the molecular geometry. Vibrational averaging is found to increase bond distances, as expected, but it does not affect the qualitative nature of the bonding. The CCSD(T)/spdf harmonic frequencies of cis-FONO support our previous assertion that a band observed at 1200 /cm is a combination band (upsilon(sub 3) + upsilon(sub 4)), and not a fundamental.

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 Cis

Biosynthesis of adipic acid via microaerobic hydrogenation of cis,cis-muconic acid by oxygen-sensitive enoate reductase.

PubMed

Sun, Jing; Raza, Muslim; Sun, Xinxiao; Yuan, Qipeng

2018-06-06

Adipic acid (AA) is an important dicarboxylic acid used for the manufacture of nylon and polyurethane plastics. In this study, a novel adipic acid biosynthetic pathway was designed by extending the cis,cis-muconic acid (MA) biosynthesis through biohydrogenation. Enoate reductase from Clostridium acetobutylicum (CaER), an oxygen-sensitive reductase, was demonstrated to have in vivo enzyme activity of converting cis,cis-muconic acid to adipic acid under microaerobic condition. Engineered Escherichia coli strains were constructed to express the whole pathway and accumulated 5.8 ± 0.9 mg/L adipic acid from simple carbon sources. Considering the different oxygen demands between cis,cis-muconic acid biosynthesis and its degradation, a co-culture system was constructed. To improve production, T7 promoter instead of lac promoter was used for higher level expression of the key enzyme CaER and the titer of adipic acid increased to 18.3 ± 0.6 mg/L. To decrease the oxygen supply to downstream strains expressing CaER, Vitreoscilla hemoglobin (VHb) was introduced to upstream strains for its ability on oxygen obtaining. This attempt further improved the production of this novel pathway and 27.6 ± 1.3 mg/L adipic acid was accumulated under microaerobic condition. Copyright © 2018. Published by Elsevier B.V.

Photon induced facile synthesis and growth of CuInS2 absorber thin film for photovoltaic applications

NASA Astrophysics Data System (ADS)

Singh, Manjeet; Jiu, Jinting; Suganuma, Katsuaki

2016-04-01

In this paper, we demonstrate the use of high intensity pulsed light technique for the synthesis of phase pure CuInS2 (CIS) thin film at room temperature. The intense pulse of light is used to induce sintering of binary sulfides CuS and In2S3 to produce CIS phase without any direct thermal treatment. Light energy equivalent to the 706 mJ/cm2 is found to be the best energy to convert the CIS precursor film deposited at room temperature into CIS pure phase and well crystalline film. The CIS absorber film thus prepared is useful in making printed solar cell at room temperature on substrate with large area.

Quantitative Infrared Absorption Spectra and Vibrational Assignments of Crotonaldehyde and Methyl Vinyl Ketone Using Gas-Phase Mid-Infrared, Far-Infrared, and Liquid Raman Spectra: s-cis vs s-trans Composition Confirmed via Temperature Studies and ab Initio Methods.

PubMed

Lindenmaier, Rodica; Williams, Stephen D; Sams, Robert L; Johnson, Timothy J

2017-02-16

Methyl vinyl ketone (MVK) and crotonaldehyde are chemical isomers; both are also important species in tropospheric chemistry. We report quantitative vapor-phase infrared spectra of crotonaldehyde and MVK vapors over the 540-6500 cm -1 range. Vibrational assignments of all fundamental modes are made for both molecules on the basis of far- and mid-infrared vapor-phase spectra, liquid Raman spectra, along with density functional theory and ab initio MP2 and high energy-accuracy compound theoretical models (W1BD). Theoretical results indicate that at room temperature the crotonaldehyde equilibrium mixture is approximately 97% s-trans and only 3% s-cis conformer. Nearly all observed bands are thus associated with the s-trans conformer, but a few appear to be uniquely associated with the s-cis conformer, notably ν 16 c at 730.90 cm -1 , which displays a substantial intensity increase with temperature (70% upon going from 5 to 50 o C). The intensity of the corresponding mode of the s-trans conformer decreases with temperature. Under the same conditions, the MVK equilibrium mixture is approximately 69% s-trans conformer and 31% s-cis. W1BD calculations indicate that for MVK this is one of those (rare) cases where there are comparable populations of both conformers, approximately doubling the number of observed bands and exacerbating the vibrational assignments. We uniquely assign the bands associated with both the MVK s-cis conformer as well as those of the s-trans, thus completing the vibrational analyses of both conformers from the same set of experimental spectra. Integrated band intensities are reported for both molecules along with global warming potential values. Using the quantitative IR data, potential bands for atmospheric monitoring are also discussed.

Quantitative Infrared Absorption Spectra and Vibrational Assignments of Crotonaldehyde and Methyl Vinyl Ketone Using Gas-Phase Mid-Infrared, Far-Infrared, and Liquid Raman Spectra: s-cis vs s-trans Composition Confirmed via Temperature Studies and ab Initio Methods

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

Lindenmaier, Rodica; Williams, Stephen D.; Sams, Robert L.

Methyl vinyl ketone (MVK) and crotonaldehyde are chemical isomers; both are also important species in tropospheric chemistry. We report quantitative vapor-phase infrared spectra of crotonaldehyde and MVK vapors over the 540-6500 cm-1 range. Vibrational assignments of all fundamental modes are made for both molecules based on far- and mid-infrared vapor-phase spectra, liquid Raman spectra, along with density functional theory and ab initio MP2 and high energy-accuracy compound theoretical models (W1BD). Theoretical results indicate that at room temperature the crotonaldehyde equilibrium mixture is approximately 97% s-trans and only 3% s-cis conformer. Nearly all observed bands are thus associated with the s-transmore » conformer, but a few appear to be uniquely associated the s-cis conformer, notably ν16c at 730.90 cm-1, which displays a substantial intensity increase with temperature (62% upon going from 5 to 50 oC). The intensity of the corresponding mode of the s-trans conformer decreases with temperature. Under the same conditions, the MVK equilibrium mixture is approximately 69% s-trans conformer and 31% s-cis. W1BD calculations indicate that for MVK this is one of those (rare) cases where there are comparable populations of both conformers, ~doubling the number of observed bands and exacerbating the vibrational assignments. We uniquely assign the bands associated with both the MVK s-cis conformer as well as those of the s-trans, thus completing the vibrational analyses of both conformers from the same set of experimental spectra. Integrated band intensities are reported for both molecules along with global warming potential values. Using the quantitative IR data, potential bands for atmospheric monitoring are also discussed.« less

Identification and quantitation of all-trans- and 13-cis-retinoic acid and 13-cis-4-oxoretinoic acid in human plasma.

PubMed

Eckhoff, C; Nau, H

1990-08-01

Human plasma was analyzed by high performance liquid chromatography for the presence of retinoic acid and 4-oxoretinoic acid isomers. Peaks that coeluted with the reference compounds all-trans-retinoic acid, 13-cis-retinoic acid, and 13-cis-4-oxoretinoic acid were routinely observed in human plasma. These retinoids were unequivocally identified by the following methods: comigration with reference compounds under several high performance liquid chromatographic conditions; comparison of ultraviolet spectra with those of reference compounds; derivatization with diazomethane and coelution of the methyl esters with reference compounds in a high performance liquid chromatographic system as well as in a gas chromatography system with a mass selective detector. In vitro formation of 13-cis-retinoic acid and 13-cis-4-oxoretinoic acid as artifacts during the analytical procedure was excluded by control experiments. The mean plasma concentrations of the vitamin A metabolites in ten male volunteers were: all-trans-retinoic acid: 1.32 +/- 0.46 ng/ml; 13-cis-retinoic acid: 1.63 +/- 0.85 ng/ml; and 13-cis-4-oxoretinoic acid: 3.68 +/- 0.99 ng/ml. After oral dosing with vitamin A (833 IU/kg body weight) in five male volunteers, mean plasma all-trans-retinoic acid increased to 3.92 +/- 1.40 ng/ml and 13-cis-retinoic acid increased to 9.75 +/- 2.18 ng/ml. Maximal plasma 13-cis-4-oxoretinoic acid concentrations (average 7.60 +/- 1.45 ng/ml) were observed 6 h after dosing which was the last time point in this study. Concentrations of all-trans-4-oxoretinoic acid were low or not detectable. Our findings suggest that, in addition to all-trans-retinoic acid, 13-cis-retinoic acid and 13-cis-4-oxoretinoic acid are present in normal human plasma as metabolites of vitamin A.

The rate of cis-trans conformation errors is increasing in low-resolution crystal structures.

PubMed

Croll, Tristan Ian

2015-03-01

Cis-peptide bonds (with the exception of X-Pro) are exceedingly rare in native protein structures, yet a check for these is not currently included in the standard workflow for some common crystallography packages nor in the automated quality checks that are applied during submission to the Protein Data Bank. This appears to be leading to a growing rate of inclusion of spurious cis-peptide bonds in low-resolution structures both in absolute terms and as a fraction of solved residues. Most concerningly, it is possible for structures to contain very large numbers (>1%) of spurious cis-peptide bonds while still achieving excellent quality reports from MolProbity, leading to concerns that ignoring such errors is allowing software to overfit maps without producing telltale errors in, for example, the Ramachandran plot.

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.

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

DOE PAGES

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

2015-03-22

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

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.

Low density supercritical fluids precipitation of 9-cis and all trans-β-carotenes enriched particulates from Dunaliella salina.

PubMed

Chen, Jian-Ren; Wu, Jia-Jiuan; Lin, Justin Chun-Te; Wang, Yuan-Chuen; Young, Chiu-Chung; Shieh, Chwen-Jen; Hsu, Shih-Lan; Chang, Cheih-Ming J

2013-07-19

In this study, supercritical anti-solvent (SAS) pulverization coupled with reverse phase elution chromatography was employed to isolate 9-cis and trans-β-carotenes from Dunaliella salina. Total concentration of 9-cis (134.7mg/g) and trans-β-carotene (204.2mg/g) was increased from 338.9mg/g of the ultrasonic extract to 859.7mg/g (338.9 for 9-cis and 520.8 for trans) of the elution fraction. The SAS pulverization of the collected fraction further produced submicron-sized particulates containing 932.1mg/g (355.6 for 9-cis and 576.5 for trans) of total β-carotenes with a recovery of 86.3% (83.9% for cis and 87.8% for trans). Effects of two SAS operational conditions on the purity, recovery of total β-carotenes, mean size and morphology of the precipitates were obtained from an experimentally designed method. Generation of micronized particulates enriched with 9-cis and trans-β-carotenes by low-density SAS was proved to be feasible and environmental benign. Copyright © 2013 Elsevier B.V. All rights reserved.

The twilight zone of cis element alignments.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-02-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

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

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

9-cis Retinoic Acid is the ALDH1A1 Product that Stimulates Melanogenesis

PubMed Central

Paterson, Elyse K.; Ho, Hsiang; Kapadia, Rubina; Ganesan, Anand K.

2013-01-01

Aldehyde dehydrogenase 1A1 (ALDH1A1), an enzyme that catalyzes the conversion of lipid aldehydes to lipid carboxylic acids, plays pleiotropic roles in UV-radiation resistance, melanogenesis, and stem cell maintenance. In this study, a combination of RNAi and pharmacologic approaches were used to determine which ALDH1A1 substrates and products regulate melanogenesis. Initial studies revealed that neither the UV-induced lipid aldehyde 4-hydroxy-2-nonenal nor the ALDH1A1 product all-trans retinoic acid appreciably induced melanogenesis. In contrast, both the ALDH1A1 substrate 9-cis retinal and its corresponding product 9-cis retinoic acid potently induced the accumulation of MITF mRNA, Tyrosinase mRNA, and melanin. ALDH1A1 depletion inhibited the ability of 9-cis retinal but not 9-cis retinoic acid to stimulate melanogenesis, indicating that ALDH1A1 regulates melanogenesis by catalyzing the conversion of 9-cis retinal to 9-cis retinoic acid. The addition of potent ALDH1A inhibitors (cyanamide or Angeli’s salt) suppressed Tyrosinase and MITF mRNA accumulation in vitro and also melanin accumulation in skin equivalents, suggesting that 9-cis retinoids regulate melanogenesis in the intact epidermis. Taken together, these studies not only identify cyanamide as a potential novel treatment for hyperpigmentary disorders, but also identify 9-cis retinoic acid as a pigment stimulatory agent that may have clinical utility in the treatment of hypopigmentary disorders, such as vitiligo. PMID:23489423

ATR-FTIR spectroscopic investigation of the cis- and trans-bis-(α-amino acids) copper(II) complexes

NASA Astrophysics Data System (ADS)

Berestova, Tatyana V.; Kuzina, Lyudmila G.; Amineva, Natalya A.; Faizrakhmanov, Ilshat S.; Massalimov, Ismail A.; Mustafin, Akhat G.

2017-06-01

The crystalline phases of the trans-(a) and cis-(b)-isomers of bis-(α-amino acids) copper(II) complexes [Cu(bL)2] 1-5 (bL - bidentate ligand: gly (1), S-ala (2), R,S-val (3), (±)-thr (4), R,S-phe (5)) were studied by ATR-FTIR spectroscopy in the mid region IR spectrum. It was established that asymmetric νas(COO) and symmetric νs(COO) stretching vibrations of carboxylic groups of 1-5 are sensitive to change of the geometric structure and have a different maxima for the trans(a)- and cis(b)-isomers. It found that νas(COO) and νs(COO) stretching vibrations of cis-isomers are broadened and shifted to longer wavelengths (b) as compared with trans-isomers (a). Shown that peculiarities of crystal packing molecules of geometric isomers may affect on carboxylate stretching vibration bis-α-amino acids complexes copper(II) 1-5 a,b.

The twilight zone of cis element alignments

PubMed Central

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-01-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments. PMID:23268451

Production of isopropyl cis-6-hexadecenoate by regiospecific desaturation of isopropyl palmitate by a double mutant of a Rhodococcus strain.

PubMed

Koike, K; Takaiwa, M; Ara, K; Inoue, S; Kimura, Y; Ito, S

2000-02-01

Resting cells of a double mutant noted as KSM-MT66, derived from Rhodococcus sp. strain KSM-B-3 by UV irradiation, were found to cis-desaturate isopropyl hexadecanoate, yielding isopropyl cis-6-hexadecenoate. Addition of sodium glutamate (1.0%), Mg SO4 (2 mM), and thiamine (2 mM) increased the productivity of the unsaturated product in phosphate buffer. Optimal temperature and pH for the reaction were around 26 degrees C and 7, respectively. Under the optimized conditions, more than 50 g/l of isopropyl cis-6-hexadecenoate was produced after a 3-day incubation by resting cells of the mutant. Thus, cis-6-hexadecenoic acid, the main component of human sebaceous lipids, can be manufactured economically by the rhodococcal bioconversion.

Fatty acids attached to all-trans-astaxanthin alter its cis-trans equilibrium, and consequently its stability, upon light-accelerated autoxidation.

PubMed

de Bruijn, Wouter J C; Weesepoel, Yannick; Vincken, Jean-Paul; Gruppen, Harry

2016-03-01

Fatty acid esterification, common in naturally occurring astaxanthin, has been suggested to influence both colour stability and degradation of all-trans-astaxanthin. Therefore, astaxanthin stability was studied as influenced by monoesterification and diesterification with palmitate. Increased esterification decelerated degradation of all-trans-astaxanthin (RP-UHPLC-PDA), whereas, it had no influence on colour loss over time (spectrophotometry). This difference might be explained by the observation that palmitate esterification influenced the cis-trans equilibrium. Free astaxanthin produced larger amounts of 9-cis isomer whereas monopalmitate esterification resulted in increased 13-cis isomerization. The molar ratios of 9-cis:13-cis after 60min were 1:1.7 (free), 1:4.8 (monopalmitate) and 1:2.6 (dipalmitate). The formation of 9-cis astaxanthin, with its higher molar extinction coefficient than that of all-trans-astaxanthin, might compensate for colour loss induced by conjugated double bond cleavage. As such, it was concluded that spectrophotometry is not an accurate measure of the degradation of the all-trans-astaxanthin molecule. Copyright © 2015 Elsevier Ltd. All rights reserved.

Klyuchevskaya, Volcano, Kamchatka Peninsula, CIS

NASA Technical Reports Server (NTRS)

1991-01-01

Klyuchevskaya, Volcano, Kamchatka Peninsula, CIS (56.0N, 160.5E) is one of several active volcanoes in the CIS and is 15,584 ft. in elevation. Fresh ash fall on the south side of the caldera can be seen as a dirty smudge on the fresh snowfall. Just to the north of the Kamchatka River is Shiveluch, a volcano which had been active a short time previously. There are more than 100 volcanic edifices recognized on Kamchatka, 15 of which are still active.

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.

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

Thermal decomposition and isomerization of cis-permethrin and beta-cypermethrin in the solid phase.

PubMed

González Audino, Paola; Licastro, Susana A; Zerba, Eduardo

2002-02-01

The stability to heart of cis-permethrin and beta-cypermethrin in the solid phase was studied and the decomposition products identified. Samples heated at 210 degrees C in an oven in the dark showed that, in the absence of potassium chlorate (the salt present in smoke-generating formulations of these pyrethroids), cis-permethrin was not isomerized, although in the presence of that salt, decomposition was greater and thermal isomerization occurred. Other salts of the type KXO3 or NaXO3, with X being halogen or nitrogen, also led to a considerable thermal isomerization. Heating the insecticides in solution in the presence of potassium chlorate did not produce isomerization in any of the solvents assayed. Salt-catalysed thermal cis-trans isomerization was also found for other pyrethroids derived from permethrinic or deltamethrinic acid but not for those derived from chrysanthemic acid. The main thermal degradation processes of cis-permethrin and beta-cypermethrin decomposition when potassium chlorate was present were cyclopropane isomerization, ester cleavage and subsequent oxidation of the resulting products. Permethrinic acid, 3-phenoxybenzyle chloride, alcohol, aldehyde and acid were identified in both cases, as well as 3-phenoxybenzyl cyanide from beta-cypermethrin. A similar decomposition pattern occurred after combustion of pyrethroid fumigant formulations.

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.

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.

Environmental testing of CIS based modules

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

Willett, D.

1995-11-01

This report describes environmental testing of Siemen`s CIS modules. Charts and diagrams are presented on data concerning: temporary power loss of laminated mini-modules; the 50 thermal cycle test; the 10 humidity freeze cycle test; results after 1000 hours of exposure to damp heat; and interconnect test structures in damp heat testing. It is concluded that moisture ingress causes permanent increases in the series resistance of modules, and that improved packaging is needed for better high humidity reliability. Also, dry dark heat caused temporary power losses which were recovered in sunlight.

Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages

NASA Astrophysics Data System (ADS)

Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H.

2016-09-01

Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides.

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

Evaluating the economic viability of CdTe/CIS and CIGS/CIS tandem photovoltaic modules

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

Nanayakkara, Sanjini U.; Horowitz, Kelsey; Kanevce, Ana

In this paper, we analyze the potential cost competitiveness of two frameless, glass–glass thin-film tandem photovoltaic module structures, cadmium telluride (CdTe)/CuInSe 2 (CIS) and CuIn 0.3Ga 0.7Se 2 (CIGS)/CIS, based on the demonstrated cost of manufacturing the respective component cell technologies in high volume. To consider multiple economic scenarios, we base the CdTe/CIS module efficiency on the current industrial production of CdTe modules, while for CIGS/CIS, we use an aspirational estimate for CIGS efficiency. We focus on four-terminal mechanically stacked structures, thus avoiding the need to achieve current matching between the two cells. The top cell in such a tandemmore » must have a transparent back contact, which has not been successfully implemented to date. However, for the purpose of understanding the economic viability of both tandems, we assume that this can be implemented at a cost similar to that of sputtered indium tin oxide. The cost of both tandem module structures was found to be nearly identical on an equal-area basis and approximately $30/m 2 higher than the single-junction alternatives. Both tandem modules are about 4% (absolute) more efficient than a module by using the top-cell material alone. We find that these tandem modules might reduce total system cost by as much as 11% in applications having a high area-related balance-of-system cost, such as area-constrained residential systems; however, the relative advantage of tandems decreases in the cases where balance-of-system costs are lower, such as in commercial and utility scale systems.« less

Evaluating the economic viability of CdTe/CIS and CIGS/CIS tandem photovoltaic modules

DOE PAGES

Nanayakkara, Sanjini U.; Horowitz, Kelsey; Kanevce, Ana; ...

2017-01-20

In this paper, we analyze the potential cost competitiveness of two frameless, glass–glass thin-film tandem photovoltaic module structures, cadmium telluride (CdTe)/CuInSe 2 (CIS) and CuIn 0.3Ga 0.7Se 2 (CIGS)/CIS, based on the demonstrated cost of manufacturing the respective component cell technologies in high volume. To consider multiple economic scenarios, we base the CdTe/CIS module efficiency on the current industrial production of CdTe modules, while for CIGS/CIS, we use an aspirational estimate for CIGS efficiency. We focus on four-terminal mechanically stacked structures, thus avoiding the need to achieve current matching between the two cells. The top cell in such a tandemmore » must have a transparent back contact, which has not been successfully implemented to date. However, for the purpose of understanding the economic viability of both tandems, we assume that this can be implemented at a cost similar to that of sputtered indium tin oxide. The cost of both tandem module structures was found to be nearly identical on an equal-area basis and approximately $30/m 2 higher than the single-junction alternatives. Both tandem modules are about 4% (absolute) more efficient than a module by using the top-cell material alone. We find that these tandem modules might reduce total system cost by as much as 11% in applications having a high area-related balance-of-system cost, such as area-constrained residential systems; however, the relative advantage of tandems decreases in the cases where balance-of-system costs are lower, such as in commercial and utility scale systems.« less

Mandarin compound vowels produced by prelingually deafened children with cochlear implants.

PubMed

Yang, Jing; Xu, Li

2017-06-01

Compound vowels including diphthongs and triphthongs have complex, dynamic spectral features. The production of compound vowels by children with cochlear implants (CIs) has not been studied previously. The present study examined the dynamic features of compound vowels in native Mandarin-speaking children with CIs. Fourteen prelingually deafened children with CIs (aged 2.9-8.3 years old) and 14 age-matched, normal-hearing (NH) children produced monosyllables containing six Mandarin compound vowels (i.e., /aɪ/, /aʊ/, /uo/, /iɛ/, /iaʊ/, /ioʊ/). The frequency values of the first two formants were measured at nine equidistant time points over the course of the vowel duration. All formant frequency values were normalized and then used to calculate vowel trajectory length and overall spectral rate of change. The results revealed that the CI children produced significantly longer durations for all six compound vowels. The CI children's ability to produce formant movement for the compound vowels varied considerably. Some CI children produced relatively static formant trajectories for certain diphthongs, whereas others produced certain vowels with greater formant movement than did the NH children. As a group, the CI children roughly followed the NH children on the pattern of magnitude of formant movement, but they showed a slower rate of formant change than did the NH children. The findings suggested that prelingually deafened children with CIs, during the early stage of speech acquisition, had not established appropriate targets and articulatory coordination for compound vowel productions. This preliminary study may shed light on rehabilitation of prelingually deafened children with CIs. Copyright © 2017 Elsevier B.V. All rights reserved.

In vitro and in vivo metabolism of all-trans- and 13-cis-retinoic acid in hamsters. Identification of 13-cis-4-oxoretinoic acid.

PubMed

Frolik, C A; Roller, P P; Roberts, A B; Sporn, M B

1980-09-10

Administration of either all-trans-[3H]- or 13-cis-[3H]retinoic acid to hamsters fed a normal diet results in the formation of a number of polar metabolites. At least one of these metabolites has been shown to be common to both isomers of retinoic acid and can be generated in a hamster liver 10,000 X g supernatant system using 13-cis-retinoic acid as substrate. It has been identified as 13-cis-4-oxoretinoic acid by mass spectral, ultraviolet absorption, and proton NMR characteristics, as well as by its co-migration with synthetic 13-cis-4-oxoretinoic acid in two different high pressure liquid chromatographic systems. In addition, its metabolic precursor, 13-cis-4-hydroxyretinoic acid, has been tentatively identified. These compounds are believed to be early metabolites in the elimination pathway of retinoic acid from the body.

Trans-cis molecular photoswitching in interstellar space

NASA Astrophysics Data System (ADS)

Cuadrado, S.; Goicoechea, J. R.; Roncero, O.; Aguado, A.; Tercero, B.; Cernicharo, J.

2016-11-01

As many organic molecules, formic acid (HCOOH) has two conformers (trans and cis). The energy barrier to internal conversion from trans to cis is much higher than the thermal energy available in molecular clouds. Thus, only the most stable conformer (trans) is expected to exist in detectable amounts. We report the first interstellar detection of cis-HCOOH. Its presence in ultraviolet (UV) irradiated gas exclusively (the Orion Bar photodissociation region), with a low trans-to-cis abundance ratio of 2.8 ± 1.0, supports a photoswitching mechanism: a given conformer absorbs a stellar photon that radiatively excites the molecule to electronic states above the interconversion barrier. Subsequent fluorescent decay leaves the molecule in a different conformer form. This mechanism, which we specifically study with ab initio quantum calculations, was not considered in Space before but likely induces structural changes of a variety of interstellar molecules submitted to UV radiation. This paper makes use of observations obtained with the IRAM-30 m telescope. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain).

The role of 11-cis-retinyl esters in vertebrate cone vision.

PubMed

Babino, Darwin; Perkins, Brian D; Kindermann, Aljoscha; Oberhauser, Vitus; von Lintig, Johannes

2015-01-01

A cycle of cis-to-trans isomerization of the chromophore is intrinsic to vertebrate vision where rod and cone photoreceptors mediate dim- and bright-light vision, respectively. Daylight illumination can greatly exceed the rate at which the photoproduct can be recycled back to the chromophore by the canonical visual cycle. Thus, an additional supply pathway(s) must exist to sustain cone-dependent vision. Two-photon microscopy revealed that the eyes of the zebrafish (Danio rerio) contain high levels of 11-cis-retinyl esters (11-REs) within the retinal pigment epithelium. HPLC analyses demonstrate that 11-REs are bleached by bright light and regenerated in the dark. Pharmacologic treatment with all-trans-retinylamine (Ret-NH2), a potent and specific inhibitor of the trans-to-cis reisomerization reaction of the canonical visual cycle, impeded the regeneration of 11-REs. Intervention with 11-cis-retinol restored the regeneration of 11-REs in the presence of all-trans-Ret-NH2. We used the XOPS:mCFP transgenic zebrafish line with a functional cone-only retina to directly demonstrate that this 11-RE cycle is critical to maintain vision under bright-light conditions. Thus, our analyses reveal that a dark-generated pool of 11-REs helps to supply photoreceptors with the chromophore under the varying light conditions present in natural environments. © FASEB.

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

The Community Intercomparison Suite (CIS)

NASA Astrophysics Data System (ADS)

Watson-Parris, Duncan; Schutgens, Nick; Cook, Nick; Kipling, Zak; Kershaw, Phil; Gryspeerdt, Ed; Lawrence, Bryan; Stier, Philip

2017-04-01

Earth observations (both remote and in-situ) create vast amounts of data providing invaluable constraints for the climate science community. Efficient exploitation of these complex and highly heterogeneous datasets has been limited however by the lack of suitable software tools, particularly for comparison of gridded and ungridded data, thus reducing scientific productivity. CIS (http://cistools.net) is an open-source, command line tool and Python library which allows the straight-forward quantitative analysis, intercomparison and visualisation of remote sensing, in-situ and model data. The CIS can read gridded and ungridded remote sensing, in-situ and model data - and many other data sources 'out-of-the-box', such as ESA Aerosol and Cloud CCI product, MODIS, Cloud CCI, Cloudsat, AERONET. Perhaps most importantly however CIS also employs a modular plugin architecture to allow for the reading of limitless different data types. Users are able to write their own plugins for reading the data sources which they are familiar with, and share them within the community, allowing all to benefit from their expertise. To enable the intercomparison of this data the CIS provides a number of operations including: the aggregation of ungridded and gridded datasets to coarser representations using a number of different built in averaging kernels; the subsetting of data to reduce its extent or dimensionality; the co-location of two distinct datasets onto a single set of co-ordinates; the visualisation of the input or output data through a number of different plots and graphs; the evaluation of arbitrary mathematical expressions against any number of datasets; and a number of other supporting functions such as a statistical comparison of two co-located datasets. These operations can be performed efficiently on local machines or large computing clusters - and is already available on the JASMIN computing facility. A case-study using the GASSP collection of in-situ aerosol observations

IRIS Toxicological Review of Cis-& Trans-1,2-Dichloroethylene (Final Report)

EPA Science Inventory

EPA has finalized the Toxicological Review of cis- & trans-1,2-Dichloroethylene: in support of the Integrated Risk Information System (IRIS). Now final, this assessment may be used by EPA’s program and regional offices to inform decisions to protect human health.

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.

Dipeptide cis-cyclo(Leucyl-Tyrosyl) produced by sponge associated Penicillium sp. F37 inhibits biofilm formation of the pathogenic Staphylococcus epidermidis.

PubMed

Scopel, Marina; Abraham, Wolf-Rainer; Henriques, Amélia T; Macedo, Alexandre J

2013-02-01

Infections associated to microbial biofilms are involved in 80% of human infections and became a challenge concerning public health. Infections related to Staphylococcus epidermidis biofilms are presently commonly associated to medical devices, increasing treatment costs for this type of infection. Alternatives to eliminate this kind of disease have been employed in screening programs using diverse marine-derived fungi source of bioactive compounds capable to combat biofilm formation. In this work was isolated the dipeptide cis-cyclo(Leucyl-Tyrosyl) from a sponge associated Penicillium sp. possessing a remarkable inhibition up to 85% of biofilm formation without interfering with bacterial growth, confirmed by scanning electron microscopy. This is the first demonstration that cis-cyclo(Leucyl-Tyrosyl) is able to specifically inhibit biofilm formation adding another aspect to the broad spectrum of bioactivities of cyclic dipeptides. Copyright © 2012 Elsevier Ltd. All rights reserved.

Improved packing of protein side chains with parallel ant colonies.

PubMed

Quan, Lijun; Lü, Qiang; Li, Haiou; Xia, Xiaoyan; Wu, Hongjie

2014-01-01

The accurate packing of protein side chains is important for many computational biology problems, such as ab initio protein structure prediction, homology modelling, and protein design and ligand docking applications. Many of existing solutions are modelled as a computational optimisation problem. As well as the design of search algorithms, most solutions suffer from an inaccurate energy function for judging whether a prediction is good or bad. Even if the search has found the lowest energy, there is no certainty of obtaining the protein structures with correct side chains. We present a side-chain modelling method, pacoPacker, which uses a parallel ant colony optimisation strategy based on sharing a single pheromone matrix. This parallel approach combines different sources of energy functions and generates protein side-chain conformations with the lowest energies jointly determined by the various energy functions. We further optimised the selected rotamers to construct subrotamer by rotamer minimisation, which reasonably improved the discreteness of the rotamer library. We focused on improving the accuracy of side-chain conformation prediction. For a testing set of 442 proteins, 87.19% of X1 and 77.11% of X12 angles were predicted correctly within 40° of the X-ray positions. We compared the accuracy of pacoPacker with state-of-the-art methods, such as CIS-RR and SCWRL4. We analysed the results from different perspectives, in terms of protein chain and individual residues. In this comprehensive benchmark testing, 51.5% of proteins within a length of 400 amino acids predicted by pacoPacker were superior to the results of CIS-RR and SCWRL4 simultaneously. Finally, we also showed the advantage of using the subrotamers strategy. All results confirmed that our parallel approach is competitive to state-of-the-art solutions for packing side chains. This parallel approach combines various sources of searching intelligence and energy functions to pack protein side chains

Improved packing of protein side chains with parallel ant colonies

PubMed Central

2014-01-01

Introduction The accurate packing of protein side chains is important for many computational biology problems, such as ab initio protein structure prediction, homology modelling, and protein design and ligand docking applications. Many of existing solutions are modelled as a computational optimisation problem. As well as the design of search algorithms, most solutions suffer from an inaccurate energy function for judging whether a prediction is good or bad. Even if the search has found the lowest energy, there is no certainty of obtaining the protein structures with correct side chains. Methods We present a side-chain modelling method, pacoPacker, which uses a parallel ant colony optimisation strategy based on sharing a single pheromone matrix. This parallel approach combines different sources of energy functions and generates protein side-chain conformations with the lowest energies jointly determined by the various energy functions. We further optimised the selected rotamers to construct subrotamer by rotamer minimisation, which reasonably improved the discreteness of the rotamer library. Results We focused on improving the accuracy of side-chain conformation prediction. For a testing set of 442 proteins, 87.19% of X1 and 77.11% of X12 angles were predicted correctly within 40° of the X-ray positions. We compared the accuracy of pacoPacker with state-of-the-art methods, such as CIS-RR and SCWRL4. We analysed the results from different perspectives, in terms of protein chain and individual residues. In this comprehensive benchmark testing, 51.5% of proteins within a length of 400 amino acids predicted by pacoPacker were superior to the results of CIS-RR and SCWRL4 simultaneously. Finally, we also showed the advantage of using the subrotamers strategy. All results confirmed that our parallel approach is competitive to state-of-the-art solutions for packing side chains. Conclusions This parallel approach combines various sources of searching intelligence and energy

Investigation of cis-4-[18F]Fluoro-D-Proline Uptake in Human Brain Tumors After Multimodal Treatment.

PubMed

Verger, Antoine; Stoffels, Gabriele; Galldiks, Norbert; Lohmann, Philipp; Willuweit, Antje; Neumaier, Bernd; Geisler, Stefanie; Langen, Karl-Josef

2018-04-23

Cis-4-[ 18 F]fluoro-D-proline (D-cis-[ 18 F]FPro) has been shown to pass the intact blood-brain barrier and to accumulate in areas of secondary neurodegeneration and necrosis in the rat brain while uptake in experimental brain tumors is low. This pilot study explores the uptake behavior of D-cis-[ 18 F]FPro in human brain tumors after multimodal treatment. In a prospective study, 27 patients with suspected recurrent brain tumor after treatment with surgery, radiotherapy, and/or chemotherapy (SRC) were investigated by dynamic positron emission tomography (PET) using D-cis-[ 18 F]FPro (22 high-grade gliomas, one unspecified glioma, and 4 metastases). Furthermore, two patients with untreated lesions were included (one glioblastoma, one reactive astrogliosis). Data were compared with the results of PET using O-(2-[ 18 F]fluoroethyl)-L-tyrosine ([ 18 F]FET) which detects viable tumor tissue. Tracer distribution, mean and maximum lesion-to-brain ratios (LBR mean , LBR max ), and time-to-peak (TTP) of the time activity curve (TAC) of tracer uptake were evaluated. Final diagnosis was determined by histology (n = 9), clinical follow-up (n = 10), or by [ 18 F]FET PET (n = 10). D-cis-[ 18 F]FPro showed high uptake in both recurrent brain tumors (n = 11) and lesions classified as treatment-related changes (TRC) only (n = 16) (LBR mean 2.2 ± 0.7 and 2.1 ± 0.6, n.s.; LBR max 3.4 ± 1.2 and 3.2 ± 1.3, n.s.). The untreated glioblastoma and the lesion showing reactive astrogliosis exhibited low D-cis-[ 18 F]FPro uptake. Distribution of [ 18 F]FET and D-cis-[ 18 F]FPro uptake was discordant in 21/29 cases indicating that the uptake mechanisms are different. The high accumulation of D-cis-[ 18 F]FPro in pretreated brain tumors and TRC supports the hypothesis that tracer uptake is related to cell death. Further studies before and after therapy are needed to assess the potential of D-cis-[ 18 F]FPro for treatment monitoring.

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.

On the effect of tether composition on cis/trans selectivity in intramolecular Diels-Alder reactions.

PubMed

Paddon-Row, Michael N; Longshaw, Alistair I; Willis, Anthony C; Sherburn, Michael S

2009-01-05

Intramolecular Diels-Alder (IMDA) transition structures (TSs) and energies have been computed at the B3LYP/6-31+G(d) and CBS-QB3 levels of theory for a series of 1,3,8-nonatrienes, H(2)C=CH-CH=CH-CH(2)-X-Z-CH=CH(2) [-X-Z- = -CH(2)-CH(2)- (1); -O-C(=O)- (2); -CH(2)-C(=O)- (3); -O-CH(2)- (4); -NH-C(=O)- (5); -S-C(=O)- (6); -O-C(=S)- (7); -NH-C(=S)- (8); -S-C(=S)- (9)]. For each system studied (1-9), cis- and trans-TS isomers, corresponding, respectively, to endo- and exo-positioning of the -C-X-Z- tether with respect to the diene, have been located and their relative energies (E(rel) (TS)) employed to predict the cis/trans IMDA product ratio. Although the E(rel) (TS) values are modest (typically <3 kJ mol(-1)), they follow a clear and systematic trend. Specifically, as the electronegativity of the tether group X is reduced (X=O --> NH or S), the IMDA cis stereoselectivity diminishes. The predicted stereochemical reaction preferences are explained in terms of two opposing effects operating in the cis-TS, namely (1) unfavorable torsional (eclipsing) strain about the C4-C5 bond, that is caused by the -C-X-C(=Y)- group's strong tendency to maintain local planarity; and (2) attractive electrostatic and secondary orbital interactions between the endo-(thio)carbonyl group, C=Y, and the diene. The former interaction predominates when X is weakly electronegative (X=N, S), while the latter is dominant when X is more strongly electronegative (X=O), or a methylene group (X=CH(2)) which increases tether flexibility. These predictions hold up to experimental scrutiny, with synthetic IMDA reactions of 1, 2, 3, and 4 (published work) and 5, 6, and 8 (this work) delivering ratios close to those calculated. The reactions of thiolacrylate 5 and thioamide 8 represent the first examples of IMDA reactions with tethers of these types. Our results point to strategies for designing tethers, which lead to improved cis/trans-selectivities in IMDAs that are normally only weakly selective

Chemiluminescence Study of the Autoxidation of cis-1,4-Polyisoprene

NASA Technical Reports Server (NTRS)

Mendenhall, G. David; Nathan, Richard A.; Golub, Morton A.

1978-01-01

The free-radical mechanism for the autoxidation of cis-1,4-polyisoprene (natural rubber or its synthetic counterpart) has been investigated extensively. An important feature of this mechanism, and indeed also of the autoxidation of hydrocarbons generally, is that it is a chain process propagated by alkyl and peroxy radicals and terminated through bimolecular reactions involving these same radicals. In the usual oxidation situation, that is, at all oxygen pressures greater than a few torr, the alkyl radicals are rapidly converted to peroxy radicals, and the termination step proceeds almost exclusively through the latter radicals. The bimolecular decay of the peroxy radicals is accompanied by a weak emission of light or chemiluminescence. Kinetic evidence is consistent with an electronically excited ketone produced in the termination reaction as the source of the emission. The first observation of chemiluminescence from the oxidative degradation of polymers was reported by Ashby, who dealt mainly with polypropylene but made passing mention of several other polymers. Subsequently, a number of papers have appeared dealing with oxidative chemiluminescence from a variety of polymers. In this paper we report the first detailed study of the chemiluminescence emitted in the autoxidation of cis-1,4-polyisoprene. The chemiluminescence technique is extremely sensitive and can follow rates of oxidation that are too slow to be measured conveniently by other means. This work thus offered the potential of throwing new light on the autoxidation of cis-1,4-polyisoprene, especially in the very early stages or under ambient conditions where conventional spectroscopic procedures are rather insensitive.

Comparison of Insect Kinin Analogs With cis-Peptide Bond Motif 4-Aminopyroglutamate Identifies Optimal Stereochemistry for Diuretic Activity

DTIC Science & Technology

2006-01-01

Amino acid side-chain-protecting groups were Pbf for Arg and Boc for Trp. The coupling of Fmoc-4-amino- pyroglutamic acids (Fmoc-aPy-OH, Fmoc-apy-OH...Inc. Biopolymers (Pept Sci) 88:1–7, 2007. Keywords: 4-aminopyroglutamic acid ; cis-peptide bond; b-turn mimetic; constrained insect kinin analog...analogs containing three stereochemical var- iants of the (2S, 4S)-4-aminopyroglutamic acid (APy) com- ponent (see Figure 1), a mimic of the cis-peptide

DBMS UTILIZATION: A Corporate Information System (CIS) development approach

NASA Technical Reports Server (NTRS)

Rozett, P.

1983-01-01

The Corporate Information System (CIS), an integrated information system intended to tie the corporation together as a functioning entity, is described. In addition to being a major upgraded automated data processing system, the CIS is a management philosophy which recognizes data as a valuable corporate resource and which distinguishes between data and selected data, or information. It further recognizes that different users need different kinds of information. Plans for CIS development are discussed. It will offer its users not just after-the-fact data, but timely information in a format that is meaningful and useful to the particular user, so that the information can be applied in planning, controlling, and decision making by all levels of management. In effect, CIS will help the corporation itself to function as a total, integrated system by typing together administrative activities through information exchange. The CIS supports the operational, tactical control, and strategic planning functions of the corporation. Operational functions are the day-to-day processing necessary to support the corporation's work, such as purchasing and payroll.

Resonance Raman spectra of bacteriorhodopsin's primary photoproduct: evidence for a distorted 13-cis retinal chromophore.

PubMed Central

Braiman, M; Mathies, R

1982-01-01

We have obtained the resonance Raman spectrum of bacteriorhodopsin's primary photoproduct K with a novel low-temperature spinning sample technique. Purple membrane at 77 K is illuminated with spatially separated actinic (pump) and probe laser beams. The 514-nm pump beam produces a photostationary steady-state mixture of bacteriorhodopsin and K. This mixture is then rotated through the red (676 nm) probe beam, which selectively enhances the Raman scattering from K. The essential advantage of our successive pump-and-probe technique is that it prevents the fluorescence excited by the pump beam from masking the red probe Raman scattering. K exhibits strong Raman lines at 1516, 1294, 1194, 1012, 957, and 811 cm-1. The effects of C15 deuteration on K's fingerprint lines correlate well with those seen in 13-cis model compounds, indicating that K has a 13-cis chromophore. However, the presence of unusually strong "low-wavenumber" lines at 811 and 957 cm-1, attributable to hydrogen out-of-plane wags, indicates that the protein holds the chromophore in a distorted conformation after trans leads to cis isomerization. PMID:6281770

Mechanistic insight into peroxydisulfate reactivity: Oxidation of the cis,cis-[Ru(bpy) 2(OH 2)] 2O 4+ "Blue Dimmer"

DOE PAGES

Hurst, James K.; Roemeling, Margo D.; Lymar, Sergei V.

2015-04-10

One-electron oxidation of the μ-oxo dimer (cis,cis-[Ru III(bpy) 2(OH 2)] 2O 4+, {3,3}) to {3,4} by S 2O 8 2- can be described by three concurrent reaction pathways corresponding to the three protic forms of {3,3}. Free energy correlations of the rate constants, transient species dynamics determined by pulse radiolysis, and medium and temperature dependencies of the alkaline pathway all suggest that the rate determining step in these reactions is a strongly non-adiabatic dissociative electron transfer within a precursor ion pair leading to the {3,4}|SO 4 2-|SO 4 •- ion triple. As deduced from the SO 4 •- scavenging experimentsmore » with 2-propanol, the SO 4 •- radical then either oxidizes {3,4} to {4,4} within the ion triple, effecting a net two-electron oxidation of {3,3}, or escapes in solution with ~25 % probability to react with additional {3,3} and {3,4}, that is, effecting sequential one-electron oxidations. The reaction model presented also invokes rapid {3,3} + {4,4} → 2 {3,4} comproportionation, for which k com ~5×10 7 M -1 s -1 was independently measured. The model provides an explanation for the observation that despite favorable energetics, no oxidation beyond the {3,4} state was detected. As a result, the indiscriminate nature of oxidation by SO 4 •- indicates that its fate must be quantitatively determined when using S 2O 8 2- as an oxidant« less

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

Electronic structure description of the cis-MoOS unit in models for molybdenum hydroxylases.

PubMed

Doonan, Christian J; Rubie, Nick D; Peariso, Katrina; Harris, Hugh H; Knottenbelt, Sushilla Z; George, Graham N; Young, Charles G; Kirk, Martin L

2008-01-09

The molybdenum hydroxylases catalyze the oxidation of numerous aromatic heterocycles and simple organics and, unlike other hydroxylases, utilize water as the source of oxygen incorporated into the product. The electronic structures of the cis-MoOS units in CoCp2[TpiPrMoVOS(OPh)] and TpiPrMoVIOS(OPh) (TpiPr = hydrotris(3-isopropylpyrazol-1-yl)borate), new models for molybdenum hydroxylases, have been studied in detail using S K-edge X-ray absorption spectroscopy, vibrational spectroscopy, and detailed bonding calculations. The results show a highly delocalized Mo=S pi* LUMO redox orbital that is formally Mo(dxy) with approximately 35% sulfido ligand character. Vibrational spectroscopy has been used to quantitate Mo-Ssulfido bond order changes in the cis-MoOS units as a function of redox state. Results support a redox active molecular orbital that has a profound influence on MoOS bonding through changes to the relative electro/nucleophilicity of the terminal sulfido ligand accompanying oxidation state changes. The bonding description for these model cis-MoOS systems supports enzyme mechanisms that are under orbital control and dominantly influenced by the unique electronic structure of the cis-MoOS site. The electronic structure of the oxidized enzyme site is postulated to play a role in polarizing a substrate carbon center for nucleophilic attack by metal activated water and acting as an electron sink in the two-electron oxidation of substrates.

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.

A randomized phase II chemoprevention trial of 13-CIS retinoic acid with or without alpha tocopherol or observation in subjects at high risk for lung cancer.

