The ENIGMA Consortium: Large-scale collaborative analyses of neuroimaging and genetic data

The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience, genetics, and medicine, ENIGMA studies have analyzed neuroimaging data from over 12,826 subjects. In addition, data from 12,171 individuals were provided by the CHARGE consortium for replication of findings, in a total of 24,997 subjects. By meta-analyzing results from many sites, ENIGMA has detected factors that affect the brain that no individual site could detect on its own, and that require larger numbers of subjects than any individual neuroimaging study has currently collected. ENIGMA's first project was a genome-wide association study identifying common variants in the genome associated with hippocampal volume or intracranial volume. Continuing work is exploring genetic associations with subcortical volumes (ENIGMA2) and white matter microstructure (ENIGMA-DTI). Working groups also focus on understanding how schizophrenia, bipolar illness, major depression and attention deficit/hyperactivity disorder (ADHD) affect the brain. We review the current progress of the ENIGMA Consortium, along with challenges and unexpected discoveries made on the way.

A preliminary investigation into adrenal responsiveness and outcomes in patients with cardiogenic shock after acute myocardial infarction

PURPOSE: This study investigated the significance of baseline cortisol levels and adrenal response to corticotropin in shocked patients after acute myocardial infarction (AMI). METHODS: A short corticotropin stimulation test was performed in 35 patients with cardiogenic shock after AMI by intravenously injecting of 250 μg of tetracosactrin (Synacthen). Blood samples were obtained at baseline (T0) before and at 30 (T30) and 60 (T60) minutes after the test to determine plasma total cortisol (TC) and free cortisol concentrations. The main outcome measure was in-hospital mortality and its association with T0 TC and maximum response to corticotropin (maximum difference [Δ max] in cortisol levels between T0 and the highest value between T30 and T60). RESULTS: The in-hospital mortality was 37%, and the median time to death was 4 days (interquartile range, 3-9 days). There was some evidence of an increased mortality in patients with T0 TC concentrations greater than 34 μg/dL (P=.07). Maximum difference by itself was not an independent predictor of death. Patients with a T0 TC 34 μg/dL or less and Δ max greater than 9 μg/dL appeared to have the most favorable survival (91%) when compared with the other 2 groups: T0 34 μg/dL or less and Δ max 9 μg/dL or less or T0 34 μg/dL or higher and Δ max greater than 9 μg/dL (75%; P=.8) and T0 greater than 34 μg/dL and Δ max 9 μg/dL or less (60%; P=.02). Corticosteroid therapy was associated with an increased mortality (P=.03). There was a strong correlation between plasma TC and free cortisol (r=0.85). CONCLUSIONS: A high baseline plasma TC was associated with a trend toward increased mortality in patients with cardiogenic shock post-AMI. Patients with lower baseline TC, but with an inducible adrenal response, appeared to have a survival benefit. A prognostic system based on basal TC and Δ max similar to that described in septic shock appears feasible in this cohort. Corticosteroid therapy was associated with adverse outcomes. These findings require further validation in larger studies.

