Vegetation succession and pedogenesis on the Yukon-Kuskokwim Delta near St. Mary's, Alaska

Thesis (M.S.) University of Alaska Fairbanks, 2015Arctic lowlands of Alaska are known to contain large stores of soil organic carbon (SOC) in organic-rich wetland systems and in the permafrost. Vegetation succession that follows floodplain and wetland development strongly affects the organic carbon stores and distribution of permafrost. Due to recent climate warming there has been losses of permafrost, and much of the SOC stored in Arctic lowlands is at risk for transfer within the global carbon budget. The vast Arctic lowland system in western Alaska is within the zone of discontinuous permafrost. It is anticipated to lose most of the permafrost within this century, yet it is inadequately studied due to the lack of road system connecting the region. This study is the first designed to explore the relationships between vegetation succession and soil development at different stages of sediment deposition. The study area is near St. Mary's at the north part of the Yukon-Kuskokwim Coastal Plain in western Alaska. Soil development is weak due to frequent flooding events and prolonged saturation. The irregular distribution of organic carbon and detritus, silt dominated particle size distribution, and nearly uniform composition of clay minerals with depth attest the alluvial deposition due to flooding events. Cryaquents were found in poor to very-poorly drained raised alluvial bars, Cryaquepts were found on somewhat poorly drained levees, Historthels were found on an abandoned floodplain, and Cryofibrists in very poorly drained depressions. Carbon stores range from 27.7 kg C m⁻² on raised alluvial bars and levees and 40.9 to 45.3 kg C m⁻² on oxbow depressions and the abandoned floodplain. It is crucial to have reliable measurements of SOC stores in order to estimate the potential impact of climate change on the global carbon budget. Soil development and nutrient level in response to vegetation succession are also reported for the area near St. Mary's, Alaska to add to the current understanding of soils in the region and the global carbon budget

CFD and aeroelastic analysis of the MEXICO wind turbine

This paper presents an aerodynamic and aeroelastic analysis of the MEXICO wind turbine, using the compressible HMB solver of Liverpool. The aeroelasticity of the blade, as well as the effect of a low-Mach scheme were studied for the zero-yaw 15m/s wind case and steady- state computations. The wake developed behind the rotor was also extracted and compared with the experimental data, using the compressible solver and a low-Mach scheme. It was found that the loads were not sensitive to the Mach number effects, although the low-Mach scheme improved the wake predictions. The sensitivity of the results to the blade structural properties was also highlighted

