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.

On the structure of the seminal receptacle in cyclopids (Copepoda, Cyclopoida). [Translation from: Informatsionnyi Byulleten Biologiya Vnutrennikh Vod (6) 26-31, 1970.]

The seminal bag, or seminal receptacle, forms a characteristic organ of cyclopids, serving for retention of the sperms discharged from the spermatophores. The structure of the seminal receptacle, more precisely its form, is fairly widely used in diagnosis and undoubtedly can be more widely applied in the systematics of the group. Within the limits of the family Cyclopidae it is possible to distinguish crustaceans with three basic types of seminal bag. The differences consist of the position which this organ occupies in the genital segment. of one species, we carried out a series of observations on its formation in ontogenesis and during the life of the adult stage. As material for observation the study used laboratory cultures of three species; Acanthocyclops americanus (Marsh) from the plankton of the Moscow River, Cyclops vicinus Uljan and Mesocyclops leuckarti Glaus from the plankton of the channel section of the upper part of the Gorkovsk reservoir. The author concluded that the irreversibility of the changes in the seminal receptacle presents the possibility of utilising this structure as one of the indicators of the growth of the individual.

Electronic structure in five-coordinate complexes of nickel(II) with heavy-donor ligands

I.

Various studies designed to elucidate the electronic structure of the arsenic donor ligand, o-phenylenebisdimethylarsine (diarsine), have been carried out. The electronic spectrum of diarsine has been measured at 300 and 77˚K. Electronic spectra of the molecular complexes of various substituted organoarsines and phosphines with tetracyanoethylene have been measured and used to estimate the relative ionization potentials of these molecules.

Uv photolysis of arsines in frozen solution (96˚K) has yielded thermally labile, paramagnetic products. These include the molecular cations of the photolyzed compounds. The species (diars)⁺ exhibits hyper-fine splitting due to two equivalent ⁷⁵As(I=3/2) nuclei. Resonances due to secondary products are reported and assignments discussed.

Evidence is presented for the involvement of d-orbitals in the bonding of arsines. In (diars)⁺ there is mixing of arsenic “lone-pair” orbitals with benzene ring π-orbitals.

II.

Detailed electronic spectral measurements at 300 and 77˚K have been carried out on five-coordinate complexes of low-spin nickel(II), including complexes of both trigonal bipyramidal (TBP) and square pyramidal (SPY) geometry. TBP complexes are of the form NiLX⁺ (X=halide or cyanide,

L = Qƭ(CH₂)₃As(CH₃)₂]₃ or

P [hexagon - Q'CH₃] , Q = P, As,

Q’=S, Se).

The electronic spectra of these compounds exhibit a novel feature at low temperature. The first ligand field band, which is asymmetric in the room temperature solution spectrum, is considerably more symmetrical at 77˚K. This effect is interpreted in terms of changes in the structure of the complex.

The SPY complexes are of the form Ni(diars)₂X^z (X=CL, Br, CNS, CN, thiourea, NO₂, As). On the basis of the spectral results, the d-level ordering is concluded to be xy ˂ xz, yz ˂ z² ˂˂ x² - y². Central to this interpretation is identification of the symmetry-allowed ¹A₁ → ¹E (xz, yz → x² - y²) transition. This assignment was facilitated by the low temperature measurements.

An assignment of the charge-transfer spectra of the five-coordinate complexes is reported, and electronic spectral criteria for distinguishing the two limiting geometries are discussed.

Optical properties and structure of Sb-rich AgInSbTe phase change thin films

A new composition content quaternary-alloy-based phase change thin film, Sb-rich AgInSbTe, has been prepared by DC-magnetron sputtering on a K9 glass substrate. After the film has been subsequently annealed at 200degreesC for 30 min, it becomes a crystalline thin film. The diffraction peak of antimony (Sb) are observed by shallow (0.5 degree) x-ray diffraction in the quaternary alloy thin film. The analyses of the measurement from differential scanning calorimetry (DSC) show that the crystallization temperature of the phase change thin film is about 190degreesC and increases with the heating rate. By Kissinger plot, the activation energy for crystallization is determined to be 3.05eV. The reflectivity, refractive index and extinction coefficient of the crystalline and amorphous phase change thin films are presented. The optical absorption coefficient of the phase change thin films as a function of photon energy is obtained from the extinction coefficient. The optical band gaps of the amorphous and crystallization phase change thin films are 0.265eV and 1.127eV, respectively.