Molecular Biomonitoring during Rhizoremediation of Oil-Contaminated Soil

Rhizoremediation is the use of microbial populations present in the rhizosphere of plants for environmental cleanup. The idea of this work was that bacteria living in the rhizosphere of a nitrogen-fixing leguminous plant, goat's rue (Galega orientalis), could take part in the degradation of harmful monoaromatic hydrocarbons, such as benzene, toluene and xylene (BTEX), from oil-contaminated soils. In addition to chemical (e.g. pollutant concentration) and physical (e.g. soil structure) information, the knowledge of biological aspects (e.g. bacteria and their catabolic genes) is essential when developing the rhizoremediation into controlled and effective bioremediation practice. Therefore, the need for reliable biomonitoring methods is obvious. The main aims of this thesis were to evaluate the symbiotic G. orientalis - Rhizobium galegae system for rhizoremediation of oil-contaminated soils, to develop molecular methods for biomonitoring, and to apply these methods for studying the microbiology of rhizoremediation. In vitro, Galega plants and rhizobia remained viable in m-toluate concentrations up to 3000 mg/l. Plant growth and nodulation were inhibited in 500 mg/l m-toluate, but were restored when plants were transferred to clean medium. In the greenhouse, Galega showed good growth, nodulation and nitrogen fixation, and developed a strong rhizosphere in soils contaminated with oil or spiked with 2000 mg/l m-toluate. The high aromatic tolerance of R. galegae and the viability of Galega plants in oil-polluted soils proved this legume system to be a promising method for the rhizoremediation of oil-contaminated soils. Molecular biomonitoring methods were designed and/or developed further for bacteria and their degradation genes. A combination of genomic fingerprinting ((GTG)5-PCR), taxonomic ribotyping of 16S rRNA genes and partial 16S rRNA gene sequencing were chosen for molecular grouping of culturable, heterogeneous rhizosphere bacteria. PCR primers specific for the xylE gene were designed for TOL plasmid detection. Amplified enzyme-coding DNA restriction analysis (AEDRA) with AluI was used to profile both TOL plasmids (xylE primers) and, in general, aromatics-degrading plasmids (C230 primers). The sensitivity of the direct monitoring of TOL plasmids in soil was enhanced by nested C23O-xylE-PCR. Rhizosphere bacteria were isolated from the greenhouse and field lysimeter experiments. High genetic diversity was observed among the 50 isolated, m-toluate tolerating rhizosphere bacteria in the form of five major lineages of the Bacteria domain. Gram-positive Rhodococcus, Bacillus and Arthrobacter and gram-negative Pseudomonas were the most abundant genera. The inoculum Pseudomonas putida PaW85/pWW0 was not found in the rhizosphere samples. Even if there were no ecological niches available for the bioaugmentation bacterium itself, its conjugative catabolic plasmid might have had some additional value for other bacterial species and thus, for rhizoremediation. Only 10 to 20% of the isolated, m-toluate tolerating bacterial strains were also able to degrade m-toluate. TOL plasmids were a major group of catabolic plasmids among these bacteria. The ability to degrade m-toluate by using enzymes encoded by a TOL plasmid was detected only in species of the genus Pseudomonas, and the best m-toluate degraders were these Pseudomonas species. Strain-specific differences in degradation abilities were found for P.oryzihabitans and P. migulae: some of these strains harbored a TOL plasmid - a new finding observed in this work, indicating putative horizontal plasmid transfer in the rhizosphere. One P. oryzihabitans strain harbored the pWW0 plasmid that had probably conjugated from the bioaugmentation Pseudomonas. Some P. migulae and P. oryzihabitans strains seemed to harbor both the pWW0- and the pDK1-type TOL plasmid. Alternatively, they might have harbored a TOL plasmid with both the pWW0- and the pDK1-type xylE gene. The breakdown of m-toluate by gram-negative bacteria was not restricted to the TOL pathway. Also some gram-positive Rhodococcus erythropolis and Arthrobacter aurescens strains were able to degrade m-toluate in the absence of a TOL plasmid. Three aspects of the rhizosphere effect of G. orientalis were manifested in oil-contaminated soil in the field: 1) G. orientalis and Pseudomonas bioaugmentation increased the amount of rhizosphere bacteria. G. orientalis especially together with Pseudomonas bioaugmentation increased the numbers of m-toluate utilizing and catechol positive bacteria indicating an increase in degradation potential. 2) Also the bacterial diversity, when measured as the amount of ribotypes, was increased in the Galega rhizosphere with or without Pseudomonas bioaugmentation. However, the diversity of m-toluate utilizing bacteria did not significantly increase. At the community level, by using the 16S rRNA gene PCR-DGGE method, the highest diversity of species was also observed in vegetated soils compared with non-vegetated soils. Diversified communities may best guarantee the overall success in rhizoremediation by offering various genetic machineries for catabolic processes. 3) At the end of the experiment, no TOL plasmid could be detected by direct DNA analysis in soil treated with both G. orientalis and Pseudomonas. The detection limit for TOL plasmids was encountered indicating decreased amount of degradation plasmids and thus, the success of rhizoremediation. The use of G. orientalis for rhizoremediation is unique. In this thesis new information was obtained about the rhizosphere effect of Galega orientalis in BTEX contaminated soils. The molecular biomonitoring methods can be applied for several purposes within environmental biotechnology, such as for evaluating the intrinsic biodegradation potential, monitoring the enhanced bioremediation, and estimating the success of bioremediation. Environmental protection by using nature's own resources and thus, acting according to the principle of sustainable development, would be both economically and environmentally beneficial for society. Keywords: molecular biomonitoring, genetic fingerprinting, soil bacteria, bacterial diversity, TOL plasmid, catabolic genes, horizontal gene transfer, rhizoremediation, rhizosphere effect, Galega orientalis, aerobic biodegradation, petroleum hydrocarbons, BTEX

