Structural elucidation and antisense properties of a sugar-modified DNA analogue

Antisense oligonucleotides deserve great attention as potential drug candidates for the treatment of genetic disorders. For example, muscle dystrophy can be treated successfully in mice by antisense-induced exon skipping in the pre-mRNA coding for the structural protein dystrophin in muscle cells. For this purpose a sugar- and backbone-modified DNA analogue was designed, in which a tricyclic ring system substitutes the deoxyribose. These chemical modifications stabilize the dimers formed with the targeted RNA relative to native nucleic acid duplexes and increase the biostability of the antisense oligonucleotide. While evading enzymatic degradation constitutes an essential property of antisense oligonucleotides for therapeutic application, it renders the oligonucleotide inaccessible to biochemical sequencing techniques and requires the development of alternative methods based on mass spectrometry. The set of sequences studied includes tcDNA oligonucleotides ranging from 10 to 15 nucleotides in length as well as their hybrid duplexes with DNA and RNA complements. All samples were analyzed on a LTQ Orbitrap XL instrument equipped with a nano-electrospray source. For tandem mass spectrometric experiments collision-induced dissociation was performed, using helium as collision gas. Mass spectrometric sequencing of tcDNA oligomers manifests the applicability of the technique to substrates beyond the scope of enzyme-based methods. Sequencing requires the formation of characteristic backbone fragments, which take the form of a-B- and w-ions in the product ion spectra of tcDNA. These types of product ions are typically associated with unmodified DNA, which suggests a DNA-like fragmentation mechanism in tcDNA. The loss of nucleobases constitutes the second prevalent dissociation pathway observed in tcDNA. Comparison of partially and fully modified oligonucleotides indicates a pronounced impact of the sugar-moiety on the base loss. As this event initiates cleavage of the backbone, the presented results provide new mechanistic insights into the fragmentation of DNA in the gas-phase. The influence of the sugar-moiety on the dissociation extends to tcDNA:DNA and tcDNA:RNA hybrid duplexes, where base loss was found to be much more prominent from sugar-modified oligonucleotides than from their natural complements. Further prominent dissociation channels are strand separation and backbone cleavage of the single strands, as well as the ejection of backbone fragments from the intact duplex. The latter pathway depends noticeably on the base sequence. Moreover, it gives evidence of the high stability of the hybrid dimers, and thus directly reflects the affinity of tcDNA for its target in the cell. As the cellular target of tcDNA is a pre-mRNA, the structure was designed to discriminate RNA from DNA complements, which could be demonstrated by mass spectrometric experiments.

Sedimentological, physical, bulk geochemical, elemental and rock magnetic properties of the Middle to Late Pleistocene Rodderberg (Eifel/Germany)

The sediment record from Rodderberg potentially provides a climate and environmental record spanning at least the last ca 130 ka. Results from a low resolution pilot study reveal characteristic fluctuations that can be related to global climate variability as reflected in marine isotope stages and document the potential of this site for continuous and high-resolution investigations of the Middle to Late Pleistocene. Here we document the tentative lithology drilled, and show how the elemental composition can be interpreted with regard to lake level fluctuations, related redox conditions, but also to grain-size distribution and changes in lacustrine productivity. Finally, based on major lithological changes, a preliminary depth/age model is suggested that allows reassessing published luminescence ages from the same site.

Magnetic properties and chemical composition at DSDP Hole 77-538A

Magnetic properties of doleritic and some metamorphic basement rocks underlying Catoche Knoll are studied. Doleritic rocks show a high saturation magnetic moment (2-5 emu/g) compared to metamorphic rocks (0.1-1 emu/g). Magnetic minerals of rocks from this hole show a high stability when heated in vacuo up to 600°C at a fixed rate of heating. Curie temperatures are distributed close to 550°C. These properties differ markedly from those of common submarine basalts observed before. X-ray microprobe analysis techniques were used to determine internal structures of ferromagnetic minerals; in most of ferromagnetic minerals there exist two different types of magnetic phases (i.e., products of high-temperature and low-temperature oxidations). Interpretations on the coexisting, seemingly contradictory, phases can be made based upon present analyses.

Magnetic properties of Cenozoic MORB and Cretaceous MORB from DSDP and ODP holes

The fact that the natural remanent magnetization (NRM) intensity of mid-oceanic-ridge basalt (MORB) samples shows systematic variations as a function of age has long been recognized: maximum as well as average intensities are generally high for very young samples, falling off rather rapidly to less than half the recent values in samples between 10 and 30 Ma, whereupon they slowly rise in the early Tertiary and Cretaceous to values that approach those of the very young samples. NRM intensities measured in this study follow the same trends as those observed in previous publications. In this study, we take a statistical approach and examine whether this pattern can be explained by variations in one or more of all previously proposed mechanisms: chemical composition of the magnetic minerals, abundance of these magnetization carriers, vectorial superposition of parallel or antiparallel components of magnetization, magnetic grain or domain size patterns, low-temperature oxidation to titanomaghemite, or geomagnetic field behavior. We find that the samples do not show any compositional, petrological, rock-magnetic, or paleomagnetic patterns that can explain the trends. Geomagnetic field intensity is the only effect that cannot be directly tested on the same samples, but it shows a similar pattern as our measured NRM intensities. We therefore conclude that the geomagnetic field strength was, on-average, significantly greater during the Cretaceous than during the Oligocene and Miocene.