Combination of web usage, content and structure information for diverse web mining applications in the tourism context and the context of users with disabilities

188 p.

Special effects of YbF3 on the structural changes for fluorophosphate glass

From Raman and IR spectra, obvious differences of the glass structure were observed in non-Yb3+-doped and Yb3+ -doped fluorophosphate glasses. Results showed that Yb3+ ions can induce, in a better glass, polymerization and network uniformity. Compared with the monophosphate-mastered Yb3+-free glass, Yb3+-doped glass has a pyrophosphate environment. The main building blocks in Yb3+ -doped samples are metaphosphate groups, pyrophosphate groups (P-2(O,F)(7),PO3F), Al[F-6]+Al[O,F](6) and F3Al-O-AlF3 while those of the Yb3+ -free glasses are monophosphate groups P(O,F)(4), little pyrophosphate groups, Al[F-4]+Al[F-6]+Al[O,F](4)+Al[O,F](6) and F3Al-O-AlF3. The DSC analysis also showed a slight increase in crystallization stability. (c) 2005 Elsevier B.V. All rights reserved.

Diversidade e padrões estruturais da vegetação halófila-psamófila das restingas do Rio de Janeiro

As restingas do Estado do Rio de Janeiro são áreas de sedimentação predominantemente quaternária, descontínuas geograficamente, formadas em função das mudanças paleoclimáticas, flutuações do nível do mar e transporte longitudinal de sedimentos. A diversidade e a estrutura da vegetação halófila-psamófila presente nestas restingas são os principais focos deste estudo, onde foram analisadas a similaridade florística, as formas de vida e síndrome de dispersão, o padrão de riqueza e diversidade, a distribuição das espécies e os parâmetros de cobertura vegetal, serrapilheira, solo desnudo e salinidade da água do mar. Foram amostradas nove áreas de restinga, a saber, Praia do Sul, Marambaia, Grumari, Marapendi, Maricá, Massambaba, Barra de São João, Jurubatiba e São João da Barra. Foram encontradas 90 espécies, distribuídas em 33 famílias, 69 gêneros, sendo as famílias de maior riqueza específica: Asteraceae (10), Poaceae (9 espécies), Fabaceae (9) e Rubiaceae (6). Foi registrada uma baixa riqueza de espécies nas áreas avaliadas, variando de 25 a 48. Somente 11 espécies ocorreram em todas as áreas (Alternanthera maritima, Blutaparon portulacoides, Canavalia rosea, Cereus fernambucensis, Euphorbia hyssopifolia, Ipomoea imperati, Ipomoea pes-caprae, Panicum racemosum, Remirea maritima, Sporobolus virginicus, Stenotaphrum secundatum), e 12 são dominantes, em uma ou mais áreas (Allagoptera arenaria, Alternanthera maritima, Blutaparon portulacoides, Canavalia rosea, Ipomoea imperati, Ipomoea pes-caprae, Mollugo verticillata, Panicum racemosum, Remirea maritima, Spermacoce capitata, Sporobolus virginicus, Stenotaphrum secundatum), existindo um grande número de espécies raras. O índice de diversidade de Shannon variou de 1,49 a 2,40, e a equabilidade de Pielou de 0,82 a 0,60. O agrupamento formou dois grandes grupos, sendo o primeiro constituído por Barra de São João, Praia do Sul, Marambaia, Grumari e Marapendi, e o segundo por Jurubatiba, São João da Barra, Maricá e Massambaba. As áreas mais similares floristicamente foram Maricá e Massambaba (58%), Grumari e Marapendi (56%), e Barra de São João e Praia do Sul (50%). A vegetação apresenta uma flora característica, com diferença na composição entre as áreas, e similaridade entre áreas geograficamente mais próximas. Um terço das espécies identificadas são caméfitos (34,56%), seguida por fanerófitos (20,98%), geófitos (16,04%), hemicriptófitos (12,34%), terófitos (13,58%) e duas lianas. Na dispersão predomina a autocoria (41,97%), anemocoria (33,33%) e zoocoria (24,69%). O tamanho das áreas perpendicularmente ao mar não está relacionado com aumento da riqueza, nem apresenta o padrão de aumento com o distanciamento do mar. Existem diferenças da riqueza e da diversidade entre as áreas, não havendo uma homogeneidade ao longo do litoral. Há uma zonação, com espécies distribuídas próximas ao mar (Allagoptera arenaria, Alternanthera maritima, Blutaparon portulacoides, Canavalia rosea, Cassytha filiformis, Cereus fernambucensis, Hydrocotyle bonariensis, Ipomoea pes-caprae, Schinus terebinthifolia, Sophora tomentosa, Stenotaphrum secundatum, Cyrtocymura scorpioides), e ao longo do gradiente perpendicular ao mar (Chamaecrista flexuosa, Euphorbia hyssopifolia, Ipomoea imperati, Mollugo verticillata, Panicum racemosum, Paspalum maritimum, Remirea maritima, Sporobolus virginicus). O modelo de série logarítmica é o que melhor representa a vegetação, independente da diversidade ou riqueza. A cobertura vegetal variou entre as áreas. A serrapilheira e o solo desnudo estão estreitamente relacionados com a cobertura vegetal, havendo variação entre as áreas.

