Are Marine Migrations of Striped Bass Genetically Pre-determined? : An investigation of Albemarle Sound-Roanoke River Striped Bass Migratory Patterns

Striped bass, Morone saxatilis, is one of the most thoroughly studied anadromous fish species in the United States, with records governing the management of the species dating back to the late 1600s. However, management of this species has been difficult because of the species' anadromous behavior that takes it between fresh and marine waters, crossing numerous geopolitical boundaries. In the 20th century, the fishery experienced two dramatic declines in abundance. Studying the fishery after the declines resulted in major advancements in scientific understanding and management for this species, and striped bass is now an example of a successfully rebuilt fishery, key questions about population dynamics and migration patterns still persist. These unanswered questions reduce confidence in managing the species as a whole, and instead encouraging precautionary measures applied to small geographic areas, such as a natal river.  This dissertation begins with a thorough review of the history of striped bass, including the key scientific findings and management measures instrumental in its recent recovery. Chapter 2 explores how scientists have approached the major challenge in striped bass management: defining the management unit so allocations can be made fairly and sustainably. The array of genetic techniques that have been employed, their limitations, and the populations studied with those techniques, is reviewed. Among the studies reviewed is one suggesting North Carolina striped bass migration may be genetically linked; this suggestion forms the basis for this dissertation's hypothesis. Answering this question can help resource managers better understand population dynamics, genetic interplay, and migration patterns - important for creating effective management and fair allocation between states. Chapter 3 explores the biotic and abiotic factors that can influence the results of an otolith microchemistry analysis, and Chapter 4 contains the discussion of the findings about the 112 striped bass examined.  With biases accounted for, this dissertation concludes that marine migration was not linked to the genes examined. However, an interesting post-hoc observation can be made: though the behavior was not found to be genetically linked, striped bass in the first year of life proved to be residents, stagers, or sprinters, with different growth rates associated with these behaviors.  Ph.D

Rapid Circumstellar Disk Evolution and an Accelerating Star Formation Rate in the Infrared Dark Cloud M17 SWex

We present a catalog of 840 X-ray sources and first results from a 100 ks Chandra X-ray Observatory imaging study of the filamentary infrared dark cloud G014.225$-$00.506, which forms the central regions of a larger cloud complex known as the M17 southwest extension (M17 SWex). In addition to the rich population of protostars and young stellar objects with dusty circumstellar disks revealed by Spitzer Space Telescope archival data, we discover a population of X-ray-emitting, intermediate-mass pre--main-sequence stars (IMPS) that lack infrared excess emission from circumstellar disks. We model the infrared spectral energy distributions of this source population to measure its mass function and place new constraints on the inner dust disk destruction timescales for 2-8 $M_{\odot}$ stars. We also place a lower limit on the star formation rate (SFR) and find that it is quite high ($\dot{M}\ge 0.007~M_{\odot}$ yr$^{-1}$), equivalent to several Orion Nebula Clusters in G14.225$-$0.506 alone, and likely accelerating. The cloud complex has not produced a population of massive, O-type stars commensurate with its SFR. This absence of very massive (${\ge}20~M_{\odot}$) stars suggests that either (1) M17 SWex is an example of a distributed mode of star formation that will produce a large OB association dominated by intermediate-mass stars but relatively few massive clusters, or (2) the massive cores are still in the process of accreting sufficient mass to form massive clusters hosting O stars.Comment: 29 pages, 9 figures, accepted to Ap

Using productivity and susceptibility indices to assess the vulnerability of United States fish stocks to overfishing

Assessing the vulnerability of stocks to fishing practices in U.S. federal waters was recently highlighted by the National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration, as an important factor to consider when 1) identifying stocks that should be managed and protected under a fishery management plan; 2) grouping data-poor stocks into relevant management complexes; and 3) developing precautionary harvest control rules. To assist the regional fishery management councils in determining vulnerability, NMFS elected to use a modified version of a productivity and susceptibility analysis (PSA) because it can be based on qualitative data, has a history of use in other fisheries, and is recommended by several organizations as a reasonable approach for evaluating risk. A number of productivity and susceptibility attributes for a stock are used in a PSA and from these attributes, index scores and measures of uncertainty are computed and graphically displayed. To demonstrate the utility of the resulting vulnerability evaluation, we evaluated six U.S. fisheries targeting 162 stocks that exhibited varying degrees of productivity and susceptibility, and for which data quality varied. Overall, the PSA was capable of differentiating the vulnerability of stocks along the gradient of susceptibility and productivity indices, although fixed thresholds separating low-, moderate-, and highly vulnerable species were not observed. The PSA can be used as a flexible tool that can incorporate regional-specific information on fishery and management activity

