Journal articles: 'Heavy Element Containing Molecules'

1

Thomas, Reji, and Nobuyuki Tamaoki. "Determination of the absolute stereostructure of a cyclic azobenzene from the crystal structure of the precursor containing a heavy element." Beilstein Journal of Organic Chemistry 12 (October 19, 2016): 2211–15. http://dx.doi.org/10.3762/bjoc.12.212.

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Single crystal X-ray diffraction has been used as one of the common methods for the unambiguous determination of the absolute stereostructure of chiral molecules. However, this method is limited to molecules containing heavy atoms or to molecules with the possibility of functionalization with heavy elements or chiral internal references. Herein, we report the determination of the absolute stereostructure of the enantiomers of molecule (E)-2, which lacks the possibility of functionalization, using a reverse method, i.e., defunctionalization of its precursor of known stereostructure with bromine substitution (S-(−)-(E)-1). A reductive debromination of S-(−)-(E)-1 results in formation of one of the enantiomers of (E)-2. Using a combination of HPLC and CD spectroscopy we could safely assign the stereostructure of one of the enantiomers of (E)-2, the reduced product R-(−)-(E)-1.

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2

Scott, Gregory E., and Karl K. Irikura. "Electron-Impact Ionization Cross Sections of Molecules Containing Heavy Elements (Z> 10)." Journal of Chemical Theory and Computation 1, no. 6 (November 2005): 1153–61. http://dx.doi.org/10.1021/ct050077j.

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3

Bazett-Jones, D. P., and M. J. Hendzel. "High resolution mapping of nucleic acid containing complexes in vitro and in situ." Proceedings, annual meeting, Electron Microscopy Society of America 54 (August 11, 1996): 48–49. http://dx.doi.org/10.1017/s0424820100162703.

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Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.

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Bischoff, Florian A., Sebastian Höfener, Andreas Glöß, and Wim Klopper. "Explicitly correlated second-order perturbation theory calculations on molecules containing heavy main-group elements." Theoretical Chemistry Accounts 121, no. 1-2 (April 8, 2008): 11–19. http://dx.doi.org/10.1007/s00214-008-0441-8.

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Wang, Fan, and Lemin Li. "Numerical examination of performance of some exchange-correlation functionals for molecules containing heavy elements." Journal of Computational Chemistry 25, no. 5 (2004): 669–77. http://dx.doi.org/10.1002/jcc.10421.

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Oura, M., T. Gejo, K. Nagaya, Y. Kohmura, K. Tamasaku, L. Journel, M. N. Piancastelli, and M. Simon. "Hard x-ray photoelectron spectroscopy on heavy atoms and heavy-element containing molecules using synchrotron radiation up to 35 keV at SPring-8 undulator beamlines." New Journal of Physics 21, no. 4 (April 12, 2019): 043015. http://dx.doi.org/10.1088/1367-2630/ab09a3.

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Andreocci, Marco V., Carla Cauletti, Stefano Stranges, Bernd Wrackmeyer, and Carin Stader. "UV Photoelectron Spectra and Pseudopotential “ab initio” Calculations of Some 4-Membered Cyclic Amides of Group XIV Elements." Zeitschrift für Naturforschung B 46, no. 1 (January 1, 1991): 39–46. http://dx.doi.org/10.1515/znb-1991-0109.

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Gas-phase He I and He II photoelectron spectroscopy and Pseudopotential “ab initio” calculations were used to determine the electronic structure of some 4-membered cyclic amides containing Si, Sn and Pb.The IE splitting on the non-bonding nitrogen-localized m .o .s ., nNasym(a2) and nNsym(b2), due to the “through space” interaction is critically affected by the planar ring molecular structure and the coordination of the silicon and tin atoms of the ring.The pseudopotential “ab initio” model resulted successful in describing the electronic structure of the molecules containing heavy atoms, at a Koopmans’ approximation level.

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Lloyd, Austin, Helen Moylan, and Joseph McDouall. "Modelling the Effect of Zero-Field Splitting on the 1H, 13C and 29Si Chemical Shifts of Lanthanide and Actinide Compounds." Magnetochemistry 5, no. 1 (January 11, 2019): 3. http://dx.doi.org/10.3390/magnetochemistry5010003.

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The prediction of paramagnetic NMR (pNMR) chemical shifts in molecules containing heavy atoms presents a significant challenge to computational quantum chemistry. The importance of meeting this challenge lies in the central role that NMR plays in the structural characterisation of chemical systems. Hence there is a need for reliable assignment and prediction of chemical shifts. In a previous study [Trends in Physical Chemistry, 17, 25–57, (2017)] we looked at the computation of pNMR chemical shifts in lanthanide and actinide complexes using a spin Hamiltonian approach. In that study we were principally concerned with molecules with S = 1/2 ground states. In the present work we extend that study by looking at the effect of zero field splitting (ZFS) for six complexes with S = 3/2 ground states. It is shown that the inclusion of ZFS can produce substantial shifts in the predicted chemical shifts. The computations presented are typically sufficient to enable assignment of experimental spectra. However for one case, in which the peaks are closely clustered, the inclusion of ZFS re-orders the chemical shifts making assignment quite difficult. We also observe, and echo, the previously reported importance of including the paramagnetic spin-orbit hyperfine interaction for 13 C and 29 Si atoms, when these are directly bound to a heavy element and thus subject to heavy-atom-light-atom effects. The necessary computations are very demanding, and more work is needed to find theoretical and computational approaches that simplify the evaluation of this term. We discuss the computation of each term required in the spin Hamiltonian. The systems we study in this work are restricted to a single heavy atom ion (one Nd(III) and five U(III) complexes), but typify some of the computational complexity encountered in lanthanide and actinide containing molecules.

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Gaul, Konstantin, and Robert Berger. "Quasi-relativistic study of nuclear electric quadrupole coupling constants in chiral molecules containing heavy elements." Molecular Physics 118, no. 19-20 (August 3, 2020): e1797199. http://dx.doi.org/10.1080/00268976.2020.1797199.

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10

Märkl, Raphael S., Nuri Hohn, Emanuel Hupf, Lorenz Bießmann, Volker Körstgens, Lucas P. Kreuzer, Gaetano Mangiapia, et al. "Comparing the backfilling of mesoporous titania thin films with hole conductors of different sizes sharing the same mass density." IUCrJ 7, no. 2 (February 12, 2020): 268–75. http://dx.doi.org/10.1107/s2052252520000913.

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Efficient infiltration of a mesoporous titania matrix with conducting organic polymers or small molecules is one key challenge to overcome for hybrid photovoltaic devices. A quantitative analysis of the backfilling efficiency with time-of-flight grazing incidence small-angle neutron scattering (ToF-GISANS) and scanning electron microscopy (SEM) measurements is presented. Differences in the morphology due to the backfilling of mesoporous titania thin films are compared for the macromolecule poly[4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)benzo[1,2-b;4,5-b′]dithiophene-2,6-diyl-alt-(4-(2-ethylhexyl)-3-fluorothieno[3,4-b]thiophene-)-2-carboxylate-2-6-diyl)] (PTB7-Th) and the heavy-element containing small molecule 2-pinacolboronate-3-phenylphenanthro[9,10-b]tellurophene (PhenTe-BPinPh). Hence, a 1.7 times higher backfilling efficiency of almost 70% is achieved for the small molecule PhenTe-BPinPh compared with the polymer PTB7-Th despite sharing the same volumetric mass density. The precise characterization of structural changes due to backfilling reveals that the volumetric density of backfilled materials plays a minor role in obtaining good backfilling efficiencies and interfaces with large surface contact.

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11

Johnson, D. R., and J. S. Pober. "HLA class I heavy-chain gene promoter elements mediating synergy between tumor necrosis factor and interferons." Molecular and Cellular Biology 14, no. 2 (February 1994): 1322–32. http://dx.doi.org/10.1128/mcb.14.2.1322.

