Dissecting the Relation between a Nuclear Receptor and GATA: Binding Affinity Studies of Thyroid Hormone Receptor and GATA2 on TSH beta Promoter

Background: Much is known about how genes regulated by nuclear receptors (NRs) are switched on in the presence of a ligand. However, the molecular mechanism for gene down-regulation by liganded NRs remains a conundrum. The interaction between two zinc-finger transcription factors, Nuclear Receptor and GATA, was described almost a decade ago as a strategy adopted by the cell to up-or down-regulate gene expression. More recently, cell-based assays have shown that the Zn-finger region of GATA2 (GATA2-Zf) has an important role in down-regulation of the thyrotropin gene (TSH beta) by liganded thyroid hormone receptor (TR). Methodology/Principal Findings: In an effort to better understand the mechanism that drives TSH beta down-regulation by a liganded TR and GATA2, we have carried out equilibrium binding assays using fluorescence anisotropy to study the interaction of recombinant TR and GATA2-Zf with regulatory elements present in the TSH beta promoter. Surprisingly, we observed that ligand (T3) weakens TR binding to a negative regulatory element (NRE) present in the TSH beta promoter. We also show that TR may interact with GATA2-Zf in the absence of ligand, but T3 is crucial for increasing the affinity of this complex for different GATA response elements (GATA-REs). Importantly, these results indicate that TR complex formation enhances DNA binding of the TR-GATA2 in a ligand-dependent manner. Conclusions: Our findings extend previous results obtained in vivo, further improving our understanding of how liganded nuclear receptors down-regulate gene transcription, with the cooperative binding of transcription factors to DNA forming the core of this process.

NMR quadrupolar system described as Bose-Einstein-condensate-like system

This paper presents a description of nuclear magnetic resonance (NMR) of quadrupolar systems using the Holstein-Primakoff (HP) formalism and its analogy with a Bose-Einstein condensate (BEC) system. Two nuclear spin systems constituted of quadrupolar nuclei I=3/2 ((23)Na) and I=7/2 ((133)Cs) in lyotropic liquid crystals were used for experimental demonstrations. Specifically, we derived the conditions necessary for accomplishing the analogy, executed the proper experiments, and compared with quantum mechanical prediction for a Bose system. The NMR description in the HP representation could be applied in the future as a workbench for BEC-like systems, where the statistical properties may be obtained using the intermediate statistic, first established by Gentile. The description can be applied for any quadrupolar systems, including new developed solid-state NMR GaAS nanodevices.

Haplotype distribution of five nuclear genes based on network genealogies and Bayesian inference indicates that Trypanosoma cruzi hybrid strains are polyphyletic

Chagas disease is still a major public health problem in Latin America. Its causative agent, Trypanosoma cruzi, can be typed into three major groups, T. cruzi I, T. cruzi II and hybrids. These groups each have specific genetic characteristics and epidemiological distributions. Several highly virulent strains are found in the hybrid group; their origin is still a matter of debate. The null hypothesis is that the hybrids are of polyphyletic origin, evolving independently from various hybridization events. The alternative hypothesis is that all extant hybrid strains originated from a single hybridization event. We sequenced both alleles of genes encoding EF-1 alpha, actin and SSU rDNA of 26 T. cruzi strains and DHFR-TS and TR of 12 strains. This information was used for network genealogy analysis and Bayesian phylogenies. We found T. cruzi I and T. cruzi II to be monophyletic and that all hybrids had different combinations of T. cruzi I and T. cruzi II haplotypes plus hybrid-specific haplotypes. Bootstrap values (networks) and posterior probabilities (Bayesian phylogenies) of clades supporting the monophyly of hybrids were far below the 95% confidence interval, indicating that the hybrid group is polyphyletic. We hypothesize that T. cruzi I and T. cruzi II are two different species and that the hybrids are extant representatives of independent events of genome hybridization, which sporadically have sufficient fitness to impact on the epidemiology of Chagas disease.

Application of electron paramagnetic resonance Spectroscopy for validation of the novel (AN plus DN) solvent polarity scale

Based on solvation studies of polymers, the sum (1: 1) of the electron acceptor (AN) and electron donor (DN) values of solvents has been proposed as an alternative polarity scale. To test this, the electron paramagnetic resonance isotropic hyperfine splitting constant, a parameter known to be dependent on the polarity/proticity of the medium, was correlated with the (AN+DN) term using three paramagnetic probes. The linear regression coefficient calculated for 15 different solvents was approximately 0.9, quite similar to those of other well-known polarity parameters, attesting to the validity of the (AN+DN) term as a novel ""two-parameter"" solvent polarity scale.

