Bathymetry of Lake Constance – a High-Resolution Survey in a Large, Deep Lake

Within the project “Tiefenschärfe – hochauflösende Vermes- sung Bodensee” a high-resolution seamless terrain model is created using airborne topobathymetric laserscanning and multibeam echosounder (MBES) techniques. The project visu- alizes the enormous wealth of features of underwater land- scapes of lakes. The combination of hydroacoustic (multibeam echosounder) and laser-optic (topobathymetric laserscan- ning) methods was used for the first time in a freshwater body of this size. Opportunities, limitations and restrictions of these high-resolution methods are presented.

A 4 Mb high resolution BAC contig on bovine chromosome 1q12 and comparative analysis with human chromosome 21q22

The bovine RPCI-42 BAC library was screened to construct a sequence-ready ~4 Mb single contig of 92 BAC clones on BTA 1q12. The contig covers the region between the genes KRTAP8P1 and CLIC6. This genomic segment in cattle is of special interest as it contains the dominant gene responsible for the hornless or polled phenotype in cattle. The construction of the BAC contig was initiated by screening the bovine BAC library with heterologous cDNA probes derived from 12 human genes of the syntenic region on HSA 21q22. Contig building was facilitated by BAC end sequencing and chromosome walking. During the construction of the contig, 165 BAC end sequences and 109 single-copy STS markers were generated. For comparative mapping of 25 HSA 21q22 genes, genomic PCR primers were designed from bovine EST sequences and the gene-associated STSs mapped on the contig. Furthermore, bovine BAC end sequence comparisons against the human genome sequence revealed significant matches to HSA 21q22 and allowed the in silico mapping of two new genes in cattle. In total, 31 orthologues of human genes located on HSA 21q22 were directly mapped within the bovine BAC contig, of which 16 genes have been cloned and mapped for the first time in cattle. In contrast to the existing comparative bovine-human RH maps of this region, these results provide a better alignment and reveal a completely conserved gene order in this 4 Mb segment between cattle, human and mouse. The mapping of known polled linked BTA 1q12 microsatellite markers allowed the integration of the physical contig map with existing linkage maps of this region and also determined the exact order of these markers for the first time. Our physical map and transcript map may be useful for positional cloning of the putative polled gene in cattle.

Late-Holocene climate variability and ecosystem responses in Alaska inferred from high-resolution multiproxy sediment analyses at Grizzly Lake

The late-Holocene shift from Picea glauca (white spruce) to Picea mariana (black spruce) forests marked the establishment of modern boreal forests in Alaska. To understand the patterns and drivers of this vegetational change and the associated late-Holocene environmental dynamics, we analyzed radiocarbon-dated sediments from Grizzly Lake for chironomids, diatoms, pollen, macrofossils, charcoal, element composition, particle size, and magnetic properties for the period 4100–1800 cal BP. Chironomid assemblages reveal two episodes of decreased July temperature, at ca. 3300–3150 (ca −1 °C) and 2900–2550 cal BP (ca −2 °C). These episodes coincided with climate change elsewhere in the Northern Hemisphere, atmospheric reorganization, and low solar activity. Diatom-inferred lake levels dropped by ca. 5 m at 3200 cal BP, suggesting dry conditions during the period 3200–1800 cal BP. P. glauca declined and P. mariana expanded at ca. 3200 cal BP; this vegetational change was linked to diatom-inferred low lake levels and thus decreased moisture availability. Forest cover declined at 3300–3100, 2800–2500 and 2300–2100 cal BP and soil erosion as inferred from increased values of Al, K, Si, Ti, and Ca intensified, when solar irradiance was low. Plant taxa adapted to disturbance and cold climate (e.g. Alnus viridis, shrub Betula, Epilobium) expanded during these periods of reduced forest cover. This open vegetation type was associated with high fire activity that peaked at 2800 cal BP, when climatic conditions were particularly cold and dry. Forest recovery lagged behind subsequent climate warming (≤+3 °C) by ca. 75–225 years. Our multiproxy data set suggests that P. glauca was dominant under warm-moist climatic conditions, whereas P. mariana prevailed under cold-dry and warm-dry conditions. This pattern implies that climatic warming, as anticipated for this century, may promote P. glauca expansions, if moisture availability will be sufficiently high, while P. mariana may expand under dry conditions, possibly exacerbating climate impacts on the fire regime.