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The cytokines tumor necrosis factor (TNF), beta interferon (IFN-beta), and IFN-gamma increase major histocompatibility complex class I molecule expression. A greater than additive (i.e., synergistic) induction of class I heavy-chain mRNA is observed in HeLa cells treated with TNF in combination with either type of IFN. To define the cis-acting elements mediating cytokine synergy, the promoter of a human major histocompatibility complex class I heavy-chain gene (HLA-B7) was placed in front of a reporter gene and transfected into HeLa cells. Deletion analysis mapped the elements required for synergy to a 40-bp region containing a kappa B-like element, which is necessary for the response to TNF, and an interferon consensus sequence (ICS), which is necessary for the responses to IFNs. When the orientation of these elements was reversed or their normal 20-bp spacing was reduced by 5 or 10 bp, i.e., one half or one full turn of the DNA helix, essentially equivalent responses were obtained, suggesting that these parameters are not critical. In electromobility shift assays, a p50-containing NF-kappa B nuclear factor from TNF-treated cells binds kappa B-containing probes, and ISGF-2 from IFN-gamma-treated cells binds ICS-containing probes. A probe containing both the kappa B and ICS elements (kappa B-ICS) forms a novel complex with nuclear factors isolated from cells treated with both TNF and IFN-gamma; this complex also forms when nuclear factors from individually cytokine-treated cells are mixed in vitro. The natural variant ICS found in HLA-A responds to IFN-gamma and can mediate synergy with TNF. However, the variant kappa B found in HLA-C does not respond to TNF, nor can it mediate synergy between TNF and IFN-gamma. These observations suggest that synergy between TNF and IFNs in the induction of HLA class I gene expression results from the sum of individual interactions of cytokine-activated enhancer-binding factors with the transcription initiation complex.

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Johnson, D. R., and J. S. Pober. "HLA class I heavy-chain gene promoter elements mediating synergy between tumor necrosis factor and interferons." Molecular and Cellular Biology 14, no. 2 (February 1994): 1322–32. http://dx.doi.org/10.1128/mcb.14.2.1322-1332.1994.

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The cytokines tumor necrosis factor (TNF), beta interferon (IFN-beta), and IFN-gamma increase major histocompatibility complex class I molecule expression. A greater than additive (i.e., synergistic) induction of class I heavy-chain mRNA is observed in HeLa cells treated with TNF in combination with either type of IFN. To define the cis-acting elements mediating cytokine synergy, the promoter of a human major histocompatibility complex class I heavy-chain gene (HLA-B7) was placed in front of a reporter gene and transfected into HeLa cells. Deletion analysis mapped the elements required for synergy to a 40-bp region containing a kappa B-like element, which is necessary for the response to TNF, and an interferon consensus sequence (ICS), which is necessary for the responses to IFNs. When the orientation of these elements was reversed or their normal 20-bp spacing was reduced by 5 or 10 bp, i.e., one half or one full turn of the DNA helix, essentially equivalent responses were obtained, suggesting that these parameters are not critical. In electromobility shift assays, a p50-containing NF-kappa B nuclear factor from TNF-treated cells binds kappa B-containing probes, and ISGF-2 from IFN-gamma-treated cells binds ICS-containing probes. A probe containing both the kappa B and ICS elements (kappa B-ICS) forms a novel complex with nuclear factors isolated from cells treated with both TNF and IFN-gamma; this complex also forms when nuclear factors from individually cytokine-treated cells are mixed in vitro. The natural variant ICS found in HLA-A responds to IFN-gamma and can mediate synergy with TNF. However, the variant kappa B found in HLA-C does not respond to TNF, nor can it mediate synergy between TNF and IFN-gamma. These observations suggest that synergy between TNF and IFNs in the induction of HLA class I gene expression results from the sum of individual interactions of cytokine-activated enhancer-binding factors with the transcription initiation complex.

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13

Kepert, David L., Peter C. Junk, Brian W. Skelton, and Allan H. White. "Structural Systematics of Rare Earth Complexes. XIII (‘Maximally’) Hydrated (Heavy) Rare Earth Nitrates." Australian Journal of Chemistry 52, no. 6 (1999): 497. http://dx.doi.org/10.1071/ch98044.

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Room-temperature single-crystal X-ray structure determinations are known for a number of ‘maximally hydrated" nitrates of, in particular, the lighter lanthanoid elements; in all cases, all nitrates coordinate as O,O′-bidentate ligands so that the series may be represented at the outset as Ln(O2NO)3.x H2O. Two distinct triclinic P 1 hexahydrate phases of similar cell dimensions are recognized, the most distinctive distinguishing feature being that in the La, Ce phase the 11-coordinate Ln is surrounded by three O,O′-bidentate nitrate and five O-unidentate water molecule ligands; the domain of the other, with four coordinated water molecules, extends from Ln = Pr to Ln = Dy (inclusive of Y). At local ambience, we have crystallized heavier members of the series as pentahydrates, isomorphous with the previously characterized Ln = Eu example, also containing a molecule of the form [Ln(O2NO)3(OH2)4] (with a molecule of water of crystallization), but a different stereoisomer to that found in the Ln = Pr(-)Dy array. Structure determinations are recorded for Ln = Dy, Er, Yb, conventional R on |F| 0·042, 0·034, 0·029 for No = 3858, 3980, 3935 independent ‘observed’ (I > 3σ(I)) diffractometer reflections. For Ln = Lu a new tetrahydrate phase is described, monoclinic P21/n, a 7·379(7), b 10·364(5), c 14·26(1) Å, β 96·09(7)°, Z = 4, R 0·048 for No 2324, together with a new triclinic P 1 trihydrate, a 12·591(4), b 12·144(3), c 7·355(2) Å, α 80·22(2), β 77·68(3), γ 62·30(2)°, Z = 4, R 0·051 for No 4552. In both of the latter, Lu is nine-coordinate, with three bidentate nitrate groups and three coordinated water molecules; remarkably, the two independent molecules of the asymmetric unit in the triclinic phase are distinct isomers, one having the water molecules fac, derivative of the 10-coordinate array of the Pr(-)Yb series with quasi-3 symmetry, while the other, like that in the monoclinic phase, is mer.

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Mongkolrattanothai, Kanokporn, Susan Boyle, Trudy V. Murphy, and Robert S. Daum. "Novel Non-mecA-Containing Staphylococcal Chromosomal Cassette Composite Island Containing pbp4 and tagF Genes in a Commensal Staphylococcal Species: a Possible Reservoir for Antibiotic Resistance Islands in Staphylococcus aureus." Antimicrobial Agents and Chemotherapy 48, no. 5 (May 2004): 1823–36. http://dx.doi.org/10.1128/aac.48.5.1823-1836.2004.

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ABSTRACT Among methicillin-resistant Staphylococcus aureus isolates, a staphylococcal chromosomal cassette containing the mecA gene (SCCmec) is integrated into the chromosome at a unique site. SCCmec also contains unique ccrAB recombinase genes mediating its integration and excision from the genome and is flanked by characteristic left and right direct- and inverted-repeat sequences. A few non-mecA-containing SCC elements that have the other molecular features described above have recently been described. The origin of these cassettes is not clear. We have identified two new members of the SCC family integrated within orfX in Staphylococcus epidermidis strain ATCC 12228, neither of which carries mecA. One is a 57-kb element flanked by a unique 28-bp SCC direct repeat. It was called the SCC composite island (SCC-CI) because it carries a 19-kb SCC element (SCCpbp4) nested within it. SCCpbp4 contains pbp4 and tagF genes, as well as one pair of ccrAB genes (allotype 2) flanked by classical SCC-specific terminal repeats. External to SCCpbp4, SCC-CI contains a second pair of ccrAB genes (allotype 4), three IS431 elements, and genes mediating resistance to heavy metals. Genes mediating restriction-modification that may facilitate horizontal transfer are also present within SCC-CI, both within and outside SCCpbp4. Several novel arrangements of the SCC direct and inverted repeats were identified. Several long stretches of homology with other SCCs were found within and outside SCCpbp4. In view of the fact that SCC-CI was found in a commensal species, it may represent a reservoir for sequences involved in genetic shuffling between staphylococci and may contribute to the diversity found in SCC elements.

