Benthic foraminifera of surface sediments from the continental slope off Sierra Leone, North-West Africa

On "Meteor" cruise 30 (1973) 22 piston-cores were collected off Sierra Leone from water-depths between about 5000 m (Sierra Leone Basin) and 500 m (upper continental slope) with the objective to study the sediment composition and age as well as processes of sedimentation on the continental slope in a tropical humid region. Granulometric analysis and determinations of the carbonate contents of the sediment samples were carried out, as well as qualitative and quantitative analysis of the components of the grain size fractions > 63 µm and of the planktonic and benthonic foraminifera > 160 µm. Presently, the cold Canary Current influences the composition of the planktonic foraminifera within the northwestern area of investigation (profile A), whereas the planktonic fauna of the eastern area (profile C) seems to be truly tropical. In all Quaternary sediments from the continental slope off Sierra Leone, species of Globorotalia are less abundant than in truly pelagic sediments. For that reason, the zonation of the Pleistocene sediments based on the presence or absence of Globorotalia cultrata does not always agree with the climatic changes reflected in the sediments. Concerning past climates better results can be obtained by using the changes in percentage abundances of Globigerina sp. sp. and Globigerinoides sp. sp. as indicators for cool and warm temperatures. The Tertiary sediments contain a pelagic foraminiferal assemblage. In the Holocene sediments the benthonic foraminifera do not only serve as good paleodepth indicators, but their communities are also restricted to defined water masses, which change their positions in accordance with climatic changes. Thus, Cassidulina carinata in the area of investigation is an excellent indicator for sediments deposited during times, which were cooler than today; this is true for all cores from the continental slope off Sierra Leone independent of water-depth although this species presently abounds at water-depths around 600 m. The cores from the continental rise and from the Sierra Leone Basin (M30-261, M30-146, M30-147) were deposited below the calcium carbonate compensation depth. Only small sections of the cores consist of the original carbonate-free sediments, whereas the main part of the sediment column is redeposited material, rich in foraminifera, which normally live on the upper continental slope, or even on the shelf. From these cores only M30-261 can be subdivided into biostratigraphic zones ranging from zone V to zone Y. In all cores from the middle and upper continental slope of the eastern area of investigation (profile C; KL 230, 209-204) and in cores KL 183 and KL 184 from the northwestern area (profile A) we observed an undisturbed succession of sediments from the biostratigraphic zones X (partly), Y and Z. All cores from the central area (M30-181, M30-182, M30-262 to 264) and M30-187 from the upper slope of profile A show variable hiatuses in the sedimentary record. Locally, high velocity bottom currents were probably responsible for erosion, nondeposition or minimal sedimentation rates. These currents might have been initiated partly by the somewhat exposed position of this part of the continental slope, where the shelf edge bends from a northwest towards an eastern direction, and partly by very young tectonic movements. Fracture zones with vertically displaced fault blocs are frequent at Sierra Leone continental margin. According to seismic measurements by McMaster et al. (1975) the sites of the central area are located on an uplifted fault bloc explaining the reduced sediment rates or erosion. Unlike the central area, the eastern area (profile C) is situated on a downfaulted bloc with high sediment rates. The sediments from the cores of profile B as well as the turbiditic deep-sea sediments were deposited under a higher flow regime; therefore they are coarser than the extremely fine-grained sediments of the cores from profile C. Since the sand fraction (> 63 µm) is mainly composed of foraminifera, besides pteropods and light-colored fecal pellets, the carbonate content increases with the increasing percentage of the coarse grain fraction. Higher concentrations of quartz were only observed in core sections with considerable carbonate dissolution (mainly in the X-Zone), and, in general, in all sediments from the eastern area with higher terrigenous input including larger concentration of mica. Especially during times transitional between glacials and interglacials (or interstadials) the bottom currents were intensified. The percentages of coarse fraction and carbonate increase with increasing current velocities. Calcium carbonate dissolution becomes important in water depths > 3500 m. During cooler times the lysokline is depressed. Light-colored fecal pellets were redeposited from Late Neogene sediments (M30-187, M30-181). In the area of investigation they occur in the Holocene and mainly the Pleistocene sediments of the cores from the northwestern and central area because only here Tertiary sediments have been eroded at the uppermost continental slope. In the central area there are at least two periods of non-sedimentation and/or erosion which can be confined as being (1) not older than middle Pliocene and not younger than zone V and (2) younger than zone W. The local character of the erosion is documented by the fact that a complete Late Quaternary section is present in the cores of the northwestern and eastern area, each within less than 100 km from incomplete cores from the central area.

