Anthropogenic Effects on Tidal Distortion in a Tidal River

Tidal rivers are landward portions of estuarine systems constituting the union between coastal, tidally controlled settings and rivers, where fluvial processes dominate. In these reaches, river discharge (mean flow) and tides are the two most important mechanisms in controlling geophysical flows. The processes governing water levels and current amplitudes in tidal rivers are highly nonlinear and modulated by external forcings- thus requiring sophisticated techniques for accurate prediction and forecasting. Physical oceanographers and estuarine physicists tend to limit their study area to the maximum extent of the horizontal tide (salinity intrusion), not the most landward point influenced by tidal water levels. This is in part because landward reaches are complicated by freshwater tributary inputs, tidal reflection, abrupt hydrographic changes, and backwater dynamics. Understanding river-tide interaction in tidal rivers is important for geomorphology as this synergism impacts salinity intrusion, sediment transport, pollutant fate, channel bifurcation, and deltaic deposition. This thesis aims to satisfy two objectives: (1) to characterize the Penobscot River Estuarine (PRE) system and present field measurements collected in the tidal river section near the extent of salinity intrusion; and (2) to demonstrate the mechanism creating unexpected overtide patterns near the flood limit. To accomplish these objectives, long-term water levels, meteorological, and river discharge datasets are used in conjunction with measurements collected during a field campaign conducted on September 21st, 2021. The results of this research effort reveal the modulations of the D2 tidal species with respect to mean flow and the emergence of hydrographic tidal reflection as a mechanism for the generation of D6. The discussion presents a theory explaining momentum transfer to the D6 band under high mean flow conditions, where contributions from quadratic friction are known to decrease. This has implications in sediment transport, backwater dynamics, and longitudinal shifts of river-tide dynamics

K-band Spectroscopy of Clusters in NGC 4038/4039

Integral field spectroscopy in the K-band (1.9-2.4um) was performed on four IR-bright star clusters and the two nuclei in NGC 4038/4039 (``The Antennae''). Two of the clusters are located in the overlap region of the two galaxies, and together comprise ~25% of the total 15um and ~10% of the total 4.8 GHz emission from this pair of merging galaxies. The other two clusters, each of them spatially resolved into two components, are located in the northern galaxy, one in the western and one in the eastern loop of blue clusters. Comparing our analysis of Brgamma, CO band-heads, He I (2.058um), Halpha (from archival HST data), and V-K colors with stellar population synthesis models indicates that the clusters are extincted (A_V ~ 0.7 - 4.3 mags) and young, displaying a significant age spread (4-13 Myrs). The starbursts in the nuclei are much older (65 Myrs), with the nucleus of NGC 4038 displaying a region of recent star formation northward of its K-band peak. Using our derived age estimates and assuming the parameters of the IMF (Salpeter slope, upper mass cut-off of 100 M_sun, Miller-Scalo between 1 M_sun and 0.1 M_sun), we find that the clusters have masses between 0.5 and 5 * 10^6M_sun.Comment: 10 pages, 3 figures, ApJ accepte

Pyrite cloning: a single tube and programmed reaction cloning with restriction enzymes

Insertion of engineered DNA fragments into bacterial vectors is the foundation of recombinant DNA technology, yet existing methods are still laborious, require many steps, depend on specific vector configuration, or require expensive reagents. We have developed a method, called “Pyrite” cloning that combines the traditional restriction enzyme digestion and ligation reaction in a single tube and uses a programmed thermocycler reaction, allowing rapid and flexible cloning in a single tube. After the Pyrite reaction and transformation, approximately 50% colonies contain the expected insert, which can be easily and quickly determined by colony PCR or blue-white colony screening. We also demonstrated that Pyrite cloning can be applied for different cloning purposes. The Pyrite cloning method reported here is a single tube and programmed reaction cloning with restriction enzymes. Compared to other cloning methods, Pyrite cloning is flexible, inexpensive, simple, and highly efficient.https://doi.org/10.1186/s13007-018-0359-

Comparison of T-cell Receptor Diversity of people with Myalgic Encephalomyelitis versus controls