PubMed

Kelly, Karen; Kittelson, John; Franklin, Wilbur A; Kennedy, Timothy C; Klein, Catherine E; Keith, Robert L; Dempsey, Edward C; Lewis, Marina; Jackson, Mary K; Hirsch, Fred R; Bunn, Paul A; Miller, York E

2009-05-01

No chemoprevention strategies have been proven effective for lung cancer. We evaluated the effect of 13-cis retinoic acid (13-cis RA), with or without alpha tocopherol, as a lung cancer chemoprevention agent in a phase II randomized controlled clinical trial of adult subjects at high risk for lung cancer as defined by the presence of sputum atypia, history of smoking, and airflow obstruction, or a prior surgically cured nonsmall cell lung cancer (disease free, >3 years). Subjects were randomly assigned to receive either 13-cis RA, 13-cis RA plus alpha tocopherol (13-cis RA/alpha toco) or observation for 12 months. Outcome measures are derived from histologic evaluation of bronchial biopsy specimens obtained by bronchoscopy at baseline and follow-up. The primary outcome measure is treatment "failure" defined as histologic progression (any increase in the maximum histologic score) or failure to return for follow-up bronchoscopy. Seventy-five subjects were randomized (27/22/26 to observations/13-cis RA/13-cis RA/alpha toco); 59 completed the trial; 55 had both baseline and follow-up bronchoscopy. The risk of treatment failure was 55.6% (15 of 27) and 50% (24 of 48) in the observation and combined (13 cis RA plus 13 cis RA/alpha toco) treatment arms, respectively (odds ratio adjusted for baseline histology, 0.97; 95% confidence interval, 0.36-2.66; P = 0.95). Among subjects with complete histology data, maximum histology score in the observation arm increased by 0.37 units and by 0.03 units in the treated arms (difference adjusted for baseline, -0.18; 95% confidence interval, -1.16 to 0.81; P = 0.72). Similar (nonsignificant) results were observed for treatment effects on endobronchial proliferation as assessed by Ki-67 immunolabeling. Twelve-month treatment with 13-cis RA produced nonsignificant changes in bronchial histology, consistent with results in other trials. Agents advancing to phase III randomized trials should produce greater histologic changes. The

A Randomized Phase II Chemoprevention Trial of 13-CIS Retinoic Acid with Or without α Tocopherol or Observation in Subjects at High Risk for Lung Cancer

PubMed Central

Kelly, Karen; Kittelson, John; Franklin, Wilbur A.; Kennedy, Timothy C.; Klein, Catherine E.; Keith, Robert L.; Dempsey, Edward C.; Lewis, Marina; Jackson, Mary K.; Hirsch, Fred R.; Bunn, Paul A.; Miller, York E.

2011-01-01

No chemoprevention strategies have been proven effective for lung cancer. We evaluated the effect of 13-cis retinoic acid (13-cis RA), with or without α tocopherol, as a lung cancer chemoprevention agent in a phase II randomized controlled clinical trial of adult subjects at high risk for lung cancer as defined by the presence of sputum atypia, history of smoking, and airflow obstruction, or a prior surgically cured nonsmall cell lung cancer (disease free, >3 years). Subjects were randomly assigned to receive either 13-cis RA, 13-cis RA plus α tocopherol (13-cis RA/α toco) or observation for 12 months. Outcome measures are derived from histologic evaluation of bronchial biopsy specimens obtained by bronchoscopy at baseline and follow-up. The primary outcome measure is treatment “failure” defined as histologic progression (any increase in the maximum histologic score) or failure to return for follow-up bronchoscopy. Seventy-five subjects were randomized (27/22/26 to obervations/13-cis RA/13-cis RA/α toco); 59 completed the trial; 55 had both baseline and follow-up bronchoscopy. The risk of treatment failure was 55.6% (15 of 27) and 50% (24 of 48) in the observation and combined (13 cis RA plus 13 cis RA/α toco) treatment arms, respectively (odds ratio adjusted for baseline histology, 0.97; 95% confidence interval, 0.36–2.66; P = 0.95). Among subjects with complete histology data, maximum histology score in the observation arm increased by 0.37 units and by 0.03 units in the treated arms (difference adjusted for baseline, −0.18; 95% confidence interval, −1.16 to 0.81; P = 0.72). Similar (nonsignificant) results were observed for treatment effects on endobronchial proliferation as assessed by Ki-67 immunolabeling. Twelve-month treatment with 13-cis RA produced nonsignificant changes in bronchial histology, consistent with results in other trials. Agents advancing to phase III randomized trials should produce greater histologic changes. The addition of �

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)

Molecular cloning and characterization of tetrahydroprotoberberine cis-N-methyltransferase, an enzyme involved in alkaloid biosynthesis in opium poppy.

PubMed

Liscombe, David K; Facchini, Peter J

2007-05-18

S-Adenosyl-l-methionine:tetrahydroprotoberberine cis-N-methyltransferase (EC 2.1.1.122) catalyzes the conversion of (S)-stylopine to the quaternary ammonium alkaloid, (S)-cis-N-methylstylopine, as a key step in the biosynthesis of protopine and benzophenanthridine alkaloids in plants. A full-length cDNA encoding a protein exhibiting 45 and 48% amino acid identity with coclaurine N-methyltransferase from Papaver somniferum (opium poppy) and Coptis japonica, respectively, was identified in an elicitor-treated opium poppy cell culture expressed sequence tag data base. Phylogenetic analysis showed that the protein belongs to a unique clade of enzymes that includes coclaurine N-methyltransferase, the predicated translation products of the Arabidopsis thaliana genes, At4g33110 and At4g33120, and bacterial S-adenosyl-L-methionine-dependent cyclopropane fatty acid synthases. Expression of the cDNA in Escherichia coli produced a recombinant enzyme able to convert the protoberberine alkaloids stylopine, canadine, and tetrahydropalmatine to their corresponding N-methylated derivatives. However, the protoberberine alkaloids tetrahydroxyberbine and scoulerine, and simple isoquinoline, benzylisoquinoline, and pavine alkaloids were not accepted as substrates, demonstrating the strict specificity of the enzyme. The apparent K(m) values for (R,S)-stylopine and S-adenosyl-L-methionine were 0.6 and 11.5 microm, respectively. TNMT gene transcripts and enzyme activity were detected in opium poppy seedlings and all mature plant organs and were induced in cultured opium poppy cells after treatment with a fungal elicitor. The enzyme was detected in cell cultures of other members of the Papaveraceae but not in species of related plant families that do not accumulate protopine and benzophenanthridine alkaloids.

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.

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

Property study of poly nitro compounds of cis-syn-cis-2, 6-dioxodecahydro-lH, 5H-diimidazo [4, 5-b: 4', 5'-e] pyrazine

NASA Astrophysics Data System (ADS)

Liu, Yang; Xu, Zhibin; Xu, Yudong; Xu, Liang; Meng, Zihui

2017-03-01

Poly nitro group substituted cis-syn-cis-2, 6-dioxodecahydro-lH, 5H-diimidazo [4, 5-b: 4', 5'-e] pyrazine derivatives are synthesized by modified method and adequately characterized. All compounds have good performance both in density (ρ> 1.85 g/cm3) and high detonation velocity (vD > 8800 m/s, calculated). Some representative compounds, for example, 4 (vD: 9405 ms-1; P: 41.6 GPa) and 5 (vD:9781 ms-1; P: 45.6 GPa) exhibit excellent detonation performances, which are comparable with current energetic compounds such as RDX (vD: 8724 ms-1; P: 35.2 GPa) and HMX (vD:9059 ms-1; P: 39.2 GPa). Considering the sensitivity increasing with the number of nitro group, two componds with tetranitro groups (2 and 3) are worthy of deep research.

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.

Differential role of CYP2E1-mediated metabolism in the lethal and vestibulotoxic effects of cis-crotononitrile in the mouse

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

Boadas-Vaello, Pere; Jover, Eric; Diez-Padrisa, Nuria

2007-12-15

Several alkylnitriles are toxic to sensory systems, including the vestibular system, through yet undefined mechanisms. This study addressed the hypothesis that the vestibular toxicity of cis-crotononitrile depends on CYP2E1-mediated bioactivation. Wild-type (129S1) and CYP2E1-null female mice were exposed to cis-crotononitrile at 0, 2, 2.25 or 2.5 mmol/kg (p.o.) in either a baseline condition or following exposure to 1% acetone in drinking water to induce CYP2E1 expression. The exposed animals were assessed for vestibular toxicity using a behavioral test battery and through surface observation of the vestibular sensory epithelia by scanning electron microscopy. In parallel groups, concentrations of cis-crotononitrile and cyanidemore » were assessed in whole blood. Contrary to our hypothesis, CYP2E1-null mice were slightly more susceptible to the vestibular toxicity of cis-crotononitrile than were control 129S1 mice. Similarly, rather than enhance vestibular toxicity, acetone pretreatment actually reduced it slightly in 129S1 controls, although not in CYP2E1-null mice. In addition, significant differences in mortality were recorded, with the greatest mortality occurring in 129S1 mice after acetone pretreatment. The highest mortality recorded in the 129S1 + acetone mice was associated with the lowest blood concentrations of cis-crotononitrile and the highest concentrations of cyanide at 6 h after nitrile exposure, the time when deaths were initially recorded. We conclude that cis-crotononitrile is a CYP2E1 substrate as hypothesized, but that CYP2E1-mediated metabolism of this nitrile is not necessary for vestibular toxicity; rather, this metabolism constitutes a major pathway for cyanide release and subsequent lethality.« less

Phosphatidic Acid Sequesters Sec18p from cis-SNARE Complexes to Inhibit Priming.

PubMed

Starr, Matthew L; Hurst, Logan R; Fratti, Rutilio A

2016-10-01

Yeast vacuole fusion requires the activation of cis-SNARE complexes through priming carried out by Sec18p/N-ethylmaleimide sensitive factor and Sec17p/α-SNAP. The association of Sec18p with vacuolar cis-SNAREs is regulated in part by phosphatidic acid (PA) phosphatase production of diacylglycerol (DAG). Inhibition of PA phosphatase activity blocks the transfer of membrane-associated Sec18p to SNAREs. Thus, we hypothesized that Sec18p associates with PA-rich membrane microdomains before transferring to cis-SNARE complexes upon PA phosphatase activity. Here, we examined the direct binding of Sec18p to liposomes containing PA or DAG. We found that Sec18p preferentially bound to liposomes containing PA compared with those containing DAG by approximately fivefold. Additionally, using a specific PA-binding domain blocked Sec18p binding to PA-liposomes and displaced endogenous Sec18p from isolated vacuoles. Moreover, the direct addition of excess PA blocked the priming activity of isolated vacuoles in a manner similar to chemically inhibiting PA phosphatase activity. These data suggest that the conversion of PA to DAG facilitates the recruitment of Sec18p to cis-SNAREs. Purified vacuoles from yeast lacking the PA phosphatase Pah1p showed reduced Sec18p association with cis-SNAREs and complementation with plasmid-encoded PAH1 or recombinant Pah1p restored the interaction. Taken together, this demonstrates that regulating PA concentrations by Pah1p activity controls SNARE priming by Sec18p. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Communication: An accurate calculation of the S 1 C 2H 2 cis-trans isomerization barrier height

DOE PAGES

Baraban, Joshua H.; Matthews, Devin A.; Stanton, John F.

2016-03-16

In this study, a high level ab initio calculation of the cis-trans isomerization barrier height in the first excited singlet electronic state of acetylene is found to agree very well with a recent experimental determination.

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.

Organocatalytic, Diastereo- and Enantioselective Synthesis of Nonsymmetric cis-Stilbene Diamines: A Platform for the Preparation of Single-Enantiomer cis-Imidazolines for Protein–Protein Inhibition

PubMed Central

2015-01-01

The finding by scientists at Hoffmann-La Roche that cis-imidazolines could disrupt the protein–protein interaction between p53 and MDM2, thereby inducing apoptosis in cancer cells, raised considerable interest in this scaffold over the past decade. Initial routes to these small molecules (i.e., Nutlin-3) provided only the racemic form, with enantiomers being enriched by chromatographic separation using high-pressure liquid chromatography (HPLC) and a chiral stationary phase. Reported here is the first application of an enantioselective aza-Henry approach to nonsymmetric cis-stilbene diamines and cis-imidazolines. Two novel mono(amidine) organocatalysts (MAM) were discovered to provide high levels of enantioselection (>95% ee) across a broad range of substrate combinations. Furthermore, the versatility of the aza-Henry strategy for preparing nonsymmetric cis-imidazolines is illustrated by a comparison of the roles of aryl nitromethane and aryl aldimine in the key step, which revealed unique substrate electronic effects providing direction for aza-Henry substrate–catalyst matching. This method was used to prepare highly substituted cis-4,5-diaryl imidazolines that project unique aromatic rings, and these were evaluated for MDM2-p53 inhibition in a fluorescence polarization assay. The diversification of access to cis-stilbene diamine-derived imidazolines provided by this platform should streamline their further development as chemical tools for disrupting protein–protein interactions. PMID:25017623

Structural effects in fluorinated cyclopropanes: A microwave study of cis-1,1,2,3-tetrafluorocyclopropane

NASA Astrophysics Data System (ADS)

Beauchamp, R. N.; Gillies, C. W.; Gillies, J. Z.

1990-12-01

Microwave and RFMDR spectra of cis- overlineCHFCHFCF 2, cis- 13overlineCHFCHFCF 2, cis- overlineCDFCDFCF 2, and cis- 13overlineCDFCDFCF 2 have been measured between 26.5 and 40.0 GHz using an HP 8400C spectrometer. The a- and c-type transitions were assigned and fit to the quartic Watson Hamiltonian giving A = 3450.445(2) MHz, B = 2402.831(3) MHz, C = 2060.247(3) MHz, Δ J = 0.39(3) kHz, Δ JK = 0.26(1) kHz, δK = 1.606(9) kHz, δJ = 0.059(1) kHz, and δJK = -0.58(2) kHz for cis- overlineCHFCHFCF 2. A structure is derived from the moment of inertia data by fixing three parameters associated with the CF 2 group. The rS parameters for the CHFCHF segment of the molecule in the overlineCHFCHFCF 2 isotopic frame are r (C 2C 3) = 1.533(3) Å, r (C 2,3H) = 1.099(3) Å, r (F 2 ⋯ F 3) = 2.775(2) Å, and r (H 2 ⋯ H 3) = 2.622(2) Å. Two algorithms describing the CC and CF bond distances are fitted to gas phase structural data for a series of fluorinated cyclopropane derivatives. A partial test of these algorithms is obtained from the structure of cis- overlineCHFCHFCF 2. The structural results are related to theoretical studies of fluorination effects in cyclopropane derivatives.

Enzymatic and free radical formation of cis- and trans- epoxyeicosatrienoic acids in vitro and in vivo.

PubMed

Aliwarga, Theresa; Raccor, Brianne S; Lemaitre, Rozenn N; Sotoodehnia, Nona; Gharib, Sina A; Xu, Libin; Totah, Rheem A

2017-11-01

Epoxyeicosatrienoic acids (EETs) are metabolites of arachidonic acid (AA) oxidation that have important cardioprotective and signaling properties. AA is an ω-6 polyunsaturated fatty acid (PUFA) that is prone to autoxidation. Although hydroperoxides and isoprostanes are major autoxidation products of AA, EETs are also formed from the largely overlooked peroxyl radical addition mechanism. While autoxidation yields both cis- and trans-EETs, cytochrome P450 (CYP) epoxygenases have been shown to exclusively catalyze the formation of all regioisomer cis-EETs, on each of the double bonds. In plasma and red blood cell (RBC) membranes, cis- and trans-EETs have been observed, and both have multiple physiological functions. We developed a sensitive ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) assay that separates cis- and trans- isomers of EETs and applied it to determine the relative distribution of cis- vs. trans-EETs in reaction mixtures of AA subjected to free radical oxidation in benzene and liposomes in vitro. We also determined the in vivo distribution of EETs in several tissues, including human and mouse heart, and RBC membranes. We then measured EET levels in heart and RBC of young mice compared to old. Formation of EETs in free radical reactions of AA in benzene and in liposomes exhibited time- and AA concentration-dependent increase and trans-EET levels were higher than cis-EETs under both conditions. In contrast, cis-EET levels were overall higher in biological samples. In general, trans-EETs increased with mouse age more than cis-EETs. We propose a mechanism for the non-enzymatic formation of cis- and trans-EETs involving addition of the peroxyl radical to one of AA's double bonds followed by bond rotation and intramolecular homolytic substitution (S H i). Enzymatic formation of cis-EETs by cytochrome P450 most likely occurs via a one-step concerted mechanism that does not allow bond rotation. The ability to accurately measure

Proton irradiation of the CIS115 for the JUICE mission

NASA Astrophysics Data System (ADS)

Soman, M. R.; Allanwood, E. A. H.; Holland, A. D.; Winstone, G. P.; Gow, J. P. D.; Stefanov, K.; Leese, M.

2015-09-01

The CIS115 is one of the latest CMOS Imaging Sensors designed by e2v technologies, with 1504x2000 pixels on a 7 μm pitch. Each pixel in the array is a pinned photodiode with a 4T architecture, achieving an average dark current of 22 electrons pixel-1 s-1 at 21°C measured in a front-faced device. The sensor aims for high optical sensitivity by utilising e2v's back-thinning and processing capabilities, providing a sensitive silicon thickness approximately 9 μm to 12 μm thick with a tuned anti-reflective coating. The sensor operates in a rolling shutter mode incorporating reset level subtraction resulting in a mean pixel readout noise of 4.25 electrons rms. The full well has been measured to be 34000 electrons in a previous study, resulting in a dynamic range of up to 8000. These performance characteristics have led to the CIS115 being chosen for JANUS, the high-resolution and wide-angle optical camera on the JUpiter ICy moon Explorer (JUICE). The three year science phase of JUICE is in the harsh radiation environment of the Jovian magnetosphere, primarily studying Jupiter and its icy moons. Analysis of the expected radiation environment and shielding levels from the spacecraft and instrument design predict the End Of Life (EOL) displacement and ionising damage for the CIS115 to be equivalent to 1010 10 MeV protons cm-2 and 100 krad(Si) respectively. Dark current and image lag characterisation results following initial proton irradiations are presented, detailing the initial phase of space qualification of the CIS115. Results are compared to the pre-irradiation performance and the instrument specifications and further qualification plans are outlined.

Isolation of pyrrolocins A-C: cis- and trans-decalin tetramic acid antibiotics from an endophytic fungal-derived pathway.

PubMed

Jadulco, Raquel C; Koch, Michael; Kakule, Thomas B; Schmidt, Eric W; Orendt, Anita; He, Haiyin; Janso, Jeffrey E; Carter, Guy T; Larson, Erica C; Pond, Christopher; Matainaho, Teatulohi K; Barrows, Louis R

2014-11-26

Three new decalin-type tetramic acid analogues, pyrrolocins A (1), B (2), and C (3), were defined as products of a metabolic pathway from a fern endophyte, NRRL 50135, from Papua New Guinea. NRRL 50135 initially produced 1 but ceased its production before chemical or biological evaluation could be completed. Upon transfer of the biosynthetic pathway to a model host, 1-3 were produced. All three compounds are structurally related to equisetin-type compounds, with 1 and 3 having a trans-decalin ring system, while 2 has a cis-fused decalin. All were active against Mycobacterium tuberculosis, with the trans-decalin analogues 1 and 3 exhibiting lower MICs than the cis-decalin analogue 2. Here we report the isolation, structure elucidation, and antimycobacterial activities of 1-3 from the recombinant expression as well as the isolation of 1 from the wild-type fungus NRRL 50135.

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.

LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint

PubMed Central

Dimitrova, Nadya; Zamudio, Jesse R.; Jong, Robyn M.; Soukup, Dylan; Resnick, Rebecca; Sarma, Kavitha; Ward, Amanda J.; Raj, Arjun; Lee, Jeannie; Sharp, Phillip A.; Jacks, Tyler

2014-01-01

SUMMARY The p53-regulated long non-coding RNA lincRNA-p21 has been proposed to act in trans via several mechanisms ranging from repressing genes in the p53 transcriptional network to regulating mRNA translation and protein stability. To further examine lincRNA-p21 function we generated a conditional knockout mouse model. We find that lincRNA-p21 predominantly functions in cis to activate expression of its neighboring gene, p21. Mechanistically, we show that lincRNA-p21 acts in concert with hnRNP-K as a co-activator for p53-dependent p21 transcription. Additional phenotypes of lincRNA-p21 deficiency could be attributed to diminished p21 levels, including deregulated expression and altered chromatin state of some Polycomb target genes, defective G1/S checkpoint, increased proliferation rates, and enhanced reprogramming efficiency. These findings indicate that lincRNA-p21 affects global gene expression and influences the p53 tumor suppressor pathway by acting in cis as a locus-restricted co-activator for p53-mediated p21 expression. PMID:24857549

Large-area copper indium diselenide (CIS) process, control and manufacturing

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

Gillespie, T.J.; Lanning, B.R.; Marshall, C.H.

1997-12-31

Lockheed Martin Astronautics (LMA) has developed a large-area (30x30cm) sequential CIS manufacturing approach amenable to low-cost photovoltaics (PV) production. A prototype CIS manufacturing system has been designed and built with compositional uniformity (Cu/In ratio) verified within {+-}4 atomic percent over the 30x30cm area. CIS device efficiencies have been measured by the National Renewable Energy Laboratory (NREL) at 7% on a flexible non-sodium-containing substrate and 10% on a soda-lime-silica (SLS) glass substrate. Critical elements of the manufacturing capability include the CIS sequential process selection, uniform large-area material deposition, and in-situ process control. Details of the process and large-area manufacturing approach aremore » discussed and results presented.« less

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

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.

Supercritical fluid extraction of 13-cis retinoic acid and its photoisomers from selected pharmaceutical dosage forms.

PubMed

Simmons, B R; Chukwumerije, O; Stewart, J T

1997-11-01

13-Cis retinoic acid (Accutane) was extracted from a cream, gel, capsule and beadlet dosage from using supercritical carbon dioxide modified with 5% methanol as the mobile phase. The pump pressure and the extraction chamber and restrictor temperature were experimentally optimized at 325 atm and 45 degrees C, respectively. A 2.5-min static and 5-min dynamic extraction time were used. The supercritical fluid extraction (SFE) eluent was trapped in methanol, injected into the high-performance liquid chromatographic (HPLC) system, and quantitated by ultraviolet detection at 360 nm. Application of the SFE method to spiked placebo dosage forms gave 13-cis retinoic acid recoveries of 98.8, 98.9, 98.8 and 100% for the cream, gel, capsule and beadlet, respectively, with R.S.D.s in the range 0.6-0.9% (n = 4). Inter-day percent error and precision of the extraction were 1.1-2.0 and 0.2-2.4% (n = 3), respectively, and intra-day percent error and precision were 1.0-3.0 and 0.3-2.1% (n = 8), respectively. Percent error and precision data for spiked celite samples in the 0.05-1.0 microgram ml-1 range were 0.59-4.75 and 1.8-2.1% (n = 3), respectively. The extraction method was applied to commercial 13-cis retinoic acid dosage forms and the results compared to unextracted samples. Linear regression analysis of concentration versus peak height gave a correlation coefficient of 0.9991 with a slope of 7.468 and a y-intercept of 0.1923. The percent error and precision data were 1.3-5.3 and 0.2-1.5% (n = 4), respectively. The photoisomers of 13-cis retinoic acid were also extracted with the method and recoveries of 90.4-92.4% with R.S.D.s of 1.5-3.4% were obtained (n = 4).

Sex Pheromone of the Almond Moth and the Indian Meal Moth: cis-9, trans-12-Tetradecadienyl Acetate.

PubMed

Kuwahara, Y; Kitamura, C; Takashi, S; Hara, H; Ishii, S; Fukami, H

1971-02-26

Female moths of different species but belonging to the same subfamily produce an identical compound as their sex pheromone. The sex pheromone of the almond moth, Cadra cautella (Walker), and the Indian meal moth, Plodia interpunctella (Hübner), has been isolated and identified as cis-9, trans-12-tetradecadienyl acetate.

The high sensitivity of the rabbit to the teratogenic effects of 13-cis-retinoic acid (isotretinoin) is a consequence of prolonged exposure of the embryo to 13-cis-retinoic acid and 13-cis-4-oxo-retinoic acid, and not of isomerization to all-trans-retinoic acid.

PubMed

Tzimas, G; Bürgin, H; Collins, M D; Hummler, H; Nau, H

1994-01-01

Previous studies suggested that the rabbit is much more susceptible to the teratogenic action of 13-cis-retinoic acid (13-cis-RA) than the mouse or the rat, while the teratogenicity of all-trans-RA was comparable in these species. In the present study we investigated if pharmacokinetics can explain these species- and structure-related differences. The embryotoxic and teratogenic potential of all-trans-retinoic acid (all-trans-RA) and 13-cis-RA were evaluated in the Swiss hare rabbit after oral administration of daily doses of the two drugs throughout organogenesis, from gestation day (GD) 6 to 18 (plug day = GD 0). All-trans-RA was given at dose levels of 0.7, 2 or 6 mg/kg body weight per day and 13-cis-RA at 3, 7.5 or 10 mg/kg per day. The doses needed to elicit a minimum teratogenic response were found to be 6 mg/kg per day for all-trans-RA and 10 mg/kg per day for 13-cis-RA. Using these doses, transplacental pharmacokinetics of all-trans- and 13-cis-RA were performed. Pregnant rabbits were treated once daily from GD 7 to 12 and plasma and embryo samples were collected for HPLC analysis at various time intervals after the final dose. The main plasma metabolites of all-trans- and 13-cis-RA were all-trans-beta-glucuronide (all-trans-RAG) and 13-cis-4-oxo-RA, respectively. The elimination of 13-cis-RA and its metabolites from maternal plasma were much slower than of all-trans-RA resulting in accumulation of the 13-cis-isomers in plasma. Marked differences in the placental transfer of the two drugs and their metabolites were observed. All-trans-RA and all-trans-4-oxo-RA were efficiently transferred to the rabbit embryo, reaching concentrations similar to the plasma levels. On the contrary, the 13-cis-isomers reached the embryo to a lesser extent. Despite its limited placental transfer, a considerable embryonic exposure to 13-cis-RA and 13-cis-4-oxo-RA was noticed after treatment with isotretinoin, as indicated by their area-under-the-concentration-time-curve (AUC

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.

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

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.

Mono- and bifunctional binding of cis-diamminedichloroplatinum(II) to dinucleotides.

PubMed

Försti, A; Laatikainen, R; Hemminki, K

1987-01-01

cis-Diamminedichloroplatinum(II) (cis-Pt) was reacted with four homodinucleotides (GpG, ApA, CpC, and UpU) and six heterodinucleotides (GpC, CpG, GpU, UpG, GpA, and ApG) at pH 6, and the reaction products were purified by HPLC. The most important products were characterized by 1H-NMR spectra. In all the heterodinucleotides except the ones containing uridine the main Pt-adduct was an intramolecular cross-link, but monofunctional adducts and intermolecular cross-links were also detected. Intramolecular cross-links were also formed with GpU and UpG but the amounts of them were about the same as the amounts of intermolecular cross-links. In the case of homodinucleotides GpG gave almost entirely intramolecular cross-links, in which cis-Pt was chelated between the N-7 atoms of two guanines. cis-Pt reacted also with ApA forming both monofunctional and bifunctional Pt-adducts. The main adducts were intramolecular cross-links. cis-Pt reacted equally well with all guanosine-containing dinucleotides, while the reaction with ApA was much slower. With CpC and UpU no reaction products were formed.

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.

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.

The Clinical Interview Schedule-Revised (CIS-R)-Malay Version, Clinical Validation.

PubMed

Subramaniam, Kavitha; Krishnaswamy, Saroja; Jemain, Abdul Aziz; Hamid, Abdul; Patel, Vikram

2006-01-01

Use of instruments or questionnaires in different cultural settings without proper validation can result in inaccurate results. Issues like reliability, validity, feasibility and acceptability should be considered in the use of an instrument. The study aims to determine the usefulness of the CIS-R Malay version in detecting common mental health problems specifically to establish the validity. The CIS-R instrument (PROQSY* format) was translated through the back translation process into Malay. Inter rater reliability was established for raters who were medical students. Cases and controls for the study were psychiatric in patients, out patient and relatives or friends accompanying the patients to the clinic or visiting the inpatients. The Malay version of CIS-R was administered to all cases and controls. All cases and controls involved in the study were rated by psychiatrists for psychiatric morbidity using the SCID as a guideline. Specificity and sensitivity of the CIS-R to the assessment by the psychiatrist were determined. The Malay version of CIS-R showed 100% sensitivity and 96.15% specificity at a cut off score of 9. The CIS-R can be a useful instrument for clinical and research use in the Malaysian population for diagnosing common mental disorders like depression and anxiety.

Understanding and managing health and environmental risks of CIS, CGS, and CdTe photovoltaic module production and use: A workshop

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

Moskowitz, P.D.; Zweibel, K.; DePhillips, M.P.

1994-04-28

Environmental, health and safety (EH&S) risks presented by CIS, CGS and CdTe photovoltaic module production, use and decommissioning have been reviewed and discussed by several authors. Several EH&S concerns exit. The estimated EH&S risks are based on extrapolations of toxicity, environmental mobility, and bioavailability data for other related inorganic compounds. Sparse data, however, are available for CIS, CGS or CdTe. In response to the increased interest in these materials, Brookhaven National Laboratory (BNL) has been engaged in a cooperative research program with the National Renewable Energy Laboratory (NREL), the Fraunhofer Institute for Solid State Technology (IFT), the Institute of Ecotoxicitymore » of the GSF Forschungszentrum fair Umwelt und Gesundheit, and the National Institute of Environmental Health Sciences (NIEHS) to develop fundamental toxicological and environmental data for these three compounds. This workshop report describes the results of these studies and describes their potential implications with respect to the EH&S risks presented by CIS, CGS, and CdTe module production, use and decommissioning.« less

Abundant raw material for cis-regulatory evolution in humans

NASA Technical Reports Server (NTRS)

Rockman, Matthew V.; Wray, Gregory A.

2002-01-01

Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (<13,000), in part because of an overrepresentation among the former in multiallelic tandem repeat variation, especially (AC)(n) dinucleotide microsatellites. The role of microsatellites in gene expression variation may provide a larger store of heritable phenotypic variation, and a more rapid mutational input of such variation, than has been realized. Finally, we outline the distinctive consequences of cis-regulatory variation for the genotype-phenotype relationship, including ubiquitous epistasis and genotype-by-environment interactions, as well as underappreciated modes of pleiotropy and overdominance. Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.

Structural analysis of conjugated linoleic acid produced by Lactobacillus plantarum, and factors affecting isomer production.

PubMed

Kishino, Shigenobu; Ogawa, Jun; Ando, Akinori; Iwashita, Takashi; Fujita, Tsuyoshi; Kawashima, Hiroshi; Shimizu, Sakayu

2003-01-01

An isomer of the conjugated linoleic acid (CLA) produced from linoleic acid by Lactobacillus plantarum was identified as cis-9,trans-11-octadecadienoic acid by proton nuclear magnetic resonance spectroscopy. Together with earlier results, we concluded that the bacterium produces two CLA isomers, cis-9,trans-11- and trans-9,trans-11-octadecadienoic acid from linoleic acid. The addition of L-serine, glucose, AgNO3, or NaCl to the reaction mixture reduced production of the latter.

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

A Cis-Lunar Propellant Infrastructure for Flexible Path Exploration and Space Commerce

NASA Technical Reports Server (NTRS)

Oeftering, Richard C.

2012-01-01

This paper describes a space infrastructure concept that exploits lunar water for propellant production and delivers it to users in cis-lunar space. The goal is to provide responsive economical space transportation to destinations beyond low Earth orbit (LEO) and enable in-space commerce. This is a game changing concept that could fundamentally affect future space operations, provide greater access to space beyond LEO, and broaden participation in space exploration. The challenge is to minimize infrastructure development cost while achieving a low operational cost. This study discusses the evolutionary development of the infrastructure from a very modest robotic operation to one that is capable of supporting human operations. The cis-lunar infrastructure involves a mix of technologies including cryogenic propellant production, reusable lunar landers, propellant tankers, orbital transfer vehicles, aerobraking technologies, and electric propulsion. This cislunar propellant infrastructure replaces Earth-launched propellants for missions beyond LEO. It enables users to reach destinations with smaller launchers or effectively multiplies the user s existing payload capacity. Users can exploit the expanded capacity to launch logistics material that can then be traded with the infrastructure for propellants. This mutually beneficial trade between the cis-lunar infrastructure and propellant users forms the basis of in-space commerce.

Design study of an S-band RF cavity of a dual-energy electron LINAC for the CIS

NASA Astrophysics Data System (ADS)

Lee, Byeong-No; Park, Hyungdal; Song, Ki-baek; Li, Yonggui; Lee, Byung Cheol; Cha, Sung-su; Lee, Jong-Chul; Shin, Seung-Wook; Chai, Jong-seo

2014-01-01

The design of a resonance frequency (RF) cavity for the dual-energy S-band electron linear accelerator (LINAC) has been carried out for the cargo inspection system (CIS). This Standing-wave-type RF cavity is operated at a frequency under the 2856-MHz resonance frequency and generates electron beams of 9 MeV (high mode) and 6 MeV (low mode). The electrons are accelerated from the initial energy of the electron gun to the target energy (9 or 6 MeV) inside the RF cavity by using the RF power transmitted from a 5.5-MW-class klystron. Then, electron beams with a 1-kW average power (both high mode and low mode) bombard an X-ray target a 2-mm spot size. The proposed accelerating gradient was 13 MV/m, and the designed Q value was about 7100. On going research on 15-MeV non-destructive inspections for military or other applications is presented.

9-cis-retinoic acid increases apolipoprotein AI secretion and mRNA expression in HepG2 cells.

PubMed

Haghpassand, M; Moberly, J B

1995-10-01

HepG2 cells were studied as a model for regulation of hepatic apolipoprotein AI (apo AI) secretion and gene expression by 9-cis-retinoic acid. HepG2 cells cultured on plastic dishes were exposed to 9-cis-retinoic acid (9-cis-RA) for 48 h with a complete media change at 24 h. Apo AI mass in cultured media was determined by ELISA, by quantitative immunoblotting and by steady-state 35S-methionine labeling. Messenger RNA levels were determined by RNase protection using probes for apo AI and the housekeeping gene, glyceraldehyde 3-phosphate dehydrogenase (G3PDH). 9-cis-RA increased secretion of apo AI by 52% at doses of 10 and 1 microM (6.3 +/- 0.6 vs. 4.2 +/- 0.3; P < 0.005; 6.1 +/- 0.3 vs. 4.0 +/- 0.7 ng of apo AI/mg cell protein, P < 0.05) and by 35% at 0.1 microM (5.5 +/- 0.6 vs. 4.1 +/- 0.4 ng apo AI/mg protein, P < 0.05, n = 4). Immunoblotting results were consistent with results from ELISA (70% increase at 10 microM 9-cis-RA, P < 0.001; 34% increase at 1 microM, P < 0.005, n = 3). Metabolically labeled apoAI in the medium was increased by 39% following steady-state labeling in the presence of 10 microM 9-cis-RA (597 +/- 7 vs. 430 +/- 13 DPM/microliters media; P < 0.001; n = 4). 9-cis-RA (10 microM) also increased HepG2 cell apo AI mRNA expression by 76% (68 700 +/- 400 vs. 38 900 +/- 2700 DPM, P < 0.01, n = 4), whereas expression of G3PDH mRNA was slightly decreased (14%, P < 0.05). Thus, 9-cis-RA stimulates apo AI expression in HepG2 cells, suggesting a role for retinoids in activating endogenous apo AI gene expression.

Entry and Exit Mechanisms at the cis-Face of the Golgi Complex

PubMed Central

Lorente-Rodríguez, Andrés; Barlowe, Charles

2011-01-01

Vesicular transport of protein and lipid cargo from the endoplasmic reticulum (ER) to cis-Golgi compartments depends on coat protein complexes, Rab GTPases, tethering factors, and membrane fusion catalysts. ER-derived vesicles deliver cargo to an ER-Golgi intermediate compartment (ERGIC) that then fuses with and/or matures into cis-Golgi compartments. The forward transport pathway to cis-Golgi compartments is balanced by a retrograde directed pathway that recycles transport machinery back to the ER. How trafficking through the ERGIC and cis-Golgi is coordinated to maintain organelle structure and function is poorly understood and highlights central questions regarding trafficking routes and organization of the early secretory pathway. PMID:21482742

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

Directed evolution of toluene dioxygenase from Pseudomonas putida for improved selectivity toward cis-indandiol during indene bioconversion.

PubMed

Zhang, N; Stewart, B G; Moore, J C; Greasham, R L; Robinson, D K; Buckland, B C; Lee, C

2000-10-01

Toluene dioxygenase (TDO) from Pseudomonas putida F1 converts indene to a mixture of cis-indandiol (racemic), 1-indenol, and 1-indanone. The desired product, cis-(1S,2R)-indandiol, is a potential key intermediate in the chemical synthesis of indinavir sulfate (Crixivan), Merck's HIV-1 protease inhibitor for the treatment of AIDS. To reduce the undesirable byproducts 1-indenol and 1-indanone formed during indene bioconversion, the recombinant TDO expressed in Escherichia coli was evolved by directed evolution using the error-prone polymerase chain reaction (epPCR) method. High-throughput fluorometric and spectrophotometric assays were developed for rapid screening of the mutant libraries in a 96-well format. Mutants with reduced 1-indenol by-product formation were identified, and the individual indene bioconversion product profiles of the selected mutants were confirmed by HPLC. Changes in the amino acid sequence of the mutant enzymes were identified by analyzing the nucleotide sequence of the genes. A mutant with the most desirable product profile from each library, defined as the most reduced 1-indenol concentration and with the highest cis-(1S,2R)-indandiol enantiomeric excess, was used to perform each subsequent round of mutagenesis. After three rounds of mutagenesis and screening, mutant 1C4-3G was identified to have a threefold reduction in 1-indenol formation over the wild type (20% vs 60% of total products) and a 40% increase of product (cis-indandiol) yield.

Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes.

PubMed

Infante, Carlos R; Mihala, Alexandra G; Park, Sungdae; Wang, Jialiang S; Johnson, Kenji K; Lauderdale, James D; Menke, Douglas B

2015-10-12

The amniote phallus and limbs differ dramatically in their morphologies but share patterns of signaling and gene expression in early development. Thus far, the extent to which genital and limb transcriptional networks also share cis-regulatory elements has remained unexplored. We show that many limb enhancers are retained in snake genomes, suggesting that these elements may function in non-limb tissues. Consistent with this, our analysis of cis-regulatory activity in mice and Anolis lizards reveals that patterns of enhancer activity in embryonic limbs and genitalia overlap heavily. In mice, deletion of HLEB, an enhancer of Tbx4, produces defects in hindlimbs and genitalia, establishing the importance of this limb-genital enhancer for development of these different appendages. Further analyses demonstrate that the HLEB of snakes has lost hindlimb enhancer function while retaining genital activity. Our findings identify roles for Tbx4 in genital development and highlight deep similarities in cis-regulatory activity between limbs and genitalia. Copyright © 2015 Elsevier Inc. All rights reserved.

Outcome of High-Risk Stage 3 Neuroblastoma with Myeloablative Therapy and 13-cis-Retinoic Acid: A Report from the Children’s Oncology Group

PubMed Central

Park, Julie R.; Villablanca, Judith G.; London, Wendy B.; Gerbing, Robert B.; Haas-Kogan, Daphne; Stanton Adkins, E.; Attiyeh, Edward F.; Maris, John M.; Seeger, Robert C.; Patrick Reynolds, C.; Matthay, Katherine K.

2009-01-01

Background The components of therapy required for patients with INSS Stage 3 neuroblastoma and high risk features remain controversial. Procedure A retrospective cohort design was used to determine if intensive chemoradiotherapy with purged autologous bone marrow rescue (ABMT) and/or 13-cis-retinoic acid (13-cis-RA) improved outcome for patients with high-risk neuroblastoma that was not metastatic to distant sites. We identified 72 patients with INSS Stage 3 neuroblastoma enrolled between 1991 and 1996 on the Phase III CCG 3891 randomized trial. Patients were analyzed on an intent-to-treat basis using a log-rank test. Results The 5-year event-free survival (EFS) and overall survival (OS) rates for patients with Stage 3 neuroblastoma were 55 +/- 6% and 59% +/- 6%, respectively (n=72). Patients randomized to ABMT (n=20) had 5-year EFS of 65% +/- 11% and OS of 65% +/- 11% compared to 41% +/- 11 (p=0.21) and 46% +/- 11% (p=0.23) for patients randomized to CC (n=23), respectively. Patients randomized to 13-cis-RA (n=23) had 5-year EFS of 70% +/- 10% and OS of 78% +/- 9% compared to 63% +/- 12% (p=0.67) and 67% +/- 12% (p=0.55) for those receiving no further therapy (n=16), respectively. Patients randomized to both ABMT and 13-cis-RA (n=6) had a 5-year EFS of 80% ± 11% and OS of 100%. Conclusion Patients with high-risk Stage 3 neuroblastoma have an overall poor prognosis despite aggressive chemoradiotherapy. Further studies are warranted to determine if myeloablative consolidation followed by 13-cis-RA maintenance therapy statistically significantly improves outcome. PMID:18937318

40 CFR 721.2250 - 1,4-Cyclohexanediamine, cis- and trans-.

Code of Federal Regulations, 2011 CFR

2011-07-01

... § 721.125 (a), (b), (c), (f), (g), (h), (i), and (k) are applicable to manufacturers, importers, and... 40 Protection of Environment 31 2011-07-01 2011-07-01 false 1,4-Cyclohexanediamine, cis- and trans... Substances § 721.2250 1,4-Cyclohexanediamine, cis- and trans-. (a) Chemical substances and significant new...

Deciphering the transcriptional cis-regulatory code.

PubMed

Yáñez-Cuna, J Omar; Kvon, Evgeny Z; Stark, Alexander

2013-01-01

Information about developmental gene expression resides in defined regulatory elements, called enhancers, in the non-coding part of the genome. Although cells reliably utilize enhancers to orchestrate gene expression, a cis-regulatory code that would allow their interpretation has remained one of the greatest challenges of modern biology. In this review, we summarize studies from the past three decades that describe progress towards revealing the properties of enhancers and discuss how recent approaches are providing unprecedented insights into regulatory elements in animal genomes. Over the next years, we believe that the functional characterization of regulatory sequences in entire genomes, combined with recent computational methods, will provide a comprehensive view of genomic regulatory elements and their building blocks and will enable researchers to begin to understand the sequence basis of the cis-regulatory code. Copyright © 2012 Elsevier Ltd. All rights reserved.

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.

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.

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

Photoionization and trans-to-cis isomerization of β-cyclodextrin-encapsulated azobenzene induced by two-color two-laser-pulse excitation.

PubMed

Takeshita, Tatsuya; Hara, Michihiro

2018-03-15

Azobenzene (1) and the complex resulting from the incorporation of 1 with cyclodextrin (1/CD) are attractive for light-driven applications such as micromachining and chemical biology tools. The highly sensitive photoresponse of 1 is crucial for light-driven applications containing both 1 and 1/CD to reach their full potential. In this study, we investigated the photoionization and trans-to-cis isomerization of 1/CD induced by one- and two-color two-laser pulse excitation. Photoionization of 1/CD, which was induced by stepwise two-photon absorption, was observed using laser pulse excitation at 266nm. Additionally, simultaneous irradiation with 266 and 532nm laser pulses increased the trans-to-cis isomerization yield (Υ t→c ) by 27%. It was concluded that the increase in Υ t→c was caused by the occurrence of trans-to-cis isomerization in the higher-energy singlet state (S n ), which was reached by S 1 →S n transition induced by laser pulse excitation at 532nm. The results of this study are potentially applicable in light-driven applications such as micromachining and chemical biology tools. Copyright © 2018 Elsevier B.V. All rights reserved.

Pharmacology of 13-cis-retinoic acid in humans.

PubMed

Kerr, I G; Lippman, M E; Jenkins, J; Myers, C E

1982-05-01

Vitamin A and its analogs (retinoids) have shown great promise for the chemoprevention of cancer as well as being a possible new class of chemotherapeutic agents. A Phase I and II trial of 13-cis-retinoic acid in advanced cancers was initiated, and the clinical pharmacology of the drug was studied. All patients received p.o. 13-cis-retinoic acid starting at 0.5 mg/kg/day, escalating over 4 weeks to a maximum dose of 8 mg/kg/day in divided doses. Although there was a linear correlation of plasma concentration with dose escalation, large inter-individual variations in peak plasma concentrations were noted. At the maximum drug dose, the mean peak plasma concentration was 4 X 10(-6) M. There was little drug accumulation on this schedule, as trough concentrations between p.o. doses often dropped below 1 X 10(-6) M. The drug was metabolized extensively to a metabolite, the concentrations of which exceeding parent 13-cis-retinoic acid concentrations with chronic dosing. Retinol concentrations were below the normal range.

Crystal structures of the diastereomeric salt pair of the prostaglandin intermediate 1 R, 2 S(+)- cis-2-hydroxycyclopent-4-enylacetic acid with S- and R- 1-phenylethylamine

NASA Astrophysics Data System (ADS)

Czugler, Mátyás; Csöregh, Ingeborg; Kálmán, Alajos; Faigl, Ferenc; Ács, Mária

1989-05-01

Crystal structures of an enantiomeric salt pair formed between 1 R,2 S- cis-2-hydroxycyclopent-4-enylacetic acid ( S-HCA) and R(+)-1-phenylethylamine ( R-PEA) and the corresponding S-PEA salt have been determined by X-ray crystallography. The S-HCA: R-PEA 1:1 salt ( R-HCA-PEA hereafter) is orthorhombic, P2 12 12 1, with the unit-cell parameters a = 5.806(1), b = 9.261(1), c = 27.624(2) Å and R = 0.056 for 1162 reflections at ambient temperature. The S-HCA: S-PEA 1:1 salt ( S-HCAPEA) is also orthorhombic, P2 12 12 1, with the unit-cell data a = 6.034(2), b = 11.840(7), c = 20.198(11) Å at 170 K, R = 0.082 for 1196 data measured at low temperatures (170 K). The R-HCAPEA salt has its two components assembled into an elongated rod-like shape via two-dimensional hydrogen bonding between cations and anions thus forming a well-ordered crystal. In contrast, the cation and anion in the S-HCAPEA salt forms a more globular aggregate and displays orientation disorder in the five-membered ring part of the anion and maintains an essentially one-dimensional hydrogen-bond network, while the total number of hydrogen bonds between cationic and anionic species remains three in both crystals.

Highly Luminescent Water-Dispersible NIR-Emitting Wurtzite CuInS2/ZnS Core/Shell Colloidal Quantum Dots

PubMed Central

2017-01-01

Copper indium sulfide (CIS) quantum dots (QDs) are attractive as labels for biomedical imaging, since they have large absorption coefficients across a broad spectral range, size- and composition-tunable photoluminescence from the visible to the near-infrared, and low toxicity. However, the application of NIR-emitting CIS QDs is still hindered by large size and shape dispersions and low photoluminescence quantum yields (PLQYs). In this work, we develop an efficient pathway to synthesize highly luminescent NIR-emitting wurtzite CIS/ZnS QDs, starting from template Cu2-xS nanocrystals (NCs), which are converted by topotactic partial Cu+ for In3+ exchange into CIS NCs. These NCs are subsequently used as cores for the overgrowth of ZnS shells (≤1 nm thick). The CIS/ZnS core/shell QDs exhibit PL tunability from the first to the second NIR window (750–1100 nm), with PLQYs ranging from 75% (at 820 nm) to 25% (at 1050 nm), and can be readily transferred to water upon exchange of the native ligands for mercaptoundecanoic acid. The resulting water-dispersible CIS/ZnS QDs possess good colloidal stability over at least 6 months and PLQYs ranging from 39% (at 820 nm) to 6% (at 1050 nm). These PLQYs are superior to those of commonly available water-soluble NIR-fluorophores (dyes and QDs), making the hydrophilic CIS/ZnS QDs developed in this work promising candidates for further application as NIR emitters in bioimaging. The hydrophobic CIS/ZnS QDs obtained immediately after the ZnS shelling are also attractive as fluorophores in luminescent solar concentrators. PMID:28638177

Emerging roles in plant defense for cis-jasmone-induced cytochrome P450 CYP81D11.