TolA mediates the differential detergent resistance pattern between the Salmonella enterica subsp enterica serovars Typhi and Typhimurium

The tol-pal genes are essential for maintaining the outer membrane integrity and detergent resistance in various Gram-negative bacteria, including Salmonella. The role of TolA has been well established for the bile resistance of Salmonella enterica subsp. enterica serovar Typhimurium. We compared the bile resistance pattern between the S. enterica serovars Typhi and Typhimurium and observed that Typhi is more resistant to bile-mediated damage. A closer look revealed a significant difference in the TolA sequence between the two serovars which contributes to the differential detergent resistance. The tolA knockout of both the serovars behaves completely differently in terms of membrane organization and morphology. The role of the Pal proteins and difference in LPS organization between the two serovars were verified and were found to have no direct connection with the altered bile resistance. In normal Luria broth (LB), S. Typhi Delta tolA is filamentous while S. Typhimurium Delta tolA grows as single cells, similar to the wildtype. In low osmolarity LB, however, S. Typhimurium Delta tolA started chaining and S. Typhi Delta tolA showed no growth. Further investigation revealed that the chaining phenomenon observed was the result of failure of the outer membrane to separate in the dividing cells. Taken together, the results substantiate the evolution of a shorter TolA in S. Typhi to counteract high bile concentrations, at the cost of lower osmotic tolerance.

Tailoring the Magnetic and Optical Characteristics of Nanocrystalline BiFeO3 by Ce Doping

The Ce-doped BiFeO3 (BFO) nanoparticles (NPs) were synthesized using a facile solgel route with varying Ce concentrations in the range of 15 mol%. Ferroelectric transition temperature was found to shift from 723 degrees C +/- 5 degrees C for pristine BFO NPs to 534 degrees C +/- 3 degrees C for 5 mol% Ce-doped BFO NPs. UVVis absorption spectra of BFO NPs showed a significant blue shift of similar to 100 nm on Ce doping. The Fourier transformed infrared (FTIR) spectrum centered similar to 550 cm(-1) becomes considerably broadened on Ce doping which is due to additional closely spaced vibrational peaks as revealed by the second derivative FTIR analysis. High-frequency EPR measurements indicated that clustering occurs at high dopant levels, and that Fe is present as Fe(3+)corroborating Mossbauer measurements. The values of saturation and remanent magnetization for 3% Ce-doped BFO NPs are 3.03 and 0.49 emu/g, respectively, which are quite significant at room temperature, making it more suitable for technological applications.

Ferrimagnetism and magnetic phase separation in Nd1-xYxMnO3 studied by magnetization and high frequency electron paramagnetic resonance

Ferrimagnetism and metamagnetic features tunable by composition are observed in the magnetic response of Nd1-xYxMnO3, for x=0.1-0.5. For all values of x in the series, the compound crystallizes in orthorhombic Pbnm space group similar to NdMnO3. Magnetization studies reveal a phase transition of the Mn-sublattice below T-N(Mn) approximate to 80 K for all compositions, which, decreases up on diluting the Nd-site with Yttrium. For x=0.35, ferrimagnetism is observed. At 5 K, metamagnetic transition is observed for all compositions x < 0.4. The evolution of magnetic ground states and appearance of ferrimagnetism in Nd1-xYxMnO3 can be accounted for by invoking the scenario of magnetic phase separation. The high frequency electron paramagnetic resonance measurements on x=0.4 sample, which is close to the critical composition for phase separation, revealed complex temperature dependent lineshapes clearly supporting the assumption of magnetic phase separation. (C) 2014 Elsevier B.V. All rights reserved.

Design, Synthesis, and Study of Novel Platforms for Iron-N2 Chemistry and Photoinduced, Copper-mediated C-N Bond Formation

