Amino acid in Deep Sea Drilling Project cores

Several amino acid diagenetic reactions, which take place in the deep-sea sedimentary environment, were investigated, using various Deep Sea Drilling Project (DSDP) cores. Initially it was found that essentially all the amino acids in sediments are bound in peptide linkages; but, with increasing age, the peptide bonds undergo slow hydrolysis that results in an increasingly larger fraction of amino acids in the free state. The hydrolysis half-life in calcareous sediments was estimated to be ~1-2 million years, while in non-carbonate sediment the hydrolysis rate may be considerably slower. The amino acid compositions and the extent of racemization of several amino acids were determined in various fractions isolated from the sediments. These analyses demonstrated that the mechanism, kinetics, and rate of amino acid diagenesis are highly dependent upon the physical state (i.e., free, bound, etc.) in which the amino acids exist in the sedimentary environment. In the free state, serine and threonine were found to decompose primarily by a dehydration reaction, while in the bound state (residue or HCl-insoluble fraction) a reversible aldol-cleavage reaction is the main decomposition pathway of these amino acids. The change in amino acid composition of the residue fraction with time was suggested to be due to the hydrolysis of peptide bonds, while in foraminiferal tests the compositional changes over geological time are the result of various decomposition reactions. Reversible first-order racemization kinetics are not observed for free amino acids in sediments. The explanation for these anomalous kinetics involves a complex reaction series which includes the hydrolysis of peptide bonds and the very rapid racemization of free amino acids. The racemization rates of free amino acids in sediments were found to be many orders of magnitude faster than those predicted from elevated temperature experiments using free amino acids in aqueous solution. The racemization rate enhancement of free amino acids in sediments may be due to the catalysis of the reaction by trace metals. Reversible first-order kinetics are followed for amino acids in the residue fraction isolated from sediments; the rate of racemization in this fraction is slower than that predicted for protein-bound amino acids. Various applications of amino acid diagenetic reactions are discussed. Racemization and the decomposition reaction of serine and threonine can both be used, with certain limitations, to make rough age estimates of deep-sea sediments back to several million years. The extent of racemization in foraminiferal tests which have been dated by some other independent technique can be used to estimate geothermal gradients, and thus heat flows, and to evaluate the bottom water temperature history in certain oceanic areas.

The influence of quantum dot size on the sub-bandgap intraband photocurrent in intermediate band solar cells

The effect of quantum dot (QD) size on the performance of quantum dot intermediate band solar cells is investigated. A numerical model is used to calculate the bound state energy levels and the absorption coefficient of transitions from the ground state to all other states in the conduction band. Comparing with the current state of the art, strong absorption enhancements are found for smaller quantum dots, as well as a better positioning of the energy levels, which is expected to reduce thermal carrier escape. It is concluded that reducing the quantum dot size can increase sub-bandgap photocurrent and improve voltage preservation.

Photon Management Structures for Absorption Enhancement in Intermediate Band Solar Cells and Crystalline Silicon Solar Cells