PubMed

Matthes, Michaela; Bruce, Toby; Chamberlain, Keith; Pickett, John; Napier, Johnathan

2011-04-01

cis-Jasmone is a volatile organic compound emitted constitutively by flowers or leaves of several plant species where it acts as an attractant for pollinators and as a chemical cue for host localisation (or avoidance) for insects. ( 1-3) It is also released by some plant species after feeding damage inflicted by herbivorous insects and in this case might serve as a chemical cue for parasitoids to guide them to their prey (so called "indirect defense"). ( 4,5) Moreover, we have recently shown that plants can perceive cis-jasmone and that it acts as a signaling molecule in A. thaliana, inducing a discrete and distinctive suite of genes, of which a large subset is putatively involved in metabolism and defense responses. ( 6) Cytochrome P450s feature prominently in these functional subsets and of these the highest fold change upon cis-jasmone treatment occurred with the cytochrome CYP81D11 (At3g28740). ( 6) Hence this gene was chosen for a more thorough analysis of the potential biological relevance of the cis-jasmone induced defense response. Although the precise function of CYP81D11 remains to be determined, we could previously demonstrate its involvement in the indirect defense response in Arabidopsis, as plants exposed to cis-jasmone ceased to be attractive to the aphid parasitoid Aphidius ervi when this P450 was inactivated by T-DNA insertion mutagenesis. ( 6) Here we report additional experiments which give further support to a role of CYP81D11 in the direct or indirect defense response of A. thaliana.

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.

Anharmonic vibrational analysis of s-trans and s-cis conformers of acryloyl fluoride using numerical-analytic Van Vleck operator perturbation theory

NASA Astrophysics Data System (ADS)

Krasnoshchekov, Sergey V.; Craig, Norman C.; Koroleva, Lidiya A.; Stepanov, Nikolay F.

2018-01-01

A new gas-phase infrared (IR) spectrum of acryloyl fluoride (ACRF, CH2dbnd CHsbnd CFdbnd O) with a resolution of 0.1 cm- 1 in the range 4000-450 cm- 1 was measured. Theoretical ab initio molecular structures, full quartic potential energy surfaces (PES), and cubic surfaces of dipole moments and polarizability tensor components (electro-optical properties, EOP) of the s-trans and s-cis conformers of the ACRF were calculated by the second-order Møller-Plesset electronic perturbation theory with a correlation consistent Dunning triple-ζ basis set. The numerical-analytic implementation of the second-order operator canonical Van Vleck perturbation theory was employed for predicting anharmonic IR and Raman scattering (RS) spectra of ACRF. To improve the anharmonic predictions, harmonic frequencies were replaced by their counterparts evaluated with the higher-level CCSD(T)/cc-pVTZ model, to form a ;hybrid; PES. The original operator representation of the Hamiltonian is analytically reduced to a quasi-diagonal form, integrated in the harmonic oscillator basis and diagonalized to account for strong resonance couplings. Double canonical transformations of EOP expansions enabled prediction of integral intensities of both fundamental and multi-quanta transitions in IR/RS spectra. Enhanced band shape analysis reinforced the assignments. A thorough interpretation of the new IR experimental spectra and existing matrix-isolation literature data for the mixture of two conformers of ACRF was accomplished, and a number of assignments clarified.

Workstation Designs for a Cis-Lunar Deep Space Habitat

NASA Technical Reports Server (NTRS)

Howe, A. Scott

2014-01-01

Using the International Standard Payload Rack (ISPR) system, a suite of workstations required for deep space missions have been proposed to fill out habitation functions in an International Space Station (ISS) derived Cis-lunar Deep Space Habitat. This paper introduces the functional layout of the Cis-lunar habitat design, and describes conceptual designs for modular deployable work surfaces, General Maintenance Workstation (GMWS), In-Space Manufacturing Workstation (ISMW), Intra-Vehicular Activity Telerobotics Work Station (IVA-TRWS), and Galley / Wardroom.

Design of cyclic peptides featuring proline predominantly in the cis conformation under physiological conditions.

PubMed

Malešević, Miroslav; Schumann, Michael; Jahreis, Günther; Fischer, Gunter; Lücke, Christian

2012-09-24

Turns are secondary-structure elements that are omnipresent in natively folded polypeptide chains. A large variety of four-residue β-turns exist, which differ mainly in the backbone dihedral angle values of the two central residues i+1 and i+2. The βVI-type turns are of particular biological interest because the i+2 residue is always a proline in the cis conformation and might thus serve as target of peptidyl prolyl cis/trans isomerases (PPIases). We have designed cyclic hexapeptides containing two proline residues that predominantly adopt the cis conformation in aqueous solution. NMR data and MD calculations indicated that the cyclic peptide sequences c-(-DXaa-Ser-Pro-DXaa-Lys-Pro-) result in highly symmetric backbone structures when both prolines are in the cis conformation and the D-amino acids are either alanine or phenylalanine residues. Replacement of the serine residue either by phosphoserine or by tyrosine compromises this symmetry, but further increases the cis conformation content of both prolines. As a result, we obtained a cyclic hexapeptide that exists almost exclusively as the cis-Pro/cis-Pro conformer but shows no cis/trans interconversion even in the presence of the PPIase Pin1, apparently due to an energetically quite favorable but highly restricted conformational space. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Columbia River Coordinated Information System (CIS), 1992-1993 Annual Report.

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

Rowe, Mike; Roger, Phillip B.; O'Connor, Dick

1993-11-01

The purposes of this report are to: (1) describe the project to date; (2) to document the work and accomplishments of the (CIS) project for Fiscal Year 1993; and (3) to provide a glimpse of future project direction. The concept of a Coordinated Information System (CIS) as an approach to meeting the growing needs for regionally standardized anadromous fish information.

Recombinant human glutathione S-transferases catalyse enzymic isomerization of 13-cis-retinoic acid to all-trans-retinoic acid in vitro.

PubMed Central

Chen, H; Juchau, M R

1998-01-01

The steric conversion of 13-cis-retinoic acid (13-cRA) to all-trans-retinoic acid (t-RA) has been proposed as an activation mechanism for the observed therapeutic and teratogenic activities of 13-cRA. Here we have investigated the catalysis of isomerization of 13-cRA to t-RA by recombinant human glutathione S-transferases (GSTs). Substrate was incubated with GST in 0.1 M sodium phosphate buffer, pH 7.5, at 37 degrees C in total darkness. The t-RA generated was measured quantitatively by HPLC. Under the reaction conditions used, GSTP1-1 was far more effective than human GSTM1-1 or human GSTA1-1 in catalysing the isomerization reaction. The reaction catalysed by GSTP1-1 showed substrate saturation and the Km and Vmax values for the reaction were approx. 7 microM and 650 pmol/min per nmol respectively. The reaction rate increased linearly with increasing enzyme concentration. The reaction was inhibited both by heat treatment and by S-decylglutathione (a potent inhibitor of transferase activity associated with GST). Additions of polyclonal rabbit antiserum for human GSTP1-1 to the reaction resulted in a significant decrease in generation of t-RA (70-80%). In addition, ethacrynic acid, a selective substrate for Pi isoforms of GST, also inhibited the isomerization of 13-cRA to t-RA catalysed by GSTP1-1. Under the same reaction conditions, GSTP1-1 was much less effective in catalysing the steric conversion of 9-cis-retinoic acid to t-RA, indicating that the enzyme was stereospecific for the conversion of 13-cRA to t-RA. These observations suggest that enzymic catalysis was the primary mechanism for the GSTP1-1-dependent conversion of 13-cRA to t-RA. Reactions catalysed by a purified rat hepatic GST Pi isoenzyme proceeded more slowly than reactions catalysed by human GSTP1-1. Comparative studies also showed that there were marked species differences in catalytic activities between various purified mammalian hepatic GST mixtures. PMID:9806904

Recombinant human glutathione S-transferases catalyse enzymic isomerization of 13-cis-retinoic acid to all-trans-retinoic acid in vitro.

PubMed

Chen, H; Juchau, M R

1998-11-15

The steric conversion of 13-cis-retinoic acid (13-cRA) to all-trans-retinoic acid (t-RA) has been proposed as an activation mechanism for the observed therapeutic and teratogenic activities of 13-cRA. Here we have investigated the catalysis of isomerization of 13-cRA to t-RA by recombinant human glutathione S-transferases (GSTs). Substrate was incubated with GST in 0.1 M sodium phosphate buffer, pH 7.5, at 37 degrees C in total darkness. The t-RA generated was measured quantitatively by HPLC. Under the reaction conditions used, GSTP1-1 was far more effective than human GSTM1-1 or human GSTA1-1 in catalysing the isomerization reaction. The reaction catalysed by GSTP1-1 showed substrate saturation and the Km and Vmax values for the reaction were approx. 7 microM and 650 pmol/min per nmol respectively. The reaction rate increased linearly with increasing enzyme concentration. The reaction was inhibited both by heat treatment and by S-decylglutathione (a potent inhibitor of transferase activity associated with GST). Additions of polyclonal rabbit antiserum for human GSTP1-1 to the reaction resulted in a significant decrease in generation of t-RA (70-80%). In addition, ethacrynic acid, a selective substrate for Pi isoforms of GST, also inhibited the isomerization of 13-cRA to t-RA catalysed by GSTP1-1. Under the same reaction conditions, GSTP1-1 was much less effective in catalysing the steric conversion of 9-cis-retinoic acid to t-RA, indicating that the enzyme was stereospecific for the conversion of 13-cRA to t-RA. These observations suggest that enzymic catalysis was the primary mechanism for the GSTP1-1-dependent conversion of 13-cRA to t-RA. Reactions catalysed by a purified rat hepatic GST Pi isoenzyme proceeded more slowly than reactions catalysed by human GSTP1-1. Comparative studies also showed that there were marked species differences in catalytic activities between various purified mammalian hepatic GST mixtures.

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.

Communication: An accurate calculation of the S{sub 1} C{sub 2}H{sub 2} cis-trans isomerization barrier height

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

Baraban, Joshua H.; Matthews, Devin A.; Stanton, John F.

2016-03-21

A high level ab initio calculation of the cis-trans isomerization barrier height in the first excited singlet electronic state of acetylene is found to agree very well with a recent experimental determination.

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

Characterization of a cis-Golgi matrix protein, GM130

PubMed Central

1995-01-01

Antisera raised to a detergent- and salt-resistant matrix fraction from rat liver Golgi stacks were used to screen an expression library from rat liver cDNA. A full-length clone was obtained encoding a protein of 130 kD (termed GM130), the COOH-terminal domain of which was highly homologous to a Golgi human auto-antigen, golgin-95 (Fritzler et al., 1993). Biochemical data showed that GM130 is a peripheral cytoplasmic protein that is tightly bound to Golgi membranes and part of a larger oligomeric complex. Predictions from the protein sequence suggest that GM130 is an extended rod-like protein with coiled-coil domains. Immunofluorescence microscopy showed partial overlap with medial- and trans-Golgi markers but almost complete overlap with the cis-Golgi network (CGN) marker, syntaxin5. Immunoelectron microscopy confirmed this location showing that most of the GM130 was located in the CGN and in one or two cisternae on the cis-side of the Golgi stack. GM130 was not re-distributed to the ER in the presence of brefeldin A but maintained its overlap with syntaxin5 and a partial overlap with the ER- Golgi intermediate compartment marker, p53. Together these results suggest that GM130 is part of a cis-Golgi matrix and has a role in maintaining cis-Golgi structure. PMID:8557739

Physiological and Chemical Investigations into Microbial Degradation of Synthetic Poly(cis-1,4-isoprene)

PubMed Central

Bode, Helge B.; Zeeck, Axel; Plückhahn, Kirsten; Jendrossek, Dieter

2000-01-01

Streptomyces coelicolor 1A and Pseudomonas citronellolis were able to degrade synthetic high-molecular-weight poly(cis-1,4-isoprene) and vulcanized natural rubber. Growth on the polymers was poor but significantly greater than that of the nondegrading strain Streptomyces lividans 1326 (control). Measurement of the molecular weight distribution of the polymer before and after degradation showed a time-dependent increase in low-molecular-weight polymer molecules for S. coelicolor 1A and P. citronellolis, whereas the molecular weight distribution for the control (S. lividans 1326) remained almost constant. Three degradation products were isolated from the culture fluid of S. coelicolor 1A grown on vulcanized rubber and were identified as (6Z)-2,6-dimethyl-10-oxo-undec-6-enoic acid, (5Z)-6-methyl-undec-5-ene-2,9-dione, and (5Z,9Z)-6,10-dimethyl-pentadec-5,9-diene-2,13-dione. An oxidative pathway from poly(cis-1,4-isoprene) to methyl-branched diketones is proposed. It includes (i) oxidation of an aldehyde intermediate to a carboxylic acid, (ii) one cycle of β-oxidation, (iii) oxidation of the conjugated double bond resulting in a β-keto acid, and (iv) decarboxylation. PMID:10966376

Cis-regulatory landscapes of four cell types of the retina.

PubMed

Hartl, Dominik; Krebs, Arnaud R; Jüttner, Josephine; Roska, Botond; Schübeler, Dirk

2017-11-16

The retina is composed of ∼50 cell-types with specific functions for the process of vision. Identification of the cis-regulatory elements active in retinal cell-types is key to elucidate the networks controlling this diversity. Here, we combined transcriptome and epigenome profiling to map the regulatory landscape of four cell-types isolated from mouse retinas including rod and cone photoreceptors as well as rare inter-neuron populations such as horizontal and starburst amacrine cells. Integration of this information reveals sequence determinants and candidate transcription factors for controlling cellular specialization. Additionally, we refined parallel reporter assays to enable studying the transcriptional activity of large collection of sequences in individual cell-types isolated from a tissue. We provide proof of concept for this approach and its scalability by characterizing the transcriptional capacity of several hundred putative regulatory sequences within individual retinal cell-types. This generates a catalogue of cis-regulatory regions active in retinal cell types and we further demonstrate their utility as potential resource for cellular tagging and manipulation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Rapid baseline separation of enantiomers and a mesoform of all-trans-astaxanthin, 13-cis-astaxanthin, adonirubin, and adonixanthin in standards and commercial supplements.

PubMed

Wang, Chunlei; Armstrong, Daniel W; Chang, Chau-Dung

2008-06-20

Astaxanthin (3,3'-dihydroxy-beta,beta-carotene-4,4'-dione) is widely used as important colorant in the aquaculture feed industry, and as nutraceuticals in human health products. Synthetic all-trans-astaxanthin consists of a mixture of a pair of enantiomers (3R,3'R and 3S,3'S) and a mesoform (3R,3'S). A high-performance liquid chromatography (HPLC) method for direct, rapid, and baseline separation of three stereoisomers of all-trans-astaxanthin is described for the first time on an immobilized cellulosic column (Chiralpak IC). Enantiomers of two important precursors in the biosynthetic pathway of astaxanthin, adonirubin and adonixanthin, were also directly separated. In addition, the major cis form of astaxanthin (13-cis-astaxanthin) resulted from isomerization was isolated with preparative C18 separation, and the separation of all four stereoisomers of 13-cis-astaxanthin is achieved. Finally, a stereoisomeric purity test of commercial astaxanthin supplements confirmed that they were from a natural source, although their levels were quite low.

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.

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

Glutathione S-transferases act as isomerases in isomerization of 13-cis-retinoic acid to all-trans-retinoic acid in vitro.

PubMed

Chen, H; Juchau, M R

1997-11-01

A discovery that rapid enzymic isomerization of 13-cis-retinoic acid (13-cRA) to all-trans-retinoic acid (t-RA) can be catalysed by purified hepatic glutathione S-transferases (GSTs; EC 2.5.1.18) from rat is now reported. Rates of cis-trans isomerization were determined quantitatively by HPLC. GST-catalysed reactions reached equilibrium rapidly, in marked contrast with uncatalysed or GSH-catalysed isomerizations. The GST-catalysed reaction exhibited substrate saturation kinetics with a Km of approx. 8 microM. The maximal velocity of the reaction and the catalytic efficiency of GSTs were determined. The initial rate of the reaction increased linearly as a function of enzyme concentration. Catalysis by GSTs was independent of the presence of GSH, indicating that GSTs act as GSH-independent isomerases as well as transferases. Incubation with guanidine (7-8 M) or heat-inactivation of GSTs (100 degrees C for 3 min) decreased isomerase activities by approx. 50% and 75% respectively. The same heat treatment did not significantly inhibit isomerization catalysed by GSH and apoferritin, indicating that the observed decrease in isomerase activity by heat inactivation was not primarily due to oxidation of protein thiol groups in the GSTs. The specific activity of GSTs was approx. 23- and 340-fold those of GSH and apoferritin respectively when comparisons were made on the basis of free thiol concentrations, indicating that free thiol in GSTs cannot account for the majority of observed isomerase activities and suggesting that specific conformations of GSTs are important for such activities. Complete inhibition of the reaction by low concentrations of N-ethylmaleimide (10 microM) demonstrated that intact protein thiols are required for the isomerase activities of GSTs.

Decrease of blood anti-α1,3 Galactose Abs levels in multiple sclerosis (MS) and clinically isolated syndrome (CIS) patients.

PubMed

Le Berre, L; Rousse, J; Gourraud, P-A; Imbert-Marcille, B-M; Salama, A; Evanno, G; Semana, G; Nicot, A; Dugast, E; Guérif, P; Adjaoud, C; Freour, T; Brouard, S; Agbalika, F; Marignier, R; Brassat, D; Laplaud, D-A; Drouet, E; Van Pesch, V; Soulillou, J-P

2017-07-01

The etiology of multiple sclerosis (MS) remains elusive. Among the possible causes, the increase of anti-Neu5Gc antibodies during EBV primo-infection of Infectious mononucleosis (IMN) may damage the integrity of the blood-brain barrier facilitating the transfer of EBV-infected B cells and anti-EBV T cell clones in the brain. We investigated the change in titers of anti-Neu5Gc and anti-α1,3 Galactose antibodies in 49 IMN, in 76 MS, and 73 clinically isolated syndrome (CIS) patients, as well as age/gender-matched healthy individuals. Anti-Gal and anti-Neu5Gc are significantly increased during IMN (p=0.02 and p<1.10 -4 respectively), but not in acute CMV primo-infection. We show that, whereas there was no change in anti-Neu5Gc in MS/CIS, the two populations exhibit a significant decrease in anti-Gal (combined p=2.7.10 -3 ), in contrast with patients with non-MS/CIS central nervous system pathologies. Since anti-Gal result from an immunization against α1,3 Gal, lacking in humans but produced in the gut, our data suggest that CIS and MS patients have an altered microbiota or an altered response to this microbiotic epitope. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

PDSS/IMC CIS user's guide

NASA Technical Reports Server (NTRS)

1984-01-01

The Spacelab Payload Development Support System PDSS Image Motion Compensator (IMC) computer interface simulation (CIS) user's manual is given. The software provides a real time interface simulation for the following IMC subsystems: the Dry Rotor Reference Unit, the Advanced Star/Target Reference Optical sensor, the Ultra Violet imaging telescope, the Wisconson Ultraviolet Photopolarimetry Experiment, the Cruciform Power distributor, and the Spacelab Experiment Computer Operating System.

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

Structural Elucidation of cis / trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry

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

Zheng, Xueyun; Renslow, Ryan S.; Makola, Mpho M.

Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/transmore » isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.« less

Ethical Challenges of Educational Leadership in the Countries of the CIS

ERIC Educational Resources Information Center

Zagoumennov, Iouri

2010-01-01

There is no school administrators' pre-service training in the CIS (Former USSR) countries. As for the in-service training, it has been traditionally focused on educational management. As a result, schools in the CIS countries are run as well-oiled machines but there is a big question mark over whether these machines are running in the right…

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.

PubMed

Mathelier, Anthony; Lefebvre, Calvin; Zhang, Allen W; Arenillas, David J; Ding, Jiarui; Wasserman, Wyeth W; Shah, Sohrab P

2015-04-23

With the rapid increase of whole-genome sequencing of human cancers, an important opportunity to analyze and characterize somatic mutations lying within cis-regulatory regions has emerged. A focus on protein-coding regions to identify nonsense or missense mutations disruptive to protein structure and/or function has led to important insights; however, the impact on gene expression of mutations lying within cis-regulatory regions remains under-explored. We analyzed somatic mutations from 84 matched tumor-normal whole genomes from B-cell lymphomas with accompanying gene expression measurements to elucidate the extent to which these cancers are disrupted by cis-regulatory mutations. We characterize mutations overlapping a high quality set of well-annotated transcription factor binding sites (TFBSs), covering a similar portion of the genome as protein-coding exons. Our results indicate that cis-regulatory mutations overlapping predicted TFBSs are enriched in promoter regions of genes involved in apoptosis or growth/proliferation. By integrating gene expression data with mutation data, our computational approach culminates with identification of cis-regulatory mutations most likely to participate in dysregulation of the gene expression program. The impact can be measured along with protein-coding mutations to highlight key mutations disrupting gene expression and pathways in cancer. Our study yields specific genes with disrupted expression triggered by genomic mutations in either the coding or the regulatory space. It implies that mutated regulatory components of the genome contribute substantially to cancer pathways. Our analyses demonstrate that identifying genomically altered cis-regulatory elements coupled with analysis of gene expression data will augment biological interpretation of mutational landscapes of cancers.

Stable and Flexible CuInS2/ZnS:Al-TiO2 Film for Solar-Light-Driven Photodegradation of Soil Fumigant.

PubMed

Yan, Lili; Li, Zhichun; Sun, Mingxing; Shen, Guoqing; Li, Liang

2016-08-10

Semiconductor quantum dots (QDs) are suitable light absorbers for photocatalysis because of their unique properties. However, QDs generally suffer from poor photochemical stability against air, limiting their applications in photocatalysis. In this study, a stable solar-light-driven QDs-containing photocatalytic film was developed to facilitate photocatalytic degradation of the soil fumigant 1,3-dichloropropene (1,3-D). Highly stable CuInS2/ZnS:Al core/shell QDs (CIS/ZnS:Al QDs) were synthesized by doping Al into the ZnS shell and controlling ZnS:Al shell thickness; the CIS/ZnS:Al QDs were subsequently combined with TiO2 to form a CIS/ZnS:Al-TiO2 photocatalyst. The optimized ZnS:Al shell thickness for 1,3-D photodegradation was approximately 1.3 nm, which guaranteed and balanced the good photocatalytic activity and stability of the CIS/ZnS:Al-TiO2 photocatalyst. The photodegradation efficiency of 1,3-D can be maintained up to more than 80% after five cycles during recycling experiment. When CIS/ZnS:Al-TiO2 was deposited as photocatalytic film on a flexible polyethylene terephthalate substrate, over 99% of cis-1,3-D and 98% of trans-1,3-D were depleted as they passed through the film during 15 h of irradiation under natural solar light. This study demonstrated that the stable CIS/ZnS:Al-TiO2 photocatalyst both in powder and film form is a promising agent for photodegradation and emission reduction of soil fumigants.

13-cis retinoic acid and isomerisation in paediatric oncology--is changing shape the key to success?

PubMed

Armstrong, Jane L; Redfern, Christopher P F; Veal, Gareth J

2005-05-01

Retinoic acid isomers have been used with some success as chemotherapeutic agents, most recently with 13-cis retinoic acid showing impressive clinical efficacy in the paediatric malignancy neuroblastoma. The aim of this commentary is to review the evidence that 13-cis retinoic acid is a pro-drug, and consider the implications of retinoid metabolism and isomerisation for the further development of retinoic acid for cancer therapy. The low binding affinity of 13-cis retinoic acid for retinoic acid receptors, low activity in gene expression assays and the accumulation of the all-trans isomer in cells treated with 13-cis retinoic acid, coupled with the more-favourable pharmacokinetic profile of 13-cis retinoic acid compared to other isomers, suggest that intracellular isomerisation to all-trans retinoic acid is the key process underlying the biological activity of 13-cis retinoic acid. Intracellular metabolism of all-trans retinoic acid by a positive auto-regulatory loop may result in clinical resistance to retinoic acid. Agents that block or reduce the metabolism of all-trans retinoic acid are therefore attractive targets for drug development. Devising strategies to deliver 13-cis retinoic acid to tumour cells and facilitate the intracellular isomerisation of 13-cis retinoic acid, while limiting metabolism of all-trans retinoic acid, may have a major impact on the efficacy of 13-cis retinoic acid in paediatric oncology.

The retina visual cycle is driven by cis retinol oxidation in the outer segments of cones

PubMed Central

Sato, Shinya; Frederiksen, Rikard; Cornwall, M. Carter; Kefalov, Vladimir J.

2017-01-01

Vertebrate rod and cone photoreceptors require continuous supply of chromophore for regenerating their visual pigments after photoactivation. Cones, which mediate our daytime vision, demand a particularly rapid supply of 11-cis retinal chromophore in order to maintain their function in bright light. An important contribution to this process is thought to be the chromophore precursor 11-cis retinol, which is supplied to cones from Müller cells in the retina and subsequently oxidized to 11-cis retinal as part of the retina visual cycle. However, the molecular identity of the cis retinol oxidase in cones remains unclear. Here, as a first step in characterizing this enzymatic reaction, we sought to determine the subcellular localization of this activity in salamander red cones. We found that the onset of dark adaptation of isolated salamander red cones was substantially faster when exposing directly their outer vs. their inner segment to 9-cis retinol, an analogue of 11-cis retinol. In contrast, this difference was not observed when treating the outer vs. inner segment with 9-cis retinal, a chromophore analogue which can directly support pigment regeneration. These results suggest, surprisingly, that the cis-retinol oxidation occurs in the outer segments of cone photoreceptors. Confirming this notion, pigment regeneration with exogenously added 9-cis retinol was directly observed in the truncated outer segments of cones, but not in rods. We conclude that the enzymatic machinery required for the oxidation of recycled cis retinol as part of the retina visual cycle is present in the outer segments of cones. PMID:28359344

Structure of H/ACA RNP protein Nhp2p reveals cis/trans isomerization of a conserved proline at the RNA and Nop10 binding interface

PubMed Central

Koo, Bon-Kyung; Park, Chin-Ju; Fernandez, Cesar F.; Chim, Nicholas; Ding, Yi; Chanfreau, Guillaume; Feigon, Juli

2011-01-01

H/ACA small nucleolar and Cajal body ribonucleoproteins (RNPs) function in site-specific pseudouridylation of eukaryotic rRNA and snRNA, rRNA processing, and vertebrate telomerase biogenesis. Nhp2, one of four essential protein components of eukaryotic H/ACA RNPs, forms a core trimer with the pseudouridylase Cbf5 and Nop10 that specifically binds to H/ACA RNAs. Crystal structures of archaeal H/ACA RNPs have revealed how the protein components interact with each other and with the H/ACA RNA. However, in place of Nhp2p, archaeal H/ACA RNPs contain L7Ae, which binds specifically to an RNA K-loop motif absent in eukaryotic H/ACA RNPs, while Nhp2 binds a broader range of RNA structures. We report solution NMR studies of S. cerevisiae Nhp2 (Nhp2p), which reveal that Nhp2p exhibits two major conformations in solution due to cis/trans isomerization of the evolutionarily conserved Pro83. The equivalent proline is in the cis conformation in all reported structures of L7Ae and other homologous proteins. Nhp2p has the expected α-β-α fold, but the solution structures of the major conformation of Nhp2p with trans Pro83 and of Nhp2p-S82W with cis Pro83 reveal that Pro83 cis/trans isomerization affects the positions of numerous residues at the Nop10- and RNA-binding interface. An S82W substitution, which stabilizes the cis conformation, also stabilizes the association of Nhp2p with H/ACA snoRNPs in vivo. We propose that Pro83 plays a key role in the assembly of the eukaryotic H/ACA RNP, with the cis conformation locking in a stable Cbf5-Nop10-Nhp2 ternary complex and positioning the protein backbone to interact with the H/ACA RNA. PMID:21708174

On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions

NASA Astrophysics Data System (ADS)

Tarpine, Ryan; Istrail, Sorin

The regulatory genome is about the “system level organization of the core genomic regulatory apparatus, and how this is the locus of causality underlying the twin phenomena of animal development and animal evolution” (E.H. Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Academic Press, 2006). Information processing in the regulatory genome is done through regulatory states, defined as sets of transcription factors (sequence-specific DNA binding proteins which determine gene expression) that are expressed and active at the same time. The core information processing machinery consists of modular DNA sequence elements, called cis-modules, that interact with transcription factors. The cis-modules “read” the information contained in the regulatory state of the cell through transcription factor binding, “process” it, and directly or indirectly communicate with the basal transcription apparatus to determine gene expression. This endowment of each gene with the information-receiving capacity through their cis-regulatory modules is essential for the response to every possible regulatory state to which it might be exposed during all phases of the life cycle and in all cell types. We present here a set of challenges addressed by our CYRENE research project aimed at studying the cis-regulatory code of the regulatory genome. The CYRENE Project is devoted to (1) the construction of a database, the cis-Lexicon, containing comprehensive information across species about experimentally validated cis-regulatory modules; and (2) the software development of a next-generation genome browser, the cis-Browser, specialized for the regulatory genome. The presentation is anchored on three main computational challenges: the Gene Naming Problem, the Consensus Sequence Bottleneck Problem, and the Logic Function Inference Problem.

Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters.

PubMed

Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo

2005-02-01

cis-Acting regulatory elements are important molecular switches involved in the transcriptional regulation of a dynamic network of gene activities controlling various biological processes, including abiotic stress responses, hormone responses and developmental processes. In particular, understanding regulatory gene networks in stress response cascades depends on successful functional analyses of cis-acting elements. The ever-improving accuracy of transcriptome expression profiling has led to the identification of various combinations of cis-acting elements in the promoter regions of stress-inducible genes involved in stress and hormone responses. Here we discuss major cis-acting elements, such as the ABA-responsive element (ABRE) and the dehydration-responsive element/C-repeat (DRE/CRT), that are a vital part of ABA-dependent and ABA-independent gene expression in osmotic and cold stress responses.

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

Glutathione S-transferases act as isomerases in isomerization of 13-cis-retinoic acid to all-trans-retinoic acid in vitro.

PubMed Central

Chen, H; Juchau, M R

1997-01-01

A discovery that rapid enzymic isomerization of 13-cis-retinoic acid (13-cRA) to all-trans-retinoic acid (t-RA) can be catalysed by purified hepatic glutathione S-transferases (GSTs; EC 2.5.1.18) from rat is now reported. Rates of cis-trans isomerization were determined quantitatively by HPLC. GST-catalysed reactions reached equilibrium rapidly, in marked contrast with uncatalysed or GSH-catalysed isomerizations. The GST-catalysed reaction exhibited substrate saturation kinetics with a Km of approx. 8 microM. The maximal velocity of the reaction and the catalytic efficiency of GSTs were determined. The initial rate of the reaction increased linearly as a function of enzyme concentration. Catalysis by GSTs was independent of the presence of GSH, indicating that GSTs act as GSH-independent isomerases as well as transferases. Incubation with guanidine (7-8 M) or heat-inactivation of GSTs (100 degrees C for 3 min) decreased isomerase activities by approx. 50% and 75% respectively. The same heat treatment did not significantly inhibit isomerization catalysed by GSH and apoferritin, indicating that the observed decrease in isomerase activity by heat inactivation was not primarily due to oxidation of protein thiol groups in the GSTs. The specific activity of GSTs was approx. 23- and 340-fold those of GSH and apoferritin respectively when comparisons were made on the basis of free thiol concentrations, indicating that free thiol in GSTs cannot account for the majority of observed isomerase activities and suggesting that specific conformations of GSTs are important for such activities. Complete inhibition of the reaction by low concentrations of N-ethylmaleimide (10 microM) demonstrated that intact protein thiols are required for the isomerase activities of GSTs. PMID:9581548

Combining anti-cancer drugs with artificial sweeteners: synthesis and anti-cancer activity of saccharinate (sac) and thiosaccharinate (tsac) complexes cis-[Pt(sac)2(NH3)2] and cis-[Pt(tsac)2(NH3)2].

PubMed

Al-Jibori, Subhi A; Al-Jibori, Ghassan H; Al-Hayaly, Lamaan J; Wagner, Christoph; Schmidt, Harry; Timur, Suna; Baris Barlas, F; Subasi, Elif; Ghosh, Shishir; Hogarth, Graeme

2014-12-01

The new platinum(II) complexes cis-[Pt(sac)2(NH3)2] (sac=saccharinate) and cis-[Pt(tsac)2(NH3)2] (tsac=thiosaccharinate) have been prepared, the X-ray crystal structure of cis-[Pt(sac)2(NH3)2] x H2O reveals that both saccharinate anions are N-bound in a cis-arrangement being inequivalent in both the solid-state and in solution at room temperature. Preliminary anti-cancer activity has been assessed against A549 human alveolar type-II like cell lines with the thiosaccharinate complex showing good activity. Copyright © 2014 Elsevier Inc. All rights reserved.

Latex Clearing Protein—an Oxygenase Cleaving Poly(cis-1,4-Isoprene) Rubber at the cis Double Bonds

PubMed Central

Hiessl, Sebastian; Böse, Dietrich; Oetermann, Sylvia; Eggers, Jessica; Pietruszka, Jörg

2014-01-01

Gordonia polyisoprenivorans strain VH2, a potent rubber-degrading actinomycete, harbors two latex clearing proteins (Lcps), which are known to be essential for the microbial degradation of rubber. However, biochemical information on the exact role of this protein in the degradation of polyisoprene was lacking. In this study, the gene encoding Lcp1VH2 was heterologously expressed in strains of Escherichia coli, the corresponding protein was purified, and its role in rubber degradation was examined by measurement of oxygen consumption as well as by chromatographic and spectroscopic methods. It turned out that active Lcp1VH2 is a monomer and is responsible for the oxidative cleavage of poly(cis-1,4-isoprene) in synthetic as well as in natural rubber by the addition of oxygen (O2) to the cis double bonds. The resulting oligomers possess repetitive isoprene units with aldehyde (CHO-CH2—) and ketone (—CH2-CO-CH3) functional groups at the termini. Two fractions with average isoprene contents of 18 and 10, respectively, were isolated, thus indicating an endocleavage mechanism. The activity of Lcp1VH2 was determined by applying a polarographic assay. Alkenes, acyclic terpenes, or other rubber-like polymers, such as poly(cis-1,4-butadiene) or poly(trans-1,4-isoprene), are not oxidatively cleaved by Lcp1VH2. The pH and temperature optima of the enzyme are at pH 7 and 30°C, respectively. Furthermore, it was demonstrated that active Lcp1VH2 is a Cu(II)-containing oxygenase that exhibits a conserved domain of unknown function which cannot be detected in any other hitherto-characterized enzyme. The results presented here indicate that this domain might represent a new protein family of oxygenases. PMID:24928880

Hydroperoxide-dependent cooxidation of 13-cis-retinoic acid by prostaglandin H synthase.

PubMed

Samokyszyn, V M; Marnett, L J

1987-10-15

Reverse phase high pressure liquid chromatography was employed to separate the major products resulting from the hydroperoxide-dependent cooxidation of 13-cis-retinoic acid by microsomal and purified prostaglandin H (PGH) synthase. Several major oxygenated metabolites including 4-hydroxy-, 5,6-epoxy-, and 5,8-oxy-13-cis-retinoic acid were unambiguously identified on the basis of cochromatography with authentic standards, uv spectra, and mass spectral analysis. Identical product profiles were generated regardless of the type of oxidizing substrate employed, and heat-denatured microsomes or enzyme did not support oxidation. In addition, several geometric isomers including all trans-retinoic acid were identified. Isomerization to all trans-retinoic acid in microsomes occurred in the absence of exogenous hydroperoxide, was insensitive to inhibition by antioxidant, and was eliminated when heat-denatured preparations were substituted for intact microsomes. Conversely, isomerization to at least one other isomer required the addition of hydroperoxide and was sensitive to antioxidant inhibition. Addition of antioxidant to microsomal incubation mixtures inhibited the hydroperoxide-dependent generation of 5,6-epoxy- and 5,8-oxy-13-cis-retinoic acid and other oxygenated metabolites but stimulated the formation of 4-hydroxy-13-cis-retinoic acid. Under standard conditions, 77% of the original retinoid was metabolized resulting in products containing 1.25 oxygen atoms/oxygenated metabolite, and two dioxygen molecules were consumed per hydroperoxide reduced. Purified PGH synthase also supported O2 uptake during cooxidation of 13-cis-retinoic acid by H2O2 or 5-phenyl-4-pentenyl-1-hydroperoxide, and the initial velocities of O2 uptake were directly proportional to enzyme concentration. 13-cis-Retinoic acid effectively inhibited peroxidase-dependent cooxidation of guaiacol indicating a direct interaction of retinoid with peroxidase iron-oxo intermediates, and EPR spin trapping

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

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.

Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus

PubMed Central

Sundaram, Vasavi; Choudhary, Mayank N. K.; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A.; Wang, Ting

2017-01-01

Cis-regulatory modules contain multiple transcription factor (TF)-binding sites and integrate the effects of each TF to control gene expression in specific cellular contexts. Transposable elements (TEs) are uniquely equipped to deposit their regulatory sequences across a genome, which could also contain cis-regulatory modules that coordinate the control of multiple genes with the same regulatory logic. We provide the first evidence of mouse-specific TEs that encode a module of TF-binding sites in mouse embryonic stem cells (ESCs). The majority (77%) of the individual TEs tested exhibited enhancer activity in mouse ESCs. By mutating individual TF-binding sites within the TE, we identified a module of TF-binding motifs that cooperatively enhanced gene expression. Interestingly, we also observed the same motif module in the in silico constructed ancestral TE that also acted cooperatively to enhance gene expression. Our results suggest that ancestral TE insertions might have brought in cis-regulatory modules into the mouse genome. PMID:28348391

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.

Mechanistic Studies on the Cis to Trans Epimerization of Trisubstituted-1,2,3,4-Tetrahydro-β-Carbolines

PubMed Central

Van Linn, Michael L.; Cook, James M.

2010-01-01

It is well known that Nb-benzyl tryptophan alkyl esters undergo the Pictet-Spengler reaction with aldehydes to furnish both cis and trans 1,2,3,4-tetrahydro-β-carbolines, with the trans isomer predominating. Epimerization at C-1 took place under acidic conditions to produce, exclusively, the thermodynamically more stable trans diastereomer via internal asymmetric induction. Recent kinetic experiments provided insight into the cis to trans epimerization mechanism involved in the Pictet-Spengler reaction of 1,2,3-trisubsituted tetrahydro-β-carbolines. Since the epimerization reaction had been shown to be sensitive to electronic effects at C-1, the rate data for a series of 1-phenyl-substituted-1,2,3,4-tetrahydro-β-carbolines was investigated via a Hammett study. Analysis of the data supported the presence of a positively charged intermediate with a ρ value of −1.4, although the existence of an iminium ion intermediate or a carbocationic intermediate could not be determined from this data alone. Analysis of the rate of epimerization demonstrated first-order kinetics with respect to TFA following the initial protonation of the substrate. This observation was consistent with the formation of a doubly protonated intermediate as the rate determining step in the carbocation-mediated cis to trans epimerization process. In addition, the observed first-order rate dependence was inconsistent with the retro Pictet-Spengler mechanism since protonation at the indole-2 position was not rate determining as demonstrated by kinetic isotope effects. Based on this kinetic data, the retro Pictet-Spengler pathway was ruled out for the cis to trans epimerization of 1,2,3-trisubstituted-1,2,3,4-tetrahydro-β-carbolines, while the olefinic mechanism had been ruled out by experiments carried out in TFA-d. PMID:20429580

Perception of Speech Produced by Native and Nonnative Talkers by Listeners with Normal Hearing and Listeners with Cochlear Implants

ERIC Educational Resources Information Center

Ji, Caili; Galvin, John J.; Chang, Yi-ping; Xu, Anting; Fu, Qian-Jie

2014-01-01

Purpose: The aim of this study was to evaluate the understanding of English sentences produced by native (English) and nonnative (Spanish) talkers by listeners with normal hearing (NH) and listeners with cochlear implants (CIs). Method: Sentence recognition in noise was measured in adult subjects with CIs and subjects with NH, all of whom were…

A CIS (Clinical Information System) Quality Evaluation Tool for Nursing Care Services

ERIC Educational Resources Information Center

Lee, Seon Ah

2010-01-01

The purpose of this study was to develop a tool to evaluate the quality of a clinical information system (CIS) conceived by nurses and conduct a pilot test with the developed tool as an initial assessment. CIS quality is required for successful implementation in information technology (IT) environments. The study started with the realization that…

Cis and trans RET signaling control the survival and central projection growth of rapidly adapting mechanoreceptors

PubMed Central

Fleming, Michael S; Vysochan, Anna; Paixão, Sόnia; Niu, Jingwen; Klein, Rüdiger; Savitt, Joseph M; Luo, Wenqin

2015-01-01

RET can be activated in cis or trans by its co-receptors and ligands in vitro, but the physiological roles of trans signaling are unclear. Rapidly adapting (RA) mechanoreceptors in dorsal root ganglia (DRGs) express Ret and the co-receptor Gfrα2 and depend on Ret for survival and central projection growth. Here, we show that Ret and Gfrα2 null mice display comparable early central projection deficits, but Gfrα2 null RA mechanoreceptors recover later. Loss of Gfrα1, the co-receptor implicated in activating RET in trans, causes no significant central projection or cell survival deficit, but Gfrα1;Gfrα2 double nulls phenocopy Ret nulls. Finally, we demonstrate that GFRα1 produced by neighboring DRG neurons activates RET in RA mechanoreceptors. Taken together, our results suggest that trans and cis RET signaling could function in the same developmental process and that the availability of both forms of activation likely enhances but not diversifies outcomes of RET signaling. DOI: http://dx.doi.org/10.7554/eLife.06828.001 PMID:25838128

Separation of Cis-Trans Phospholipid Isomers using Reversed Phase LC with High Resolution MS Detection

PubMed Central

Bird, Susan S.; Marur, Vasant R.; Stavrovskaya, Irina G.; Kristal, Bruce S.

2012-01-01

The increased presence of synthetic trans fatty acids into western diets has been shown to have deleterious effects on physiology and raising an individual’s risk of developing metabolic disease, cardiovascular disease, and stroke. The importance of these fatty acids for health and the diversity of their (patho) physiological effects suggest that not only should the free trans fatty acids be studied, but that monitoring the presence of these fats into the side-chains of biological lipids, such as glycerophospholipids, is also essential. We developed a high resolution LC-MS method that quantitatively monitors the major lipid classes found in biospecimens in an efficient, sensitive and robust manner while also characterizing individual lipid side-chains through the use of HCD fragmentation and chromatographic alignment. We herein show how this previously described reversed phase method can baseline separate the cis-trans isomers of phosphatidylglycerol and phosphatidylcholine (PC) with two 18:1 side chains, in both positive and negative mode, as neat solutions and when spiked into a biological matrix. Endogenous PC (18:1/18:1) cis and PC (18:1/18:1) trans isomers were examined in mitochondrial and serum profiling studies, where rats were fed diets enriched in either trans 18:1 fatty acids, or cis 18:1 fatty acids. In this study, we determined the cis:trans isomer ratios of PC (18:1/18:1) and related this ratio to dietary composition. This generalized LC-MS method enables the monitoring of trans fats in biological lipids in the context of a non-targeted method, allowing for relative quantitation and enhanced identification of unknown lipids in complex matrices. PMID:22656324

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.

Molecular dynamics simulations of trans- and cis- N-acetyl- N'-methylamides of XaaPro dipeptides

NASA Astrophysics Data System (ADS)

Hoon Choi, Seung; Yun Yu, Jeong; Kwang Shin, Jae; Shik Jhon, Mu

1994-07-01

The occurrence of cis imide bonds in proteins is much higher than that of cis amide bonds due to the unique properties of proline. In order to examine the relationship between the high occurrence of these cis imide bonds and the residues preceding the proline, we perform molecular dynamics simulations of trans- and cis- N-acetyl- N'-methylamides of XaaPro dipeptides (AcXaaProNHMe). We investigate the conformational energies and structures of trans- and cis-AcXaa where Xaa has 12 amino acids in the vacuum state and 5 amino acids in the solution state. It is found that the occurrence of the cis imide bonds is strongly affected by the residue preceding the proline, and the dihedral angles (φ,ψ) of the backbone in AcXaaProNHMe are influenced by the configuration of the imide bond. We also find that the equilibrium properties of XaaPro in solution simulations are more similar to the statistics of X-ray crystallographic data than are those in vacuum simulations and solvation causes a remarkable change in the conformation of the pyrrolidine ring from the endo to the exo form.

Connectivity patterns and rotamer states of nucleobases determine acid-base properties of metalated purine quartets.

PubMed

Lüth, Marc Sven; Freisinger, Eva; Kampf, Gunnar; Garijo Anorbe, Marta; Griesser, Rolf; Operschall, Bert P; Sigel, Helmut; Lippert, Bernhard

2015-07-01

Potentiometric pH titrations and pD dependent (1)H NMR spectroscopy have been applied to study the acidification of the exocyclic amino group of adenine (A) model nucleobases (N9 position blocked by alkyl groups) when carrying trans-a2Pt(II) (with a=NH3 or CH3NH2) entities both at N1 and N7 positions. As demonstrated, in trinuclear complexes containing central A-Pt-A units, it depends on the connectivity pattern of the adenine bases (N7/N7 or N1/N1) and their rotamer states (head-head or head-tail), how large the acidifying effect is. Specifically, a series of trinuclear complexes with (A-N7)-Pt-(N7-A) and (A-N1)-Pt-(N1-A) cross-linking patterns and terminal 9-alkylguanine ligands (9MeGH, 9EtGH) have been analyzed in this respect, and it is shown that, for example, the 9MeA ligands in trans-,trans-,trans-[Pt(NH3)2(N7-9MeA-N1)2{Pt(NH3)2(9EtGH-N7)}2](ClO4)6·6H2O (4a) and trans-,trans-,trans-[Pt(NH3)2(N7-9EtA-N1)2{Pt(CH3NH2)2(9-MeGH-N7)}2](ClO4)6·3H2O (4b) are more acidic, by ca. 1.3 units (first pKa), than the linkage isomer trans-,trans-,trans-[Pt(CH3NH2)2(N1-9MeA-N7)2{Pt(NH3)2(9MeGH-N7)}2](NO3)6·6.25H2O (1b). Overall, acidifications in these types of complexes amount to 7-9 units, bringing the pKa values of such adenine ligands in the best case close to the physiological pH range. Comparison with pKa values of related trinuclear Pt(II) complexes having different co-ligands at the Pt ions, confirms this picture and supports our earlier proposal that the close proximity of the exocyclic amino groups in a head-head arrangement of (A-N7)-Pt-(N7-A), and the stabilization of the resulting N6H(-)⋯H2N6 unit, is key to this difference. Copyright © 2015 Elsevier Inc. All rights reserved.

