The genetic structure and mating system of Acrocomia aculeata (Arecaceae)

Acrocomia aculeata is a perennial, fruit-producing palm tree, native to tropical forests. Its fruits have spurred interest because of their significant potential for use in the cosmetic industry and as feedstock for biofuel. In the present study, the genetic structure and mating system in Acrocomia aculeata were analyzed, using eight nuclear microsatellite loci and samples from Sao Paulo and Minas Gerais states, Brazil. By means of Bayesian analysis, these populations were clustered into two or three groups. A high multilocus outcrossing rate suggests that outcrosses were predominant, although a certain degree of biparental inbreeding also occurred. Thus, although monoecious and self-compatible, there is every indication that A. aculeata bears a mixed reproductive system, with a predominance of outcrossing. Given the genetic structure revealed hereby, future conservation strategies and germplasm collecting should be focussed on sampling and preserving individuals from different clusters.

Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes, Laridae) from the Brazilian coast

Several phylogeographic studies of seabirds have documented low genetic diversity that has been attributed to bottleneck events or individual capacity for dispersal. Few studies have been done in seabirds on the Brazilian coast and all have shown low genetic differentiation on a wide geographic scale. The Kelp Gull is a common species with a wide distribution in the Southern Hemisphere. In this study, we used mitochondrial and nuclear markers to examine the genetic variability of Kelp Gull populations on the Brazilian coast and compared this variability with that of sub-Antarctic island populations of this species. Kelp Gulls showed extremely low genetic variability for nnitochondrial markers (cytb and ATPase) and high diversity for a nuclear locus (intron 7 of the beta-fibrinogen). The intraspecific evolutionary history of Kelp Gulls showed that the variability found in intron 7 of the beta-fibrinogen gene was compatible with the variability expected under neutral evolution but suggested an increase in population size during the last 10,000 years. However, none of the markers revealed evidence of a bottleneck population. These findings indicate that the recent origin of Kelp Gulls is the main explanation for their nuclear diversity, although selective pressure on the mtDNA of this species cannot be discarded.

Preparation, characterization and structure of ruthenium phosphine complexes containing non-innocent ligands

Phosphine ruthenate complexes containing the non-innocent ligands 4-chloro-1,2-phenylenediamine (opda-CI) and 3,3',4,4'-tetraamminebiphenyl (diopda) were synthesized and characterized by means of X-ray diffraction, electrochemistry, P-31{H-1} NMR and electronic spectroscopies. Crystals of cis-[RuCl2 (dppb)(bqdi-CI)] complex were isolated as a mixture of two conformational isomers due to different positions of the chlorine atoms of the o-phenylene ligand in relation to the P1 atom of the phosphine moiety. (C) 2011 Elsevier Ltd. All rights reserved.

Spectroscopic characterization and crystal structure of cis-Bis(N-(2-benzoyl)-N ',N '-diphenylthioureato-k O-2,S)nickel(II)

The title compound [Ni(C20H15N2OS)(2)] is prepared by the reaction of metal acetate with the corresponding acylthiourea derivative. The complex is characterized by elemental analysis, IR, H-1 and C-13 NMR, and its structure is determined by single crystal X-ray diffraction. The Ni(II) ion is coordinated by the S and O atoms of two N-benzoyl-N',N'-diphenylthiourea ligands in a slightly distorted square-planar coordination geometry. The two O and two S atoms are mutually cis to each other. The substance crystallizes triclinic (P-1 space group) with cell dimensions a = 10.7262(9) , b = 12.938(3) , c = 14.2085(12) , alpha = 74.650(4)A degrees, beta = 78.398(4)A degrees, gamma = 68.200(5)A degrees, and two formula units in the unit cell. The structure is very close to the related N-(2-furoyl) Ni complex reported previously.