El objetivo de la tesis es investigar los beneficios que el atrapamiento de la luz mediante fenómenos difractivos puede suponer para las células solares de silicio cristalino y las de banda intermedia. Ambos tipos de células adolecen de una insuficiente absorción de fotones en alguna región del espectro solar. Las células solares de banda intermedia son teóricamente capaces de alcanzar eficiencias mucho mayores que los dispositivos convencionales (con una sola banda energética prohibida), pero los prototipos actuales se resienten de una absorción muy débil de los fotones con energías menores que la banda prohibida. Del mismo modo, las células solares de silicio cristalino absorben débilmente en el infrarrojo cercano debido al carácter indirecto de su banda prohibida. Se ha prestado mucha atención a este problema durante las últimas décadas, de modo que todas las células solares de silicio cristalino comerciales incorporan alguna forma de atrapamiento de luz. Por razones de economía, en la industria se persigue el uso de obleas cada vez más delgadas, con lo que el atrapamiento de la luz adquiere más importancia. Por tanto aumenta el interés en las estructuras difractivas, ya que podrían suponer una mejora sobre el estado del arte. Se comienza desarrollando un método de cálculo con el que simular células solares equipadas con redes de difracción. En este método, la red de difracción se analiza en el ámbito de la óptica física, mediante análisis riguroso con ondas acopladas (rigorous coupled wave analysis), y el sustrato de la célula solar, ópticamente grueso, se analiza en los términos de la óptica geométrica. El método se ha implementado en ordenador y se ha visto que es eficiente y da resultados en buen acuerdo con métodos diferentes descritos por otros autores. Utilizando el formalismo matricial así derivado, se calcula el límite teórico superior para el aumento de la absorción en células solares mediante el uso de redes de difracción. Este límite se compara con el llamado límite lambertiano del atrapamiento de la luz y con el límite absoluto en sustratos gruesos. Se encuentra que las redes biperiódicas (con geometría hexagonal o rectangular) pueden producir un atrapamiento mucho mejor que las redes uniperiódicas. El límite superior depende mucho del periodo de la red. Para periodos grandes, las redes son en teoría capaces de alcanzar el máximo atrapamiento, pero sólo si las eficiencias de difracción tienen una forma peculiar que parece inalcanzable con las herramientas actuales de diseño. Para periodos similares a la longitud de onda de la luz incidente, las redes de difracción pueden proporcionar atrapamiento por debajo del máximo teórico pero por encima del límite Lambertiano, sin imponer requisitos irrealizables a la forma de las eficiencias de difracción y en un margen de longitudes de onda razonablemente amplio. El método de cálculo desarrollado se usa también para diseñar y optimizar redes de difracción para el atrapamiento de la luz en células solares. La red propuesta consiste en un red hexagonal de pozos cilíndricos excavados en la cara posterior del sustrato absorbente de la célula solar. La red se encapsula en una capa dieléctrica y se cubre con un espejo posterior. Se simula esta estructura para una célula solar de silicio y para una de banda intermedia y puntos cuánticos. Numéricamente, se determinan los valores óptimos del periodo de la red y de la profundidad y las dimensiones laterales de los pozos para ambos tipos de células. Los valores se explican utilizando conceptos físicos sencillos, lo que nos permite extraer conclusiones generales que se pueden aplicar a células de otras tecnologías. Las texturas con redes de difracción se fabrican en sustratos de silicio cristalino mediante litografía por nanoimpresión y ataque con iones reactivos. De los cálculos precedentes, se conoce el periodo óptimo de la red que se toma como una constante de diseño. Los sustratos se procesan para obtener estructuras precursoras de células solares sobre las que se realizan medidas ópticas. Las medidas de reflexión en función de la longitud de onda confirman que las redes cuadradas biperiódicas consiguen mejor atrapamiento que las uniperiódicas. Las estructuras fabricadas se simulan con la herramienta de cálculo descrita en los párrafos precedentes y se obtiene un buen acuerdo entre la medida y los resultados de la simulación. Ésta revela que una fracción significativa de los fotones incidentes son absorbidos en el reflector posterior de aluminio, y por tanto desaprovechados, y que este efecto empeora por la rugosidad del espejo. Se desarrolla un método alternativo para crear la capa dieléctrica que consigue que el reflector se deposite sobre una superficie plana, encontrándose que en las muestras preparadas de esta manera la absorción parásita en el espejo es menor. La siguiente tarea descrita en la tesis es el estudio de la absorción de fotones en puntos cuánticos semiconductores. Con la aproximación de masa efectiva, se calculan los niveles de energía de los estados confinados en puntos cuánticos de InAs/GaAs. Se emplea un método de una y de cuatro bandas para el cálculo de la función de onda de electrones y huecos, respectivamente; en el último caso se utiliza un hamiltoniano empírico. La regla de oro de Fermi permite obtener la intensidad de las transiciones ópticas entre los estados confinados. Se investiga el efecto de las dimensiones del punto cuántico en los niveles de energía y la intensidad de las transiciones y se obtiene que, al disminuir la anchura del punto cuántico respecto a su valor en los prototipos actuales, se puede conseguir una transición más intensa entre el nivel intermedio fundamental y la banda de conducción. Tomando como datos de partida los niveles de energía y las intensidades de las transiciones calculados como se ha explicado, se desarrolla un modelo de equilibrio o balance detallado realista para células solares de puntos cuánticos. Con el modelo se calculan las diferentes corrientes debidas a transiciones ópticas entre los numerosos niveles intermedios y las bandas de conducción y de valencia bajo ciertas condiciones. Se distingue de modelos de equilibrio detallado previos, usados para calcular límites de eficiencia, en que se adoptan suposiciones realistas sobre la absorción de fotones para cada transición. Con este modelo se reproducen datos publicados de eficiencias cuánticas experimentales a diferentes temperaturas con un acuerdo muy bueno. Se muestra que el conocido fenómeno del escape térmico de los puntos cuánticos es de naturaleza fotónica; se debe a los fotones térmicos, que inducen transiciones entre los estados excitados que se encuentran escalonados en energía entre el estado intermedio fundamental y la banda de conducción. En el capítulo final, este modelo realista de equilibrio detallado se combina con el método de simulación de redes de difracción para predecir el efecto que tendría incorporar una red de difracción en una célula solar de banda intermedia y puntos cuánticos. Se ha de optimizar cuidadosamente el periodo de la red para equilibrar el aumento de las diferentes transiciones intermedias, que tienen lugar en serie. Debido a que la absorción en los puntos cuánticos es extremadamente débil, se deduce que el atrapamiento de la luz, por sí solo, no es suficiente para conseguir corrientes apreciables a partir de fotones con energía menor que la banda prohibida en las células con puntos cuánticos. Se requiere una combinación del atrapamiento de la luz con un incremento de la densidad de puntos cuánticos. En el límite radiativo y sin atrapamiento de la luz, se necesitaría que el número de puntos cuánticos de una célula solar se multiplicara por 1000 para superar la eficiencia de una célula de referencia con una sola banda prohibida. En cambio, una