Structure-Function Studies of Nicotinic Acetylcholine Receptors Using Selective Agonists and Positive Allosteric Modulators

This dissertation primarily describes chemical-scale studies of nicotinic acetylcholine receptors (nAChRs) in order to better understand ligand-receptor selectivity and allosteric modulation influences during receptor activation. Electrophysiology coupled with canonical and non-canonical amino acids mutagenesis is used to probe subtle changes in receptor function.

The first half of this dissertation focuses on differential agonist selectivity of α4β2-containing nAChRs. The α4β2 nAChR can assemble in alternative stoichiometries as well as assemble with other accessory subunits. Chapter 2 identifies key structural residues that dictate binding and activation of three stoichiometry-dependent α4β2 receptor ligands: sazetidine-A, cytisine, and NS9283. These do not follow previously suggested hydrogen-bonding patterns of selectivity. Instead, three residues on the complementary subunit strongly influence binding ability of a ligand and receptor activation. Chapter 3 involves isolation of a α5α4β2 receptor-enriched population to test for a potential alternative agonist binding location at the α5 α4 interface. Results strongly suggest that agonist occupation of this site is not necessary for receptor activation and that the α5 subunit only incorporates at the accessory subunit location.

The second half of this dissertation seeks to identify residue interactions with positive allosteric modulators (PAMs) of the α7 nAChR. Chapter 4 focuses on methods development to study loss of potentiation of Type I PAMs, which indicate residues vital to propagation of PAM effects and/or binding. Chapter 5 investigates α7 receptor modulation by a Type II PAM (PNU 120596). These results show that PNU 120596 does not alter the agonist binding site, thus is relegated to influencing only the gating component of activation. From this, we were able to map a potential network of residues from the agonist binding site to the proposed PNU 120596 binding site that are essential for receptor potentiation.

Study of the transmitter antenna gain for intersatellite laser communications

The gain of a transmitter for intersatellite communications is closely related to the performance of all the links. We calculate the transmitter telescope's gain with the help of the rigorous scalar diffraction theory and equivalent optical layout method. Furthermore, a comparison is performed with the conventional imaging method. The results show that the stop inside the telescope can affect the gain of the telescope. Finally, the gain is calculated under the condition of the aberrations. We find that different aberrations cause different effects. (C) 2006 Society of Photo-Optical Instrumentation Engineers.

Study of the transmitter antenna gain for intersatellite laser communications

The gain of a transmitter for intersatellite communications is closely related to the performance of all the links. We calculate the transmitter telescope's gain with the help of the rigorous scalar diffraction theory and equivalent optical layout method. Furthermore, a comparison is performed with the conventional imaging method. The results show that the stop inside the telescope can affect the gain of the telescope. Finally, the gain is calculated under the condition of the aberrations. We find that different aberrations cause different effects. (C) 2006 Society of Photo-Optical Instrumentation Engineers.

Design for Survival: Sustainability for Planet and Structure

Buildings in Port Aransas encounter drastic environmental challenges: the potential catastrophic storm surge and high winds from a hurricane, and daily conditions hostile to buildings, vehicles, and even most vegetation. Its location a few hundred feet from the Gulf of Mexico and near-tropical latitude expose buildings to continuous high humidity, winds laden with scouring sand and corrosive salt, and extremes of temperature and ultraviolet light. Building construction methods are able to address each of these, but doing so in a sustainable way creates significant challenges. The new research building at the Marine Science Institute has been designed and is being constructed to meet the demand for both survivability and sustainability. It is tracking towards formal certification as a LEED Gold structure while being robust and resistant to the harsh coastal environment. The effects of a hurricane are mitigated by elevating buildings and providing a windproof envelope. Ground-level enclosures are designed to be sacrificial and non-structural so they can wash or blow away without imposing damage on the upper portions of the building, and only non-critical functions and equipment will be supported within them. Design features that integrate survivability with sustainability include: orientation of building axis; integral shading from direct summer sunlight; light wells; photovoltaic arrays; collection of rainwater and air conditioning condensate for use in landscape irrigation; reduced impervious cover; xeriscaping and indigenous plants; recycling of waste heat from air conditioning systems; roofing system that reflects light and heat; long life, low maintenance stainless steel, high-tensile vinyl, hard-anodized aluminum and hot-dipped galvanized mountings throughout; chloride-resistant concrete; reduced visual impact; recycling of construction materials.