Ligand- and Structure-Based Drug Design Strategies and PPAR delta/alpha Selectivity

Peroxisome-proliferator-activated receptors are a class of nuclear receptors with three subtypes: a, ? and d. Their main function is regulating gene transcription related to lipid and carbohydrate metabolism. Currently, there are no peroxisome-proliferator-activated receptors d drugs being marketed. In this work, we studied a data set of 70 compounds with a and d activity. Three partial least square models were created, and molecular docking studies were performed to understand the main reasons for peroxisome-proliferator-activated receptors d selectivity. The obtained results showed that some molecular descriptors (log P, hydration energy, steric and polar properties) are related to the main interactions that can direct ligands to a particular peroxisome-proliferator-activated receptors subtype.

N-4-Phenyl-substituted 2-acetylpyridine thiosemicarbazones: Cytotoxicity against human tumor cells, structure-activity relationship studies and investigation on the mechanism of action

N-4-Phenyl 2-acetylpyridine thiosemicarbazone (H2Ac4Ph; N-(phenyl)-2-(1-(pyridin-2-yl)ethylidene) hydrazinecarbothioamide) and its N-4-ortho-, -meta- and -para-fluorophenyl (H2Ac4oFPh, H2Ac4mFPh, H2Ac4pFPh), N-4-ortho-, -meta- and -para-chlorophenyl (H2Ac4oClPh, H2Ac4mClPh, H2Ac4pClPh), N-4-ortho-, -meta- and -para-iodophenyl (H2Ac4oIPh, H2Ac4mIPh, H2Ac4pIPh) and N-4-ortho-, -meta- and -para-nitrophenyl (H2Ac4oNO(2)Ph, H2Ac4mNO(2)Ph, H2Ac4pNO(2)Ph) derivatives were assayed for their cytotoxicity against human malignant breast (MCF-7) and glioma (T98G and U87) cells. The compounds were highly cytotoxic against the three cell lineages (IC50: MCF-7, 52-0.16 nM; T98G, 140-1.0 nM; U87, 160-1.4 nM). All tested thiosemicarbazones were more cytotoxic than etoposide and did not present any haemolytic activity at up to 10(-5) M. The compounds were able to induce programmed cell death. H2Ac4pClPh partially inhibited tubulin assembly at high concentrations and induced cellular microtubule disorganization. (C) 2012 Elsevier Ltd. All rights reserved.

Synthesis and characterization of [Ru(eta(6)-C10H14)(dppf)X][PF6] (X = Cl, Br, I, SnF3) compounds: The X-ray structure of [Ru(eta(6)-C10H14)(dppf)Cl][SnCl3]center dot 0.45CH(2)Cl(2)

The arene-ruthenium complex [Ru(eta(6)-C10H14)(dppf)Cl]PF6 (1) was used as a precursor for the syntheses of the [Ru(eta(6)-C10H14)(dppf)Br]PF6 (2), [Ru(eta(6)-C10H14)(dppf)I]PF6 (3). [Ru(eta(6)-C10H14)(dppf)SnF3]PF6 (4) and [Ru(eta(6)-C10H14)(dppf)Cl][SnCl3]center dot 0.45CH(2)Cl(2) (5) complexes by its reactions with KBr, Kl, SnF2 and SnCl2. respectively. All of the compounds were characterized by NMR, IR, Fe-57 and Sn-119-Mossbauer spectroscopy, and cyclic voltammetry. The single-crystal X-ray structure analysis of the [Ru(eta(6)-C10H14)(dppf)Cl] [SnCl3]center dot 0.45CH(2)Cl(2) complex revealed the expected piano-stool geometry. Cyclic voltammograms of the complexes showed only one quasi-reversible electrochemical process, involving the oxidation of Fe(II) and Ru(II) at the same potential, which was confirmed by exhaustive electrolysis experiments. Fe-57-Mossbauer parameters obtained for the complexes (1-5) were fitted with one doublet corresponding to a site of one iron(II). The Sn-119-Mossbauer parameters of the complex (4) indicate that tin is tetra covalent. (c) 2012 Elsevier Ltd. All rights reserved.