Strong reduction of V(4+) amount in vanadium oxide/hexadecylamine nanotubes by doping with Co(2+) and Ni(2+) ions: Electron paramagnetic resonance and magnetic studies

In this work we present a complete characterization and magnetic study of vanadium oxide/hexadecylamine nanotubes (VO(x)/Hexa NT's) doped with Co(2)+ and Ni(2+) ions. The morphology of the NT's has been characterized by transmission electron microscopy, while the metallic elements have been quantified by the instrumental neutron activation analysis technique. The static and dynamic magnetic properties were studied by collecting data of magnetization as a function of magnetic field and temperature and by electron paramagnetic resonance. At difference of the majority reports in the literature, we do not observe magnetic dimers in vanadium oxide nanotubes. Also, we observed that the incorporation of metallic ions (Co(2+), S = 3/2 and Ni(2+), S = 1) decreases notably the amount of V(4+) ions in the system, from 14-16% (nondoped case) to 2%-4%, with respect to the total vanadium atoms (fact corroborated by XPS experiments) anyway preserving the tubular nanostructure. The method to decrease the amount of V(4+) in the nanotubes improves considerably their potential technological applications as Li-ion batteries cathodes. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3580252]

The electronic states of SeF: A reinterpretation of the chemiluminescent emission of the reaction of selenium with fluorine

The low-lying doublet and quartet electronic states of the species SeF correlating with the first dissociation channel are investigated theoretically at a high-level of electronic correlation treatment, namely, the complete active space self-consistent field/multireference single and double excitations configuration interaction (CASSCF/MRSDCI) using a quintuple-zeta quality basis set including a relativistic effective core potential for the selenium atom. Potential energy curves for (Lambda+S) states and the corresponding spectroscopic properties are derived that allows for an unambiguous assignment of the only spectrum known experimentally as due to a spin-forbidden X (2)Pi-a (4)Sigma(-) transition, and not a A (2)Pi-X (2)Pi transition as assumed so far. For the bound excited doublets, yet unknown experimentally, this study is the first theoretical characterization of their spectroscopic properties. Also the spin-orbit coupling constant function for the X (2)Pi state is derived as well as the spin-orbit coupling matrix element between the X (2)Pi and a (4)Sigma(-) states. Dipole moment functions and vibrationally averaged dipole moments show SeF to be a very polar species. An overview of the lowest-lying spin-orbit (Omega) states completes this description. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3426315]

Spectroscopic, structural, and functional characterization of the alternative low-spin state of horse heart cytochrome c

The alternative low-spin states of Fe3+ and Fe2+ cytochrome c induced by SDS or AOT/hexane reverse micelles exhibited the heme group in a less rhombic symmetry and were characterized by electron paramagnetic resonance, UV-visible, CD, magnetic CD, fluorescence, and Raman resonance. Consistent with the replacement of Met 80 by another strong field ligand at the sixth heme iron coordination position, Fe3+ ALSScytc exhibited 1-nm Soret band blue shift and e enhancement accompanied by disappearance of the 695-nm charge transfer band. The Raman resonance, CD, and magnetic CD spectra of Fe3+ and Fe2+ ALSScytc exhibited significant changes suggestive of alterations in the heme iron microenvironment and conformation and should not be assigned to unfold because the Trp(59) fluorescence remained quenched by the neighboring heme group. ALSScytc was obtained with His(33) and His(26) carboxyethoxylated horse cytochrome c and with tuna cytochrome c (His(33) replaced by Asn) pointing out Lys(79) as the probable heme iron ligand. Fe3+ ALSScytc retained the capacity to cleave tert-butylhydroperoxide and to be reduced by dithiothreitol and diphenylacetaldehyde but not by ascorbate. Compatible with a more open heme crevice, ALSScytc exhibited a redox potential similar to 200 mV lower than the wild-type protein (1220 mV) and was more susceptible to the attack of free radicals.