Several new ligand platforms designed to support iron dinitrogen chemistry have been developed. First, we report Fe complexes of a tris(phosphino)alkyl (CP^iPr₃) ligand featuring an axial carbon donor intended to conceptually model the interstitial carbide atom of the nitrogenase iron-molybdenum cofactor (FeMoco). It is established that in this scaffold, the iron center binds dinitrogen trans to the C_alkyl anchor in three structurally characterized oxidation states. Fe-C_alkyl lengthening is observed upon reduction, reflective of significant ionic character in the Fe-C_alkyl interaction. The anionic (CP^iPr₃)FeN₂^- species can be functionalized by a silyl electrophile to generate (CP^iPr₃)Fe-N₂SiR₃. This species also functions as a modest catalyst for the reduction of N₂ to NH₃. Next, we introduce a new binucleating ligand scaffold that supports an Fe(μ-SAr)Fe diiron subunit that coordinates dinitrogen (N₂-Fe(μ-SAr)Fe-N₂) across at least three oxidation states (Fe^IIFe^II, Fe^IIFe^I, and Fe^IFe^I). Despite the sulfur-rich coordination environment of iron in FeMoco, synthetic examples of transition metal model complexes that bind N₂ and also feature sulfur donor ligands remain scarce; these complexes thus represent an unusual series of low-valent diiron complexes featuring thiolate and dinitrogen ligands. The (N₂-Fe(μ-SAr)Fe-N₂) system undergoes reduction of the bound N₂ to produce NH₃ (~50% yield) and can efficiently catalyze the disproportionation of N₂H₄ to NH₃ and N₂. The present scaffold also supports dinitrogen binding concomitant with hydride as a co-ligand. Next, inspired by the importance of secondary-sphere interactions in many metalloenzymes, we present complexes of iron in two new ligand scaffolds ([SiP^NMe₃] and [SiP^iPr₂P^NMe]) that incorporate hydrogen-bond acceptors (tertiary amines) which engage in interactions with nitrogenous substrates bound to the iron center (NH₃ and N₂H₄). Cation binding is also facilitated in anionic Fe(0)-N₂ complexes. While Fe-N₂ complexes of a related ligand ([SiP^iPr₃]) lacking hydrogen-bond acceptors produce a substantial amount of ammonia when treated with acid and reductant, the presence of the pendant amines instead facilitates the formation of metal hydride species.

Additionally, we present the development and mechanistic study of copper-mediated and copper-catalyzed photoinduced C-N bond forming reactions. Irradiation of a copper-amido complex, ((m-tol)₃P)₂Cu(carbazolide), in the presence of aryl halides furnishes N-phenylcarbazole under mild conditions. The mechanism likely proceeds via single-electron transfer from an excited state of the copper complex to the aryl halide, generating an aryl radical. An array of experimental data are consistent with a radical intermediate, including a cyclization/stereochemical investigation and a reactivity study, providing the first substantial experimental support for the viability of a radical pathway for Ullmann C-N bond formation. The copper complex can also be used as a precatalyst for Ullmann C-N couplings. We also disclose further study of catalytic C_alkyl-N couplings using a CuI precatalyst, and discuss the likely role of [Cu(carbazolide)₂]^- and [Cu(carbazolide)₃]^- species as intermediates in these reactions.

Finally, we report a series of four-coordinate, pseudotetrahedral P₃Fe^II-X complexes supported by tris(phosphine)borate ([PhBP₃Fe^R]^-) and phosphiniminato X-type ligands (-N=PR'₃) that in combination tune the spin-crossover behavior of the system. Low-coordinate transition metal complexes such as these that undergo reversible spin-crossover remain rare, and the spin equilibria of these systems have been studied in detail by a suite of spectroscopic techniques.

Análise do perfil de genes relacionados ao SST5 e SST6, formação de biofilme e invasão em cepas de Escherichia coli enteroagregativa

