Binding site size limitations of imidazole-pyrrole polyamides for recognition in the minor groove of DNA

The discovery that the three ring polyamide Im-Py-Py-Dp containing imidazole (Im) and pyrrole (Py) carboxamides binds the DNA sequence 5'-(A,T)G(A,T)C(A,T)-3' as an antiparallel dimer offers a new model for the design of ligands for specific recognition of sequences in the minor groove containing both G,C and A,T base pairs. In Chapter 2, experiments are described in which the sequential addition of five N- methylpyrrolecarboxamides to the imidazole-pyrrole polyamide Im-Py-Py-Dp affords a series of six homologous polyamides, Im-(Py)_2-7-Dp, that differ in the size of their binding site, apparent first order binding affinity, and sequence specificity. These results demonstrate that DNA sequences up to nine base pairs in length can be specifically recognized by imidazole-pyrrole polyamides containing three to seven rings by 2:1 polyamide-DNA complex formation in the minor groove. Recognition of a nine base pair site defines the new lower limit of the binding site size that can be recognized by polyamides containing exclusively imidazole and pyrrolecarboxamides. The results of this study should provide useful guidelines for the design of new polyamides that bind longer DNA sites with enhanced affinity and specificity.

In Chapter 3 the design and synthesis of the hairpin polyamide Im-Py-Im-Py-γ-Im- Py-Im-Py-Dp is described. Quantitative DNase I footprint titration experiments reveal that Im-Py-Im-Py-γ-Im-Py-Im-Py-Dp binds six base pair 5'-(A,T)GCGC(A,T)-3' sequences with 30-fold higher affinity than the unlinked polyamide Im-Py-Im-Py-Dp. The hairpin polyamide does not discriminate between A•T and T•A at the first and sixth positions of the binding site as three sites 5'-TGCGCT-3', 5'-TGCGCA-3', and 5 'AGCGCT- 3' are bound with similar affinity. However, Im-Py-Im-Py-γ-Im-Py-Im-PyDp is specific for and discriminates between G•C and C•G base pairs in the 5'-GCGC-3' core as evidenced by lower affinities for the mismatched sites 5'-AACGCA-3', 5'- TGCGTT-3', 5'-TGCGGT-3', and 5'-ACCGCT-3'.

In Chapter 4, experiments are described in which a kinetically stable hexa-aza Schiff base La³⁺ complex is covalently attached to a Tat(49-72) peptide which has been shown to bind the HIV-1 TAR RNA sequence. Although these metallo-peptides cleave TAR site-specifically in the hexanucleotide loop to afford products consistent with hydrolysis, a series of control experiments suggests that the observed cleavage is not caused by a sequence-specifically bound Tat(49-72)-La(L)³⁺ peptide.

Impact of laser-accelerated micron-size projectile on dense plasma

The impact of a laser-accelerated micron-size projectile on a dense plasma target is studied using two-dimensional particle-in-cell simulations. The projectile is first accelerated by an ultraintense laser. It then impinges on the dense plasma target and merges with the latter. Part of the kinetic energy of the laser-accelerated ions in the projectile is deposited in the fused target, and an extremely high concentration of plasma ions with a mean kinetic energy needed for fusion reaction is induced. The interaction is thus useful for laser-driven impact fusion and as a compact neutron source.

Reconstructing Past Depositional and Diagenetic Processes through Quantitative Stratigraphic Analysis of the Martian Sedimentary Rock Record

High-resolution orbital and in situ observations acquired of the Martian surface during the past two decades provide the opportunity to study the rock record of Mars at an unprecedented level of detail. This dissertation consists of four studies whose common goal is to establish new standards for the quantitative analysis of visible and near-infrared data from the surface of Mars. Through the compilation of global image inventories, application of stratigraphic and sedimentologic statistical methods, and use of laboratory analogs, this dissertation provides insight into the history of past depositional and diagenetic processes on Mars. The first study presents a global inventory of stratified deposits observed in images from the High Resolution Image Science Experiment (HiRISE) camera on-board the Mars Reconnaissance Orbiter. This work uses the widespread coverage of high-resolution orbital images to make global-scale observations about the processes controlling sediment transport and deposition on Mars. The next chapter presents a study of bed thickness distributions in Martian sedimentary deposits, showing how statistical methods can be used to establish quantitative criteria for evaluating the depositional history of stratified deposits observed in orbital images. The third study tests the ability of spectral mixing models to obtain quantitative mineral abundances from near-infrared reflectance spectra of clay and sulfate mixtures in the laboratory for application to the analysis of orbital spectra of sedimentary deposits on Mars. The final study employs a statistical analysis of the size, shape, and distribution of nodules observed by the Mars Science Laboratory Curiosity rover team in the Sheepbed mudstone at Yellowknife Bay in Gale crater. This analysis is used to evaluate hypotheses for nodule formation and to gain insight into the diagenetic history of an ancient habitable environment on Mars.

Some observations on the temporal variations of size of copepods and some answers to questions on their biology. [Translation from: Internationale Revue der Gesamten Hydrobiologie und Hydrographie 17 99-114, 1927.]

Until now observations on the temporal variation of size of freshwater copepods have not provided much information. Other observers only mention in passing this or that phenomenon from which it is possible to deduct termporal variations. In this study Cyclops strenuus s.l., a freshwater species of fairly wide distribution, is studied in two water bodies. The author studies the systematic, placing of inhabitants described as C. strenuus Fischer in both locations, their annual life cycle, and their annual size variations.

