Azotobacter genomes: the genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)

The genome of the soil-dwelling heterotrophic N2-fixing Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 (ATCC 4412) (Ac-8003) has been determined. It consists of 7 circular replicons totalling 5,192,291 bp comprising a circular chromosome of 4,591,803 bp and six plasmids pAcX50a, b, c, d, e, f of 10,435 bp, 13,852, 62,783, 69,713, 132,724, and 311,724 bp respectively. The chromosome has a G+C content of 66.27% and the six plasmids have G+C contents of 58.1, 55.3, 56.7, 59.2, 61.9, and 62.6% respectively. The methylome has also been determined and 5 methylation motifs have been identified. The genome also contains a very high number of transposase/inactivated transposase genes from at least 12 of the 17 recognised insertion sequence families. The Ac-8003 genome has been compared with that of Azotobacter vinelandii ATCC BAA-1303 (Av-DJ), a derivative of strain O, the only other member of the Azotobacteraceae determined so far which has a single chromosome of 5,365,318 bp and no plasmids. The chromosomes show significant stretches of synteny throughout but also reveal a history of many deletion/insertion events. The Ac-8003 genome encodes 4628 predicted protein-encoding genes of which 568 (12.2%) are plasmid borne. 3048 (65%) of these show > 85% identity to the 5050 protein-encoding genes identified in Av-DJ, and of these 99 are plasmid-borne. The core biosynthetic and metabolic pathways and macromolecular architectures and machineries of these organisms appear largely conserved including genes for CO-dehydrogenase, formate dehydrogenase and a soluble NiFe-hydrogenase. The genetic bases for many of the detailed phenotypic differences reported for these organisms have also been identified. Also many other potential phenotypic differences have been uncovered. Properties endowed by the plasmids are described including the presence of an entire aerobic corrin synthesis pathway in pAcX50f and the presence of genes for retro-conjugation in pAcX50c. All these findings are related to the potentially different environmental niches from which these organisms were isolated and to emerging theories about how microbes contribute to their communities.

On mathematical and physical principles of transformations of the coherent radar backscatter matrix

The congruential rule advanced by Graves for polarization basis transformation of the radar backscatter matrix is now often misinterpreted as an example of consimilarity transformation. However, consimilarity transformations imply a physically unrealistic antilinear time-reversal operation. This is just one of the approaches found in literature to the description of transformations where the role of conjugation has been misunderstood. In this paper, the different approaches are examined in particular in respect to the role of conjugation. In order to justify and correctly derive the congruential rule for polarization basis transformation and properly place the role of conjugation, the origin of the problem is traced back to the derivation of the antenna height from the transmitted field. In fact, careful consideration of the role played by the Green’s dyadic operator relating the antenna height to the transmitted field shows that, under general unitary basis transformation, it is not justified to assume a scalar relationship between them. Invariance of the voltage equation shows that antenna states and wave states must in fact lie in dual spaces, a distinction not captured in conventional Jones vector formalism. Introducing spinor formalism, and with the use of an alternate spin frame for the transmitted field a mathematically consistent implementation of the directional wave formalism is obtained. Examples are given comparing the wider generality of the congruential rule in both active and passive transformations with the consimilarity rule.

Asymmetric oxidation of vinyl- and ethynyl terthiophene ligands in triruthenium complexes

A series of ruthenium(II) complexes [{RuCl(CO)(PMe3)3(–CHvCH–)}nX], 1a–1c (1a: n = 3, X = 3,3’’- dimethyl-2,2’:3’,2’’-terthiophene; 1b: n = 2, X = 2,2’-bithiophene; 1c: n = 2, X = 2,3-bis(3-methylthiophen- 2-yl)benzothiophene) and [{Cp*(dppe)2Ru(–CuC–)}3X], 1d (X = 3,3’’-dimethyl-2,2’:3’,2’’- terthiophene), were prepared and characterized by 1H, 13C and 31P NMR. Their redox, spectroscopic and bonding properties were studied with a range of spectro-electrochemical methods in combination with density functional theory calculations. The first two anodic steps observed for 1a and 1d are largely localized on the lateral frameworks of the molecular triangle, the direct conjugation between them being precluded due to the photostable open form of the dithienyl ethene moiety. The third anodic step is then mainly localized on the centerpiece of the triangular structure, affecting both bithiophene laterals. The experimental IR and UV-vis-NIR spectroelectrochemical data and, largely, also DFT calculations account for this explanation, being further supported by direct comparison with the anodic behavior of reference diruthenium complexes 1b and 1c.