Crystal structure and spectroscopic properties of polymeric adducts of the tetra-mu-haloaspirinate-dicopper(II)

Eight new copper(II) complexes with halo-aspirinate anions have been synthesized: [Cu-2(Fasp)(4)(MeCN)(2)] center dot 2MeCN (1), [Cu-2(Clasp)(4)(MeCN)(2)]center dot 2MeCN (2), [Cu-2(Brasp)(4) (MeCn)(2)] center dot 2MeCn (3), {[Cu-2(Fasp)(4)(Pyrz)] center dot 2MeCN}(n) (4) {[Cu-2(Clasp)(4)(Pyrz)] center dot 2MeCN}(n) (5), [Cu-2(Brasp)(4)(Pyrz)](n) (6), [Cu-2(Clasp)(4)(4,4'-Bipy)](n) (7), and [Cu-2(Brasp)(4)(4,4'-Bipy)](n) (8) (Fasp: fluor-aspirinate; Clasp: chloro-aspirinate; Brasp: bromo-aspirinate; MeCN: acetonitrile; Pyrz: pyrazine; 4,4'-Bipy: 4,4'-bipyridine). The crystal structure of two 2 and 4 have been determined by X-ray diffraction methods. All compounds have been studied employing elemental analysis, IR, and UV-Visible spectroscopic techniques. The results have been compared with previous data reported for complexes with similar structures.

Structure and luminescent investigation of the Ln(III)-beta-diketonate complexes containing tertiary amides

The synthesis and photoluminescent properties of Ln(III)-thenoyltrifluoroacetonate and dibenzoylmethanate complexes (Ln = Eu(III) and Gd(III) ions) containing tertiary amides such as dimethylacetamide (DMA), dimethylformamide (DMF), and dimethylbenzamide (DMB) as neutral ligands are reported. The Ln complexes were characterized by elemental analysis, complexometric titration with EDTA, and infrared spectroscopy. Single-crystal X-ray structure data of the [Eu(DBM)(3).(DMA)] compound indicates that this complex crystallizes in the triclinic system, space group PT with the following cell parameters: a = 10.2580(3) angstrom, b = 10.3843(2) angstrom, c= 22.3517(5) angstrom, alpha = 78.906(2)degrees, beta = 78.049(2)degrees, lambda= 63.239(2)degrees, V= 2066.41(9) angstrom(3), and Z = 2. The coordination polyhedron for the Eu(III) complex may be described as an approximate C-2v distorted monocapped trigonal prism. The optical properties of the Eu(III) complexes were studied based on the intensity parameters and luminescence quantum yield (q). The values of the ohm(2) parameter of the Eu-DBM complexes are larger than those for the Eu-TTA complexes, indicating that the Eu(III) ion is in a more polarizable chemical environment in the former case. The geometries of the complexes have been optimized by using the Sparkle Model, and the results have been used to perform theoretical predictions of the ligand-to-metal energy transfer via direct and exchange Coulomb mechanisms. (C) 2012 Elsevier Ltd. All rights reserved.

Unraveling the structure of sugarcane bagasse after soaking in concentrated aqueous ammonia (SCAA) and ethanol production by Scheffersomyces (Pichia) stipitis