Effect of grassland management on soil carbon sequestration in Rondonia and Mato Grosso states, Brazil

Grassland management affects soil organic carbon (SOC) content and a variety of management options have been proposed to sequester carbon. However, studies conducted in Brazilian pastures have shown divergent responses for the SOC depending on management practices. Our objective was to evaluate the effects of management on SOC stocks in grasslands of the Brazilian states of Rondonia and Mato Grosso, and to derive region-specific factors for soil C stock change associated with different management conditions. Compared to SOC stocks in native vegetation, degraded grassland management decreased SOC by a factor of 0.91 +/- 0.14, nominal grassland management reduced SOC stock for Oxisols by a relatively small factor of 0.99 +/- 0.08, whereas, SOC storage increased by a factor of 1.24 +/- 0.07 with nominal management for other soil types. Improved grassland management on Oxisols increased SOC storage by 1.19 +/- 0.07, relative to native stocks, but there were insufficient data to evaluate the impact of improved grassland management for other soil types. Using these results, we also evaluated the potential for grassland management to sequester or emit C to the atmosphere, and found that degraded grassland management decreased stocks by about 0.27-0.28 Mg C ha(-1) yr(-1); nominal management on Oxisols decreased C at a rate of 0.03 Mg C ha(-1) yr(-1), while nominal management on others soil types and improved management on Oxisols increased stocks by 0.72 Mg C ha(-1) yr(-1) and 0.61 Mg C ha(-1) yr(-1), respectively. Therefore, when well managed or improved, grasslands in Rondonia and Mato Grosso states have the potential to sequester C. (c) 2008 Elsevier B.V. All rights reserved.

Changes in optical properties caused by UV-irradiation of aquatic humic substances from the amazon river basin: Seasonal variability evaluation

Aquatic humic substances (AHS) isolated from two characteristic seasons of the Negro river, winter and summer corresponding to floody and dry periods, were structurally characterized by (13)C nuclear magnetic ressonance. Subsequently, AHS aqueous solutions were irradiated with a polychromatic lamp (290-475 nm) and monitored by its total organic carbon (TOC) content, ultraviolet-visible (UV-vis) absorbance, fluorescence and Fourier transformed infrared spectroscopy (FTIR). As a result, a photobleaching upto 80% after irradiation of 48 h was observed. Conformational rearrangements and formation of low molecular complexity structures were formed during the irradiation, as deduced from the pH decrement and the fluorescence shifting to lower wavelengths. Additionally a significant mineralization with the formation Of CO(2), CO, and inorganic carbon compounds was registered, as assumed by TOC losses of up to 70%. The differences in photodegradation between samples expressed by photobleaching efficiency were enhanced in the summer sample and related to its elevated aromatic content. Aromatic structures are assumed to have high autosensitization capacity effects mediated by the free radical generation from quinone and phenolic moieties.

Multiple synchronous states in static delay-free mutually connected PLL networks

In many engineering applications, the time coordination of geographically separated events is of fundamental importance, as in digital telecommunications and integrated digital circuits. Mutually connected (MC) networks are very good candidates for some new types of application, such as wireless sensor networks. This paper presents a study on the behavior of MC networks of digital phase-locked loops (DPLLs). Analytical results are derived showing that, even for static networks without delays, different synchronous states may exist for the network. An upper bound for the number of such states is also presented. Numerical simulations are used to show the following results: (i) the synchronization precision in MC DPLLs networks; (ii) the existence of synchronous states for the network does not guarantee its achievement and (iii) different synchronous states may be achieved for different initial conditions. These results are important in the neural computation context. as in this case, each synchronous state may be associated to a different analog memory information. (C) 2010 Elsevier B.V. All rights reserved.

Molecular evidence of phytoplasma associated with witches` broom on passion fruit in five Brazilian States

Phytoplasmas are cell wall-less prokaryotes and phloem-inhabitants associated with diseases that affect several crops. Passion fruit is a tropical plant species cultivated in various Brazilian regions. Diseases are among the factors that may cause damage to this crop, and witches` broom is a very important one. This disease, associated with a phytoplasma, has been reported only in Brazil, where it was described in Rio de Janeiro and Pernambuco States at the beginning of the 1980`s. In 2005-2006, symptomatic plants Suspected of phytoplasma infection were sampled in areas located in Sao Paulo, Parana, Rio de Janeiro, Sergipe and Bahia. Amplification of DNA fragments of 1.2kb from nested PCR primed by the pairs 16mF2/mR1 and 16F2n/R2 revealed the presence of phytoplasma in the tissue of plants from all sampled regions. Molecular detection of the agent allowed confirmation of the diagnosis based on the symptomatology; demonstrated the strong association between diseased plants and a phytoplasma, confirming previous investigations based on electron microscopy;, and revealed the present occurrence of the agent in the States of Bahia, Parana, Rio de Janeiro, Sergipe, and Sao Paulo.