Germinating the 2050 Cis-Lunar Econosphere

NASA Technical Reports Server (NTRS)

Scott, David W.; Curreri, Peter A.; Ferguson, Cynthia K.; Nall, Mark E.; Tinker, Michael L.; Wright, Gregory M.

2015-01-01

In early 2013, Marshall Space Flight Center's upper management chartered a diverse team for a six-week 'sprint' to speculate (in a disciplined manner) and paint (with broad brush strokes) a picture of how earth, space, and public/private entities might be operating and relating to each other... in the year 2100. Two 12-person groups of civil servants, one with members having 15 years or less of NASA experience and the other with more senior members, worked independently and then compared and integrated their conclusions. In 2014, the 'Space 2100' team, with some new team members and different group boundaries, ran a longer sprint to a) develop more detailed estimates of the operations and economics of space activities in the vicinity of the Earth and Moon in the 2050 time frame, b) identify evolutionary paths, barriers, and opportunities, and c) suggest actions and philosophies to enable and invigorate progress towards the vision. This paper explores Space 2100's first two sprints and their projections of NASA's role in what will likely be a highly networked, international space industry and cis-lunar infrastructure.

Cluster Ion Spectrometry (CIS) Data Archiving in the CAA

NASA Astrophysics Data System (ADS)

Dandouras, I. S.; Barthe, A.; Penou, E.; Brunato, S.; Reme, H.; Kistler, L. M.; Blagau, A.; Facsko, G.; Kronberg, E.; Laakso, H. E.

2009-12-01

The Cluster Active Archive (CAA) aims at preserving the four Cluster spacecraft data, so that they are usable in the long-term by the scientific community as well as by the instrument team PIs and Co-Is. This implies that the data are filed together with the descriptive and documentary elements making it possible to select and interpret them. The CIS (Cluster Ion Spectrometry) experiment is a comprehensive ionic plasma spectrometry package onboard the four Cluster spacecraft, capable of obtaining full three-dimensional ion distributions (about 0 to 40 keV/e) with a time resolution of one spacecraft spin (4 sec) and with mass-per-charge composition determination. The CIS package consists of two different instruments, a Hot Ion Analyser (HIA) and a time-of-flight ion Composition Distribution Function (CODIF) analyser. For the archival of the CIS data a multi-level approach has been adopted. The CAA archival includes processed raw data (Level 1 data), moments of the ion distribution functions (Level 2 data), and calibrated high-resolution data in a variety of physical units (Level 3 data). The latter are 3-D ion distribution functions and 2-D pitch-angle distributions. In addition, a software package has been developed to allow the CAA user to interactively calculate partial or total moments of the ion distributions. Instrument cross-calibration has been an important activity in preparing the data for archival. The CIS data archive includes also experiment documentation, graphical products for browsing through the data, and data caveats. In addition, data quality indexes are under preparation, to help the user. Given the complexity of an ion spectrometer, and the variety of its operational modes, each one being optimised for a different magnetospheric region or measurement objective, consultation of the data caveats by the end user will always be a necessary step in the data analysis.

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

The role of tachysterol in vitamin D photosynthesis - a non-adiabatic molecular dynamics study

NASA Astrophysics Data System (ADS)

Cisneros, Cecilia; Thompson, Travis; Baluyot, Noel; Smith, Adam C.; Tapavicza, Enrico

To investigate the role of tachysterol in the photophysical/chemical regulation of vitamin D photosynthesis, we studied its electronic absorption properties and excited state dynamics using time-dependent density functional theory (TDDFT), coupled cluster theory (CC2), and non-adiabatic molecular dynamics. In excellent agreement with experiments, the simulated electronic spectrum shows a broad absorption band covering the spectra of the other vitamin D photoisomers. The broad band stems from the spectral overlap of four different ground state rotamers. After photoexcitation, the first excited singlet state (S1) decays within 882 fs. The S1 dynamics is characterized by a strong twisting of the central double bond. 96% of all trajectories relax without chemical transformation to the ground state. In 2.3 % of the trajectories we observed [1,5]-sigmatropic hydrogen shift forming the partly deconjugated toxisterol D1. 1.4 % previtamin D formation is observed via hula-twist double bond isomerization. We find a strong dependence between photoreactivity and dihedral angle conformation: hydrogen shift only occurs in cEc and cEt rotamers and double bond isomerization occurs mainly in cEc rotamers. Our study confirms the hypothesis that cEc rotamers are more prone to previtamin D formation than other isomers. We also observe the formation of a cyclobutene-toxisterol in the hot ground state (0.7 %). Due to its strong absorption and unreactive behavior, tachysterol acts mainly as a sun shield suppressing previtamin D formation. Tachysterol shows stronger toxisterol formation than previtamin D. Absorption of low energy UV light by the cEc rotamer can lead to previtamin D formation. Our study reinforces a recent hypothesis that tachysterol can act as a previtamin D source when only low energy ultraviolet light is available, as it is the case in winter or in the morning and evening hours of the day.

Metabolic engineering of Pichia pastoris to produce ricinoleic acid, a hydroxy fatty acid of industrial importance[S

PubMed Central

Meesapyodsuk, Dauenpen; Chen, Yan; Ng, Siew Hon; Chen, Jianan; Qiu, Xiao

2015-01-01

Ricinoleic acid (12-hydroxyoctadec-cis-9-enoic acid) has many specialized uses in bioproduct industries, while castor bean is currently the only commercial source for the fatty acid. This report describes metabolic engineering of a microbial system (Pichia pastoris) to produce ricinoleic acid using a “push” (synthesis) and “pull” (assembly) strategy. CpFAH, a fatty acid hydroxylase from Claviceps purpurea, was used for synthesis of ricinoleic acid, and CpDGAT1, a diacylglycerol acyl transferase for the triacylglycerol synthesis from the same species, was used for assembly of the fatty acid. Coexpression of CpFAH and CpDGAT1 produced higher lipid contents and ricinoleic acid levels than expression of CpFAH alone. Coexpression in a mutant haploid strain defective in the Δ12 desaturase activity resulted in a higher level of ricinoleic acid than that in the diploid strain. Intriguingly, the ricinoleic acid produced was mainly distributed in the neutral lipid fractions, particularly the free fatty acid form, but with little in the polar lipids. This work demonstrates the effectiveness of the metabolic engineering strategy and excellent capacity of the microbial system for production of ricinoleic acid as an alternative to plant sources for industrial uses. PMID:26323290

Single-step electrodeposition of CIS thin films with the complexing agent triethanolamine

NASA Astrophysics Data System (ADS)

Chiu, Yu-Shuen; Hsieh, Mu-Tao; Chang, Chih-Min; Chen, Chun-Shuo; Whang, Thou-Jen

2014-04-01

Some difficulties have long been encountered by single-step electrodeposition such as the optimization of electrolyte composition, deposition potentials, deposition time, and pH values. The approach of introducing ternary components into single-step electrodeposition is rather challenging especially due to the different values of the equilibrium potential for each constituent. Complexing agents play an important role in single-step electrodeposition of CuInSe2 (CIS), since the equilibrium potential of every constituent can be brought closer to each other when complexing agents are employed. In this work, single-step electrodeposition of CIS was enhanced by adding triethanolamine (TEA) into deposition bath, the CIS thin films were improved consequently in the form of polycrystalline cauliflower structures through the examination of SEM images and XRD patterns. The optimum composition of the solution for single-step electrodeposition of CIS is found to be 5 mM CuCl2, 22 mM InCl3, and 22 mM SeO2 at pH 1.5 with 0.1 M TEA. The structures, compositions, and morphologies of as-deposited and of annealed films were investigated.

BIRTH DEFECTS IN FOUR U.S. WHEAT-PRODUCING STATES

EPA Science Inventory

Birth Defects in Four U.S. Wheat - Producing States
Dina M. Schreinemachers, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711

Wheat agriculture in Mi...

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

Cis-trans photoisomerization of azobenzene upon excitation to the S1 state: an ab initio molecular dynamics and QM/MM study

NASA Astrophysics Data System (ADS)

Pederzoli, Marek; Pittner, Jiří; Barbatti, Mario; Lischka, Hans

2012-10-01

The cis-trans isomerization of azobenzene upon S1(n,π*) excitation is studied both in gas phase and in solution. Our study is based on ab initio non-adiabatic dynamics simulations with the non-adiabatic effects included via the fewest-switches surface hopping method with potential-energy surfaces and couplings determined on the fly. The non-adiabatic couplings have been computed based on overlaps of CASSCF wave functions. The solvent is described using classical molecular dynamics employing the quantum mechanics/molecular mechanics (QM/MM) approach. Azobenzene photoisomerization upon S1(n,π*) excitation occurs purely as a rotational motion of the central CNNC moiety. Two non-equivalent rotational pathways, corresponding to clockwise or counterclockwise rotation, are available. The course of the rotational motion is strongly dependent on the initial conditions. The internal conversion occurs via a S0/S1 crossing seam located near the midpoint of both of these rotational pathways. Based on statistical analysis it is shown that the occurrence of one or other pathways can be completely controlled by selecting adequate initial conditions. The effect of the solvent on the reaction mechanism is small. The lifetime of the S1 state is marginally lowered; the effect does not depend on the polarity, but rather on the viscosity of the solvent. The quantum yield is solvent dependent; the simulations in water give smaller quantum yield than those obtained in n-hexane and in gas phase.

Using ruthenium sawhorse based decarboxylation to produce industrial materials from oleic acid

USDA-ARS?s Scientific Manuscript database

Ruthenium catalyzed isomerization and decarboxylation of 9-cis-octadecenoic acid are reported as part of the effort to produce valuable industrial materials from biobased sources. Initial studies have demonstrated the efficacy of ruthenium sawhorse materials and further mechanistic studies uncovered...

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.

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

Cis-oriented solvent-front EGFR G796S mutation in tissue and ctDNA in a patient progressing on osimertinib: a case report and review of the literature.

PubMed

Klempner, Samuel J; Mehta, Pareen; Schrock, Alexa B; Ali, Siraj M; Ou, Sai-Hong Ignatius

2017-01-01

Acquired resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) is a universal event and limits clinical efficacy. The third-generation EGFR inhibitor osimertinib is active in EGFR-mutant/T790M positive non-small-cell lung cancer. Mechanisms of acquired resistance are emerging, and here we describe a cis -oriented solvent-front EGFR G796S mutation as the resistance mechanism observed in a progression biopsy and circulating tumor DNA (ctDNA) from a patient with initial response followed by progression on osimertinib. This is one of the earliest reports of a sole solvent-front tertiary EGFR mutation as a resistance mechanism to osimertinib. Our case suggests a monoclonal resistance mechanism. We review the importance of the solvent-front residues across TKIs and describe known osimertinib resistance mechanisms. We observe that nearly all clinical osimertinib-resistant tertiary EGFR mutations are oriented in cis with EGFR T790M. This case highlights the importance of mutations affecting EGFR kinase domains and supports the feasibility of broad panel ctDNA assays for detection of novel acquired resistance and tumor heterogeneity in routine clinical care.

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

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

Recycling Of Cis Photovoltaic Waste

DOEpatents

Drinkard, Jr., William F.; Long, Mark O.; Goozner; Robert E.

1998-07-14

A method for extracting and reclaiming metals from scrap CIS photovoltaic cells and associated photovoltaic manufacturing waste by leaching the waste with dilute nitric acid, skimming any plastic material from the top of the leaching solution, separating glass substrate from the leachate, electrolyzing the leachate to plate a copper and selenium metal mixture onto a first cathode, replacing the cathode with a second cathode, re-electrolyzing the leachate to plate cadmium onto the second cathode, separating the copper from selenium, and evaporating the depleted leachate to yield a zinc and indium containing solid.

cis-Apa: a practical linker for the microwave-assisted preparation of cyclic pseudopeptides via RCM cyclative cleavage.

PubMed

Baron, Alice; Verdié, Pascal; Martinez, Jean; Lamaty, Frédéric

2011-02-04

A new linker cis-5-aminopent-3-enoic acid (cis-Apa) was prepared for the synthesis of cyclic pseudopeptides by cyclization-cleavage by using ring-closing methatesis (RCM). We developed a new synthetic pathway for the preparation of the cis-Apa linker that was tested in the cyclization-cleavage process of different RGD peptide sequences. Different macrocyclic peptidomimetics were prepared by using this integrated microwave-assisted method, showing that the readily available cis-Apa amino acid is well adapted as a linker in the cyclization-cleavage process.

Characterization of STAT5B phosphorylation correlating with expression of cytokine-inducible SH2-containing protein (CIS).

PubMed

Cooper, John C; Boustead, Jared N; Yu, Chao-Lan

2006-06-01

Cytokine-inducible SH2-containing protein (CIS) is the first identified member of genes encoding for the suppressor of cytokine signaling (SOCS). CIS is also a well-known target gene of signal transducer and activator of transcription 5 (STAT5) pathways, providing normal negative feedback control of signaling by cytokines and growth factors. Three other SOCS genes, SOCS1, SOCS2, and SOCS3, can be silenced by DNA hypermethylation in human cancers, suggesting a potential mechanism for constitutive STAT activation. However, it is not known whether CIS expression is similarly perturbed in tumor cells. We report here the absence of CIS expression in T lymphoma LSTRA that overexpresses the Lck protein tyrosine kinase and exhibits elevated STAT5 activity. Pervanadate-induced CIS expression and STAT5 binding to the CIS promoter in vivo over a short time course implies that mechanisms other than DNA hypermethylation may contribute to defective CIS expression in LSTRA cells. Comparison with cytokine-dependent BaF3 cells stimulated with interleukin-3 (IL-3) further reveals that CIS induction correlates with specific STAT5b post-translational modifications. It exhibits as the slowest migrating form through SDS-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. This distinctly modified STAT5b is the predominant form that binds to the consensus STAT5 sites in the CIS promoter and accumulates in the nucleus. In vitro phosphatase assays and phosphoamino acid analysis suggest the involvement of phosphorylation on residues other than the highly conserved tyrosine and serine sites in this distinct STAT5b mobility shift. All together, our results provide a novel link between incomplete STAT5b phosphorylation and defective SOCS gene expression in cancer cells.

Multiphase reactivity of gaseous hydroperoxide oligomers produced from isoprene ozonolysis in the presence of acidified aerosols

NASA Astrophysics Data System (ADS)

Riva, Matthieu; Budisulistiorini, Sri Hapsari; Zhang, Zhenfa; Gold, Avram; Thornton, Joel A.; Turpin, Barbara J.; Surratt, Jason D.

2017-03-01

Ozonolysis of alkenes results in the formation of primary ozonides (POZs), which can subsequently decompose into carbonyl compounds and stabilized Criegee intermediates (sCIs). The sCIs generated from isoprene ozonolysis include the simplest congener, formaldehyde oxide (CH2OO), and isomers of C4-sCI. Although the bimolecular reaction with H2O is expected to be the main fate of sCIs, it was reported that sCIs can also react with carboxylic acids and/or organic hydroperoxides leading to gas-phase oligomeric compounds. While the impact of the gas-phase composition (H2O, sCI scavenger) on the formation of such products was recently studied, their fate remains unclear. In the present work, formation of oligomeric hydroperoxides from isoprene ozonolysis, proposed as reaction products composed of the sCI as a chain unit and formed from the insertion of sCI into a hydroperoxide or a carboxylic acid, was systematically examined in the presence of aerosol with varying compositions. The effect of hydroxyl (OH) radicals on the gas- and particle-phase compositions was investigated using diethyl ether as an OH radical scavenger. Thirty-four oligomeric compounds resulting from the insertion of sCIs into organic hydroperoxides or carboxylic acids were identified using iodide chemical ionization high-resolution mass spectrometry. Large reactive uptake onto acidified sulfate aerosol was observed for most of the characterized gaseous oligomeric species, whereas the presence of organic coatings and the lack of aerosol water significantly reduced or halted the reactive uptake of these species. These results indicate that highly oxidized molecules, such as hydroperoxides, could undergo multiphase reactions, which are significantly influenced by the chemical composition of seed aerosol. Furthermore, in addition to functionalization and accretion, decomposition and re-volatilization should be considered in SOA formation.

9-cis-retinoic acid represses estrogen-induced expression of the very low density apolipoprotein II gene.

PubMed

Schippers, I J; Kloppenburg, M; Snippe, L; Ab, G

1994-11-01

The chicken very low density apolipoprotein II (apoVLDLII) gene is estrogen-inducible and specifically expressed in liver. We examined the possible involvement of the retinoid X receptor (RXR) and its ligand 9-cis-retinoic acid (9-cis-RA) in the activation of the apoVLDLII promoter. We first concentrated on a potential RXR recognition site, which deviates at only one position from a perfect direct A/GGGTCA repeat spaced by one nucleotide (DR-1) and was earlier identified as a common HNF-4/COUP-TF recognition site. However, band shift analysis revealed that this imperfect DR-1 motif does not interact with RXR alpha-homodimers. In accordance with this observation we found that this regulatory element does not mediate transactivation through RXR alpha in the presence of 9-cis-RA. However, our experiments revealed another, unexpected, effect of 9-cis-RA. Instead of stimulating, 9-cis-RA attenuated estrogen-induced expression of transfected estrogen-responsive VLDL-CAT reporter plasmids. This repression appeared to take place through the main estrogen response element (ERE) of the gene. Importantly, 9-cis-RA also strongly repressed the estrogen-induced expression of the endogenous apoVLDLII gene in cultured chicken hepatoma cells.

Laser Spectroscopy of Vinyl Alcohol Embedded in Helium Droplets

NASA Astrophysics Data System (ADS)

Bunn, Hayley; Raston, Paul; Douberly, Gary E.

2017-06-01

Vinyl alcohol has two rotameric forms, known as syn- and anti-vinyl alcohol, where syn is the most stable. While both have been investigated by microwave and far-infrared spectroscopy, only the syn rotamer has been investigated by mid-infrared spectroscopy. This is due to the low anti rotamer population (15%) at room temperature, in addition to the closeness in proximity of the mid-infrared bands between the rotamers; this results in overlapping bands that are dominated by syn-vinyl alcohol absorptions. In this investigation we increase the anti-vinyl alcohol population to 40% by using a high temperature "pyrolysis" source, and eliminate the spectral overlap by recording the spectra at low temperature in helium nanodroplets. We observe a number of bands of both rotamers in the OH, CH, and CO stretching regions that display rotational substructure. A highlight of this work is the observation of a Fermi dyad in the OH stretching region of anti-vinyl alcohol. Anharmonic frequency calculations suggest that this is due to a near degeneracy of the OH stretching state (νb{1}) with a triple combination involving νb{7}, νb{8}, and νb{9}. M. Rodler, J. Mol. Spec. 114, 23 (1985);S. Saito, Chem. Phys. Lett. 42, 3 (1976) H. Bunn, R. Hudson, A. S. Gentleman, and P. L. Raston, ACS Earth Space Chem. DOI: 10.1021/acsearthspacechem.6b00008 (2017) D-L Joo, A. J. Merer, D. J. Clouthier, J. Mol. Spec. 197, 68 (1999)

US/CIS integrated NTRE

NASA Astrophysics Data System (ADS)

Bulman, M. J.; Culver, D. W.; McIlwain, M. C.; Rochow, Richard; D'Yakov, E. K.; Smetannikov, V. P.

1993-06-01

The paper describes the Nuclear Thermal Energy (NTRE) engine, developed by taking advantage of mature fuel technology developed in the former Soviet Union, thus shortening the development schedule of this engine for moon and Mars explorations. The near-term NTRE engine has a number of features that provide safety, mission performance, cost, and risk benefits. These include: (1) high-temperature long-life CIS fuel, (2) high-pressure recuperated expander cycle, (3) assured restart, (4) long-life cooled nozzle with thin inner wall, (5) long-life turbopumps, (6) heat radiation and electrical power generation, and (7) component integration synergy. Diagrams of the reactor core, the recuperated bottoming cycle flow schematic, and the recuperated bottoming cycle engine schematic are presented.

Chemical characterization of organosulfates from the hydroxyl radical-initiated oxidation and ozonolysis of cis-3-hexen-1-ol

NASA Astrophysics Data System (ADS)

Barbosa, Thais S.; Riva, Matthieu; Chen, Yuzhi; da Silva, Cleyton M.; Ameida, Jose Claudino S.; Zhang, Zhenfa; Gold, Avram; Arbilla, Graciela; Bauerfeldt, Glauco F.; Surratt, Jason D.

2017-08-01

Cis-3-hexen-1-ol (cis-HXO) is a green leaf volatile emitted from plants under stress and belongs to an important class of biogenic volatile organic compounds. In this study, we have investigated the potential formation of organosulfates (OSs) from the hydroxyl radical (OH)-initiated oxidation and ozonolysis of cis-HXO using either non-acidified or acidified sulfate seed aerosols under different relative humidity (RH) conditions. For selected ozonolysis experiments, an OH scavenger was utilized. Ultra performance liquid chromatography interfaced to high-resolution quadrupole time-of-flight mass spectrometry with electrospray ionization (UPLC/ESI-HR-Q-TOFMS) was used to characterize cis-HXO-derived secondary organic aerosol (SOA) formation. Chemical characterization of cis-HXO-derived SOA products reveals that OSs were generated in significant quantity from multiphase chemistry of gas-phase oxidation products of cis-HXO. Ambient fine aerosol (PM2.5) samples collected from Rio de Janeiro, Brazil, were also analyzed. Seven cis-HXO-derived OSs identified in the lab study with molecular weights 154, 186, 170, 210, 212, 226 and 270 were also found in the PM2.5 samples collected in Brazil. This study provides direct evidence that the oxidation of cis-HXO by OH and O3 yields biogenic SOA through the formation of polar OSs.

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.

Biodegradation of cis-1,4-Polyisoprene Rubbers by Distinct Actinomycetes: Microbial Strategies and Detailed Surface Analysis

PubMed Central

Linos, Alexandros; Berekaa, Mahmoud M.; Reichelt, Rudolf; Keller, Ulrike; Schmitt, Jürgen; Flemming, Hans-Curt; Kroppenstedt, Reiner M.; Steinbüchel, Alexander

2000-01-01

Several actinomycetes isolated from nature were able to use both natural rubber (NR) and synthetic cis-1,4-polyisoprene rubber (IR) as a sole source of carbon. According to their degradation behavior, they were divided into two groups. Representatives of the first group grew only in direct contact to the rubber substrate and led to considerable disintegration of the material during cultivation. The second group consisted of weaker rubber decomposers that did not grow adhesively, as indicated by the formation of clear zones (translucent halos) around bacterial colonies after cultivation on NR dispersed in mineral agar. Taxonomic analysis of four selected strains based on 16S rRNA similarity examinations revealed two Gordonia sp. strains, VH2 and Kb2, and one Mycobacterium fortuitum strain, NF4, belonging to the first group as well as one Micromonospora aurantiaca strain, W2b, belonging to the second group. Schiff's reagent staining tests performed for each of the strains indicated colonization of the rubber surface, formation of a bacterial biofilm, and occurrence of compounds containing aldehyde groups during cultivation with NR latex gloves. Detailed analysis by means of scanning electron microscopy yielded further evidence for the two different microbial strategies and clarified the colonization efficiency. Thereby, strains VH2, Kb2, and NF4 directly adhered to and merged into the rubber material, while strain W2b produced mycelial corridors, especially on the surface of IR. Fourier transform infrared spectroscopy comprising the attenuated total reflectance technique was applied on NR latex gloves overgrown by cells of the Gordonia strains, which were the strongest rubber decomposers. Spectra demonstrated the decrease in number of cis-1,4 double bonds, the formation of carbonyl groups, and the change of the overall chemical environment, indicating that an oxidative attack at the double bond is the first metabolic step of the biodegradation process. PMID:10742254

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

Effect of Freezing Conditions on Distances and Their Distributions Derived from Double Electron Electron Resonance (DEER): A Study of Doubly-Spin-Labeled T4 Lysozyme

PubMed Central

Georgieva, Elka R.; Roy, Aritro S.; Grigoryants, Vladimir M.; Borbat, Petr P.; Earle, Keith A.; Scholes, Charles P.; Freed, Jack H.

2012-01-01

Pulsed dipolar ESR spectroscopy, DEER and DQC, require frozen samples. An important issue in the biological application of this technique is how the freezing rate and concentration of cryoprotectant could possibly affect the conformation of biomacromolecule and/or spin-label. We studied in detail the effect of these experimental variables on the distance distributions obtained by DEER from a series of doubly spin-labeled T4 lysozyme mutants. We found that the rate of sample freezing affects mainly the ensemble of spin-label rotamers, but the distance maxima remain essentially unchanged. This suggests that proteins frozen in a regular manner in liquid nitrogen faithfully maintain the distance-dependent structural properties in solution. We compared the results from rapidly freeze-quenched (≤100 μs) samples to those from commonly shock-frozen (slow freeze, 1s or longer) samples. For all the mutants studied we obtained inter-spin distance distributions, which were broader for rapidly frozen samples than for slowly frozen ones. We infer that rapid freezing trapped a larger ensemble of spin label rotamers; whereas, on the time-scale of slower freezing the protein and spin-label achieve a population showing fewer low-energy conformers. We used glycerol as a cryoprotectant in concentrations of 10% and 30% by weight. With 10% glycerol and slow freezing, we observed an increased slope of background signals, which in DEER is related to increased local spin concentration, in this case due to insufficient solvent vitrification, and therefore protein aggregation. This effect was considerably suppressed in slowly frozen samples containing 30% glycerol and rapidly frozen samples containing 10% glycerol. The assignment of bimodal distributions to tether rotamers as opposed to protein conformations is aided by comparing results using MTSL and 4-Bromo MTSL spin-labels. The latter usually produce narrower distance distributions. PMID:22341208

cis-Dioxorhenium(V/VI) Complexes Supported by Neutral Tetradentate N4 Ligands. Synthesis, Characterization, and Spectroscopy.

PubMed

Ng, Vicky Yin-Ming; Tse, Chun-Wai; Guan, Xiangguo; Chang, Xiaoyong; Yang, Chen; Low, Kam-Hung; Lee, Hung Kay; Huang, Jie-Sheng; Che, Chi-Ming

2017-12-18

A series of cis-dioxorhenium(V) complexes containing chiral tetradentate N 4 ligands, including cis-[Re V (O) 2 (pyxn)] + (1; pyxn = N,N'-dimethyl-N,N'-bis(2-pyridylmethyl)cyclohexane-1,2-diamine), cis-[Re V (O) 2 (6-Me 2 pyxn)] + (cis-2), cis-[Re V (O) 2 (R,R-pdp)] + (3; R,R-pdp = 1,1'-bis((R,R)-2-pyridinylmethyl)-2,2'-bipyrrolidine), cis-[Re V (O) 2 (R,R-6-Me 2 pdp)] + (4), and cis-[Re V (O) 2 (bqcn)] + (5; bqcn = N,N'-dimethyl-N,N'-di(quinolin-8-yl)cyclohexane-1,2-diamine), were synthesized. Their structures were established by X-ray crystallography, showing Re-O distances in the range of 1.740(3)-1.769(8) Å and O-Re-O angles of 121.4(2)-124.8(4)°. Their cyclic voltammograms in MeCN (0.1 M [NBu 4 ]PF 6 ) display a reversible Re VI/V couple at E 1/2 = 0.39-0.49 V vs SCE. In aqueous media, three proton-coupled electron transfer reactions corresponding to Re VI/V , Re V/III , and Re III/II couples were observed at pH 1. The Pourbaix diagrams of 1·OTf, 3·OTf, and 5·OTf have been examined. The electronic absorption spectra of the cis-dioxorhenium(V) complexes show three absorption bands at around 800 nm (600-1730 dm 3 mol -1 cm -1 ), 580 nm (1700-5580 dm 3 mol -1 cm -1 ), and 462-523 nm (3170-6000 dm 3 mol -1 cm -1 ). Reaction of 1 with Lewis acids (or protic acids) gave cis-[Re V (O)(OH)(pyxn)] 2+ (1·H + ), in which the Re-O distances are lengthened to 1.788(5) Å. Complex cis-2 resulted from isomerization of trans-2 at elevated temperature. cis-[Re VI (O) 2 (pyxn)](PF 6 ) 2 (1'·(PF 6 ) 2 ) was obtained by constant-potential electrolysis of 1·PF 6 in MeCN (0.1 M [NBu 4 ]PF 6 ) at 0.56 V vs SCE; it displays shorter Re-O distances (1.722(4), 1.726(4) Å) and a smaller O-Re-O angle (114.88(18)°) relative to 1 and shows a d-d transition absorption band at 591 nm (ε = 77 dm 3 mol -1 cm -1 ). With a driving force of ca. 75 kcal mol -1 , 1' oxidizes hydrocarbons with weak C-H bonds (75.5-76.3 kcal mol -1 ) via hydrogen atom abstraction. DFT and TDDFT calculations

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

PubMed Central

Freire-Pritchett, Paula; Schoenfelder, Stefan; Várnai, Csilla; Wingett, Steven W; Cairns, Jonathan; Collier, Amanda J; García-Vílchez, Raquel; Furlan-Magaril, Mayra; Osborne, Cameron S; Fraser, Peter; Rugg-Gunn, Peter J; Spivakov, Mikhail

2017-01-01

Long-range cis-regulatory elements such as enhancers coordinate cell-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. Deciphering the interplay between the promoter connectivity and activity of cis-regulatory elements during lineage commitment is crucial for understanding developmental transcriptional control. Here, we use Promoter Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements. We reveal extensive dynamics of cis-regulatory contacts upon lineage commitment, including the acquisition and loss of promoter interactions. This spatial rewiring occurs preferentially with predicted changes in the activity of cis-regulatory elements and is associated with changes in target gene expression. Our results provide a global and integrated view of promoter interactome dynamics during lineage commitment of human pluripotent cells. DOI: http://dx.doi.org/10.7554/eLife.21926.001 PMID:28332981

Differentiation of refined and virgin edible oils by means of the trans- and cis-phytol isomer distribution.

PubMed

Vetter, Walter; Schröder, Markus; Lehnert, Katja

2012-06-20

The differentiation of nonrefined (e.g., cold-pressed) and refined edible oils is an important task in food control because of the higher commercial value of the former. Here, we explored the suitability of the relative abundance of cis-phytol as a marker for authentication of nonrefined edible oils. Phytol, the tetramethyl-branched, monoenoic alcohol, is found widespread in nature as a part of chlorophyll. In chlorophyll, only trans-phytol is found. In this study, we present a method for the analysis of the phytol isomers, considering that traces of cis-phytol (contributing 0.1% to the phytol content) can be determined next to trans-phytol. For this purpose, phytol was gathered with the unsaponifiable matter from the oil, trimethylsilylated, and analyzed by gas chromatography coupled to mass spectrometry. With this method, 27 samples of edible oils (16 refined and 11 nonrefined edible oils) were analyzed for the abundance of cis-phytol relative to trans-phytol. In the nonrefined oils (e.g., olive oil, rapeseed oil, maize oil, and sunflower oil), cis-phytol contributed 0.1% (n = 3) or less (n = 8) to the phytol content. In contrast, the refined olive oils (n = 4) contained a share of 1.3-3% cis-phytol; the refined rapeseed oil (n = 3) contained a share of 0.7-1.0% cis-phytol; and the refined sunflower oil (n = 4) contained a share of 0.3-0.9% cis-phytol. Only one refined pomegranate kernel did not contain cis-phytol. The phytol concentration was not suited to distinguish nonrefined from refined oils. In contrast, our data suggest that the virtual absence of cis-phytol can be used as a marker for nonrefined (e.g., cold-pressed) edible oils.

cis-Regulatory Mutations Are a Genetic Cause of Human Limb Malformations

PubMed Central

VanderMeer, Julia E.; Ahituv, Nadav

2011-01-01

The underlying mutations that cause human limb malformations are often difficult to determine, particularly for limb malformations that occur as isolated traits. Evidence from a variety of studies shows that cis-regulatory mutations, specifically in enhancers, can lead to some of these isolated limb malformations. Here, we provide a review of human limb malformations that have been shown to be caused by enhancer mutations and propose that cis-regulatory mutations will continue to be identified as the cause of additional human malformations as our understanding of regulatory sequences improves. PMID:21509892

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.

21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

Code of Federal Regulations, 2010 CFR

2010-04-01

... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol to...

21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

Code of Federal Regulations, 2013 CFR

2013-04-01

... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol to...

21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

Code of Federal Regulations, 2012 CFR

2012-04-01

... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol to...

21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

Code of Federal Regulations, 2011 CFR

2011-04-01

... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol to...

21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

Code of Federal Regulations, 2014 CFR

2014-04-01

... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol to...

An Active Insect Kinin Analog with 4-Aminopyroglutamate, A Novel cis-Peptide Bond, Type VI beta-Turn Motif

DTIC Science & Technology

2004-01-01

2004 Wiley Periodicals, Inc.* Biopolymers 75: 412–419, 2004 Keywords: 4-aminopyroglutamic acid ; cis-peptide bond; -turn mimetic; constrained insect...biological evaluation of an insect kinin analog containing a novel, (2S,4S)-4-aminopyroglutamic acid (APy) com- ponent (Figure 1) that theoretical and...cricket diuretic bioassay system. FIGURE 1 A comparison of the structures of the tetrazole ([CN4], left) and 4-aminopyroglu- tamic acid (APy; right

Conversion of 2-chloro-cis,cis-muconate and its metabolites 2-chloro- and 5-chloromuconolactone by chloromuconate cycloisomerases of pJP4 and pAC27.

PubMed Central

Vollmer, M D; Schlömann, M

1995-01-01

2-Chloro-cis,cis-muconate, the product of ortho-cleavage of 3-chlorocatechol, was converted by purified preparations of the pJP4- and pAC27-encoded chloromuconate cycloisomerases (EC 5.5.1.7) to trans-dienelactone (trans-4-carboxymethylenebut-2-en-4-olide). The same compound was also formed when (+)-2-chloro- and (+)-5-chloromuconolactone were substrates of these enzyme preparations. Thus, the pJP4- and pAC27-encoded chloromuconate cycloisomerases are able to catalyze chloride elimination from (+)-5-chloromuconolactone. The ability to convert (+)-2-chloromuconolactone differentiates these enzymes from other groups of cycloisomerases. PMID:7751312

9-cis-Retinoic Acid Promotes Cell Adhesion Through Integrin Dependent and Independent Mechanisms Across Immune Lineages

PubMed Central

Whelan, Jarrett T.; Chen, Jianming; Miller, Jabin; Morrow, Rebekah L.; Lingo, Joshuah D.; Merrell, Kaitlin; Shaikh, Saame Raza; Bridges, Lance C.

2012-01-01

Retinoids are essential in the proper establishment and maintenance of immunity. Although retinoids are implicated in immune related processes, their role in immune cell adhesion has not been well established. In this study, the effect of 9-cis-retinoic acid (9-cis-RA) on human hematopoietic cell adhesion was investigated. 9-cis-RA treatment specifically induced cell adhesion of the human immune cell lines HuT-78, NB4, RPMI 8866, and U937. Due to the prominent role of integrin receptors in mediating immune cell adhesion, we sought to evaluate if cell adhesion was integrin-dependent. By employing a variety of integrin antagonist including function-blocking antibodies and EDTA, we establish that 9-cis-RA prompts immune cell adhesion through established integrin receptors in addition to a novel integrin-independent process. The novel integrin-independent adhesion required the presence of retinoid and was attenuated by treatment with synthetic corticosteroids. Finally, we demonstrate that 9-cis-RA treatment of primary murine B-cells induces ex vivo adhesion that persists in the absence of integrin function. Our study is the first to demonstrate that 9-cis-retinoic acid influences immune cell adhesion through at least two functionally distinct mechanisms. PMID:22925918

Evidence for cis Amide Bonds in Peptoid Nanosheets.

PubMed

Hudson, Benjamin C; Battigelli, Alessia; Connolly, Michael D; Edison, John; Spencer, Ryan K; Whitelam, Stephen; Zuckermann, Ronald N; Paravastu, Anant K

2018-05-17

Peptoid nanosheets are supramolecular protein-mimetic materials that form from amphiphilic polypeptoids with aromatic and ionic side chains. Nanosheets have been studied at the nanometer scale, but the molecular structure has been difficult to probe. We report the use of 13 C- 13 C dipolar recoupling solid-state NMR measurements to reveal the configuration of backbone amide bonds selected by 13 C isotopic labeling of adjacent α-carbons. Measurements on the same molecules in the amorphous state and in nanosheets revealed that amide bonds in the center of the amino block of peptoid (NaeNpe) 7 -(NceNpe) 7 (B28) favor the trans configuration in the amorphous state and the cis configuration in the nanosheet. This unexpected result contrasts with previous NMR and theoretical studies of short solvated peptoids. Furthermore, examination of the amide bond at the junction of the two charged blocks within B28 revealed a mixture of both cis and trans configurational states, consistent with the previously predicted brickwork-like intermolecular organization.

Effects of Cd{sup 2+} on cis-dimer structure of E-cadherin in living cells

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

Takeda, Hiroshi, E-mail: hirotake@sapmed.ac.jp

2014-02-21

Highlights: • The effects of Cd on the dimer of cadherin in living cells was analyzed. • Cd induced cadherin dimer formation was not detected in living cell with low Ca. • Ca mediated structural cooperativity and allostery in the native cadherin. • Ca concentration-dependent competitive displacement of Cd from cadherin is proposed. - Abstract: E-cadherin, a calcium (Ca{sup 2+})-dependent cell–cell adhesion molecule, plays a key role in the maintenance of tissue integrity. We have previously demonstrated that E-cadherin functions in vivo as a cis-dimer through chemical cross-linking reagents. Ca{sup 2+} plays an important role in the cis-dimer formation ofmore » cadherin. However, the molecular mechanisms by which Ca{sup 2+} interacts with the binding sites that regulate cis-dimer structures have not been completely elucidated. As expected for a Ca{sup 2+} antagonist, cadmium (Cd{sup 2+}) disrupts cadherin function by displacing Ca{sup 2+} from its binding sites on the cadherin molecules. We used Cd{sup 2+} as a probe for investigating the role of Ca{sup 2+} in the dynamics of the E-cadherin extracellular region that involve cis-dimer formation and adhesion. While cell–cell adhesion assembly was completely disrupted in the presence of Cd{sup 2+}, the amount of cis-dimers of E-cadherin that formed at the cell surface was not affected. In our “Cd{sup 2+}-switch” experiments, we did not find that Cd{sup 2+}-induced E-cadherin cis-dimer formation in EL cells when they were incubated in low-Ca{sup 2+} medium. In the present study, we demonstrated for the first time the effects of Cd{sup 2+} on the cis-dimer structure of E-cadherin in living cells using a chemical cross-link analysis.« less

Germinating the 2050 Cis-Lunar Econosphere

NASA Technical Reports Server (NTRS)

Scott, David W.; Tinker, Michael L.; Nall, Mark E.; Wright, Gregory M.

2015-01-01

In early 2013, the Marshall Space Flight Center (MSFC) Director and MSFC's Office of Strategic Analysis and Communications (OSAC) chartered a diverse team for a six-week "sprint" to speculate (in a disciplined manner) and paint (with broad brush strokes) a picture of how earth, space, and public/private entities might be operating and relating to each other...in the year 2100. Two 12-person groups of civil servants, one with members having 15 years or less of NASA experience and the other with more senior members, worked independently and then compared and integrated their conclusions. In 2014, the "Space 2100" team, with some new team members and different group boundaries, ran a longer sprint to a) develop more detailed estimates of the operations and economics of space activities in the vicinity of the Earth and Moon in the 2050 time frame, b) identify evolutionary steps and viable paths needed to make that a reality, and c) recommend actions to enable and invigorate those steps. This paper explores Space 2100's first two sprints and their projections of NASA's role in what will likely be a highly networked international space industry and cis-lunar infrastructure.

trans- cis Isomerism and acylimine formation in DsRed chromophore models: Intrinsic rotation barriers

NASA Astrophysics Data System (ADS)

Olsen, Seth; Smith, Sean C.

2006-07-01

The chromophore of the red fluorescent protein DsRed contains an acylimine substituent to a GFP-like chromophore structure. The acylimine is formed from the trans peptide linkage between residues F65 and Q66 in immature DsRed, but has a cis configuration in the mature protein. The relationship between acylimine formation and trans- cis isomerization is unresolved. We have calculated bond rotation profiles for models of mature and immature DsRed chromophores using B3LYP DFT. The isomerization barrier is substantially reduced in acylimine-substituted models, providing prima facie evidence that acylimine formation precedes trans- cis isomerization in DsRed chromophores.

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.

Cis- and trans-perfluorodecalin: Infrared spectra, radiative efficiency and global warming potential

NASA Astrophysics Data System (ADS)

Le Bris, Karine; DeZeeuw, Jasmine; Godin, Paul J.; Strong, Kimberly

2017-12-01

Perfluorodecalin (PFD) is a molecule used in various medical applications for its capacity to dissolve gases. This potent greenhouse gas was detected for the first time in the atmosphere in 2005. We present infrared absorption cross-section spectra of a pure vapour of cis- and trans-perfluorodecalin at a resolution of 0.1 cm-1. Measurements were performed in the 560-3000 cm-1 spectral range using Fourier transform spectroscopy. The spectra have been compared with previous experimental data and theoretical calculations by density functional theory. The new experimental absorption cross-sections have been used to calculate a lifetime-corrected radiative efficiency at 300 K of 0.62 W m-2 ppb-1 and 0.57 W.m-2.ppb-1 for the cis and trans isomers respectively. This leads to a 100-year time horizon global warming potential of 8030 for cis-PFD and 7440 for trans-PFD.

Cis-pent-2-ene. Electron diffraction, vibrational analysis and molecular mechanics

NASA Astrophysics Data System (ADS)

Ter Brake, J. H. M.

1984-08-01

The molecular structure of cis-pent-2-ene has been investigated by using electron diffraction, vibrational analysis and molecular mechanics. It is possible to fit a model, describing cis-pent-2-ene as a semi-rigid molecule with one conformer only, to the electron diffraction data. However, molecular mechanics, ab initio self-consistent field molecular orbital calculations and microwave spectroscopy show that cis-pent-2-ene is not a semi-rigid molecule. The large-amplitude motion is described, using all pseudo-conformers at 10° intervals around the circle of rotation. The resulting rα structure is: r[CC] = 149.0(1), r[CC] = 133.8(2), r[CC] = 156.1(2), r[CH] = 109.2(2), r[CH] = 105.8(5) pm, ∠[CCC] = 127.4(2), ∠[CCC] = 112.4(4), ∠[CCH] = 124(2), ∠[CCH] = 114.2(3)° (standard deviations given in parentheses refer to the last significant digit).

Cis-acting RNA elements in the Hepatitis C virus RNA genome

PubMed Central

Sagan, Selena M.; Chahal, Jasmin; Sarnow, Peter

2017-01-01

Hepatitis C virus (HCV) infection is a rapidly increasing global health problem with an estimated 170 million people infected worldwide. HCV is a hepatotropic, positive-sense RNA virus of the family Flaviviridae. As a positive-sense RNA virus, the HCV genome itself must serve as a template for translation, replication and packaging. The viral RNA must therefore be a dynamic structure that is able to readily accommodate structural changes to expose different regions of the genome to viral and cellular proteins to carry out the HCV life cycle. The ∼9600 nucleotide viral genome contains a single long open reading frame flanked by 5′ and 3′ non-coding regions that contain cis-acting RNA elements important for viral translation, replication and stability. Additional cis-acting RNA elements have also been identified in the coding sequences as well as in the 3′ end of the negative-strand replicative intermediate. Herein, we provide an overview of the importance of these cis-acting RNA elements in the HCV life cycle. PMID:25576644

7 CFR 272.10 - ADP/CIS Model Plan.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 4 2010-01-01 2010-01-01 false ADP/CIS Model Plan. 272.10 Section 272.10 Agriculture Regulations of the Department of Agriculture (Continued) FOOD AND NUTRITION SERVICE, DEPARTMENT OF AGRICULTURE... benefit computation (including but not limited to all household members' names, addresses, dates of birth...

Low-Temperature Chemiluminescence From cis-1,4-Polybutadiene, 1,2-Polybutadiene, and trans-Polypentenamer at Temperatures Near Ambient

NASA Technical Reports Server (NTRS)

Nathan, Richard A.; Mendenhall, G. David; Birts, Michelle A.; Ogle, Craig A.; Golub, Morton A.

1978-01-01

The chemiluminescence emission at 25-60 C was measured from films of cis-1,4-polybutadiene, 1,2-polybutadiene, and trans-polypentenamer. The polymers were autoxidized previously in air 100 C, or allowed to react with singlet molecular oxygen in solution, and then cast into films. Values of beta(or k(sub d,((1)O2 yields (3)03)/k(sub r)((1)O2 + polymer yields products)) were determined in benzene for cis-1,4-polybutadiene and cis-1,4-polyisoprene, and for model compounds cis-3-hexene and cis-3-methyl-3-hexene by independent methods. The chemiluminescence emission from irradiated films of the polymers containing a dye sensitizer showed a complicated time dependence, and the results depended on the length of irradiation.

Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution.

PubMed

Kuang, Meihua Christina; Kominek, Jacek; Alexander, William G; Cheng, Jan-Fang; Wrobel, Russell L; Hittinger, Chris Todd

2018-05-21

Repeated evolutionary events imply underlying genetic constraints that can make evolutionary mechanisms predictable. Morphological traits are thought to evolve frequently through cis-regulatory changes because these mechanisms bypass constraints in pleiotropic genes that are reused during development. In contrast, the constraints acting on metabolic traits during evolution are less well studied. Here we show how a metabolic bottleneck gene has repeatedly adopted similar cis-regulatory solutions during evolution, likely due to its pleiotropic role integrating flux from multiple metabolic pathways. Specifically, the genes encoding phosphoglucomutase activity (PGM1/PGM2), which connect GALactose catabolism to glycolysis, have gained and lost direct regulation by the transcription factor Gal4 several times during yeast evolution. Through targeted mutations of predicted Gal4-binding sites in yeast genomes, we show this galactose-mediated regulation of PGM1/2 supports vigorous growth on galactose in multiple yeast species, including Saccharomyces uvarum and Lachancea kluyveri. Furthermore, the addition of galactose-inducible PGM1 alone is sufficient to improve the growth on galactose of multiple species that lack this regulation, including Saccharomyces cerevisiae. The strong association between regulation of PGM1/2 by Gal4 even enables remarkably accurate predictions of galactose growth phenotypes between closely related species. This repeated mode of evolution suggests that this specific cis-regulatory connection is a common way that diverse yeasts can govern flux through the pathway, likely due to the constraints imposed by this pleiotropic bottleneck gene. Since metabolic pathways are highly interconnected, we argue that cis-regulatory evolution might be widespread at pleiotropic genes that control metabolic bottlenecks and intersections.