Objective: Myalgic Encephalomyelitis (ME; sometimes referred to as Chronic Fatigue Syndrome) is a chronic disease without laboratory test, detailed aetiological understanding or effective therapy. Its symptoms are diverse, but it is distinguished from other fatiguing illnesses by the experience of post-exertional malaise, the worsening of symptoms even after minor physical or mental exertion. Its frequent onset after infection suggests autoimmune involvement or that it arises from abnormal T-cell activation. Results: To test this hypothesis, we sequenced the genomic loci of and T-cell receptors (TCR) from 40 human blood samples from each of four groups: severely affected people with ME; mildly or moderately affected people with ME; people diagnosed with Multiple Sclerosis, as disease controls; and, healthy controls. Seeking to automatically classify these individuals’ samples by their TCR repertoires, we applied P-SVM, a machine learning method. However, despite working well on a simulated data set, this approach did not allow statistically significant partitioning of samples into the four subgroups. Our findings do not support the hypothesis that blood samples from people with ME frequently contain altered T-cell receptor diversity

ISO LWS Spectroscopy of M82: A Unified Evolutionary Model

We present the first complete far-infrared spectrum (43 to 197 um) of M82, the brightest infrared galaxy in the sky, taken with the Long Wavelength Spectrometer of the Infrared Space Observatory (ISO). We detected seven fine structure emission lines, [OI] 63 and 145 um, [OIII] 52 and 88 um, [NII] 122 um, [NIII] 57 um and [CII] 158 um, and fit their ratios to a combination starburst and photo-dissociation region (PDR) model. The best fit is obtained with HII regions with n = 250 cm^{-3} and an ionization parameter of 10^{-3.5} and PDRs with n = 10^{3.3} cm^{-3} and a far-ultraviolet flux of G_o = 10^{2.8}. We applied both continuous and instantaneous starburst models, with our best fit being a 3-5 Myr old instantaneous burst model with a 100 M_o cut-off. We also detected the ground state rotational line of OH in absorption at 119.4 um. No excited level OH transitions are apparent, indicating that the OH is almost entirely in its ground state with a column density ~ 4x10^{14} cm^{-2}. The spectral energy distribution over the LWS wavelength range is well fit with a 48 K dust temperature and an optical depth, tau_{Dust} proportional to lambda^{-1}.Comment: 23 pages, 4 figures, accepted by ApJ, Feb. 1, 199

Influence of Precipitation and Crop Germination on Resource Selection by Mule Deer (\u3ci\u3eOdocoileus hemionus\u3c/i\u3e) in Southwest Colorado

Mule deer (Odocoileus hemionus) populations in the western United States provide many benefits to local economies but can also cause considerable damage to agriculture, particularly damage to lucrative crops. Limited information exists to understand resource selection of mule deer in response to annual variation in crop rotation and climatic conditions. We tested the hypothesis that mule deer select certain crops, and in particular sunflower, based on annual climatic variability. Our objective was to use movements, estimates of home range, and resource selection analysis to identify resources selected by mule deer. We used annually-derived crop-specific datasets along with Global Positioning System collars to monitor 14 mule deer in an agricultural area near public lands in southwestern Colorado, USA. We estimated home ranges for two winter seasons that ranged between 7.68 and 9.88 km2, and for two summer seasons that ranged between 5.51 and 6.24 km2. Mule deer selected areas closer to forest and alfalfa for most periods during 2012, but selected areas closer to sunflower in a majority of periods during 2013. Considerable annual variation in climate patterns and precipitation levels appeared to influence selection by mule deer because of variability in crop rotation and success of germination of specific crops

High-excitation OH and H_2O lines in Markarian 231: the molecular signatures of compact far-infrared continuum sources

The ISO/LWS far-infrared spectrum of the ultraluminous galaxy Mkn 231 shows OH and H_2O lines in absorption from energy levels up to 300 K above the ground state, and emission in the [O I] 63 micron and [C II] 158 micron lines. Our analysis shows that OH and H_2O are radiatively pumped by the far-infrared continuum emission of the galaxy. The absorptions in the high-excitation lines require high far-infrared radiation densities, allowing us to constrain the properties of the underlying continuum source. The bulk of the far-infrared continuum arises from a warm (T_dust=70-100 K), optically thick (tau_100micron=1-2) medium of effective diameter 200-400 pc. In our best-fit model of total luminosity L_IR, the observed OH and H2O high-lying lines arise from a luminous (L/L_IR~0.56) region with radius ~100 pc. The high surface brightness of this component suggests that its infrared emission is dominated by the AGN. The derived column densities N(OH)>~10^{17} cm^{-2} and N(H_2O)>~6x10^{16} cm^{-2} may indicate XDR chemistry, although significant starburst chemistry cannot be ruled out. The lower-lying OH, [C II] 158 micron, and [O I] 63 micron lines arise from a more extended (~350 pc) starburst region. We show that the [C II] deficit in Mkn 231 is compatible with a high average abundance of C+ because of an extreme overall luminosity to gas mass ratio. Therefore, a [C II] deficit may indicate a significant contribution to the luminosity by an AGN, and/or by extremely efficient star formation.Comment: 16 pages, 6 figures, accepted for publication in The Astrophysical Journa

