Isolation of yeast artificial chromosomes free of endogenous yeast chromosomes: construction of alternate hosts with defined karyotypic alterations.

An intrinsic feature of yeast artificial chromosomes (YACs) is that the cloned DNA is generally in the same size range (i.e., approximately 200-2000 kb) as the endogenous yeast chromosomes. As a result, the isolation of YAC DNA, which typically involves separation by pulsed-field gel electrophoresis, is frequently confounded by the presence of a comigrating or closely migrating endogenous yeast chromosome(s). We have developed a strategy that reliably allows the isolation of any YAC free of endogenous yeast chromosomes. Using recombination-mediated chromosome fragmentation, a set of Saccharomyces cerevisiae host strains was systematically constructed. Each strain contains defined alterations in its electrophoretic karyotype, which provide a large-size interval devoid of endogenous chromosomes (i.e., a karyotypic "window"). All of the constructed strains contain the kar1-delta 15 mutation, thereby allowing the efficient transfer of a YAC from its original host into an appropriately selected window strain using the kar1-transfer procedure. This approach provides a robust and efficient means to obtain relatively pure YAC DNA regardless of YAC size.

Genomic DNA fingerprinting by restriction fragment end labeling.

A typing method for bacteria was developed and applied to several species, including Escherichia coli and Actinobacillus actinomycetemcomitans. Total genomic DNA was digested with a restriction endonuclease, and fragments were enabled with [alpha-32P]dATP by using the Klenow fragment of DNA polymerase and separated by electrophoresis in 6% polyacrylamide/8 M urea (sequencing gel). Depending on the restriction endonuclease and the bacterium, the method produced approximately 30-50 well-separated fragments in the size range of 100-400 nucleotides. For A. actinomycetemcomitans, all strains had bands in common. Nevertheless, many polymorphisms could be observed, and the 31 strains tested could be classified into 29 distinct types. Furthermore, serotype-specific fragments could be assigned for the three serotypes investigated. The method described is very sensitive, allowing more distinct types to be distinguished than other commonly used typing methods. When the method was applied to 10 other clinically relevant bacterial species, both species-specific bands and strain-specific bands were found. Isolates from different locations of one patient showed indistinguishable patterns. Computer-assisted analysis of the DNA fingerprints allowed the determination of similarity coefficients. It is concluded that genomic fingerprinting by restriction fragment end labeling (RFEL) is a powerful and generally applicable technique to type bacterial species.

Impacts on particles and ozone by transport processes recorded at urban and high-altitude monitoring stations

In order to evaluate the influence of particle transport episodes on particle number concentration temporal trends at both urban and high-altitude (Aitana peak-1558 m a.s.l.) stations, a simultaneous sampling campaign from October 2011 to September 2012 was performed. The monitoring stations are located in southeastern Spain, close to the Mediterranean coast. The annual average value of particle concentration obtained in the larger accumulation mode (size range 0.25–1 μm) at the mountain site, 55.0 ± 3.0 cm− 3, was practically half that of the value obtained at the urban station (112.0 ± 4.0 cm− 3). The largest difference between both stations was recorded during December 2011 and January 2012, when particles at the mountain station registered the lowest values. It was observed that during urban stagnant episodes, particle transport from urban sites to the mountain station could take place under specific atmospheric conditions. During these transports, the major particle transfer is produced in the 0.5–2 μm size range. The minimum difference between stations was recorded in summer, particularly in July 2012, which is most likely due to several particle transport events that affected only the mountain station. The particle concentration in the coarse mode was very similar at both monitoring sites, with the biggest difference being recorded during the summer months, 0.4 ± 0.1 cm− 3 at the urban site and 0.9 ± 0.1 cm− 3 at the Aitana peak in August 2012. Saharan dust outbreaks were the main factor responsible for these values during summer time. The regional station was affected more by these outbreaks, recording values of > 4.0 cm− 3, than the urban site. This long-range particle transport from the Sahara desert also had an effect upon O3 levels measured at the mountain station. During periods affected by Saharan dust outbreaks, ozone levels underwent a significant decrease (3–17%) with respect to its mean value.

Novel particulate BCG-loaded delivery system for mucosal immunization against tuberculosis

Tese de doutoramento, Farmácia (Tecnologia Farmacêutica), Universidade de Lisboa, Faculdade de Farmácia, 2016

Light sheet fluorescence microscopy for in situ cell interaction analysis in mouse lymph nodes.