Far-Infrared Spectroscopy of Anti-Vinyl Alcohol

NASA Astrophysics Data System (ADS)

Raston, Paul; Bunn, Hayley

2016-06-01

Vinyl alcohol can exist in two rotameric forms, known as syn- and anti- vinyl alcohol, where syn is the most stable. Both rotamers have been observed in the interstellar medium towards Sagittarius B2(N) making them of particular astrophysical importance. Vinyl alcohol has been subject to various spectroscopic investigations, however, the anti rotamer has only been obsvered in the microwave region. We report the high resolution (0.001 wn) FTIR spectrum of anti-vinyl alcohol collected at the infrared beamline facility of the Australian Synchrotron. Vinyl alcohol was produced via the pyrolysis of 2-chloroethanol at 900°C, and its far infrared spectrum reveals the presence of the strong νb{15} fundamental and hot band of anti-vinyl alcohol. Rotational and centrifugal distortion constants of this higher energy rotamer have since been determined for the νb{15} and 2νb{15} states, and the ground state constants have been refined. B. E. Turner, A. J. Apponi, ApJ 561, 207 (2001) M. Rodler, J. Mol. Spec. 114, 23 (1985) D-L Joo, et al., J. Mol. Spec. 197, 68 (1999)

Single-dose pharmacokinetic study of 13-cis-retinoic acid in man.

PubMed

Besner, J G; Leclaire, R; Band, P; Meloche, S; Deschamps, M; Mailhot, S; Moisan, R; Diorio, G

1985-03-01

A pharmacokinetic study of 13-cis-retinoic acid was performed in nine patients following administration of a single oral dose of 80 mg. An average lag time of 1.2 hours was observed, followed by fast absorption, with a mean half-life of 0.5 hour. Peak plasmatic concentration of 733 ng/ml occurred at 2.3 hours. The disposition profile showed a rapid distribution half-life of 1.3 hours and a terminal elimination half-life of 24.7 hours. No 13-cis-retinoic acid was detected unchanged in urine. An important interpatient variability was noted.

A chiral HPLC method for the simultaneous separation of configurational isomers of the predominant cis/trans forms of astaxanthin.

PubMed

Abu-Lafi, S; Turujman, S A

1997-01-01

We report an HPLC method that allows the simultaneous separation of configurational isomers of the predominant cis/trans forms of astaxanthin. The configurational isomers of the all-trans-, and most of the configurational isomers of the 9-cis-, 13-cis- and 15-cis-astaxanthin were separated on a Sumichiral OA-2000 column, which is manufactured and packed in Japan with a Pirkle covalent D-phenylglycine chiral stationary phase (CSP). The large separation of the cis isomers from the all-trans isomers that we report here ensure the suitability of this method for the routine determination of the ratio of the configurational isomers of all-trans-astaxanthin.

Interleukin-6 inhibits hepatic growth hormone signaling via upregulation of Cis and Socs-3.

PubMed

Denson, Lee A; Held, Matthew A; Menon, Ram K; Frank, Stuart J; Parlow, Albert F; Arnold, Dodie L

2003-04-01

Cytokines may cause an acquired growth hormone (GH) resistance in patients with inflammatory diseases. Anabolic effects of GH are mediated through activation of STAT5 transcription factors. We have reported that TNF-alpha suppresses hepatic GH receptor (GHR) gene expression, whereas the cytokine-inducible SH2-containing protein 1 (Cis)/suppressors of cytokine signaling (Socs) genes are upregulated by TNF-alpha and IL-6 and inhibit GH activation of STAT5. However, the relative importance of these mechanisms in inflammatory GH resistance was not known. We hypothesized that IL-6 would prevent GH activation of STAT5 and that this would involve Cis/Socs protein upregulation. GH +/- LPS was administered to TNF receptor 1 (TNFR1) or IL-6 null mice and wild-type (WT) controls. STAT5, STAT3, GHR, Socs 1-3, and Cis phosphorylation and abundance were assessed by using immunoblots, EMSA, and/or real time RT-PCR. TNF-alpha and IL-6 abundance were assessed by using ELISA. GH activated STAT5 in WT and TNFR1 or IL-6 null mice. LPS pretreatment prevented STAT5 activation in WT and TNFR1 null mice; however, STAT5 activation was preserved in IL-6 null mice. GHR abundance did not change with LPS administration. Inhibition of STAT5 activation by LPS was temporally associated with phosphorylation of STAT3 and upregulation of Cis and Socs-3 protein in WT and TNFR1 null mice; STAT3, Cis, and Socs-3 were not induced in IL-6 null mice. IL-6 inhibits hepatic GH signaling by upregulating Cis and Socs-3, which may involve activation of STAT3. Therapies that block IL-6 may enhance GH signaling in inflammatory diseases.

Govt. Pubs: U.S. Government Produced Audiovisual Materials.

ERIC Educational Resources Information Center

Korman, Richard

1981-01-01

Describes the availability of United States government-produced audiovisual materials and discusses two audiovisual clearinghouses--the National Audiovisual Center (NAC) and the National Library of Medicine (NLM). Finding aids made available by NAC, NLM, and other government agencies are mentioned. NAC and the U.S. Government Printing Office…

Assessing Produced Water Management Issues with Increasing U.S. Tight Oil Production

NASA Astrophysics Data System (ADS)

Scanlon, B. R.; Reedy, R. C.; Murray, K. E.; Weingarten, M.

2017-12-01

U.S. oil fields have been producing about 10 times more water than oil for decades; however, problems with managing this produced water, including over-pressuring and induced seismicity, have only become apparent with the recent increases in oil production from unconventional reservoirs. This study involved quantifying spatial and temporal variability in produced water volumes and evaluating issues with managing this produced water using data from the major U.S. unconventional/conventional oil plays (Bakken, Permian, and Eagle Ford plays, and Oklahoma). The primary difference between recent and historical produced water management is the inability to inject the produced water back into the unconventional low permeability or dewatered oil reservoirs. Disposing of this produced water into non-oil producing horizons using salt water disposal wells has been linked to over-pressuring in shallow geologic units in the Bakken and Permian basins and to induced seismicity in Oklahoma. These issues with produced water management can be partially alleviated by reusing/recycling produced water for hydraulic fracturing, which seems particularly promising in the Permian Basin.

Ring[bond]chain tautomerism of 2-Aryl-substituted cis- and trans-decahydroquinazolines.

PubMed

Lázár, László; Göblyös, Anikó; Martinek, Tamás A; Fülöp, Ferenc

2002-07-12

In CDCl(3) at 300 K, 2-aryl-substituted cis- and trans-3-isopropyldecahydroquinazolines and trans-3-phenyldecahydroquinazolines proved to be three-component (r(1)[bond]o[bond]r(2)) ring[bond]chain tautomeric mixtures, whereas only ring-closed tautomers could be detected for the 3-methyl-substituted analogues. The proportions of the ring-chain tautomeric forms at equilibrium were strongly influenced by the N-substitutents and the cis-trans ring junction and could be described by the equation log K(X) = rho sigma(+) + log K(X=H). These are the first examples among 2-aryl-1,3-N,N-heterocycles of a three-component ring-chain tautomeric equilibrium characterized by a Hammett-type equation. The stabilities of the ring-closed forms of cis- and trans-2-aryldecahydroquinazolines and the corresponding 3,1-benzoxazines were found to increase in the following sequence of the heteroatom at position 3: NPh < N-i-Pr < O < NMe.

1H NMR Measurement of the Trans Cis Photoisomerization of Cinnamic Acid Derivatives

NASA Astrophysics Data System (ADS)

Danylec, Basil; Iskander, Magdy N.

2002-08-01

1H NMR spectroscopy was used to follow the course of the photochemical conversion of methyl p-hydroxy-trans-cinnamate to the thermodynamically less stable cis isomer. Integration of the new olefinic cis proton doublet (5.66 ppm, J = 12.9 Hz), which was then compared to the trans isomer (6.15 ppm, J = 15.9 Hz), allowed the determination of the relative amounts of these two isomers.

Both cis and trans Activities of Foot-and-Mouth Disease Virus 3D Polymerase Are Essential for Viral RNA Replication.

PubMed

Herod, Morgan R; Ferrer-Orta, Cristina; Loundras, Eleni-Anna; Ward, Joseph C; Verdaguer, Nuria; Rowlands, David J; Stonehouse, Nicola J

2016-08-01

The Picornaviridae is a large family of positive-sense RNA viruses that contains numerous human and animal pathogens, including foot-and-mouth disease virus (FMDV). The picornavirus replication complex comprises a coordinated network of protein-protein and protein-RNA interactions involving multiple viral and host-cellular factors. Many of the proteins within the complex possess multiple roles in viral RNA replication, some of which can be provided in trans (i.e., via expression from a separate RNA molecule), while others are required in cis (i.e., expressed from the template RNA molecule). In vitro studies have suggested that multiple copies of the RNA-dependent RNA polymerase (RdRp) 3D are involved in the viral replication complex. However, it is not clear whether all these molecules are catalytically active or what other function(s) they provide. In this study, we aimed to distinguish between catalytically active 3D molecules and those that build a replication complex. We report a novel nonenzymatic cis-acting function of 3D that is essential for viral-genome replication. Using an FMDV replicon in complementation experiments, our data demonstrate that this cis-acting role of 3D is distinct from the catalytic activity, which is predominantly trans acting. Immunofluorescence studies suggest that both cis- and trans-acting 3D molecules localize to the same cellular compartment. However, our genetic and structural data suggest that 3D interacts in cis with RNA stem-loops that are essential for viral RNA replication. This study identifies a previously undescribed aspect of picornavirus replication complex structure-function and an important methodology for probing such interactions further. Foot-and-mouth disease virus (FMDV) is an important animal pathogen responsible for foot-and-mouth disease. The disease is endemic in many parts of the world with outbreaks within livestock resulting in major economic losses. Propagation of the viral genome occurs within

Both cis and trans Activities of Foot-and-Mouth Disease Virus 3D Polymerase Are Essential for Viral RNA Replication

PubMed Central

Herod, Morgan R.; Ferrer-Orta, Cristina; Loundras, Eleni-Anna; Ward, Joseph C.; Verdaguer, Nuria; Rowlands, David J.

2016-01-01

ABSTRACT The Picornaviridae is a large family of positive-sense RNA viruses that contains numerous human and animal pathogens, including foot-and-mouth disease virus (FMDV). The picornavirus replication complex comprises a coordinated network of protein-protein and protein-RNA interactions involving multiple viral and host-cellular factors. Many of the proteins within the complex possess multiple roles in viral RNA replication, some of which can be provided in trans (i.e., via expression from a separate RNA molecule), while others are required in cis (i.e., expressed from the template RNA molecule). In vitro studies have suggested that multiple copies of the RNA-dependent RNA polymerase (RdRp) 3D are involved in the viral replication complex. However, it is not clear whether all these molecules are catalytically active or what other function(s) they provide. In this study, we aimed to distinguish between catalytically active 3D molecules and those that build a replication complex. We report a novel nonenzymatic cis-acting function of 3D that is essential for viral-genome replication. Using an FMDV replicon in complementation experiments, our data demonstrate that this cis-acting role of 3D is distinct from the catalytic activity, which is predominantly trans acting. Immunofluorescence studies suggest that both cis- and trans-acting 3D molecules localize to the same cellular compartment. However, our genetic and structural data suggest that 3D interacts in cis with RNA stem-loops that are essential for viral RNA replication. This study identifies a previously undescribed aspect of picornavirus replication complex structure-function and an important methodology for probing such interactions further. IMPORTANCE Foot-and-mouth disease virus (FMDV) is an important animal pathogen responsible for foot-and-mouth disease. The disease is endemic in many parts of the world with outbreaks within livestock resulting in major economic losses. Propagation of the viral genome

Ni supported CdIn2S4 spongy-like spheres: a noble metal free high-performance sunlight driven photocatalyst for hydrogen production.

PubMed

Vu, Manh-Hiep; Nguyen, Chinh-Chien; Sakar, M; Do, Trong-On

2017-11-08

Nickel supported CdIn 2 S 4 (Ni-CIS) spongy-like spheres have been developed using alcoholysis followed by a sulfidation process. The formation of nanocrystalline-single phase CdIn 2 S 4 was confirmed using X-ray diffraction studies. Electron microscopy images showed that the spongy-like spheres are composed of CdIn 2 S 4 nanoparticles with average sizes of around 25 nm. X-ray photoelectron spectra indicated the presence of elements with their respective stable oxidation states that led to the formation of single phase CdIn 2 S 4 with enhanced structural integrity and chemical composition. The absorption spectra indicated the visible light activity of the material and the band gap energy is deduced to be 2.23 eV. The photocatalytic efficiency of the synthesized Ni-CIS in relation to its ability to produce hydrogen under solar light irradiation is estimated to be 1060 μmol g -1 h -1 , which is around 5.5 and 3.6 fold higher than that of Pt-CIS (180 μmol g -1 h -1 ) and Pd-CIS (290 μmol g -1 h -1 ), respectively, as obtained in this study. Accordingly, the mechanism of the observed efficiency of the Ni-CIS nanoparticles is also proposed. The recyclability test showed consistent hydrogen evolution efficiency over 3 cycles (9 h), which essentially revealed the excellent photo- and chemical-stability of the photocatalyst. The strategy to utilize non-noble metals such as Ni, rather than noble-metals, as a co-catalyst opens up a new possibility to develop low cost and high-performance sunlight-driven photocatalysts as achieved in this study.

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.

Isolation and Characterization of the cis-trans-Unsaturated Fatty Acid Isomerase of Pseudomonas oleovorans GPo12

PubMed Central

Pedrotta, Valerian; Witholt, Bernard

1999-01-01

Pseudomonas oleovorans contains an isomerase which catalyzes the cis-trans conversion of the abundant unsaturated membrane fatty acids 9-cis-hexadecenoic acid (palmitoleic acid) and 11-cis-octadecenoic acid (vaccenic acid). We purified the isomerase from the periplasmic fraction of Pseudomonas oleovorans. The molecular mass of the enzyme was estimated to be 80 kDa under denaturing conditions and 70 kDa under native conditions, suggesting a monomeric structure of the active enzyme. N-terminal sequencing showed that the isomerase derives from a precursor with a signal sequence which is cleaved from the primary translation product in accord with the periplasmic localization of the enzyme. The purified isomerase acted only on free unsaturated fatty acids and not on esterified fatty acids. In contrast to the in vivo cis-trans conversion of lipids, this in vitro isomerization of free fatty acids did not require the addition of organic solvents. Pure phospholipids, even in the presence of organic solvents, could not serve as substrate for the isomerase. However, when crude membranes from Pseudomonas or Escherichia coli cells were used as phospholipid sources, a cis-trans isomerization was detectable which occurred only in the presence of organic solvents. These results indicate that isolated membranes from Pseudomonas or E. coli cells must contain factors which, activated by the addition of organic solvents, enable and control the cis-trans conversion of unsaturated acyl chains of membrane phospholipids by the periplasmic isomerase. PMID:10322030

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

PubMed Central

Yang, Fan; Wang, Jiebiao; Pierce, Brandon L.; Chen, Lin S.

2017-01-01

The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their biological mechanisms. One common trans-eQTLs mechanism is “mediation” by a local (cis) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are “cis-mediators” of trans-eQTLs, including those “cis-hubs” involved in regulation of many trans-genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans-eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multitissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis-mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis-hubs and trans-eQTL regulation across tissue types. PMID:29021290

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.

PubMed

Yang, Fan; Wang, Jiebiao; Pierce, Brandon L; Chen, Lin S

2017-11-01

The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes ( cis -eQTLs). More research is needed to identify effects of genetic variation on distant genes ( trans -eQTLs) and understand their biological mechanisms. One common trans -eQTLs mechanism is "mediation" by a local ( cis ) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are " cis -mediators" of trans -eQTLs, including those " cis -hubs" involved in regulation of many trans -genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans -eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multitissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis -mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis -hubs and trans -eQTL regulation across tissue types. © 2017 Yang et al.; Published by Cold Spring Harbor Laboratory Press.

The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits.

PubMed

Yeo, Seungeun; Hodgkinson, Colin A; Zhou, Zhifeng; Jung, Jeesun; Leung, Ming; Yuan, Qiaoping; Goldman, David

2016-08-11

Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL's for complex phenotypes. We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. Additionally several novel DAE-QTLs not identified as cis-eQTLs were identified suggesting that there are differences in sensitivity and specificity for QTL detection between the two methodologies. Strain specific DAE QTLs in B6/DBAF1 mice were located in excess at candidate genes for alcohol use disorders, seizures, and angiogenesis previously implicated by genetic linkage in C57BL/6J × DBA/2JF2 mice or BXD RI strains. Via a survey for differential allele expression in F1 mice, a substantial proportion of genes were found to have alleles altering expression in cis-acting fashion. Comparing forebrain and kidney, many or most of these alleles were

Measurement and analysis of the conversion gain degradation of the CIS detectors in harsh radiation environments

NASA Astrophysics Data System (ADS)

Wang, Zujun; Xue, Yuanyuan; Guo, Xiaoqiang; Bian, Jingying; Yao, Zhibin; He, Baoping; Ma, Wuying; Sheng, Jiangkun; Dong, Guantao; Liu, Yan

2018-07-01

The conversion gain of the CMOS image sensor (CIS) is one of the most important key parameters to the CIS detector. The conversion gain degradation induced by radiation damage will seriously affect the performances of the CIS detector. The experiments of the CISs irradiated by protons, neutrons, and gamma rays are presented. The CISs have 4 Megapixels and pinned photodiode (PPD) pixel architecture with a standard 0.18 μm CMOS technology. The conversion gains versus the proton fluence (including the proton ionizing dose), neutron fluence and gamma total ionizing dose are presented, respectively. The mechanisms of the conversion gain degradation induced by radiation damage are analyzed in details. The investigations will help to improve the PPD CIS detector design, reliability and applicability for applications in the harsh radiation environments such as space and nuclear environments.

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.

Planning "and" Sprinting: Use of a Hybrid Project Management Methodology within a CIS Capstone Course

ERIC Educational Resources Information Center

Baird, Aaron; Riggins, Frederick J.

2012-01-01

An increasing number of information systems projects in industry are managed using hybrid project management methodologies, but this shift in project management methods is not fully represented in our CIS curriculums. CIS capstone courses often include an applied project that is managed with traditional project management methods (plan first,…

Laticifer-specific cis-prenyltransferase silencing affects the rubber, triterpene, and inulin content of Taraxacum brevicorniculatum.

PubMed

Post, Janina; van Deenen, Nicole; Fricke, Julia; Kowalski, Natalie; Wurbs, David; Schaller, Hubert; Eisenreich, Wolfgang; Huber, Claudia; Twyman, Richard M; Prüfer, Dirk; Gronover, Christian Schulze

2012-03-01

Certain Taraxacum species, such as Taraxacum koksaghyz and Taraxacum brevicorniculatum, produce large amounts of high-quality natural rubber in their latex, the milky cytoplasm of specialized cells known as laticifers. This high-molecular mass biopolymer consists mainly of poly(cis-1,4-isoprene) and is deposited in rubber particles by particle-bound enzymes that carry out the stereospecific condensation of isopentenyl diphosphate units. The polymer configuration suggests that the chain-elongating enzyme (rubber transferase; EC 2.5.1.20) is a cis-prenyltransferase (CPT). Here, we present a comprehensive analysis of transgenic T. brevicorniculatum plants in which the expression of three recently isolated CPTs known to be associated with rubber particles (TbCPT1 to -3) was heavily depleted by laticifer-specific RNA interference (RNAi). Analysis of the CPT-RNAi plants by nuclear magnetic resonance, size-exclusion chromatography, and gas chromatography-mass spectrometry indicated a significant reduction in rubber biosynthesis and a corresponding 50% increase in the levels of triterpenes and the main storage carbohydrate, inulin. Transmission electron microscopy revealed that the laticifers in CPT-RNAi plants contained fewer and smaller rubber particles than wild-type laticifers. We also observed lower activity of hydroxymethylglutaryl-coenzyme A reductase, the key enzyme in the mevalonate pathway, reflecting homeostatic control of the isopentenyl diphosphate pool. To our knowledge, this is the first in planta demonstration of latex-specific CPT activity in rubber biosynthesis.

Characteristics of step-defined physical activity categories in U.S. adults..

PubMed

Sisson, Susan B; Camhi, Sarah M; Tudor-Locke, Catrine; Johnson, William D; Katzmarzyk, Peter T

2012-01-01

Descriptive physical activity epidemiology of the U.S. population is critical for program development and resource allocation. The purpose of this project was to describe step-defined categories (as measured by accelerometer) of U.S. adults and to determine predictors of sedentary classification (<5000 steps/d). The National Health and Nutrition Examination Survey (NHANES) is an annual, nationally representative survey used to determine the health status of the U.S. populace. In-home interviews and physical examination components of NHANES. Overall, 4372 eligible adults wore accelerometers in the 2005-2006 NHANES; 628 were excluded, which yielded 3744 adults (of which 46.8% were men). Steps per day; body mass index (BMI); demographic, household and behavioral variables. Means and frequencies were calculated. Logistic regression was utilized to determine predictors of sedentary classification. Overall, 36.1% were sedentary (i.e., <5000 steps/d); 47.6% were low to somewhat active (5000-9999 steps/d); 16.3% were active to highly active (≥10,000 steps/d). Advancing age (odds ratio [OR], 1.95; confidence intervals [CIs], 1.78, 2.13), higher BMI (OR, 1.40; CIs, 1.23, 1.59), female sex (OR, 1.86; CIs, 1.46, 2.36), African-American versus European-American ethnicity (OR, 1.36; CIs, 1.13, 1.65), household income versus ≥$45,000 (<$25,000: OR, 1.94; CIs, 1.40, 2.69; $25,000-$44,000: OR, 1.51; CIs, 1.23, 1.85), and current versus never smoker (OR, 1.53; CIs, 1.26, 1.86) variables had higher odds of sedentary classification. Usual daily occupational/domestic physical activity categories of standing/walking (OR, .51; CIs, .38, .69); lifting/climbing (OR, .26; CIs, .17, .38); and heavy loads/labor (OR, .16; CIs, .10, .26) had lower odds of sedentary classification than sitting. Over one-third of the U.S. population was classified as sedentary by accelerometer-determined steps per day, and several characteristics predicted sedentary classification.

ZFPL1, a novel ring finger protein required for cis-Golgi integrity and efficient ER-to-Golgi transport.

PubMed

Chiu, Chi-Fang; Ghanekar, Yashoda; Frost, Laura; Diao, Aipo; Morrison, Daniel; McKenzie, Eddie; Lowe, Martin

2008-04-09

The Golgi apparatus occupies a central position within the secretory pathway, but the molecular mechanisms responsible for its assembly and organization remain poorly understood. We report here the identification of zinc finger protein-like 1 (ZFPL1) as a novel structural component of the Golgi apparatus. ZFPL1 is a conserved and widely expressed integral membrane protein with two predicted zinc fingers at the N-terminus, the second of which is a likely ring domain. ZFPL1 directly interacts with the cis-Golgi matrix protein GM130. Depletion of ZFPL1 results in the accumulation of cis-Golgi matrix proteins in the intermediate compartment (IC) and the tubulation of cis-Golgi and IC membranes. Loss of ZFPL1 function also impairs cis-Golgi assembly following brefeldin A washout and slows the rate of cargo trafficking into the Golgi apparatus. Effects upon Golgi matrix protein localization and cis-Golgi structure can be rescued by wild-type ZFPL1 but not mutants defective in GM130 binding. Together, these data suggest that ZFPL1 has an important function in maintaining the integrity of the cis-Golgi and that it does so through interactions with GM130.

Chronic treatment with 13-cis-retinoic acid changes aggressive behaviours in the resident-intruder paradigm in rats.

PubMed

Trent, Simon; Drew, Cheney J G; Mitchell, Paul J; Bailey, Sarah J

2009-12-01

Retinoids, vitamin A related compounds, have an established role in the development of the nervous system and are increasingly recognized to play a role in adult brain function. The synthetic retinoid, 13-cis-retinoic acid (13-cis-RA, Roaccutane) is widely used to treat severe acne but has been linked to an increased risk of neuropsychiatric side effects, including depression. Here we report that chronic administration with 13-cis-RA (1 mg/kg i.p. daily, 7-14 days) in adult rats reduced aggression- and increased flight-related behaviours in the resident-intruder paradigm. However, in the forced swim, sucrose consumption and open field tests treatment for up to 6 weeks with 13-cis-RA did not modify behaviour in adult or juvenile animals. The behavioural change observed in the resident-intruder paradigm is directly opposite to that observed with chronic antidepressant administration. These findings indicate that when a suitably sensitive behavioural test is employed then chronic administration of 13-cis-RA in adult rats induces behavioural changes consistent with a pro-depressant action.

Antibody side chain conformations are position-dependent.

PubMed

Leem, Jinwoo; Georges, Guy; Shi, Jiye; Deane, Charlotte M

2018-04-01

Side chain prediction is an integral component of computational antibody design and structure prediction. Current antibody modelling tools use backbone-dependent rotamer libraries with conformations taken from general proteins. Here we present our antibody-specific rotamer library, where rotamers are binned according to their immunogenetics (IMGT) position, rather than their local backbone geometry. We find that for some amino acid types at certain positions, only a restricted number of side chain conformations are ever observed. Using this information, we are able to reduce the breadth of the rotamer sampling space. Based on our rotamer library, we built a side chain predictor, position-dependent antibody rotamer swapper (PEARS). On a blind test set of 95 antibody model structures, PEARS had the highest average χ 1 and χ1+2 accuracy (78.7% and 64.8%) compared to three leading backbone-dependent side chain predictors. Our use of IMGT position, rather than backbone ϕ/ψ, meant that PEARS was more robust to errors in the backbone of the model structure. PEARS also achieved the lowest number of side chain-side chain clashes. PEARS is freely available as a web application at http://opig.stats.ox.ac.uk/webapps/pears. © 2018 Wiley Periodicals, Inc.

Effect of time between x-irradiation and chemotherapy on the growth of three solid mouse tumors. III. Cis-diamminedichloroplatinum

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

Twentyman, P.R.; Kallman, R.F.; Brown, J.M.

1979-08-01

Experiments have been carried out to determine the effect of different time intervals between the administration of x-irradiation (1200 rad) and cis-diamminedichloroplatinum (cis-DDP) (7 mg/kg) on the growth delay produced in three mouse tumors. The tumors used were the EMT6 tumor in BALB/c mice and the KHT and RIF-1 sarcomas in C3H mice. All tumors were grown intramuscularly in the gastrocnemius muscle and treatment was carried out at a mean tumor weight of 450 mg. Time to reach 2X (for KHT) or 4X (for EMT6 and RIF-1) treatment volume was used as the endpoint of response. The drug was administeredmore » by the intraperitoneal route either 24, 6, or 2 h before radiation, immediately before the start of radiation, or 3, 6, or 24 h after radiation. All irradiations were carried out in unanesthetized mice. The growth delays due to the drug alone were 2, 10, and 2 days for the EMT6, RIF-1, and KHT tumors, respectively. In the RIF-1 and KHT tumors, the combined modality groups tend to show longer growth delays than predicted by the addition of the growth delays for the single agents. For the EMT6 tumor, however, the trend is in the opposite direction. There is no particular timing between irradiation and drug administration which appears to produce consistently longer or shorter growth delays from system to system.« less

Identification of unique cis-element pattern on simulated microgravity treated Arabidopsis by in silico and gene expression

NASA Astrophysics Data System (ADS)

Soh, Hyuncheol; Choi, Yongsang; Lee, Taek-Kyun; Yeo, Up-Dong; Han, Kyeongsik; Auh, Chungkyun; Lee, Sukchan

2012-08-01

Arabidopsis gene expression microarray (44 K) was used to detect genes highly induced under simulated microgravity stress (SMS). Ten SMS-inducible genes were selected from the microarray data and these 10 genes were found to be abundantly expressed in 3-week-old plants. Nine out of the 10 SMS-inducible genes were also expressed in response to the three abiotic stresses of drought, touch, and wounding in 3-week-old Arabidopsis plants respectively. However, WRKY46 was elevated only in response to SMS. Six other WRKY genes did not respond to SMS. To clarify the characteristics of the genes expressed at high levels in response to SMS, 20 cis-elements in the promoters of the 40 selected genes including the 10 SMS-inducible genes, the 6 WRKY genes, and abiotic stress-inducible genes were analyzed and their spatial positions on each promoter were determined. Four cis-elements (M/T-G-T-P from MYB1AT or TATABOX5, GT1CONSENSUS, TATABOX5, and POLASIG1) showed a unique spatial arrangement in most SMS-inducible genes including WRKY46. Therefore the M/T-G-T-P cis-element patterns identified in the promoter of WRKY46 may play important roles in regulating gene expression in response to SMS. The presences of the cis-element patterns suggest that the order or spatial positioning of certain groups of cis-elements is more important than the existence or numbers of specific cis-elements. Taken together, our data indicate that WRKY46 is a novel SMS inducible transcription factor and the unique spatial arrangement of cis-elements shown in WRKY46 promoter may play an important role for its response to SMS.

Enantioselective synthesis of cis-decalins using organocatalysis and sulfonyl Nazarov reagents.

PubMed

Peña, Javier; Silveira-Dorta, Gastón; Moro, Rosalina F; Garrido, Narciso M; Marcos, Isidro S; Sanz, Francisca; Díez, David

2015-04-10

The first organocatalytic synthesis of cis-decalins using sulfonyl Nazarov reagents is reported. The Jørgensen's catalyst directs this highly enantioselective synthesis using different cyclohexenal derivatives.

Thermodynamics of the clusterization process of cis isomers of unsaturated fatty acids at the air/water interface.

PubMed

Vysotsky, Yu B; Belyaeva, E A; Fainerman, V B; Vollhardt, D; Aksenenko, E V; Miller, R

2009-04-02

In the framework of the semiempirical PM3 method, the thermodynamic parameters of cis isomers of unsaturated carboxylic acids at the air/water interface are studied. The model systems used are unsaturated cis fatty acid of the composition Delta = 12-15 and omega = 6-11, where Delta and omega refer to the number of carbon atoms between the functional group and double bond, and that between the double bond and methyl group, respectively. For dimers, trimers, and tetramers of the four acid series, the thermodynamic parameters of clusterization are calculated. It is shown that the position of the double bond does not significantly affect the values of thermodynamic parameters of formation and clusterization of carboxylic acids for equal chain lengths (n = Delta + omega). The calculated results show that for cis unsaturated fatty acid with odd Delta values the spontaneous clusterization threshold corresponds to n = 17-18 carbon atoms in the alkyl chain, while for monounsaturated acids with even Delta values this threshold corresponds to n = 18-19 carbon atoms in the alkyl chain. These differences in the clusterization threshold between the acids with even and odd Delta values are attributed to the formation of additional intermolecular hydrogen bonds between the ketonic oxygen atom of one monomer and the hydrogen atom linked to the alpha-carbon atom of the second monomer for the acids with odd Delta values or between the hydroxyl oxygen atom of one monomer and hydrogen atom linked to the alpha-carbon atom of the second monomer for the acids with even Delta values. The results obtained in the study agree satisfactorily with our experimental data for cis unsaturated nervonic (Delta15, omega9) and erucic acids (Delta13, omega9), and published data for some fatty acids, namely cis-16-heptadecenoic (Delta16, omega1), cis-9-hexadecenoic (Delta7, omega9), cis-11-eicosenoic (Delta11, omega9) and cis-9-octadecenoic acid (Delta9, omega9).

Photodissociation of cis-, trans-, and 1,1-dichloroethylene in the ultraviolet range: characterization of Cl((2)P(J)) elimination.

PubMed

Hua, Linqiang; Zhang, Xiaopeng; Lee, Wei-Bin; Chao, Meng-Hsuan; Zhang, Bing; Lin, King-Chuen

2010-01-14

By using photofragment velocity imaging detection coupled with a (2 + 1) resonance-enhanced multiphoton ionization technique, the elimination channel of spin-orbit chlorine atoms in photodissociation of cis-, trans-, and 1,1-dichloroethylene at two photolysis wavelengths of 214.5 and 235 nm is investigated. Translational energy and angular distributions of Cl((2)P(J)) fragmentation are acquired. The Cl((2)P(J)) fragments are produced by two competing channels. The fast dissociation component with higher translational energy is characterized by a Gaussian distribution, resulting from a curve crossing of the initially excited (pi, pi*) state to nearby repulsive (pi, sigma*) and/or (n, sigma*). In contrast, the slow component with a lower translational energy is characterized by a Boltzmann distribution, which dissociates on the vibrationally hot ground state relaxed from the (pi, pi*) state via internal conversion. cis-C(2)H(2)Cl(2) is found to have a larger branching of Boltzmann component than the other two isomers. The fraction of available energy partitioning into translation increases along the trend of cis- < trans- < 1,1-C(2)H(2)Cl(2). This trend may be fitted by a rigid radical model and interpreted by means of a torque generated during the C-Cl bond cleavage. The anisotropy parameters are determined, and the transition dipole moments are expected to be essentially along the C horizontal lineC bond axis. The results are also predicted theoretically. The relative quantum yields of Cl((2)P(J)) have a similar value for the three isomers at the two photolysis wavelengths.

Mutation of NgBR, a subunit of cis-prenyltransferase, causes a congenial disorder of glycosylation

PubMed Central

Park, Eon Joo; Grabińska, Kariona A.; Guan, Ziqiang; Stránecký, Viktor; Hartmannová, Hana; Hodaňová, Kateřina; Barešová, Veronika; Sovová, Jana; Jozsef, Levente; Ondrušková, Nina; Hansíková, Hana; Honzík, Tomáš; Zeman, Jiří; Hůlková, Helena; Wen, Rong; Kmoch, Stanislav; Sessa, William C.

2014-01-01

Summary Dolichol is an obligate carrier of glycans for N-linked protein glycosylation, O-mannosylation, and GPI anchor biosynthesis. Cis-prenyltransferase (cis-PTase) is the first enzyme committed to the synthesis of dolichol. However, the proteins responsible for mammalian cis-PTase activity have not been delineated. Here we show that Nogo-B receptor (NgBR) is a subunit required for dolichol synthesis in yeast, mice and man. Moreover, we describe a family with a congenital disorder of glycosylation caused by a loss of function mutation in the conserved C terminus of NgBR-R290H and show that fibroblasts isolated from patients exhibit reduced dolichol profiles and enhanced accumulation of free cholesterol identically to fibroblasts from mice lacking NgBR. Mutation of NgBR-R290H in man and orthologs in yeast proves the importance of this evolutionarily conserved residue for mammalian cis-PTase activity and function. Thus, these data provides a genetic basis for the essential role of NgBR in dolichol synthesis and protein glycosylation. PMID:25066056

Coordination chemistry of highly hemilabile bidentate sulfoxide N-heterocyclic carbenes with palladium(II).

PubMed

Yu, Kuo-Hsuan; Wang, Chia-Ching; Chang, I-Hsin; Liu, Yi-Hung; Wang, Yu; Elsevier, Cornelis J; Liu, Shiuh-Tzung; Chen, Jwu-Ting

2014-12-01

Imidazolium salts, [RS(O)-CH2 (C3 H3 N2 )Mes]Cl (R=Me (L1a), Ph (L1b)); Mes=mesityl), make convenient carbene precursors. Palladation of L1a affords the monodentate dinuclear complex, [(PdCl2 {MeS(O)CH2 (C3 H2 N2 )Mes})2 ] (2a), which is converted into trans-[PdCl2 (NHC)2] (trans-4a; N-heterocyclic carbene) with two rotamers in anti and syn configurations. Complex trans-4a can isomerize into cis-4a(anti) at reflux in acetonitrile. Abstraction of chlorides from 4a or 4b leads to the formation of a new dication: trans-[Pd{RS(O)CH2(C3H2N2)Mes}2](PF6)2 (R=Me (5a), Ph (5b)). The X-ray structure of 5a provides evidence that the two bidentate SO-NHC ligands at palladium(II) are in square-planar geometry. Two sulfoxides are sulfur- and oxygen-bound, and constitute five- and six-membered chelate rings with the metal center, respectively. In acetonitrile, complexes 5a or 5b spontaneously transform into cis-[Pd(NHC)2(NCMe)2](PF6)2. Similar studies of thioether-NHCs have also been examined for comparison. The results indicate that sulfoxides are more labile than thioethers. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Density functional theory study of structural and electronic properties of trans and cis structures of thiothixene as a nano-drug.

PubMed

Noori Tahneh, Akram; Bagheri Novir, Samaneh; Balali, Ebrahim

2017-11-25

The geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, natural charge distribution, MEP analysis and thermodynamic properties of the trans and cis structures of the drug thiothixene were investigated using density functional theory (DFT) and time-dependent DFT (TDDFT) methods with the B3LYP hybrid functional and 6-311 + G(d,p) basis set. The results of the calculations demonstrate that the cis structure of thiothixene has appropriate quantum properties that can act as an active medicine. The relative energies of trans and cis structures of thiothixene shows that the cis structure is more stable than the trans structure, with a small energy difference. TDDFT calculations show that the cis structure of thiothixene has the best absorption properties. The calculated NLO properties show that the NLO properties of the cis structure of thiothixene are higher than the trans structure, and the fact that the chemical hardness of the cis structure is lower than that of the trans structure that indicates that the reactivity and charge transfer of the cis isomer of thiothixene is higher than that of trans thiothixene. The molecular electrostatic potential (MEP) maps of both structures of thiothixene demonstrate that the oxygen atoms of the molecule are appropriate areas for electrophilic reactions. The vibrational frequencies of the two conformations of thiothixene demonstrate that both structures of thiothixene have almost similar modes of vibrations. The calculated thermodynamic parameters show that these quantities increase with enhancing temperature due to the enhancement of molecular vibrational intensities with temperature. Graphical abstract Trans/Cis isomerization of thiothixene drug.

40 CFR 180.296 - Dimethyl phosphate of 3-hydroxy-N-methyl-cis-crotonamide; tolerances for residues.

Code of Federal Regulations, 2010 CFR

2010-07-01

...-methyl-cis-crotonamide; tolerances for residues. 180.296 Section 180.296 Protection of Environment... RESIDUES IN FOOD Specific Tolerances § 180.296 Dimethyl phosphate of 3-hydroxy-N-methyl-cis-crotonamide; tolerances for residues. (a) General. Tolerances are established for residues of the insecticide Dimethyl...

Hydrogenation of fluoroarenes: Direct access to all-cis-(multi)fluorinated cycloalkanes.

PubMed

Wiesenfeldt, Mario P; Nairoukh, Zackaria; Li, Wei; Glorius, Frank

2017-09-01

All-c is -multifluorinated cycloalkanes exhibit intriguing electronic properties. In particular, they display extremely high dipole moments perpendicular to the aliphatic ring, making them highly desired motifs in material science. Very few such motifs have been prepared, as their syntheses require multistep sequences from diastereoselectively prefunctionalized precursors. Herein we report a synthetic strategy to access these valuable materials via the rhodium-cyclic (alkyl)(amino)carbene (CAAC)-catalyzed hydrogenation of readily available fluorinated arenes in hexane. This route enables the scalable single-step preparation of an abundance of multisubstituted and multifluorinated cycloalkanes, including all- cis -1,2,3,4,5,6-hexafluorocyclohexane as well as cis-configured fluorinated aliphatic heterocycles. Copyright © 2017, American Association for the Advancement of Science.

Genome sequences of three tunicamycin-producing Streptomyces strains; S. chartreusis NRRL 12338, S. chartreusis NRRL 3882, and S. lysosuperificus ATCC 31396

USDA-ARS?s Scientific Manuscript database

S. chartreusis strains NRRL 12338 and NRRL 3882, S. clavuligerus NRRL 3585, and S. lysosuperificus ATCC 31396, are known producers of tunicamycins, and also of charteusins, clavulinate, cephalosporins, holomycins, and calcimycin. Here we announce the sequencing of the S. lysosuperificus and the two...

Enhanced luminescence of Cu-In-S nanocrystals by surface modification.

PubMed

Kim, Young-Kuk; Cho, Young-Sang; Chung, Kookchae; Choi, Chul-Jin; Shin, Pyung-Woo

2012-04-01

We have synthesized highly luminescent Cu-In-S nanocrystals by heating the mixture of metal carboxylates and alkylthiol under inert atmosphere. We modified the surface of CIS nanocrystals with zinc carboxylate and subsequent injection of alkylthiol. As a result of the surface modification, highly luminescent CIS@ZnS core/shell nanocrystals were synthesized. The luminescence quantum yield (QY) of best CIS@ZnS nanocrystals was above 50%, which is more than 10 times higher than the initial QY of CIS nanocrystals before surface modification (QY = 3%). Detailed study on the luminescence mechanism implies that etching of the surface of nanocrystals by dissociated carboxylate group (CH3COO-) and formation of epitaxial shell by Zn with sulfur from alkylthiol efficiently removed the surface defects which are major non-radiative recombination sites in semiconductor nanocrystals. In this study, we developed a novel surface modification route for monodispersed highly luminescent Cu-In-S nanocrystals with less toxic and highly stable precursors.

Brasilenyne and cis-dihydrorhodophytin: Antifeedant medium-ring haloethers from a sea hare (Aplysia brasiliana)

PubMed Central

Kinnel, R. B.; Dieter, R. K.; Meinwald, J.; Van Engen, D.; Clardy, J.; Eisner, T.; Stallard, M. O.; Fenical, W.

1979-01-01

Two straight-chain C15 fish antifeedants have been isolated from the sea hare Aplysia brasiliana. Chemical, spectral, and x-ray diffraction studies led to the characterization of these medium-ring ethers as brasilenyne (2) and cis-dihydrorhodophytin (3). The oxonin ring system of 2 is novel in nature. Biosynthetic considerations permit the postulation that a third compound, a noncrystalline congener of these compounds, is cis-isodihydrohodophytin (4). PMID:16592687

A conserved C-terminal RXG motif in the NgBR subunit of cis-prenyltransferase is critical for prenyltransferase activity.

PubMed

Grabińska, Kariona A; Edani, Ban H; Park, Eon Joo; Kraehling, Jan R; Sessa, William C

2017-10-20

cis -Prenyltransferases ( cis -PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. In eukaryotes and archaea, cis -PT is the first enzyme committed to the synthesis of dolichyl phosphate, an obligate lipid carrier in protein glycosylation reactions. The homodimeric bacterial enzyme, undecaprenyl diphosphate synthase, generates 11 isoprene units and has been structurally and mechanistically characterized in great detail. Recently, we discovered that unlike undecaprenyl diphosphate synthase, mammalian cis -PT is a heteromer consisting of NgBR (Nus1) and hCIT (dehydrodolichol diphosphate synthase) subunits, and this composition has been confirmed in plants and fungal cis -PTs. Here, we establish the first purification system for heteromeric cis -PT and show that both NgBR and hCIT subunits function in catalysis and substrate binding. Finally, we identified a critical R X G sequence in the C-terminal tail of NgBR that is conserved and essential for enzyme activity across phyla. In summary, our findings show that eukaryotic cis -PT is composed of the NgBR and hCIT subunits. The strong conservation of the R X G motif among NgBR orthologs indicates that this subunit is critical for the synthesis of polyprenol diphosphates and cellular function. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

PBPK modeling of the cis- and trans-permethrin isomers and their major urinary metabolites in rats

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

Willemin, Marie-Emilie; Sorbonne University, Université de Technologie de Compiègne, CNRS, UMR 7338 Biomechanics and Bioengineering, Centre de recherche Royallieu CS 60319,60203 Compiègnee Cedex; Desmots, Sophie

2016-03-01

Permethrin, a pyrethroid insecticide, is suspected to induce neuronal and hormonal disturbances in humans. The widespread exposure of the populations has been confirmed by the detection of the urinary metabolites of permethrin in biomonitoring studies. Permethrin is a chiral molecule presenting two forms, the cis and the trans isomers. Because in vitro studies indicated a metabolic interaction between the trans and cis isomers of permethrin, we adapted and calibrated a PBPK model for trans- and cis-permethrin separately in rats. The model also describes the toxicokinetics of three urinary metabolites, cis- and trans-3-(2,2 dichlorovinyl)-2,2-dimethyl-(1-cyclopropane) carboxylic acid (cis- and trans-DCCA), 3-phenoxybenzoic acidmore » (3-PBA) and 4′OH-phenoxybenzoic acid (4′-OH-PBA). In vivo experiments performed in Sprague–Dawley rats were used to calibrate the PBPK model in a Bayesian framework. The model captured well the toxicokinetics of permethrin isomers and their metabolites including the rapid absorption, the accumulation in fat, the extensive metabolism of the parent compounds, and the rapid elimination of metabolites in urine. Average hepatic clearances in rats were estimated to be 2.4 and 5.7 L/h/kg for cis- and trans-permethrin, respectively. High concentrations of the metabolite 4′-OH-PBA were measured in urine compared to cis- and trans-DCCA and 3-PBA. The confidence in the extended PBPK model was then confirmed by good predictions of published experimental data obtained using the isomers mixture. The extended PBPK model could be extrapolated to humans to predict the internal dose of exposure to permethrin from biomonitoring data in urine. - Highlights: • A PBPK model of isomers of permethrin and its urinary metabolites was developed. • A quantitative link was established for permethrin and its biomarkers of exposure. • The bayesian framework allows getting confidence interval on the estimated parameters. • The PBPK model can be

Synthesis and bacterial metabolism of cis- and trans-2-alkyl analogues of sodium cyclamate.

PubMed

Wiley, R A; Pearson, D A; Schmidt, V; Wesche, S B; Roxon, J J

1983-07-01

Sodium cyclamate is an effective artificial sweetner, which has been banned from the U.SD. market because of alleged carcinogenic properties. It appears that cyclohexylamine, liberated from cyclamate as a result of bacterial mtabolism, is the proximate carcinogen. In an effort to elucidate the extent to which analogues of cyclamate would enter into the bacterial metabolic pathway, as well as any stereochemical requirements which might exist, several 2-alkaly analogues of sodium cyclamate were prepared. It was found that trans-N-(2-methylcyclohexyl)sulfamate (trans-2a) and trans-N-(2-ethylcyclohexyl)sulfamate were hydrolyzed by freshly collected fecal suspensions from rats fed cyclamate, but not from control rats, at the same rate as cyclamate itself. trans-N-(2-Isopropylcyclohexyl)sulfamate (trans-2c) was not hydrolyzed at all. Surprisingly, two of the analogous cis compounds (cis-2a and cis-2c, respectively) were hydrolyzed by fecal suspensions from control, as well as from cyclamate-fed, rats. Moreover, cis-2a was hydrolyzed by incubating it in medium only. Thus, it is apparent that stereochemical influences on the chemical properties of these compounds are substantial. These results do not appear to point the way toward a safe, nonmetabolizable sweetening agent.

