Spatial and temporal distribution of sperm whales (Physeter macrocephalus) within the Kaikoura submarine canyon in relation to oceanographic variables

The Kaikoura area is a valuable feeding spot for sperm whales with the presence of a submarine canyon close to shore. Male sperm whales can be found there year around, close to the shore and exhibiting almost constant foraging activities. This thesis investigates the distribution and habitat use, both spatially and temporally, of sperm whales (Physeter macrocephalus) within the Kaikoura submarine canyon, New Zealand. The primary aim was to determine which oceanographic variables and bathymetric features influence the sperm whale distribution patterns off Kaikoura. A theodolite was used to track surfacing and movement of sperm whales from a shore-based station. The accuracy of positions recorded by the theodolite was investigated by comparing theodolite measurements of an object of known position. A calibration technique was then developed as the vertical angle was not accurately determined by the theodolite. In addition to investigating the distribution of sperm whales, the daily abundance of sperm whales within the Kaikoura submarine canyon was estimated. Distance sampling and mark-resight models showed an average of 4 (SEM = 0.13) individuals present in the study area at any given time. The mark-resight technique using photo-identification was not possible from a shore-based station so a spatio-temporal model was built in order to track the identity of individuals. The model was tested using photo-identification of sperm whales collected from a boat-based station. Results showed that 88% of the modeled identifications corresponded to the photo-identification database. Sperm whales off Kaikoura were strongly associated with depth, slope and distance from the nearest coast. They were found in waters between 500 m to 1250 m deep and preferred shallower waters in winter. In spring, sperm whales occurred further from the coast, mainly in the Hikurangi Trough, north-east of the shore-based station. Generalized Additive Models (GAM) were used to identify significant oceanographic variables predicting the presence of sperm whales off Kaikoura. Models indicated that sea surface temperature (SST), chlorophylla (Chla) and distance from sea surface temperature fronts were all important parameters in predicting sperm whales presence. Results showed that sperm whales aggregated in the section of the study area with the lowest SST and near SST fronts. This study provides a detailed insight into the use of the Kaikoura submarine canyon by male sperm whales

The effect of solvent dynamics on the low frequency collective motions of DNA in solution and unoriented films

Infrared spectroscopy is used to probe the dynamics of invitro samples of DNA prepared as solutions and as solid unoriented films.The lowest frequency DNA mode identified in the far-infrared spectra ofthe DNA samples is found to shift in frequency when the solvent influencein the hydration shell is altered. The lowest frequency mode also hascharacteristics that are similar to beta - relaxations identified inother glass forming polymers

Chemical Imaging on Liver Steatosis Using Synchrotron Infrared and ToF-SIMS Microspectroscopies

Fatty liver or steatosis is a frequent histopathological change. It is a precursor for steatohepatitis that may progress to cirrhosis and in some cases to hepatocellular carcinoma. In this study we addressed the in situ composition and distribution of biochemical compounds on tissue sections of steatotic liver using both synchrotron FTIR (Fourier transform infrared) and ToF-SIMS (time of flight secondary ion mass spectrometry) microspectroscopies. FTIR is a vibrational spectroscopy that allows investigating the global biochemical composition and ToF-SIMS lead to identify molecular species in particular lipids. Synchrotron FTIR microspectroscopy demonstrated that bands linked to lipid contribution such as -CH3 and -CH2 as well as esters were highly intense in steatotic vesicles. Moreover, a careful analysis of the -CH2 symmetric and anti-symmetric stretching modes revealed a slight downward shift in spectra recorded inside steatotic vesicles when compared to spectra recorded outside, suggesting a different lipid environment inside the steatotic vesicles. ToF-SIMS analysis of such steatotic vesicles disclosed a selective enrichment in cholesterol as well as in diacylglycerol (DAG) species carrying long alkyl chains. Indeed, DAG C36 species were selectively localized inside the steatotic vesicles whereas DAG C30 species were detected mostly outside. Furthermore, FTIR detected a signal corresponding to olefin (C = C, 3000-3060 cm−1) and revealed a selective localization of unsaturated lipids inside the steatotic vesicles. ToF-SIMS analysis definitely demonstrated that DAG species C30, C32, C34 and C36 carrying at least one unsaturated alkyl chain were selectively concentrated into the steatotic vesicles. On the other hand, investigations performed on the non-steatotic part of the fatty livers have revealed important changes when compared to the normal liver. Although the non-steatotic regions of fatty livers exhibited normal histological aspect, IR spectra demonstrated an increase in the lipid content and ToF-SIMS detected small lipid droplets corresponding most likely to the first steps of lipid accretion

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl–DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium