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Colovic, Mirjana B., Vesna M. Vasic, Dragan M. Djuric, and Danijela Z. Krstic. "Sulphur-containing Amino Acids: Protective Role Against Free Radicals and Heavy Metals." Current Medicinal Chemistry 25, no. 3 (January 30, 2018): 324–35. http://dx.doi.org/10.2174/0929867324666170609075434.

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Background: Sulphur is an abundant element in biological systems, which plays an important role in processes essential for life as a constituent of proteins, vitamins and other crucial biomolecules. The major source of sulphur for humans is plants being able to use inorganic sulphur in the purpose of sulphur-containing amino acids synthesis. Sulphur-containing amino acids include methionine, cysteine, homocysteine, and taurine. Methionine and cysteine are classified as proteinogenic, canonic amino acids incorporated in protein structure. Sulphur amino acids are involved in the synthesis of intracellular antioxidants such as glutathione and N-acetyl cysteine. Moreover, naturally occurring sulphur-containing ligands are effective and safe detoxifying agents, often used in order to prevent toxic metal ions effects and their accumulation in human body. Methods: Literature search for peer-reviewed articles was performed using PubMed and Scopus databases, and utilizing appropriate keywords. Results: This review is focused on sulphur-containing amino acids – methionine, cysteine, taurine, and their derivatives – glutathione and N-acetylcysteine, and their defense effects as antioxidant agents against free radicals. Additionally, the protective effects of sulphur-containing ligands against the toxic effects of heavy and transition metal ions, and their reactivation role towards the enzyme inhibition are described. Conclusion: Sulphur-containing amino acids represent a powerful part of cell antioxidant system. Thus, they are essential in the maintenance of normal cellular functions and health. In addition to their worthy antioxidant action, sulphur-containing amino acids may offer a chelating site for heavy metals. Accordingly, they may be supplemented during chelating therapy, providing beneficial effects in eliminating toxic metals.

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Matsumura, Mio, Yuki Matsuhashi, Masato Kawakubo, Tadashi Hyodo, Yuki Murata, Masatoshi Kawahata, Kentaro Yamaguchi, and Shuji Yasuike. "Synthesis, Structural Characterization, and Optical Properties of Benzene-Fused Tetracyclic and Pentacyclic Stiboles." Molecules 26, no. 1 (January 4, 2021): 222. http://dx.doi.org/10.3390/molecules26010222.

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The expectation that antimony (Sb) compounds should display phosphorescence emissions based on the “heavy element effect” prompted our interest in the introduction of antimony to a biaryl as the bridging atom in a fused heterole system. Herein, the synthesis, molecular structures, and optical properties of novel benzene-fused heteroacenes containing antimony or arsenic atoms are described. The stiboles and arsole were prepared by the condensation of dibromo(phenyl)stibane or dichloro(phenyl)arsine with dilithium intermediates derived from the corresponding dibromo compounds. Nuclear magnetic resonance (NMR) spectroscopy and X-ray crystal analysis revealed that the linear pentacyclic stibole was highly symmetric in both the solution and crystal states. In contrast, the curved pentacyclic stibole adopted a helical structure in solution, and surprisingly, only M helical molecules were crystallized from the racemate. All synthesized compounds produced very weak or no emissions at room temperature or in the solid state. In contrast, the linear penta- and tetracyclic stiboles exhibited clear phosphorescence emissions in the CHCl3 frozen matrix at 77 K under aerobic conditions.

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17

Erman, Batu, Marta Cortes, Barbara S. Nikolajczyk, Nancy A. Speck, and Ranjan Sen. "ETS-Core Binding Factor: a Common Composite Motif in Antigen Receptor Gene Enhancers." Molecular and Cellular Biology 18, no. 3 (March 1, 1998): 1322–30. http://dx.doi.org/10.1128/mcb.18.3.1322.

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ABSTRACT A tripartite domain of the murine immunoglobulin μ heavy-chain enhancer contains the μA and μB elements that bind ETS proteins and the μE3 element that binds leucine zipper-containing basic helix-loop-helix (bHLH-zip) factors. Analysis of the corresponding region of the human μ enhancer revealed high conservation of the μA and μB motifs but a striking absence of the μE3 element. Instead of bHLH-zip proteins, we found that the human enhancer bound core binding factor (CBF) between the μA and μB elements; CBF binding was shown to be a common feature of both murine and human enhancers. Furthermore, mutant enhancers that bound prototypic bHLH-zip proteins but not CBF did not activate transcription in B cells, and conversely, CBF transactivated the murine enhancer in nonlymphoid cells. Taking these data together with the earlier analysis of T-cell-specific enhancers, we propose that ETS-CBF is a common composite element in the regulation of antigen receptor genes. In addition, these studies identify the first B-cell target of CBF, a protein that has been implicated in the development of childhood pre-B-cell leukemias.

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18

Oleynichenko, Alexander V., Andréi Zaitsevskii, Leonid V. Skripnikov, and Ephraim Eliav. "Relativistic Fock Space Coupled Cluster Method for Many-Electron Systems: Non-Perturbative Account for Connected Triple Excitations." Symmetry 12, no. 7 (July 2, 2020): 1101. http://dx.doi.org/10.3390/sym12071101.

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The Fock space relativistic coupled cluster method (FS-RCC) is one of the most promising tools of electronic structure modeling for atomic and molecular systems containing heavy nuclei. Until recently, capabilities of the FS-RCC method were severely restricted by the fact that only single and double excitations in the exponential parametrization of the wave operator were considered. We report the design and the first computer implementation of FS-RCC schemes with full and simplified non-perturbative account for triple excitations in the cluster operator. Numerical stability of the new computational scheme and thus its applicability to a wide variety of molecular electronic states is ensured using the dynamic shift technique combined with the extrapolation to zero-shift limit. Pilot applications to atomic (Tl, Pb) and molecular (TlH) systems reported in the paper indicate that the breakthrough in accuracy and predictive power of the electronic structure calculations for heavy-element compounds can be achieved. Moreover, the described approach can provide a firm basis for high-precision modeling of heavy molecular systems with several open shells, including actinide compounds.

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19

Gupta, Madhu, Radovan Zak, Towia A. Libermann, and Mahesh P. Gupta. "Tissue-Restricted Expression of the Cardiac α-Myosin Heavy Chain Gene Is Controlled by a Downstream Repressor Element Containing a Palindrome of Two Ets-Binding Sites." Molecular and Cellular Biology 18, no. 12 (December 1, 1998): 7243–58. http://dx.doi.org/10.1128/mcb.18.12.7243.

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ABSTRACT The expression of the α-myosin heavy chain (MHC) gene is restricted primarily to cardiac myocytes. To date, several positive regulatory elements and their binding factors involved in α-MHC gene regulation have been identified; however, the mechanism restricting the expression of this gene to cardiac myocytes has yet to be elucidated. In this study, we have identified by using sequential deletion mutants of the rat cardiac α-MHC gene a 30-bp purine-rich negative regulatory (PNR) element located in the first intronic region that appeared to be essential for the tissue-specific expression of the α-MHC gene. Removal of this element alone elevated (20- to 30-fold) the expression of the α-MHC gene in cardiac myocyte cultures and in heart muscle directly injected with plasmid DNA. Surprisingly, this deletion also allowed a significant expression of the α-MHC gene in HeLa and other nonmuscle cells, where it is normally inactive. The PNR element required upstream sequences of the α-MHC gene for negative gene regulation. By DNase I footprint analysis of the PNR element, a palindrome of two high-affinity Ets-binding sites (CTTCCCTGGAAG) was identified. Furthermore, by analyses of site-specific base-pair mutation, mobility gel shift competition, and UV cross-linking, two different Ets-like proteins from cardiac and HeLa cell nuclear extracts were found to bind to the PNR motif. Moreover, the activity of the PNR-binding factor was found to be increased two- to threefold in adult rat hearts subjected to pressure overload hypertrophy, where the α-MHC gene is usually suppressed. These data demonstrate that the PNR element plays a dual role, both downregulating the expression of the α-MHC gene in cardiac myocytes and silencing the muscle gene activity in nonmuscle cells. Similar palindromic Ets-binding motifs are found conserved in the α-MHC genes from different species and in other cardiac myocyte-restricted genes. These results are the first to reveal a role of the Ets class of proteins in controlling the tissue-specific expression of a cardiac muscle gene.