Photoluminescence of CuInS2 nanocrystals: effect of surface modification

NASA Astrophysics Data System (ADS)

Kim, Young-Kuk; Cho, Young-Sang; Chung, Kookchae; Choi, Chul-Jin

2011-09-01

We have synthesized highly luminescent Cu-In-S(CIS) nanocrystals (NCs) by heating the mixture of metal carboxylates and alkylthiol under inert atmosphere. We modified the surface of CIS NCs with zinc carboxylate and subsequent injection of alkylthiol. As a result of the surface modification, highly luminescent CIS@ZnS core/shell nanocrystals were synthesized. The luminescence quantum yield (QY) of best CIS@ZnS NCs was above 50%, which is 10 times higher than the initial QY of CIS NCs before surface modification (QY=3%). Detailed study on the luminescence mechanism implies that etching of the surface of NCs by dissociated carboxylate group (CH3COO-) and formation of epitaxial shell by Zn with sulfur from alkylthiol efficiently removed the surface defects which are known to be major non-radiative recombination sites in semiconductor nanocrystals. In this study, we developed a novel surface modification route for monodispersed highly luminescent Cu-In-S NCs with less toxic and highly stable precursors. Investigation with the timeand the temperature-dependent photoluminescence showed that the trap related emission was minimized by surface modification and the donor-acceptor pair recombination was enhanced by controlling copper stoichiometry.xb

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

Combined removal of a BTEX, TCE, and cis-DCE mixture using Pseudomonas sp. immobilized on scrap tyres.

PubMed

Lu, Qihong; de Toledo, Renata Alves; Xie, Fei; Li, Junhui; Shim, Hojae

2015-09-01

The simultaneous aerobic removal of a mixture of benzene, toluene, ethylbenzene, and o,m,p-xylene (BTEX); cis-dichloroethylene (cis-DCE); and trichloroethylene (TCE) from the artificially contaminated water using an indigenous bacterial isolate identified as Pseudomonas plecoglossicida immobilized on waste scrap tyres was investigated. Suspended and immobilized conditions were compared for the removal of these volatile organic compounds. For the immobilized system, toluene, benzene, and ethylbenzene were completely removed, while the highest removal efficiencies of 99.0 ± 0.1, 96.8 ± 0.3, 73.6 ± 2.5, and 61.6 ± 0.9% were obtained for o-xylene, m,p-xylene, TCE, and cis-DCE, respectively. The sorption kinetics of contaminants towards tyre surface was also evaluated, and the sorption capacity generally followed the order of toluene > benzene > m,p-xylene > o-xylene > ethylbenzene > TCE > cis-DCE. Scrap tyres showed a good capability for the simultaneous sorption and bioremoval of BTEX/cis-DCE/TCE mixture, implying a promising waste material for the removal of contaminant mixture from industrial wastewater or contaminated groundwater.

A Survey of Current Computer Information Science (CIS) Students.

ERIC Educational Resources Information Center

Los Rios Community Coll. District, Sacramento, CA. Office of Institutional Research.

This document is a survey designed to be completed by current students of Computer Information Science (CIS) in the Los Rios Community College District (LRCCD), which consists of three community colleges: American River College, Cosumnes River College, and Sacramento City College. The students are asked about their educational goals and how…

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.

History and Status of the CIS Customs Union

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

Lawson, T.M.; Erickson, S.A.

1999-08-31

This report explores the history of the CIS Customs Union and the major obstacles the Union faces in its implementation. Investigation of the Customs Union is necessary as its implementation could effect the Second Line of Defense (SLD) Program. Russian Customs contends that radiation detectors should not be installed along the Customs Union members borders of as the borders will be dissolved when the Union is implemented.

Thermal degradation kinetics of all-trans and cis-carotenoids in a light-induced model system.

PubMed

Xiao, Ya-Dong; Huang, Wu-Yang; Li, Da-Jing; Song, Jiang-Feng; Liu, Chun-Quan; Wei, Qiu-Yu; Zhang, Min; Yang, Qiu-Ming

2018-01-15

Thermal degradation kinetics of lutein, zeaxanthin, β-cryptoxanthin, β-carotene was studied at 25, 35, and 45°C in a model system. Qualitative and quantitative analyses of all-trans- and cis-carotenoids were conducted using HPLC-DAD-MS technologies. Kinetic and thermodynamic parameters were calculated by non-linear regression. A total of 29 geometrical isomers and four oxidation products were detected, including all-trans-, keto compounds, mono-cis- and di-cis-isomers. Degradations of all-trans-lutein, zeaxanthin, β-cryptoxanthin, and β-carotene were described by a first-order kinetic model, with the order of rate constants as k β -carotene >k β -cryptoxanthin >k lutein >k zeaxanthin . Activation energies of zeaxanthin, lutein, β-cryptoxanthin, and β-carotene were 65.6, 38.9, 33.9, and 8.6kJ/moL, respectively. cis-carotenoids also followed with the first-order kinetic model, but they did not show a defined sequence of degradation rate constants and activation energies at different temperatures. A possible degradation pathway of four carotenoids was identified to better understand the mechanism of carotenoid degradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electro-optic and radiation damage performance of the CIS115, an imaging sensor for the JANUS optical camera onboard JUICE

NASA Astrophysics Data System (ADS)

Soman, M. R.; Allanwood, E. A. H.; Holland, A. D.; Stefanov, K.; Pratlong, J.; Leese, M.; Gow, J. P. D.; Smith, D. R.

2016-08-01

The Jupiter Icy Moon Explorer (JUICE) has been officially adopted as the next Large class mission by the European Space Agency, with a launch date of 2022. The science payload includes an optical camera, JANUS, which will perform imaging and mapping observations of Jupiter, its moons and icy rings. A 13 slot filter wheel will be used to provide spectral information in order for the JANUS experiment to study the geology and physical properties of Ganymede, Europa and Io, and to investigate processes and structures in the atmosphere of Jupiter. The sensor selected for JANUS is the back-thinned CIS115, a 3 MPixel CMOS Image Sensor from e2v technologies. The CIS115 has a 4-Transistor pixel design with a pinned photodiode to improve signal to noise performance by reducing dark current and allowing for reset level subtraction. The JUICE mission will consist of an 8 year cruise phase followed by a 3 year science phase in the Jovian system. Models of the radiation environment throughout the JUICE mission predict that the End of Life (EOL) non-ionising damage will be equivalent to 1010 protons cm-2 (10 MeV) and the EOL ionising dose will be 100 krad(Si), once the shielding from the spacecraft and instrument design is taken into account. An extensive radiation campaign is therefore being carried out to qualify and characterise the CIS115 for JANUS, as well as other space and terrestrial applications. Radiation testing to take the CIS115 to twice the ionising dose and displacement damage levels was completed in 2015 and the change in sensor performance has been characterised. Good sensor performance has been observed following irradiation and a summary of the key results from the campaign using gamma irradiation (ionising dose) will be presented here, including its soft X-ray detection capabilities, flat-band voltage shift and readout noise. In 2016, further radiation campaigns on flight-representative CIS115s will be undertaken and their results will be disseminated in

Effect of toluene concentration and hydrogen peroxide on Pseudomonas plecoglossicida cometabolizing mixture of cis-DCE and TCE in soil slurry.

PubMed

Li, Junhui; Lu, Qihong; de Toledo, Renata Alves; Lu, Ying; Shim, Hojae

2015-12-01

An indigenous Pseudomonas sp., isolated from the regional contaminated soil and identified as P. plecoglossicida, was evaluated for its aerobic cometabolic removal of cis-1,2-dichloroethylene (cis-DCE) and trichloroethylene (TCE) using toluene as growth substrate in a laboratory-scale soil slurry. The aerobic simultaneous bioremoval of the cis-DCE/TCE/toluene mixture was studied under different conditions. Results showed that an increase in toluene concentration level from 300 to 900 mg/kg prolonged the lag phase for the bacterial growth, while the bioremoval extent for cis-DCE, TCE, and toluene declined as the initial toluene concentration increased. In addition, the cometabolic bioremoval of cis-DCE and TCE was inhibited by the presence of hydrogen peroxide as the additional oxygen source, while the bioremoval of toluene (900 mg/kg) was enhanced after 9 days of incubation. The subsequent addition of toluene did not improve the cometabolic bioremoval of cis-DCE and TCE. The obtained results would help to enhance the applicability of bioremediation technology to the mixed waste contaminated sites.

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.

PubMed

Babak, Tomas; Garrett-Engele, Philip; Armour, Christopher D; Raymond, Christopher K; Keller, Mark P; Chen, Ronghua; Rohl, Carol A; Johnson, Jason M; Attie, Alan D; Fraser, Hunter B; Schadt, Eric E

2010-08-13

Identifying associations between genotypes and gene expression levels using microarrays has enabled systematic interrogation of regulatory variation underlying complex phenotypes. This approach has vast potential for functional characterization of disease states, but its prohibitive cost, given hundreds to thousands of individual samples from populations have to be genotyped and expression profiled, has limited its widespread application. Here we demonstrate that genomic regions with allele-specific expression (ASE) detected by sequencing cDNA are highly enriched for cis-acting expression quantitative trait loci (cis-eQTL) identified by profiling of 500 animals in parallel, with up to 90% agreement on the allele that is preferentially expressed. We also observed widespread noncoding and antisense ASE and identified several allele-specific alternative splicing variants. Monitoring ASE by sequencing cDNA from as little as one sample is a practical alternative to expression genetics for mapping cis-acting variation that regulates RNA transcription and processing.

Identification of cis-suppression of human disease mutations by comparative genomics

PubMed Central

Jordan, Daniel M.; Frangakis, Stephan G.; Golzio, Christelle; Cassa, Christopher A.; Kurtzberg, Joanne; Davis, Erica E.; Sunyaev, Shamil R.; Katsanis, Nicholas

2015-01-01

Patterns of amino acid conservation have served as a tool for understanding protein evolution1. The same principles have also found broad application in human genomics, driven by the need to interpret the pathogenic potential of variants in patients2. Here we performed a systematic comparative genomics analysis of human disease-causing missense variants. We found that an appreciable fraction of disease-causing alleles are fixed in the genomes of other species, suggesting a role for genomic context. We developed a model of genetic interactions that predicts most of these to be simple pairwise compensations. Functional testing of this model on two known human disease genes3,4 revealed discrete cis amino acid residues that, although benign on their own, could rescue the human mutations in vivo. This approach was also applied to ab initio gene discovery to support the identification of a de novo disease driver in BTG2 that is subject to protective cis-modification in more than 50 species. Finally, on the basis of our data and models, we developed a computational tool to predict candidate residues subject to compensation. Taken together, our data highlight the importance of cis-genomic context as a contributor to protein evolution; they provide an insight into the complexity of allele effect on phenotype; and they are likely to assist methods for predicting allele pathogenicity5,6. PMID:26123021

Identification of cis-suppression of human disease mutations by comparative genomics.

PubMed

Jordan, Daniel M; Frangakis, Stephan G; Golzio, Christelle; Cassa, Christopher A; Kurtzberg, Joanne; Davis, Erica E; Sunyaev, Shamil R; Katsanis, Nicholas

2015-08-13

Patterns of amino acid conservation have served as a tool for understanding protein evolution. The same principles have also found broad application in human genomics, driven by the need to interpret the pathogenic potential of variants in patients. Here we performed a systematic comparative genomics analysis of human disease-causing missense variants. We found that an appreciable fraction of disease-causing alleles are fixed in the genomes of other species, suggesting a role for genomic context. We developed a model of genetic interactions that predicts most of these to be simple pairwise compensations. Functional testing of this model on two known human disease genes revealed discrete cis amino acid residues that, although benign on their own, could rescue the human mutations in vivo. This approach was also applied to ab initio gene discovery to support the identification of a de novo disease driver in BTG2 that is subject to protective cis-modification in more than 50 species. Finally, on the basis of our data and models, we developed a computational tool to predict candidate residues subject to compensation. Taken together, our data highlight the importance of cis-genomic context as a contributor to protein evolution; they provide an insight into the complexity of allele effect on phenotype; and they are likely to assist methods for predicting allele pathogenicity.

Creating a Collaborative Learning Community in the CIS Sandbox

ERIC Educational Resources Information Center

Frydenberg, Mark

2013-01-01

Purpose: The purpose of this paper is to investigate the impact of transforming a traditional university computer lab to create a collaborative learning community known as the CIS Sandbox, by remodeling a physical space and supporting it with a virtual presence through the use of social media tools. The discussion applies Selander's "designs for…

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

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.

Detecting cis-regulatory binding sites for cooperatively binding proteins

PubMed Central

van Oeffelen, Liesbeth; Cornelis, Pierre; Van Delm, Wouter; De Ridder, Fedor; De Moor, Bart; Moreau, Yves

2008-01-01

Several methods are available to predict cis-regulatory modules in DNA based on position weight matrices. However, the performance of these methods generally depends on a number of additional parameters that cannot be derived from sequences and are difficult to estimate because they have no physical meaning. As the best way to detect cis-regulatory modules is the way in which the proteins recognize them, we developed a new scoring method that utilizes the underlying physical binding model. This method requires no additional parameter to account for multiple binding sites; and the only necessary parameters to model homotypic cooperative interactions are the distances between adjacent protein binding sites in basepairs, and the corresponding cooperative binding constants. The heterotypic cooperative binding model requires one more parameter per cooperatively binding protein, which is the concentration multiplied by the partition function of this protein. In a case study on the bacterial ferric uptake regulator, we show that our scoring method for homotypic cooperatively binding proteins significantly outperforms other PWM-based methods where biophysical cooperativity is not taken into account. PMID:18400778

Active Ageing in CIS Countries: Semantics, Challenges, and Responses

PubMed Central

Sidorenko, Alexandre; Zaidi, Asghar

2013-01-01

Although the CIS countries are connected together by the legacy of breaking away from the Soviet Union, they have had a distinctive transition course and are rather diverse in terms of the population ageing challenges and policy responses in place. The commonality is that a comprehensive national strategy on ageing is lacking, and many of necessary reforms were put aside owing to political uncertainties, lack of societal consensus, and financial instability. The notion of active ageing is associated with the term “accelerated ageing,” which is understood to be an individual living a life under harsh living conditions or a society experiencing rapid increases in the relative number of older persons, and therefore it carries a negative connotation. Yet, in the same spirit as the European Year for Active Ageing and Solidarity between Generations 2012, the CIS countries have initiated sectoral programmes towards enhancing employment of older workers, social participation of older people in the society in a wider sense and also measures promoting health and independent living of older persons. PMID:23346109

Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin.

PubMed

Xiong, Jie; Gao, Shan; Dui, Wen; Yang, Wentao; Chen, Xiao; Taverna, Sean D; Pearlman, Ronald E; Ashlock, Wendy; Miao, Wei; Liu, Yifan

2016-12-01

The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impact of these nucleosomes on the mutational and transcriptional landscape, and driven by evolutionary selection. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mutation of Nogo-B receptor, a subunit of cis-prenyltransferase, causes a congenital disorder of glycosylation.

PubMed

Park, Eon Joo; Grabińska, Kariona A; Guan, Ziqiang; Stránecký, Viktor; Hartmannová, Hana; Hodaňová, Kateřina; Barešová, Veronika; Sovová, Jana; Jozsef, Levente; Ondrušková, Nina; Hansíková, Hana; Honzík, Tomáš; Zeman, Jiří; Hůlková, Helena; Wen, Rong; Kmoch, Stanislav; Sessa, William C

2014-09-02

Dolichol is an obligate carrier of glycans for N-linked protein glycosylation, O-mannosylation, and GPI anchor biosynthesis. cis-prenyltransferase (cis-PTase) is the first enzyme committed to the synthesis of dolichol. However, the proteins responsible for mammalian cis-PTase activity have not been delineated. Here we show that Nogo-B receptor (NgBR) is a subunit required for dolichol synthesis in yeast, mice, and man. Moreover, we describe a family with a congenital disorder of glycosylation caused by a loss of function mutation in the conserved C terminus of NgBR-R290H and show that fibroblasts isolated from patients exhibit reduced dolichol profiles and enhanced accumulation of free cholesterol identically to fibroblasts from mice lacking NgBR. Mutation of NgBR-R290H in man and orthologs in yeast proves the importance of this evolutionarily conserved residue for mammalian cis-PTase activity and function. Thus, these data provide a genetic basis for the essential role of NgBR in dolichol synthesis and protein glycosylation. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans

PubMed Central

Fujioka, Miki; Mistry, Hemlata; Schedl, Paul; Jaynes, James B.

2016-01-01

The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible both for subdividing the chromatin into discrete domains and for determining the topological organization of these domains. Central to the architectural functions of insulators are homologous and heterologous insulator:insulator pairing interactions. The former (pairing between copies of the same insulator) dictates the process of homolog alignment and pairing in trans, while the latter (pairing between different insulators) defines the topology of looped domains in cis. To elucidate the principles governing these architectural functions, we use two insulators, Homie and Nhomie, that flank the Drosophila even skipped locus. We show that homologous insulator interactions in trans, between Homie on one homolog and Homie on the other, or between Nhomie on one homolog and Nhomie on the other, mediate transvection. Critically, these homologous insulator:insulator interactions are orientation-dependent. Consistent with a role in the alignment and pairing of homologs, self-pairing in trans is head-to-head. Head-to-head self-interactions in cis have been reported for other fly insulators, suggesting that this is a general principle of self-pairing. Homie and Nhomie not only pair with themselves, but with each other. Heterologous Homie-Nhomie interactions occur in cis, and we show that they serve to delimit a looped chromosomal domain that contains the even skipped transcription unit and its associated enhancers. The topology of this loop is defined by the heterologous pairing properties of Homie and Nhomie. Instead of being head-to-head, which would generate a circular loop, Homie-Nhomie pairing is head-to-tail. Head-to-tail pairing in cis

40 CFR 721.2250 - 1,4-Cyclohexanediamine, cis- and trans-.

Code of Federal Regulations, 2010 CFR

2010-07-01

...-. 721.2250 Section 721.2250 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.2250 1,4-Cyclohexanediamine, cis- and trans-. (a) Chemical substances and significant new...

Proximity labeling of cis-ligands of CD22/Siglec-2 reveals stepwise α2,6 sialic acid-dependent and -independent interactions.

PubMed

Alborzian Deh Sheikh, Amin; Akatsu, Chizuru; Imamura, Akihiro; Abdu-Allah, Hajjaj H M; Takematsu, Hiromu; Ando, Hiromune; Ishida, Hideharu; Tsubata, Takeshi

2018-01-01

Lectins expressed on the cell surface are often bound and regulated by the membrane molecules containing the glycan ligands on the same cell (cis-ligands). However, molecular nature and function of cis-ligands are generally poorly understood partly because of weak interaction between lectins and glycan ligands. Cis-ligands are most extensively studied in CD22 (also known as Siglec-2), an inhibitory B lymphocyte receptor specifically recognizing α2,6 sialic acids. CD22, CD45 and IgM are suggested to be ligands of CD22. Here we labeled molecules in the proximity of CD22 in situ on B cell surface using biotin-tyramide. Molecules including CD22, CD45 and IgM were labeled in wild-type but not ST6GalI -/- B cells that lack α2,6 sialic acids, indicating that these molecules associate with CD22 by lectin-glycan interaction, and are therefore cis-ligands. In ST6GalI -/- B cells, these cis-ligands are located in a slightly more distance from CD22. Thus, the lectin-glycan interaction recruits cis-ligands already located in the relative proximity of CD22 through non-lectin-glycan interaction to the close proximity. Moreover, cis-ligands are labeled in Cmah -/- B cells that lack Neu5Gc preferred by mouse CD22 as efficiently as in wild-type B cells, indicating that very low affinity lectin-glycan interaction is sufficient for recruiting cis-ligands, and can be detected by proximity labeling. Thus, proximity labeling with tyramide appears to be a useful method to identify cis-ligands and to analyze their interaction with the lectins. Copyright © 2017 Elsevier Inc. All rights reserved.

Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations.

PubMed Central

Hodel, A.; Rice, L. M.; Simonson, T.; Fox, R. O.; Brünger, A. T.

1995-01-01

Staphylococcal nuclease A exists in two folded forms that differ in the isomerization state of the Lys 116-Pro 117 peptide bond. The dominant form (90% occupancy) adopts a cis peptide bond, which is observed in the crystal structure. NMR studies show that the relatively small difference in free energy between the cis and trans forms (delta Gcis-->trans approximately 1.2 kcal/mol) results from large and nearly compensating differences in enthalpy and entropy (delta Hcis-->trans approximately delta TScis-->trans approximately 10 kcal/mol). There is evidence from X-ray crystal structures that the structural differences between the cis and the trans forms of nuclease are confined to the conformation of residues 112-117, a solvated protein loop. Here, we obtain a thermodynamic and structural description of the conformational equilibrium of this protein loop through an exhaustive conformational search that identified several substates followed by free energy simulations between the substrates. By partitioning the search into conformational substates, we overcame the multiple minima problem in this particular case and obtained precise and reproducible free energy values. The protein and water environment was implicitly modeled by appropriately chosen nonbonded terms between the explicitly treated loop and the rest of the protein. These simulations correctly predicted a small free energy difference between the cis and trans forms composed of larger, compensating differences in enthalpy and entropy. The structural predictions of these simulations were qualitatively consistent with known X-ray structures of nuclease variants and yield a model of the unknown minor trans conformation. PMID:7613463

Cis-Lunar Reusable In-Space Transportation Architecture for the Evolvable Mars Campaign

NASA Technical Reports Server (NTRS)

McVay, Eric S.; Jones, Christopher A.; Merrill, Raymond G.

2016-01-01

Human exploration missions to Mars or other destinations in the solar system require large quantities of propellant to enable the transportation of required elements from Earth's sphere of influence to Mars. Current and proposed launch vehicles are incapable of launching all of the requisite mass on a single vehicle; hence, multiple launches and in-space aggregation are required to perform a Mars mission. This study examines the potential of reusable chemical propulsion stages based in cis-lunar space to meet the transportation objectives of the Evolvable Mars Campaign and identifies cis-lunar propellant supply requirements. These stages could be supplied with fuel and oxidizer delivered to cis-lunar space, either launched from Earth or other inner solar system sources such as the Moon or near Earth asteroids. The effects of uncertainty in the model parameters are evaluated through sensitivity analysis of key parameters including the liquid propellant combination, inert mass fraction of the vehicle, change in velocity margin, and change in payload masses. The outcomes of this research include a description of the transportation elements, the architecture that they enable, and an option for a campaign that meets the objectives of the Evolvable Mars Campaign. This provides a more complete understanding of the propellant requirements, as a function of time, that must be delivered to cis-lunar space. Over the selected sensitivity ranges for the current payload and schedule requirements of the 2016 point of departure of the Evolvable Mars Campaign destination systems, the resulting propellant delivery quantities are between 34 and 61 tonnes per year of hydrogen and oxygen propellant, or between 53 and 76 tonnes per year of methane and oxygen propellant, or between 74 and 92 tonnes per year of hypergolic propellant. These estimates can guide future propellant manufacture and/or delivery architectural analysis.

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

Regioselective cis-trans isomerization of arachidonic double bonds by thiyl radicals: the influence of phospholipid supramolecular organization.

PubMed

Ferreri, Carla; Samadi, Abdelouahid; Sassatelli, Fabio; Landi, Laura; Chatgilialoglu, Chryssostomos

2004-02-04

Trans unsaturated fatty acids in humans may be originated by two different contributions. The exogenous track is due to dietary supplementation of trans fats and the endogenous path deals with free-radical-catalyzed cis-trans isomerization of fatty acids. Arachidonic acid residue (5c,8c,11c,14c-20:4), which has only two out of the four double bonds deriving from the diet, was used to differentiate the two paths and to assess the importance of a radical reaction. A detailed study on the formation of trans phospholipids catalyzed by the HOCH2CH2S* radical was carried out on L-alpha-phosphatidylcholine from egg lecithin and 1-stearoyl-2-arachidonoyl-L-alpha-phosphatidylcholine (SAPC) in homogeneous solution or in large unilamellar vesicles (LUVET). Thiyl radicals were generated from the corresponding thiol by either gamma-irradiation or UV photolysis, and the reaction course was followed by GC, Ag/TLC, and 13C NMR analyses. The isomerization was found to be independent of cis double bond location (random process) in i-PrOH solution. In the case of vesicles, the supramolecular organization of lipids produced a dramatic change of the isomerization outcome: (i) in egg lecithin, the reactivity of arachidonate moieties is higher than that of oleate and linoleate residues, (ii) in the linoleate residues of egg lecithin, the 9t,12c-18:2 isomer prevailed on the 9c,12t-18:2 isomer (3:1 ratio), and (iii) a regioselective isomerization of SAPC arachidonate residues occurred in the 5 and 8 positions. This effect of "positional preference" indicates that thiyl radicals entering the hydrophobic region of the membrane bilayer start to isomerize polyunsaturated fatty acid residues having the double bonds nearest to the membrane surfaces. We propose that arachidonic acid and its trans isomers can function as biomarkers in membranes for distinguishing the two trans fatty acid-forming pathways.

75 FR 68728 - Establishment of a U.S. Honey Producer Research, Promotion, and Consumer Information Order...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-09

... U.S. Honey Producer Research, Promotion, and Consumer Information Order; Withdrawal of a Proposed..., 2010, that proposed a new U.S. honey producer funded research and promotion program under the Commodity Promotion, Research, and Information Act of 1996 (1996 Act). The proposed U.S. Honey Producer Research...

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.

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation

PubMed Central

2010-01-01

Background Identifying associations between genotypes and gene expression levels using microarrays has enabled systematic interrogation of regulatory variation underlying complex phenotypes. This approach has vast potential for functional characterization of disease states, but its prohibitive cost, given hundreds to thousands of individual samples from populations have to be genotyped and expression profiled, has limited its widespread application. Results Here we demonstrate that genomic regions with allele-specific expression (ASE) detected by sequencing cDNA are highly enriched for cis-acting expression quantitative trait loci (cis-eQTL) identified by profiling of 500 animals in parallel, with up to 90% agreement on the allele that is preferentially expressed. We also observed widespread noncoding and antisense ASE and identified several allele-specific alternative splicing variants. Conclusion Monitoring ASE by sequencing cDNA from as little as one sample is a practical alternative to expression genetics for mapping cis-acting variation that regulates RNA transcription and processing. PMID:20707912

A DFT Study of the cis-Dihydroxylation of Nitroaromatic Compounds Catalyzed by Nitrobenzene Dioxygenase

PubMed Central

2014-01-01

The mechanism of cis-dihydroxylation of nitrobenzene and 2-nitrotoluene catalyzed by nitrobenzene 1,2-dioxygenase (NBDO), a member of the naphthalene family of Rieske non-heme iron dioxygenases, was studied by means of the density functional theory method using four models of the enzyme active site. Different possible reaction pathways for the substrate dioxygenation initiated either by the FeIII–OOH or HO–FeV=O attack on the aromatic ring were considered and the computed activation barriers compared with the Gibbs free energy of activation for the oxygen–oxygen cleavage leading to the formation of the iron(V)–oxo species from its ferric hydroperoxo precursor. The mechanism of the substrate cis-dihydroxylation leading to the formation of a cis-dihydrodiol was then investigated, and the most feasible mechanism was found to be starting with the attack of the high-valent iron–oxo species on the substrate ring yielding a radical intermediate, which further evolves toward the final product. PMID:24624972

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

Holographic recording materials development. [development of cis-trans isomerization for holographic memory

NASA Technical Reports Server (NTRS)

1974-01-01

Developments in the area of organic cis-trans isomerization systems for holographic memory applications are reported. The chemical research effort consisted of photochemical studies leading to the selection of a stilbene derivative and a polymer matrix system which have greatly improved refractive index differences between the cis and trans isomers as well as demonstrated efficiency of the photoisomerization process. In work on lithium niobate effects of sample stoichiometry and of read and write beam polarizations on recording efficiency were investigated. LiNbO3 was used for a study of angular sensitivity and of capability for simultaneous recording of extended objects without interference. The current status of LiNbO3 as a holographic recording material is summarized.

Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis

USDA-ARS?s Scientific Manuscript database

/Cis/-nat-siRNAs are a recently characterized class of small regulatory RNAs that are widespread in eukaryotes. Despite their abundance the importance of their regulatory activity is largely unknown. The only functional role for eukaryotic /cis/-nat-siRNAs that has been described to date is in envir...

The Autographa californica Multiple Nucleopolyhedrovirus ac83 Gene Contains a cis-Acting Element That Is Essential for Nucleocapsid Assembly.

PubMed

Huang, Zhihong; Pan, Mengjia; Zhu, Silei; Zhang, Hao; Wu, Wenbi; Yuan, Meijin; Yang, Kai

2017-03-01

Baculoviridae is a family of insect-specific viruses that have a circular double-stranded DNA genome packaged within a rod-shaped capsid. The mechanism of baculovirus nucleocapsid assembly remains unclear. Previous studies have shown that deletion of the ac83 gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) blocks viral nucleocapsid assembly. Interestingly, the ac83 -encoded protein Ac83 is not a component of the nucleocapsid, implying a particular role for ac83 in nucleocapsid assembly that may be independent of its protein product. To examine this possibility, Ac83 synthesis was disrupted by insertion of a chloramphenicol resistance gene into its coding sequence or by deleting its promoter and translation start codon. Both mutants produced progeny viruses normally, indicating that the Ac83 protein is not required for nucleocapsid assembly. Subsequently, complementation assays showed that the production of progeny viruses required the presence of ac83 in the AcMNPV genome instead of its presence in trans Therefore, we reasoned that ac83 is involved in nucleocapsid assembly via an internal cis -acting element, which we named the nucleocapsid assembly-essential element (NAE). The NAE was identified to lie within nucleotides 1651 to 1850 of ac83 and had 8 conserved A/T-rich regions. Sequences homologous to the NAE were found only in alphabaculoviruses and have a conserved positional relationship with another essential cis -acting element that was recently identified. The identification of the NAE may help to connect the data of viral cis -acting elements and related proteins in the baculovirus nucleocapsid assembly, which is important for elucidating DNA-protein interaction events during this process. IMPORTANCE Virus nucleocapsid assembly usually requires specific cis -acting elements in the viral genome for various processes, such as the selection of the viral genome from the cellular nucleic acids, the cleavage of concatemeric viral genome

Trans- and cis-octadecenoic acid isomers in the hump and milk lipids from Camelus dromedarius.

PubMed

Wolff, R L; Precht, D; Nasser, B; El Kebbaj, M S

2001-10-01

The distribution profiles of individual trans- as well as cis-18:1 isomers from the fat prepared from the hump adipose tissue and the milk from Camelus dromedarius (the single-humped Arabian species) are described. Gas-liquid chromatography on two capillary columns with different polarities and lengths were used for this purpose in combination with argentation thin-layer chromatography. A comparison of the profiles established is made with that of true ruminant fats. In the fats from the dromedarius as well as from true ruminants, the trans-18:1 isomers have their ethylenic bonds in all positions between delta4 and delta16. The prominent trans isomer is the 11-18:1 (vaccenic) acid in all species, and the complete distribution profiles are quite similar. Concerning the cis isomers, the prominent isomer is oleic acid, followed by cis-vaccenic acid, as in true ruminant fats. Other cis isomers encompass the delta6-8 and the delta12 to delta15 isomers. Camelidae (suborder Tylopoda) and Bovidae (suborder Ruminantia) have evolved independently since the Eocene, that is for approximately 50 million years. Despite this considerable period, and the profound differences in anatomy, morphology, physiology, ecological and dietary habits between the extant species of these suborders, the rumen microflora has continued to synthesize the same trans- and cis-octadecenoic acid isomers, in comparable proportions, at least as deduced from their composition profiles. We conclude that the trans-18:1 acid profile is not intrinsically species-dependent, but it can be affected by the nature and the proportions of dietary unsaturated fatty acids that themselves depend on the feed, and that may be species-specific.

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation

PubMed Central

O'Connor, Timothy R.; Bailey, Timothy L.

2014-01-01

Predicting which genomic regions control the transcription of a given gene is a challenge. We present a novel computational approach for creating and validating maps that associate genomic regions (cis-regulatory modules–CRMs) with genes. The method infers regulatory relationships that explain gene expression observed in a test tissue using widely available genomic data for ‘other’ tissues. To predict the regulatory targets of a CRM, we use cross-tissue correlation between histone modifications present at the CRM and expression at genes within 1 Mbp of it. To validate cis-regulatory maps, we show that they yield more accurate models of gene expression than carefully constructed control maps. These gene expression models predict observed gene expression from transcription factor binding in the CRMs linked to that gene. We show that our maps are able to identify long-range regulatory interactions and improve substantially over maps linking genes and CRMs based on either the control maps or a ‘nearest neighbor’ heuristic. Our results also show that it is essential to include CRMs predicted in multiple tissues during map-building, that H3K27ac is the most informative histone modification, and that CAGE is the most informative measure of gene expression for creating cis-regulatory maps. PMID:25200088

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

Requirement of Multiple cis-Acting Elements in the Human Cytomegalovirus Major Immediate-Early Distal Enhancer for Viral Gene Expression and Replication

PubMed Central

Meier, Jeffery L.; Keller, Michael J.; McCoy, James J.

2002-01-01

We have shown previously that the human cytomegalovirus (HCMV) major immediate-early (MIE) distal enhancer is needed for MIE promoter-dependent transcription and viral replication at low multiplicities of infection (MOI). To understand how this region works, we constructed and analyzed a series of HCMVs with various distal enhancer mutations. We show that the distal enhancer is composed of at least two parts that function independently to coordinately activate MIE promoter-dependent transcription and viral replication. One such part is contained in a 47-bp segment that has consensus binding sites for CREB/ATF, SP1, and YY1. At low MOI, these working parts likely function in cis to directly activate MIE gene expression, thus allowing viral replication to ensue. Three findings support the view that these working parts are likely cis-acting elements. (i) Deletion of either part of a bisegmented distal enhancer only slightly alters MIE gene transcription and viral replication. (ii) Reversing the distal enhancer’s orientation largely preserves MIE gene transcription and viral replication. (iii) Placement of stop codons at −300 or −345 in all reading frames does not impair MIE gene transcription and viral replication. Lastly, we show that these working parts are dispensable at high MOI, partly because of compensatory stimulation of MIE promoter activity and viral replication that is induced by a virion-associated component(s) present at a high viral particle/cell ratio. We conclude that the distal enhancer is a complex multicomponent cis-acting region that is required to augment both MIE promoter-dependent transcription and HCMV replication. PMID:11739696

CIS and Information Technology Certifications: Education Program Trends and Implications

ERIC Educational Resources Information Center

Andersson, David; Reimers, Karl

2009-01-01

The fields of Computer Information Systems (CIS) and Information Technology (IT) are experiencing rapid change. In 2003, an analysis of IT degree programs and those of competing disciplines at 10 post-secondary institutions concluded that an information technology program is perceived differently from information systems and computer science. In…

Investigation of cis-trans isomer dependent dermatotoxicokinetics of UV filter ethylhexyl methoxycinnamate through stratum corneum in vivo.

PubMed

Sharma, Anežka; Bányiová, Katarína; Vrana, Branislav; Justan, Ivan; Čupr, Pavel

2017-11-01

2-Ethylhexyl methoxycinnamate (EHMC) is one of the most used ultraviolet filters in personal care products. It undergoes cis/trans isomerization in sunlight, and there is limited toxicological understanding of the effects of the cis-isomer. It is known that two geometric isomers of one compound can have different physico-chemical properties and effects. However, there are no studies focusing on toxicokinetics of EHMC isomerization products to compare their potential difference in dermal exposure to cis-EHMC and trans-EHMC due to the difference in their dermatotoxicokinetics. In this study, dermal absorption of the parental trans-EHMC and its cis isomer was studied. A commercially available sunscreen lotion containing trans-EHMC and spiked with laboratory-prepared cis-EHMC was locally applied on the forearm skin of two volunteers. After 8 h of skin exposure, the stratum corneum (SC) layer was removed by tape stripping. The removed thickness of the SC was determined spectrophotometrically using a total protein assay. The concentration of both isomers in the removed SC was measured by HPLC-DAD. A new diffusion and permeability coefficient of both EHMC isomers in SC were determined by Fick's second law of diffusion in vivo. The difference in dermatotoxicokinetic parameters between the two isomers was not statistically significant. However, separate toxicological studies of isomeric forms and the determination of their dermatotoxicokinetic parameters are crucial for refinement of human risk assessment.

RDH13L, an enzyme responsible for the aldehyde-alcohol redox coupling reaction (AL-OL coupling reaction) to supply 11-cis retinal in the carp cone retinoid cycle.

PubMed

Sato, Shinya; Miyazono, Sadaharu; Tachibanaki, Shuji; Kawamura, Satoru

2015-01-30

Cone photoreceptors require effective pigment regeneration mechanisms to maintain their sensitivity in the light. Our previous studies in carp cones suggested the presence of an unconventional and very effective mechanism to produce 11-cis retinal, the necessary component in pigment regeneration. In this reaction (aldehyde-alcohol redox coupling reaction, AL-OL coupling reaction), formation of 11-cis retinal, i.e. oxidation of 11-cis retinol is coupled to reduction of an aldehyde at a 1:1 molar ratio without exogenous NADP(H) which is usually required in this kind of reaction. Here, we identified carp retinol dehydrogenase 13-like (RDH13L) as an enzyme catalyzing the AL-OL coupling reaction. RDH13L was partially purified from purified carp cones, identified as a candidate protein, and its AL-OL coupling activity was confirmed using recombinant RDH13L. We further examined the substrate specificity, subcellular localization, and expression level of RDH13L. Based on these results, we concluded that RDH13L contributes to a significant part, but not all, of the AL-OL coupling activity in carp cones. RDH13L contained tightly bound NADP(+) which presumably functions as a cofactor in the reaction. Mouse RDH14, a mouse homolog of carp RDH13L, also showed the AL-OL coupling activity. Interestingly, although carp cone membranes, carp RDH13L and mouse RDH14 all showed the coupling activity at 15-37 °C, they also showed a conventional NADP(+)-dependent 11-cis retinol oxidation activity above 25 °C without addition of aldehydes. This dual mechanism of 11-cis retinal synthesis attained by carp RDH13L and mouse RDH14 probably contribute to effective pigment regeneration in cones that function in the light. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Elovl5 regulates the mTORC2-Akt-FOXO1 pathway by controlling hepatic cis-vaccenic acid synthesis in diet-induced obese mice[S

PubMed Central

Tripathy, Sasmita; Jump, Donald B.

2013-01-01

Elevated hepatic expression of fatty acid elongase-5 (Elovl5) induces FoxO1 phosphorylation, lowers FoxO1 nuclear content, and suppresses expression of genes involved in gluconeogenesis (GNG). In this report, we define the molecular and metabolic basis of Elovl5 control of FoxO1 phosphorylation. Adenoviral-mediated (Ad-Elovl5) induction of hepatic Elovl5 in diet-induced obese, glucose-intolerant mice and HepG2 cells increased the phosphorylation of Akt2-S473 [mammalian target of rapamycin complex-2 (mTORC2) site], but not Akt2-T308 (PDK1 site). The Akt2 inhibitor Akti1/2 blocked Elovl5 induction of FoxO1-S256 phosphorylation in HepG2 cells. Elevated Elovl5 activity in liver and HepG2 cells induced rictor mRNA, rictor protein, and rictor-mTOR interaction, whereas rictor knockdown (siRNA) attenuated Elovl5 induction of Akt2-S473 and FoxO1-S256 phosphorylation in HepG2 cells. FA analysis revealed that the abundance of cis-vaccenic acid (18:1,n-7) was increased in livers of obese mice and HepG2 cells following Ad-Elovl5 infection. Treating HepG2 cells with Elovl5 substrates established that palmitoleic acid (16:1,n-7), but not γ-linolenic acid (18:3,n-6), induced rictor protein, Akt-S473, and FoxO1-S256 phosphorylation. Inhibition of FA elongation blocked 16:1,n-7 but not 18:1,n-7 induction of rictor protein and Akt-S473 and FoxO1-S256 phosphorylation. These results establish a novel link between Elovl5-mediated synthesis of 18:1,n-7 and GNG through the control of the mTORC2-Akt-FoxO1 pathway. PMID:23099444

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

Hidden regularity and universal classification of fast side chain motions in proteins

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

Rajeshwar, Rajitha; Smith, Jeremy C.; Krishnam, Marimuthu

Proteins display characteristic dynamical signatures that appear to be universal across all proteins regardless of topology and size. Here, we systematically characterize the universal features of fast side chain motions in proteins by examining the conformational energy surfaces of individual residues obtained using enhanced sampling molecular dynamics simulation (618 free energy surfaces obtained from 0.94 s MD simulation). The side chain conformational free energy surfaces obtained using the adaptive biasing force (ABF) method for a set of eight proteins with different molecular weights and secondary structures are used to determine the methyl axial NMR order parameters (O axis 2), populationsmore » of side chain rotamer states (ρ), conformational entropies (S conf), probability fluxes, and activation energies for side chain inter-rotameric transitions. The free energy barriers separating side chain rotamer states range from 0.3 to 12 kcal/mol in all proteins and follow a trimodal distribution with an intense peak at ~5 kcal/mol and two shoulders at ~3 and ~7.5 kcal/mol, indicating that some barriers are more favored than others by proteins to maintain a balance between their conformational stability and flexibility. The origin and the influences of the trimodal barrier distribution on the distribution of O axis 2 and the side chain conformational entropy are discussed. A hierarchical grading of rotamer states based on the conformational free energy barriers, entropy, and probability flux reveals three distinct classes of side chains in proteins. A unique nonlinear correlation is established between O axis 2 and the side chain rotamer populations (ρ). In conclusion, the apparent universality in O axis 2 versus correlation, trimodal barrier distribution, and distinct characteristics of three classes of side chains observed among all proteins indicates a hidden regularity (or commonality) in the dynamical heterogeneity of fast side chain motions in proteins.« less

Separation behavior of octadecadienoic acid isomers and identification of cis- and trans-isomers using gas chromatography.

PubMed

Shibamoto, Shigeaki; Gooley, Andrew; Yamamoto, Kouhei

2015-01-01

Using a strongly polar cyanopropyl capillary column we have investigated the gas chromatography (GC) separation behaviors of 24 octadecadienoic acid methyl ester (18:2ME) isomers compared against saturated methyl stearate (18:0ME) and arachidic acid methyl ester (20:0ME), and the dependency on the GC column temperature. The 24 isomers were obtained by performing cis-to trans-isomerization of six regioisomers: five of the 18:2ME isomers were prepared by the partial reduction of methyl α-linolenate and methyl γ-linolenate C18 trienoic acids with different double bond positions, whereas the sixth isomer, 18:2ME (c5, c9), was obtained from a raw constituent fatty acid methyl ester (FAME) sample extracted from Japanese yew seeds. There are no reference standards commercially available for 18:2ME isomers, and in elucidating the elution order of these isomers this study should help the future identification of cis- and trans-type of 18:2ME. We also report the identification method of cis- and trans-type of FAME using equivalent chain lengths and attempt the identification of cis- and trans-type of 18:2ME isomers from partially hydrogenated canola oil.

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

Synthesis, spectroscopic and TD-DFT quantum mechanical study of azo-azomethine dyes. A laser induced trans-cis-trans photoisomerization cycle

NASA Astrophysics Data System (ADS)

Georgiev, Anton; Kostadinov, Anton; Ivanov, Deyan; Dimov, Deyan; Stoyanov, Simeon; Nedelchev, Lian; Nazarova, Dimana; Yancheva, Denitsa

2018-03-01

This paper describes the synthesis, spectroscopic characterization and quantum mechanical calculations of three azo-azomethine dyes. The dyes were synthesized via condensation reaction between 4-(dimethylamino)benzaldehyde and three different 4-aminobenzene azo dyes. Quantum chemical calculations on the optimized molecular geometry and electron densities of the trans (E) and cis (Z) isomers and their vibrational frequencies have been computed by using DFT/B3LYP density-functional theory with 6-311 ++G(d,p) basis set in vacuo. The thermodynamic parameters such as total electronic energy E (RB3LYP), enthalpy H298 (sum of electronic and thermal enthalpies), free Gibbs energy G298 (sum of electronic and thermal free Gibbs energies) and dipole moment μ were computed for trans (E) and cis (Z) isomers in order to estimate the ΔEtrans → cis, Δμtrans → cis,ΔHtrans → cis, ΔGtrans → cis and ΔStrans → cis values. After molecular geometry optimization the electronic spectra have been obtained by TD-DFT calculations at same basis set and correlated with the spectra of vapour deposited nanosized films of the dyes. The NBO analysis was performed in order to understand the intramolecular charge transfer and energy of resonance stabilization. Solvatochromism was investigated by UV-VIS spectroscopy in five different organic solvents with increasing polarity. The dynamic photoisomerization experiments have been performed in DMF by pump lasers λ = 355 nm (mostly E → Z) and λ = 491 nm (mostly Z → E) in spectral region 300 nm - 800 nm at equal concentrations and times of illumination in order to investigate the photodynamical trans-cis-trans properties of the sbnd CHdbnd Nsbnd and sbnd Ndbnd Nsbnd chromophore groups of the dyes.

Comparison of the Photodesorption Activities of cis-Butene, trans-Butene and Isobutene on the Rutile TiO 2(110) Surface

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

Henderson, Michael A.

2013-10-17

The chemical and photochemical properties of three butene molecules (cis-butene, trans-butene and isobutene) were explored on the clean rutile TiO 2(110) surface using temperature programmed desorption (TPD) and photon simulated desorption (PSD). At the low coverage limit, trans-butene was the most strongly bound butene on the TiO 2(110) surface, desorbing at ~ 210 K, however increased intermolecular repulsions between trans-butene molecules at higher coverage diminished its binding. Both cis-butene and isobutene saturated the first layer on TiO 2(110) at a coverage of ~0.50 ML in a single TPD feature at 184 and 192 K, respectively. In contrast, the maximum coveragemore » that trans-butene could achieve in its 210 K peak was ~1/3 ML, with higher coverages resulting a low temperature desorption at ~137 K. Coverages of these molecules above 0.50 ML resulted in population of second layer and multilayer states. The instability of trans-butene at a coverage of 0.5 ML on the surface was linked to the inversion center in its symmetry. In the absence of coadsorbed oxygen, the primary photochemical pathway of each butene molecule on TiO 2(110) was photodesorption. The photoactivities of these molecules on TiO 2(110) at an initial coverage of 0.50 ML followed the trend: isobutene > cis-butene > trans-butene. In contrast, the photoactivities of low coverages of cis-butene and trans-butene exceeded those measured at 0.50 ML. These data suggest that intermolecular interactions (repulsions) play a significant role in diminishing the photoactivities of weakly bound molecules on TiO 2 photocatalysts. Work reported here was supported by the U.S. Department of Energy, Office of Basic Energy Science, Division of Chemical Sciences, Geosciences, and Biosciences, and performed in the Williams R. Wiley Environmental Molecular Science Laboratory (EMSL), a Department of Energy user facility funded by the Office of Biological and Environmental Research. Pacific Northwest National

Preparation and characterization of fluorophenylboronic acid-functionalized affinity monolithic columns for the selective enrichment of cis-diol-containing biomolecules.