Reactive lymph nodes (LNs) are sites where pMHC-loaded dendritic cells (DCs) interact with rare cognate T cells, leading to their clonal expansion. While DC interactions with T cell subsets critically shape the ensuing immune response, surprisingly little is known on their spatial orchestration at physiologically T cell low precursor frequencies. Light sheet fluorescence microscopy and one of its implementations, selective plane illumination microscopy (SPIM), is a powerful method to obtain precise spatial information of entire organs of 0.5-10mm diameter, the size range of murine LNs. Yet, its usefulness for immunological research has thus far not been comprehensively explored. Here, we have tested and defined protocols that preserve fluorescent protein function during lymphoid tissue clearing required for SPIM. Reconstructions of SPIM-generated 3D data sets revealed that calibrated numbers of adoptively transferred T cells and DCs are successfully detected at a single cell level within optically cleared murine LNs. Finally, we define parameters to quantify specific interactions between antigen-specific T cells and pMHC-bearing DCs in murine LNs. In sum, our studies describe the successful application of light sheet fluorescence microscopy to immunologically relevant tissues.

Ash layers, hyaloclastite, and alteration of basaltic glass at DSDP Leg 65 Holes

Three types of tephra deposits were recovered on Leg 65 of the Deep Sea Drilling Project (DSDP) from three drill sites at the mouth of the Gulf of California: (1) a series of white ash layers at Sites 483, 484, and 485; (2) a layer of plagioclase- phyric sideromelane shards at Site 483; and (3) an indurated, cross-bedded hyaloclastite in Hole 483B. The ash layers in (1) are composed of colorless, fresh rhyolitic glass shards with minor dacitic and rare basaltic shards. These are thought to be derived from explosive volcanoes on the Mexican mainland. Most of the shards in (2) are fresh, but some show marginal to complete alteration to palagonite. The composition of the glass is that of a MORB-type tholeiite, low in Fe and moderately high in Ti, and possibly erupted from off-axis seamounts. Basaltic glass shards occurring in silt about 45 meters above the basement at Site 484 A in the Tamayo Fracture Zone show a distinctly alkalic composition similar to that of the single basement basalt specimen drilled at this site. The hyaloclastite in (3) is made up chiefly of angular sideromelane shards altered to smectite and zeolites (mainly phillipsite) and minor admixtures of terrigenous silt. A very high K and Ba content indicates significant uptake of at least these elements from seawater. Nevertheless, the unusual chemical composition of the underlying massive basalt flow is believed to be reflected in that of the hyaloclastite. This is a powerful argument for interpreting the massive basalt as a surface flow rather than an intrusion. Glass alteration is different in the glassy margins of flows than in thicker glassy pillow rinds. Also, it appears to proceed faster in coarse- than fine-grained sediments.

(Table 2) Planktic foraminifera and their diversity indices of sediment surface samples from the Atlantic Ocean

Species distribution patterns in planktonic foraminiferal assemblages are fundamental to the understanding of the determinants of their ecology. Until now, data used to identify such distribution patterns was mainly acquired using the standard >150 µm sieve size. However, given that assemblage shell size-range in planktonic foraminifera is not constant, this data acquisition practice could introduce artefacts in the distributional data. Here, we investigated the link between assemblage shell size-range and diversity in Recent planktonic foraminifera by analysing multiple sieve-size fractions in 12 samples spanning all bioprovinces of the Atlantic Ocean. Using five diversity indices covering various aspects of community structure, we found that counts from the >63 µm fraction in polar oceans and the >125 µm elsewhere sufficiently approximate maximum diversity in all Recent assemblages. Diversity values based on counts from the >150 µm fraction significantly underestimate maximum diversity in the polar and surprisingly also in the tropical provinces. Although the new methodology changes the shape of the diversity/sea-surface temperature (SST) relationship, its strength appears unaffected. Our analysis reveals that increasing diversity in planktonic foraminiferal assemblages is coupled with a progressive addition of larger species that have distinct, offset shell-size distributions. Thus, the previously documented increase in overall assemblage shell size-range towards lower latitudes is linked to an expanding shell-size disparity between species from the same locality. This observation supports the idea that diversity and shell size-range disparity in foraminiferal assemblages are the result of niche separation. Increasing SST leads to enhanced surface water stratification and results in vertical niche separation, which permits ecological specialisation. Specific deviations from the overall diversity and shell-size disparity latitudinal pattern are seen in regions of surface-water instability, indicating that coupled shell-size and diversity measurements could be used to reconstruct water column structures of past oceans.