A Escherichia coli enteroagregativa (EAEC) é um patotipo emergente e heterogêneo que causa a diarréia aguda ou persistente em indivíduos de diferentes faixas etárias e em pacientes imunocomprometidos. Além disso, EAEC é um dos principais agentes etiológicos da diarréia dos viajantes. O padrão de aderência agregativa de EAEC está associado ao plasmídeo de aderência agregativa (pAA). Genes presentes no plasmídeo e no cromossomo codificam proteínas envolvidas na secreção extracelular de fatores de virulência na superfície ou diretamente na célula hospedeira. A capacidade de produção de muco e biofilme, elaboração de toxinas, aderência e indução de inflamação intensa na mucosa intestinal são importantes características da patogenicidade de EAEC. Nesse estudo, determinamos o perfil genotípico de genes do sistema de secreção Tipo V (SST5) e sistema de secreção Tipo VI (SST6) em cepas de EAEC. Os genes do SST5 ocorreram com mais frequência que os genes do SST6. A presença de pelo menos um gene do SST5 foi detectada em 79% das cepas, enquanto que os genes relacionados ao SST6 foram detectados em apenas 42% das cepas analisadas. A produção de biofilme foi observada em teste quantitativo e verificamos que 67% das cepas produziram biofilme. No teste qualitativo, o tipo de biofilme que predomina é o biofilme moderado (11 cepas), seguido do biofilme forte (9 cepas) e do biofilme discreto (4 cepas). A presença ou ausência de genes do SST5 e SST6 não parece interferir com a capacidade de produção de biofilme, nem com o tipo de biofilme formado. Em ensaios de citotoxicidade, apenas 25% das cepas EAEC (sobrenadante) causaram redução significativa na viabilidade de células T84 avaliada pelo teste de redução com MTT. Nossos resultados mostram que as cepas EAEC isoladas de crianças com diarréia aguda ou de grupo controle são invasoras para células T84. Ao compararmos a capacidade invasora das cepas clinicas e controle, observamos que a média do índice de internalização obtido nas 15 cepas do grupo clinico foi de 5,7% 1,7 e para as 9 cepas do grupo controle foi de 2.4 % 0,7; entretanto essa diferença observada não foi estatisticamente significativa. Não foi possível correlacionar o perfil genotípico dos genes do SST5 e SST6 com o perfil fenotípico analisado (formação de biofilme, citotoxicidade e invasão).O que pode ser atribuído a heterogeneidade genotípica e fenotípica, uma característica relevante de cepas EAEC.

Estudo do reparo das lesões induzidas no DNA de Escherichia coli pela radiação ultravioleta C (UVC)

Didaticamente, podemos dividir o espectro da radiação ultravioleta (UV) em três faixas: UVA (400 a 320 nm), UVB (320 a 290 nm) e UVC (290 a 100 nm). Apesar do UVC ou UV-curto ser eficientemente filtrado pela camada de ozônio da Terra e sua atmosfera, este é uma das faixas do espectro de UV mais usadas para explorar as consequências de danos causados ao DNA, já que a letalidade induzida por este agente está relacionada aos danos diretos no genoma celular, como as lesões dímero de pirimidina, que são letais se não reparadas. Contudo, demonstrou-se que a radiação UVC pode gerar espécies reativas de oxigênio (ERO), como o oxigênio singleto (1O2). Embora, o radical hidroxil (OH) cause modificações oxidativas nas bases de DNA, alguns trabalhos indicam que o 1O2 também está envolvido nos danos oxidativos no DNA. Esta ERO é produzida por vários sistemas biológicos e reações fotossensibilização, quando cromóforos são expostos à luz visível ou são excitados pela luz UV, permitindo que essa energia possa ser transferida para o oxigênio sendo convertido em 1O2, que é conhecido por modificar resíduos de guanina, gerando 8-oxoG, que caso não seja reparada pode gerar uma transversão GC-TA. O objetivo deste trabalho foi o de elucidar a participação de ERO nos efeitos genotóxicos e mutagênicos gerados pela radiação UVC, assim como as enzimas envolvidas no processo de reparação destas lesões em células de Escherichia coli. Nos ensaios as culturas foram irradiadas com o UVC (254 nm; 15W General Electric G15T8 germicidal lamp, USA). Nossos resultados mostram que o uso de quelantes de ferro não alterou a letalidade induzida pelo UVC. A azida sódica, um captador de 1O2, protegeu as cepas contra os danos genotóxicos gerados pelo UVC e também diminuiu a frequência de mutações induzidas no teste com rifampicina. A reversão específica GC-TA foi induzida mais de 2,5 vezes no ensaio de mutagênese. A cepa deficiente na proteína de reparo Fpg, enzima que corrige a lesão 8-oxoG, apresentou menos quebras no DNA do que a cepa selvagem no ensaio de eletroforese alcalina. A letalidade induzida pelo UVC foi aumentada nos mutantes transformados com o plasmídeo pFPG, ao mesmo tempo que representou uma redução na indução mutagênica. Houve dimuição na eficiência de transformação com plasmídeo pUC 9.1 na cepa fpg quando comparado a cepa selvagem. Assim como, um aumento da sensibilidade ao UVC na associação entre mutantes fpg e uvrA. Estes resultados mostram que o 1O2 participa dos danos induzidos pelo UVC, através da geração da lesão 8-oxoG, uma lesão mutagênica, que é reparada pela proteína Fpg

Caracterização de beta-lactamases de espectro ampliado (ESBLs), genes de resistência aos antimicrobianos e conteúdo plasmidial em cepas de Escherichia coli e Salmonella spp. não tifóides isoladas do ambiente hospitalar e da comunidade