Age-related association of rDNA and telomeres with the nuclear matrix in mouse hepatocytes

Transcribed sequences have been suggested to be associated with the nuclear matrix, differing from non-transcribing sequences, which have been reported to be contained in DNA loops. However, although a dozen of genes have their expression level affected by aging, data on chromatin-nuclear matrix interactions under this physiological condition are still scarce. In the present study, liver imprints from young, adult and old mice were subjected to FISH (fluorescence in situ hybridization) for 45S rDNA and telomeric sequences, with or without a lysis treatment to produce extended chromatin fibres. There was an increased amount of 45S rDNA sequences located in DNA loops as the animals grow older, while telomeric sequences were always observed in DNA loops irrespective of the animal age. We assume that active rRNA genes associate with the nuclear matrix, while DNA loops contain silent sequences. Transcription of each 45S rDNA repeat unit is suggested to be dependent on its interaction with the nuclear matrix.

Adaptation of an apple sooty blotch and flyspeck warning system for the Upper Midwest United States

A warning system for sooty blotch and flyspeck (SBFS) of apple, developed in the southeastern United States, uses cumulative hours of leaf wetness duration (LWD) to predict the timing of the first appearance of signs. In the Upper Midwest United States, however, this warning system has resulted in sporadic disease control failures. The purpose of the present study was to determine whether the warning system`s algorithm could be modified to provide more reliable assessment of SBFS risk. Hourly LWD, rainfall, relative humidity (RH), and temperature data were collected from orchards in Iowa, North Carolina, and Wisconsin in 2005 and 2006. Timing of the first appearance of SBFS signs was determined by weekly scouting. Preliminary analysis using scatterplots and boxplots suggested that Cumulative hours of RH >= 97% could be a useful predictor of SBFS appearance. Receiver operating characteristic curve analysis was used to compare the predictive performance of cumulative LWD and cumulative hours of RH >= 97%. Cumulative hours of RH >= 97% was a more conservative and accurate predictor than cumulative LWD for 15 site years in the Upper Midwest, but not for four site years in North Carolina. Performance of the SBFS warning system in the Upper Midwest and climatically similar regions may be improved if cumulative hours of RH >= 97% were substituted for cumulative LWD to predict the first appearance of SBFS.

Overwintering of Sclerotium rolfsii and S-rolfsii var. delphinii in different latitudes of the United States

Previously known only from the southern United States, hosta petiole rot recently appeared in the northern United States. Sclerotium rolfsii var. delphinii is believed to be the predominant petiole rot pathogen in the northern United States, whereas S. rolfsii is most prevalent in the southern United States. In order to test the hypothesis that different tolerance to climate extremes affects the geographic distribution of these fungi, the survival of S. rolfsii and S. rolfsii var. delphinii in the northern and southeastern United States was investigated. At each of four locations, nylon screen bags containing sclerotia were placed on the surface of bare soil and at 20-cm depth. Sclerotia were recovered six times from November 2005 to July 2006 in North Dakota and Iowa, and from December 2005 to August 2006 in North Carolina and Georgia. Survival was estimated by quantifying percentage of sclerotium survival on carrot agar. Sclerotia of S. rolfsii var. delphinii survived until at least late July in all four states. In contrast, no S. rolfsii sclerotia survived until June in North Dakota or Iowa, whereas 18.5% survived until August in North Carolina and 10.3% survived in Georgia. The results suggest that inability to tolerate low temperature extremes limits the northern range of S. rolfsii.

Effects of glutamine on the nuclear factor-kappaB signaling pathway of murine peritoneal macrophages

The aim of this study was to evaluate the effect of glutamine on the expression of proteins involved in the nuclear factor-kappaB (NF-kappa B) signaling pathway of murine peritoneal macrophages. Since glutamine is essential for the normal functioning of macrophages, it was hypothesized that in vitro glutamine supplementation would increase NF-kappa B activation. Peritoneal macrophages were pretreated with glutamine (0, 0.6, 2 and 10 mM) before incubation with lipopolysaccharide (LPS), and the effects of glutamine on the production of tumor necrosis factor-alpha and on the expression and activity of proteins involved in the NF-kappa B signaling pathway were studied by an enzyme linked immuno-sorbent assay, Western blotting, and an electrophoretic mobility shift assay. Glutamine treatment (2 and 10 mM) increased the activation of NF-kappa B in LPS-stimulated peritoneal macrophages (P < 0.05). In non-stimulated cells, glutamine treatment (2 and 10 mM) significantly reduced I kappa B-alpha protein expression (P < 0.05). Glutamine modulates NF-kappa B signaling pathway by reducing the level of I kappa B-alpha, leading to an increase in NF-kappa B within the nucleus in peritoneal macrophages.