Long Bay hypoxia study: A collaborative and multidisciplinary approach

The nearshore waters along the Myrtle Beach area are oceanographically referred to as Long Bay. Long Bay is the last in a series of semi-circular indentations located along the South Atlantic seaboard. The Bay extends for approximately 150 km from the Cape Fear River in North Carolina to Winyah Bay in South Carolina and has a number of small inlets (Figure 1). This region of the S.C. coast, commonly referred to as the “Grand Strand,” has a significant tourism base that accounts for a substantial portion of the South Carolina economy (i.e., 40% of the state’s total in 2002) (TIAA 2003). In 2004, the Grand Strand had an estimated 13.2 million visitors of which 90% went to the beach (MBCC 2006). In addition, Long Bay supports a shore-based hook and line fishery comprised of anglers fishing from recreational fishing piers, the beach, and small recreational boats just offshore. (PDF contains 4 pages)

Seismic structure above and below the core-mantle boundary

Seismic structure above and below the core-mantle boundary (CMB) has been studied through use of travel time and waveform analyses of several different seismic wave groups. Anomalous systematic trends in observables document mantle heterogeneity on both large and small scales. Analog and digital data has been utilized, and in many cases the analog data has been optically scanned and digitized prior to analysis.

Differential travel times of S - SKS are shown to be an excellent diagnostic of anomalous lower mantle shear velocity (V s) structure. Wavepath geometries beneath the central Pacific exhibit large S- SKS travel time residuals (up to 10 sec), and are consistent with a large scale 0(1000 km) slower than average V_s region (≥3%). S - SKS times for paths traversing this region exhibit smaller scale patterns and trends 0(100 km) indicating V_s perturbations on many scale lengths. These times are compared to predictions of three tomographically derived aspherical models: MDLSH of Tanimoto [1990], model SH12_WM13 of Suet al. [1992], and model SH.10c.17 of Masters et al. [1992]. Qualitative agreement between the tomographic model predictions and observations is encouraging, varying from fair to good. However, inconsistencies are present and suggest anomalies in the lower mantle of scale length smaller than the present 2000+ km scale resolution of tomographic models. 2-D wave propagation experiments show the importance of inhomogeneous raypaths when considering lateral heterogeneities in the lowermost mantle.

A dataset of waveforms and differential travel times of S, ScS, and the arrival from the D" layer, Scd, provides evidence for a laterally varying V_s velocity discontinuity at the base of the mantle. Two different localized D" regions beneath the central Pacific have been investigated. Predictions from a model having a V_s discontinuity 180 km above the CMB agree well with observations for an eastern mid-Pacific CMB region. This thickness differs from V_s discontinuity thicknesses found in other regions, such as a localized region beneath the western Pacific, which average near 280 km. The "sharpness" of the V_s jump at the top of D", i.e., the depth range over which the V_s increase occurs, is not resolved by our data, and our data can in fact may be modeled equally well by a lower mantle with the increase in V_s at the top of D" occurring over a 100 krn depth range. It is difficult at present to correlate D" thicknesses from this study to overall lower mantle heterogeneity, due to uncertainties in the 3-D models, as well as poor coverage in maps of D" discontinuity thicknesses.

P-wave velocity structure (V_p) at the base of the mantle is explored using the seismic phases SKS and SPdKS. SPdKS is formed when SKS waves at distances around 107° are incident upon the CMB with a slowness that allows for coupling with diffracted P-waves at the base of the mantle. The P-wave diffraction occurs at both the SKS entrance and exit locations of the outer core. SP_dKS arrives slightly later in time than SKS, having a wave path through the mantle and core very close to SKS. The difference time between SKS and SP_dKS strongly depends on V_p at the base of the mantle near SK Score entrance and exit points. Observations from deep focus Fiji-Tonga events recorded by North American stations, and South American events recorded by European and Eurasian stations exhibit anomalously large SP_dKS - SKS difference times. SKS and the later arriving SP_dKS phase are separated by several seconds more than predictions made by 1-D reference models, such as the global average PREM [Dziewonski and Anderson, 1981] model. Models having a pronounced low-velocity zone (5%) in V_p in the bottom 50-100 km of the mantle predict the size of the observed SP_dK S-SKS anomalies. Raypath perturbations from lower mantle V_s structure may also be contributing to the observed anomalies.