Enterobactérias produtoras de ESBLs são descritas tanto no ambiente hospitalar quanto na comunidade em todo o mundo. No Brasil, esses microrganismos também têm emergido como uma causa importante de infecções, sendo as enzimas CTX-M as prevalentes. O objetivo deste estudo foi analisar diferentes aspectos genotípicos relacionados à expressão da resistência aos antimicrobianos em cepas Escherichia coli e de Salmonella spp, tais como: a diversidade de ESBLs, os genes de resistência aos antimicrobianos e o conteúdo plasmidial. Os aspectos epidemiológicos das cepas produtoras de ESBLs também foram investigados. Foram estudadas 88 cepas de enterobactérias, sendo 43 E. coli e 45 cepas de Salmonella spp., de origem hospitalar e da comunidade (principalmente alimentos), isoladas na cidade do Rio de Janeiro. A expressão de ESBL foi observada em sete cepas de E. coli (7/43, 16,3%) e em uma cepa de Salmonella Typhimurium (1/45, 2,3%) e as enzimas foram identificadas como variantes de CTX-M e SHV-5, respectivamente. Entre as cepas de E. coli, a enzima CTX-M-2 foi a mais frequente (n = 4), sendo detectada em cepas isoladas de swab retal de pacientes hospitalizados, enquanto as enzimas CTX-M-59 (uma variante de CTX-M) (n = 1) e CTX-M-9 (n = 2) foram identificadas em cepas isoladas a partir de espécimes clínicos. Salmonella Typhimurium produtora de SHV-5 foi isolada do ambiente hospitalar (fórmula infantil). As cepas de E. coli produtoras das enzimas CTX-M pertenceram a grupos filogenéticos (A, B1, D) e STs (ST34, ST69, ST101) diferentes, sendo os genes blaCTX-M identificados em plasmídeos com tipo de replicon IncA/C de cerca de 150 kb (blaCTX-M-2, blaCTX-M-9, blaCTX-M-59) ou 80 kb (blaCTX-M-2). A cepa de S. Typhimurium produtora de SHV-5 pertenceu a um único clone (A-ST19) e o gene blaSHV-5 foi identificado em plasmídeo com o replicon IncL/M com aproximadamente 55Kb. Foi identificado pela primeira vez no Brasil o ST313 em um clone de S. Typhimurium (D-ST313), comumente associado com doenças invasivas severas, particulamente no continente africano. Genes que codificam para a resistência aos antimicrobianos não-beta-lactâmicos e integrons classe 1 foram identificados entre as cepas de E. coli e de Salmonella spp. multirresistentes produtoras ou não de ESBLs. Em conclusão: i) nossos resultados referentes à E. coli confirmaram a disseminação de enzimas CTX-M (principalmente variantes do grupo CTX-M-2) desde, pelo menos, o ano de 2000, em hospitais no Rio de Janeiro; demonstraram a implicação dos plasmídeos IncA/C na disseminação de genes blaCTX-M; indicaram a possível evolução intra-plasmídeo de blaCTX-M-59 a partir de blaCTX-M-2; a observação da diversidade e multiplicidade de plasmídeos poderiam fornecer plataformas genéticas para a dispersão de diferentes genes e/ou elementos de resistência aos antimicrobianos; ii) em relação à Salmonella spp. este estudo descreveu, pela primeira vez, o isolamento, a partir de fórmula infantil, de uma cepa de S. Typhimurium produtora de ESBL; foi demonstrada a associação do gene blaSHV-5 com plasmídeo do tipo IncL/M, que é considerado epidêmico; foi identificado o clone D-ST313 de S. Typhimurium, que está associado a doenças invasivas severas no continente africano, que reuniu cepas isoladas exclusivamente do ambiente hospitalar.

Fracturing of sand in compensation grouting

The phenomenon of fracturing in sand as a result of compensation grouting was studied. Processes of fracture initiation and propagation were explained and a parametric study was conducted in order to investigate the factors that cause sand fracturing to occur. Experimental results indicate that fracture initiation requires the existence of a local inhomogeneity around the injection position. Grout mixture in terms of water-cement ratio and fines content had major roles in sand fracturing, whereas injection rate had a minor influence under the tested conditions. © 2009 Taylor & Francis Group.