Abstract Background Fuel ethanol production from sustainable and largely abundant agro-residues such as sugarcane bagasse (SB) provides long term, geopolitical and strategic benefits. Pretreatment of SB is an inevitable process for improved saccharification of cell wall carbohydrates. Recently, ammonium hydroxide-based pretreatment technologies have gained significance as an effective and economical pretreatment strategy. We hypothesized that soaking in concentrated aqueous ammonia-mediated thermochemical pretreatment (SCAA) would overcome the native recalcitrance of SB by enhancing cellulase accessibility of the embedded holocellulosic microfibrils. Results In this study, we designed an experiment considering response surface methodology (Taguchi method, L8 orthogonal array) to optimize sugar recovery from ammonia pretreated sugarcane bagasse (SB) by using the method of soaking in concentrated aqueous ammonia (SCAA-SB). Three independent variables: ammonia concentration, temperature and time, were selected at two levels with center point. The ammonia pretreated bagasse (SCAA-SB) was enzymatically hydrolysed by commercial enzymes (Celluclast 1.5 L and Novozym 188) using 15 FPU/g dry biomass and 17.5 Units of β-glucosidase/g dry biomass at 50°C, 150 rpm for 96 h. A maximum of 28.43 g/l reducing sugars corresponding to 0.57 g sugars/g pretreated bagasse was obtained from the SCAA-SB derived using a 20% v/v ammonia solution, at 70°C for 24 h after enzymatic hydrolysis. Among the tested parameters, pretreatment time showed the maximum influence (p value, 0.053282) while ammonia concentration showed the least influence (p value, 0.612552) on sugar recovery. The changes in the ultra-structure and crystallinity of native SCAA-SB and enzymatically hydrolysed SB were observed by scanning electron microscopy (SEM), x-ray diffraction (XRD) and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. The enzymatic hydrolysates and solid SCAA-SB were subjected to ethanol fermentation under separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) by Scheffersomyces (Pichia) stipitis NRRL Y-7124 respectively. Higher ethanol production (10.31 g/l and yield, 0.387 g/g) was obtained through SSF than SHF (3.83 g/l and yield, 0.289 g/g). Conclusions SCAA treatment showed marked lignin removal from SB thus improving the accessibility of cellulases towards holocellulose substrate as evidenced by efficient sugar release. The ultrastructure of SB after SCAA and enzymatic hydrolysis of holocellulose provided insights of the degradation process at the molecular level.

New insights regarding HCV-NS5A structure/function and indication of genotypic differences

Abstract Background HCV is prevalent throughout the world. It is a major cause of chronic liver disease. There is no effective vaccine and the most common therapy, based on Peginterferon, has a success rate of ~50%. The mechanisms underlying viral resistance have not been elucidated but it has been suggested that both host and virus contribute to therapy outcome. Non-structural 5A (NS5A) protein, a critical virus component, is involved in cellular and viral processes. Methods The present study analyzed structural and functional features of 345 sequences of HCV-NS5A genotypes 1 or 3, using in silico tools. Results There was residue type composition and secondary structure differences between the genotypes. In addition, second structural variance were statistical different for each response group in genotype 3. A motif search indicated conserved glycosylation, phosphorylation and myristoylation sites that could be important in structural stabilization and function. Furthermore, a highly conserved integrin ligation site was identified, and could be linked to nuclear forms of NS5A. ProtFun indicated NS5A to have diverse enzymatic and nonenzymatic activities, participating in a great range of cell functions, with statistical difference between genotypes. Conclusion This study presents new insights into the HCV-NS5A. It is the first study that using bioinformatics tools, suggests differences between genotypes and response to therapy that can be related to NS5A protein features. Therefore, it emphasizes the importance of using bioinformatics tools in viral studies. Data acquired herein will aid in clarifying the structure/function of this protein and in the development of antiviral agents.

Phylogeography of the neotropical Anopheles triannulatus complex (Diptera: Culicidae) supports deep structure and complex patterns

Abstract Background The molecular phylogenetic relationships and population structure of the species of the Anopheles triannulatus complex: Anopheles triannulatus s.s., Anopheles halophylus and the putative species Anopheles triannulatus C were investigated. Methods The mitochondrial COI gene, the nuclear white gene and rDNA ITS2 of samples that include the known geographic distribution of these taxa were analyzed. Phylogenetic analyses were performed using Bayesian inference, Maximum parsimony and Maximum likelihood approaches. Results Each data set analyzed septely yielded a different topology but none provided evidence for the seption of An. halophylus and An. triannulatus C, consistent with the hypothesis that the two are undergoing incipient speciation. The phylogenetic analyses of the white gene found three main clades, whereas the statistical parsimony network detected only a single metapopulation of Anopheles triannulatus s.l. Seven COI lineages were detected by phylogenetic and network analysis. In contrast, the network, but not the phylogenetic analyses, strongly supported three ITS2 groups. Combined data analyses provided the best resolution of the trees, with two major clades, Amazonian (clade I) and trans-Andean + Amazon Delta (clade II). Clade I consists of multiple subclades: An. halophylus + An. triannulatus C; trans-Andean Venezuela; central Amazonia + central Bolivia; Atlantic coastal lowland; and Amazon delta. Clade II includes three subclades: Panama; cis-Andean Colombia; and cis-Venezuela. The Amazon delta specimens are in both clades, likely indicating local sympatry. Spatial and molecular variance analyses detected nine groups, corroborating some of subclades obtained in the combined data analysis. Conclusion Combination of the three molecular markers provided the best resolution for differentiation within An. triannulatus s.s. and An. halophylus and C. The latest two species seem to be very closely related and the analyses performed were not conclusive regarding species differentiation. Further studies including new molecular markers would be desirable to solve this species status question. Besides, results of the study indicate a trans-Andean origin for An. triannulatus s.l. The potential implications for malaria epidemiology remain to be investigated.