célula con red de difracción precisaría un incremento del número de puntos en un factor 10 a 100, dependiendo del nivel de la absorción parásita en el reflector posterior. Abstract The purpose of this thesis is to investigate the benefits that diffractive light trapping can offer to quantum dot intermediate band solar cells and crystalline silicon solar cells. Both solar cell technologies suffer from incomplete photon absorption in some part of the solar spectrum. Quantum dot intermediate band solar cells are theoretically capable of achieving much higher efficiencies than conventional single-gap devices. Present prototypes suffer from extremely weak absorption of subbandgap photons in the quantum dots. This problem has received little attention so far, yet it is a serious barrier to the technology approaching its theoretical efficiency limit. Crystalline silicon solar cells absorb weakly in the near infrared due to their indirect bandgap. This problem has received much attention over recent decades, and all commercial crystalline silicon solar cells employ some form of light trapping. With the industry moving toward thinner and thinner wafers, light trapping is becoming of greater importance and diffractive structures may offer an improvement over the state-of-the-art. We begin by constructing a computational method with which to simulate solar cells equipped with diffraction grating textures. The method employs a wave-optical treatment of the diffraction grating, via rigorous coupled wave analysis, with a geometric-optical treatment of the thick solar cell bulk. These are combined using a steady-state matrix formalism. The method has been implemented computationally, and is found to be efficient and to give results in good agreement with alternative methods from other authors. The theoretical upper limit to absorption enhancement in solar cells using diffractions gratings is calculated using the matrix formalism derived in the previous task. This limit is compared to the so-called Lambertian limit for light trapping with isotropic scatterers, and to the absolute upper limit to light trapping in bulk absorbers. It is found that bi-periodic gratings (square or hexagonal geometry) are capable of offering much better light trapping than uni-periodic line gratings. The upper limit depends strongly on the grating period. For large periods, diffraction gratings are theoretically able to offer light trapping at the absolute upper limit, but only if the scattering efficiencies have a particular form, which is deemed to be beyond present design capabilities. For periods similar to the incident wavelength, diffraction gratings can offer light trapping below the absolute limit but above the Lambertian limit without placing unrealistic demands on the exact form of the scattering efficiencies. This is possible for a reasonably broad wavelength range. The computational method is used to design and optimise diffraction gratings for light trapping in solar cells. The proposed diffraction grating consists of a hexagonal lattice of cylindrical wells etched into the rear of the bulk solar cell absorber. This is encapsulated in a dielectric buffer layer, and capped with a rear reflector. Simulations are made of this grating profile applied to a crystalline silicon solar cell and to a quantum dot intermediate band solar cell. The grating period, well depth, and lateral well dimensions are optimised numerically for both solar cell types. This yields the optimum parameters to be used in fabrication of grating equipped solar cells. The optimum parameters are explained using simple physical concepts, allowing us to make more general statements that can be applied to other solar cell technologies. Diffraction grating textures are fabricated on crystalline silicon substrates using nano-imprint lithography and reactive ion etching. The optimum grating period from the previous task has been used as a design parameter. The substrates have been processed into solar cell precursors for optical measurements. Reflection spectroscopy measurements confirm that bi-periodic square gratings offer better absorption enhancement than uni-periodic line gratings. The fabricated structures have been simulated with the previously developed computation tool, with good agreement between measurement and simulation results. The simulations reveal that a significant amount of the incident photons are absorbed parasitically in the rear reflector, and that this is exacerbated by the non-planarity of the rear reflector. An alternative method of depositing the dielectric buffer layer was developed, which leaves a planar surface onto which the reflector is deposited. It was found that samples prepared in this way suffered less from parasitic reflector absorption. The next task described in the thesis is the study of photon absorption in semiconductor quantum dots. The bound-state energy levels of in InAs/GaAs quantum dots is calculated using the effective mass approximation. A one- and four- band method is applied to the calculation of electron and hole wavefunctions respectively, with an empirical Hamiltonian being employed in the latter case. The strength of optical transitions between the bound states is calculated using the Fermi golden rule. The effect of the quantum dot dimensions on the energy levels and transition strengths is investigated. It is found that a strong direct transition between the ground intermediate state and the conduction band can be promoted by decreasing the quantum dot width from its value in present prototypes. This has the added benefit of reducing the ladder of excited states between the ground state and the conduction band, which may help to reduce thermal escape of electrons from quantum dots: an undesirable phenomenon from the point of view of the open circuit voltage of an intermediate band solar cell. A realistic detailed balance model is developed for quantum dot solar cells, which uses as input the energy levels and transition strengths calculated in the previous task. The model calculates the transition currents between the many intermediate levels and the valence and conduction bands under a given set of conditions. It is distinct from previous idealised detailed balance models, which are used to calculate limiting efficiencies, since it makes realistic assumptions about photon absorption by each transition. The model is used to reproduce published experimental quantum efficiency results at different temperatures, with quite good agreement. The much-studied phenomenon of thermal escape from quantum dots is found to be photonic; it is due to thermal photons, which induce transitions between the ladder of excited states between the ground intermediate state and the conduction band. In the final chapter, the realistic detailed balance model is combined with the diffraction grating simulation method to predict the effect of incorporating a diffraction grating into a quantum dot intermediate band solar cell. Careful optimisation of the grating period is made to balance the enhancement given to the different intermediate transitions, which occur in series. Due to the extremely weak absorption in the quantum dots, it is found that light trapping alone is not sufficient to achieve high subbandgap currents in quantum dot solar cells. Instead, a combination of light trapping and increased quantum dot density is required. Within the radiative limit, a quantum dot solar cell with no light trapping requires a 1000 fold increase in the number of quantum dots to supersede the efficiency of a single-gap reference cell. A quantum dot solar cell equipped with a diffraction grating requires between a 10 and 100 fold increase in the number of quantum dots, depending on the level of parasitic absorption in the rear reflector.