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Scott, Gregory E., and Karl K. Irikura. "Performance of binary-encounter-Bethe (BEB) theory for electron-impact ionization cross sections of molecules containing heavy elements (Z > 10)." Surface and Interface Analysis 37, no. 11 (2005): 973–77. http://dx.doi.org/10.1002/sia.2091.

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21

Culotta, V. C., and D. H. Hamer. "Fine mapping of a mouse metallothionein gene metal response element." Molecular and Cellular Biology 9, no. 3 (March 1989): 1376–80. http://dx.doi.org/10.1128/mcb.9.3.1376-1380.1989.

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Metal-regulated transcription of metallothionein (MT) genes in higher eucaryotes involves multiple copies of a highly conserved 17-base-pair metal-regulatory element (MRE). We have assayed by transient transfection the ability of mouse MT-I element d (MREd) to confer metal responsivity to constructs containing the mouse MT-I TATA box and the bacterial chloramphenicol acetyltransferase indicator gene. A single copy of MREd works bidirectionally to afford a three- to fourfold induction, and dual copies act cooperatively to yield a 10- to 20-fold response. Element d responds to the same spectrum of heavy metals as doses the complete MT gene promoter. The sequences involved in induction by metals were delineated by analyzing point mutations in MREd. While nucleotides of the highly conserved core sequence TGCPuCXC are critical, substitutions in the less conserved regions affect the induction response only marginally. These sequences include residues of a potential Sp1-binding site, suggesting that if Sp1 binds to MREd, it has little if any role in induction by metals.

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22

Felli, M. P., A. Vacca, D. Meco, I. Screpanti, A. R. Farina, M. Maroder, S. Martinotti, E. Petrangeli, L. Frati, and A. Gulino. "Retinoic acid-induced down-regulation of the interleukin-2 promoter via cis-regulatory sequences containing an octamer motif." Molecular and Cellular Biology 11, no. 9 (September 1991): 4771–78. http://dx.doi.org/10.1128/mcb.11.9.4771-4778.1991.

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Retinoic acid (RA) is known to influence the proliferation and differentiation of a wide variety of transformed and developing cells. We found that RA and the specific RA receptor (RAR) ligand Ch55 inhibited the phorbol ester and calcium ionophore-induced expression of the T-cell growth factor interleukin-2 (IL-2) gene. Expression of transiently transfected chloramphenicol acetyltransferase vectors containing the 5'-flanking region of the IL-2 gene was also inhibited by RA. RA-induced down-regulation of the IL-2 enhancer is mediated by RAR, since overexpression of transfected RARs increased RA sensitivity of the IL-2 promoter. Functional analysis of chloramphenicol acetyltransferase vectors containing either internal deletion mutants of the region from -317 to +47 bp of the IL-2 enhancer or multimerized cis-regulatory elements showed that the RA-responsive element in the IL-2 promoter mapped to sequences containing an octamer motif. RAR also inhibited the transcriptional activity of the octamer motif of the immunoglobulin heavy chain enhancer. In spite of the transcriptional inhibition of the IL-2 octamer motif, RA did not decrease the in vitro DNA-binding capability of octamer-1 protein. These results identify a regulatory pathway within the IL-2 promoter which involves the octamer motif and RAR.

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Jacobs, Y., X. Q. Xin, K. Dorshkind, and C. Nelson. "Pan/E2A expression precedes immunoglobulin heavy-chain expression during B lymphopoiesis in nontransformed cells, and Pan/E2A proteins are not detected in myeloid cells." Molecular and Cellular Biology 14, no. 6 (June 1994): 4087–96. http://dx.doi.org/10.1128/mcb.14.6.4087-4096.1994.

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A newly developed rat long-term bone marrow culture system was used to study the role of Pan/E2A basic helix-loop-helix transcription factors during B-cell development. In this system, B-lymphocyte progenitors actively differentiate into mature B cells. Monoclonal (Yae) and polyclonal (anti-Pan) antibodies were employed to characterize the expression of Pan proteins by Western blot assay during hematopoiesis and to examine the components of immunoglobulin heavy-chain gene enhancer element-binding species by electrophoretic mobility shift assay. During B-cell development, the appearance of Pan/E2A proteins preceded the expression of immunoglobulin heavy-chain protein. A Pan-containing immunoglobulin heavy-chain enhancer element (mu E5)-binding species (BCF1), composed of immunoreactive Pan-1/E47 but not Pan-2/E12, was observed concomitantly with the detection of Pan/E2A proteins. In addition to BCF1, other mu E5-binding species were detected which were not recognized by the Yae antibody. Two of these species were present in primary B-lymphocyte and myeloid cultures and were recognized by an anti-upstream stimulatory factor antiserum. Although Pan/E2A proteins have been proposed to be ubiquitous, Pan/E2A proteins were not detected in primary myeloid cultures composed mainly of granulocytes and macrophages or in the macrophage cell line J774. The absence of Pan/E2A proteins in differentiated myeloid cells correlated with low steady-state levels of Pan/E2A RNA. However, Pan/E2A proteins were present in a promyeloid cell line, 32DCL3, suggesting that extinction of Pan/E2A expression may play a role in myelopoiesis.

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Varshney, U., N. Jahroudi, R. Foster, and L. Gedamu. "Structure, organization, and regulation of human metallothionein IF gene: differential and cell-type-specific expression in response to heavy metals and glucocorticoids." Molecular and Cellular Biology 6, no. 1 (January 1986): 26–37. http://dx.doi.org/10.1128/mcb.6.1.26-37.1986.

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We describe a human genomic clone containing the metallothionein (MT) IF and MT IG genes. Southern blot analysis and partial DNA sequence determinations show that these genes are organized in a head-to-head fashion and are located approximately 7.0 kilobases apart from each other. Sequence analysis shows that the MT IF gene contains three exons separated by two introns. All of the intron-exon junctions are defined by the GT-AG rule. The 5' flanking region shows the presence of a duplicated metal regulatory element (TGCGC CCGGCCC) important in heavy-metal induction of this gene and a sequence for its basal level expression (GCGGGGCGGGTGCAAAG). The 5' flanking region is also highly G + C rich (approximately 75%) and contains several GC boxes (GGGCGG), probably important in the binding of transcription factors. The TATAA box and the AATAAA sequence are represented by their variants, the TATCAA box and the AATTAA sequence, respectively. This gene is functional and inducible by heavy metals but not by dexamethasone in mouse LMTK- cells after its transfer on a plasmid containing the herpes simplex virus thymidine kinase gene. Further studies on various human cell lines show that this gene is not expressed in a splenic lymphoblastoid cell line (WI-L2) but is expressed in two hepatoma cell lines (Hep 3B2 and Hep G2) in response to cadmium, zinc, and copper. Dexamethasone appears to have no significant effect on its expression. The studies suggest that the MT IF gene shows cell-type-specific expression and is differentially regulated by heavy metals and glucocorticoids.

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Ekker, Marc, Noelle Doyen, Marie Leblond-Francillard, and François Rougeon. "A mouse renin promoter containing the conserved decanucleotide element binds the same B-cell factors as an authentic immunoglobulin heavy chain promoter." FEBS Letters 222, no. 2 (October 5, 1987): 337–40. http://dx.doi.org/10.1016/0014-5793(87)80397-6.

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Wang, Bin, Michael S. Thompson, and Kevin M. Adkins. "Characteristics of the Iron-responsive Element (IRE) Stems in the Untranslated Regions of Animal mRNAs." Open Biochemistry Journal 15, no. 1 (May 3, 2021): 26–37. http://dx.doi.org/10.2174/1874091x02115010026.