Imaging the earth with ambient noise and earthquakes

In this thesis, I develop the velocity and structure models for the Los Angeles Basin and Southern Peru. The ultimate goal is to better understand the geological processes involved in the basin and subduction zone dynamics. The results are obtained from seismic interferometry using ambient noise and receiver functions using earthquake- generated waves. Some unusual signals specific to the local structures are also studied. The main findings are summarized as follows:

(1) Los Angeles Basin

The shear wave velocities range from 0.5 to 3.0 km/s in the sediments, with lateral gradients at the Newport-Inglewood, Compton-Los Alamitos, and Whittier Faults. The basin is a maximum of 8 km deep along the profile, and the Moho rises to a depth of 17 km under the basin. The basin has a stretch factor of 2.6 in the center decreasing to 1.3 at the edges, and is in approximate isostatic equilibrium. This "high-density" (~1 km spacing) "short-duration" (~1.5 month) experiment may serve as a prototype experiment that will allow basins to be covered by this type of low-cost survey.

(2) Peruvian subduction zone

Two prominent mid-crust structures are revealed in the 70 km thick crust under the Central Andes: a low-velocity zone interpreted as partially molten rocks beneath the Western Cordillera – Altiplano Plateau, and the underthrusting Brazilian Shield beneath the Eastern Cordillera. The low-velocity zone is oblique to the present trench, and possibly indicates the location of the volcanic arcs formed during the steepening of the Oligocene flat slab beneath the Altiplano Plateau.

The Nazca slab changes from normal dipping (~25 degrees) subduction in the southeast to flat subduction in the northwest of the study area. In the flat subduction regime, the slab subducts to ~100 km depth and then remains flat for ~300 km distance before it resumes a normal dipping geometry. The flat part closely follows the topography of the continental Moho above, indicating a strong suction force between the slab and the overriding plate. A high-velocity mantle wedge exists above the western half of the flat slab, which indicates the lack of melting and thus explains the cessation of the volcanism above. The velocity turns to normal values before the slab steepens again, indicating possible resumption of dehydration and ecologitization.

(3) Some unusual signals

Strong higher-mode Rayleigh waves due to the basin structure are observed in the periods less than 5 s. The particle motions provide a good test for distinguishing between the fundamental and higher mode. The precursor and coda waves relative to the interstation Rayleigh waves are observed, and modeled with a strong scatterer located in the active volcanic area in Southern Peru. In contrast with the usual receiver function analysis, multiples are extensively involved in this thesis. In the LA Basin, a good image is only from PpPs multiples, while in Peru, PpPp multiples contribute significantly to the final results.

Automatically exposing OpenLifeData via SADI semantic Web Services

Background: Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. Results: We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. Conclusions: We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

The role of syllables in sign language production

The aim of the present study was to investigate the functional role of syllables in sign language and how the different phonological combinations influence sign production. Moreover, the influence of age of acquisition was evaluated. Deaf signers (native and non-native) of Catalan Signed Language (LSC) were asked in a picture-sign interference task to sign picture names while ignoring distractor-signs with which they shared two phonological parameters (out of three of the main sign parameters: Location, Movement, and Handshape). The results revealed a different impact of the three phonological combinations. While no effect was observed for the phonological combination Handshape-Location, the combination Handshape-Movement slowed down signing latencies, but only in the non-native group. A facilitatory effect was observed for both groups when pictures and distractors shared Location-Movement. Importantly, linguistic models have considered this phonological combination to be a privileged unit in the composition of signs, as syllables are in spoken languages. Thus, our results support the functional role of syllable units during phonological articulation in sign language production.