Purification of plasmid DNA for use in human gene therapy

Two key issues defined the focus of this research in manufacturing plasmid DNA for use In human gene therapy. First, the processing of E.coli bacterial cells to effect the separation of therapeutic plasmid DNA from cellular debris and adventitious material. Second, the affinity purification of the plasmid DNA in a Simple one-stage process. The need arises when considering the concerns that have been recently voiced by the FDA concerning the scalability and reproducibility of the current manufacturing processes in meeting the quality criteria of purity, potency, efficacy, and safety for a recombinant drug substance for use in humans. To develop a preliminary purification procedure, an EFD cross-flow micro-filtration module was assessed for its ability to effect the 20-fold concentration, 6-time diafiltration, and final clarification of the plasmid DNA from the subsequent cell lysate that is derived from a 1 liter E.coli bacterial cell culture. Historically, the employment of cross-flow filtration modules within procedures for harvesting cells from bacterial cultures have failed to reach the required standards dictated by existing continuous centrifuge technologies, frequently resulting in the rapid blinding of the membrane with bacterial cells that substantially reduces the permeate flux. By challenging the EFD module, containing six helical wound tubular membranes promoting centrifugal instabilities known as Dean vortices, with distilled water between the Dean number's of 187Dn and 818Dn,and the transmembrane pressures (TMP) of 0 to 5 psi. The data demonstrated that the fluid dynamics significantly influenced the permeation rate, displaying a maximum at 227Dn (312 Imh) and minimum at 818Dn (130 Imh) for a transmembrane pressure of 1 psi. Numerical studies indicated that the initial increase and subsequent decrease resulted from a competition between the centrifugal and viscous forces that create the Dean vortices. At Dean numbers between 187Dn and 227Dn , the forces combine constructively to increase the apparent strength and influence of the Dean vortices. However, as the Dean number in increases above 227 On the centrifugal force dominates the viscous forces, compressing the Dean vortices into the membrane walls and reducing their influence on the radial transmembrane pressure i.e. the permeate flux reduced. When investigating the action of the Dean vortices in controlling tile fouling rate of E.coli bacterial cells, it was demonstrated that the optimum cross-flow rate at which to effect the concentration of a bacterial cell culture was 579Dn and 3 psi TMP, processing in excess of 400 Imh for 20 minutes (i.e., concentrating a 1L culture to 50 ml in 10 minutes at an average of 450 Imh). The data demonstrated that there was a conflict between the Dean number at which the shear rate could control the cell fouling, and the Dean number at which tile optimum flux enhancement was found. Hence, the internal geometry of the EFD module was shown to sub-optimal for this application. At 579Dn and 3 psi TMP, the 6-fold diafiltration was shown to occupy 3.6 minutes of process time, processing at an average flux of 400 Imh. Again, at 579Dn and 3 psi TMP the clarification of the plasmid from tile resulting freeze-thaw cell lysate was achieved at 120 Iml1, passing 83% (2,5 mg) of the plasmid DNA (6,3 ng μ-1 10.8 mg of genomic DNA (∼23,00 Obp, 36 ng μ-1 ), and 7.2 mg of cellular proteins (5-100 kDa, 21.4 ngμ-1 ) into the post-EFD process stream. Hence the EFD module was shown to be effective, achieving the desired objectives in approximately 25 minutes. On the basis of its ability to intercalate into low molecular weight dsDNA present in dilute cell lysates, and be electrophoresed through agarose, the fluorophore PicoGreen was selected for the development of a suitable dsDNA assay. It was assesseel for its accuracy, and reliability, In determining the concentration and identity of DNA present in samples that were eleclrophoresed through agarose gels. The signal emitted by intercalated PicoGreen was shown to be constant and linear, and that the mobility of the PicaGreen-DNA complex was not affected by the intercalation. Concerning the secondary purification procedure, various anion-exchange membranes were assessed for their ability to capture plasmid DNA from the post-EFD process stream. For a commercially available Sartorius Sartobind Q15 membrane, the reduction in the equilibriumbinding capacity for  ctDNA in buffer of increasing ionic demonstrated that DNA was being.adsorbed by electrostatic  interactions only. However, the problems associated with fluid distribution across the membrane demonstrated that the membrane housing was the predominant cause of the .erratic breakthrough curves. Consequently, this would need to be rectified before such a membrane could be integrated into the current system, or indeed be scaled beyond laboratory scale. However, when challenged with the process material, the data showed that considerable quantities of protein (1150 μg) were adsorbed preferentially to the plasmid DNA (44 μg). This was also shown for derived Pall Gelman UltraBind US450 membranes that had been functionalised by varying molecular weight poly-L~lysine and polyethyleneimine ligands. Hence the anion-exchange membranes were shown to be ineffective in capturing plasmid DNA from the process stream. Finally, work was performed to integrate a sequence-specific DNA·binding protein into a single-stage DNA chromatography, isolating plasmid DNA from E.coli cells whilst minimising the contamination from genomic DNA and cellular protein. Preliminary work demonstrated that the fusion protein was capable of isolating pUC19 DNA into which the recognition sequence for the fusion-protein had been inserted (pTS DNA) when in the presence of the conditioned process material. Althougth the pTS recognition sequence differs from native pUC19 sequences by only 2 bp, the fusion protein was shown to act as a highly selective affinity ligand for pTS DNA alone. Subsequently, the scale of the process was scaled 25-fold and positioned directly following the EFD system. In conclusion, the integration of the EFD micro-filtration system and zinc-finger affinity purification technique resulted in the capture of approximately 1 mg of plasmid DNA was purified from 1L of E.coli  culture in a simple two stage process, resulting in the complete removal of genomic DNA and 96.7% of cellular protein in less than 1 hour of process time

The Distribution of Lya-Emitting Galaxies at z=2.3

We present the detection of 34 Ly-alpha emission-line galaxy candidates in a 80x80x60 co-moving Mpc region surrounding the known z=2.38 galaxy cluster J2143-4423. The space density of Ly-alpha emitters is comparable to that found by Steidel et al. when targeting a cluster at redshift 3.09, but is a factor of 5.8 +/- 2.5 greater than that found by field samples at similar redshifts. The distribution of these galaxy candidates contains several 5-10 Mpc scale voids. We compare our observations with mock catalogs derived from the VIRGO consortium Lambda-CDM n-body simulations. Fewer than 1% of the mock catalogues contain voids as large as we observe. Our observations thus tentatively suggest that the galaxy distribution at redshift 2.38 contains larger voids than predicted by current models. Three of the candidate galaxies and one previously discovered galaxy have the large luminosities and extended morphologies of "Ly-alpha blobs".Comment: 10 pages, 8 figures, emulateapj5, Accepted for publication in Ap

