Chemical and physical properties of Amazonian aerosol particles

- ZUSAMMENFASSUNG:Die vorliegende Dissertation befasst sich mit der Bestimmung der chemischen und physikalischen Eigenschaften von Aerosolpartikeln im Amazonasbecken, die während Zeiten mit Biomasseverbrennung und bei Hintergrundbedingungen bestimmt wurden. Die Messungen wurden während zwei Kampagnen im Rahmen des europäischen Beitrags zum LBA-EUSTACH Experiment in Amazonien. Die Daten umfassen Messungen der Anzahlkonzentrationen, Größenverteilungen, optischen Eigenschaften sowie Elementzusammensetzungen und Kohlenstoffgehalte der gesammelten Aerosole. Die Zusammensetzung des Aerosols wies auf folgende drei Quellen hin: natürlichen biogenen, Mineralstaub, und pyrogenes Aerosol. Aller drei Komponenten trugen signifikant zur Extinktion des Sonnenlichts bei. Insgesamt ergab sich eine Steigerung der Meßwerte um ca. das Zehnfache während der Trockenzeit im Vergleich zur Regenzeit, was auf eine massive Einbringung von Rauchpartikeln im Submikrometerbereich in die Atmosphäre während der Trockenzeit zurückzuführen ist. Dementsprechend sank die Einzelstreualbedo von ca. 0,97 auf 0,91. Der Brechungsindex der Aerosolpartikel wurde mit einer neuen iterative Methoden, basierend auf der Mie-Theorie berechnet. Es ergaben sich durchschnittliche Werte von 1,42 – 0,006i für die Regenzeit und 1,41 – 0,013i für die Trockenperiode. Weitere klimatisch relevante Parameterergaben für Hintergrundaerosole und für Aerosole aus Biomasseverbrennung folgende Werte: Asymmetrieparameter von 0,63 ± 0,02 bzw. 0,70 ± 0,03 und Rückstreuungsverhältnisse von 0,12 ± 0,01 bzw. 0,08 ± 0,01. Diese Veränderungen haben das Potential, das regionale und globale Klima über die Variierung der Extinktion der Sonneneinstrahlung als auch der Wolkeneigenschaften zu beeinflussen.

Identification of stock units of Mullus barbatus (Linnaeus, 1758) in the Italian seas: development of genomic 2b-RAD markers and biological variation analysis.

This thesis is settled within the STOCKMAPPING project, which represents one of the studies that were developed in the framework of RITMARE Flagship project. The main goals of STOCKMAPPING were the creation of a genomic mapping for stocks of demersal target species and the assembling of a database of population genomic, in order to identify stocks and stocks boundaries. The thesis focuses on three main objectives representing the core for the initial assessment of the methodologies and structure that would be applied to the entire STOCKMAPPING project: individuation of an analytical design to identify and locate stocks and stocks boundaries of Mullus barbatus, application of a multidisciplinary approach to validate biological methods and an initial assessment and improvement for the genotyping by sequencing technique utilized (2b-RAD). The first step is the individuation of an analytical design that has to take in to account the biological characteristics of red mullet and being representative for STOCKMAPPING commitments. In this framework a reduction and selection steps was needed due to budget reduction. Sampling areas were ranked according the individuation of four priorities. To guarantee a multidisciplinary approach the biological data associated to the collected samples were used to investigate differences between sampling areas and GSAs. Genomic techniques were applied to red mullet for the first time so an initial assessment of molecular protocols for DNA extraction and 2b-RAD processing were needed. At the end 192 good quality DNAs have been extracted and eight samples have been processed with 2b-RAD. Utilizing the software Stacks for sequences analyses a great number of SNPs markers among the eight samples have been identified. Several tests have been performed changing the main parameter of the Stacks pipeline in order to identify the most explicative and functional sets of parameters.