Read-only memory disk with AgOx and AgInSbTe superresolution mask layer

Two novel read-only memory (ROM) disks, one with an AgOx mask layer and the other with an AgInSbTe mask layer, are proposed and studied. The AgOx and the AgInSbTe films sputtered on the premastered substrates with pit depths of 50 nm and pit lengths (space) of 380 nm are studied by atomic force microscopy. Disk readout measurement is carried out using a dynamic setup with a laser wavelength of 632.8 nm and an object lens numerical aperture (NA) of 0.40. Results show that the superresolution effect happens only at a suitable oxygen flow ratio for the AgOx ROM disk. The best superresolution readout effect is achieved at an oxygen flow ratio of 0.5 with the smoothest film surface. Compared with the AgOx ROM disk, the AgInSbTe ROM disk has a much smoother film surface and better superresolution effect. A carrier-to-noise ratio (CNR) of above 40 dB can be obtained at an appropriate readout power and readout velocity. The readout CNR of both the AgOx and AgInSbTe ROM disks have a nonlinear dependence on the readout power. The superresolution readout mechanisms for these ROM disks are analyzed and compared as well. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

Read-only memory disk with AgOx super-resolution mask layer

A novel read-only memory (ROM) disk with an AgOx mask layer was proposed and studied in this letter. The AgOx films sputtered on the premastered substrates, with pits depth of 50 nm and pits length of 380 nm, were studied by an atomic force microscopy. The transmittances of these AgOx films were also measured by a spectrophotometer. Disk measurement was carried out by a dynamic setup with a laser wavelength of 632.8 nm and a lens numerical aperture (NA) of 0.40. The readout resolution limit of this setup was λ/(4NA) (400 nm). Results showed that the super-resolution readout happened only when the oxygen flow ratios were at suitable values for these disks. The best super-resolution performance was achieved at the oxygen flow ratio of 0.5 with the smoothest film surface. The super-resolution readout mechanism of these ROM disks was analyzed as well.

Read-only memory disk with AgOx and AgInSbTe superresolution mask layer

Two novel read-only memory (ROM) disks, one with an AgOx mask layer and the other with an AgInSbTe mask layer, are proposed and studied. The AgOx and the AgInSbTe films sputtered on the premastered substrates with pit depths of 50 nm and pit lengths (space) of 380 nm are studied by atomic force microscopy. Disk readout measurement is carried out using a dynamic setup with a laser wavelength of 632.8 nm and an object lens numerical aperture (NA) of 0.40. Results show that the superresolution effect happens only at a suitable oxygen flow ratio for the AgOx ROM disk. The best superresolution readout effect is achieved at an oxygen flow ratio of 0.5 with the smoothest film surface. Compared with the AgOx ROM disk, the AgInSbTe ROM disk has a much smoother film surface and better superresolution effect. A carrier-to-noise ratio (CNR) of above 40 dB can be obtained at an appropriate readout power and readout velocity. The readout CNR of both the AgOx and AgInSbTe ROM disks have a nonlinear dependence on the readout power. The superresolution readout mechanisms for these ROM disks are analyzed and compared as well. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

Gestão do trabalho na Estratégia Saúde da Família em municípios do Estado do Rio de Janeiro com mais de 500 mil habitantes: o caso do Rio de Janeiro e Duque de Caxias