PubMed

Li, Qianjin; Liu, Zhen

2015-01-01

Boronate affinity monolithic columns have been developed into an important means for the selective recognition and capture of cis-diol-containing biomolecules, such as glycoproteins, nucleosides and saccharides. The ligands of boronic acids are playing an important role in boronate affinity monolithic columns. Although several boronate affinity monoliths with high affinity toward cis-diol-containing biomolecules have been reported, only few publications are focused on their detailed procedures for preparation and characterization. This chapter describes in detail the preparation and characterization of a boronate affinity monolithic column applying 2,4-difluoro-3-formyl-phenylboronic acid (DFFPBA) as a ligand. The DFFPBA-functionalized monolithic column not only exhibited an ultrahigh boronate affinity toward cis-diol-containing biomolecules, but also showed great potential for the selective enrichment of cis-diol-containing biomolecules in real samples.

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

A sensitive high-pressure liquid chromatography/particle beam/mass spectrometry assay for the determination of all-trans-retinoic acid and 13-cis-retinoic acid in human plasma.

PubMed

Lehman, P A; Franz, T J

1996-03-01

A highly sensitive assay for the measurement of all-trans-retinoic acid (tretinoin) and 13-cis-retinoic acid (isotretinoin) has been developed. Collected plasma samples were protein precipitated with 2-propanol followed by solid phase extraction. The retinoic acids were subsequently derivatized to their pentafluorobenzyl esters followed by separation and isolation by reverse phase high-pressure liquid chromatography. The HPLC eluate was directed to a mass spectrometer via a particle beam interface. Selected ion monitoring (299 m/z) for the retinoic acid's carboxylate anion produced by negative chemical ionization using methane reagent gas achieved minimum detection limits of 25 pg injected. Endogenous blood levels in 19 male and 9 female subjects were measured. It was found that females have significantly more all-trans-retinoic acid than males and that both sexes demonstrate significantly more all-trans-retinoic acid then 13-cis-retinoic acid.

City of Troitsk and Sooty Snow, Chelyabinsk, CIS

NASA Technical Reports Server (NTRS)

1992-01-01

This view shows the industrial pollution around the Siberian city of Troitsk (54.0N, 61.0E). Troitsk is the smallest of a group of three heavy industrial cities east of the Urals, the others being Magnitogorsk and Chelyabinsk. All have been cited as being some of the worst industrial polluted cities in the CIS. Despite being the smallest of the three, Troitsk has the largest area of soot blackened snow. Respiratory diseases among the citizens are chronic.

Pre-Steady State Kinetic Analysis of cis-3-Chloroacrylic Acid Dehalogenase: Analysis and Implications†

PubMed Central

Robertson, Brooklyn A.; Schroeder, Gottfried K.; Jin, Zhinan; Johnson, Kenneth A.; Whitman, Christian P.

2009-01-01

Isomer-specific 3-chloroacrylic acid dehalogenases catalyze the hydrolytic dehalogenation of the cis- and trans-isomers of 3-chloroacrylate to yield malonate semialdehyde. These reactions represent key steps in the degradation of the nematocide, 1,3-dichloropropene. The kinetic mechanism of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) has now been examined using stopped-flow and chemical-quench techniques. Stopped-flow analysis of the reaction, following the fluorescence of an active site tryptophan, is consistent with a minimal three-step model involving substrate binding, chemistry, and product release. Chemical quench experiments show burst kinetics, indicating that product release is at least partially rate limiting. Global fitting of all of the kinetic results by simulation is best accommodated by a four-step mechanism. In the final kinetic model, the enzyme binds substrate and isomerizes to an alternate fluorescent form, chemistry occurs, and is followed by the ordered release of two products, with the release of the first product as the rate-limiting step. Bromide ion is a competitive inhibitor of the reaction indicating that it binds to the free enzyme rather than to the enzyme with one product still bound. This observation suggests that malonate semialdehyde is the first product released by the enzyme (rate limiting), followed by halide. A comparison of the unliganded cis-CaaD crystal structure with that of an inactivated cis-CaaD where the prolyl nitrogen of Pro-1 is covalently attached to (R)-2-hydroxypropanoate provides a possible explanation for the isomerization step. The structure of the covalently modified enzyme shows that a 7-residue loop comprised of residues 32-38 is closed down on the active site cavity where the backbone amides of two residues (Phe-37 and Leu-38) interact with the carboxylate group of the adduct. In the unliganded form, the same loop points away from the active site cavity. Similarly, substrate binding may cause this loop

Au plasmonics in a WS{sub 2}-Au-CuInS{sub 2} photocatalyst for significantly enhanced hydrogen generation

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

Cheng, Zhongzhou; School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083; Wang, Zhenxing, E-mail: wangzx@nanoctr.cn, E-mail: hej@nanoctr.cn

2015-11-30

Promoting the activities of photocatalysts is still the critical challenge in H{sub 2} generation area. Here, a Au plasmon enhanced photocatalyst of WS{sub 2}-Au-CuInS{sub 2} is developed by inserting Au nanoparticles between WS{sub 2} nanotubes and CuInS{sub 2} (CIS) nanoparticles. Due to the localized surface plasmonic resonance properties from Au nanoparticles, WS{sub 2}-Au-CIS shows the best performance as compared to Au-CIS, CIS, WS{sub 2}-CIS, CIS-Au, WS{sub 2}-Au, and WS{sub 2}-CIS-Au. The surface plasmonic resonance effects dramatically intensify the absorption of visible light and help to inject hot electrons into the semiconductors. Our findings open up an efficient method to optimizemore » the type-II structures for photocatalytic water splitting.« less

Simultaneous analysis of retinol, all-trans- and 13-cis-retinoic acid and 13-cis-4-oxoretinoic acid in plasma by liquid chromatography using on-column concentration after single-phase fluid extraction.

PubMed

Teerlink, T; Copper, M P; Klaassen, I; Braakhuis, B J

1997-06-20

A reversed-phase high-performance liquid chromatographic method for the simultaneous analysis of retinol, all-trans-retinoic acid, 13-cis-retinoic acid and 13-cis-4-oxoretinoic acid in human plasma and cell culture medium is described. Sample preparation involves precipitation of proteins and extraction of retinoids with 60% acetonitrile. After centrifugation, the acetonitrile content of the supernatant is reduced to 45%, allowing on-column concentration of analytes. Injection volumes up to 2.0 ml (equivalent to 0.525 ml of sample) can be used without compromising chromatographic resolution of all-trans-retinoic acid and 13-cis-retinoic acid. Retinoids were stable in this extract and showed no isomerization when stored in the dark in a cooled autosampler, allowing automated analysis of large series of samples. Recoveries from spiked plasma samples were between 95 and 103%. Although no internal standard was used, the inter-assay precision for all retinoids was better than 6% and 4% at concentrations of 30 nM and 100 nM, respectively. The method is a valuable tool for the study of cellular metabolism of all-trans-retinoic acid, as polar metabolites of this compound can be detected with high sensitivity in cell culture media.

Probing the Early Stages of Solvation of cis-Pinate Dianions by Water, Acetonitrile, and Methanol: A Photoelectron Spectroscopy and Theoretical Study

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

Hou, Gao-Lei; Kong, Xiang-Tao; Valiev, Marat

2016-01-01

Cis-pinic acid is one of the most important oxidation products of α-pinene – a key monoterpene compound in biogenic emission processes affecting the atmosphere. Molecular level understanding of interactions involved in the cluster formations around cis-pinic acid is an important and necessary prerequisite toward ascertaining its role in the aerosol formation processes. In this work, we studied the structures and energetics of the solvated clusters of cis-pinate (cis-PA²⁻), the doubly deprotonated dicarboxylate of cis-pinic acid, with H₂O, CH₃OH, and CH₃CN by negative ion photoelectron spectroscopy and ab initio theoretical calculations. We found that cis-PA²⁻ prefers being solvated alternately on themore » two -CO₂⁻ groups with increase of solvent coverage, a well-known solvation pattern that has been observed in microhydrated linear dicarboxylate dianion (DC n²⁻) clusters. Experiments and calculations further reveal an intriguing feature for the existence of the asymmetric type isomers for cis-PA2–(H2O)2 and cis-PA²⁻(CH₃OH)₂, in which both solvent molecules interact with only one of the -CO²⁻ groups – a phenomena that has not been observed in DCn²⁻ water clusters and exhibits the subtle effect of the rigid four-membered carbon ring brought in on the cis-PA²⁻ solvation. The dominant interactions between cis-PA²⁻ and solvent molecules are forming bidentate O–···H–O H-bonds for H₂O, O–···H–O and O–···H–C H-bonds for CH₃OH, and tridentate O–···H–C H-bonds for CH₃CN. The formation of inter-solvent H-bonds between H₂O and CH₃CN is found to be favorable in mixed solvent clusters, distinctly different from that between H₂O and CH₃OH. These findings have important implications for understanding the mechanism of cluster growth and nucleation of atmospheric organic aerosols and the nature of structure-function relationship of proteins containing carboxylate groups under various solvent

Distinct Conformations of Ly49 Natural Killer Cell Receptors Mediate MHC Class I Recognition in Trans and Cis

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

Back, J.; Malchiodi, E; Cho, S

2009-01-01

Certain cell-surface receptors engage ligands expressed on juxtaposed cells and ligands on the same cell. The structural basis for trans versus cis binding is not known. Here, we showed that Ly49 natural killer (NK) cell receptors bound two MHC class I (MHC-I) molecules in trans when the two ligand-binding domains were backfolded onto the long stalk region. In contrast, dissociation of the ligand-binding domains from the stalk and their reorientation relative to the NK cell membrane allowed monovalent binding of MHC-I in cis. The distinct conformations (backfolded and extended) define the structural basis for cis-trans binding by Ly49 receptors andmore » explain the divergent functional consequences of cis versus trans interactions. Further analyses identified specific stalk segments that were not required for MHC-I binding in trans but were essential for inhibitory receptor function. These data identify multiple distinct roles of stalk regions for receptor function.« less

Big U. S. gas producing states fan prorationing controversy

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

Not Available

This paper reports that the biggest gas producing states in the U.S. are embracing wholesale changes in prorationing rules. And their actions have stirred controversy and warnings among key energy lawmakers in Washington. The Texas Railroad Commission last week unanimously approved new rules for setting production volumes for gas wells. Texas is the country's No. 1 gas producer. TRC commissioners eliminated a system that prorated production based on monthly nominations by gas purchasers. The Office of Conservation in Louisiana, No. 2 ranked producer, recently conducted a hearing on a prorationing proposal supported by Gov. Edwin Edwards. Conservation Commissioner Herbert W.more » Thompson is expected to disclose the state's plans by the end of this month. No. 3 Oklahoma enacted a law last March restricting production from unallocated wells in the 4 winter months to the greater of 1 MMcfd or 40% of the calculated absolute open flow and the rest of the year to the greater of 750 Mcfd or 25% of the calculated absolute open flow.« less

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.

Probing the early stages of solvation of cis-pinate dianions by water, acetonitrile, and methanol: a photoelectron spectroscopy and theoretical study.

PubMed

Hou, Gao-Lei; Kong, Xiang-Tao; Valiev, Marat; Jiang, Ling; Wang, Xue-Bin

2016-02-07

cis-Pinic acid is one of the most important oxidation products of α-pinene--a key monoterpene compound in biogenic emission processes. Molecular level understanding of its interaction with water in cluster formation is an important and necessary prerequisite for ascertaining its role in the aerosol formation processes. In this work, we studied the structures and energetics of the solvated clusters of cis-pinate (cis-PA(2-)), the doubly deprotonated dicarboxylate of cis-pinic acid, with H2O, CH3OH, and CH3CN by negative ion photoelectron spectroscopy and ab initio theoretical calculations. We found that cis-PA(2-) prefers being solvated alternately on the two -CO2(-) groups with increase of solvent coverage, a well-known solvation pattern that has been observed in microhydrated linear dicarboxylate dianion (DCn(2-)) clusters. Experiments and calculations further reveal an intriguing feature for the existence of the asymmetric type isomers for cis-PA(2-)(H2O)2 and cis-PA(2-)(CH3OH)2, in which both solvent molecules interact with only one of the -CO2(-) groups, a phenomenon that has not been observed in DCn(2-) water clusters and exhibits that the subtle effect of the rigid four-membered carbon ring brought on the cis-PA(2-) solvation. The dominant interactions between cis-PA(2-) and solvent molecules form bidentate O(-)...H-O H-bonds for H2O, O(-)...H-O and O(-)...H-C H-bonds for CH3OH, and tridentate O(-)...H-C H-bonds for CH3CN. The formation of inter-solvent H-bonds between H2O and CH3CN is found to be favorable in mixed solvent clusters, different from that between H2O and CH3OH. These findings have important implications for understanding the mechanism of cluster growth and the formation of atmospheric organic aerosols, as well as for rationalizing the nature of structure-function relationship of proteins containing carboxylate groups in various solvent environments.

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

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

Steady state pharmacokinetics of oral treatment with 13-cis-retinoic acid or all-trans-retinoic acid in male and female adult rats.

PubMed

Ferguson, Sherry A; Siitonen, Paul H; Cisneros, F Javier; Gough, Bobby; Young, John F

2006-06-01

Male and female Sprague-Dawley rats were orally gavaged with 13-cis-retinoic acid (7.5 or 15 mg/kg) or all-trans-retinoic acid (10 or 15 mg/kg) for 7 consecutive days. Blood was collected out to 8 hr after the last gavage on day 7. HPLC serum concentrations of 13-cis-retinoic acid, all-trans-retinoic acid, and 13-cis-4-oxo-retinoic acid were subjected to model independent pharmacokinetic analyses. Peak serum levels of 563 to 1640 ng/ml were observed for rats treated with 13-cis-retinoic acid at 1.5-2 hr after gavage. Peak serum levels of 183 to 267 ng/ml at 1.5 hr after gavage were observed for all-trans-retinoic acids. The elimination half-life of 13-cis-retinoic acid was about 1.5 hr while the elimination half-life of all-trans-retinoic acid was slightly longer. There were no sex differences for any parameter. Serum levels resulting from the 7.5 mg/kg 13-cis-retinoic acid were similar to those of human Accutane users.

In vitro studies on the degradation of poly(cis-1,4-isoprene).

PubMed

Andler, R; Altenhoff, A-L; Mäsing, F; Steinbüchel, A

2018-03-31

Cleavage of the backbone of poly(cis-1,4-isoprene) (IR) in solid rubber material was accomplished by the addition of partially purified latex clearing protein (Lcp1 VH2 ) using a 200-mL enzyme reactor. Two strategies for the addition of Lcp1 VH2 were studied revealing that the daily addition of 50 µg mL -1 of Lcp1 VH2 for 5 days was clearly a more efficient regime in comparison to a one-time addition of 250 µg of Lcp1 VH2 at the beginning. Soluble oligo(cis-1,4-isoprene) molecules occurred as degradation products and were identified by ESI-MS and GPC. Oxygenase activity of Lcp1 VH2 with solid IR particles as substrate was shown for the first time by measuring the oxygen consumption in the reaction medium. A strong decrease of the dissolved oxygen concentration was detected at the end of the assay, which indicates an increase in the number of cleavage reactions. The oligo(cis-1,4-isoprene) molecules comprised 1 to 11 isoprene units and exhibited an average molecular weight (M n ) of 885 g mol -1 . Isolation of the oligo(cis-1,4-isoprene) molecules was achieved by using silica gel column chromatography. The relative quantification of the isolated products was performed by HPLC-MS after derivatization with 2,4-dinitrophenilhydrazyne yielding a concentration of total degradation products of 1.62 g L -1 . Analysis of the polymer surface in samples incubated for 3 days with Lcp1 VH2 via ATR-FTIR indicated the presence of carbonyl groups, which occurred upon the cleavage reaction. This study presents a cell-free bioprocess as an alternative rubber treatment that can be applied for the partial degradation of the polymer. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 2018. © 2018 American Institute of Chemical Engineers.

Annatto Constituent Cis-Bixin Has Selective Antimyeloma Effects Mediated by Oxidative Stress and Associated with Inhibition of Thioredoxin and Thioredoxin Reductase

PubMed Central

Tibodeau, Jennifer D.; Isham, Crescent R.

2010-01-01

Abstract In pursuit of the anticancer effects of seeds of the rain forest plant Bixa orellana (annatto), we found that its constituent cis-bixin induced cytotoxicity in a wide variety of tumor cell lines (IC50 values from 10 to 50 μM, 24-h exposures) and, importantly, also selectively killed freshly collected patient multiple myeloma cells and highly drug-resistant multiple myeloma cell lines. Mechanistic studies indicated that cis-bixin–induced cytotoxicity was greatly attenuated by co-treatment with glutathione or N-acetylcysteine (NAC); whereas fluorescence-activated cell sorting (FACS) assays using the cell-permeable dyes 5-(and-6) chloromethyl-2′,7′-dichlorodihydrofluorescein diacetate, acetyl ester (CM-H2DCFDA), or dihydroethidium demonstrated that cis-bixin rapidly induced cellular reactive oxygen species (ROS) in dose- and time-dependent fashions, collectively implicating ROS as contributory to cis-bixin–induced cytotoxicity. In pursuit of potential contributors to ROS imposition by cis-bixin, we found that cis-bixin inhibited both thioredoxin (Trx) and thioredoxin reductase (TrxR1) activities at concentrations comparable to those required for cytotoxicity, implicating the inhibition of these redox enzymes as potentially contributing to its ability to impose cellular ROS and to kill cancer cells. Collectively, our studies indicate that the annatto constituent cis-bixin has intriguing selective antimyeloma activity that appears to be mediated through effects on redox signaling. Antioxid. Redox Signal. 13, 987–997. PMID:20170403

Improved performance of low cost CuInS2 superstrate-type solar cells using Zinc assisted spray pyrolysis processing

NASA Astrophysics Data System (ADS)

Cheshme Khavar, Amir Hossein; Mahjoub, Ali Reza; Taghavinia, Nima

2017-12-01

Superstrate configuration CuInS2 (CIS) solar cells are fabricated using a spray pyrolysis method. We avoided selenization process, cyanide etching and CdS buffer layer, to keep the process ‘green’. CIS layers are formed by spray pyrolysis of an aqueous precursor ink containing metal chloride salts and thiourea at 350 °C. We investigated the effect of intentional Zn doping on structural, morphological and photovoltaic response of the fabricated CIS films by dissolving ZnCl2 in aqueous precursor solution. At a zinc doping level ranging between 0.25 and 1.00 mol%, Zn doping is found to improve the CIS crystal growth and surface morphology of CIS films. Compared with the performance of the non-doped CIS cell, the Zn-doped CIS solar cell displayed a remarkable efficiency enhancement of 58-97% and the maximum enhancement was obtained at a Zn content of 0.5 mol%. The device structure consists of  S3/CIS/carbon  >  and show promising PCE of 4.29 % without any anti-reflection coating. Over the course of 300 d under ambient condition, the fabricated device showed only 1% loss in efficiency.

Cis-regulatory landscapes of four cell types of the retina

PubMed Central

Hartl, Dominik; Jüttner, Josephine

2017-01-01

Abstract The retina is composed of ∼50 cell-types with specific functions for the process of vision. Identification of the cis-regulatory elements active in retinal cell-types is key to elucidate the networks controlling this diversity. Here, we combined transcriptome and epigenome profiling to map the regulatory landscape of four cell-types isolated from mouse retinas including rod and cone photoreceptors as well as rare inter-neuron populations such as horizontal and starburst amacrine cells. Integration of this information reveals sequence determinants and candidate transcription factors for controlling cellular specialization. Additionally, we refined parallel reporter assays to enable studying the transcriptional activity of large collection of sequences in individual cell-types isolated from a tissue. We provide proof of concept for this approach and its scalability by characterizing the transcriptional capacity of several hundred putative regulatory sequences within individual retinal cell-types. This generates a catalogue of cis-regulatory regions active in retinal cell types and we further demonstrate their utility as potential resource for cellular tagging and manipulation. PMID:29059322

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging.

PubMed

Ablikim, Utuq; Bomme, Cédric; Xiong, Hui; Savelyev, Evgeny; Obaid, Razib; Kaderiya, Balram; Augustin, Sven; Schnorr, Kirsten; Dumitriu, Ileana; Osipov, Timur; Bilodeau, René; Kilcoyne, David; Kumarappan, Vinod; Rudenko, Artem; Berrah, Nora; Rolles, Daniel

2016-12-02

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C 2 H 2 Br 2 ). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. The experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model.

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

PubMed Central

Ablikim, Utuq; Bomme, Cédric; Xiong, Hui; Savelyev, Evgeny; Obaid, Razib; Kaderiya, Balram; Augustin, Sven; Schnorr, Kirsten; Dumitriu, Ileana; Osipov, Timur; Bilodeau, René; Kilcoyne, David; Kumarappan, Vinod; Rudenko, Artem; Berrah, Nora; Rolles, Daniel

2016-01-01

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C2H2Br2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. The experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model. PMID:27910943

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

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

Ablikim, Utuq; Bomme, Cédric; Xiong, Hui

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C 2H 2Br 2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. Lastly, the experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model.

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

DOE PAGES

Ablikim, Utuq; Bomme, Cédric; Xiong, Hui; ...

2016-12-02

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C 2H 2Br 2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. Lastly, the experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model.

Assessment of TD-DFT methods and of various spin scaled CIS(D) and CC2 versions for the treatment of low-lying valence excitations of large organic dyes

NASA Astrophysics Data System (ADS)

Goerigk, Lars; Grimme, Stefan

2010-05-01

We present an extension of our previously published benchmark set for low-lying valence transitions of large organic dyes [L. Goerigk et al., Phys. Chem. Chem. Phys. 11, 4611 (2009)]. The new set comprises in total 12 molecules, including two charged species and one with a clear charge-transfer transition. Our previous study on TD-DFT methods is repeated for the new test set with a larger basis set. Additionally, we want to shed light on different spin-scaled variants of the configuration interaction singles with perturbative doubles correction [CIS(D)] and the approximate coupled cluster singles and doubles method (CC2). Particularly for CIS(D) we want to clarify, which of the proposed versions can be recommended. Our results indicate that an unpublished SCS-CIS(D) variant, which is implemented into the TURBOMOLE program package, shows worse results than the original CIS(D) method, while other modified versions perform better. An SCS-CIS(D) version with a parameterization, that has already been used in an application by us recently [L. Goerigk and S. Grimme, ChemPhysChem 9, 2467 (2008)], yields the best results. Another SCS-CIS(D) version and the SOS-CIS(D) method [Y. M. Rhee and M. Head-Gordon, J. Phys. Chem. A 111, 5314 (2007)] perform very similar, though. For the electronic transitions considered herein, there is no improvement observed when going from the original CC2 to the SCS-CC2 method but further adjustment of the latter seems to be beneficial. Double-hybrid density functionals belong to best methods tested here. Particularly B2GP-PLYP provides uniformly good results for the complete set and is considered to be close to chemical accuracy within an ab initio theory of color. For conventional hybrid functionals, a Fock-exchange mixing parameter of about 0.4 seems to be optimum in TD-DFT treatments of large chromophores. A range-separated functional such as, e.g., CAM-B3LYP seems also to be promising.

Static and ELF magnetic fields enhance the in vivo anti-tumor efficacy of cis-platin against lewis lung carcinoma, but not of cyclophosphamide against B16 melanotic melanoma.

PubMed

Tofani, S; Barone, D; Berardelli, M; Berno, E; Cintorino, M; Foglia, L; Ossola, P; Ronchetto, F; Toso, E; Eandi, M

2003-07-01

Previous works showed that exposure to static and extremely low frequency (ELF) magnetic fields (MF) over 3 mT slows down the growth kinetics of human tumors engrafted s.c. in immunodeficient mice, reducing their metastatizing power and prolonging mouse survival. In the experiments reported here, immunocompetent mice bearing murine Lewis Lung carcinomas (LLCs) or B16 melanotic melanomas were exposed to MF and treated respectively with two commonly used anti-cancer drugs: cis-diamminedichloroplatinum (cis-platin) and N,N-bis (2-chloroethyl)tetra-hydro-2H-1,3,2-oxazaphosphorin-2-amine 2-oxide (cyclophosphamide). The experiment endpoint was survival time. The survival time of mice treated with cis-platin (3mg/kg i.p.) and exposed to MF was significantly (P<0.01) longer than that of mice treated only with cis-platin or only exposed to MF, superimposing that of mice treated with 10mg/kg i.p. of the drug, showing that MF act synergically with the pharmacological treatment. On the contrary, when mice treated with cyclophosphamide (50mg/kg i.p.) were exposed to MF no synergic effects were observed, the survival curve being exactly the same as that of mice treated with the drug alone. No clinical signs or toxicity were seen in any of the mice exposed to MF alone or along with cis-platin or cyclophosphamide treatment, compared to mice given only the two known drugs.A possible explanation for the synergic effect of MF being found in mice treated with cis-platin could be that the platinum ion stimulates radical production and that MF enhance active oxygen production bringing about changes in tumor cell membrane permeability, influencing positively the drug uptake. Alternatively, or in addition to this, it has been demonstrated that the rate of conversion of cis-platin to reactive species able to bind to DNA, is increased by localized production of free radicals by MF.

The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans.

PubMed

Zhan, Yingqian Ada; Ytreberg, F Marty

2015-06-01

The cis and trans conformations of the Xaa-Pro (Xaa: any amino acid) peptide bond are thermodynamically stable while other peptide bonds strongly prefer trans. The effect of proline cis-trans isomerization on protein binding has not been thoroughly investigated. In this study, computer simulations were used to calculate the absolute binding affinity for a p53 peptide (residues 17-29) to MDM2 for both cis and trans isomers of the p53 proline in position 27. Results show that the cis isomer of p53(17-29) binds more weakly to MDM2 than the trans isomer, and that this is primarily due to the difference in the free energy cost associated with the loss of conformational entropy of p53(17-29) when it binds to MDM2. The population of cis p53(17-29) was estimated to be 0.8% of the total population in the bound state. The stronger binding of trans p53(17-29) to MDM2 compared to cis may leave a minimal level of p53 available to respond to cellular stress. This study demonstrates that it is feasible to estimate the absolute binding affinity for an intrinsically disordered protein fragment binding to an ordered protein that are in good agreement with experimental results. Copyright © 2015 Elsevier Inc. All rights reserved.

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

Enantiodiscrimination of flexible cyclic solutes using NMR spectroscopy in polypeptide chiral mesophases: investigation of cis-decalin and THF.

PubMed

Aroulanda, Christie; Lafon, Olivier; Lesot, Philippe

2009-08-06

The conformational dynamics and orientational behavior of two model cyclic molecules, cis-decalin (cis-dec) and tetrahydrofurane (THF), dissolved in weakly ordering, polypeptidic chiral liquid crystals (CLCs) are theoretically discussed and experimentally investigated using deuterium and carbon-13 NMR spectroscopies. The analysis of enantiomeric and enantiotopic discriminations in these compounds is shown to depend on the rate of conformational exchange regime, slow or fast. The slow exchange regime is illustrated through the case of cis-dec at low temperature (243 K). We show that the deuterium NMR spectra in this regime can be qualitatively and quantitatively interpreted by restricting the conformational pathway of cis-dec to two enantiomeric conformers of C(2)-symmetry. The orientational order parameters of these interconverting enantiomers are calculated by matching the (2)H quadrupolar splittings with calculated conformer structures. The fast exchange regime is investigated through the examples of cis-dec at high temperature (356 K) and THF at room temperature (300 K). The (2)H NMR spectra above the coalescence temperature are analyzed by introducing the concept of "average molecular structure". This fictitious structure allows easily identifying NMR equivalences of solutes dissolved in CLC. However, it cannot be applied to determine consistent orientational order parameters. This study emphasizes that enantiotopic discriminations observed for flexible molecules in the fast exchange regime can be quantitatively interpreted only by considering the orientational order of each conformer.

Synthesis of diazatricyclic core of Madangamines from cis-perhydroisoquinolines.

PubMed

Quirante, Josefina; Paloma, Laura; Diaba, Faïza; Vila, Xavier; Bonjoch, Josep

2008-01-18

Synthesis of the tricyclic core of madangamine alkaloids has been achieved in a 10-step sequence starting from a 4-(aminomethyl)anisole derivative. A Birch reduction and acylation with cyanoacetic acid followed by an intramolecular Michael process renders a polyfunctionalized cis-perhydroisoquinoline. A diastereoselective allylation and reduction of amide, nitrile, and ketone groups leads to a bicyclic alcohol, which undergoes aminocyclization through the nosyl derivative to the diazatricyclic ring.

Antagonism of cytotoxic chemotherapy in neuroblastoma cell lines by 13-cis-retinoic acid is mediated by the anti-apoptotic Bcl-2 family proteins

PubMed Central

Hadjidaniel, Michael Daniel; Reynolds, Charles Patrick

2010-01-01

13-cis-retinoic acid (13-cis-RA), is given at completion of cytotoxic therapy to control minimal residual disease in neuroblastoma. We investigated the effect of combining 13-cis-RA with cytotoxic agents employed in neuroblastoma therapy using a panel of 6 neuroblastoma cell lines. The effect of 13-cis-RA on the mitochondrial apoptotic pathway, was studied by flow cytometry, cytotoxicity by DIMSCAN, and protein expression by immuoblotting. Pre-treatment and direct combination of 13-cis-RA with etoposide, topotecan, cisplatin, melphalan, or doxorubicin markedly antagonized the cytotoxicity of those agents in 4 out of 6 tested neuroblastoma cell lines, increasing fractional cell survival by 1 to 3 logs. The inhibitory concentration of drugs (IC99) increased from clinically achievable levels to non-achievable levels: > 5-fold (cisplatin) to > 7-fold (etoposide). In SMS-KNCR neuroblastoma cells, 13-cis-RA upregulated expression of Bcl-2 and Bcl-xL RNA and protein, and this was associated with protection from etoposide-mediated apoptosis at the mitochondrial level. A small molecule inhibitor of the Bcl-2 family of proteins (ABT-737) restored mitochondrial membrane potential loss and apoptosis in response to cytotoxic agents in 13-cis-RA treated cells. Prior selection for resistance to RA did not diminish the response to cytotoxic treatment. Thus, combining 13-cis-RA with cytotoxic chemotherapy significantly reduced the cytotoxiciity for neuroblastoma in vitro, mediated at least in part via the anti-apoptotic Bcl-2 family of proteins. PMID:21159604

Metabolic characteristics of 13-cis-retinoic acid (isotretinoin) and anti-tumour activity of the 13-cis-retinoic acid metabolite 4-oxo-13-cis-retinoic acid in neuroblastoma

PubMed Central

Sonawane, Poonam; Cho, Hwang Eui; Tagde, Ashujit; Verlekar, Dattesh; Yu, Alice L; Reynolds, C Patrick; Kang, Min H

2014-01-01

Background and Purpose Isotretinoin (13-cis-retinoic acid; 13-cRA) is a differentiation inducer used to treat minimal residual disease after myeloablative therapy for high-risk neuroblastoma. However, more than 40% of children develop recurrent disease during or after 13-cRA treatment. The plasma concentrations of 13-cRA in earlier studies were considered subtherapeutic while 4-oxo-13-cis-RA (4-oxo-13-cRA), a metabolite of 13-cRA considered by some investigators as inactive, were greater than threefold higher than 13-cRA. We sought to define the metabolic pathways of 13-cRA and investigated the anti-tumour activity of its major metabolite, 4-oxo-13-cRA. Experimental Approach Effects of 13-cRA and 4-oxo-13-cRA on human neuroblastoma cell lines were assessed by DIMSCAN and flow cytometry for cell proliferation, MYCN down-regulation by reverse transcription PCR and immunoblotting, and neurite outgrowth by confocal microscopy. 13-cRA metabolism was determined using tandem MS in human liver microsomes and in patient samples. Key Results Six major metabolites of 13-cRA were identified in patient samples. Of these, 4-oxo-13-cRA was the most abundant, and 4-oxo-13-cRA glucuronide was also detected at a higher level in patients. CYP3A4 was shown to play a major role in catalysing 13-cRA to 4-oxo-13-cRA. In human neuroblastoma cell lines, 4-oxo-13-cRA and 13-cRA were equi-effective at inducing neurite outgrowth, inhibiting proliferation, decreasing MYCN mRNA and protein, and increasing the expression of retinoic acid receptor-β mRNA and protein levels. Conclusions and Implications We showed that 4-oxo-13-cRA is as active as 13-cRA against neuroblastoma cell lines. Plasma levels of both 13-cRA and 4-oxo-13-cRA should be evaluated in pharmacokinetic studies of isotretinoin in neuroblastoma. PMID:25039756

Metabolic characteristics of 13-cis-retinoic acid (isotretinoin) and anti-tumour activity of the 13-cis-retinoic acid metabolite 4-oxo-13-cis-retinoic acid in neuroblastoma.

PubMed

Sonawane, Poonam; Cho, Hwang Eui; Tagde, Ashujit; Verlekar, Dattesh; Yu, Alice L; Reynolds, C Patrick; Kang, Min H

2014-12-01

Isotretinoin (13-cis-retinoic acid; 13-cRA) is a differentiation inducer used to treat minimal residual disease after myeloablative therapy for high-risk neuroblastoma. However, more than 40% of children develop recurrent disease during or after 13-cRA treatment. The plasma concentrations of 13-cRA in earlier studies were considered subtherapeutic while 4-oxo-13-cis-RA (4-oxo-13-cRA), a metabolite of 13-cRA considered by some investigators as inactive, were greater than threefold higher than 13-cRA. We sought to define the metabolic pathways of 13-cRA and investigated the anti-tumour activity of its major metabolite, 4-oxo-13-cRA. Effects of 13-cRA and 4-oxo-13-cRA on human neuroblastoma cell lines were assessed by DIMSCAN and flow cytometry for cell proliferation, MYCN down-regulation by reverse transcription PCR and immunoblotting, and neurite outgrowth by confocal microscopy. 13-cRA metabolism was determined using tandem MS in human liver microsomes and in patient samples. Six major metabolites of 13-cRA were identified in patient samples. Of these, 4-oxo-13-cRA was the most abundant, and 4-oxo-13-cRA glucuronide was also detected at a higher level in patients. CYP3A4 was shown to play a major role in catalysing 13-cRA to 4-oxo-13-cRA. In human neuroblastoma cell lines, 4-oxo-13-cRA and 13-cRA were equi-effective at inducing neurite outgrowth, inhibiting proliferation, decreasing MYCN mRNA and protein, and increasing the expression of retinoic acid receptor-β mRNA and protein levels. We showed that 4-oxo-13-cRA is as active as 13-cRA against neuroblastoma cell lines. Plasma levels of both 13-cRA and 4-oxo-13-cRA should be evaluated in pharmacokinetic studies of isotretinoin in neuroblastoma. © 2014 The British Pharmacological Society.

Conceptual biotransformation of 4-oxo-all-trans-retinoic acid, 4-oxo-13-cis-retinoic acid and all-trans-retinoyl-beta-glucuronide in rat whole embryo culture.

PubMed

Creech Kraft, J; Juchau, M R

1992-05-28

In cultured rat conceptuses, intraamniotic microinjections of 2500 ng/mL of 4-oxo-13-cis-retinoic acid, 600 ng/mL 4-oxo-all-trans-retinoic acid or 4000 ng/mL all-trans-retinoyl-beta-glucuronide, produce qualitatively and quantitatively similar patterns of dysmorphogenesis as those reported after the intraamniotic microinjection of 250 ng/mL all-trans-retinoic acid [Lee et al., Teratology 44: 313-323, 1991; Creech Kraft et al., Teratology 45: 259-270, 1992]. In the present study, we utilized HPLC techniques to analyze retinoid levels in cultured rat conceptuses, 1.5 hr after intraamniotic microinjections of 4-oxo-13-cis-retinoic acid (2500 ng/mL), 4-oxo-all-trans-retinoic acid (600 ng/mL) or all-trans-retinoyl-beta-glucuronide (4000 ng/mL). Our findings show that, after the microinjections of 4-oxo-all-trans-retinoic acid or 4-oxo-13-cis-retinoic acid (at these selected concentrations), 4-oxo-all-trans-retinoic acid was predominant in the embryos proper at concentrations of about 200 nM. This was roughly equivalent to the levels of all-trans-retinoic acid assayed after microinjections of all-trans-retinoyl-beta-glucuronide (4000 ng/mL). We conclude from these studies that both 4-oxo-all-trans-retinoic acid and all-trans-retinoic acid behave as ultimate or proximate dysmorphogens.

IRIS Toxicological Review of Cis-& Trans-1,2-Dichloroethylene (External Review Draft)

EPA Science Inventory

EPA is conducting a peer review of the scientific basis supporting the human health hazard and dose-response assessment of cis- and trans-1,2-dichloroethylene that will appear in the Integrated Risk Information System (IRIS) database.

Randomized Subspace Learning for Proline Cis-Trans Isomerization Prediction.

PubMed

Al-Jarrah, Omar Y; Yoo, Paul D; Taha, Kamal; Muhaidat, Sami; Shami, Abdallah; Zaki, Nazar

2015-01-01

Proline residues are common source of kinetic complications during folding. The X-Pro peptide bond is the only peptide bond for which the stability of the cis and trans conformations is comparable. The cis-trans isomerization (CTI) of X-Pro peptide bonds is a widely recognized rate-limiting factor, which can not only induces additional slow phases in protein folding but also modifies the millisecond and sub-millisecond dynamics of the protein. An accurate computational prediction of proline CTI is of great importance for the understanding of protein folding, splicing, cell signaling, and transmembrane active transport in both the human body and animals. In our earlier work, we successfully developed a biophysically motivated proline CTI predictor utilizing a novel tree-based consensus model with a powerful metalearning technique and achieved 86.58 percent Q2 accuracy and 0.74 Mcc, which is a better result than the results (70-73 percent Q2 accuracies) reported in the literature on the well-referenced benchmark dataset. In this paper, we describe experiments with novel randomized subspace learning and bootstrap seeding techniques as an extension to our earlier work, the consensus models as well as entropy-based learning methods, to obtain better accuracy through a precise and robust learning scheme for proline CTI prediction.

Photochemistry of furyl- and thienyldiazomethanes: spectroscopic characterization of triplet 3-thienylcarbene.

PubMed

Pharr, Caroline R; Kopff, Laura A; Bennett, Brian; Reid, Scott A; McMahon, Robert J

2012-04-11

Photolysis (λ > 543 nm) of 3-thienyldiazomethane (1), matrix isolated in Ar or N(2) at 10 K, yields triplet 3-thienylcarbene (13) and α-thial-methylenecyclopropene (9). Carbene 13 was characterized by IR, UV/vis, and EPR spectroscopy. The conformational isomers of 3-thienylcarbene (s-E and s-Z) exhibit an unusually large difference in zero-field splitting parameters in the triplet EPR spectrum (|D/hc| = 0.508 cm(-1), |E/hc| = 0.0554 cm(-1); |D/hc| = 0.579 cm(-1), |E/hc| = 0.0315 cm(-1)). Natural Bond Orbital (NBO) calculations reveal substantially differing spin densities in the 3-thienyl ring at the positions adjacent to the carbene center, which is one factor contributing to the large difference in D values. NBO calculations also reveal a stabilizing interaction between the sp orbital of the carbene carbon in the s-Z rotamer of 13 and the antibonding σ orbital between sulfur and the neighboring carbon-an interaction that is not observed in the s-E rotamer of 13. In contrast to the EPR spectra, the electronic absorption spectra of the rotamers of triplet 3-thienylcarbene (13) are indistinguishable under our experimental conditions. The carbene exhibits a weak electronic absorption in the visible spectrum (λ(max) = 467 nm) that is characteristic of triplet arylcarbenes. Although studies of 2-thienyldiazomethane (2), 3-furyldiazomethane (3), or 2-furyldiazomethane (4) provided further insight into the photochemical interconversions among C(5)H(4)S or C(5)H(4)O isomers, these studies did not lead to the spectroscopic detection of the corresponding triplet carbenes (2-thienylcarbene (11), 3-furylcarbene (23), or 2-furylcarbene (22), respectively). © 2012 American Chemical Society

Brief report: EGFR L858M/L861Q cis mutations confer selective sensitivity to afatinib

PubMed Central

Saxon, Jamie A.; Sholl, Lynette M.; Jänne, Pasi A.

2017-01-01

Introduction Tyrosine kinase inhibitors (TKIs) have been developed to treat patients with epidermal growth factor receptor (EGFR)-mutant lung cancers. However, the therapeutic efficacy of TKIs in patients with uncommon EGFR mutations remains unclear. Methods Next-generation sequencing was performed on a patient’s lung adenocarcinoma tumor sample, revealing rare combined in cis (on the same allele) EGFR mutations. Stable Ba/F3 and NIH-3T3 cell lines harboring the mutations were established to investigate the effect of first, second, and third generation EGFR TKIs on cell proliferation by MTS assay and EGFR phosphorylation by Western blotting. Results EGFR L858M/L861Q mutations in cis were detected in a non-small cell lung cancer patient’s tumor. The patient demonstrated primary resistance to erlotinib and was subsequently treated with afatinib, which caused tumor regression. In in vitro studies, first and third generation TKIs exhibited a decreased capacity to prevent EGFR phosphorylation and inhibit cell proliferation in EGFR L858M/L861Q cells compared to cells harboring the common EGFR L858R point mutation. In contrast, afatinib treatment reduced proliferation and inhibited EGFR phosphorylation in L858M/L861Q and L858R mutant cells at similar concentrations. Conclusions Afatinib may be a beneficial therapeutic option for a subset of lung cancer patients with rare EGFR mutations in their tumors. Understanding how uncommon mutations affect protein structure and TKI binding will be important for identifying effective targeted therapies for these patients. PMID:28088511

Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

PubMed Central

Richards, Stephen; Liu, Yue; Bettencourt, Brian R.; Hradecky, Pavel; Letovsky, Stan; Nielsen, Rasmus; Thornton, Kevin; Hubisz, Melissa J.; Chen, Rui; Meisel, Richard P.; Couronne, Olivier; Hua, Sujun; Smith, Mark A.; Zhang, Peili; Liu, Jing; Bussemaker, Harmen J.; van Batenburg, Marinus F.; Howells, Sally L.; Scherer, Steven E.; Sodergren, Erica; Matthews, Beverly B.; Crosby, Madeline A.; Schroeder, Andrew J.; Ortiz-Barrientos, Daniel; Rives, Catharine M.; Metzker, Michael L.; Muzny, Donna M.; Scott, Graham; Steffen, David; Wheeler, David A.; Worley, Kim C.; Havlak, Paul; Durbin, K. James; Egan, Amy; Gill, Rachel; Hume, Jennifer; Morgan, Margaret B.; Miner, George; Hamilton, Cerissa; Huang, Yanmei; Waldron, Lenée; Verduzco, Daniel; Clerc-Blankenburg, Kerstin P.; Dubchak, Inna; Noor, Mohamed A.F.; Anderson, Wyatt; White, Kevin P.; Clark, Andrew G.; Schaeffer, Stephen W.; Gelbart, William; Weinstock, George M.; Gibbs, Richard A.

2005-01-01

We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25–55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species—but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila. PMID:15632085

Characterization of a novel and potentially lethal designer drug (±)-cis-para-methyl-4-methylaminorex (4,4'-DMAR, or 'Serotoni').

PubMed

Brandt, Simon D; Baumann, Michael H; Partilla, John S; Kavanagh, Pierce V; Power, John D; Talbot, Brian; Twamley, Brendan; Mahony, Olivia; O'Brien, John; Elliott, Simon P; Archer, Roland P; Patrick, Julian; Singh, Kuldip; Dempster, Nicola M; Cosbey, Simon H

2014-01-01

During the second half of 2013, a total of 26 deaths involving para-methyl-4-methylaminorex (4,4'-DMAR) were reported to the European Monitoring Centre for Drugs and Drug Addiction. While aminorex and 4-methylaminorex (4-MAR) are known psychostimulants, nothing is known about the comparatively new para-methyl analog. Analytical characterization of two independent samples obtained from online vendors confirmed the presence of the (±)-cis isomer that also appeared to be associated with at least 18 of the 26 deaths. Extensive characterizations included crystal structure analysis, single, tandem, and high-resolution mass spectrometry, liquid and gas chromatography, and nuclear magnetic resonance spectroscopy. For the work described here, both the (±)-cis and (±)-trans racemates were also synthesized, confirming that the differentiation between these two forms was straight-forward. Monoamine transporter activity was studied using rat brain synaptosomes which included the comparison with d-amphetamine, aminorex and (±)-cis-4-MAR. (±)-cis-4,4'-DMAR was a potent, efficacious substrate-type releaser at transporters for dopamine, norepinephrine and serotonin with EC50 values of 8.6 ± 1.1 nM (DAT), 26.9 ± 5.9 nM (NET) and 18.5 ± 2.8 nM (SERT), respectively. The potency of (±)-cis-4,4'-DMAR at DAT and NET rivalled that of other psychomotor stimulant drugs like d-amphetamine and aminorex. However, (±)-cis-4,4'-DMAR had much more potent actions at SERT and activity at SERT varied more than 100-fold across the four drugs. The potent releasing activity of (±)-cis-4,4'-DMAR at all three monoamine transporters predicts a potential for serious side-effects such as psychotic symptoms, agitation, hyperthermia and cardiovascular stimulation, especially after high-dose exposure or following combination with other psychostimulants. Copyright © 2014 John Wiley & Sons, Ltd.

Network-directed cis-mediator analysis of normal prostate tissue expression profiles reveals downstream regulatory associations of prostate cancer susceptibility loci.

PubMed

Larson, Nicholas B; McDonnell, Shannon K; Fogarty, Zach; Larson, Melissa C; Cheville, John; Riska, Shaun; Baheti, Saurabh; Weber, Alexandra M; Nair, Asha A; Wang, Liang; O'Brien, Daniel; Davila, Jaime; Schaid, Daniel J; Thibodeau, Stephen N

2017-10-17

Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis -acting associations due to study limitations. While trans -eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans -eQTL associations are mediated by cis -regulated genes, such as transcription factors. Leveraging a data-driven gene co-expression network, we conducted a comprehensive cis -mediator analysis using RNA-Seq data from 471 normal prostate tissue samples to identify downstream regulatory associations of previously identified prostate cancer risk variants. We discovered multiple trans -eQTL associations that were significantly mediated by cis -regulated transcripts, four of which involved risk locus 17q12, proximal transcription factor HNF1B , and target trans -genes with known HNF response elements ( MIA2 , SRC , SEMA6A , KIF12 ). We additionally identified evidence of cis -acting down-regulation of MSMB via rs10993994 corresponding to reduced co-expression of NDRG1 . The majority of these cis -mediator relationships demonstrated trans -eQTL replicability in 87 prostate tissue samples from the Gene-Tissue Expression Project. These findings provide further biological context to known risk loci and outline new hypotheses for investigation into the etiology of prostate cancer.