Outer core structure is investigated using the family of SmKS (m=2,3,4) seismic waves. SmKS are waves that travel as S-waves in the mantle, P-waves in the core, and reflect (m-1) times on the underside of the CMB, and are well-suited for constraining outermost core V_p structure. This is due to closeness of the mantle paths and also the shallow depth range these waves travel in the outermost core. S3KS - S2KS and S4KS - S3KS differential travel times were measured using the cross-correlation method and compared to those from reflectivity synthetics created from core models of past studies. High quality recordings from a deep focus Java Sea event which sample the outer core beneath the northern Pacific, the Arctic, and northwestern North America (spanning 1/8th of the core's surface area), have SmKS wavepaths that traverse regions where lower mantle heterogeneity is pre- dieted small, and are well-modeled by the PREM core model, with possibly a small V_p decrease (1.5%) in the outermost 50 km of the core. Such a reduction implies chemical stratification in this 50 km zone, though this model feature is not uniquely resolved. Data having wave paths through areas of known D" heterogeneity (±2% and greater), such as the source-side of SmKS lower mantle paths from Fiji-Tonga to Eurasia and Africa, exhibit systematic SmKS differential time anomalies of up to several seconds. 2-D wave propagation experiments demonstrate how large scale lower mantle velocity perturbations can explain long wavelength behavior of such anomalous SmKS times. When improperly accounted for, lower mantle heterogeneity maps directly into core structure. Raypaths departing from homogeneity play an important role in producing SmKS anomalies. The existence of outermost core heterogeneity is difficult to resolve at present due to uncertainties in global lower mantle structure. Resolving a one-dimensional chemically stratified outermost core also remains difficult due to the same uncertainties. Restricting study to higher multiples of SmKS (m=2,3,4) can help reduce the affect of mantle heterogeneity due to the closeness of the mantle legs of the wavepaths. SmKS waves are ideal in providing additional information on the details of lower mantle heterogeneity.

A genetic and biochemical analysis of pre-mRNA splicing in Saccharomyces cerevisiae

Pre-mRNA splicing requires interaction of cis- acting intron sequences with trans -acting factors: proteins and small nuclear ribonucleoproteins (snRNPs). The assembly of these factors into a large complex, the spliceosome, is essential for the subsequent two step splicing reaction. First, the 5' splice site is cleaved and free exon 1 and a lariat intermediate (intron- exon2) form. In the second reaction the 3' splice site is cleaved the exons ligated and lariat intron released. A combination of genetic and biochemical techniques have been used here to study pre-mRNA splicing in yeast.

Yeast introns have three highly conserved elements. We made point mutations within these elements and found that most of them affect splicing efficiency in vivo and in vitro, usually by inhibiting spliceosome assembly.

To study trans -acting splicing factors we generated and screened a bank of temperature- sensitive (ts) mutants. Eleven new complementation groups (prp17 to prp27) were isolated. The four phenotypic classes obtained affect different steps in splicing and accumulate either: 1) pre-mRNA, 2) lariat intermediate, 3) excised intron or 4) both pre-mRNA and intron. The latter three classes represent novel phenotypes. The excised intron observed in one mutant: prp26 is stabilized due to protection in a snRNP containing particle. Extracts from another mutant: prpl8 are heat labile and accumulate lariat intermediate and exon 1. This is especially interesting as it allows analysis of the second splicing reaction. In vitro complementation of inactivated prp18 extracts does not require intact snRNPs. These studies have also shown the mutation to be in a previously unknown splicing protein. A specific requirement for A TP is also observed for the second step of splicing. The PRP 18 gene has been cloned and its polyadenylated transcript identified.