Não obstante ao aumento do número de equipes de Saúde da Família no território brasileiro há disparidade na implantação da Estratégia Saúde da Família (ESF) em municípios de grande porte. Outras dificuldades enfrentadas referem-se aos recursos humanos em saúde (RHS). Nesse sentido, esta pesquisa objetivou analisar o cenário atual da gestão do trabalho na ESF nos municípios do Rio de Janeiro e Duque de Caxias. Metodologia: Estudo exploratório, de investigação narrativa, bibliográfica e documental, de abordagem qualitativa. A coleta de dados se deu em duas fases: pesquisa de material bibliográfico nas bases: LILACS, PAHO e WHOLIS, e de editais de processos seletivos e concursos públicos dos anos 2000, com vistas à contratação de profissionais de saúde para a ESF e; entrevistas semiestruturadas com gestores da ESF. O período de coleta perdurou entre agosto de 2010 e dezembro de 2011. Os documentos foram analisados à luz da estatística descritiva e as entrevistas submetidas à análise de conteúdo. Resultados: Escassez de literatura sobre a ESF nos municípios de Duque de Caxias e Rio de Janeiro. As contratações no Rio de Janeiro obedeceram a dois momentos: prefeitura e Organizações Sociais (OS) como contratantes. Em Duque de Caxias a contratação foi exclusividade da Prefeitura. No Rio de Janeiro os salários dos profissionais variaram entre R$ 728,59 (Agentes Comunitários de Saúde - ACS) e R$ 7.773,69 (médicos), contrastando com a isonomia salarial adotada em Duque de Caxias, com vencimentos ao redor de R$ 700,00 para os ACS, R$ 800,00 para nível técnico e; aproximadamente R$ 5.000,00 aos profissionais de nível superior. Os gestores sugerem que a maior rotatividade entre os médicos é motivada por carga horária excessiva; más condições de trabalho e, localização da unidade em áreas de risco social. As estratégias para atração e fixação profissional incluem: processos seletivos; garantia dos direitos trabalhistas e; abonos salariais, no caso do Rio de Janeiro e; flexibilização de carga horária, melhorias em infraestrutura e estratégias de qualificação, em Duque de Caxias. Entrevistas revelaram as maiores dificuldades na gestão da ESF: alta rotatividade, formação médica destoante com o SUS e, infraestrutura precária. Acrescenta-se o baixo salário para médicos em Duque de Caxias e, vínculos e salários distintos entre profissionais que exercem mesma função no Rio de Janeiro. Conclusões: A expansão da ESF nos grandes centros urbanos encontra obstáculos relacionados à gestão do trabalho que fragilizam sua consolidação. O Rio de Janeiro mostra-se mais atraente para os profissionais da ESF. O único diferencial de Duque de Caxias, sobretudo para odontólogos e enfermeiros, refere-se à contratação direta pela Prefeitura com vinculação estatutária, ainda que, eventual aumento salarial esteja atrelado ao de todos os servidores municipais. No Rio de Janeiro, a contratação sob regime da Consolidação das Leis do Trabalho revela-se uma proteção, posto que diante da possibilidade de perda de profissionais as OS elevam seus salários. Dentre as recomendações para fixação profissional incluem-se: incentivos salariais para atuação em regiões vulneráveis, melhorias em infraestrutura e, acoplação entre Instituições de Ensino Superior e rede de saúde.

Insight on how fishing bats discern prey and adjust their mechanic and sensorial features during the attack sequence

Several insectivorous bats have included fish in their diet, yet little is known about the processes underlying this trophic shift. We performed three field experiments with wild fishing bats to address how they manage to discern fish from insects and adapt their hunting technique to capture fish. We show that bats react only to targets protruding above the water and discern fish from insects based on prey disappearance patterns. Stationary fish trigger short and shallow dips and a terminal echolocation pattern with an important component of the narrowband and low frequency calls. When the fish disappears during the attack process, bats regulate their attack increasing the number of broadband and high frequency calls in the last phase of the echolocation as well as by lengthening and deepening their dips. These adjustments may allow bats to obtain more valuable sensorial information and to perform dips adjusted to the level of uncertainty on the location of the submerged prey. The observed ultrafast regulation may be essential for enabling fishing to become cost-effective in bats, and demonstrates the ability of bats to rapidly modify and synchronise their sensorial and motor features as a response to last minute stimulus variations.

