Topography of lacUV5 initiation complexes

Formation of a transcriptionally competent open complex is a highly regulated multistep process involving at least two intermediates. The rate of formation and stability of the intermediate complexes often determine promoter strength. However, the detailed mechanism of formation of the open complex and the high resolution structures of these intermediates are not known. In this study the structures of the open and intermediate complexes formed on the lacUV5 promoter by Escherichia coli RNA polymerase were analyzed using ‘zero length’ DNA–protein cross-linking. In both the open and the intermediate complexes the core subunits (β′ and β) interact with lacUV5 DNA in a similar way, forming DNA–protein contacts flanking the initiation site. At the same time, the recognition (σ70) subunit closely interacts with the promoter only in the open complex. In combination with our previous results, the data suggest that during promoter recognition contacts of the σ subunit with core RNA polymerase and promoter DNA are rearranged in concert. These rearrangements constitute a landmark of transition from the intermediate to the open complex, identifying the σ subunit as a key player directing formation of the open complex.

Considerations of transcriptional control mechanisms: Do TFIID–core promoter complexes recapitulate nucleosome-like functions?

The general transcription initiation factor TFIID was originally identified, purified, and characterized with a biochemical assay in which accurate transcription initiation is reconstituted with multiple, chromatographically separable activities. Biochemical analyses have demonstrated that TFIID is a multiprotein complex that directs preinitiation complex assembly on both TATA box-containing and TATA-less promoters, and some TFIID subunits have been shown to be molecular targets for activation domains in DNA-binding regulatory proteins. These findings have most commonly been interpreted to support the view that transcriptional activation by upstream factors is the result of enhanced TFIID recruitment to the core promoter. Recent insights into the architecture and cell-cycle regulation of the multiprotein TFIID complex prompt both a reassessment of the functional role of TFIID in gene activation and a review of some of the less well-appreciated literature on TFIID. We present a speculative model for diverse functional roles of TFIID in the cell, explore the merits of the model in the context of published data, and suggest experimental approaches to resolve unanswered questions. Finally, we point out how the proposed functional roles of TFIID in eukaryotic class II transcription fit into a model for promoter recognition and activation that applies to both eubacteria and eukaryotes.

Nuclear particles containing RNA polymerase III complexes associated with the junctional plaque protein plakophilin 2

Plakophilin 2, a member of the arm-repeat protein family, is a dual location protein that occurs both in the cytoplasmic plaques of desmosomes as an architectural component and in an extractable form in the nucleoplasm. Here we report the existence of two nuclear particles containing plakophilin 2 and the largest subunit of RNA polymerase (pol) III (RPC155), both of which colocalize and are coimmunoselected with other pol III subunits and with the transcription factor TFIIIB. We also show that plakophilin 2 is present in the pol III holoenzyme, but not the core complex, and that it binds specifically to RPC155 in vitro. We propose the existence of diverse nuclear particles in which proteins known as plaque proteins of intercellular junctions are complexed with specific nuclear proteins.

Human cyclin-dependent kinase-activating kinase exists in three distinct complexes.

Transcription factor IIH (TFIIH) is a multisubunit complex required for transcription and for DNA nucleotide excision repair. TFIIH possesses three enzymatic activities: (i) an ATP-dependent DNA helicase, (ii) a DNA-dependent ATPase, and (iii) a kinase with specificity for the carboxyl-terminal domain of RNA polymerase II. The kinase activity was recently identified as the cdk (cyclin-dependent kinase) activating kinase, CAK, composed of cdk7, cyclin H, and MAT-1. Here we report the isolation and characterization of three distinct CAK-containing complexes from HeLa nuclear extracts: CAK, a novel CAK-ERCC2 complex, and TFIIH. CAK-ERCC2 can efficiently associate with core-TFIIH to reconstitute holo-TFIIH transcription activity. We present evidence proposing a critical role for ERCC2 in mediating the association of CAK with core TFIIH subunits.

DNA loops induced by cooperative binding of transcriptional activator proteins and preinitiation complexes.

DNA conformational changes are essential for the assembly of multiprotein complexes that contact several DNA sequence elements. An approach based on atomic force microscopy was chosen to visualize specific protein-DNA interactions occurring on eukaryotic class II nuclear gene promoters. Here we report that binding of the transcription regulatory protein Jun to linearized plasmid DNA containing the consensus AP-1 binding site upstream of a class II gene promoter leads to bending of the DNA template. This binding of Jun was found to be essential for the formation of preinitiation complexes (PICs). The cooperative binding of Jun and PIC led to looping of DNA at the protein binding sites. These loops were not seen in the absence of either PICs, Jun, or the AP-1 binding site, suggesting a direct interaction between DNA-bound Jun homodimers and proteins bound to the core promoter. This direct visualization of functional transcriptional complexes confirms the theoretical predictions for the mode of gene regulation by trans-activating proteins.