Deterioration and fragmentation of rivers in Malta

Malta, situated in the Mediterranean Sea south of Sicily, is a small island of less than 300 km2. Two hundred years ago Malta was a wet and sodden country. The limestone was like a sponge, with numerous perennial springs, great and small, and so full of water that most flat areas did not drain, but were marsh. Water from springs, rivers and marshes was in ample supply. In the space of two centuries, Malta's rivers have passed from being good, spring-regulated watercourses with a mixed community of clean limewater plants, to the present-day situation where many if not all are on the verge of extinction. This is the result of human impact, not climate change, and is set to continue and increase. Unfortunately the best wetland-type valley communities were scheduled to be destroyed in 1997 but, after a change of Government and vigorous representations, these may now be spared. However, there is at least a great opportunity to prevent further fragmentation of remaining rivers and to reclaim some of the fragmented portions.

Resolution and noise in ghost imaging with classical thermal light

The resolution and classical noise in ghost imaging with a classical thermal light are investigated theoretically. For ghost imaging with a Gaussian Schell model source, the dependences of the resolution and noise on the spatial coherence of the source and the aperture in the imaging system are discussed and demonstrated by using numerical simulations. The results show that an incoherent source and a large aperture will lead to a good image quality and small noise.

Computational Predictions of G Protein-Coupled Receptor Structures and Binding Sites

G protein-coupled receptors (GPCRs) are the largest family of proteins within the human genome. They consist of seven transmembrane (TM) helices, with a N-terminal region of varying length and structure on the extracellular side, and a C-terminus on the intracellular side. GPCRs are involved in transmitting extracellular signals to cells, and as such are crucial drug targets. Designing pharmaceuticals to target GPCRs is greatly aided by full-atom structural information of the proteins. In particular, the TM region of GPCRs is where small molecule ligands (much more bioavailable than peptide ligands) typically bind to the receptors. In recent years nearly thirty distinct GPCR TM regions have been crystallized. However, there are more than 1,000 GPCRs, leaving the vast majority of GPCRs with limited structural information. Additionally, GPCRs are known to exist in a myriad of conformational states in the body, rendering the static x-ray crystal structures an incomplete reflection of GPCR structures. In order to obtain an ensemble of GPCR structures, we have developed the GEnSeMBLE procedure to rapidly sample a large number of variations of GPCR helix rotations and tilts. The lowest energy GEnSeMBLE structures are then docked to small molecule ligands and optimized. The GPCR family consists of five subfamilies with little to no sequence homology between them: class A, B1, B2, C, and Frizzled/Taste2. Almost all of the GPCR crystal structures have been of class A GPCRs, and much is known about their conserved interactions and binding sites. In this work we particularly focus on class B1 GPCRs, and aim to understand that family’s interactions and binding sites both to small molecules and their native peptide ligands. Specifically, we predict the full atom structure and peptide binding site of the glucagon-like peptide receptor and the TM region and small molecule binding sites for eight other class B1 GPCRs: CALRL, CRFR1, GIPR, GLR, PACR, PTH1R, VIPR1, and VIPR2. Our class B1 work reveals multiple conserved interactions across the B1 subfamily as well as a consistent small molecule binding site centrally located in the TM bundle. Both the interactions and the binding sites are distinct from those seen in the more well-characterized class A GPCRs, and as such our work provides a strong starting point for drug design targeting class B1 proteins. We also predict the full structure of CXCR4 bound to a small molecule, a class A GPCR that was not closely related to any of the class A GPCRs at the time of the work.

Solar System Small-Body Demographics with the Palomar Transient Factory Survey

Observational studies of our solar system's small-body populations (asteroids and comets) offer insight into the history of our planetary system, as these minor planets represent the left-over building blocks from its formation. The Palomar Transient Factory (PTF) survey began in 2009 as the latest wide-field sky-survey program to be conducted on the 1.2-meter Samuel Oschin telescope at Palomar Observatory. Though its main science program has been the discovery of high-energy extragalactic sources (such as supernovae), during its first five years PTF has collected nearly five million observations of over half a million unique solar system small bodies. This thesis begins to analyze this vast data set to address key population-level science topics, including: the detection rates of rare main-belt comets and small near-Earth asteroids, the spin and shape properties of asteroids as inferred from their lightcurves, the applicability of this visible light data to the interpretation of ultraviolet asteroid observations, and a comparison of the physical properties of main-belt and Jovian Trojan asteroids. Future sky-surveys would benefit from application of the analytical techniques presented herein, which include novel modeling methods and unique applications of machine-learning classification. The PTF asteroid small-body data produced in the course of this thesis work should remain a fertile source of solar system science and discovery for years to come.