Interaction of spatially overlapping standing electromagnetic solitons in plasmas

Numerical investigations on mutual interactions between two spatially overlapping standing electromagnetic solitons in a cold unmagnetized plasma are reported. It is found that an initial state comprising of two overlapping standing solitons evolves into different end states, depending on the amplitudes of the two solitons and the phase difference between them. For small amplitude solitons with zero phase difference, we observe the formation of an oscillating bound state whose period depends on their initial separation. These results suggest the existence of a bound state made of two solitons in the relativistic cold plasma fluid model.

Structural basis of an embryonically lethal single Ala → Thr mutation in the vnd/NK-2 homeodomain

The structural and DNA binding behavior is described for an analog of the vnd/NK-2 homeodomain, which contains a single amino acid residue alanine to threonine replacement in position 35 of the homeodomain. Multidimensional nuclear magnetic resonance, circular dichroism, and electrophoretic gel retardation assays were carried out on recombinant 80-aa residue proteins that encompass the wild-type and mutant homeodomains. The mutant A35T vnd/NK-2 homeodomain is unable to adopt a folded conformation free in solution at temperatures down to −5°C in contrast to the behavior of the corresponding wild-type vnd/NK-2 homeodomain, which is folded into a functional three-dimensional structure below 25°C. The A35T vnd/NK-2 binds specifically to the vnd/NK-2 target DNA sequence, but with an affinity that is 50-fold lower than that of the wild-type homeodomain. Although the three-dimensional structure of the mutant A35T vnd/NK-2 in the DNA bound state shows characteristic helix–turn–helix behavior similar to that of the wild-type homeodomain, a notable structural deviation in the mutant A35T analog is observed for the amide proton of leucine-40. The wild-type homeodomain forms an unusual i,i-5 hydrogen bond with the backbone amide oxygen of residue 35. In the A35T mutant this amide proton resonance is shifted upfield by 1.27 ppm relative to the resonance frequency for the wild-type analog, thereby indicating a significant alteration of this i,i-5 hydrogen bond.