Intimal smooth muscle cells are a source but not a sensor of anti-inflammatory CYP450 derived oxylipins

AbstractVascular pathologies are associated with changes in the presence and expression of morphologically distinct vascular smooth muscle cells. In particular, in complex human vascular lesions and models of disease in pigs and rodents, an intimal smooth muscle cell (iSMC) which exhibits a stable epithelioid or rhomboid phenotype in culture is often found to be present in high numbers, and may represent the reemergence of a distinct developmental vascular smooth muscle cell phenotype. The CYP450-oxylipin - soluble epoxide hydrolase (sEH) pathway is currently of great interest in targeting for cardiovascular disease. sEH inhibitors limit the development of hypertension, diabetes, atherosclerosis and aneurysm formation in animal models. We have investigated the expression of CYP450-oxylipin-sEH pathway enzymes and their metabolites in paired intimal (iSMC) and medial (mSMC) cells isolated from rat aorta. iSMC basally released significantly larger amounts of epoxy-oxylipin CYP450 products from eicosapentaenoic acid > docosahexaenoic acid > arachidonic acid > linoleic acid, and expressed higher levels of CYP2C12, CYP2B1, but not CYP2J mRNA compared to mSMC. When stimulated with the pro-inflammatory TLR4 ligand LPS, epoxy-oxylipin production did not change greatly in iSMC. In contrast, LPS induced epoxy-oxylipin products in mSMC and induced CYP2J4. iSMC and mSMC express sEH which metabolizes primary epoxy-oxylipins to their dihydroxy-counterparts. The sEH inhibitors TPPU or AUDA inhibited LPS-induced NFκB activation and iNOS induction in mSMC, but had no effect on NFκB nuclear localization or inducible nitric oxide synthase in iSMC; effects which were recapitulated in part by addition of authentic epoxy-oxylipins. iSMCs are a rich source but not a sensor of anti-inflammatory epoxy-oxylipins. Complex lesions that contain high levels of iSMCs may be more resistant to the protective effects of sEH inhibitors

Design of nucleotide-mimetic and non-nucleotide inhibitors of the translation initiation factor eIF4E: Synthesis, structural and functional characterisation.

Eukaryotic translation initiation factor 4E (eIF4E) is considered as the corner stone in the cap-dependent translation initiation machinery. Its role is to recruit mRNA to the ribosome through recognition of the 5'-terminal mRNA cap structure (m7GpppN, where G is guanosine, N is any nucleotide). eIF4E is implicated in cell transformation, tumourigenesis, and angiogenesis by facilitating translation of oncogenic mRNAs; it is thus regarded as an attractive anticancer drug target. We have used two approaches to design cap-binding inhibitors of eIF4E by modifying the N7-substituent of m7GMP and replacing the phosphate group with isosteres such as squaramides, sulfonamides, and tetrazoles, as well as by structure-based virtual screening aimed at identifying non-nucleotide cap-binding antagonists. Phosphomimetic nucleotide derivatives and highly ranking virtual hits were evaluated in a series of in vitro and cell-based assays to identify the first non-nucleotide eIF4E cap-binding inhibitor with activities in cell-based assays, N-[(5,6-dihydro-6-oxo-1,3-dioxolo[4,5-g]quinolin-7-yl)methyl]-N'-(2-methyl-propyl)-N-(phenyl-methyl)thiourea (14), including down-regulation of oncogenic proteins and suppression of RNA incorporation into polysomes. Although we did not observe cellular activity with any of our modified m7GMP phosphate isostere compounds, we obtained X-ray crystallography structures of three such compounds in complex with eIF4E, 5'-deoxy-5'-(1,2-dioxo-3-hydroxycyclobut-3-en-4-yl)amino-N7-methyl-guanosine (4a), N7-3-chlorobenzyl-5'-deoxy-5'-(1,2-dioxo-3-hydroxy-cyclobut-3-en-4-yl)amino-guanosine (4f), and N7-benzyl-5'-deoxy-5'-(trifluoromethyl-sulfamoyl)guanosine (7a). Collectively, the data we present on structure-based design of eIF4E cap-binding inhibitors should facilitate the optimisation of such compounds as potential anticancer agents