Azo-group dihedral angle torsion dependence on temperature: A theorerical-experimental study

Quantum chemical calculations were carried out to explain the observed shifts in the absorption spectrum of different azo-aromatic compounds due to changes in the dihedral angle of the azo-group. Our results reveal that the pi-pi* transition presents a hypsochromic shift and an oscillator strength drop upon increase of the dihedral angle. Nevertheless, the pi-pi* transition exhibits the opposite behavior. This effect is attributed to the reduction in the pi-electron conjugation length of the molecule. Experimentally, we performed temperature dependence measurements of the linear absorption spectrum. Both the theoretical and experimental results demonstrate that small energy changes are mirrored in the electronic transitions of conjugated linear molecules. (C) 2010 Elsevier B.V. All rights reserved.

Excited State Absorption of Doped and Undoped Polyanyline

Polyaniline is a conducting polymer with appealing electrical and optical properties, arising from the -conjugation along the polymer backbone. The understanding of its excited state absorption is of prime importance for designing and fabricating optical devices. Here, we report on the study of the excited state absorption of doped and undoped PANI by using femtosecond pulses in the spectral range from 450nm up to 850nm. For undoped PANI, we observed saturation of absorption as well as reverse saturable absorption, depending on the excitation wavelength. For doped PANI, however, only saturable absorption was observed.

Controlling the absorption and emission properties of polyparaphenylenevinylene films

In this work we used the conversion process of a precursor polymer into polyparaphenylenevinylene (PPV) at low temperatures in order to control the effective conjugation degree of spin-casted PPV films. The absorption and emission spectra of the films were studied by following a partial substitution of chloride counterions from poly(xylylidene tetrahydrothiophenium chloride) (PTHT), used as a precursor, by sodium acid dodecyl benzenesulfonate (DBS), added as a surfactant salt. Upon controlling the DBS amount and conversion temperature (T-c) of PTHT/DBS to PPV films, the band gap of PPV changed from 409 to 506 nm, and 505 to 532 nm, values obtained from absorbance and emission measurements, respectively. Based on these experimental data, we proposed a physical model which represents the chemical structure of PPV as a distribution of conjugated chain segments (like oligomers) alternated by non-conjugated segments (structural defects and/or from the precursor polymer). (C) 2008 Elsevier B.V. All rights reserved.

Intermolecular Contacts Influencing the Conformational and Geometric Features of the Pharmaceutically Preferred Mebendazole Polymorph C

Mebendazole (MBZ) is a common benzimidazole anthelmintic that exists in three different polymorphic forms, A, B, and C. Polymorph C is the pharmaceutically preferred form due to its adequated aqueous solubility. No single crystal structure determinations depicting the nature of the crystal packing and molecular conformation and geometry have been performed on this compound. The crystal structure of mebendazole form C is resolved for the first time. Mebendazole form C crystallizes in the triclinic centrosymmetric space group and this drug is practically planar, since the least-squares methyl benzimidazolylcarbamate plane is much fitted on the forming atoms. However, the benzoyl group is twisted by 31(1)degrees from the benzimidazole ring, likewise the torsional angle between the benzene and carbonyl moieties is 27(1)degrees. The formerly described bends and other interesting intramolecular geometry features were viewed as consequence of the intermolecular contacts occurring within mebendazole C structure. Among these features, a conjugation decreasing through the imine nitrogen atom of the benzimidazole core and a further resonance path crossing the carbamate one were described. At last, the X-ray powder diffractogram of a form C rich mebendazole mixture was overlaid to the calculated one with the mebendazole crystal structure. (C) 2008 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:2336-2344, 2009

Cloning, expression, purification and characterization of recombinant glutathione-S-transferase from Xylella fastidiosa

Xylella fastidiosa is an important pathogen bacterium transmitted by xylem-feedings leafhoppers that colonizes the xylem of plants and causes diseases on several important crops including citrus variegated chlorosis (CVC) in orange and lime trees. Glutathione-S-transferases (GST) form a group of multifunctional isoenzymes that catalyzes both glutathione (GSH)-dependent conjugation and reduction reactions involved in the cellular detoxification of xenobiotic and endobiotic compounds. GSTs are the major detoxification enzymes found in the intracellular space and mainly in the cytosol from prokaryotes to mammals, and may be involved in the regulation of stress-activated signals by suppressing apoptosis signal-regulating kinase 1. In this study, we describe the cloning of the glutathione-S-transferase from X. fastidiosa into pET-28a(+) vector, its expression in Escherichia coli, purification and initial structural characterization. The purification of recombinant xfGST (rxfGST) to near homogeneity was achieved using affinity chromatography and size-exclusion chromatography (SEC). SEC demonstrated that rxfGST is a homodimer in solution. The secondary and tertiary structures of recombinant protein were analyzed by circular dichroism and fluorescence spectroscopy, respectively. The enzyme was assayed for activity and the results taken together indicated that rxfGST is a stable molecule, correctly folded, and highly active. Several members of the GST family have been extensively studied. However, xfGST is part of a less-studied subfamily which yet has not been structurally and biochemically characterized. In addition, these studies should provide a useful basis for future studies and biotechnological approaches of rxfGST. (C) 2008 Elsevier Inc. All rights reserved.