Supramolecular coordination complexes as building blocks for porous and magnetic materials

In this work, new coordination polymers based on two different classes of synthons are presented. In addition, manganese-based metallacrowns of magnetic interest are studied, both in the solid state and in solution. Firstly, functionalized bispyrazolylmethane derivatives are employed as bridging ligands for the establishment of silver-based coordination polymers; the influence of the substituent groups and of the counterions on the supramolecular packing is also investigated. Secondly, the use of metallacrown (MC) complexes as building blocks for porous coordination polymers is discussed. The design of a new metallacrown species is presented, which shows the tendency of aggregating in the solid state to form coordination polymers. Two new coordination polymers are indeed reported, of which one is the first MC-based permanently porous coordination network ever presented. The solid resists solvent evacuation and exhibits gas uptake ability. Furthermore, the isolation and characterization of a new metallacryptate species based on manganese ions is described. The metal-rich structure comprises nine Mn(II)/Mn(III) ions and presents an inverse metallacrown core subunit that binds a μ3-O2- ion. The metallacryptate is isolated in high yields and stable in solution. Lastly, a family of 3d-4f heterometallic metallacrowns is characterized in solution by means of UV-Vis spectrophotometry and of paramagnetically shifted 1H-NMR. The lanthanide-induced shifts observed in the spectra are employed to describe the molecules behaviour in solution and are qualitatively related to the magnetic properties of the compounds.

Síntese e caracterização de nanomateriais superparamagnéticos do tipo core-shell para aplicação em catálise e biomedicina

As diversas aplicações tecnológicas de nanopartículas magnéticas (NPM) vêm intensificando o interesse por materiais com propriedades magnéticas diferenciadas, como magnetização de saturação (MS) intensificada e comportamento superparamagnético. Embora MNP metálicas de Fe, Co e bimetálicas de FeCo e FePt possuam altos valores de MS, sua baixa estabilidade química dificulta aplicações em escala nanométrica. Neste trabalho foram sintetizadas NPM de Fe, Co, FeCo e FePt com alta estabilidade química e rigoroso controle morfológico. NPM de óxido metálicos (Fe e Co) também foram obtidas. Dois métodos de síntese foram empregados. Usando método baseado em sistemas nanoheterogêneos (sistemas micelares ou de microemulsão inversa), foram sintetizadas NPM de Fe3O4 e Co metálico. Foram empregados surfactantes cátion-substituídos: dodecil sulfato de ferro(III) (FeDS) e dodecil sulfato de cobalto(II) (CoDS). Para a síntese das NPM, foram estudados e determinados a concentração micelar crítica do FeDS em 1-octanol (cmc = 0,90 mmol L-1) e o diagrama de fases pseudoternário para o sistema n-heptano/CoDS/n-butanol/H2O. NPM esferoidais de magnetita com3,4 nm de diâmetro e comportamento quase-paramagnético foram obtidas usando sistemas micelares de FeDS em 1-octanol. Já as NPM de Co obtidas via microemulsão inversa, apesar da larga distribuição de tamanho e baixa MS, são quimicamente estáveis e superparamagnéticas. O segundo método é baseado na decomposição térmica de complexos metálicos, pelo qual foram preparadas NPM esféricas de FePt e de óxidos metálicos (Fe3O4, FeXO1-X, (Co,Fe)XO1-X e CoFe2O4) com morfologia controlada e estabilidade química. O método não mostrou a mesma efetividade na síntese de NPM de FeAg e FeCo: a liga FeAg não foi obtida enquanto que NPM de FeCo com estabilidade química foram obtidas sem controle morfológico. NPM de Fe e FeCo foram preparadas a partir da redução térmica de NPM de Fe3O4 e CoFe2O4, as quais foram previamente recobertas com sílica. A sílica previne a sinterização inter-partículas, além de proporcionar caráter hidrofílico e biocompatibilidade ao material. As amostras reduzidas apresentaram aumento dos valores de MS (entre 21,3 e 163,9%), o qual é diretamente proporcional às dimensões das NPM. O recobrimento com sílica foi realizado via hidrólise de tetraetilortosilicato (TEOS) em sistema de microemulsão inversa. A espessura da camada de sílica foi controlada variando-se o tempo de reação e as concentrações de TEOS e de NPM, sendo então proposto um mecanismo do processo de recobrimento. Algumas amostras receberam um recobrimento adicional de TiO2 na fase anatase, para o qual foi empregado etilenoglicol como solvente e ligante para formação de glicolato de Ti como precursor. A espessura da camada de TiO2 (2-12 nm) é controlada variando as quantidades relativas entre NPM e o precursor de Ti. Ensaios de hipertermia magnética foram realizados para as amostras recobertas com sílica. Ensaios de hipertermia magnéticas mostram grande aumento da taxa de aquecimento das amostras após a redução térmica, mesmo para dispersões diluídas de NPM (0,6 a 4,5 mg mL-1). Taxas de aquecimento entre 0,3 e 3,0oC min-1 e SAR entre 37,2 e 96,3 W g-1. foram obtidos. A atividade fotocatalítica das amostras recobertas foram próximas à da fase anatase pura, com a vantagem de possuir um núcleo magnético que permite a recuperação do catalisador pela simples aplicação de campos magnéticos externos. Os resultados preliminares dos ensaios de hipertermia magnética e fotocatálise indicam um forte potencial dos materiais aqui relatados para aplicações em biomedicina e em fotocatálise.