Preliminary mineralogy and ore petrology of the intermediate-sulfidation pallancata deposit, Ayacucho, Peru

Se investiga la compleja mineralogía del Yacimiento de Pallancata (6º productor de plata del mundo) y se establecen las condiciones de formación (P.T) basadas en la petrología de las menas comparada con los datos de mineralogía experimental y en la petrografía y microtermometría de inclusiones fluídas en la ganga silicatada, resultando un depósito típicamente caracterizado como epitermal de sulfuración intermedia.ABSTRACT:Pallancata is a world-class intermediate-sulfidation epithermal deposit, hosted by upper Miocene volcanics of the south-central Peruvian Andes in a sinuous N70ºW, ∼75º SW strike-slip structure, with wide (up to 35 m) pull-apart dilation zones related to bends of the vein strike. The structural evolution of the vein from earlier brecciation to later open space infill resembles the Shila Paula district (Chauvet et al. 2006). Fluid inclusion petrography and microthermometry show that ore deposition is related to protracted boiling of very diluted, mainly meteoric fluids, starting at 250–260 ºC, under ∼300 m hydrostatic head. The mineralogical-petrological study reveals a complex sequence of mineralization (eight stages) and mineral reactions consistent with Ag2S enrichment or Sb2S3 depletion, or both, during cooling over the temperature range 250–200 ºC: pyrite, sphalerite, galena, miargyrite, pyrargyrite-proustite, chalcopyrite, polybasite-pearceite, argentite (now acanthite), and Au–Ag alloy (“electrum”). This Ag2S enrichment and Sb2S3depletion during cooling may be explained by decay of a Ag-rich galena precursor at deeper levels (Pb2S2–AgSbS2 solid solution), which rapidly becomes unstable with decreasing temperature, producing residual (stoichiometric) PbS and more mobile Ag and Sb sulfide phases, which migrated upward and laterally away from the thermal core of the system. The core is still undisclosed by mining works, but the available geochemical evidence (logAg/log Pb ratios decreasing at depth) is consistent with this interpretation, implying a deeper potential resource. Data from sulfide geothermometry, based on mineral equilibria, document the thermal evolution of the system below 200 ºC (stephanite, uytenbogaardtite, jalpaite, stromeyerite, mckinstryite, among others). The end of the most productive stages (3, 4, and 5) is marked by the precipitation of stephanite at temperatures below 197 ± 5 ºC, but precipitation of residual silver continues through the waning stages of the hydrothermal system down to <93.3 ºC (stromeyerite) or in a supergene redistribution (stage 8, acanthite II).

Strained DNA is kinked by low concentrations of Zn2+

A novel atomic force microscope with a magnetically oscillated tip has provided unprecedented resolution of small DNA fragments spontaneously adsorbed to mica and imaged in situ in the presence of divalent ions. Kinks (localized bends of average angle 78°) were observed in axially strained minicircles consisting of tandemly repeated d(A)5 and d(GGGCC[C]) sequences. The frequency of kinks in identical minicircles increased 4-fold in the presence of 1 mM Zn2+ compared with 1 mM Mg2+. Kinking persisted in mixed Mg2+/Zn2+ electrolytes until the Zn2+ concentration dropped below 100 μM, indicating that this type of kinking may occur under physiological conditions. Kinking appears to replace intrinsic bending, and statistical analysis shows that kinks are not localized within any single sequence element. A surprisingly small free energy is associated with kink formation.