Influence of oxygen partial pressure on the structure and photoluminescence of direct current reactive magnetron sputtering ZnO thin films

The effects of oxygen partial pressure on the structure and photoluminescence (PL) of ZnO films were studied. The films were prepared by direct current (DC) reactive magnetron sputtering with various oxygen concentrations at room temperature. With increasing oxygen ratio, the structure of films changes from zinc and zinc oxide phases, single-phase ZnO, to the (002) orientation, and the mechanical stresses exhibit from tensile stress to compressive stress. Films deposited at higher oxygen pressure show weaker emission intensities, which may result from the decrease of the oxygen vacancies and zinc interstitials in the film. This indicates that the emission in ZnO film originates from the oxygen vacancy and zinc interstitial-related defects. From optical transmittance spectra of ZnO films, the plasma edge shifts towards the shorter wavelength with the improvement of film stoichiometry. (C) 2004 Elsevier B.V. All rights reserved.

Length and sex effects on the spatial structure of catches of Pacific halibut (Hippoglossus stenolepis) on longline gear

Field experiments were conducted to test the hypotheses that Pacific halibut (Hippoglossus stenolepis) display small-scale spatial structure within longline catches, relative to other species and empty hooks, or within-species based on sex or length. Sequential hook-by-hook inventories, along with length and sex data, were taken at thirty-one survey stations. Two-dimensional spatial statistics were used to test for 1) aggregation, defined as the clustering of individuals within a given demographic of size or sex over small intervals of distance; and 2) segregation, defined as the sequential occurrence of individuals within a given demographic of size or sex, uninterrupted by other observations, irrespective of the distance between individuals. Statistically significant structure was detected within catches that is more commonly associated with fish length than sex. Significant spatial structuring occurred at 60% of all stations tested. Significant aggregation of halibut of legal length for commercial retention (≥82 cm) was detected at 44% of stations and aggregation of sublegal-size halibut was detected at 11%. Maleand female-based aggregations were observed at 22% and 11% of stations, respectively. Significant segregation of females was observed at 20% of stations, male segregation occurred at 8% of stations, and segregation by size at 16% of stations. Understanding small-scale spatial structure within longline catches may help us interpret changes in survey and commercial catch data. If structure is generated by behavior, then observed size-at-age or relative sex-ratios may be biased relative to underlying distributions. Although physical processes such as gape limitation should remain stable over the time, dynamic processes may be spatially and temporally variabl