Paleomagnetic and rock magnetic properties of ODP Leg 173 sites, west Iberia continental margin

We present detailed paleomagnetic and rock magnetic results of rock samples recovered during Leg 173. The Leg 173 cores display a multicomponent magnetization nature. Variations in magnetic properties correlate with changes in lithology that result from differences in the abundance and size of magnetic minerals. The combined investigation suggests that the magnetic properties of the "fresher" peridotite samples from Site 1070 are controlled mainly by titanomagnetite, with a strong Verwey transition in the vicinity of 110 K, and with field- and frequency-dependent susceptibility curves that resemble those of titanomagnetites. These results are in excellent agreement with thermomagnetic characteristics where titanomagnetites with Curie temperature ~580°C were identified from the "fresher" peridotites. In contrast to the magnetic properties observed from the "fresher" peridotites, the low-temperature curves for the "altered" peridotites did not show any Verwey transition. Thermomagnetic analysis using the high-temperature vibrating sample magnetometer also failed to show evidence for titanomagnetites. The remanent magnetization is carried by a thermally unstable mineral that breaks down at ~420°C, probably maghemite. The field- and frequency-dependent relationships are also directly opposite to those in the reversal zone, with no signs of titanomagnetite characteristics. Altogether, these rock magnetic data seem to be sensitive indicators of alteration and support the contention that maghemite is responsible for the magnetic signatures displayed in the altered peridotites of the upper section. The magnetic minerals of the basement rocks from Sites 1068, 1069, and 1070 are of variable particle size but fall within the pseudo-single-domain size range (0.2-14 µm). The average natural remanent magnetization (NRM) intensity of recovered serpenitinized peridotite is typically on the order of 20 mA/m for samples from Site 1068, but ~120 mA/m for samples from Site 1070. The much stronger magnetization intensity of Site 1070 is apparently in excellent agreement with the observed magnetic anomaly high. Nearly half of the NRM intensity remained after 400°C demagnetization, suggesting that the remanence can contribute significantly to the marine magnetic anomaly.

Activity and biomass of small benthic biota in the central Arctic Ocean

Sediment samples collected during the expedition "Arctic Ocean '96" with the Swedish ice-breaker ODEN were investigated to estimate for the first time heterotrophic activity and total microbial biomass (size range from bacteria to small metazoans) from the perennially ice-covered central Arctic Ocean. Benthic activities and biomass were evaluated analysing a series of biogenic sediment compounds (i.e. bacterial exoenzymes, total adenylates, DNA, phospholipids, particulate proteins). In contrast to the very time-consuming sorting, enumeration and weight determination, analyses of biochemical sediment parameters may represent a useful method for obtaining rapid information on the ecological situation in a given benthic system. Bacterial cell numbers and biomass were estimated for comparison with biochemically determined biomass data, to evaluate the contribution of the bacterial biomass to the total microbial biomass. It appeared that bacterial biomass made up only 8-31% (average of all stations = 20%) of the total microbial biomass, suggesting a large fraction of other small infaunal organisms within the sediment samples (most probably fungi, yeasts, protozoans such as flagellates, ciliates or amoebae, as well as a fraction of small metazoans). Activity and biomass values determined within this study were generally extremely low, and often even slightly lower than those given for other deep oceanic regions, thus characterizing the seafloor of the central Arctic Ocean as a "benthic desert". Nevertheless, some clear trends in the data could be found, e.g. generally sharply decreasing values within the sediment column, a vague tendency for declining values with increasing water depth of sampling stations, and also differences between various Arctic deep-sea regions.

Biochemical investigation of multicorer sediment profile PS74/109-2

To detect and track the impact of large-scale environmental changes in a the transition zone between the northern North Atlantic and the central Arctic Ocean, and to determine experimentally the factors controlling deep-sea biodiversity, the Alfred- Wegener-Institute for Polar and Marine Research (AWI) established the deep-sea long-term observatory HAUSGARTEN, which constitutes the first, and until now only open-ocean long-term station in a polar region. Virtually undisturbed sediment samples have been taken using a video-guided multiple corer (MUC) at 13 HAUSGARTEN stations along a bathymetric (1,000 - 4,000 m water depth) and a latitudinal transect in 2,500 m water depth as well as two stations at 230 and 1,200 m water depth within the framework of the KONGHAU project. Various biogenic sediment compounds were analyzed to estimate the input of organic matter from phytodetritus sedimentation, benthic activities (e.g. bacterial exoenzymatic activity), and the total biomass of the smallest sediment-inhabiting organisms (size range: bacteria to meiofauna).