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Background: Iron-responsive Elements (IREs) are hairpin structures located in the 5’ or 3’ untranslated region of some animal mRNAs. IREs have a highly conserved terminal loop and a UGC/C or C bulge five bases upstream of the terminal loop, which divides the hairpin stem into an upper stem and a lower stem. Objective: The objective of this study was to investigate the base-pair composition of the upper and lower stems of IREs to determine whether they are highly conserved among mRNAs from different genes. Methods: The mRNA sequences of six 5’IREs and five 3’IREs from several animal species were retrieved from the National Center for Biotechnology Information. The folding free energy of each IRE mRNA sequence was predicted using the RNAfold WebServer. Results: We found that the upper and lower stems of IREs are not highly conserved among the mRNAs of different genes. There are no statistically significant differences in the IRE structures or folding free energies between mammalian and non-mammalian species relative to either the ferritin heavy chain 5’IRE or ferroportin 5’IRE. There are no overall significant differences in the folding free energies between UGC/C-containing 5’IREs and C-bulge-containing 5’IREs, or between 5’IREs and 3’IREs. Conclusion: Further studies are needed to investigate whether the variations in IRE stem composition are responsible for fine-tuning the IRE/Iron-Regulatory Protein interactions among different mRNAs to maintain the balance of cellular iron metabolism, and to identify whether evolutionary processes drive the base-pair composition of the upper and lower stems of IREs toward any particular configuration.

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Nasluzov, Vladimir A., and Notker Rösch. "Density functional based structure optimization for molecules containing heavy elements: analytical energy gradients for the Douglas-Kroll-Hess scalar relativistic approach to the LCGTO-DF method." Chemical Physics 210, no. 3 (October 1996): 413–25. http://dx.doi.org/10.1016/0301-0104(96)00137-1.

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Navankasattusas, S., M. Sawadogo, M. van Bilsen, C. V. Dang, and K. R. Chien. "The basic helix-loop-helix protein upstream stimulating factor regulates the cardiac ventricular myosin light-chain 2 gene via independent cis regulatory elements." Molecular and Cellular Biology 14, no. 11 (November 1994): 7331–39. http://dx.doi.org/10.1128/mcb.14.11.7331-7339.1994.

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Previous studies have documented that 250 bp of the rat cardiac ventricular myosin light-chain 2 (MLC-2v) promoter is sufficient to confer cardiac muscle-specific expression on a luciferase reporter gene in both transgenic mice and primary cultured neonatal rat myocardial cells. Utilizing ligation-mediated PCR to perform in vivo dimethyl sulfate footprinting, the present study has identified protein-DNA interaction within the position from -176 to -165. This region, identified as MLE1, contains a core sequence, CACGTG, which conforms to the consensus E-box site and is identical to the upstream stimulating factor (USF)-binding site of the adenovirus major late promoter. Transient assays of luciferase reporter genes containing point mutations of the site demonstrate the importance of this cis regulatory element in the transcriptional activation of this cardiac muscle gene in ventricular muscle cells. The protein complex that occupies this site is capable of binding to HF-1a and PRE B sites which are known to be required for cardiac muscle-specific expression of rat MLC-2v and alpha-myosin heavy-chain genes, respectively. This study provides direct evidence that USF, a member of the basic helix-loop-helix leucine zipper family, binds to MLE1, HF-1a, and PRE B sites and suggests that it is a component of protein complexes that may coordinately control the expression of MLC-2v and alpha-myosin heavy-chain genes. The current study also provides evidence that USF can positively and negatively regulate the MLC-2v gene via independent cis regulatory elements.

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29

Ghoshal, Kalpana, Sarmila Majumder, Qin Zhu, John Hunzeker, Jharna Datta, Manisha Shah, John F. Sheridan, and Samson T. Jacob. "Influenza Virus Infection Induces Metallothionein Gene Expression in the Mouse Liver and Lung by Overlapping but Distinct Molecular Mechanisms." Molecular and Cellular Biology 21, no. 24 (December 15, 2001): 8301–17. http://dx.doi.org/10.1128/mcb.21.24.8301-8317.2001.

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ABSTRACT Metallothionein I (MT-I) and MT-II have been implicated in the protection of cells against reactive oxygen species (ROS), heavy metals, and a variety of pathological and environmental stressors. Here, we show a robust increase in MT-I/MT-II mRNA level and MT proteins in the livers and lungs of C57BL/6 mice exposed to the influenza A/PR8 virus that infects the upper respiratory tract and lungs. Interleukin-6 (IL-6) had a pronounced effect on the induction of these genes in the liver but not the lung. Treatment of the animals with RU-486, a glucocorticoid receptor antagonist, inhibited induction of MT-I/MT-II in both liver and lung, revealing a direct role of glucocorticoid that is increased upon infection in this induction process. In vivo genomic footprinting (IVGF) analysis demonstrated involvement of almost all metal response elements, major late transcription factor/antioxidant response element (MLTF/ARE), the STAT3 binding site on the MT-I upstream promoter, and the glucocorticoid responsive element (GRE1), located upstream of the MT-II gene, in the induction process in the liver and lung. In the lung, inducible footprinting was also identified at a unique gamma interferon (IFN-γ) response element (γ-IRE) and at Sp1 sites. The mobility shift analysis showed activation of STAT3 and the glucocorticoid receptor in the liver and lung nuclear extracts, which was consistent with the IVGF data. Analysis of the newly synthesized mRNA for cytokines in the infected lung by real-time PCR showed a robust increase in the levels of IL-10 and IFN-γ mRNA that can activate STAT3 and STAT1, respectively. A STAT1-containing complex that binds to the γ-IRE in vitro was activated in the infected lung. No major change in MLTF/ARE DNA binding activity in the liver and lung occurred after infection. These results have demonstrated that MT-I and MT-II can be induced robustly in the liver and lung following experimental influenza virus infection by overlapping but distinct molecular mechanisms.

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Olevska, Yu B., V. I. Olevskyi, K. I. Timchy, and О. V. Olevskyi. "The method of fuzzy determination of the concentration of heavy metals in the atomic absorption spectral analysis of bottom sediments." Computer Modeling: Analysis, Control, Optimization 7, no. 1 (2020): 29–36. http://dx.doi.org/10.32434/2521-6406-2020-1-7-29-36.

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Due to the technogenic impact on the biosphere and its components, a significant amount of heavy metals and radionuclides ends up in the environment. One of the main directions for improving the ecological components of environmental safety is the biotransformation of bottom sediments of reservoirs containing heavy metals, with the help of vermiculture, into biologically safe organic fertilizer. Assessment of the concentration of heavy metals in bottom sediments is an urgent task, the solution of which will allow preserving the natural environment, improving the condition of soils and, as a result, human health. The problem of using bottom deposits in this case is the accuracy of determining the content of various heavy metals in them, which affect the vital activity of earthworms. The gross and mobile forms of heavy metals in experimental substrates can be most accurately determined by atomic absorption spectral analysis. Atomic absorption analysis is a method of analytical chemistry based on the selective absorption of electromagnetic radiation of a certain wavelength by neutral atoms of the element being determined free of all molecular bonds. In the process of absorption, an electron moves from the main energy level to a higher one as a result of photon excitation. In this case, the intensity of the exciting light of a given frequency decreases. Accurate quantification is often hampered by significant matrix interference and non-uniform analyte distribution. To achieve the accuracy and reliability of the method required for vermicultivation, this work proposes a modification of the analysis method by applying fuzzy modeling of the experimental results. From a mathematical point of view, the process of constructing a calibration graph can be implemented using the procedure for constructing a fuzzy scale in the method for decoding the weight of proteins during electrophoresis. An algorithm is described for determining the fuzzy concentration of a metal from the atomic absorption signal data, followed by defuzzification of the obtained fuzzy concentration for analysis and practical use. Keywords: fuzzy modeling, spectral analysis, heavy metals.