Diet changes of Pacific cod (Gadus macrocephalus) in Alaska between 1980 and 1995

The diet of Pacific cod (Gadus macrocephalus) in the area of Pavlof Bay, Alaska, was studied in the early 1980s by Albers and Anderson (1985). They found that the dominant prey species were forage species like pandalid shrimp, capelin (Mallotus villosus), and walleye pollock (Theragra chalcogramma). The shrimp fishery in Pavlof Bay began in 1968 and closed in 1980 because of low shrimp abundance (Ruccio and Worton1). Survey data indicate that, during the period between 1972 and 1997, the abundance of forage species such as pandalid shrimp and capelin declined and higher trophic-level groundfish such as Pacific cod increased. There is a general recognition that a long-term ocean climate shift in the Gulf of Alaska has been partially responsible for the observed reorganization of the community structure (Anderson and Piatt, 1999).

Changes over time in the spatial distribution of walleye pollock (Theragra chalcogramma) in the Gulf of Alaska, 1984-1996

Triennial bottom trawl survey data from 1984 to 1996 were used to evaluate changes in the summer distribution of walleye pollock in the western and central Gulf of Alaska. Differences between several age groups of pollock were evaluated. Distribution was examined in relation to several physical characteristics, including bottom depth and distance from land. Interspecies associations were also analyzed with the Bray-Curtis clustering technique to better understand community structure. Our results indicated that although the population numbers decreased, high concentrations of pollock remained in the same areas during 1984–96. However, there was an increase in the number of stations where low-density pollock concentrations of all ages were observed, which resulted in a decrease in mean population density of pollock within the GOA region. Patterns emerging from our data suggested an alternative to Mac-Call’s “basin hypothesis” which states that as population numbers decrease, there should be a contraction of the population range to optimal habitats. During 1984–96 there was a concurrent precipitous decline in Steller sea lions in the Gulf of Alaska. The results of our study suggest that decreases in the mean density of adult pollock, the main food in the Steller sea lion diet, combined with slight changes in the distribution of pollock (age-1 pollock in particular) in the mid-1980s, may have contributed to decreased foraging efficiency in Steller sea lions. Our results support the prevailing conceptual model for pollock ontogeny, although there is evidence that substantial spawning may also occur outside of Shelikof Strait.

Climate-related long-term faunal changes in a California rocky intertidal community [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): The effects of gradual climate change (ie, multi-decadal) on biological communities are not well understood for most natural systems, owing principally to the lack of quantitative observations in early studies. ... We resurveyed invertebrate species on an intertidal transect in central California, first established and surveyed in 1931, to assess shifts in community structure.

The zooplankton population structure and their trend of variations in the southern of Caspian Sea (Iranian waters)