Investigations into the effect of nucleoside modifications on the physicochemical properties and biological function of DNA and RNA

This thesis explores the effect of chemical nucleoside modification on the physicochemical and biological properties of nucleic acids. Positional alteration on the Watson-Crick edge of purines and pyrimidines, the “C-H” edge of pyrimidines, as well as both the Hoogsteen and sugar edges of purines were attempted by means of copper catalyzed azide-alkyne cycloaddition. For this purpose, nucleic acid building blocks carrying terminal alkynes were synthesized and introduced into oligonucleotides by solid-phase oligonucleotide chemistry. rnOf particular interest was the effect of nucleoside modification on hydrogen bond formation with complementary nucleosides. The attachment of propargyl functionalities onto the N2 of guanosine and the N4 of 5-methylcytosine, respectively, followed by incorporation of the modified analogs into oligonucleotides, was successfully achieved. Temperature dependent UV-absorption melting measurements with duplexes formed between modified oligonucleotides and a variety of complementary strands resulted in melting temperatures for the respective duplexes. As a result, the effect that both the nature and the site of nucleoside modification have on base pairing properties could thus be assisted. rnTo further explore the enzymatic recognition of chemically modified nucleosides, the oligonucleotide containing the N2-modified guanosine derivative on the 5’-end, which was clicked to a fluorescent dye, was subjected to knockdown analyses of the eGFP reporter gene in the presence of increasing concentrations of siRNA duplexes. From these dose-dependent experiments, a clear effect of 5’-labeling on the knockdown efficiency could be seen. In contrast, 3’-labeling was found to be relatively insignificant.rn

Stationary in-situ measurements of aerosols, gaseous pollutants and meteorology : chemical and physical characterization of natural and anthropogenic sources

Natural and anthropogenic emissions of gaseous and particulate matter affect the chemical composition of the atmosphere, impact visibility, air quality, clouds and climate. Concerning climate, a comprehensive characterization of the emergence, composition and transformation of aerosol particles is relevant as their influence on the radiation budget is still rarely understood. Regarding air quality and therefore human health, the formation of atmospheric aerosol particles is of particular importance as freshly formed, small particles penetrate into the human alveolar region and can deposit. Additionally, due to the long residence times of aerosol particles in the atmosphere it is crucial to examine their chemical and physical characteristics.This cumulative dissertation deals with stationary measurements of particles, trace gases and meteorological parameters during the DOMINO (Diel Oxidant Mechanism In relation to Nitrogen Oxide) campaign at the southwest coast of Spain in November/December 2008 and the ship emission campaign on the banks of the Elbe in Freiburg/Elbe in April 2011. Measurements were performed using the Mobile research Laboratory “MoLa” which is equipped with state-of-the-art aerosol particle and trace gas instruments as well as a meteorological station.

Lead discovery, chemistry optimization, and biological evaluation studies of novel biamide derivatives as CB2 receptor inverse agonists and osteoclast inhibitors

N,N'-((4-(Dimethylamino)phenyl)methylene)bis(2-phenylacetamide) was discovered by using 3D pharmacophore database searches and was biologically confirmed as a new class of CB(2) inverse agonists. Subsequently, 52 derivatives were designed and synthesized through lead chemistry optimization by modifying the rings A-C and the core structure in further SAR studies. Five compounds were developed and also confirmed as CB(2) inverse agonists with the highest CB(2) binding affinity (CB(2)K(i) of 22-85 nM, EC(50) of 4-28 nM) and best selectivity (CB(1)/CB(2) of 235- to 909-fold). Furthermore, osteoclastogenesis bioassay indicated that PAM compounds showed great inhibition of osteoclast formation. Especially, compound 26 showed 72% inhibition activity even at the low concentration of 0.1 μM. The cytotoxicity assay suggested that the inhibition of PAM compounds on osteoclastogenesis did not result from its cytotoxicity. Therefore, these PAM derivatives could be used as potential leads for the development of a new type of antiosteoporosis agent.