On the methods of determining size/weight characteristics of food organisms of fish. (Determination of the length of Copepoda in larval stages by egg-laying females of the free living freshwater Copepoda). [Translation from: Voprosy Ikhtiologii 14, 182-194, 1960. ]

As is known, copepods play an important role in the nutrition of fish. Therefore with a view to facilitating research on the study of the quantitative side of feeding, there have recently appeared a considerable number of papers devoted to the development of methods for determining the wet. weight of these crustaceans. For the further facilitating of research in the nutrition of fish it would be of great interest to clarify the problem, is there not some kind of rule in the growth of the crustaceans during metamorphosis, and if there is such a rule is it not possible, to determine the length of the larvae at each stage, not by measuring them, but by using the formulae derived on the basis of these rules. This article examines the growth curves of different species of freshwater Copepoda, obtained on the basis of experimental observations in cultures or by way of measurement of mass material at all stages of development in samples from water-bodies. The authors study in particular the ratio of the mean diameter of the eggs to the mean length of the egg-bearing females.

Studies on the mouth size of fish larvae. Method and conclusions only [Translation from: Bulletin of the Japanese Society of Scientific Fisheries 36, 353-368, 1970]

This study was conducted to look into the relationship between mouth size and the total length of larval fish, and the growth in total length of larval fish in one or within a one-year period. Study material was gathered in the South China Sea, the Bay of Bangkok and the Vietnamese coast. This translation focuses on methods and conclusions of the original (longer) paper.

Ecological significance of seasonal variation in clutch-size of Arctodiaptomus bacillifer in alpine lakes of high altitudes (Val Bognanco) [Translation from: Bollettino di Zoologia 37 491-492, 1970]

This brief paper describes the significance of seasonal variation in clutch-size of the copepod Arctodiaptomus bacillifer in alpine lakes of high altitudes (Val Bognanco). Seasonal dynamics of the zooplankton of these lakes was studied during summer and autumn of 1968 and 1969and results are summarised.

The relationship between boat size and fish catches in the gillnet fishery of Lake Victoria, Uganda

The number and size composition of gillnets, fishing grounds, and the quantity and composition of fish catches were related to the size of fishing boat. The overall number of gillnets per boat increased from 20.9 + or - 2.3 nets in 5-6 m long boats to 88.6 + or - 11.8 nets in 11-12 m long boats. The proportion of large mesh sizes, + or more than 127 mm, also increased from 40% in 5-6 m long boats to 100% in boats longer than 10 m. Fish catches are related to the size of boat and this should be considered when formulating management guidelines of the lake's fishery. Promotion of large fishing boats 8 m or longer and restriction on the number and/or mesh size of gillnets of smaller boats could increase ecological and socio-economic benefits.

I. Stokes flow past a thin screen. II. Viscous flows past porous bodies of finite size

Part I

The slow, viscous flow past a thin screen is analyzed based on Stokes equations. The problem is reduced to an associated electric potential problem as introduced by Roscoe. Alternatively, the problem is formulated in terms of a Stokeslet distribution, which turns out to be equivalent to the first approach.

Special interest is directed towards the solution of the Stokes flow past a circular annulus. A "Stokeslet" formulation is used in this analysis. The problem is finally reduced to solving a Fredholm integral equation of the second kind. Numerical data for the drag coefficient and the mean velocity through the hole of the annulus are obtained.

Stokes flow past a circular screen with numerous holes is also attempted by assuming a set of approximate boundary conditions. An "electric potential" formulation is used, and the problem is also reduced to solving a Fredholm integral equation of the second kind. Drag coefficient and mean velocity through the screen are computed.

Part II

The purpose of this investigation is to formulate correctly a set of boundary conditions to be prescribed at the interface between a viscous flow region and a porous medium so that the problem of a viscous flow past a porous body can be solved.

General macroscopic equations of motion for flow through porous media are first derived by averaging Stokes equations over a volume element of the medium. These equations, including viscous stresses for the description, are more general than Darcy's law. They reduce to Darcy's law when the Darcy number becomes extremely small.

The interface boundary conditions of the first kind are then formulated with respect to the general macroscopic equations applied within the porous region. An application of such equations and boundary conditions to a Poiseuille shear flow problem demonstrates that there usually exists a thin interface layer immediately inside the porous medium in which the tangential velocity varies exponentially and Darcy's law does not apply.

With Darcy's law assumed within the porous region, interface boundary conditions of the second kind are established which relate the flow variables across the interface layer. The primary feature is a jump condition on the tangential velocity, which is found to be directly proportional to the normal gradient of the tangential velocity immediately outside the porous medium. This is in agreement with the experimental results of Beavers, et al.

The derived boundary conditions are applied in the solutions of two other problems: (1) Viscous flow between a rotating solid cylinder and a stationary porous cylinder, and (2) Stokes flow past a porous sphere.

Core size scaling of helical-core optical fibres

The mode-area, scaling properties of helical-core optical fibres are numerically studied and the limit of core size for achievable single-mode operation is explored. By appropriate design, helical-core fibres can operate in a single mode with possible scaling up to 300 mu m in core diameter with numerical aperture 0.1.

Effect of the A cation size disorder and synthesis conditions on the properties of an iron perovskite series

Póster presentado en The Energy and Materials Research Conference - EMR2015 celebrado en Madrid (España) entre el 25-27 de febrero de 2015