Building damage and repair due to leakage in a deep excavation

The north-south line in Amsterdam is being built underneath the historic centre of the city. Three deep stations are being constructed in deep excavations supported by diaphragm walls. During the excavation for Vijzelgracht station, leakage through the wall resulted in large settlements and damage to historic buildings, which threatened continuation of the project. The authors analysed the cause of the leakage and the damage to the buildings. With the application of robust preventative measures at two of the deep excavations it was possible to continue the project. This paper reports on the cause of the events, the damage to the buildings and the counter-measures taken. It includes lessons learned for the project and for the foundations industry.

长期水分胁迫下氮、钾对夏玉米叶片光合特性的影响

采用2种不同夏玉米基因型(陕单9号,抗旱品种;陕单911,不抗旱品种)的盆栽试验,研究了长期水分胁迫下氮、钾对各生育期叶片净光合速率、蒸腾速率、胞间二氧化碳浓度和叶绿素含量的影响,旨在从光合生理特性揭示这些因子的抗旱机理。结果表明,长期水分胁迫下叶片净光合速率,蒸腾速率、胞间二氧化碳浓度(除成熟期)和叶绿素含量显著降低,不抗旱品种降幅更甚。抗旱品种的净光合速率和叶绿素含量大于不抗旱品种,而蒸腾速率和胞间二氧化碳浓度则相反。两品种苗期光合作用较弱,净光合速率和叶绿素含量均较低,抽雄期达到高峰。施氮能不同程度降低水分胁迫下玉米叶片的蒸腾速率,增加叶绿素含量.提高净光合速率,从而减缓水分胁迫对光合作用的伤害。随氮肥用量增加,不抗旱品种净光合速率和叶绿素含量显著升高,蒸腾速率和胞间二氧化碳浓度明显降低,两种氮肥用量间有显著差异;抗旱品种在低氮用量时效果显著,但高低氮用量间无显著区别。钾对受水分胁迫的玉米表现出比氮肥更突出的效果。相反,在适量供水条件下,氮、钾肥的作用明显下降。以上结果表明,适当用量的氮、钾肥可以有效地改善水分胁迫下作物叶片的光合特性,从而增强作物的抗旱性。