Long-term hydrological dynamics and fire history over the last 2000 years in CE Europe reconstructed from a high-resolution peat archive

Sphagnum peatlands in the oceanic-continental transition zone of Poland are currently influenced by climatic and anthropogenic factors that lead to peat desiccation and susceptibility to fire. Little is known about the response of Sphagnum peatland testate amoebae (TA) to the combined effects of drought and fire. To understand the relationships between hydrology and fire dynamics, we used high-resolution multi-proxy palaeoecological data to reconstruct 2000 years of mire history in northern Poland. We employed a new approach for Polish peatlands – joint TA-based water table depth and charcoal-inferred fire activity reconstructions. In addition, the response of most abundant TA hydrological indicators to charcoal-inferred fire activity was assessed. The results show four hydrological stages of peatland development: moderately wet (from ∼35 BC to 800 AD), wet (from ∼800 to 1390 AD), dry (from ∼1390 to 1700 AD) and with an instable water table (from ∼1700 to 2012 AD). Fire activity has increased in the last millennium after constant human presence in the mire surroundings. Higher fire activity caused a rise in the water table, but later an abrupt drought appeared at the onset of the Little Ice Age. This dry phase is characterized by high ash contents and high charcoal-inferred fire activity. Fires preceded hydrological change and the response of TA to fire was indirect. Peatland drying and hydrological instability was connected with TA community changes from wet (dominance of Archerella flavum, Hyalosphenia papilio, Amphitrema wrightianum) to dry (dominance of Cryptodifflugia oviformis, Euglypha rotunda); however, no clear fire indicator species was found. Anthropogenic activities can increase peat fires and cause substantial hydrology changes. Our data suggest that increased human fire activity was one of the main factors that influenced peatland hydrology, though the mire response through hydrological changes towards drier conditions was delayed in relation to the surrounding vegetation changes.

Quantification of water content across a cement-clay interface using high resolution neutron radiography

In many designs for radioactive waste repositories, cement and clay will come into direct contact. The geochemical contrast between cement and clay will lead to mass fluxes across the interface, which consequently results in alteration of structural and transport properties of both materials that may affect the performance of the multi-barrier system. We present an experimental approach to study cement-clay interactions with a cell to accommodate small samples of cement and clay. The cell design allows both in situ measurement of water content across the sample using neutron radiography and measurement of transport parameters using through-diffusion tracer experiments. The aim of the high- resolution neutron radiography experiments was to monitor changes in water content (porosity) and their spatial extent. Neutron radiographs of several evolving cement-clay interfaces delivered quantitative data which allow resolving local water contents within the sample domain. In the present work we explored the uncertainties of the derived water contents with regard to various input parameters and with regard to the applied image correction procedures. Temporal variation of measurement conditions created absolute uncertainty of the water content in the order of ±0.1 (m3/m3), which could not be fully accounted for by correction procedures. Smaller relative changes in water content between two images can be derived by specific calibrations to two sample regions with different, invariant water contents.

Southern Hemisphere high-resolution palaeoclimate records of the last 2000 years

This study presents a comprehensive assessment of high-resolution Southern Hemisphere (SH) paleoarchives covering the last 2000 years. We identified 174 monthly to annually resolved climate proxy (tree ring, coral, ice core, documentary, speleothem and sedimentary) records from the Hemisphere. We assess the interannual and decadal sensitivity of each proxy record to large-scale circulation indices from the Pacific, Indian and Southern Ocean regions over the twentieth century. We then analyse the potential of this newly expanded palaeoclimate network to collectively represent predictands (sea surface temperature, sea level pressure, surface air temperature and precipitation) commonly used in climate reconstructions. The key dynamical centres-of-action of the equatorial Indo-Pacific are well captured by the palaeoclimate network, indicating that there is considerable reconstruction potential in this region, particularly in the post AD 1600 period when a number of long coral records are available. Current spatiotemporal gaps in data coverage and regions where significant potential for future proxy collection exists are discussed. We then highlight the need for new and extended records from key dynamical regions of the Southern Hemisphere. Although large-scale climate field reconstructions for the SH are in their infancy, we report that excellent progress in the development of regional proxies now makes plausible estimates of continental- to hemispheric-scale climate variations possible.

Analytic validation of a gas chromatography-mass spectrometry method for quantification of six amino acids in canine serum samples.

OBJECTIVE To analytically validate a gas concentration of chromatography-mass spectrometry (GC-MS) method for measurement of 6 amino acids in canine serum samples and to assess the stability of each amino acid after sample storage. SAMPLES Surplus serum from 80 canine samples submitted to the Gastrointestinal Laboratory at Texas A&M University and serum samples from 12 healthy dogs. PROCEDURES GC-MS was validated to determine precision, reproducibility, limit of detection, and percentage recovery of known added concentrations of 6 amino acids in surplus serum samples. Amino acid concentrations in serum samples from healthy dogs were measured before (baseline) and after storage in various conditions. RESULTS Intra- and interassay coefficients of variation (10 replicates involving 12 pooled serum samples) were 13.4% and 16.6% for glycine, 9.3% and 12.4% for glutamic acid, 5.1% and 6.3% for methionine, 14.0% and 15.1% for tryptophan, 6.2% and 11.0% for tyrosine, and 7.4% and 12.4% for lysine, respectively. Observed-to-expected concentration ratios in dilutional parallelism tests (6 replicates involving 6 pooled serum samples) were 79.5% to 111.5% for glycine, 80.9% to 123.0% for glutamic acid, 77.8% to 111.0% for methionine, 85.2% to 98.0% for tryptophan, 79.4% to 115.0% for tyrosine, and 79.4% to 110.0% for lysine. No amino acid concentration changed significantly from baseline after serum sample storage at -80°C for ≤ 7 days. CONCLUSIONS AND CLINICAL RELEVANCE GC-MS measurement of concentration of 6 amino acids in canine serum samples yielded precise, accurate, and reproducible results. Sample storage at -80°C for 1 week had no effect on GC-MS results.