Alpha cluster structure in 16O.

The alpha cluster phenomenon in the light nuclei structure has been the subject of a longtime investigation since the proposal of the Ikeda diagrams, however the mechanism of the cluster formation is still not completely understood. In fact, if the clusters have a fairly rigid crystal-like or a gas-like structure remains an open question. The interpretation of the Hoyle state as an α condensate brought a renewed interest to this subject, in particular to resonances analogous to the Hoyle state. In this context the study of the experimental evolution of the α-cluster phenomenon through (6Li,d) transfer reactions has been performed in São Paulo. Particularly important are the regions around the nα thresholds where the α-cluster structure states are predicted. The resonant states around the 4α threshold in the nucleus 16O are the focus of the present contribution. The 12C(6Li,d)16O reaction was measured at a bombarding energy of 25.5 MeV employing the São Paulo Pelletron-Enge-Spectrograph facility and the nuclear emulsion detection technique. Resonant states above the α threshold were measured and an energy resolution of 15-30 keV allows to define states previously unresolved. The angular distributions of the absolute cross sections were determined in a range of 4-40 degree in the center of mass system and up to 17 MeV excitation energy. The upper limit for the resonance widths in the crucial region of the 4α threshold was obtained. These values revealed to be at least a factor three smaller than the ones previously reported in the literature, indicating that the α cluster structure information on this region should be revised.

ScPdZn and ScPtZn with YAlGe type structure: group-subgroup relation and 45Sc solid state NMR spectroscopy

The intermetallic compounds ScPdZn and ScPtZn were prepared from the elements by high-frequency melting in sealed tantalum ampoules. Both structures were refined from single crystal X-ray diffractometer data: YAlGe type, Cmcm, a = 429.53(8), b = 907.7(1), c = 527.86(1) pm, wR2 = 0.0375, 231 F2 values, for ScPdZn and a = 425.3(1), b = 918.4(2), c = 523.3(1) pm, wR2 = 0.0399, 213 F2 values for ScPtZn with 14 variables per refinement. The structures are orthorhombically distorted variants of the AlB2 type. The scandium and palladium (platinum atoms) build up ordered networks Sc3Pd3 and Sc3Pt3 (boron networks) which are slightly shifted with respect to each other. These networks are penetrated by chains of zinc atoms (262 pm in ScPtZn) which correspond to the aluminum positions, i.e. Zn(ScPd) and Zn(ScPt). The corresponding group-subgroup scheme and the differences in chemical bonding with respect to other AlB2-derived REPdZn and REPtZn compounds are discussed. 45Sc solid state NMR spectra confirm the single crystallographic scandium sites. From electronic band structure calculations the two compounds are found metallic with free electron like behavior at the Fermi level. A larger cohesive energy for ScPtZn suggests a more strongly bonded intermetallic than ScPdZn. Electron localization and overlap population analyses identify the largest bonding for scandium with the transition metal (Pd, Pt).