Magnetic properties and oxide petrography of ODP Hole 111-504B

Magnetic properties measurements were performed on 47 samples drilled during Leg 111 of the Ocean Drilling Program and oxide petrography was studied in 32 samples taken at depths throughout the sheeted dike complex in Hole 504B. Integration of these data with results from previous DSDP legs shows that while natural remanent magnetization is constant with depth, magnetic susceptibility increases and median demagnetizing field and the Q ratio decrease with depth in the section. These trends appear to be a result of an increase in deuteric oxidation and a decrease in hydrothermal alteration of primary titanomagnetite with depth. A distinct change in stable magnetic inclination occurs between the extrusive basalts and the sheeted dikes and may be a result of tectonic rotation of the upper extrusive basalts.

Electromagnetic, rock magnetic, and geochemical properties of surficial sediments in Eckernförde Bay

Submarine groundwater discharge in coastal settings can massively modify the hydraulic and geochemical conditions of the seafloor. Resulting local anomalies in the morphology and physical properties of surface sediments are usually explored with seismo-acoustic imaging techniques. Controlled source electromagnetic imaging offers an innovative dual approach to seep characterization by its ability to detect pore-water electrical conductivity, hence salinity, as well as sediment magnetic susceptibility, hence preservation or diagenetic alteration of iron oxides. The newly developed electromagnetic (EM) profiler Neridis II successfully realized this concept for a first time with a high-resolution survey of freshwater seeps in Eckernförde Bay (SW Baltic Sea). We demonstrate that EM profiling, complemented and validated by acoustic as well as sample-based rock magnetic and geochemical methods, can create a crisp and revealing fingerprint image of freshwater seepage and related reductive alteration of near-surface sediments. Our findings imply that (1) freshwater penetrates the pore space of Holocene mud sediments by both diffuse and focused advection, (2) pockmarks are marked by focused freshwater seepage, underlying sand highs, reduced mud thickness, higher porosity, fining of grain size, and anoxic conditions, (3) depletion of Fe oxides, especially magnetite, is more pervasive within pockmarks due to higher concentrations of organic and sulfidic reaction partners, and (4) freshwater advection reduces sediment magnetic susceptibility by a combination of pore-water injection (dilution) and magnetite reduction (depletion). The conductivity vs. susceptibility biplot resolves subtle lateral litho- and hydrofacies variations.

Magnetic properties, grain sizes and minerals at DSDP Site 83-504B

Twenty-seven samples from the Leg 83 section of Hole 504B have been investigated using magnetic, optical, and electron optical methods. The primary magnetic mineral to crystallize was titanomagnetite of approximate composition Fe2.4Ti0.6O4 (TM60), but none survives, nor is there evidence of titanomaghemite produced by oxidation of TM60. The average measured magnetic properties can be interpreted in terms of magnetite, Fe3O4, having average grain size of <1 µm and present in average volume concentration of - 0.5%. The intensity of the natural remanent magnetization (NRM) of the rocks could also be accounted for as being a thermoremanence carried by this mineral. Although the heterogeneity of the titanomagnetite grains could be detected optically, the texture of the intergrown phases is poorly developed. In some samples from the massive units of the lower part of the section, trellis patterns were visible. The Fe3O4 present in the intergrowths is too intimately mixed with the other intergrown phases to be revealed by electron microprobe analysis that simply returns the bulk composition of the intergrowth (oxidized TM60). The path by which the mineral assemblage evolved from TM60 to an Fe304-containing intergrowth, under the temperature and pressure conditions obtaining in the Leg 83 section, makes interesting speculation. Deuteric oxidation, maghemitization/inversion, or some hypothetical low-temperature/high-pressure oxidation by a leaching-of-iron process may all play roles.

Magnetic properties of basalts and sediments of ODP Leg 135 sites

Paleomagnetic and rock-magnetic investigations of basalts from Hole 834B in the Lau backarc basin and of sediments from Holes 841A and 841B at the Tonga Ridge are reported. Three groups of blocking temperatures in the basalts suggest the presence of at least three magnetic phases: pure magnetite, a Ti-poor titanomagnetite, and a Ti-rich phase. The drill-string-induced remanence in the basalts is typically between three and six times the original normal remanent magnetization intensity, but it is mostly removed by alternating-field (AF) cleaning in 5 mT. Volume susceptibility values range from 0.04 * 10**-3 to 4 * 10**-3 cgs. The modified Q-ratio J5/sus ranges from 0.5 to 10. The drill-string-induced remanence behaves different in the two sediment cores from Holes 841A and 841B, which may be the result of differences in the sediment or caused by the different drilling equipment used. The AF-cleaned inclinations of the sediment in Holes 841A and 841B suggest a slight flattening with increasing depth (up to 6° under a load of 400 m of sediment) to be present. This flattening is likely to be caused by the differential rotation of detrital particles under compaction during diagenesis.