76 FR 14278 - U.S. Honey Producer Research, Promotion, and Consumer Information Order; Termination of...

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2011-03-16

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19 CFR 10.622 - Corrected certification by U.S. exporters or producers.

Code of Federal Regulations, 2010 CFR

2010-04-01

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Synthetic cis-jasmone exposure induces wheat and barley volatiles that repel the pest cereal leaf beetle, Oulema melanopus L.

PubMed

Delaney, Kevin J; Wawrzyniak, Maria; Lemańczyk, Grzegorz; Wrzesińska, Danuta; Piesik, Dariusz

2013-05-01

The plant semiochemical cis-jasmone primes/induces plant resistance that deters herbivores and attracts natural enemies. We studied the induction of volatile organic compounds (VOCs) in winter wheat and spring barley after exposure of plants to three synthetic cis-jasmone doses (50 μl of 1, 100, and 1 × 10(4) ng μl(-1)) and durations of exposure (1, 3, and 6 h). Cereal leaf beetle, Oulema melanopus, adult behavioral responses were examined in a Y-tube olfactometer to cis-jasmone induced plant VOC bouquets and to two synthetic blends of VOCs (3 green leaf volatiles (GLVs); 4 terpenes + indole). In both cereals, eight VOCs [(Z)-3-hexanal, (Z)-3-hexanol, (Z)-3-hexanyl acetate, (Z)-β-ocimene, linalool, β-caryophyllene, (E)-ß-farnesene, and indole] were induced 100- to 1000-fold after cis-jasmone exposure. The degree of induction in both cereals was usually positively and linearly associated with increasing exposure dose and duration. However, VOC emission rate was only ~2-fold greater from plants exposed to the highest vs. lowest cis-jasmone exposure doses (1 × 10(4) difference) or durations (6-fold difference). Male and female O. melanopus were deterred by both cereal VOC bouquets after plant exposure to the high cis-jasmone dose (1 × 10(4) ng μl(-1)), while females were also deterred after plant exposure to the low dose (1 ng μl(-1)) but attracted to unexposed plant VOC bouquets. Both O. melanopus sexes were repelled by terpene/indole and GLV blends at two concentrations (25 ng · min(-1); 125 ng · min(-1)), but attracted to the lowest dose (1 ng · min(-1)) of a GLV blend. It is possible that the biologically relevant low cis-jasmone dose has ecological activity and potential for inducing field crop VOCs to deter O. melanopus.

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

The Osmium(VIII) Oxofluoro Cations OsO(2)F(3)(+) and F(cis-OsO(2)F(3))(2)(+): Syntheses, Characterization by (19)F NMR Spectroscopy and Raman Spectroscopy, X-ray Crystal Structure of F(cis-OsO(2)F(3))(2)(+)Sb(2)F(11)(-), and Density Functional Theory Calculations of OsO(2)F(3)(+), ReO(2)F(3), and F(cis-OsO(2)F(3))(2)(+).

PubMed

Casteel, William J.; Dixon, David A.; Mercier, Hélène P. A.; Schrobilgen, Gary J.

1996-07-17

Osmium dioxide tetrafluoride, cis-OsO(2)F(4), reacts with the strong fluoride ion acceptors AsF(5) and SbF(5) in anhydrous HF and SbF(5) solutions to form orange salts. Raman spectra are consistent with the formation of the fluorine-bridged diosmium cation F(cis-OsO(2)F(3))(2)(+), as the AsF(6)(-) and Sb(2)F(11)(-) salts, respectively. The (19)F NMR spectra of the salts in HF solution are exchange-averaged singlets occurring at higher frequency than those of the fluorine environments of cis-OsO(2)F(4). The F(cis-OsO(2)F(3))(2)(+)Sb(2)F(11)(-) salt crystallizes in the orthorhombic space group Imma. At -107 degrees C, a = 12.838(3) Å, b = 10.667(2) Å, c = 11.323(2) Å, V = 1550.7(8) Å(3), and Z = 4. Refinement converged with R = 0.0469 [R(w) = 0.0500]. The crystal structure consists of discrete fluorine-bridged F(cis-OsO(2)F(3))(2)(+) and Sb(2)F(11)(-) ions in which the fluorine bridge of the F(cis-OsO(2)F(3))(2)(+) cation is trans to an oxygen atom (Os-O 1.676 Å) of each OsO(2)F(3) group. The angle at the bridge is 155.2(8) degrees with a bridging Os---F(b) distance of 2.086(3) Å. Two terminal fluorine atoms (Os-F 1.821 Å) are cis to the two oxygen atoms (Os-O 1.750 Å), and two terminal fluorine atoms of the OsO(2)F(3) group are trans to one another (1.813 Å). The OsO(2)F(3)(+) cation was characterized by (19)F NMR and by Raman spectroscopy in neat SbF(5) solution but was not isolable in the solid state. The NMR and Raman spectroscopic findings are consistent with a trigonal bipyramidal cation in which the oxygen atoms and a fluorine atom occupy the equatorial plane and two fluorine atoms are in axial positions. Density functional theory calculations show that the crystallographic structure of F(cis-OsO(2)F(3))(2)(+) is the energy-minimized structure and the energy-minimized structures of the OsO(2)F(3)(+) cation and ReO(2)F(3) are trigonal bipyramidal having C(2)(v)() point symmetry. Attempts to prepare the OsOF(5)(+) cation by oxidative fluorination of cis

Swipe In, Tap Out: Advancing Student Entrepreneurship in the CIS Sandbox

ERIC Educational Resources Information Center

Charlebois, Conner; Hentschel, Nicholas; Frydenberg, Mark

2014-01-01

The Computer Information Systems Learning and Technology Sandbox (CIS Sandbox) opened as a collaborative learning lab during the fall 2011 semester at a New England business university. The facility employs 24 student workers, who, in addition to providing core tutoring services, are encouraged to explore new technologies and take on special…

Cloning and characterization of farnesyl pyrophosphate synthase from the highly branched isoprenoid producing diatom Rhizosolenia setigera.

PubMed

Ferriols, Victor Marco Emmanuel N; Yaginuma, Ryoko; Adachi, Masao; Takada, Kentaro; Matsunaga, Shigeki; Okada, Shigeru

2015-05-21

The diatom Rhizosolenia setigera Brightwell produces highly branched isoprenoid (HBI) hydrocarbons that are ubiquitously present in marine environments. The hydrocarbon composition of R. setigera varies between C25 and C30 HBIs depending on the life cycle stage with regard to auxosporulation. To better understand how these hydrocarbons are biosynthesized, we characterized the farnesyl pyrophosphate (FPP) synthase (FPPS) enzyme of R. setigera. An isolated 1465-bp cDNA clone contained an open reading frame spanning 1299-bp encoding a protein with 432 amino acid residues. Expression of the RsFPPS cDNA coding region in Escherichia coli produced a protein that exhibited FPPS activity in vitro. A reduction in HBI content from diatoms treated with an FPPS inhibitor, risedronate, suggested that RsFPPS supplies precursors for HBI biosynthesis. Product analysis by gas chromatography-mass spectrometry also revealed that RsFPPS produced small amounts of the cis-isomers of geranyl pyrophosphate and FPP, candidate precursors for the cis-isomers of HBIs previously characterized. Furthermore, RsFPPS gene expression at various life stages of R. setigera in relation to auxosporulation were also analyzed. Herein, we present data on the possible role of RsFPPS in HBI biosynthesis, and it is to our knowledge the first instance that an FPPS was cloned and characterized from a diatom.

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.

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.

Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella

PubMed Central

Steige, Kim A.; Reimegård, Johan; Koenig, Daniel; Scofield, Douglas G.; Slotte, Tanja

2015-01-01

The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis-regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts. PMID:26318184

The dopamine antagonist cis-flupenthixol blocks the expression of the conditioned positive but not the negative effects of cocaine in rats

PubMed Central

Wenzel, Jennifer M.; Su, Zu-In; Shelton, Kerisa; Dominguez, Hiram M.; von Furstenberg, Victoria A.; Ettenberg, Aaron

2013-01-01

Human cocaine users report that the initial “high” produced by cocaine administration is followed by an anxiogenic “crash”. Given that cocaine has such robust and opposing properties, it is likely that both the positive and negative effects of cocaine contribute to an individual’s motivation to administer the drug. Despite this likelihood, the neurobiology underlying cocaine’s dual processes remains unclear. While much literature supports a role for dopamine (DA) in cocaine reward, it is uncertain if DA also contributes to the drug’s negative effects. Our laboratory has extensively utilized a modified conditioned place test to explore cocaine’s opponent processes. In this paradigm rats develop conditioned place preferences (CPPs) for an environment paired with the immediate/positive effects of cocaine, and conditioned place aversions (CPAs) for an environment paired with the delayed/negative effects present 15-min after i.v. injection. In the current study rats were conditioned to associate an environment with either the immediate or delayed effects of i.v. cocaine (1 mg/kg/0.1 ml) three hours after i.p. pre-treatment with either the DA D1/D2 receptor antagonist cis-flupenthixol (0.5 mg/kg/ml) or saline vehicle. As expected, vehicle-treated control animals developed the normal pattern of CPPs for cocaine’s immediate effects or CPAs for the delayed effects of cocaine. However, while DA receptor antagonism prevented the expression of cocaine CPPs it did not alter the expression of cocaine-induced CPAs. These data confirm a role for DA transmission in cocaine reward but suggest that different neural pathways mediate the drug’s negative/anxiogenic properties. PMID:24012795

The identification of cis-regulatory elements: A review from a machine learning perspective.

PubMed

Li, Yifeng; Chen, Chih-Yu; Kaye, Alice M; Wasserman, Wyeth W

2015-12-01

The majority of the human genome consists of non-coding regions that have been called junk DNA. However, recent studies have unveiled that these regions contain cis-regulatory elements, such as promoters, enhancers, silencers, insulators, etc. These regulatory elements can play crucial roles in controlling gene expressions in specific cell types, conditions, and developmental stages. Disruption to these regions could contribute to phenotype changes. Precisely identifying regulatory elements is key to deciphering the mechanisms underlying transcriptional regulation. Cis-regulatory events are complex processes that involve chromatin accessibility, transcription factor binding, DNA methylation, histone modifications, and the interactions between them. The development of next-generation sequencing techniques has allowed us to capture these genomic features in depth. Applied analysis of genome sequences for clinical genetics has increased the urgency for detecting these regions. However, the complexity of cis-regulatory events and the deluge of sequencing data require accurate and efficient computational approaches, in particular, machine learning techniques. In this review, we describe machine learning approaches for predicting transcription factor binding sites, enhancers, and promoters, primarily driven by next-generation sequencing data. Data sources are provided in order to facilitate testing of novel methods. The purpose of this review is to attract computational experts and data scientists to advance this field. Crown Copyright © 2015. Published by Elsevier Ireland Ltd. All rights reserved.

A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitness[C][W

PubMed Central

Jabnoune, Mehdi; Secco, David; Lecampion, Cécile; Robaglia, Christophe; Shu, Qingyao; Poirier, Yves

2013-01-01

cis-natural antisense transcripts (cis-NATs) are widespread in plants and are often associated with downregulation of their associated sense genes. We found that a cis-NAT positively regulates the level of a protein critical for phosphate homeostasis in rice (Oryza sativa). PHOSPHATE1;2 (PHO1;2), a gene involved in phosphate loading into the xylem in rice, and its associated cis-NATPHO1;2 are both controlled by promoters active in the vascular cylinder of roots and leaves. While the PHO1;2 promoter is unresponsive to the plant phosphate status, the cis-NATPHO1;2 promoter is strongly upregulated under phosphate deficiency. Expression of both cis-NATPHO1;2 and the PHO1;2 protein increased in phosphate-deficient plants, while the PHO1;2 mRNA level remained stable. Downregulation of cis-NATPHO1;2 expression by RNA interference resulted in a decrease in PHO1;2 protein, impaired the transfer of phosphate from root to shoot, and decreased seed yield. Constitutive overexpression of NATPHO1;2 in trans led to a strong increase of PHO1;2, even under phosphate-sufficient conditions. Under all conditions, no changes occurred in the level of expression, sequence, or nuclear export of PHO1;2 mRNA. However, expression of cis-NATPHO1;2 was associated with a shift of both PHO1;2 and cis-NATPHO1;2 toward the polysomes. These findings reveal an unexpected role for cis-NATPHO1;2 in promoting PHO1;2 translation and affecting phosphate homeostasis and plant fitness. PMID:24096344

Slime-producing Staphylococcus epidermidis and S. aureus in acute bacterial conjunctivitis in soft contact lens wearers.

PubMed

Catalanotti, Piergiorgio; Lanza, Michele; Del Prete, Antonio; Lucido, Maria; Catania, Maria Rosaria; Gallè, Francesca; Boggia, Daniela; Perfetto, Brunella; Rossano, Fabio

2005-10-01

In recent years, an increase in ocular pathologies related to soft contact lens has been observed. The most common infectious agents were Staphylococcus spp. Some strains produce an extracellular polysaccharidic slime that can cause severe infections. Polysaccharide synthesis is under genetic control and involves a specific intercellular adhesion (ica) locus, in particular, icaA and icaD genes. Conjunctival swabs from 97 patients with presumably bacterial bilateral conjunctivitis, wearers of soft contact lenses were examined. We determined the ability of staphylococci to produce slime, relating it to the presence of icaA and icaD genes. We also investigated the antibiotic susceptibility and Pulsed Field Gel Electrophoresis (PFGE) patterns of the clinical isolates. We found that 74.1% of the S. epidermidis strains and 61.1% of the S. aureus strains isolated were slime producers and showed icaA and icaD genes. Both S. epidermidis and S. aureus slime-producing strains exhibited more surface hydrophobicity than non-producing slime strains. The PFGE patterns overlapped in S. epidermidis strains with high hydrophobicity. The similar PFGE patterns were not related to biofilm production. We found scarce matching among the Staphylococcus spp. studied, slime production, surface hydrophobicity and antibiotic susceptibility.

Biodistribution and Subcellular Localization of an Unnatural Boron-Containing Amino Acid (Cis-ABCPC) by Imaging Secondary Ion Mass Spectrometry for Neutron Capture Therapy of Melanomas and Gliomas

PubMed Central

Chandra, Subhash; Barth, Rolf F.; Haider, Syed A.; Yang, Weilian; Huo, Tianyao; Shaikh, Aarif L.; Kabalka, George W.

2013-01-01

The development of new boron-delivery agents is a high priority for improving the effectiveness of boron neutron capture therapy. In the present study, 1-amino-3-borono-cyclopentanecarboxylic acid (cis-ABCPC) as a mixture of its L- and D- enantiomers was evaluated in vivo using the B16 melanoma model for the human tumor and the F98 rat glioma as a model for human gliomas. A secondary ion mass spectrometry (SIMS) based imaging instrument, CAMECA IMS 3F SIMS Ion Microscope, was used for quantitative imaging of boron at 500 nm spatial resolution. Both in vivo and in vitro studies in melanoma models demonstrated that boron was localized in the cytoplasm and nuclei with some cell-to-cell variability. Uptake of cis-ABCPC in B16 cells was time dependent with a 7.5:1 partitioning ratio of boron between cell nuclei and the nutrient medium after 4 hrs. incubation. Furthermore, cis-ABCPC delivered boron to cells in all phases of the cell cycle, including S-phase. In vivo SIMS studies using the F98 rat glioma model revealed an 8:1 boron partitioning ratio between the main tumor mass and normal brain tissue with a 5:1 ratio between infiltrating tumor cells and contiguous normal brain. Since cis-ABCPC is water soluble and can cross the blood-brain-barrier via the L-type amino acid transporters (LAT), it may accumulate preferentially in infiltrating tumor cells in normal brain due to up-regulation of LAT in high grade gliomas. Once trapped inside the tumor cell, cis-ABCPC cannot be metabolized and remains either in a free pool or bound to cell matrix components. The significant improvement in boron uptake by both the main tumor mass and infiltrating tumor cells compared to those reported in animal and clinical studies of p-boronophenylalanine strongly suggest that cis-ABCPC has the potential to become a novel new boron delivery agent for neutron capture therapy of gliomas and melanomas. PMID:24058680

Structure Determination of an Inter-strand-type cis-anti Cyclobutane Thymine Dimer Produced in High Yield by UVB Light in an Oligodeoxynucleotide at Acidic pH

PubMed Central

Su, Dian G. T.; Kao, Jeffrey L.-F.; Gross, Michael L.; Taylor, John-Stephen A.

2009-01-01

UVB irradiation of DNA produces photodimers in adjacent DNA bases and on rare occasions in non-adjacent bases. UVB irradiation (312 nm) of d(GTATCATGAGGTGC) gave rise to an unknown DNA photoproduct in approximately 40% yield at acidic pH of about 5. This product has a much shorter retention time in reverse phase HPLC compared to known dipyrimidine photoproducts of this sequence. A large upfield shift of two thymine H6 NMR signals and photoreversion to the parent ODN upon irradiation with 254 nm light indicates that the photoproduct is a cyclobutane thymine dimer. Exonuclease-coupled MS assay establishes that the photodimer forms between T2 and T7, which was confirmed by tandem mass spectrometric MS/MS identification of the endonuclease P1 digestion product d(T2[A3])=pd(T7[G8]). Acidic hydrolysis of the photoproduct gave a product with the same retention time on reverse phase HPLC and the same MS/MS fragmentation pattern as authentic Thy[c,a]Thy. 2D NOE NMR data are consistent with a cis-anti cyclobutane dimer between the 3′-sides of T2 and T7 in anti glycosyl conformations that had to have arisen from an inter-stand type reaction. In addition to pH-dependent, the photoproduct yield is highly sequence specific and concentration dependent, indicating that it results from a higher order folded structure. The efficient formation of this inter-strand-type photoproduct suggests the existence of a new type of folding motif and the possibility that this type of photoproduct might also form in other folded structures, such as G-quadruplexes and i-motif structures which can be now studied by the methods described. PMID:18680367

Distal regulatory regions restrict the expression of cis-linked genes to the tapetal cells.

PubMed

Franco, Luciana O; de O Manes, Carmem Lara; Hamdi, Said; Sachetto-Martins, Gilberto; de Oliveira, Dulce E

2002-04-24

The oleosin glycine-rich protein genes Atgrp-6, Atgrp-7, and Atgrp-8 occur in clusters in the Arabidopsis genome and are expressed specifically in the tapetum cells. The cis-regulatory regions involved in the tissue-specific gene expression were investigated by fusing different segments of the gene cluster to the uidA reporter gene. Common distal regulatory regions were identified that coordinate expression of the sequential genes. At least two of these genes were regulated spatially by proximal and distal sequences. The cis-acting elements (122 bp upstream of the transcriptional start point) drive the uidA expression to floral tissues, whereas distal 5' upstream regions restrict the gene activity to tapetal cells.

How does the trans-cis photoisomerization of azobenzene take place in organic solvents?

PubMed

Tiberio, Giustiniano; Muccioli, Luca; Berardi, Roberto; Zannoni, Claudio

2010-04-06

The trans-cis photoisomerization of azobenzene-containing materials is key to a number of photomechanical applications, but the actual conversion mechanism in condensed phases is still largely unknown. Herein, we study the n, pi* isomerization in a vacuum and in various solvents via a modified molecular dynamics simulation adopting an ab initio torsion-inversion force field in the ground and excited states, while allowing for electronic transitions and a stochastic decay to the fundamental state. We determine the trans-cis photoisomerization quantum yield and decay times in various solvents (n-hexane, anisole, toluene, ethanol, and ethylene glycol), and obtain results comparable with experimental ones where available. A profound difference between the isomerization mechanism in vacuum and in solution is found, with the often neglected mixed torsional-inversion pathway being the most important in solvents.

Untangling Risk of Maltreatment from Events of Maltreatment: An Analysis of the 2008 Canadian Incidence Study of Reported Child Abuse and Neglect (CIS-2008)

ERIC Educational Resources Information Center

Fallon, Barbara; Trocme, Nico; MacLaurin, Bruce; Sinha, Vandna; Black, Tara

2011-01-01

This paper describes the methodological changes that occurred across cycles of the Canadian Incidence Study of Reported Child Abuse and Neglect (CIS), specifically outlining the rationale for tracking investigations of families with children at risk of maltreatment in the CIS-2008 cycle. This paper also presents analysis of data from the CIS-2008…

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.

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

Laticifer-Specific cis-Prenyltransferase Silencing Affects the Rubber, Triterpene, and Inulin Content of Taraxacum brevicorniculatum12[C][W

PubMed Central

Post, Janina; van Deenen, Nicole; Fricke, Julia; Kowalski, Natalie; Wurbs, David; Schaller, Hubert; Eisenreich, Wolfgang; Huber, Claudia; Twyman, Richard M.; Prüfer, Dirk; Gronover, Christian Schulze

2012-01-01

Certain Taraxacum species, such as Taraxacum koksaghyz and Taraxacum brevicorniculatum, produce large amounts of high-quality natural rubber in their latex, the milky cytoplasm of specialized cells known as laticifers. This high-molecular mass biopolymer consists mainly of poly(cis-1,4-isoprene) and is deposited in rubber particles by particle-bound enzymes that carry out the stereospecific condensation of isopentenyl diphosphate units. The polymer configuration suggests that the chain-elongating enzyme (rubber transferase; EC 2.5.1.20) is a cis-prenyltransferase (CPT). Here, we present a comprehensive analysis of transgenic T. brevicorniculatum plants in which the expression of three recently isolated CPTs known to be associated with rubber particles (TbCPT1 to -3) was heavily depleted by laticifer-specific RNA interference (RNAi). Analysis of the CPT-RNAi plants by nuclear magnetic resonance, size-exclusion chromatography, and gas chromatography-mass spectrometry indicated a significant reduction in rubber biosynthesis and a corresponding 50% increase in the levels of triterpenes and the main storage carbohydrate, inulin. Transmission electron microscopy revealed that the laticifers in CPT-RNAi plants contained fewer and smaller rubber particles than wild-type laticifers. We also observed lower activity of hydroxymethylglutaryl-coenzyme A reductase, the key enzyme in the mevalonate pathway, reflecting homeostatic control of the isopentenyl diphosphate pool. To our knowledge, this is the first in planta demonstration of latex-specific CPT activity in rubber biosynthesis. PMID:22238421

CIS Program Redesign Driven by IS2010 Model: A Case Study

ERIC Educational Resources Information Center

Surendran, Ken; Amer, Suhair; Schwieger, Dana

2012-01-01

The release of the IS2010 Model Curriculum has triggered review of existing Information Systems (IS) programs. It also provides an opportunity to replace low enrollment IS programs with flexible ones that focus on specific application domains. In this paper, the authors present a case study of their redesigned Computer Information Systems (CIS)…

Pharmacokinetics and metabolism of all-trans- and 13-cis-retinoic acid in pulmonary emphysema patients.

PubMed

Muindi, Josephia R; Roth, Michael D; Wise, Robert A; Connett, John E; O'Connor, George T; Ramsdell, Joe W; Schluger, Neil W; Romkes, Marjorie; Branch, Robert A; Sciurba, Frank C

2008-01-01

Retinoids promote lung alveolarization in animal models and were administered to patients as part of the Feasibility of Retinoid Therapy for Emphysema (FORTE) study. This FORTE substudy investigated the pharmacokinetic profiles of 2 retinoic acid isomers-all-trans-retinoic acid (ATRA) and 13-cis-retinoic acid (13-cRA)-in subjects with emphysema, evaluated strategies to overcome self-induced ATRA catabolism, and identified pharmacodynamic relationships. Comprehensive and limited pharmacokinetics were obtained at multiple visits in emphysema subjects treated with placebo (n = 30), intermittent dosing (4 days/week) with low-dose ATRA (1 mg/kg/day, n = 21), or high-dose ATRA (2 mg/kg/day, n = 25) or daily administration of 13-cRA (1 mg/kg/day, n = 40). High-dose ATRA produced the highest peak plasma ATRA Cmax. However, at follow-up, plasma ATRA C(max) was significantly decreased from baseline in subjects whose day 1 levels exceeded 100 ng/mL (P < .0001). In contrast, administration of 13-cRA produced lower plasma ATRA C(max) (<100 ng/mL), but the levels were significantly higher at follow-up than those on day 1 (P < .001). Plasma ATRA levels as determined on day 1 correlated with changes in pulmonary diffusing capacity at 6 months, consistent with concentration-dependent biologic effects (r2 = -0.25). The authors conclude that intermittent therapy with high-dose ATRA produced the greatest ATRA exposure, but alternative approaches for limiting self-induced ATRA catabolism should be sought.

NMR analysis of cleaved Escherichia coli thioredoxin (1-73/74-108) and its P76A variant: cis/trans peptide isomerization.

PubMed Central

Yu, W. F.; Tung, C. S.; Wang, H.; Tasayco, M. L.

2000-01-01

Inspection of high resolution three-dimensional (3D) structures from the protein database reveals an increasing number of cis-Xaa-Pro and cis-Xaa-Yaa peptide bonds. However, we are still far from being able to predict whether these bonds will remain cis upon single-site substitution of Pro or Yaa and/or cleavage of a peptide bond close to it in the sequence. We have chosen oxidized Escherichia coli thioredoxin (Trx), a member of the Trx superfamily with a single alpha/beta domain and cis P76 to determine the effect of single-site substitution and/or cleavage on this isomer. Standard two-dimensional (2D) NMR analysis were performed on cleaved Trx (1-73/74-108) and its P76A variant. Analysis of the NOE connectivities indicates remarkable similarity between the secondary and supersecondary structure of the noncovalent complexes and Trx. Analysis of the 2D version of the HCCH-TOCSY and HMQC-NOESY-HMQC and 13C-filtered HMQC-NOESY spectra of cleaved Trx with uniformly 13C-labeled 175 and P76 shows surprising conservation of both cis P76 and packing of 175 against W31. A similar NMR analysis of its P76A variant provides no evidence for cis A76 and shows only subtle local changes in both the packing of 175 and the interstrand connectivities between its most protected hydrophobic strands (beta2 and beta4). Indeed, a molecular simulation model for the trans P76A variant of Trx shows only subtle local changes around the substitution site. In conclusion, cleavage of R73 is insufficient to provoke cis/trans isomerization of P76, but cleavage and single-site substitution (P76A) favors the trans isomer. PMID:10739243

Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana.

PubMed

Zhang, Weixiong; Ruan, Jianhua; Ho, Tuan-Hua David; You, Youngsook; Yu, Taotao; Quatrano, Ralph S

2005-07-15

A fundamental problem of computational genomics is identifying the genes that respond to certain endogenous cues and environmental stimuli. This problem can be referred to as targeted gene finding. Since gene regulation is mainly determined by the binding of transcription factors and cis-regulatory DNA sequences, most existing gene annotation methods, which exploit the conservation of open reading frames, are not effective in finding target genes. A viable approach to targeted gene finding is to exploit the cis-regulatory elements that are known to be responsible for the transcription of target genes. Given such cis-elements, putative target genes whose promoters contain the elements can be identified. As a case study, we apply the above approach to predict the genes in model plant Arabidopsis thaliana which are inducible by a phytohormone, abscisic acid (ABA), and abiotic stress, such as drought, cold and salinity. We first construct and analyze two ABA specific cis-elements, ABA-responsive element (ABRE) and its coupling element (CE), in A.thaliana, based on their conservation in rice and other cereal plants. We then use the ABRE-CE module to identify putative ABA-responsive genes in A.thaliana. Based on RT-PCR verification and the results from literature, this method has an accuracy rate of 67.5% for the top 40 predictions. The cis-element based targeted gene finding approach is expected to be widely applicable since a large number of cis-elements in many species are available.

Persistence of an Oncogenic Papillomavirus Genome Requires cis Elements from the Viral Transcriptional Enhancer

PubMed Central

Van Doorslaer, Koenraad; Chen, Dan; Chapman, Sandra; Khan, Jameela

2017-01-01

ABSTRACT Human papillomavirus (HPV) genomes are replicated and maintained as extrachromosomal plasmids during persistent infection. The viral E2 proteins are thought to promote stable maintenance replication by tethering the viral DNA to host chromatin. However, this has been very difficult to prove genetically, as the E2 protein is involved in transcriptional regulation and initiation of replication, as well as its assumed role in genome maintenance. This makes mutational analysis of viral trans factors and cis elements in the background of the viral genome problematic and difficult to interpret. To circumvent this problem, we have developed a complementation assay in which the complete wild-type HPV18 genome is transfected into primary human keratinocytes along with subgenomic or mutated replicons that contain the minimal replication origin. The wild-type genome provides the E1 and E2 proteins in trans, allowing us to determine additional cis elements that are required for long-term replication and partitioning of the replicon. We found that, in addition to the core replication origin (and the three E2 binding sites located therein), additional sequences from the transcriptional enhancer portion of the URR (upstream regulatory region) are required in cis for long-term genome replication. PMID:29162712

Synthesis and biological evaluation of cis-locked vinylogous combretastatin-A4 analogues: derivatives with a cyclopropyl-vinyl or a cyclopropyl-amide bridge.

PubMed

Ty, Nancy; Kaffy, Julia; Arrault, Alban; Thoret, Sylviane; Pontikis, Renée; Dubois, Joelle; Morin-Allory, Luc; Florent, Jean-Claude

2009-03-01

A series of novel combretastatin A4 analogues, in which the cis-olefinic bridge is replaced by a cyclopropyl-vinyl or a cyclopropyl-amide moiety, were synthesized and evaluated for inhibition of tubulin polymerization and antiproliferative activity. The derivative 9a with a (cis,E)-cyclopropyl-vinyl unit is the most promising compound. As expected, molecular docking of 9a has shown that only one of the cis-cyclopropyl enantiomers is a good ligand for tubulin.

Diastereoselective intramolecular Ritter reaction: generation of a cis-fused hexahydro-4aH-indeno[1,2-b]pyridine ring system with 4a,9b-diangular substituents.

PubMed

Van Emelen, K; De Wit, T; Hoornaert, G J; Compernolle, F

2000-10-05

Indanol intermediates 5, prepared via Michael addition of 1-indanone beta-ketoester and acrylonitrile followed by reduction or Grignard reaction of the ketone group, were submitted to intramolecular Ritter reaction using various acid reaction conditions to produce tricyclic lactams 4. This cis-fused hexahydro-4aH-indeno[1,2-b]pyridine ring system, substituted at both angular positions 4a and 9b, provides access to constrained analogues of non-peptide NK(1)-antagonists with monocyclic piperidine structure.

A user-centered, object-oriented methodology for developing Health Information Systems: a Clinical Information System (CIS) example.

PubMed

Konstantinidis, Georgios; Anastassopoulos, George C; Karakos, Alexandros S; Anagnostou, Emmanouil; Danielides, Vasileios

2012-04-01

The aim of this study is to present our perspectives on healthcare analysis and design and the lessons learned from our experience with the development of a distributed, object-oriented Clinical Information System (CIS). In order to overcome known issues regarding development, implementation and finally acceptance of a CIS by the physicians we decided to develop a novel object-oriented methodology by integrating usability principles and techniques in a simplified version of a well established software engineering process (SEP), the Unified Process (UP). A multilayer architecture has been defined and implemented with the use of a vendor application framework. Our first experiences from a pilot implementation of our CIS are positive. This approach allowed us to gain a socio-technical understanding of the domain and enabled us to identify all the important factors that define both the structure and the behavior of a Health Information System.

Synthesis and cytotoxic activities of novel 4-methoxy-substituted and 5-methyl-substituted (3′S,4′S)-(−)-cis-khellactone derivatives that induce apoptosis via the intrinsic pathway

PubMed Central

Chen, Jingrun; Liu, Junjie; Cui, Dongxiao; Yan, Chaoqun; Meng, Liqiang; Sun, Liqian; Ban, Shurong; Ge, Rui; Liang, Taigang; Li, Qingshan

2017-01-01

This study deals with the design and synthesis of a series of novel 4-methoxy-substituted and 5-methyl-substituted (3′S,4′S)-(−)-cis-khellactones. The newly synthesized compounds were characterized by 1H nuclear magnetic resonance (NMR), 13C-NMR, mass spectrometry, and elemental analysis. All the derivatives were subjected to in vitro cytotoxicity screening against HEPG-2 (human liver carcinoma), SGC-7901 (human gastric carcinoma), and LS174T (human colon carcinoma), by using the MTT assay. The results revealed that several of the 4-methoxy-substituted compounds exhibited potent cytotoxicity. Among these, compound 12e showed the highest activity against cancer cells which 50% inhibitory concentration (IC50) values were in the range of 6.1–9.2 μM with low toxicity on normal human hepatocyte. Preliminary investigation of possible mechanisms of action of compound 12e against HEPG-2 cells indicated possible induction of apoptosis, as determined by morphological observations and Annexin V/propidium iodide (PI) double staining, in addition to apparent dissipation of mitochondrial membrane potential (MMP), as measured by 5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethyl-imidacarbocyanine iodide (JC-1) staining in combination with the activation of caspase-9 and caspase-3 by Western blot analysis. Overall, the data suggest that compound 12e may be a promising potential anti-cancer agent that could act primarily by inducing apoptosis through the mitochondria-mediated intrinsic pathway in human hepatoma cells. PMID:28694689

Speech entrainment enables patients with Broca’s aphasia to produce fluent speech

PubMed Central

Hubbard, H. Isabel; Hudspeth, Sarah Grace; Holland, Audrey L.; Bonilha, Leonardo; Fromm, Davida; Rorden, Chris

2012-01-01

A distinguishing feature of Broca’s aphasia is non-fluent halting speech typically involving one to three words per utterance. Yet, despite such profound impairments, some patients can mimic audio-visual speech stimuli enabling them to produce fluent speech in real time. We call this effect ‘speech entrainment’ and reveal its neural mechanism as well as explore its usefulness as a treatment for speech production in Broca’s aphasia. In Experiment 1, 13 patients with Broca’s aphasia were tested in three conditions: (i) speech entrainment with audio-visual feedback where they attempted to mimic a speaker whose mouth was seen on an iPod screen; (ii) speech entrainment with audio-only feedback where patients mimicked heard speech; and (iii) spontaneous speech where patients spoke freely about assigned topics. The patients produced a greater variety of words using audio-visual feedback compared with audio-only feedback and spontaneous speech. No difference was found between audio-only feedback and spontaneous speech. In Experiment 2, 10 of the 13 patients included in Experiment 1 and 20 control subjects underwent functional magnetic resonance imaging to determine the neural mechanism that supports speech entrainment. Group results with patients and controls revealed greater bilateral cortical activation for speech produced during speech entrainment compared with spontaneous speech at the junction of the anterior insula and Brodmann area 47, in Brodmann area 37, and unilaterally in the left middle temporal gyrus and the dorsal portion of Broca’s area. Probabilistic white matter tracts constructed for these regions in the normal subjects revealed a structural network connected via the corpus callosum and ventral fibres through the extreme capsule. Unilateral areas were connected via the arcuate fasciculus. In Experiment 3, all patients included in Experiment 1 participated in a 6-week treatment phase using speech entrainment to improve speech production

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.

Combined optical and photoelectric study of the photocycle of 13-cis bacteriorhodopsin.

PubMed Central

Gergely, C; Ganea, C; Váró, G

1994-01-01

The photocycle of the 13-cis retinal containing bacteriorhodopsin was studied by three different techniques. The optical multichannel analyzer monitored the spectral changes during the photocycle and gave information about the number and the spectrum of the intermediates. The absorption kinetic measurements provided the possibility of following the absorbance changes at several characteristic wavelengths. The electric signal provided information about the charge motions during the photocycle. The results reveal the existence of two intermediates in the 13-cis photocycle, one with a short lifetime having an average of 1.7 microseconds and an absorption maximum at 620 nm. The other, a long-living intermediate, has a lifetime of about 50 ms and an absorption maximum around 585 nm. The data analysis suggests that these intermediates are in two parallel branches of the photocycle, and branching from the intermediate with the shorter lifetime might be responsible for the light-adaptation process. PMID:7948698

Cumene oxidation by cis-[RuIV(bpy)2(py)(O)]2+, revisited.

PubMed

Bryant, Jasmine R; Matsuo, Takashi; Mayer, James M

2004-02-23

cis-[RuIV(bpy)2(py)(O)]2+ oxidizes cumene (2-phenylpropane) in acetonitrile solution primarily to cumyl alcohol (2-phenyl-2-propanol), alpha-methylstyrene, and acetophenone. Contrary to a prior report, the rate of the reaction is not accelerated by added nucleophiles. There is thus no evidence for the hydride transfer mechanism originally proposed. Instead, the results are consistent with a mechanism of initial hydrogen atom transfer from cumene to the ruthenium oxo group. This is indicated by the correlation of rate with C-H bond strength and by the various products observed. The formation of acetophenone, with one carbon less than cumene, is suggested to occur via a multistep pathway involving decarbonylation of the acyl radical from 2-phenylpropanal. An alternative mechanism involving beta-scission of cumyloxyl radical is deemed unlikely because of the difficulty of generating alkoxyl radicals under anaerobic conditions and the lack of rearranged products in the oxidation of triphenylmethane by cis-[RuIV(bpy)2(py)(O)]2+.

Comparative teratology and transplacental pharmacokinetics of all-trans-retinoic acid, 13-cis-retinoic acid, and retinyl palmitate following daily administrations in rats.

PubMed

Collins, M D; Tzimas, G; Hummler, H; Bürgin, H; Nau, H

1994-07-01

The retinoids are teratogenic in a wide variety of species. In the rat, 13-cis-retinoic acid and retinyl palmitate are significantly less potent teratogens than all-trans-retinoic acid. This investigation questioned whether differing teratogenic potencies of these moieties can be correlated with the concentrations of these drugs and/or metabolites in the embryonic compartment. Approximately equipotent teratogenic doses of these three retinoids were administered and the pharmacokinetics in maternal plasma and embryo of the most prevalent vitamin A metabolites were measured. The glucuronides of the respective retinoids were the predominant metabolites in the maternal plasma, but were not detected in the embryo. Also, the transport of 13-cis-retinoic acid across the placenta occurred to a much lesser extent than the transport of all-trans-retinoic acid. Administration of either all-trans- or 13-cis-retinoic acid causes a depression in the endogenous retinol concentration. This depression is more pronounced in the maternal plasma than in the embryo. The depression of the retinol level in both plasma and embryo after 13-cis-retinoic acid administration (75 mg/kg/day) was greater than the depression after all-trans-retinoic acid (6 mg/kg/day), corroborating the inferential teratological data that the 13-cis-retinoic acid dose was more embryotoxic than the all-trans-retinoic acid dose. Although the dose of all-trans-retinoic acid was less embryotoxic than that of either 13-cis-retinoic acid or retinyl palmitate, the embryonic exposure to all-trans-retinoic acid was considerably larger, as determined by maximum concentration or area under the concentration-versus-time curve, after administration of all-trans-retinoic acid than after either retinyl palmitate or 13-cis-retinoic acid application. These results suggest that embryonic retinoids other than all-trans-retinoic acid--including the administered substances themselves--are important in the teratogenic process induced

Process optimization for enhancing production of cis-4-hydroxy-L-proline by engineered Escherichia coli.

PubMed

Chen, Kequan; Pang, Yang; Zhang, Bowen; Feng, Jiao; Xu, Sheng; Wang, Xin; Ouyang, Pingkai

2017-11-22

Understanding the bioprocess limitations is critical for the efficient design of biocatalysts to facilitate process feasibility and improve process economics. In this study, a proline hydroxylation process with recombinant Escherichia coli expressing L-proline cis-4-hydroxylase (SmP4H) was investigated. The factors that influencing the metabolism of microbial hosts and process economics were focused on for the optimization of cis-4-hydroxy-L-proline (CHOP) production. In recombinant E. coli, SmP4H synthesis limitation was observed. After the optimization of expression system, CHOP production was improved in accordance with the enhanced SmP4H synthesis. Furthermore, the effects of the regulation of proline uptake and metabolism on whole-cell catalytic activity were investigated. The improved CHOP production by repressing putA gene responsible for L-proline degradation or overexpressing L-proline transporter putP on CHOP production suggested the important role of substrate uptake and metabolism on the whole-cell biocatalyst efficiency. Through genetically modifying these factors, the biocatalyst activity was significantly improved, and CHOP production was increased by twofold. Meanwhile, to further improve process economics, a two-strain coupling whole-cell system was established to supply co-substrate (α-ketoglutarate, α-KG) with a cheaper chemical L-glutamate as a starting material, and 13.5 g/L of CHOP was successfully produced. In this study, SmP4H expression, and L-proline uptake and degradation, were uncovered as the hurdles for microbial production of CHOP. Accordingly, the whole-cell biocatalysts were metabolically engineered for enhancing CHOP production. Meanwhile, a two-strain biotransformation system for CHOP biosynthesis was developed aiming at supplying α-KG more economically. Our work provided valuable insights into the design of recombinant microorganism to improve the biotransformation efficiency that catalyzed by Fe

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

Increased concentrations of endogenous 13-cis- and all-trans-retinoic acids in diffuse idiopathic skeletal hyperostosis, as demonstrated by HPLC.

PubMed

Periquet, B; Lambert, W; Garcia, J; Lecomte, G; De Leenheer, A P; Mazieres, B; Thouvenot, J P; Arlet, J

1991-11-09

Endogenous 13-cis- and all-trans-retinoic acids have been quantitated in human serum using a solvent extraction procedure followed by isocratic reversed phase high performance liquid chromatography and UV detection. In healthy adults, after an overnight fasting period, the concentrations of 13-cis- and all-trans-retinoic acids yielded 5.3 +/- 2.43 nmol/l and 11.8 +/- 3.3 nmol/l, respectively (mean +/- SD). The method has been successfully applied to the analysis of both isomers in serum from patients with idiopathic skeletal hyperostosis in whom, the 13-cis- as well as all-trans-retinoic acid levels were raised as compared to the control group.

The Effect of Bornyl cis-4-Hydroxycinnamate on Melanoma Cell Apoptosis Is Associated with Mitochondrial Dysfunction and Endoplasmic Reticulum Stress

PubMed Central

Yang, Tzu-Yen; Wu, Yu-Jen; Chang, Chi-I; Wu, Mei-Li

2018-01-01

Bornyl cis-4-hydroxycinnamate, an active compound isolated from Piper betle stems, was investigated in terms of its effects on A2058 and A375 melanoma cell proliferation and protein expression in this study. We used flow cytometric analysis to examine the early stages of apoptosis induced by bornyl cis-4-hydroxycinnamate in the two melanoma cell lines and employed comparative proteomic analysis to investigate the effects of this compound on protein expression in A375 cells. Master maps generated by PDQuest software from two-dimensional electrophoresis (2-DE) analysis of A375 cells showed that the expression levels of 35 proteins were significantly altered, with 18 proteins upregulated and 17 downregulated. The proteomics study identified several proteins that are involved in mitochondrial dysfunction and endoplasmic reticulum stress (ER stress), in addition to apoptosis-associated proteins, including prohibitin, hypoxia-upregulated protein 1, stress 70 protein, 78 kDa glucose-regulated protein (GRP78), and protein deglycase DJ-1 (protein DJ-1) in melanoma cells exposed to bornyl cis-4-hydroxycinnamate. The treatment also resulted in a marked decline of the mitochondrial membrane potential, in cytochrome C release into the cytosol, in the activation of Bcl-2-associated X protein (Bax), Bcl-2-associated death promoter protein (Bad), caspase-3, and caspase-9, and in the decreased expression of p-Bad, B-cell lymphoma 2 (Bcl-2), Bcl-xl, and induced myeloid leukemia cell differentiation protein-1 (Mcl-1), indicating that apoptosis induced by bornyl cis-4-hydroxycinnamate was mediated by the mitochondria through the caspase-dependent pathway. Also, salubrinal (an eukaryotic initiation factor 2α inhibitor; eIF2α inhibitor) was able to protect the cells from bornyl cis-4-hydroxycinnamate-induced apoptosis. Bornyl cis-4-hydroxycinnamate-related cell death also implied that the protein kinase R-like endoplasmic reticulum kinase (PERK)–eIF2α–ATF4–CHOP signal pathways

Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript.

PubMed

Fedak, Halina; Palusinska, Malgorzata; Krzyczmonik, Katarzyna; Brzezniak, Lien; Yatusevich, Ruslan; Pietras, Zbigniew; Kaczanowski, Szymon; Swiezewski, Szymon

2016-11-29

Seed dormancy is one of the most crucial process transitions in a plant's life cycle. Its timing is tightly controlled by the expression level of the Delay of Germination 1 gene (DOG1). DOG1 is the major quantitative trait locus for seed dormancy in Arabidopsis and has been shown to control dormancy in many other plant species. This is reflected by the evolutionary conservation of the functional short alternatively polyadenylated form of the DOG1 mRNA. Notably, the 3' region of DOG1, including the last exon that is not included in this transcript isoform, shows a high level of conservation at the DNA level, but the encoded polypeptide is poorly conserved. Here, we demonstrate that this region of DOG1 contains a promoter for the transcription of a noncoding antisense RNA, asDOG1, that is 5' capped, polyadenylated, and relatively stable. This promoter is autonomous and asDOG1 has an expression profile that is different from known DOG1 transcripts. Using several approaches we show that asDOG1 strongly suppresses DOG1 expression during seed maturation in cis, but is unable to do so in trans Therefore, the negative regulation of seed dormancy by asDOG1 in cis results in allele-specific suppression of DOG1 expression and promotes germination. Given the evolutionary conservation of the asDOG1 promoter, we propose that this cis-constrained noncoding RNA-mediated mechanism limiting the duration of seed dormancy functions across the Brassicaceae.

Zirconium-doped magnetic microspheres for the selective enrichment of cis-diol-containing ribonucleosides.

PubMed

Fan, Hua; Chen, Peihong; Wang, Chaozhan; Wei, Yinmao

2016-05-27

Zirconium-doped magnetic microspheres (Zr-Fe3O4) for the selective enrichment of cis-diol-containing biomolecules were easily synthesized via a one-step hydrothermal method. Characterization of the microspheres revealed that zirconium was successfully doped into the lattice of Fe3O4 at a doping level of 4.0 at%. Zr-Fe3O4 possessed good magnetic properties and high specificity towards cis-diol molecules, as shown using 28 compounds. For ribonucleosides, the adsorbent not only has favorable anti-interferential abilities but also has a high adsorption capacity up to 159.4μmol/g. As an example of a real application, four ribonucleosides in urine were efficiently enriched and detected via magnetic solid-phase extraction coupled with high-performance liquid chromatography. Under the optimized extraction conditions, the detection limits were determined to be between 0.005 and 0.017μg/mL, and the linearities ranged from 0.02 to 5.00μg/mL (R≥0.996) for these analytes. The accuracy of the analytical method was examined by studying the relative recoveries of the analytes in real urine samples, with recoveries varying from 77.8% to 119.6% (RSDs<10.6%, n=6). The results indicate that Zr-Fe3O4 is a suitable adsorbent for the analysis of cis-diol-containing biomolecules in practical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

CIS-lunar space infrastructure lunar technologies: Executive summary