Preparation and photoluminescence properties of functionalized silica materials incorporating europium complexes

In the present work, the surface of the Eu-BTC = [Eu(EMA)(H(2)O)(2)], [Eu(TLA)(H(2)O)(4)] and [Eu(TMA)(H(2)O)(6)] complexes (EMA = 1,2,3-benzenetricarboxylate, TLA = 1,2,4-benzenetricarboxylate and TMA = 1,3,5-benzenetricarboxylate) was modified using 3-aminopropyltriethoxysilane (APTES) by a new microwave assisted method that proved to be simple and efficient. According to our observations, the most efficient luminescence is the material based on APTES incorporating [Eu(TMA)(H(2)O)(6)] complexes, denoted as Eu-TMA-Si, shows the highest emission efficiency. Therefore, it is proposed as a promising material for molecular conjugation in clinical diagnosis. (C) 2011 Elsevier B.V. All rights reserved.

Studies on the resonance Raman spectra of polyaniline obtained with near-IR excitation

The effects of near-IR (NIR) laser power over the Raman spectra of poly(aniline) emeraldine salt (PANIES) and base (PANI-EB) were investigated. The reasons for the existence of several bands from 1324 to 1500 cm-1 in the Raman spectra of poly(aniline) obtained at NIR region were also studied. The bands from 1324 to 1375 cm-` were associated to vC-N of polarons with different conjugation lengths and the bands from 1450 to 1500 cm-1 in Raman spectra of PANI emeraldine and pernigraniline base forms were correlated to vC=N modes associated with quinoid units having different conjugation lengths. The increase of laser power at 1064.0 run causes the deprotonation of PANI-ES and the formation of cross-linking segments having phenazine and/or oxazine rings. For PANI-EB only a small spectral change is observed when the laser power is increased, owing to the low absorption of this form in the NIR region. Copyright (c) 2007 John Wiley & Sons, Ltd.

Spectroscopic investigation of conjugated polymers derived from nitroanilines

For the first time, the resonance Raman spectroscopy was used to characterize polymers derived from meta- and para-nitroanilines. In order to improve the polymer structure analysis, other techniques were also used such as FTIR, UV-vis, XRD, XPS, EPR and N K-XANES. The insertion of strong electron-withdrawing groups (NO2) in polyaniline (PANI)-like backbone causes drastic changes in the lower energy charge transfer states, related to the polymer effective conjugation length. The resonance Raman data show that the NO2 moiety has a minor contribution on the CT state in poly(meta-nitroaniline), PMN, while in the poly(para-nitroaniline), PPN, the quinoid structure induced by para-substitution increases the charge density of NO2 groups, causing a more localized chromophore. The characterization of the imine nitrogen and of the protonated segments was done by XPS, N K-XANES and EPR spectroscopies and the lower polymerization degree of PPN, in comparison to PMN, is confirmed by XRD and TG data. (C) 2007 Elsevier B.V. All rights reserved.

Biolabeling with nanoparticles based on Y(2)O(3):Nd(3+) and luminescence detection in the near-infrared

Neodymium based fluorescence presents several advantages in comparison to conventional rare earth or enzyme-substrate based fluorescence emitting sources (e.g.Tb, HRP). Based on this fact we have herein explored a Nd-based fluoroimmunoassay. We efficiently detected the presence of an oxidized low-density lipoprotein (oxLDL) in human plasma a well-known marker for cardiovascular diseases, which causes around 30% of deaths worldwide. Conventional fluoroimmunoassay uses time-resolved luminescence techniques, with detection in the visible range, to eliminate the fluorescence background from the biological specimens. By using an immunoassay based on functionalized Y(2)O(3):Nd(3+) nanoparticles, where the excitation and emission processes in the Nd(3+) ion occur in the near-infrared (NIR) region, we have succeeded in eliminating the interferences from the biological fluorescence background, avoiding the use of time-resolved techniques. This yields higher emission intensity from the Nd(3+)-nanolabels and efficient detection of anti-oxidized low-density lipoproteins (anti-oxLDL) by Y(2)O(3):Nd(3+)-antibody-antigen conjugation, leading to a novel biolabeling method. (C) 2010 Elsevier B.V. All rights reserved.