食肉目哺乳动物（Carnivora）的分子进化研究

追溯生物界不同生物类型的起源及进化关系，即重建生物类群的系统发育树是进化生物学领域中一个十分重要的内容，并日益受到广泛的关注。美国和一些欧洲国家已率先启动了类似人类基因组计划的"生命之树，，计划（TreeofLife，TOL），将对生物学研究的发展产生深远影响。本研究瞄准了"生命之树"这一国际关注的焦点问题，选择具有重要进化理论意义和保护生物学价值的食肉目进行研究，除采用流行的多个线粒体基因外，还筛选多个有效的核基因标记，通过多基因序列数据的整合分析，构建可靠的食肉目分子系统树。此外，我们在食肉目部分物种的一个内含子区域发现了SINE家族的插入，考虑到这个内含子区域可能是SINE家族序列的一个插入热点，我们还增加了一些胎盘类哺乳动物目对这个内含子区域发生的多次SINE家族插入进行了详尽的进化研究。世界现生食肉目动物共计有11科280种，一般将它们归为两大超科，犬型超科（熊科，犬科，洗熊科，锄科，海狮科，海象科和海豹科）和猫型超科（灵猫科、猫科、鼠狗科和獴科）。犬型超科由于包含的物种种类繁多而且形态差异极"大，因此物种之间的系统发育关系方面争论颇多，难以解决。我们选用四个核基因序列片段和一个线粒体蛋白编码基因（共4417个碱基）对16个大型超科食肉目代表物种进行研究，探讨这一超科中科间的系统发育关系以及两个熊猫（大，小熊猫）的位置。结果表明不同基因在各分枝上表现出不同的解决能力，核基因和线粒体基因不含有冲突的，而是含有互补的系统发育信号，因而当把它们合并在一起进行系统发育分析时得到了一个大部分分枝都有很高支持程度的系统树拓扑结构。系统发育重建支持犬科是犬型超科中最早分歧的谱系，洗熊科和勃科的关系最近。小熊猫是洗熊科和触科的姐妹群，大熊猫是熊科中最早分歧的成员。鳍脚类（海狮科，海象科和海豹科）和熊科依次是由洗熊科，融科和小熊猫组成的进化枝最近的姐妹群。其中，鳍脚类和熊科的系统发育学位置在合并所有基因片段进行的ML和贝叶斯分析方法中都有较高的支持率和后验概率，但是在孵分析中的支持率却很低。因此，鳍脚类，熊科和由洗熊科，融科，小熊猫组成的进化枝三者之间的系统发育关系的解决将是以后食肉目犬型超科科水平系统发育学研究的趋势和重点。食肉目中不仅各科之间的进化关系扑朔迷离，科内的系统发育关系也很不清楚，尤其是熊科和猫科。因为这两个科都是在非常近期才发生物种分化的类群，代表了快速的进化辐射和间隔时间非常短的物种形成事件，因而重建科内各物种之间的系统发育关系对于系统学家来说是一项艰巨，极富挑战性的任务，也是造成熊科和猫科物种系统发育关系一直无法得到完全解决的重要原因。我们首次从两个核基因的角度，并与以前发表的五个线粒体基因数据进行单独和合并分析来探讨所有熊科物种（8个）的系统发育关系（约4kb）。结果不仅证实了目前普遍接受的观点，包括眼镜熊是除大熊猫以外最早分歧的熊科物种，以及棕熊和北极熊的姐妹群关系，而且进一步支持了亚洲黑熊和美洲黑熊之间的紧密关系，但是就在大多数以前的线粒体基因研究暗示懒熊极有可能是Ursus属中分歧最早的熊科物种时，我们的核基因分析提出新的假说，强烈支持懒熊和马来熊之间的姐妹群关系，使得懒熊和马来熊的系统发育位置又要成为将来熊科系统发育学研究中讨论的热点。另外，我们也探讨了核基因和线粒体基因表现出不一致系统发育信号的可能原因。猫科物种一般分成三大谱系：家猫谱系，豹谱系和虎猫谱系。其中由Panthera属和一些中等体型大小的猫类组成的豹谱系分化时间最近而且包含的物种最多，因此围绕它的系统发育学未解决的问题也最多。我们首次使用三个核基因对猫科中豹谱系部分物种系统发育关系进行探讨，同时还测定了两个完整线粒体编码基因，并结合以前发表的其它四个线粒体基因片段进行单独和结合分析，了解猫科豹谱系物种的进化历史。另外，我们还比较了这9个基因序列片段在进化特征和猫科系统发育关系应用价值方面的异同点。通过对14个猫科部分物种，主要为豹谱系物种的多个线粒体和核基因序列片段的综合分析，得到了一些非常有价值的重要结论，包括Panthera属的单源性以及Panthera属内部物种之间新的系统发育关系，云豹与Panthera属关系最近，美洲狮和猎豹是姐妹群，兔孙仍然属于家猫谱系等等。本研究中的核基因DNA在追溯如此近期才分化的猫科类群过程中积累的序列差异较少，因而贡献非常有限，它们可能会更适合用来解决食肉目中更高水平的物种之间系统发育关系。此外，当我们使用FGB基因第七内含子进行食肉目犬型超科各科和猫科部分物种的系统发育关系研究时，发现犬科代表物种和两个猫科物种中的不同位置上都发现了SINE片段的插入。我们又增加了除食肉目以外的部分哺乳动物目代表物种（共30个分类群）来进一步分析FGB基因第七内含子发生的多次SINEs家族插入事件。我们的结果表明：在所有哺乳动物内含子中的直源位置都发现了起源于tRNA的M琅元件，除了啮齿目。研究发现啮齿目小鼠中较高的序列变异速率以及大鼠中随着寄主DNA的大段丢失而发生了罕有的遗失是造成啮齿目中MIR缺失的原因。此外，在我们分析的12个哺乳动物目中，食肉目，偶蹄目和兔形目的FGB基因第七内含子不同位置还发现了至少五次谱系特异性SINE家族的独立插入事件。在食肉目中，三个独立的CANSINEs插入支持了这个SINE家族在食肉目所有类群中都有分布的假说（即"pan-camivores"假说）。研究中最重要的发现就是那些谱系特异的sINE家族有插入到己存在的MIRs内部或MIRs附近的强烈倾向，表明MIR很有可能是其它SINEs连续插入的"热点"区域，因而使这个内含子区域有如此多的逆转座子插入。我们认为SINEs要比以前所意识到的具有更大的插入"灵活性"和区域"特异性"。另外，本论文还重点介绍了现代系统发育学中常用的系统发育重建方法和策．略以及随着基因组时代的到来，"系统发育基因组学（P坤logenomics））'这门崭新的交叉学科在"重建生命之树"方面所具有的巨大优势和潜力。