Transport of torsional stress in DNA

It is well known that transcription can induce torsional stress in DNA, affecting the activity of nearby genes or even inducing structural transitions in the DNA duplex. It has long been assumed that the generation of significant torsional stress requires the DNA to be anchored, forming a limited topological domain, because otherwise it would spin almost freely about its axis. Previous estimates of the rotational drag have, however, neglected the role of small natural bends in the helix backbone. We show how these bends can increase the drag several thousandfold relative to prior estimates, allowing significant torsional stress even in linear unanchored DNA. The model helps explain several puzzling experimental results on structural transitions induced by transcription of DNA.

Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun

Interactions among transcription factors that bind to separate sequence elements require bending of the intervening DNA and juxtaposition of interacting molecular surfaces in an appropriate orientation. Here, we examine the effects of single amino acid substitutions adjacent to the basic regions of Fos and Jun as well as changes in sequences flanking the AP-1 site on DNA bending. Substitution of charged amino acid residues at positions adjacent to the basic DNA-binding domains of Fos and Jun altered DNA bending. The change in DNA bending was directly proportional to the change in net charge for all heterodimeric combinations between these proteins. Fos and Jun induced distinct DNA bends at different binding sites. Exchange of a single base pair outside of the region contacted in the x-ray crystal structure altered DNA bending. Substitution of base pairs flanking the AP-1 site had converse effects on the opposite directions of DNA bending induced by homodimers and heterodimers. These results suggest that Fos and Jun induce DNA bending in part through electrostatic interactions between amino acid residues adjacent to the basic region and base pairs flanking the AP-1 site. DNA bending by Fos and Jun at inverted binding sites indicated that heterodimers bind to the AP-1 site in a preferred orientation. Mutation of a conserved arginine within the basic regions of Fos and transversion of the central C:G base pair in the AP-1 site to G:C had complementary effects on the orientation of heterodimer binding and DNA bending. The conformational variability of the Fos–Jun–AP-1 complex may contribute to its functional versatility at different promoters.

The leucine zipper may induce electrophoretic mobility anomalies without DNA bending

Numerous proteins bend DNA upon binding, a phenomenon of potential significance for regulation of gene expression and chromatin. DNA bending is commonly predicted from the presence of electrophoretic mobility anomalies in protein–DNA complexes. However, as compared with electrophoretic methods, several DNA binding oncoprotein families do not display comparable evidence of DNA bends in x-ray structural studies. Herein, circularization kinetics and affinity measurements with prebent DNA templates were employed to assess bending and DNA structural preferences for Max and other basic helix–loop–helix/leucine zipper proteins. In this way, proteins in the Myc/Max basic helix–loop–helix/leucine zipper family were found not to bend DNA in solution but to actually stabilize DNA in an unbent configuration that resists circularization. The mobility anomaly was found to be induced by the leucine zipper protein motif, rather than structural distortions of DNA. Thus rigid protein domain structures may induce anomalous electrophoretic mobility. Moreover, the energetic preference of non-DNA bending proteins for unbent templates suggests mechanisms whereby chromatin structure may regulate transcription.

p53-induced DNA bending and twisting: p53 tetramer binds on the outer side of a DNA loop and increases DNA twisting

DNA binding activity of p53 is crucial for its tumor suppressor function. Our recent studies have shown that four molecules of the DNA binding domain of human p53 (p53DBD) bind the response elements with high cooperativity and bend the DNA. By using A-tract phasing experiments, we find significant differences between the bending and twisting of DNA by p53DBD and by full-length human wild-type (wt) p53. Our data show that four subunits of p53DBD bend the DNA by 32–36°, whereas wt p53 bends it by 51–57°. The directionality of bending is consistent with major groove bends at the two pentamer junctions in the consensus DNA response element. More sophisticated phasing analyses also demonstrate that p53DBD and wt p53 overtwist the DNA response element by ≈35° and ≈70°, respectively. These results are in accord with molecular modeling studies of the tetrameric complex. Within the constraints imposed by the protein subunits, the DNA can assume a range of conformations resulting from correlated changes in bend and twist angles such that the p53–DNA tetrameric complex is stabilized by DNA overtwisting and bending toward the major groove at the CATG tetramers. This bending is consistent with the inherent sequence-dependent anisotropy of the duplex. Overall, the four p53 moieties are placed laterally in a staggered array on the external side of the DNA loop and have numerous interprotein interactions that increase the stability and cooperativity of binding. The novel architecture of the p53 tetrameric complex has important functional implications including possible p53 interactions with chromatin.