High-resolution MALDI-FT-ICR MS imaging for the analysis of metabolites from formalin-fixed, paraffin-embedded clinical tissue samples.

We present the first analytical approach to demonstrate the in situ imaging of metabolites from formalin-fixed, paraffin-embedded (FFPE) human tissue samples. Using high-resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR MSI), we conducted a proof-of-principle experiment comparing metabolite measurements from FFPE and fresh frozen tissue sections, and found an overlap of 72% amongst 1700 m/z species. In particular, we observed conservation of biomedically relevant information at the metabolite level in FFPE tissues. In biomedical applications, we analysed tissues from 350 different cancer patients and were able to discriminate between normal and tumour tissues, and different tumours from the same organ, and found an independent prognostic factor for patient survival. This study demonstrates the ability to measure metabolites in FFPE tissues using MALDI-FT-ICR MSI, which can then be assigned to histology and clinical parameters. Our approach is a major technical, histochemical, and clinicopathological advance that highlights the potential for investigating diseases in archived FFPE tissues.

High-resolution AMS (super 14) C dating of post-bomb peat archives of atmospheric pollutants.

Peat deposits in Greenland and Denmark were investigated to show that high-resolution dating of these archives of atmospheric deposition can be provided for the last 50 years by radiocarbon dating using the atmospheric bomb pulse. (super 14) C was determined in macrofossils from sequential one cm slices using accelerator mass spectrometry (AMS). Values were calibrated with a general-purpose curve derived from annually averaged atmospheric (super 14) CO (sub 2) values in the northernmost northern hemisphere (NNH, 30 degrees -90 degrees N). We present a through review of (super 14) C bomb-pulse data from the NNH including our own measurements made in tree rings and seeds from Arizona as well as other previously published data. We show that our general-purpose calibration curve is valid for the whole NNH producing accurate dates within 1-2 years. In consequence, (super 14) C AMS can precisely date individual points in recent peat deposits within the range of the bomb-pulse (from the mid-1950s on). Comparing the (super 14) C AMS results with the customary dating method for recent peat profiles by (super 210) Pb, we show that the use of (super 137) Cs to validate and correct (super 210) Pb dates proves to be more problematic than previously supposed. As a unique example of our technique, we show how this chronometer can be applied to identify temporal changes in Hg concentrations from Danish and Greenland peat cores.

High-resolution atomic force microscopy imaging of rhodopsin in rod outer segment disk membranes.

Atomic force microscopy (AFM) is a powerful imaging technique that allows recording topographical information of membrane proteins under near-physiological conditions. Remarkable results have been obtained on membrane proteins that were reconstituted into lipid bilayers. High-resolution AFM imaging of native disk membranes from vertebrate rod outer segments has unveiled the higher-order oligomeric state of the G protein-coupled receptor rhodopsin, which is highly expressed in disk membranes. Based on AFM imaging, it has been demonstrated that rhodopsin assembles in rows of dimers and paracrystals and that the rhodopsin dimer is the fundamental building block of higher-order structures.

Binary recombinase systems for high-resolution conditional mutagenesis.

Conditional mutagenesis using Cre recombinase expressed from tissue specific promoters facilitates analyses of gene function and cell lineage tracing. Here, we describe two novel dual-promoter-driven conditional mutagenesis systems designed for greater accuracy and optimal efficiency of recombination. Co-Driver employs a recombinase cascade of Dre and Dre-respondent Cre, which processes loxP-flanked alleles only when both recombinases are expressed in a predetermined temporal sequence. This unique property makes Co-Driver ideal for sequential lineage tracing studies aimed at unraveling the relationships between cellular precursors and mature cell types. Co-InCre was designed for highly efficient intersectional conditional transgenesis. It relies on highly active trans-splicing inteins and promoters with simultaneous transcriptional activity to reconstitute Cre recombinase from two inactive precursor fragments. By generating native Cre, Co-InCre attains recombination rates that exceed all other binary SSR systems evaluated in this study. Both Co-Driver and Co-InCre significantly extend the utility of existing Cre-responsive alleles.