The structure and organization within the membrane of the helices composing the pore-forming domain of Bacillus thuringiensis δ-endotoxin are consistent with an “umbrella-like” structure of the pore

The aim of this study was to elucidate the mechanism of membrane insertion and the structural organization of pores formed by Bacillus thuringiensis δ-endotoxin. We determined the relative affinities for membranes of peptides corresponding to the seven helices that compose the toxin pore-forming domain, their modes of membrane interaction, their structures within membranes, and their orientations relative to the membrane normal. In addition, we used resonance energy transfer measurements of all possible combinatorial pairs of membrane-bound helices to map the network of interactions between helices in their membrane-bound state. The interaction of the helices with the bilayer membrane was also probed by a Monte Carlo simulation protocol to determine lowest-energy orientations. Our results are consistent with a situation in which helices α4 and α5 insert into the membrane as a helical hairpin in an antiparallel manner, while the other helices lie on the membrane surface like the ribs of an umbrella (the “umbrella model”). Our results also support the suggestion that α7 may serve as a binding sensor to initiate the structural rearrangement of the pore-forming domain.

The kinetic mechanism of myosin V

Myosin V is an unconventional myosin proposed to be processive on actin filaments, analogous to kinesin on a microtubule [Mehta, A. D., et al. (1999) Nature (London) 400, 590–593]. To ascertain the unique properties of myosin V that permit processivity, we undertook a detailed kinetic analysis of the myosin V motor. We expressed a truncated, single-headed myosin V construct that bound a single light chain to study its innate kinetics, free from constraints imposed by other regions of the molecule. The data demonstrate that unlike any previously characterized myosin a single-headed myosin V spends most of its kinetic cycle (>70%) strongly bound to actin in the presence of ATP. This kinetic tuning is accomplished by increasing several of the rates preceding strong binding to actin and concomitantly prolonging the duration of the strongly bound state by slowing the rate of ADP release. The net result is a myosin unlike any previously characterized, in that ADP release is the rate-limiting step for the actin-activated ATPase cycle. Thus, because of a number of kinetic adaptations, myosin V is tuned for processive movement on actin and will be capable of transporting cargo at lower motor densities than any other characterized myosin.

(4-Aminomethyl)phenylguanidine derivatives as nonpeptidic highly selective inhibitors of human urokinase

Increased expression of the serine protease urokinase-type plasminogen activator (uPA) in tumor tissues is highly correlated with tumor cell migration, invasion, proliferation, progression, and metastasis. Thus inhibition of uPA activity represents a promising target for antimetastatic therapy. So far, only the x-ray crystal structure of uPA inactivated by H-Glu-Gly-Arg-chloromethylketone has been reported, thus limited data are available for a rational structure-based design of uPA inhibitors. Taking into account the trypsin-like arginine specificity of uPA, (4-aminomethyl)phenylguanidine was selected as a potential P1 residue and iterative derivatization of its amino group with various hydrophobic residues, and structure–activity relationship-based optimization of the spacer in terms of hydrogen bond acceptor/donor properties led to N-(1-adamantyl)-N′-(4-guanidinobenzyl)urea as a highly selective nonpeptidic uPA inhibitor. The x-ray crystal structure of the uPA B-chain complexed with this inhibitor revealed a surprising binding mode consisting of the expected insertion of the phenylguanidine moiety into the S1 pocket, but with the adamantyl residue protruding toward the hydrophobic S1′ enzyme subsite, thus exposing the ureido group to hydrogen-bonding interactions. Although in this enzyme-bound state the inhibitor is crossing the active site, interactions with the catalytic residues Ser-195 and His-57 are not observed, but their side chains are spatially displaced for steric reasons. Compared with other trypsin-like serine proteases, the S2 and S3/S4 pockets of uPA are reduced in size because of the 99-insertion loop. Therefore, the peculiar binding mode of the new type of uPA inhibitors offers the possibility of exploiting optimized interactions at the S1′/S2′ subsites to further enhance selectivity and potency. Because crystals of the uPA/benzamidine complex allow inhibitor exchange by soaking procedures, the structure-based design of new generations of uPA inhibitors can rely on the assistance of x-ray analysis.