A simple method for counting bacteria with active electron transport system in water and sediment samples [Translation from: Kiel. Meeresforsch. 31(2) 83-86, 1975]

Description of a simple method for counting bacteria with active electron transport systems in water and sediment samples. Sodium succinate, NADH and NADPH served as electron donors. It is possible to see several sites of electron transport in the larger cells. Especially impressive are the plankton-algae, protozoa, and small metazoa. This is a partial translation of the ”method” section only.

On the classification of lakes and lake-like bodies of the Ukraine [Translation from: Gidrobiologicheskie Zhurnal, Kiev 19(2) 100-101, 1983]

In the Ukraine there are several thousand large, medium and small lakes and lake-like reservoirs, distinguished by origin, salinity, regional position, productivity and by construction a significant number of large and small water bodies, ponds and industrial reservoirs of variable designation. The problem of national systems necessitates the creation of specific schemes and classifications. Classifying into specific types of reservoir by means of suitable specifications is required for planning national measures with the objective of the rational utilisation of natural resources. It is now necessary to consider the present-day characteristics of Ukranian lakes. In the case of the Ukraine it is possible to use two approaches - genetical and ecological. This paper uses the genetical system to classify the lake-like water bodies of the Ukraine.

Biochemical and Biophysical Characterization of Huntingtin

Huntington’s disease (HD) is a fatal autosomal dominant neurodegenerative disease. HD has no cure, and patients pass away 10-20 years after the onset of symptoms. The causal mutation for HD is a trinucleotide repeat expansion in exon 1 of the huntingtin gene that leads to a polyglutamine (polyQ) repeat expansion in the N-terminal region of the huntingtin protein. Interestingly, there is a threshold of 37 polyQ repeats under which little or no disease exists; and above which, patients invariably show symptoms of HD. The huntingtin protein is a 350 kDa protein with unclear function. As the polyQ stretch expands, its propensity to aggregate increases with polyQ length. Models for polyQ toxicity include formation of aggregates that recruit and sequester essential cellular proteins, or altered function producing improper interactions between mutant huntingtin and other proteins. In both models, soluble expanded polyQ may be an intermediate state that can be targeted by potential therapeutics.

In the first study described herein, the conformation of soluble, expanded polyQ was determined to be linear and extended using equilibrium gel filtration and small-angle X-ray scattering. While attempts to purify and crystallize domains of the huntingtin protein were unsuccessful, the aggregation of huntingtin exon 1 was investigated using other biochemical techniques including dynamic light scattering, turbidity analysis, Congo red staining, and thioflavin T fluorescence. Chapter 4 describes crystallization experiments sent to the International Space Station and determination of the X-ray crystal structure of the anti-polyQ Fab MW1. In the final study, multimeric fibronectin type III (FN3) domain proteins were engineered to bind with high avidity to expanded polyQ tracts in mutant huntingtin exon 1. Surface plasmon resonance was used to observe binding of monomeric and multimeric FN3 proteins with huntingtin.

Particle fluid mechanics in shear flows, acoustic waves, and shock waves

Three different categories of flow problems of a fluid containing small particles are being considered here. They are: (i) a fluid containing small, non-reacting particles (Parts I and II); (ii) a fluid containing reacting particles (Parts III and IV); and (iii) a fluid containing particles of two distinct sizes with collisions between two groups of particles (Part V).