Experimental arthritis: effect on growth parameters and total skeletal calcium

Aim of the study was to investigate the possible mechanisms leading to stunted growth and osteoporosis in experimental arthritis. Fourty-two female rats of 7-8 weeks of age were randomly assigned to three groups of 14 animals each: (a) controls; (b) adjuvant-inoculated (AA); and (c) adjuvant-inoculated rats receiving 10 mg cyclosporin A (CsA) orally for 30 days. Biological parameters studied were: hindpaw swelling; vertebral length progression expressed as Delta increments between days 1 and 30 as a parameter of skeletal growth, and estimation of total skeletal mineral content by dual energy X-ray absorptiometry (n=10 each group) on day 30. Endocrine parameters measured were pulsatile release of growth hormone (rGH) on day 30 following jugular cannulation and measurement of insulin-like growth factor (IGF-1) in pooled plasma from rGH profiles. Results can be summarized as follows: Untreated AA rats exhibited local signs of inflammation in comparison with controls (hindpaw diameter 8.1-8.9 mm vs. 5.3-5.6 mm in controls). Treatment with CsA normalized this parameter (4.9-5.6 mm). Vertebral growth was significantly retarded in AA rats in comparison with controls (214+/-32 vs. 473+/-33 microm; p<0.001). Administration of CsA normalized vertebral size increment with a clear tendency to overgrowth (523+/-43 microm, n.s.). There was also a marked reduction in total skeletal mineral content in diseased (AA) rats as compared to controls (5.8+/-0.1 vs. 7.5+/-0.1g [OH-apatite]; p<0.001), and a moderate but significant increment above controls in the group receiving CsA (8.0+/-0.1 vs. 7.5+/-0.1g [OH-appatite]; p<0.04). Integrated rGH profiles exhibited a significant fall in arthritic rats and were completely restored to normal under CsA treatment. A trend toward higher rGH values was observed in the latter group (2908+/-554 in AA vs. 8317+/-1492 ng/ml/240 min in controls; p<0.001, and 10940+/-222 ng/ml/240 min, n.s. in the CsA group). There was a good correlation between skeletal growth and rGH pulsatility (r=0.81; p<0.001). IGF-1 followed a similar pattern (630+/-44 in AA vs. 752+/-30 ng/ml in controls; p<0.04, and 769+/-59 ng/ml in the CsA group, n.s. vs. controls). Thus, a clear tendency to skeletal overgrowth following treatment was observed in agreement with the hormonal data. It can therefore be concluded that, in experimental arthritis, attenuated GH-spiking and reduced circulating IGF-1 appear to be causally related to growth retardation, probably mimicking signs and symptoms observed in juvenile arthritis. Therapy with CsA is followed by normalization of hormonal and biological parameters accompanied by a catch up phenomenon in skeletal growth which is also observed clinically in juvenile arthritis. Generalized osteopenia is a prominent feature seemingly connected with the growth abnormalities as they parallel each other during the evolution of the disease and respond equally to therapy.

Bioavailability of silver nanoparticles and ions: from a chemical and biochemical perspective

Owing to their antimicrobial properties, silver nanoparticles (NPs) are the most commonly used engineered nanomaterial for use in a wide array of consumer and medical applications. Many discussions are currently ongoing as to whether or not exposure of silver NPs to the ecosystem (i.e. plants and animals) may be conceived as harmful or not. Metallic silver, if released into the environment, can undergo chemical and biochemical conversion which strongly influence its availability towards any biological system. During this process, in the presence of moisture, silver can be oxidized resulting in the release of silver ions. To date, it is still debatable as to whether any biological impact of nanosized silver is relative to either its size, or to its ionic constitution. The aim of this review therefore is to provide a comprehensive, interdisciplinary overview--for biologists, chemists, toxicologists as well as physicists--regarding the production of silver NPs, its (as well as in their ionic form) chemical and biochemical behaviours towards/within a multitude of relative and realistic biological environments and also how such interactions may be correlated across a plethora of different biological organisms.