The "allosteric three-site model" of elongation cannot be confirmed in a well-defined ribosome system from Escherichia coli.

For the functional role of the ribosomal tRNA exit (E) site, two different models have been proposed. It has been suggested that transient E-site binding of the tRNA leaving the peptidyl (P) site promotes elongation factor G (EF-G)-dependent translocation by lowering the energetic barrier of tRNA release [Lill, R., Robertson, J. M. & Wintermeyer, W. (1989) EMBO J. 8, 3933-3938]. The alternative "allosteric three-site model" [Nierhaus, K.H. (1990) Biochemistry 29, 4997-5008] features stable, codon-dependent tRNA binding to the E site and postulates a coupling between E and aminoacyl (A) sites that regulates the tRNA binding affinity of the two sites in an anticooperative manner. Extending our testing of the two conflicting models, we have performed translocation experiments with fully active ribosomes programmed with heteropolymeric mRNA. The results confirm that the deacylated tRNA released from the P site is bound to the E site in a kinetically labile fashion, and that the affinity of binding, i.e., the occupancy of the E site, is increased by Mg2+ or polyamines. At conditions of high E-site occupancy in the posttranslocation complex, filling the A site with aminoacyl-tRNA had no influence on the E site, i.e., there was no detectable anticooperative coupling between the two sites, provided that second-round translocation was avoided by removing EF-G. On the basis of these results, which are entirely consistent with our previous results, we consider the allosteric three-site model of elongation untenable. Rather, as proposed earlier, the E site-bound state of the leaving tRNA is a transient intermediate and, as such, is a mechanistic feature of the classic two-state model of the elongating ribosome.

Purification and characterization of a guanine nucleotide-exchange protein for ADP-ribosylation factor from spleen cytosol.

ADP-ribosylation factors (ARFs) are 20-kDa guanine nucleotide-binding proteins and are active in the GTP-bound state and inactive with GDP bound. ARF-GTP has a critical role in vesicular transport in several cellular compartments. Conversion of ARF-GDP to ARF-GTP is promoted by a guanine nucleotide-exchange protein (GEP). We earlier reported the isolation from bovine brain cytosol of a 700-kDa protein complex containing GEP activity that was inhibited by brefeldin A (BFA). Partial purification yielded an approximately 60-kDa BFA-insensitive GEP that enhanced binding of ARF1 and ARF3 to Golgi membranes. GEP has now been purified extensively from rat spleen cytosol in a BFA-insensitive, approximately 55-kDa form. It activated class I ARFs (ARFs 1 and 3) that were N-terminally myristoylated, but not nonmyristoylated ARFs from class-I, II, or III. GEP activity required MgCl2. In the presence of 0.6-0.8 mM MgCl2 and 1 mM EDTA, binding of guanosine 5'-[gamma[35S]thio]triphosphate ([35S]GTP gamma S) by ARF1 and ARF3 was equally high without and with GEP. At higher Mg2+ concentrations, binding without GEP was much lower; with 2-5 mM MgCl2, GEP-stimulated binding was maximal. The rate of GDP binding was much less than that of GTP gamma S with and without GEP. Phospholipids were necessary for GEP activity; phosphatidylinositol was more effective than phosphatidylserine, and phosphatidic acid was less so. Other phospholipids tested were ineffective. Maximal effects required approximately 200 microM phospholipid, with half-maximal activation at 15-20 microM. Release of bound [35S]GTP gamma S from ARF3 required the presence of both GEP and unlabeled GTP or GTP gamma S; GDP was much less effective. This characterization of the striking effects of Mg2+ concentration and specific phospholipids on the purified BFA-insensitive ARF GEP should facilitate experiments to define its function in vesicular transport.

Growth hormone secretagogues: characterization, efficacy, and minimal bioactive conformation.

Another class of growth hormone (GH) secretagogues has been discovered by altering the backbone structure of a flexible linear GH-releasing peptide (GHRP). In vitro and in vivo characterization confirms these GH secretagogues as the most potent and smallest (M(r) < 500) reported. Anabolic efficacy is demonstrated in rodents with intermittent delivery. A convergent model of the bioactive conformation of GHRPs is developed and is supported by the NMR structure of a highly potent cyclic analog of GHRP-2. The model and functional data provide a logical framework for the further design of low-molecular weight secretagogues and illustrate the utility of an interdisciplinary approach to elucidating potential bound-state conformations of flexible peptide ligands.