Part I

A numerical solution is obtained for a fluid containing small particles flowing over an infinite disc rotating at a constant angular velocity. It is a boundary layer type flow, and the boundary layer thickness for the mixture is estimated. For large Reynolds number, the solution suggests the boundary layer approximation of a fluid-particle mixture by assuming W = W_p. The error introduced is consistent with the Prandtl’s boundary layer approximation. Outside the boundary layer, the flow field has to satisfy the “inviscid equation” in which the viscous stress terms are absent while the drag force between the particle cloud and the fluid is still important. Increase of particle concentration reduces the boundary layer thickness and the amount of mixture being transported outwardly is reduced. A new parameter, β = 1/Ω τ_v, is introduced which is also proportional to μ. The secondary flow of the particle cloud depends very much on β. For small values of β, the particle cloud velocity attains its maximum value on the surface of the disc, and for infinitely large values of β, both the radial and axial particle velocity components vanish on the surface of the disc.

Part II

The “inviscid” equation for a gas-particle mixture is linearized to describe the flow over a wavy wall. Corresponding to the Prandtl-Glauert equation for pure gas, a fourth order partial differential equation in terms of the velocity potential ϕ is obtained for the mixture. The solution is obtained for the flow over a periodic wavy wall. For equilibrium flows where λ_v and λ_T approach zero and frozen flows in which λ_v and λ_T become infinitely large, the flow problem is basically similar to that obtained by Ackeret for a pure gas. For finite values of λ_v and λ_T, all quantities except v are not in phase with the wavy wall. Thus the drag coefficient C_D is present even in the subsonic case, and similarly, all quantities decay exponentially for supersonic flows. The phase shift and the attenuation factor increase for increasing particle concentration.

Part III

Using the boundary layer approximation, the initial development of the combustion zone between the laminar mixing of two parallel streams of oxidizing agent and small, solid, combustible particles suspended in an inert gas is investigated. For the special case when the two streams are moving at the same speed, a Green’s function exists for the differential equations describing first order gas temperature and oxidizer concentration. Solutions in terms of error functions and exponential integrals are obtained. Reactions occur within a relatively thin region of the order of λ_D. Thus, it seems advantageous in the general study of two-dimensional laminar flame problems to introduce a chemical boundary layer of thickness λ_D within which reactions take place. Outside this chemical boundary layer, the flow field corresponds to the ordinary fluid dynamics without chemical reaction.

Part IV

The shock wave structure in a condensing medium of small liquid droplets suspended in a homogeneous gas-vapor mixture consists of the conventional compressive wave followed by a relaxation region in which the particle cloud and gas mixture attain momentum and thermal equilibrium. Immediately following the compressive wave, the partial pressure corresponding to the vapor concentration in the gas mixture is higher than the vapor pressure of the liquid droplets and condensation sets in. Farther downstream of the shock, evaporation appears when the particle temperature is raised by the hot surrounding gas mixture. The thickness of the condensation region depends very much on the latent heat. For relatively high latent heat, the condensation zone is small compared with Ʌ_D.

For solid particles suspended initially in an inert gas, the relaxation zone immediately following the compression wave consists of a region where the particle temperature is first being raised to its melting point. When the particles are totally melted as the particle temperature is further increased, evaporation of the particles also plays a role.

The equilibrium condition downstream of the shock can be calculated and is independent of the model of the particle-gas mixture interaction.

Part V

For a gas containing particles of two distinct sizes and satisfying certain conditions, momentum transfer due to collisions between the two groups of particles can be taken into consideration using the classical elastic spherical ball model. Both in the relatively simple problem of normal shock wave and the perturbation solutions for the nozzle flow, the transfer of momentum due to collisions which decreases the velocity difference between the two groups of particles is clearly demonstrated. The difference in temperature as compared with the collisionless case is quite negligible.