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Jaynes, J. B., J. E. Johnson, J. N. Buskin, C. L. Gartside, and S. D. Hauschka. "The muscle creatine kinase gene is regulated by multiple upstream elements, including a muscle-specific enhancer." Molecular and Cellular Biology 8, no. 1 (January 1988): 62–70. http://dx.doi.org/10.1128/mcb.8.1.62-70.1988.

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Muscle creatine kinase (MCK) is induced to high levels during skeletal muscle differentiation. We have examined the upstream regulatory elements of the mouse MCK gene which specify its activation during myogenesis in culture. Fusion genes containing up to 3,300 nucleotides (nt) of MCK 5' flanking DNA in various positions and orientations relative to the bacterial chloramphenicol acetyltransferase (CAT) structural gene were transfected into cultured cells. Transient expression of CAT was compared between proliferating and differentiated MM14 mouse myoblasts and with nonmyogenic mouse L cells. The major effector of high-level expression was found to have the properties of a transcriptional enhancer. This element, located between 1,050 and 1,256 nt upstream of the transcription start site, was also found to have a major influence on the tissue and differentiation specificity of MCK expression; it activated either the MCK promoter or heterologous promoters only in differentiated muscle cells. Comparisons of viral and cellular enhancer sequences with the MCK enhancer revealed some similarities to essential regions of the simian virus 40 enhancer as well as to a region of the immunoglobulin heavy-chain enhancer, which has been implicated in tissue-specific protein binding. Even in the absence of the enhancer, low-level expression from a 776-nt MCK promoter retained differentiation specificity. In addition to positive regulatory elements, our data provide some evidence for negative regulatory elements with activity in myoblasts. These may contribute to the cell type and differentiation specificity of MCK expression.

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Murano, S., R. Thweatt, R. J. Shmookler Reis, R. A. Jones, E. J. Moerman, and S. Goldstein. "Diverse gene sequences are overexpressed in werner syndrome fibroblasts undergoing premature replicative senescence." Molecular and Cellular Biology 11, no. 8 (August 1991): 3905–14. http://dx.doi.org/10.1128/mcb.11.8.3905-3914.1991.

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Genes that play a role in the senescent arrest of cellular replication are likely to be overexpressed in human diploid fibroblasts (HDF) derived from subjects with Werner syndrome (WS) because these cells have a severely curtailed replicative life span. To identify some of these genes, a cDNA library was constructed from WS HDF after they had been serum depleted and repleted (5 days in medium containing 1% serum followed by 24 h in medium containing 20% serum). Differential screening of 7,500 colonies revealed 102 clones that hybridized preferentially with [32P]cDNA derived from RNA of WS cells compared with [32P]cDNA derived from normal HDF. Cross-hybridization and partial DNA sequence determination identified 18 independent gene sequences, 9 of them known and 9 unknown. The known genes included alpha 1(I) procollagen, alpha 2(I) procollagen, fibronectin, ferritin heavy chain, insulinlike growth factor-binding protein-3 (IGFBP-3), osteonectin, human tissue plasminogen activator inhibitor type I, thrombospondin, and alpha B-crystallin. The nine unknown clones included two novel gene sequences and seven additional sequences that contained both novel segments and the Alu class of repetitive short interspersed nuclear elements; five of these seven Alu+ clones also contained the long interpersed nuclear element I (KpnI) family of repetitive elements. Northern (RNA) analysis, using the 18 sequences as probes, showed higher levels of these mRNAs in WS HDF than in normal HDF. Five selected mRNAs studied in greater detail [alpha 1(I) procollagen, fibronectin, insulinlike growth factor-binding protein-3, WS3-10, and WS9-14] showed higher mRNA levels in both WS and late-passage normal HDF than in early-passage normal HDF at various intervals following serum depletion/repletion and after subculture and growth from sparse to high-density confluent arrest. These results indicate that senescence of both WS and normal HDF is accompanied by overexpression of similar sets of diverse genes which may play a role in the senescent arrest of cellular replication and in the genesis of WS, normal biological aging, and attendant diseases.

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Scheurer, Louis, Rebecca R. Das Gupta, Annika Saebisch, Thomas Grampp, Dietmar Benke, Hanns Ulrich Zeilhofer, and Hendrik Wildner. "Expression of immunoglobulin constant domain genes in neurons of the mouse central nervous system." Life Science Alliance 4, no. 11 (August 25, 2021): e202101154. http://dx.doi.org/10.26508/lsa.202101154.

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General consensus states that immunoglobulins are exclusively expressed by B lymphocytes to form the first line of defense against common pathogens. Here, we provide compelling evidence for the expression of two heavy chain immunoglobulin genes in subpopulations of neurons in the mouse brain and spinal cord. RNA isolated from excitatory and inhibitory neurons through ribosome affinity purification revealed Ighg3 and Ighm transcripts encoding for the constant (Fc), but not the variable regions of IgG3 and IgM. Because, in the absence of the variable immunoglobulin regions, these transcripts lack the canonical transcription initiation site used in lymphocytes, we screened for alternative 5′ transcription start sites and identified a novel 5′ exon adjacent to a proposed promoter element. Immunohistochemical, Western blot, and in silico analyses strongly support that these neuronal transcripts are translated into proteins containing four Immunoglobulin domains. Our data thus demonstrate the expression of two Fc-encoding genes Ighg3 and Ighm in spinal and supraspinal neurons of the murine CNS and suggest a hitherto unknown function of the encoded proteins.

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Gimble, J. M., D. Levens, and E. E. Max. "B-cell nuclear proteins binding in vitro to the human immunoglobulin kappa enhancer: localization by exonuclease protection." Molecular and Cellular Biology 7, no. 5 (May 1987): 1815–22. http://dx.doi.org/10.1128/mcb.7.5.1815-1822.1987.

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Proteins capable of interacting with the enhancer of the immunoglobulin kappa gene in vitro have been detected in extracts of nuclei from human B cells and from human, mouse, and rabbit spleens. The experiments, based on an exonuclease protection technique, demonstrate nuclear protein factors binding to a 30- to 35-base-pair domain containing both the simian virus 40 enhancer core element (TTTCCA) and the octamer CAGGTGGC that was previously identified as the consensus sequence for protein-binding sites in the murine immunoglobulin heavy-chain enhancer. This 30- to 35-base-pair domain in the human kappa enhancer is homologous to a site of protein binding detected in the murine kappa enhancer by other investigators using a gel retardation assay. Our results complement in vivo dimethyl sulfate footprinting studies of the human immunoglobulin kappa enhancer which demonstrated B cell-specific changes in guanine reactivity immediately 5' to the consensus octamer. Together, these findings suggest that DNA-binding proteins in B-cell nuclei interact with the 5' portion of the human kappa-gene enhancer. Such proteins could play a role in the B cell-specific transcription of the human immunoglobulin kappa gene.

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35

LUCA, Antonio De, Anna SEVERINO, Paola De PAOLIS, Giuliano COTTONE, Luca De LUCA, Maria De FALCO, Antonio PORCELLINI, Massimo VOLPE, and Gianluigi CONDORELLI. "p300/cAMP-response-element-binding-protein ('CREB')-binding protein (CBP) modulates co-operation between myocyte enhancer factor 2A (MEF2A) and thyroid hormone receptor-retinoid X receptor." Biochemical Journal 369, no. 3 (February 1, 2003): 477–84. http://dx.doi.org/10.1042/bj20020057.

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Thyroid hormone receptors (TRs) and members of the myocyte enhancer factor 2 (MEF2) family are involved in the regulation of muscle-specific gene expression during myogenesis. Physical interaction between these two factors is required to synergistically activate gene transcription. p300/cAMP-response-element-binding-protein ('CREB')-binding protein (CBP) interacting with transcription factors is able to increase their activity on target gene promoters. We investigated the role of p300 in regulating the TR—MEF2A complex. To this end, we mapped the regions of these proteins involved in physical interactions and we evaluated the expression of a chloramphenicol acetyltransferase (CAT) reporter gene in U2OS cells under control of the α-myosin heavy chain promoter containing the thyroid hormone response element (TRE). Our results suggested a role of p300/CBP in mediating the transactivation effects of the TR—retenoid X receptor (RxR)—MEF2A complex. Our findings showed that the same C-terminal portion of p300 binds the N-terminal domains of both TR and MEF2A, and our in vivo studies demonstrated that TR, MEF2A and p300 form a ternary complex. Moreover, by the use of CAT assays, we demonstrated that adenovirus E1A inhibits activation of transcription by TR—RxR—MEF2A—p300 but not by TR—RxR—MEF2A. Our data suggested that p300 can bind and modulate the activity of TR—RxR—MEF2A at TRE. In addition, it is speculated that p300 might modulate the activity of the TR—RxR—MEF2A complex by recruiting a hypothetical endogenous inhibitor which may act like adenovirus E1A.