The Ran/TC4 GTPase-binding domain: identification by expression cloning and characterization of a conserved sequence motif.

Ran/TC4 is an essential, nuclear GTPase implicated in the initiation of DNA replication, entry into and exit from mitosis, and in nuclear RNA and protein transport through the nuclear pore complex. This diversity of functions suggests that Ran interacts with a large number of down-stream targets. Using an overlay assay, we detected a family of putative target proteins that associate with GTP-bound Ran. The sequence of only one such protein, HTF9a/RanBP1, is known. We have now cloned two additional Ran-binding proteins, allowing identification of a distinctive, highly conserved sequence motif of approximately 150 residues. This motif represents a minimal Ran-binding domain that stabilizes the GTP-bound state of Ran. The isolated domain also functions as a coactivator of Ran-GTPase-activating protein. Mutation of a conserved residue within the Ran-binding domain of HTF9a protein drastically reduced Ran binding. Ran-binding proteins coimmunoprecipitated with epitope-tagged Ran from cell lysates, suggesting that these proteins may associate in vivo. A previously uncharacterized Caenorhabditis elegans gene could encode a protein (96 kDa) possessing two Ran-binding domains. This open reading frame also contains similarities to nucleoporins, suggesting a functional link between Ran and nuclear pore complexes.

Synthesis and characterisation of hydrogel polymers for medical applications

A fundamental if poorly understood problem that hydrogels display is the tendency of these contact lens materials to dehydrate, causing certain complications of the corneal epithelium. However, recent studies have indicated that the evaporation rate of water from different hydrogel lenses is the same and the severity of conditions such as corneal staining is controlled by the states of water in the material. A study was therefore undertaken which concluded that increased corneal desiccating staining occurred as the proportion of water existing in the bound state decreased. The possibility of using dehydrated hydrogels as packaging materials with desiccating properties has also been investigated. As hydrogels have a high affinity for water they have adequate ability to function as a moisture scavenger in an enclosed atmosphere. It was concluded that this ability is maximised by a high total water content and an increase in the proportion of this water existing in the bound state for the material when it is fully hydrated. N-vinyl pyrrolidone has a low reactivity in vinyl polymerisation reactions which results in polymers with local domains of the same chemical type which can lead to deposition. As contact lenses comprising of this monomer are susceptible to deposition, a monomer with a higher reactivity in vinyl polymerisations is acryloylmorpholine and its incorporation in favour of NVP is encouraged. Unfortunately a large proportion of high EWC hydrogels are mechanically weak and attempts to increase this property by increasing hydrophobicity or cross-linking results in a decrease in EWC. Monomers with the potential to carry a positive charge were incorporated into a high EWC, AMO-HEMA copolymer and the physical properties were investigated. Although EWC increased, mechanical properties decreased only slightly. Therefore simultaneous incorporation of a positively charged monomer and a negatively charged monomer was investigated. The resulting copolymers showed increased water content and increased initial modulus. A technique for measuring the coefficient of friction of contact lenses during lubrication has been developed.

Nonlinear pulse shaping and polarization dynamics in mode-locked fibre lasers

We review our recent progress on the study of new nonlinear mechanisms of pulse shaping in passively mode-locked fibre lasers. These include a mode-locking regime featuring pulses with a triangular distribution of the intensity, and spectral compression arising from nonlinear pulse propagation. We also report on our recent experimental studies unveiling new families of vector solitons with precessing states of polarization for multipulsing and bound-state soliton operations in a carbon nanotube mode-locked fibre laser with anomalous dispersion cavity. © 2013 IEEE.

Nonlinear pulse shaping and polarization dynamics in mode-locked fibre lasers

We review our recent progress on the study of new nonlinear mechanisms of pulse shaping in passively mode-locked fibre lasers. These include a mode-locking regime featuring pulses with a triangular distribution of the intensity, and spectral compression arising from nonlinear pulse propagation. We also report on our recent experimental studies unveiling new families of vector solitons with precessing states of polarization for multipulsing and bound-state soliton operations in a carbon nanotube mode-locked fibre laser with anomalous dispersion cavity. © 2013 IEEE.