White spot syndrome virus (WSSV) transmission risk through infected cooked shrimp products assessed by polymerase chain reaction (PCR) and bio-inoculation studies

The aim of the study was to evaluate the resistance of white spot syndrome virus (WSSV) in shrimps (Penaeus monodon) to the process of cooking. The cooking was carried out at 1000C six different durations 5, 10, 15, 20, 25 and 30 min. The presence of WSSV was tested by single step and nested polymerase chain reaction (PCR). In the single step PCR, the primers 1s5 & 1a16 and IK1 & IK2 were used. While in the nested PCR, primers IK1 &IK2 – IK3 & IK4 were used for the detection of WSSV. WSSV was detected in the single step PCR with the primers 1s5 and 1a16 and the nested PCR with the primers IK1 and IK2 – IK3 & IK4 from the cooked shrimp samples. The cooked shrimps, which gave positive results for WSSV by PCR, were further confirmed for the viability of WSSV by conducting the bio-inoculation studies. Mortality (100%) was observed within 123 h of intra-muscular post injection (P.I) into the live healthy WSSV-free shrimps (P. monodon). These results show that the WSSV survive the cooking process and even infected cooked shrimp products may pose a transmission risk for WSSV to the native shrimp farming systems.

Central area redd project [Ribble, Hodder and Lune catchments]

Redd counting is an integral part of most Fishery Officers duties. The number and distribution of salmonid redds throughout salmonid catchments provides invaluable information on the range and extent of spawning by both salmon and sea trout. A project was initiated by the Fisheries Science and Management Team of Central Area, North West Region in England in liaison with the Flood Defence function. The main objective of this project was to assess redd count data for Central Area and attempt to quantify these data in order to produce a grading system that would highlight key salmonid spawning areas. By showing which were the main areas for salmon and sea trout spawning, better informed decisions could be made on whether or not in-stream Flood Defence works should be given the go-ahead. The main salmonid catchments in Central Area were broken into individual reaches, approximately 1 km in length. The number of redds in these individual reaches were then calculated and a density per lkm value was obtained for each reach. A grading system was devised which involved looking at the range of density per km values and dividing this by five to produce 5 classes, A - E. A sixth class (F) was used where the density per Ion value was 0.00. This grading system was calculated at two levels of detail. Grades for salmon and sea trout were produced for each individual catchment and also on an Area-wide level. Maps were produced using a range of colours to represent the grade for each reach. These maps provide a highly useful overview of the status of salmonid spawning for each catchment over individual years and highlight the key salmon and sea trout spawning areas in each catchment. These maps and the associated summary data should now provide Flood Defence and Fisheries staff with a fairly detailed overview of the status of spawning in any location within the. main salmonid catchments in Central Area. Although these maps are very useful they should only be used as a guide. The current practice of consulting with the local Fishery Officer should be continued to ensure that expert local knowledge is taken into account.

Catch rates and demographics of loggerhead sea turtles (Caretta caretta) captured from the Charleston, South Carolina, shipping channel during the period of mandatory use of turtle excluder devices (TEDs)

Trawling was conducted in the Charleston, South Carolina, shipping channel between May and August during 2004–07 to evaluate loggerhead sea turtle (Caretta caretta) catch rates and demographic distributions. Two hundred and twenty individual loggerheads were captured in 432 trawling events during eight sampling periods lasting 2–10 days each. Catch was analyzed by using a generalized linear model. Data were fitted to a negative binomial distribution with the log of standardized sampling effort (i.e., an hour of sampling with a net head rope length standardized to 30.5 m) for each event treated as an offset term. Among 21 variables, factors, and interactions, five terms were significant in the final model, which accounted for 45% of model deviance. Highly significant differences in catch were noted among sampling periods and sampling locations within the channel, with greatest catch furthest seaward consistent with historical observations. Loggerhead sea turtle catch rates in 2004–07 were greater than in 1991–92 when mandatory use of turtle excluder devices was beginning to be phased in. Concurrent with increased catch rates, loggerheads captured in 2004–07 were larger than in 1991–92. Eighty-five percent of loggerheads captured were ≤75.0 cm straight-line carapace length (nuchal notch to tip of carapace) and there was a 3.9:1 female-to-male bias, consistent with limited data for this location two decades earlier. Only juvenile loggerheads ≤75.0 cm possessed haplotypes other than CC-A01 or CC-A02 that dominate in the region. Six rare and one un-described haplotype were predominantly found in June 2004.