A Group of Red, Ly-alpha Emitting, High Redshift Galaxies

We have discovered two new high redshift (z=2.38) galaxies, near the previously known z=2.38 galaxy 2139-4434 B1 (Francis et al. 1996). All three galaxies are strong Ly-alpha emitters, and have much redder continuum colors (I-K about 5) than other optically-selected high redshift galaxies. We hypothesize that these three galaxies are QSO IIs; radio-quiet counterparts of high redshift radio galaxies, containing concealed QSO nuclei. The red colors are most easily modelled by an old (> 0.5 Gyr), massive (> 10E11 solar masses) stellar population. If true, this implies that at least one galaxy cluster of mass much greater than 3E11 solar masses had collapsed before redshift five.Comment: 12 pages, 2 figures, uses aaspp4 style file. Accepted for publication in Astrophysical Journal Letter

Mystery of the Lyα Blobs

We present Spitzer Space Telescope observations of the extended Lyman α blobs associated with the z=2.38 over-density J2143-4423, the largest known structure (110 Mpc) above z=2. We detect all 4 of the Lyα blobs in all four IRAC channels and we also detect 3 out of 4 of the blobs with MIPS 24μm. Conversion from rest-wavelength 7μm to total far-infrared luminosity using locally derived correlations suggests all the detected sources are in the class of ULIRGs or even Hyper-LIRGs. We find a weak correlation between Lyα and mid-infrared emission for the Lyα blobs (L_(Lyα)/L_(bol) = 0.05-0.2%). Nearly all Lyα blobs show some evidence for interaction, either in HST imaging, or the proximity of multiple MIPS sources within the Lyα cloud. This suggests that interaction or even mergers may be related to the production of Lyα blobs. Optical through infrared SEDs of the Lyα blobs do not show a clear 1.6μm bump, but rather are indicative of a composite of star formation and AGN energy sources

Ultraviolet-Bright, High-Redshift ULIRGS

We present Spitzer Space Telescope observations of the z=2.38 lya-emitter over-density associated with galaxy cluster J2143-4423, the largest known structure (110 Mpc) above z=2. We imaged 22 of the 37 known lya-emitters within the filament-like structure, using the MIPS 24um band. We detected 6 of the lya-emitters, including 3 of the 4 clouds of extended (>50 kpc) lyman alpha emission, also known as Lya Blobs. Conversion from rest-wavelength 7um to total far-infrared luminosity using locally derived correlations suggests all the detected sources are in the class of ULIRGs, with some reaching Hyper-LIRG energies. Lya blobs frequently show evidence for interaction, either in HST imaging, or the proximity of multiple MIPS sources within the Lya cloud. This connection suggests that interaction or even mergers may be related to the production of Lya blobs. A connection to mergers does not in itself help explain the origin of the Lya blobs, as most of the suggested mechanisms for creating Lya blobs (starbursts, AGN, cooling flows) could also be associated with galaxy interactions.Comment: 12 pages, 3 figures, accepted by ApJ Letter

Polycyclic Aromatic Hydrocarbon Emission within Lyα Blobs

We present Spitzer observations of Lyα blobs (LABs) at z = 2.38-3.09. The mid-infrared ratios (4.5 μm/8 μm and 8 μm/24 μm) indicate that ~60% of LAB infrared counterparts are cool, consistent with their infrared output being dominated by star formation and not active galactic nuclei (AGNs). The rest have a substantial hot dust component that one would expect from an AGN or an extreme starburst. Comparing the mid-infrared to submillimeter fluxes (~850 μm or rest-frame far-infrared) also indicates that a large percentage (~2/3) of the LAB counterparts have total bolometric energy output dominated by star formation, although the number of sources with submillimeter detections or meaningful upper limits remains small (~10). We obtained Infrared Spectrograph (IRS) spectra of six infrared-bright sources associated with LABs. Four of these sources have measurable polycyclic aromatic hydrocarbon (PAH) emission features, indicative of significant star formation, while the remaining two show a featureless continuum, indicative of infrared energy output completely dominated by an AGN. Two of the counterparts with PAHs are mixed sources, with PAH line-to-continuum ratios and PAH equivalent widths indicative of large energy contributions from both star formation and AGN. Most of the LAB infrared counterparts have large stellar masses, around 10^(11) M_⊙. There is a weak trend of mass upper limit with the Lyα luminosity of the host blob, particularly after the most likely AGN contaminants are removed. The range in likely energy sources for the LABs found in this and previous studies suggests that there is no single source of power that is producing all the known LABs