Sylphella puccoon gen. n., sp n. and two additional new species of aquatic oligochaetes (Lumbriculidae, Clitellata) from poorly-known lotic habitats in North Carolina (USA)

Three new species of Lumbriculidae were collected from floodplain seeps and small streams in southeastern North America. Some of these habitats are naturally acidic. Sylphella puccoon gen. n., sp. n. has prosoporous male ducts in X-XI, and spermathecae in XII-XIII. Muscular, spherical atrial ampullae and acuminate penial sheaths distinguish this monotypic new genus from other lumbriculid genera having similar arrangements of reproductive organs. Cookidrilus pocosinus sp. n. resembles its two subterranean, Palearctic congeners in the arrangement of reproductive organs, but is easily distinguished by the position of the spermathecal pores in front of the chaetae in X-XIII. Stylodrilus coreyi sp. n. differs from congeners having simple-pointed chaetae and elongate atria primarily by the structure of the male duct and the large clusters of prostate cells. Streams and wetlands of Southeastern USA have a remarkably high diversity of endemic lumbriculids, and these poorly-known invertebrates should be considered in conservation efforts.

Factors influencing cannibalism and abundance of walleye pollock (Theragra chalcogramma) on the eastern Bering Sea shelf, 1982–20

Cannibalism is thought to be an inf luential top-down process affecting walleye pollock (Theragra chalcogramma) recruitment in the eastern Bering Sea (EBS). In summer, many age-1 pollock occupy the same depths as those of adult walleye pollock, making them vulnerable to cannibalism. We examine factors that inf luence the occurrence and amount of cannibalism, as well as the abundance and co-occurrence of predator and prey walleye pollock. Large walleye pollock were generally found in deeper waters and avoided cold temperatures; whereas, age-1 walleye pollock were found in broader bottom depth and temperature ranges. The occurrence of cannibalism was highest in the area where predator and prey walleye pollock co-occurred and the amount of cannibalism was highest on the middle and outer EBS shelf. Both the occurrence and amount of cannibalism were influenced by location, bottom temperature and bottom depth, and the abundance of prey walleye pollock. The abundance of both large and small walleye pollock decreased during the 1982–2006 survey period in the EBS and, hence, the occurrence and amount of cannibalism also decreased. The occurrence and amount of cannibalism observed in the diet samples from the summer survey were good indicators of year class strength, as estimated by the stock assessment model. There was more cannibalism of age-1 walleye pollock when predicted recruit abundance was highest, indicating that summer cannibalism on age-1 walleye pollock, a top-down process, does not control walleye pollock recruitment in the EBS.

Population dynamics and exploitation of Metapenaeus affinis in Kuwaiti waters

Length-frequency data of Metapenaeus affinis collected from the trawl catches of R/V Bahith in Kuwaiti waters from 1985 to 1989 were combined with estimates of monthly total catch by the commercial and small-scale fleets operating in Kuwait, and analyzed using the Compleat ELEFAN software package. A major recruitment pulse of M. affinis occurs in spring and a minor one in autumn. Optimum relative yield per recruit (Y'/R) is obtained with the length-at-first capture (L sub(c)) of 24.4 cm CL for females and < 17.6 m CL for males. Virtual population analysis results indicated that the biomasses have decreased during the last three-year period for which data were available.

Larval development of estuary perch (Macquaria colonorum) and Australian bass (M. novemaculeata) (Perciformes: Percichthyidae), and comments on their life history

Morphological development of the larvae and small juveniles of estuary perch (Macquaria colonorum) (17 specimens, 4.8−13.5 mm body length) and Australian bass (M. novemaculeata) (38 specimens, 3.3−14.1 mm) (Family Percichthyidae) is described from channel-net and beach-seine collections of both species, and from reared larvae of M. novemaculeata. The larvae of both are characterized by having 24−25 myomeres, a large triangular gut (54−67% of BL) in postflexion larvae, small spines on the preopercle and interopercle, a smooth supraocular ridge, a small to moderate gap between the anus and the origin of the anal fin, and distinctive pigment patterns. The two species can be distinguished most easily by the different distribution of their melanophores. The adults spawn in estuaries and larvae are presumed to remain in estuaries before migrating to adult freshwater habitat. However, larvae of both species were collected as they entered a central New South Wales estuary from the ocean on flood tides; such transport may have consequences for the dispersal of larvae among estuaries. Larval morphology and published genetic evidence supports a reconsideration of the generic arrangement of the four species currently placed in the genus Macquaria.