Biochemical investigation of multicorer sediment profile PS74/113-2

To detect and track the impact of large-scale environmental changes in a the transition zone between the northern North Atlantic and the central Arctic Ocean, and to determine experimentally the factors controlling deep-sea biodiversity, the Alfred- Wegener-Institute for Polar and Marine Research (AWI) established the deep-sea long-term observatory HAUSGARTEN, which constitutes the first, and until now only open-ocean long-term station in a polar region. Virtually undisturbed sediment samples have been taken using a video-guided multiple corer (MUC) at 13 HAUSGARTEN stations along a bathymetric (1,000 - 4,000 m water depth) and a latitudinal transect in 2,500 m water depth as well as two stations at 230 and 1,200 m water depth within the framework of the KONGHAU project. Various biogenic sediment compounds were analyzed to estimate the input of organic matter from phytodetritus sedimentation, benthic activities (e.g. bacterial exoenzymatic activity), and the total biomass of the smallest sediment-inhabiting organisms (size range: bacteria to meiofauna).

Biochemical investigation of multicorer sediment profile PS74/118-2

To detect and track the impact of large-scale environmental changes in a the transition zone between the northern North Atlantic and the central Arctic Ocean, and to determine experimentally the factors controlling deep-sea biodiversity, the Alfred- Wegener-Institute for Polar and Marine Research (AWI) established the deep-sea long-term observatory HAUSGARTEN, which constitutes the first, and until now only open-ocean long-term station in a polar region. Virtually undisturbed sediment samples have been taken using a video-guided multiple corer (MUC) at 13 HAUSGARTEN stations along a bathymetric (1,000 - 4,000 m water depth) and a latitudinal transect in 2,500 m water depth as well as two stations at 230 and 1,200 m water depth within the framework of the KONGHAU project. Various biogenic sediment compounds were analyzed to estimate the input of organic matter from phytodetritus sedimentation, benthic activities (e.g. bacterial exoenzymatic activity), and the total biomass of the smallest sediment-inhabiting organisms (size range: bacteria to meiofauna).

Results of an in situ stable isotope labeling study in intertidal sediment

We report the results of an in situ tracer experiment in an intertidal sediment, where bacterial carbon was tagged with stable carbon-isotope label, after the injection of 13C-glucose. The appearance of label in bacteria (based on label incorporation in bacteria-specific, phospholipid-derived fatty acids) and subsequent transfer to meiobenthos (group level) and macrobenthos (species level) was followed for 36 days. The label dynamics of benthic taxa were either fitted with a simple-isotope model or evaluated against enrichment in bacteria, to derive the importance of bacterially derived carbon for the meiobenthos and macrobenthos. Although selective uptake of bacteria was evident, as 2.4 times more bacterial carbon was grazed as expected from indiscriminate feeding, bacterial carbon accounted on average for only 0.08 and 0.11 of the carbon requirements of meiobenthic and macrobenthic taxa, respectively. Additionally, the contribution of bacterial carbon to total carbon requirements did not depend on the living/feeding depth in the sediment or organism size (evaluated over a size range of four orders of magnitude). The observed overall low contribution of bacterial carbon implies that most intertidal benthic fauna depend primarily on other carbon resources that may assert a stronger control on the structure of intertidal-sediment communities.

Floral structure, breeding system and fruit-set in the threatened sub-shrub Tetratheca juncea Smith (Tremandraceae)

Tetratheca juncea Smith (Tremandraceae) has undergone a range contraction of approx. 50 km in the last 100 years and is now listed as a vulnerable sub-shrub restricted to the central and north coast regions of New South Wales, Australia. There are approx. 250 populations in a 110 km north-south distribution and populations are usually small with fewer than 50 plants/clumps. The reproductive ecology of the species was studied to determine why seed-set is reportedly rare. Flowers are bisexual, odourless and nectarless. Flowers are presented dependentally and there are eight stamens recurved around the pistil. Anthers are poricidal, contain viable pollen and basally contain a deep-red tapetal fluid that is slightly oily. Thus flowers are presented for buzz pollinators, although none were observed at flowers during our study. The species was found to be facultatively xenogamous with only one in 50 glasshouse flowers setting seed autogamously, i.e. without pollinator assistance. Field studies revealed fertile fruit in 24 populations but production varied significantly across sites from exceedingly low (0.6 fruits per plant clump) to low (17 fruits per plant clump). Fruit-set ranged from 0 to 65%, suggesting that pollen vectors exist or that autogamy levels in the field are variable and higher than glasshouse results. Fruit production did not vary with population size, although in three of the five populations in the south-west region more than twice as much fruit was produced as in populations elsewhere. A moderately strong relationship between foliage volume and fruit : flower ratios suggests that bigger plants may be more attractive than smaller plants to pollinators. A review of Tetratheca pollination ecology revealed that several species are poorly fecund and pollinators are rare. The habitat requirements for Tetratheca, a genus of many rare and threatened species, is discussed. (C) 2003 Annals of Botany Company.

Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae

To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50-80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in F-ST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (F-ST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low.