Noncovalent Interactions of Hydrated DNA and RNA Mapped by 2D-IR Spectroscopy

Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific electrostatic and many-body interactions. Structural fluctuations of the water shell result in fluctuating Coulomb forces on polar and/or ionic groups of the biomolecular structure and in a breaking and reformation of hydrogen bonds. Two-dimensional infrared (2D-IR) spectroscopy of vibrational modes of DNA and RNA gives insight into local hydration geometries, elementary molecular dynamics, and the mechanisms behind them. In this chapter, recent results from 2D-IR spectroscopy of native and artificial DNA and RNA are presented, together with theoretical calculations of molecular couplings and molecular dynamics simulations. Backbone vibrations of DNA and RNA are established as sensitive noninvasive probes of the complex behavior of hydrated helices. The results reveal the femtosecond fluctuation dynamics of the water shell, the short-range character of Coulomb interactions, and the strength and fluctuation amplitudes of interfacial electric fields.Comment: To appear as Chapter 8 of Springer Series in Optical Sciences: Coherent Multidimensional Spectroscopy -- Editors: Cho, Minhaeng (Ed.), 201

Ultrafast 2D-IR and optical Kerr effect spectroscopy reveal the impact of duplex melting on the structural dynamics of DNA

Changes in the structural and solvation dynamics of a 15mer AT DNA duplex upon melting of the double-helix are observed by a combination of ultrafast two-dimensional infrared (2D-IR) and optical Kerr-effect (OKE) spectroscopies. 2D-IR spectroscopy of the vibrational modes of the DNA bases reveal signature off-diagonal peaks arising from coupling and energy transfer across Watson-Crick paired bases that are unique to double-stranded DNA (ds-DNA). Spectral diffusion of specific base vibrational modes report on the structural dynamics of the duplex and the minor groove, which is predicted to contain a spine of hydration. Changes in these dynamics upon melting are assigned to increases in the degree of mobile solvent access to the bases in single-stranded DNA (ss-DNA) relative to the duplex. OKE spectra exhibit peaks that are assigned to specific long-range phonon modes of ds- and ss-DNA. Temperature-related changes in these features correlate well with those obtained from the 2D-IR spectra although the melting temperature of the ds-DNA phonon band is slightly higher than that for the Watson-Crick modes, suggesting that a degree of long-range duplex structure survives the loss of Watson-Crick hydrogen bonding. These results demonstrate that the melting of ds-DNA disrupts helix-specific structural dynamics encompassing length scales ranging from mode delocalisation in the Watson-Crick base pairs to long-range phonon modes that extend over multiple base pairs and which may play a role in molecular recognition of DNA

Microscopic structure of the polymer-induced liquid precursor for calcium carbonate

Many biomineral crystals form complex non-equilibrium shapes, often via transient amorphous precursors. Also in vitro crystals can be grown with non-equilibrium morphologies, such as thin films or nanorods. In many cases this involves charged polymeric additives that form a polymer-induced liquid precursor (PILP). Here, we investigate the CaCO3 based PILP process with a variety of techniques including cryoTEM and NMR. The initial products are 30–50 nm amorphous calcium carbonate (ACC) nanoparticles with ~2 nm nanoparticulate texture. We show the polymers strongly interact with ACC in the early stages, and become excluded during crystallization, with no liquid–liquid phase separation detected during the process. Our results suggest that “PILP” is actually a polymer-driven assembly of ACC clusters, and that its liquid-like behavior at the macroscopic level is due to the small size and surface properties of the assemblies. We propose that a similar biopolymer-stabilized nanogranular phase may be active in biomineralization

Математическое моделирование тепломассопереноса в изоляции трубопроводов тепловых сетей, эксплуатируемых в условиях затопления

The spectral range of extreme ultraviolet radiation (XUV or EUV) is an active area of research incorporating many scientific fields such as microscopy, lithography or reflectometry. During the last decade, a lot of effort has been put into transferring many of the known techniques developed at linear accelerators into the laboratory using discharge-produced plasmas (DPPs) or laser-produced plasmas (LPPs) as an alternative light source. In particular, the semiconductor industry is in need of on-site tools in the shorter wavelength range for production and inspection of structured surfaces with nanometer resolution. Here traditional charge coupled device (CCD) image sensors are inapplicable as detectors because of the strong absorption of XUV by matter prohibiting any generation of electron-hole pairs inside a deep lying p-n junction. As a solution, two-dimensional backthinned CCDs are available in the market offering high sensitivity to XUV light. Although for many applications a one-dimensional line scanning image sensor would be sufficient, they are non-existent for XUV. It is only lately that manufacturers have started to adopt the principle of backthinning to CCD line sensors to enhance sensitivity in the long wavelength UV range (>200 nm). Here we show that generally these compact sensors offer good quantum efficiencies in the XUV which make them a candidate for many spectroscopic applications and future industrial inline inspection tools for which costly two-dimensional CCDs are oversized. We have successfully implemented a compact sensor device into a laboratory XUV spectrometer and reflectometer. Our measurements compare the quantum efficiency of a state-of-the-art XUV array CCD to a phosphor-coated line sensor and a new backthinned line sensor. Additionally, we show recorded spectra from a laboratory DPP source to demonstrate the potential of a wide range of applications