Sviluppo di metodologie di localizzazione nel contesto del Comprehensive Nuclear Test-Ban Treaty

Since the first underground nuclear explosion, carried out in 1958, the analysis of seismic signals generated by these sources has allowed seismologists to refine the travel times of seismic waves through the Earth and to verify the accuracy of the location algorithms (the ground truth for these sources was often known). Long international negotiates have been devoted to limit the proliferation and testing of nuclear weapons. In particular the Treaty for the comprehensive nuclear test ban (CTBT), was opened to signatures in 1996, though, even if it has been signed by 178 States, has not yet entered into force, The Treaty underlines the fundamental role of the seismological observations to verify its compliance, by detecting and locating seismic events, and identifying the nature of their sources. A precise definition of the hypocentral parameters represents the first step to discriminate whether a given seismic event is natural or not. In case that a specific event is retained suspicious by the majority of the State Parties, the Treaty contains provisions for conducting an on-site inspection (OSI) in the area surrounding the epicenter of the event, located through the International Monitoring System (IMS) of the CTBT Organization. An OSI is supposed to include the use of passive seismic techniques in the area of the suspected clandestine underground nuclear test. In fact, high quality seismological systems are thought to be capable to detect and locate very weak aftershocks triggered by underground nuclear explosions in the first days or weeks following the test. This PhD thesis deals with the development of two different seismic location techniques: the first one, known as the double difference joint hypocenter determination (DDJHD) technique, is aimed at locating closely spaced events at a global scale. The locations obtained by this method are characterized by a high relative accuracy, although the absolute location of the whole cluster remains uncertain. We eliminate this problem introducing a priori information: the known location of a selected event. The second technique concerns the reliable estimates of back azimuth and apparent velocity of seismic waves from local events of very low magnitude recorded by a trypartite array at a very local scale. For the two above-mentioned techniques, we have used the crosscorrelation technique among digital waveforms in order to minimize the errors linked with incorrect phase picking. The cross-correlation method relies on the similarity between waveforms of a pair of events at the same station, at the global scale, and on the similarity between waveforms of the same event at two different sensors of the try-partite array, at the local scale. After preliminary tests on the reliability of our location techniques based on simulations, we have applied both methodologies to real seismic events. The DDJHD technique has been applied to a seismic sequence occurred in the Turkey-Iran border region, using the data recorded by the IMS. At the beginning, the algorithm was applied to the differences among the original arrival times of the P phases, so the cross-correlation was not used. We have obtained that the relevant geometrical spreading, noticeable in the standard locations (namely the locations produced by the analysts of the International Data Center (IDC) of the CTBT Organization, assumed as our reference), has been considerably reduced by the application of our technique. This is what we expected, since the methodology has been applied to a sequence of events for which we can suppose a real closeness among the hypocenters, belonging to the same seismic structure. Our results point out the main advantage of this methodology: the systematic errors affecting the arrival times have been removed or at least reduced. The introduction of the cross-correlation has not brought evident improvements to our results: the two sets of locations (without and with the application of the cross-correlation technique) are very similar to each other. This can be commented saying that the use of the crosscorrelation has not substantially improved the precision of the manual pickings. Probably the pickings reported by the IDC are good enough to make the random picking error less important than the systematic error on travel times. As a further justification for the scarce quality of the results given by the cross-correlation, it should be remarked that the events included in our data set don’t have generally a good signal to noise ratio (SNR): the selected sequence is composed of weak events ( magnitude 4 or smaller) and the signals are strongly attenuated because of the large distance between the stations and the hypocentral area. In the local scale, in addition to the cross-correlation, we have performed a signal interpolation in order to improve the time resolution. The algorithm so developed has been applied to the data collected during an experiment carried out in Israel between 1998 and 1999. The results pointed out the following relevant conclusions: a) it is necessary to correlate waveform segments corresponding to the same seismic phases; b) it is not essential to select the exact first arrivals; and c) relevant information can be also obtained from the maximum amplitude wavelet of the waveforms (particularly in bad SNR conditions). Another remarkable point of our procedure is that its application doesn’t demand a long time to process the data, and therefore the user can immediately check the results. During a field survey, such feature will make possible a quasi real-time check allowing the immediate optimization of the array geometry, if so suggested by the results at an early stage.