Caspian Sea has gone under a lot of changes due to human influences and the unwanted presence of a ctenophora Menomiopsis leidyi which has greatly changed the structure of planktons in the last recent years. Therefore, this study was carried out in order to determine these changes in the zooplankton community. the Sampling was done in 8 transacts in Astara, Anzali, Sefidrood, Tonekaboun, Noushahr, Babolsar, Amirabad and Bandar Torkaman coastal waters at 5 different depths including 5, 10, 20, 50 and 100 m. Sampling was carried out in four seasons of spring, summer, autumn and winter during 2008, 2009 and 2010 on board of R/V Gilan. Altogether, 12 species of zooplankton were identified in 2008, 22 species in 2009 and 14 species in 2010. The zooplankton included four groups: copepoda (4 species), cladocera (8species), rotatoria (10 species) and protozoa (2 species).The increase of diversity in 2009 was due to cladocera and rotatoria groups. The abundance of zooplankton in the spring was 5074 + 7807 ind/m3 more than other season in 2008. The abundance of copepoda in the summer reached the highest value of 3332 ind/m3 and since autumn the abundance gradually decreases and in the winter reached to the lowest value. The most abundance of cladocera was 797 ind/m3 in winter and decreased in summer and autumn. The abundance of rotatoria was 2189 ind/m3 in winter. rotifera and copepoda consisted the main population of Zooplanktons in the winter. The results of 2009 and 2010 showed that the abundance of zooplankton in winter was 2.6 fold of autumn, 1.6 fold of summer and 1.1 fold (1/9 fold in 2010)of spring. After increasing increased of temperature, phytoplankton, and zooplankton in summer, M.leidyi increased too. In the autumn M. leidyi reached to the highest rate and decreased zooplankton. The maximum population of zooplankton was in the layer 0-20 m and in the layer more than 20 meters, the abundance of zooplankton decreased very much. In 216 2008, 2009 and 2010, the abundance of zooplankton was 87, 77 and 77 percent in the layer 0-20 m respectively. In this study, the thermocline was observed in the layer 10 – 20 meters in the spring, that formed a thin layer but in the summer it was in the layer 20 to 50 meters. Temperature decreased between 11 to 15 oC in this layer. The variation of temperature between surfaces to bottom was 10 to 13 oC in spring, 19 to 21 in summer, about 9 oC in autumn and maximum 3 oC in winter. The most biomass of zooplankton was in the west. The biomass of zooplankton in central west and east of Southern of Caspian Sea was 54 %, 22 % and 24 % respectively in 2008, in 2009 was 48%, 33% and 20% respectively and in 2010 was 54 %, 29 % and 16 % respectively .The biomass decreased from west to east. The model of zooplankton designed by principal component analysis (PCA)and linear regression for Southern of Caspian Sea.

Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China

Leptobrachium ailaonicum is a vulnerable anuran restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes at mid-elevations (approximately 2000-2600 m) in the subtropical Mount Wuliang and Mount Ailao ranges in southwest China (Yunnan Province) and northern Vietnam. Given high habitat specificity and lack of suitable habitat in lower elevations between these ranges, we hypothesized limited gene flow between populations throughout its range. We used two mitochondrial genes to construct a phylogeographic pattern within this species in order to test our hypothesis. We also examined whether this phylogeographic pattern is a response to past geological events and/or climatic oscillations. A total of 1989 base pairs were obtained from 81 individuals of nine populations yielding 51 unique haplotypes. Both Bayesian and maximum parsimony phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographical regions separated by deep river valleys. These results suggest a long history of allopatric separation by vicariance. The distinct geographic distributions of four major clades and the estimated divergence time suggest spatial and temporal separations that coincide with climatic and paleogeographic changes following the orogeny and uplift of Mount Ailao during the late Miocene to mid Pliocene in southwest China. At the southern distribution, the presence of two sympatric yet differentiated clades in two areas are interpreted as a result of secondary contact between previously allopatric populations during cooler Pleistocene glacial cycles. Analysis of molecular variance indicates that most of the observed genetic variation occurs among the four regions implying long-term interruption of maternal gene flow, suggesting that L ailaonicum may represent more than one distinct species and should at least be separated into four management units corresponding to these four geographic lineages for conservation. (C) 2009 Elsevier Inc. All rights reserved.

Structure of coexisting liquid phases of supercooled water: analogy with ice polymorphs.

The structural changes occurring in supercooled liquid water upon moving from one coexisting liquid phase to the other have been investigated by computer simulation using a polarizable interaction potential model. The obtained results favorably compare with recent neutron scattering data of high and low density water. In order to assess the physical origin of the observed structural changes, computer simulation of several ice polymorphs has also been carried out. Our results show that there is a strict analogy between the structure of various disordered (supercooled) and ordered (ice) phases of water, suggesting that the occurrence of several different phases of supercooled water is rooted in the same physical origin that is responsible for ice polymorphism.