Magnetic properties and heavy metals at DSDP Hole 83-504B

We report measurements of magnetic intensity, inclination, initial susceptibility, Koenigsberger's ratio, saturation magnetization, and Curie temperatures of 68 basalt samples from the Leg 83 section of Hole 504B. As in the upper part of the hole, reversely magnetized units predominate. Intensities of natural remanent magnetization vary widely, but the range of variation is an order of magnitude less than in the upper part of the hole. This and the other properties measured indicate that the magnetic characteristics of basalts from Hole 504B have been strongly affected by hydrothermal alteration, particularly in the deeper, Leg 83 section. The alteration states of the magnetic samples were studies using Xray diffraction, electron microprobe, X-ray fluorescence, and ion coupled plasma. Our results suggest three alteration zones in Hole 504B: a low-temperature zone (274.5-890 m) and two high-temperature zones (890-1050 m and 1050- 1350 m), differing in the number of veins observed in the samples and presumably differing in the volumes of hydrothermal fluids which reacted with the basalts.

Rock magnetic properties and titanomagnetite oxydation state of ODP Hole 109-648B (Table 1)

The titanomagnetite oxidation state of "zero age" ocean floor basalts was investigated. For this purpose the oxidation parameter, z, of Hole 648B basalts was determined by SEM observation of "shrinkage cracks" in individual titanomagnetite grains and by Curie temperature measurements. A mean z-value of 0.1 has been deduced for the Hole 648B basalts. Assuming a linear relationship between titanomagnetite low-temperature oxidation state and age of the oceanic basalt, an age of 0.7 m.y. is deduced for Hole 648B.

Magnetic properties and paleomagnetism of basalts from ODP Leg 107 basalts

The basalts recovered at Holes 651A and 655B appear to carry a single component remanent magnetization, which is generally of reversed polarity. These magnetizations are consistent with eruption during the Matuyama (651A) and Gilbert (655B) polarity epochs. The blocking temperature spectra and the Js/T curves indicate that titanomaghemite is the principal remanence carrier. The lower mean destructive field (MDF) and higher susceptibility at 651A probably indicates a lower mean oxidation state at this hole relative to 655B, which may simply reflect the age difference between the two basalt sequences. At both holes, a decreasing downcore trend both in natural remanent magnetization (NRM) and susceptibility probably indicates that maghemitization (from primary titanomagnetite) increases downcore. An interval of high coercivity at hole 655B (119.80-151.45 mbsf) appears to define a magnetically distinct unit within the basalt sequence.

Magnetic properties and geochemistry in DSDP Holes 69-504B an d 69-505B

More than 60 basalt samples from two Deep Sea Drilling Project holes on the Costa Rica Rift were studied for magnetic properties and were found to have no properties significantly different from other DSDP basalts. Opaque mineralogical and thermomagnetic properties of these samples, however, to some extent show differences from normal submarine basalts; a new type of thermomagnetic curve and wide range of chemical compositions were recognized. Oxidized samples possibly containing incipient ilmenite exsolution lamellae were reduced and re-equilibrated during heating. The Curie temperatures of the re-equilibrated titanomagnetites are interpreted to be those of the original crystallized phase before oxidation.

Paleomagnetic and rock magnetic properties of IODP Expedition 318 cores

The Integrated Ocean Drilling Program Expedition 318 to the Wilkes Land margin of Antarctica recovered a sedimentary succession ranging in age from lower Eocene to the Holocene. Excellent stratigraphic control is key to understanding the timing of paleoceanographic events through critical climate intervals. Drill sites recovered the lower and middle Eocene, nearly the entire Oligocene, the Miocene from about 17 Ma, the entire Pliocene and much of the Pleistocene. The paleomagnetic properties are generally suitable for magnetostratigraphic interpretation, with well-behaved demagnetization diagrams, uniform distribution of declinations, and a clear separation into two inclination modes. Although the sequences were discontinuously recovered with many gaps due to coring, and there are hiatuses from sedimentary and tectonic processes, the magnetostratigraphic patterns are in general readily interpretable. Our interpretations are integrated with the diatom, radiolarian, calcareous nannofossils and dinoflagellate cyst (dinocyst) biostratigraphy. The magnetostratigraphy significantly improves the resolution of the chronostratigraphy, particularly in intervals with poor biostratigraphic control. However, Southern Ocean records with reliable magnetostratigraphies are notably scarce, and the data reported here provide an opportunity for improved calibration of the biostratigraphic records. In particular, we provide a rare magnetostratigraphic calibration for dinocyst biostratigraphy in the Paleogene and a substantially improved diatom calibration for the Pliocene. This paper presents the stratigraphic framework for future paleoceanographic proxy records which are being developed for the Wilkes Land margin cores. It further provides tight constraints on the duration of regional hiatuses inferred from seismic surveys of the region.