Description and chemical and mineral composition of iron oxide samples from two Finnish lakes

Fifteen iron oxide accumulations from the bottoms of two Finnish lakes ("lake ores") were found to contain as much as 50% Fe. Differential X-ray powder diffraction and selective dissolution by oxalate showed that the samples consisted of poorly crystallized goethite and ferrihydrite. The crust ores of one lake had higher ferrihydrite to goethite ratios than the nodular ores of the other lake. The higher ferrihydrite proportion was attributed to a higher rate of Fe2+ supply from the ground water and/or a higher rate of oxidation as a function of water depth and bottom-sediment permeability. Values of Al-for-Fe substitution of the goethites determined from unit-cell dimensions agreed with those obtained from chemical extraction if the unit-cell volume rather than the c dimension was used. In very small goethite crystals a slight expansion of the a unit-cell dimension is probaby compensated by a corresponding contraction of the c dimension, so that a contraction of the c dimension need not necessarily be caused by Al substitution. The goethites of the two lakes differed significantly in their Al-for-Fe substitutions and hence in their unit-cell sizes, OH-bending characteristics, dehydroxylation temperatures, dissolution kinetics, and Mössbauer parameters. The difference in Al substitution (0 vs. 7 mole %) is attributed to the Al-supplying power of the bottom sediments: the silty-clayey sediments in one lake appear to have supplied A1 during goethite formation, whereas the gravelly-sandy sediments in the other lake did not. The compositions of the goethites thus reflect their environments of formation.

(Table 1) Cation exchange capacity and other characteristics of soils common in Lower Saxony, Germany

The chemical and biochemical processes associated with the filtration of rainwater through soils, a step in groundwater recharge, were investigated. Under simulated climatic conditions in the laboratory, undisturbed soil columns of partly loamy sands, sandy soils and loess were run as lysimeters. A series of extraction procedures was carried out to determine solid matter in unaltered rock materials and in soil horizons. Drainage water and moisture movement in the columns were analysed and traced respectively. The behaviour of soluble humic substance was investigated by percolation and suspension experiments. The development of seepage-water in the unsaturated zone is closely associated with the soil genetic processes. Determining autonomous chemical and physical parameters are mineral composition and grain size distribution in the original unconsolidated host rock and prevailing climatic conditions. They influence biological activity and transport of solids, dissolved matter and gases in the unsaturated zone. Humic substances, either as amorphous solid matter or as soluble humic acids play a part in diverse sorption, solution and precipitation processes.

Chemical and isotopic compositions of ocean authigenic carbonates

Oceanic authigenic carbonates are classified according to origin of the carbonate carbon source using a complex methodology that includes methods of sedimentary petrography, mineralogy, isotope geochemistry, and microbiology. Mg-calcite (protodolomite) and aragonite predominate among the authigenic carbonates. All authigenic carbonates are depleted in 13C and enriched in 18O (in PDB system) that indicates biological fractionation of isotopes during carbonate formation. Obtained results show that authigenic carbonate formation is a biogeochemical (microbial) process, which involves carbon from ancient sedimentary rocks, abiogenic methane, and bicarbonate-ion of hydrothermal fluids into the modern carbon cycle.