Temporal Control of Leaf Complexity by miRNA-Regulated Licensing of Protein Complexes

The tremendous diversity of leaf shapes has caught the attention of naturalists for centuries. In addition to interspecific and intraspecific differences, leaf morphologies may differ in single plants according to age, a phenomenon known as heteroblasty. In Arabidopsis thaliana, the progression from the juvenile to the adult phase is characterized by increased leaf serration. A similar trend is seen in species with more complex leaves, such as the A. thaliana relative Cardamine hirsuta, in which the number of leaflets per leaf increases with age. Although the genetic changes that led to the overall simpler leaf architecture in A. thaliana are increasingly well understood, less is known about the events underlying age-dependent changes within single plants, in either A. thaliana or C. hirsuta. Here, we describe a conserved miRNA transcription factor regulon responsible for an age-dependent increase in leaf complexity. In early leaves, miR319-targeted TCP transcription factors interfere with the function of miR164-dependent and miR164-independent CUC proteins, preventing the formation of serrations in A. thaliana and of leaflets in C. hirsuta. As plants age, accumulation of miR156-regulated SPLs acts as a timing cue that destabilizes TCP-CUC interactions. The destabilization licenses activation of CUC protein complexes and thereby the gradual increase of leaf complexity in the newly formed organs. These findings point to posttranslational interaction between unrelated miRNA-targeted transcription factors as a core feature of these regulatory circuits.

Polycationic lipophilic-core dendrons as penetration enhancers for the oral administration of low molecular weight heparin

Two polycationic lipophilic-core carbohydrate-based dendrons 2a-b and five polycationic lipophilic-core peptide dendrons 3-6, containing four arginine or lysine terminal residues, were synthesized and then tested in rats as penetration enhancers for the oral delivery of low molecular weight heparin. Better results were obtained with dendrons containing terminal lysine residues than terminal arginine. A significant anti-factor Xa activity was obtained when low molecular weight heparin was coadministered with dendron 5. (c) 2005 Elsevier Ltd. All rights reserved.

Polymer-phospholipid complexes for the solubilisation and delivery of drugs to the eye

Aim: Topical application of ophthalmic drugs is very inefficient; contact lenses used as drug delivery devices could minimize the drug loss and side effects. Styrene-maleic acid copolymers (PSMA) can form polymer-phospholipid complexes with dipalmitoyl phosphatidylcholine (DMPC) in the form of nanometric vesicles, which can easily solubilise hydrophobic drugs. They can be dispersed on very thin contact lens coatings to immobilize the drug on their surface. Methods: Two types of complexes stable at different pH values (5 and 7 respectively) where synthesized and loaded with drugs of different hydrophilicities during their formation process. The drug release was studied in vitro and compared to the free drug. Results: The mean sizes of the complexes obtained by light scattering were 50 nm and 450 nm respectively with low polydispersities. However, they were affected by the drugs load and release. An increase was observed in the duration of the release in the case of hydrophobic drugs, from days to weeks, avoiding initial “burst” and with a lesser amount of total drug released due to the interaction of the drug with the phospholipid core. The size and charge of the different drugs and the complexes nature also affected the release profile. Conclusions: Polymer-phospholipid complexes in the form of nanoparticles can be used to solubilise and release hydrophobic drugs in a controlled way. The drug load and release can be optimised to reach therapeutic values in the eye.

Activity of isotopes of U, Th and Pa versus depth in bottom sediments from Core ML1_66

A sediment core from the European Basin with alternation of biogenic calcareous oozes and terrigenous sediments is studied by several methods. Isotopic age is determined by 230Th-ex and 231Pa-ex and by the radiocarbon method. Surface water paleotemperatures are reconstructed from complexes of planktic foraminifera and oxygen isotope ratios in their shells, and the ratio of biogenic and terrigenous components are investigated. Stages 1-8 of the oxygen-isotope scale are identified. Fluctuations in paleooceanic conditions in the area of coring are discussed.