Multi-layer silicon nitride-on-silicon polarization-independent grating couplers

A polarization-independent grating coupler is proposed and demonstrated in a 3-layer silicon nitride-on-silicon photonic platform. Polarization independent coupling was made possible by the supermodes and added degrees of geometric freedom unique to the 3-layer photonic platform. The grating was designed via optimization algorithms, and the simulated peak coupling efficiency was −2.1 dB with a 1 dB polarization dependent loss (PDL) bandwidth of 69 nm. The fabricated grating couplers had a peak coupling efficiency of −4.8 dB with 1 dB PDL bandwidth of over 100 nm

Further development and flight test of an autonomous precision landing system using a parafoil

NASA Dryden Flight Research Center and NASA Johnson Space Center are jointly conducting a phased program to determine the feasibility of the autonomous recovery of a spacecraft using a ram-air parafoil system for the final stages of entry from space to a precision landing. The feasibility is being studied using a flight model of a spacecraft in the generic shape of a flattened biconic that weighs approximately 120 lb and is flown under a commercially available ram-air parafoil. Key components of the vehicle include the global positioning system (GPS) guidance for navigation, a flight control computer, an electronic compass, a yaw rate gyro, and an onboard data recorder. A flight test program is being used to develop and refine the vehicle. The primary flight goal is to demonstrate autonomous flight from an altitude of 3,000 m (10,000 ft) with a lateral offset of 1.6 km (1.0 mi) to a precision soft landing. This paper summarizes the progress to date. Much of the navigation system has been tested, including a heading tracker that was developed using parameter estimation techniques and a complementary filter. The autoland portion of the autopilot is still in development. The feasibility of conducting the flare maneuver without servoactuators was investigated as a means of significantly reducing the servoactuator rate and load requirements

The maize (Zea mays L.) roothairless3 gene encodes a putative GPI-anchored, monocot-specific, COBRA-like protein that significantly affects grain yield

The rth3 (roothairless 3) mutant is specifically affected in root hair elongation. We report here the cloning of the rth3 gene via a PCR-based strategy (amplification of insertion mutagenized sites) and demonstrate that it encodes a COBRA-like protein that displays all the structural features of a glycosylphosphatidylinositol anchor. Genes of the COBRA family are involved in various types of cell expansion and cell wall biosynthesis. The rth3 gene belongs to a monocot-specific clade of the COBRA gene family comprising two maize and two rice genes. While the rice (Oryza sativa) gene OsBC1L1 appears to be orthologous to rth3 based on sequence similarity (86% identity at the protein level) and maize/rice synteny, the maize (Zea mays L.) rth3-like gene does not appear to be a functional homolog of rth3based on their distinct expression profiles. Massively parallel signature sequencing analysis detected rth3 expression in all analyzed tissues, but at relatively low levels, with the most abundant expression in primary roots where the root hair phenotype is manifested.In situ hybridization experiments confine rth3 expression to root hair-forming epidermal cells and lateral root primordia. Remarkably, in replicated field trials involving near-isogenic lines, the rth3 mutant conferred significant losses in grain yield

Monolithically Integrated Multilayer Silicon Nitride-on-Silicon Waveguide Platforms for 3-D Photonic Circuits and Devices

In this paper, we review and provide additional details about our progress on multilayer silicon nitride (SiN)-on-silicon (Si) integrated photonic platforms. In these platforms, one or more SiN waveguide layers are monolithically integrated onto a Si photonic layer. This paper focuses on the development of three-layer platforms for the O- and SCL-bands for very large-scale photonic integrated circuits requiring hundreds or thousands of waveguide crossings. Low-loss interlayer transitions and ultralow-loss waveguide crossings have been demonstrated, along with bilevel and trilevel grating couplers for fiber-to-chip coupling. The SiN and Si passive devices have been monolithically integrated with high-efficiency optical modulators, photodetectors, and thermal tuners in a single photonic platform

Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase

Citation: Nestler, J., Liu, S., Wen, T. -., Paschold, A., Marcon, C., Tang, H. M., et al. (2014). Roothairless5, which functions in maize (zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase. Retrieved from krex.k-state.edu.Root hairs are instrumental for nutrient uptake in monocot cereals. The maize (Zea mays L.) roothairless5 (rth5) mutant displays defects in root hair initiation and elongation manifested by a reduced density and length of root hairs. Map-based cloning revealed that the rth5 gene encodes a monocot-specific NADPH oxidase. RNA-Seq, in situ hybridization and qRT-PCR experiments demonstrated that the rth5 gene displays preferential expression in root hairs but also accumulates to low levels in other tissues. Immunolocalization detected RTH5 proteins in the epidermis of the elongation and differentiation zone of primary roots. Because superoxide and hydrogen peroxide levels are reduced in the tips of growing rth5 mutant root hairs as compared to wild-type, and ROS is known to be involved in tip growth, we hypothesize that the RTH5 protein is responsible for establishing the high levels of ROS in the tips of growing root hairs required for elongation. Consistent with this hypothesis, a comparative RNA-Seq analysis of 6-day-old rth5 versus wild-type primary roots, revealed significant over-representation of only two gene ontology (GO) classes related to the biological functions (i.e., oxidation/reduction and carbohydrate metabolism) among 893 differentially expressed genes (FDR <5%). Within these two classes the subgroups “response to oxidative stress” and “cellulose biosynthesis” were most prominently represented

Vascular pedicle width in acute lung injury: correlation with intravascular pressures and ability to discriminate fluid status

Abstract Introduction Conservative fluid management in patients with acute lung injury (ALI) increases time alive and free from mechanical ventilation. Vascular pedicle width (VPW) is a non-invasive measurement of intravascular volume status. The VPW was studied in ALI patients to determine the correlation between VPW and intravascular pressure measurements and whether VPW could predict fluid status. Methods This retrospective cohort study involved 152 patients with ALI enrolled in the Fluid and Catheter Treatment Trial (FACTT) from five NHLBI ARDS (Acute Respiratory Distress Syndrome) Network sites. VPW and central venous pressure (CVP) or pulmonary artery occlusion pressure (PAOP) from the first four study days were correlated. The relationships between VPW, positive end-expiratory pressure (PEEP), cumulative fluid balance, and PAOP were also evaluated. Receiver operator characteristic (ROC) curves were used to determine the ability of VPW to detect PAOP &lt;8 mmHg and PAOP ≥18 mm Hg. Results A total of 71 and 152 patients provided 118 and 276 paired VPW/PAOP and VPW/CVP measurements, respectively. VPW correlated with PAOP (r = 0.41; P &lt; 0.001) and less well with CVP (r = 0.21; P = 0.001). In linear regression, VPW correlated with PAOP 1.5-fold better than cumulative fluid balance and 2.5-fold better than PEEP. VPW discriminated achievement of PAOP &lt;8 mm Hg (AUC = 0.73; P = 0.04) with VPW ≤67 mm demonstrating 71% sensitivity (95% CI 30 to 95%) and 68% specificity (95% CI 59 to 75%). For discriminating a hydrostatic component of the edema (that is, PAOP ≥18 mm Hg), VPW ≥72 mm demonstrated 61.4% sensitivity (95% CI 47 to 74%) and 61% specificity (49 to 71%) (area under the curve (AUC) 0.69; P = 0.001). Conclusions VPW correlates with PAOP better than CVP in patients with ALI. Due to its only moderate sensitivity and specificity, the ability of VPW to discriminate fluid status in patients with acute lung injury is limited and should only be considered when intravascular pressures are unavailable

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

OP9 is a yet-uncultivated bacterial lineage found in geothermal systems, petroleum reservoirs, anaerobic digesters and wastewater treatment facilities. Here we use single-cell and metagenome sequencing to obtain two distinct, nearly complete OP9 genomes, one constructed from single cells sorted from hot spring sediments and the other derived from binned metagenomic contigs from an in situ-enriched cellulolytic, thermophilic community. Phylogenomic analyses support the designation of OP9 as a candidate phylum for which we propose the name ‘Atribacteria’. Although a plurality of predicted proteins is most similar to those from Firmicutes, the presence of key genes suggests a diderm cell envelope. Metabolic reconstruction from the core genome suggests an anaerobic lifestyle based on sugar fermentation by Embden–Meyerhof glycolysis with production of hydrogen, acetate and ethanol. Putative glycohydrolases and an endoglucanase may enable catabolism of (hemi)cellulose in thermal environments. This study lays a foundation for understanding the physiology and ecological role of the ‘Atribacteria’.United States. National Aeronautics and Space Administration (Exobiology Grant EXO-NNX11AR78G)National Science Foundation (U.S.) (Grant MCB 0546865)National Science Foundation (U.S.) (Grant OISE 0968421)United States. Dept. of Energy (Grant DE-EE-0000716)Nevada Renewable Energy ConsortiumUnited States. Dept. of Energy. Office of Science. Joint Genome Institute (Contract DE-AC02-05CH11231