Biotic and abiotic parameters and cynobacteria abundance during an experimental set-up with varying pCO2 conditions

Heterocystous cyanobacteria of the genus Nodularia form extensive blooms in the Baltic Sea and contribute substantially to the total annual primary production. Moreover, they dispense a large fraction of new nitrogen to the ecosystem when inorganic nitrogen concentration in summer is low. Thus, it is of ecological importance to know how Nodularia will react to future environmental changes, in particular to increasing carbon dioxide (CO2) concentrations and what consequences there might arise for cycling of organic matter in the Baltic Sea. Here, we determined carbon (C) and dinitrogen (N2) fixation rates, growth, elemental stoichiometry of particulate organic matter and nitrogen turnover in batch cultures of the heterocystous cyanobacterium Nodularia spumigena under low (median 315 µatm), mid (median 353 µatm), and high (median 548 µatm) CO2 concentrations. Our results demonstrate an overall stimulating effect of rising pCO2 on C and N2 fixation, as well as on cell growth. An increase in pCO2 during incubation days 0 to 9 resulted in an elevation in growth rate by 84 ± 38% (low vs. high pCO2) and 40 ± 25% (mid vs. high pCO2), as well as in N2 fixation by 93 ± 35% and 38 ± 1%, respectively. C uptake rates showed high standard deviations within treatments and in between sampling days. Nevertheless, C fixation in the high pCO2 treatment was elevated compared to the other two treatments by 97% (high vs. low) and 44% (high vs. mid) at day 0 and day 3, but this effect diminished afterwards. Additionally, elevation in carbon to nitrogen and nitrogen to phosphorus ratios of the particulate biomass formed (POC : POP and PON : POP) was observed at high pCO2. Our findings suggest that rising pCO2 stimulates the growth of heterocystous diazotrophic cyanobacteria, in a similar way as reported for the non-heterocystous diazotroph Trichodesmium. Implications for biogeochemical cycling and food web dynamics, as well as ecological and socio-economical aspects in the Baltic Sea are discussed.

Hydrographical and chemical observations during an achor station in the eastern North Atlantic

Serial observations of temperature, salinity, oxygen, alkalinity and pH are presented. They were carried out during an anchor station of R.V. "Meteor" west of Cape Sao Vincente (Portugal) in the area of the maximum Mediterranean water outflow, which follows the continental slope off Portugal. Two observational results are pointed out: The Mediterranean water masses spread out into the Atlantic Ocean, consisting of two distinct layers at depth of 700 m (T=12.0 °C, S=36.15 ?) and 1250 m (T=11.3 °C, S=36.40 ?). The salinity proved to be the most significant indicator of the observed stratification. The values of dissolved oxygen content, alkalinity and pH in the very near bottom layer (1 m above the bottom at depth of 3250 m) are different from the values at depth of 15 m to 100 m above the bottom. As this phenomenon is not observed for the salinity, the changes may be interpreted in terms of chemical and biological processes at the sediment-water interface.

Physical oceaongraphy and hydrochemistry measured on water bottle samples during METEOR cruise M84/3 in 2001

Here we report on data from an oceanographic cruise on the German research vessel Meteor covering large parts of the Mediterranean Sea during spring of 2011. The main objective of this cruise was to conduct measurements of physical, chemical and biological variables on a section across the Mediterranean Sea with the goal of producing a synoptic picture of the distribution of relevant physical and biogeochemical properties, in order to compare those to historic data sets. During the cruise, a comprehensive data set of relevant variables following the guide lines for repeat hydrography outlined by the GO-SHIP group (http://www.go-ship.org/) was collected. The measurements include salinity and temperature (CTD), an over-determined carbonate system, inorganic nutrients, oxygen, transient tracers (CFC-12, SF6), helium isotopes and tritium, and carbon isotopes. The cruise sampled all major basins of the Mediterranean Sea following roughly an east-to-west section from the coast of Lebanon through to the Strait of Gibraltar, and to the coast of Portugal. Also a south-to-north section from the Ionian Sea to the Adriatic Sea was carried out. Additionally, sampling in the Aegean, Adriatic and Tyrrhenian Seas were carried out. The sections roughly followed lines and positions that have been sampled previously during other programs, thus providing the opportunity for comparative investigations of the temporal development of various parameters.

Production characteristics and water parameters of the Kola Bay in 2004-2005

Data on chlorophyll a concentration and phytoplankton primary production in the south Kola Bay in 2004-2005 are given.