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Czarnecka, E., R. T. Nagao, J. L. Key, and W. B. Gurley. "Characterization of Gmhsp26-A, a stress gene encoding a divergent heat shock protein of soybean: heavy-metal-induced inhibition of intron processing." Molecular and Cellular Biology 8, no. 3 (March 1988): 1113–22. http://dx.doi.org/10.1128/mcb.8.3.1113-1122.1988.

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We determined the DNA sequence and mapped the corresponding transcripts of a genomic clone containing the Gmhsp26-A gene of soybean. This gene is homologous to the previously characterized cDNA clone pCE54 (E. Czarnecka, L. Edelman, F. Schöffl, and J. L. Key, Plant Mol. Biol. 3:45-58, 1984) and is expressed in response to a wide variety of physiological stresses including heat shock (HS). S1 nuclease mapping of transcripts and a comparison of the cDNA sequence with the genomic sequence indicated the presence of a soybean seedlings with either CdCl2 or CuSO4. Analysis of the 5' termini of transcripts indicated the presence of one major and at least two minor start sites. In each case, initiation occurred 27 to 30 base pairs downstream from a TATA-like motif, and thus each initiation site appears to be promoted by the activity of a separate subpromoter. The three subpromoters are all associated with sequences showing low homology to the HS consensus element of Drosophila melanogaster HS genes and are differentially induced in response to various stresses. Within the carboxyl-terminal half of the protein, hydropathy analysis of the deduced amino acid sequence indicated a high degree of relatedness to the small HS proteins. A comparison of the primary amino acid sequence of hsp26-A with sequences of the small HS proteins suggested that this stress protein is highly diverged and may therefore be specialized for stress adaptation in soybean.

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Jaynes, J. B., J. S. Chamberlain, J. N. Buskin, J. E. Johnson, and S. D. Hauschka. "Transcriptional regulation of the muscle creatine kinase gene and regulated expression in transfected mouse myoblasts." Molecular and Cellular Biology 6, no. 8 (August 1986): 2855–64. http://dx.doi.org/10.1128/mcb.6.8.2855-2864.1986.

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The muscle-specific form of creatine kinase (MCK) is induced in differentiating myoblast cultures, and a dramatic increase in mRNA levels precedes and parallels the increase in MCK protein. To study this induction, the complete MCK gene was cloned and characterized. The transcription unit was shown to span 11 kilobases and to contain seven introns. The splice junctions were identified and shown to conform to the appropriate consensus sequences. Close homology with branchpoint consensuses was found upstream of the 3' splice sites in six of seven cases. Transcriptional regulation of the gene in differentiating myoblast cultures was demonstrated by nuclear run-on experiments; increases in transcription accounted for a major part of the increased mRNA levels. Regulated expression of a transfected MCK gene containing the entire transcription unit with 3.3 kilobases of 5'-flanking sequence was also demonstrated during differentiation of the MM14 mouse myoblast cell line. The MCK 5'-flanking region was sufficient to confer transcriptional regulation to a heterologous structural gene, since chloramphenicol acetyl transferase activity was induced during differentiation of cultures transfected with an MCK-chloramphenicol acetyl transferase fusion construct. Examination of the DNA sequence immediately upstream of the transcription start site revealed a 17-nucleotide element which occurred three times. Comparisons with other muscle-specific genes which are also transcriptionally regulated during myogenesis revealed upstream homologies in the alpha-actin and myosin heavy chain genes, but not in the myosin light-chain genes, with the regions containing these repeats. We suggest that coordinate control of a subset of muscle genes may occur via recognition of these common sequences.

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Lee, John S., Peter Pushko, Michael D. Parker, Mark T. Dertzbaugh, Leonard A. Smith, and Jonathan F. Smith. "Candidate Vaccine against Botulinum Neurotoxin Serotype A Derived from a Venezuelan Equine Encephalitis Virus Vector System." Infection and Immunity 69, no. 9 (September 1, 2001): 5709–15. http://dx.doi.org/10.1128/iai.69.9.5709-5715.2001.

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ABSTRACT A candidate vaccine against botulinum neurotoxin serotype A (BoNT/A) was developed by using a Venezuelan equine encephalitis (VEE) virus replicon vector. This vaccine vector is composed of a self-replicating RNA containing all of the VEE nonstructural genes andcis-acting elements and also a heterologous immunogen gene placed downstream of the subgenomic 26S promoter in place of the viral structural genes. In this study, the nontoxic 50-kDa carboxy-terminal fragment (HC) of the BoNT/A heavy chain was cloned into the replicon vector (HC-replicon). Cotransfection of BHK cells in vitro with the HC-replicon and two helper RNA molecules, the latter encoding all of the VEE structural proteins, resulted in the assembly and release of propagation-deficient, HC VEE replicon particles (HC-VRP). Cells infected with HC-VRP efficiently expressed this protein when analyzed by either immunofluorescence or by Western blot. To evaluate the immunogenicity of HC-VRP, mice were vaccinated with various doses of HC-VRP at different intervals. Mice inoculated subcutaneously with HC-VRP were protected from an intraperitoneal challenge of up to 100,000 50% lethal dose units of BoNT/A. Protection correlated directly with serum enzyme-linked immunosorbent assay titers to BoNT/A. The duration of the immunity achieved was tested at 6 months and at 1 year postvaccination, and mice challenged at these times remained refractory to challenge with BoNT/A.

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Pierani, A., A. Heguy, H. Fujii, and R. G. Roeder. "Activation of octamer-containing promoters by either octamer-binding transcription factor 1 (OTF-1) or OTF-2 and requirement of an additional B-cell-specific component for optimal transcription of immunoglobulin promoters." Molecular and Cellular Biology 10, no. 12 (December 1990): 6204–15. http://dx.doi.org/10.1128/mcb.10.12.6204-6215.1990.

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Several distinct octamer-binding transcription factors (OTFs) interact with the sequence ATTTGCAT (the octamer motif), which acts as a transcription regulatory element for a variety of differentially controlled genes. The ubiquitous OTF-1 plays a role in expression of the cell cycle-regulated histone H2b gene as well as several other genes, while the tissue-specific OTF-2 has been implicated in the tissue-specific expression of immunoglobulin genes. In an attempt to understand the apparent transcriptional selectivity of these factors, we have investigated the physical and functional characteristics of OTF-1 purified from HeLa cells and both OTF-1 and OTF-2 purified from B cells. High-resolution footprinting and mobility shift-competition assays indicated that these factors were virtually indistinguishable in binding affinities and DNA-protein contacts on either the H2b or an immunoglobulin light-chain (kappa) promoter. In addition, each of the purified factors showed an equivalent intrinsic capacity to activate transcription from either immunoglobulin promoters (kappa and heavy chain) or the H2b promoter in OTF-depleted HeLa and B-cell extracts. However, with OTF-depleted HeLa extracts, neither factor could restore immunoglobulin gene transcription to the relatively high level observed in unfractionated B-cell extracts. Restoration of full immunoglobulin gene activity appears to require an additional B-cell regulatory component which interacts with the OTFs. The additional B-cell factor could act either by facilitating interaction of OTF activation domains with components of the general transcriptional machinery or by contributing a novel activation domain.