(Plate 3) Manganese nodules and deep-sea sediment core from Pacific Ocean

A synoptic review of the studies of well-known occurrences of palagonite tuffs is presented. Included are palagonite tuffs from Iceland, and pillow-lava palagonite complexes from Columbia River basalts and from the central Oregon coast. Additional petrologic and x-ray defraction data for selected samples are presented. Petrologic evidence shows that basaltic glass of aqueous tuffs and breccias consists of sideromelane, which is susceptible to palagonitization. It is shown that palagonitization is a selective alteration process, involving hydration, oxidation and zeolitization. Some of the manganese nodules dredged from the Pacific Ocean floor contain nucleus of palagonite-tuff breccias or of zeolite. A brief megascopic and microscopic description of nodules from the south Pacific, the Mendocino ridge and the 'Horizon' Nodule from the north Pacific is presented. Petrographic studies of palagonite-tuff breccias of manganese nodules and other palagonites suggest that migration and segregation of metallic elements occur during and subsequent to palagonitization. During the palagonitization of sideromelane, nearly 30 percent of sea water is absorbed. The hydration of sideromelane is also accompanied by oxidation of iron and other elements. These oxides may be released either in colloidal form or in true solution and tend to precipitate first from the unstable palagonite.

Mössbauer Spectroscopic Study andMagnetic Investigation of Iron(III) Complexes on a DendrimericBasis

The functionalization of the molecular surface of various dendrimer generations with a phosphorous core and external amine groups is obtained by converting those amine groups into the corresponding imines of salicylaldehyde creating multiple coordination sites for the iron atoms. Treatment with iron(III) chloride yields multinuclear iron(III) complexes on a dendrimeric basis. The obtained multinuclear molecular systems exhibit extremely high total spin values. The influence of the generation growth on this type of coordination compounds is investigated by Mossbauer spectroscopy and SQUIDmagnetometry.

Octahedral molybdenum cluster complexes with aromatic sulfonate ligands

This article describes the synthesis, structures and systematic study of the spectroscopic and redox properties of a series of octahedral molybdenum metal cluster complexes with aromatic sulfonate ligands (nBu4N)2[{Mo6X8}(OTs)6] and (nBu4N)2[{Mo6X8}(PhSO3)6] (where X- is Cl-, Br- or I-; OTs- is p-toluenesulfonate and PhSO3 - is benzenesulfonate). All the complexes demonstrated photoluminescence in the red region and an ability to generate singlet oxygen. Notably, the highest quantum yields (>0.6) and narrowest emission bands were found for complexes with a {Mo6I8}4+ cluster core. Moreover, cyclic voltammetric studies revealed that (nBu4N)2[{Mo6X8}(OTs)6] and (nBu4N)2[{Mo6X8}(PhSO3)6] confer enhanced stability towards electrochemical oxidation relative to corresponding starting complexes (nBu4N)2[{Mo6X8}X6].

New Metal Tetrazolate Complexes: Design, Synthesis, Characterization and Applications

This final thesis is aimed at summarizing the research program I have carried out during my PhD studies, that has been dealing with the design, the preparation, characterization and applications of new Re(I), Ru(II), and Ir(III) metal complexes containing anionic ligands such as 5-aryl tetrazolates [R-CN4]- or their neutral analogues, N-alkyltetrazoles [R-CN4-R1]. Chapter 1 consists of a brief introduction on tetrazoles and metal-tetrazolato complexes, and on the photophysical properties of d6 transition metal complexes. In chapter 2, the synthesis, characterization and study of the photophysical properties of new luminescent Ir(III)-tetrazolate complexes are discussed. Moreover, the application of one of the new Ir(III)-CN complexes as emissive core in the fabrication of an OLED device is reported. In chapter 3, the study of the antimicrobial activity of new Ru(II)-alkyltetrazole complexes is reported. When the pentatomic ring was substituted with a long alkyl residue, antimicrobial activity toward Deinococcus radiodurans was observed. In chapter 4, a new family of luminescent Re(I)-tetrazolate complexes is reported. In this study, different N-alkyl tetrazoles play the role of diimine (diim) ligands in the preparation of new Re(I) tricarbonyl complexes. In addition, absorption and emission titration experiments were performed to study their interaction with Bovine Serum Albumin (BSA). In chapter 5, the synthesis and characterization of new luminescent Re(I)-tetrazolate complexes are discussed. The use of sulfonated diimine ligands in the preparation of new Re(I) tricarbonyl complexes led to the first example Re(I) complexes for the luminescent staining of proteins. In chapter 6, the synthesis, a new family of Ir(III)-NO2 tetrazole complexes displaying unexpected photophysical properties are discussed. Moreover, the possibility to tune the luminescent output of such systems upon chemical modification of the pending nitro group was verified by performing reduction tests with sodium dithionite; this represents encouraging evidence for their possible application as hypoxia-responsive luminescent probes in bioimaging.