Testing Seasonal Unit Roots in Data at Any Frequency, an HEGY approach

This paper generalizes the HEGY-type test to detect seasonal unit roots in data at any frequency, based on the seasonal unit root tests in univariate time series by Hylleberg, Engle, Granger and Yoo (1990). We introduce the seasonal unit roots at first, and then derive the mechanism of the HEGY-type test for data with any frequency. Thereafter we provide the asymptotic distributions of our test statistics when different test regressions are employed. We find that the F-statistics for testing conjugation unit roots have the same asymptotic distributions. Then we compute the finite-sample and asymptotic critical values for daily and hourly data by a Monte Carlo method. The power and size properties of our test for hourly data is investigated, and we find that including lag augmentations in auxiliary regression without lag elimination have the smallest size distortion and tests with seasonal dummies included in auxiliary regression have more power than the tests without seasonal dummies. At last we apply the our test to hourly wind power production data in Sweden and shows there are no seasonal unit roots in the series.

The Isolation and Characterization of Multiply Antibiotic Resistant Strains of Fish Pathogenic Flavobacterium Species

Since the development of the first antibiotics in the 1940’s, there has been widespread overuse in both clinical and agricultural applications. Antibiotic resistance has become a significant problem as a result of subsequent dissemination of antibiotics into the environment, and multiply-resistant strains of bacteria are now a major pathogenic threat. In this study eight separate strains of Flavobacterium responsible for recent disease outbreaks in fish hatcheries throughout Maine were collected and analyzed. All eight strains were found to be resistant to high levels of a number of different antibiotics, including those used for aquaculture as well as human chemotherapeutic applications. Flavobacterium isolates were also shown phenotypically to transfer antibiotic resistance determinants using a conjugation mating system in which Flavobacterium was the donor and Escherichia coli DH5- alpha was the recipient. This experiment suggests that it may be possible for Flavobacterium strains to transfer their multiple antibiotic resistance determinants to human pathogenic bacterial strains. Importantly, none of the hatcheries from which the Flavobacterium isolates were obtained had ever used antibiotics to treat their fish stock. It is possible that there is another selective agent responsible for the development of antibiotic resistance in the absence of antibiotic pressure. Mercury is one possible candidate, as all of the strains tested were resistant to mercuric chloride and it is known that genes encoding antibiotic resistance can be carried on the same mobile genetic elements that encode for mercury resistance. Preliminary data also suggest that the majority of the Flavobacterium isolates contain genes for mercuric ion reduction, which would confirm the mercury resistance genotype.

A Broad-spectrum mer Operon in a Multi-drug Resistant Strain of the Fish Pathogen, Aeromonas salmonicida.

Aeromonas salmonicida AS03, a potential fish pathogen, was isolated from Atlantic salmon, Salmo salar, in 2003. This strain was found to be resistant to ≥1000 mM HgCl2 and ≥32 mM phenylmercuric acetate as well as multiple antimicrobials. Mercury (Hg) and antibiotic resistance genes are often located on the same mobile genetic elements, so the genetic determinants of both resistances and the possibility of horizontal gene transfer were examined. Specific PCR primers were used to amplify and sequence distinctive regions of the mer operon. A. salmonicida AS03 was found to have a pDU1358-like broad-spectrum mer operon, containing merB as well as merA, merD, merP, merR and merT, most similar to Klebsiella pneumonaie plasmid pRMH760. To our knowledge, the mer operon has never before been documented in Aeromonas spp. PCR and gene sequencing were used to identify class 1 integron associated antibiotic resistance determinants and the Tet A tetracycline resistance gene. The transposase and resolvase genes of Tn1696 were identified through PCR and sequencing with Tn21 specific PCR primers. We provide phenotypic and genotypic evidence that the mer operon, the aforementioned antibiotic resistances, and the Tn1696 transposition module are located on a single plasmid or conjugative transposon that can be transferred to E. coli DH5α through conjugation in the presence of low level Hg and absence of any antibiotic selective pressure. Additionally, the presence of low-level Hg or chloramphenicol in the mating media was found to stimulate conjugation, significantly increasing the transfer frequency of conjugation above the transfer frequency measured with mating media lacking both antibiotics and Hg. This research demonstrates that mercury indirectly selects for the dissemination of the antibiotic resistance genes of A. salmonicida AS03.