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40

Calderazzo, Fausto, Antonino Morvillo, Giancarlo Pelizzi, Rinaldo Poli, and Fausto Ungari. "Reactivity of molecules containing element-element bonds. 1. Nontransition elements." Inorganic Chemistry 27, no. 21 (October 1988): 3730–33. http://dx.doi.org/10.1021/ic00294a012.

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Calderazzo, Fausto, Alberto Juris, Rinaldo Poli, and Fausto Ungari. "Reactivity of molecules containing element-element bonds. 2. Transition elements." Inorganic Chemistry 30, no. 6 (March 1991): 1274–79. http://dx.doi.org/10.1021/ic00006a022.

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Sen, Sangita, Avijit Shee, and Debashis Mukherjee. "Inclusion of orbital relaxation and correlation through the unitary group adapted open shell coupled cluster theory using non-relativistic and scalar relativistic Hamiltonians to study the core ionization potential of molecules containing light to medium-heavy elements." Journal of Chemical Physics 148, no. 5 (February 7, 2018): 054107. http://dx.doi.org/10.1063/1.5018086.

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43

Schofield, R. M., J. H. Postlethwait, and H. W. Lefevre. "MeV-ion microprobe analyses of whole Drosophila suggest that zinc and copper accumulation is regulated storage not deposit excretion." Journal of Experimental Biology 200, no. 24 (December 1, 1997): 3235–43. http://dx.doi.org/10.1242/jeb.200.24.3235.

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We examined Drosophila spp. using a penetrative ion microprobe technique that allows us to quantify element contents in whole organs and organisms. Comparatively non-penetrative techniques, such as electron microscopy, could not have been used to make many of these measurements because material is lost during sectioning. We found that zinc was accumulated predominantly within a single organ: in the main segments of both the anterior and posterior Malpighian tubules. In contrast to zinc, iron and copper were more generally distributed throughout the body. Zinc concentrations as high as 2.8 % of dry mass were measured in cell-sized volumes of the Malpighian tubules. The large quantities of zinc (approximately 2x10(-8) g in 8-day-old male adults) were sequestered by an unidentified mechanism. We found less than 1 % of the estimated amount of consumed zinc and copper in the abdomen of flies fed food containing several hundred parts per million dry mass of these metals. Our results are inconsistent with the detoxification hypothesis that predicts that a large proportion of the heavy metals passing through the gut are absorbed and stored permanently. We found for both zinc and copper that the quantity in the abdomen was not proportional to the concentration of these metals in the consumed food but was, instead, relatively invariant. For these reasons, we suggest that regulated biological availability, not detoxification, may be the primary benefit of zinc and copper storage.

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Igel-Mann, G., H. Stoll, and H. Preuss. "Structure and ionization potentials of clusters containing heavy elements." Molecular Physics 80, no. 2 (October 10, 1993): 325–39. http://dx.doi.org/10.1080/00268979300102291.

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Igel-Mann, G., H. Stoll, and H. Preuss. "Structure and ionization potentials of clusters containing heavy elements." Molecular Physics 80, no. 2 (October 10, 1993): 341–54. http://dx.doi.org/10.1080/00268979300102301.

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46

Igel-Mann, Gudrun, and Hermann Stoll. "Structure and ionization potentials of clusters containing heavy elements." Molecular Physics 84, no. 4 (March 1995): 663–78. http://dx.doi.org/10.1080/00268979500100451.

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47

Igel-Mann, Gudrun, Rainer Schlunk, and Hermann Stoll. "Structure and ionization potentials of clusters containing heavy elements." Molecular Physics 84, no. 4 (March 1995): 679–90. http://dx.doi.org/10.1080/00268979500100461.

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48

Liu, Wenjian, and Yunlong Xiao. "Relativistic time-dependent density functional theories." Chemical Society Reviews 47, no. 12 (2018): 4481–509. http://dx.doi.org/10.1039/c8cs00175h.

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The foundations, formalisms, technicalities, and practicalities of relativistic time-dependent density functional theories (R-TD-DFT) for spinor excited states of molecular systems containing heavy elements are critically reviewed.

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49

Pokrovsky, O. S., L. S. Shirokova, J. Viers, V. V. Gordeev, V. P. Shevchenko, A. V. Chupakov, T. Y. Vorobieva, et al. "Transformation of organic carbon, trace element, and organo-mineral colloids in the mixing zone of the largest European Arctic river." Ocean Science Discussions 10, no. 5 (October 15, 2013): 1707–64. http://dx.doi.org/10.5194/osd-10-1707-2013.

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Abstract. The estuarine behavior of organic carbon (OC) and trace elements (TE) was studied for the largest European sub-Arctic river, which is the Severnaya Dvina; this river is a deltaic estuary covered in ice during several hydrological seasons: summer (July 2010, 2012) and winter (March 2009) baseflow, and the November–December 2011 ice-free period. Colloidal forms of OC and TE were assessed using three pore size cutoff (1, 10, and 50 kDa) using an in-situ dialysis procedure. Conventionally dissolved (< 0.22 μm) fractions demonstrated clear conservative behavior for Li, B, Na, Mg, K, Ca, Sr, Mo, Rb, Cs, and U during the mixing of freshwater with the White Sea; a significant (up to a factor of 10) concentration increase occurs with increases in salinity. Si and OC also displayed conservative behavior but with a pronounced decrease of concentration seawards. Rather conservative behavior, but with much smaller changes in concentration (variation within ±30%) over a full range of salinities, was observed for Ti, Ni, Cr, As, Co, Cu, Ga, Y, and heavy REE. Strong non-conservative behavior with coagulation/removal at low salinities (< 5‰) was exhibited by Fe, Al, Zr, Hf, and light REE. Finally, certain divalent metals exhibited non-conservative behavior with a concentration gain at low (~2–5‰, Ba, Mn) or intermediate (~10–15‰, Ba, Zn, Pb, Cd) salinities, which is most likely linked to TE desorption from suspended matter or sediment outflux. The most important result of this study is the elucidation of the behavior of the "truly" dissolved low molecular weight LMW< 1 kDa fraction containing Fe, OC, and a number of insoluble elements. The concentration of the LMW fraction either remains constant or increases its relative contribution to the overall dissolved (< 0.22 μm) pool as the salinity increases. Similarly, the relative proportion of colloidal (1 kDa–0.22 μm) pool for the OC and insoluble TE bound to ferric colloids systematically decreased seaward, with the largest decrease occurring at low (< 5‰) salinities. Overall, the observed decrease of the colloidal fraction may be related to the coagulation of organo-ferric colloids at the beginning of the mixing zone and therefore the replacement of the HMW1 kDa–0.22 μm portion by the LMW< 1 kDa fraction. These patterns are highly reproducible across different sampling seasons, suggesting significant enrichment of the mixing zone by the most labile (and potentially bioavailable) fraction of the OC, Fe and insoluble TE. The size fractionation of the colloidal material during estuarine mixing reflects a number of inorganic and biological processes, the relative contribution of which to element speciation varies depending on the hydrological stage and time of year. In particular, LMW< 1 kDa ligand production in the surface horizons of the mixing zone may be linked to heterotrophic mineralization of allochthonous DOM and/or photodestruction. Given the relatively low concentration of particulate vs. dissolved load of most trace elements, desorption from the river suspended material was less pronounced than in other rivers in the world. As a result, the majority of dissolved components exhibited either a conservative (OC and related elements such as divalent metals) or non-conservative, coagulation-controlled (Fe, Al, and insoluble TE associated with organo-ferric colloids) behavior. The climate warming in high latitudes is likely to intensify the production of LMW< 1 kDa organic ligands and the associated TE; therefore, the delivery of potentially bioavailable trace metal micronutrients from the land to the ocean may increase.

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Vasiliu, Monica, Kirk A. Peterson, and David A. Dixon. "Bond Dissociation Energies in Heavy Element Chalcogen and Halogen Small Molecules." Journal of Physical Chemistry A 125, no. 9 (March 1, 2021): 1892–902. http://dx.doi.org/10.1021/acs.jpca.0c11393.

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Journal articles on the topic 'Heavy Element Containing Molecules'

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