Visualization of a water-selective pore by electron crystallography in vitreous ice

The water-selective pathway through the aquaporin-1 membrane channel has been visualized by fitting an atomic model to a 3.7-Å resolution three-dimensional density map. This map was determined by analyzing images and electron diffraction patterns of lipid-reconstituted two-dimensional crystals of aquaporin-1 preserved in vitrified buffer in the absence of any additive. The aqueous pathway is characterized by a size-selective pore that is ≈4.0 ± 0.5Å in diameter, spans a length of ≈18Å, and bends by ≈25° as it traverses the bilayer. This narrow pore is connected by wide, funnel-shaped openings at the extracellular and cytoplasmic faces. The size-selective pore is outlined mostly by hydrophobic residues, resulting in a relatively inert pathway conducive to diffusion-limited water flow. The apex of the curved pore is close to the locations of the in-plane pseudo-2-fold symmetry axis that relates the N- and C-terminal halves and the conserved, functionally important N76 and N192 residues.

Deciphering the design of the tropomyosin molecule

The crystal structure at 2.0-Å resolution of an 81-residue N-terminal fragment of muscle α-tropomyosin reveals a parallel two-stranded α-helical coiled-coil structure with a remarkable core. The high alanine content of the molecule is clustered into short regions where the local 2-fold symmetry is broken by a small (≈1.2-Å) axial staggering of the helices. The joining of these regions with neighboring segments, where the helices are in axial register, gives rise to specific bends in the molecular axis. We observe such bends to be widely distributed in two-stranded α-helical coiled-coil proteins. This asymmetric design in a dimer of identical (or highly similar) sequences allows the tropomyosin molecule to adopt multiple bent conformations. The seven alanine clusters in the core of the complete molecule (which spans seven monomers of the actin helix) promote the semiflexible winding of the tropomyosin filament necessary for its regulatory role in muscle contraction.

What determines the folding of the chromatin fiber?

In this review, we attempt to summarize, in a critical manner, what is currently known about the processes of condensation and decondensation of chromatin fibers. We begin with a critical analysis of the possible mechanisms for condensation, considering both old and new evidence as to whether the linker DNA between nucleosomes bends or remains straight in the condensed structure. Concluding that the preponderance of evidence is for straight linkers, we ask what other fundamental process might allow condensation, and argue that there is evidence for linker histone-induced contraction of the internucleosome angle, as salt concentration is raised toward physiological levels. We also ask how certain specific regions of chromatin can become decondensed, even at physiological salt concentration, to allow transcription. We consider linker histone depletion and acetylation of the core histone tails, as possible mechanisms. On the basis of recent evidence, we suggest a unified model linking targeted acetylation of specific genomic regions to linker histone depletion, with unfolding of the condensed fiber as a consequence.

Fos and Jun bend the AP-1 site: effects of probe geometry on the detection of protein-induced DNA bending.

The effect of Fos and Jun binding on the structure of the AP-1 recognition site is controversial. Results from phasing analysis and phase-sensitive detection studies of DNA bending by Fos and Jun have led to opposite conclusions. The differences between these assays, the length of the spacer between two bends and the length of the sequences flanking the bends, are investigated here using intrinsic DNA bend standards. Both an increase in the spacer length as well as a decrease in the length of flanking sequences resulted in a reduction in the phase-dependent variation in electrophoretic mobilities. Probes with a wide separation between the bends and short flanking sequences, such as those used in the phase-sensitive detection studies, displayed no phase-dependent mobility variation. This shape-dependent variation in electrophoretic mobilities was reproduced by complexes formed by truncated Fos and Jun. Results from ligase-catalyzed cyclization experiments have been interpreted to indicate the absence of DNA bending in the Fos-Jun-AP-1 complex. However, truncated Fos and Jun can alter the relative rates of inter- and intramolecular ligation through mechanisms unrelated to DNA bending, confounding the interpretation of cyclization data. The analogous phase- and shape-dependence of the electrophoretic mobilities of the Fos-Jun-AP-1 complex and an intrinsic DNA bend confirm that Fos and Jun bend DNA, which may contribute to their functions in transcription regulation.

DNA bending by hexamethylene-tethered ammonium ions.

DNA is bent when complexed with certain proteins. We are exploring the hypothesis that asymmetric neutralization of phosphate charges will cause the DNA double helix to collapse toward the neutralized face. We have previously shown that DNA spontaneously bends toward one face of the double helix when it is partially substituted with neutral methylphosphonate linkages. We have now synthesized DNA duplexes in which cations are tethered by hexamethylene chains near specific phosphates. Electrophoretic phasing experiments demonstrate that tethering six ammonium ions on one helical face causes DNA to bend by approximately 5 degrees toward that face, in qualitative agreement with predictions. Ion pairing between tethered cations and DNA phosphates provides a new model for simulating the electrostatic consequences of phosphate neutralization by proteins.

On the existence and implications of an inverse folding code in proteins.

The existence of a code relating the set of possible sequences at a given position in a protein backbone to the local structure at that location is investigated. It is shown that only 73% of 4-C alpha structure fragments in a sample of 114 protein structures exhibit a preference for a particular set of sequences. The remaining structures can accommodate essentially any sequence. The structures that encode specific sequence distributions include the classical "secondary" structures, with the notable exception of planar (beta) bends. It is suggested that this has implications as to the mechanism of folding in proteins with extensive sheet/barrel structure. The possible role of structures that do not encode specific sequences as mutation hot spots is noted.

The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide.

The trans-activation response element (TAR) found near the 5' end of the viral RNA of the human immunodeficiency virus contains a 3-nt bulge that is recognized by the virally encoded trans-activator protein (Tat), an important mediator of transcriptional activation. Insertion of the TAR bulge into double-stranded RNA is known to result in reduced electrophoretic mobility, suggestive of a bulge-induced bend. Furthermore, NMR studies indicate that Arg causes a change in the structure of the TAR bulge, possibly reducing the bulge angle. However, neither of these effects has been quantified, nor have they been compared with the effects of the TAR-Tat interaction. Recently, an approach for the quantification of bulge-induced bends has been described in which hydrodynamic measurements, employing the method of transient electric birefringence, have yielded precise estimates for the angles of a series of RNA bulges, with the angles ranging from 7 degrees to 93 degrees. In the current study, transient electric birefringence measurements indicate that the TAR bulge introduces a bend of 50 degrees +/- 5 degrees in the absence of Mg2+. Addition of Arg leads to essentially complete straightening of the helix (to < 10 degrees) with a transition midpoint in the 1 mM range. This transition demonstrates specificity for the TAR bulge: no comparable transition was observed for U3 or A3 (control) bulges with differing flanking sequences. An essentially identical structural transition is observed for the Tat-derived peptide, although the transition midpoint for the latter is near 1 microM. Finally, low concentrations of Mg2+ alone reduce the bend angle by approximately 50%, consistent with the effects of Mg2+ on other pyrimidine bulges. This last observation is important in view of the fact that most previous structural/binding studies were performed in the absence of Mg2+.

Characterization and Degradation of Fatty Acid Methyl Esters and Biodiesel in Artificial Seawater Under UV Exposure Using Raman Spectroscopy

Thesis (Master's)--University of Washington, 2016-06