Computational annotation of eukaryotic gene structures: algorithms development and software systems

An important foundation for the advancement of both basic and applied biological science is correct annotation of protein-coding gene repertoires in model organisms. Accurate automated annotation of eukaryotic gene structures remains a challenging, open-ended and critical problem for modern computational biology.;The use of extrinsic (homology) information has been shown as a quite successful strategy for this task, though it is not a perfect solution, for a variety of reasons. More recently, gene prediction methods leveraging information present in syntenic genomic sequences have become favorable, though these too, have limitations.;Identifying genes by inspection of genomic sequence alone thoroughly tests our theoretical understanding of the gene recognition process as it occurs in vivo, and where we encounter failure, excellent opportunities for meaningful research are revealed.;Therefore, the continued development of methods not reliant on homology information---the so-called ab initio gene prediction methods---should help to more rapidly achieve a comprehensive understanding of gene content in our model organisms, at least.;This thesis explores the development of novel algorithms in an attempt to advance the current state-of-the-art in gene prediction, with particular emphasis on ab initio approaches.;The work has been conducted with an eye towards contributing open source, well-documented, and extensible software systems implementing the methods, and to generate novel biological knowledge with respect to plant taxa, in particular

Seasonal and Regional Animal Use of Drainage Structures to Cross Under Roadways

Road drainage structures, hereafter designated culverts, are often used by wildlife and other animals to cross under roadways. However, crossings may vary by species, culvert design, different environmental factors, and land-use and land-cover (LULC) at culvert sites. We monitored 265 culverts located throughout Maryland, USA, with motion-detecting game cameras to assess seasonal and regional effects on culvert crossing rates by wildlife and other animal species considered common to the areas. Northern raccoon (Procyon lotor) and Virginia opossum (Didelphis virginiana) exhibited lower crossing rates in culverts during winter than at other times of the year. We did not detect any difference in seasonal crossings for other species, but several species exhibited similar patterns of lower crossings/culvert/day during winter. We detected more crossings/culvert/day in the Piedmont ecoregion of Maryland for several species associated with farmland and suburbia (e.g., raccoon and red fox [Vulpes vulpes]). In contrast, opossum and free-ranging domestic cat (Felis catus) crossing rates were greater in the Appalachian Mountain ecoregion. The crossing rates for the only bird species we recorded on camera traps, the great blue heron (Ardea herodias), tended to increase from west to east, with its highest crossing rate on the Eastern Shore (lower coastal plain) of Maryland, where these birds are known to be abundant in tidal marshes. Besides a myriad of LULC and structural variables known to affect wildlife and other animal crossing rates, seasonal and regional differences in animal use must also be taken into consideration for culvert design and placement or retrofitting existing culverts to enhance crossings by particular animal species

Anomalous cooling of the massive white dwarf in U Geminorum following a narrow dwarf nova outburst

We obtained Hubble GHRS medium resolution (G160M grating) phase-resolved spectroscopic observations of the prototype dwarf nova U Geminorum during dwarf nova quiescence, 13 days and 61 days following the end of a narrow outburst. The spectral wavelength ranges were centered upon three different line regions: N V (1238\AA, 1242\AA), Si III (1300\AA) and He II (1640\AA). All of the quiescent spectra at both epochs are dominated by absorption lines and show no emission features. The Si III and He II absorption line velocities versus orbital phase trace the orbital motion of the white dwarf but the N~V absorption velocities appear to deviate from the white dwarf motion. We confirm our previously reported low white dwarf rotational velocity, V sin i= 100 km/s. We obtain a white dwarf orbital velocity semi-amplitude K1=107 km/s. Using the gamma-velocity of Wade (1981) we obtain an Einstein redshift of 80.4 km/s and hence a carbon core white dwarf mass of ~1.1 Msun. We report the first subsolar chemical abundances of C and Si for U Gem with C down by 0.05 with respect to the Sun, almost certainly a result of C depletion due to thermonuclear processing. This C-depletion is discussed within the framework of a weak TNR, contamination of the secondary during the common envelope phase, and mixing of C-depleted white dwarf gas with C-depleted matter deposited during a dwarf nova event. Remarkably the Teff of the white dwarf 13 days after outburst is only 32,000K, anomalously cooler than previous early post-outburst measurements. Extensive cooling during an extraordinarily long (210 days) quiescence followed by accretion onto an out-of-equilibrium cooled degenerate could explain the lower Teff.Comment: 16 pages AAS-Latex, 4 Figures, accepted for publication in Ap

Observations and simulations of recurrent novae: U Sco and V394 CrA

Observations and analysis of the Aug. 1987 outburst of the recurrent nova V394 CrA are presented. This nova is extremely fast and its outburst characteristics closely resemble those of the recurrent nova U Sco. Hydrodynamic simulations of the outbursts of recurrent novae were performed. Results as applied to the outbursts of V394 CrA and U Sco are summarized

Observations of classical novae in outburst

The IUE obtained ultraviolet data on novae in outburst. The characteristics of every one of the outbursts are different. Optical and infrared data on many of the same novae were also obtained. Three members of the carbon-oxygen class of novae are presented

The Effect of Two Planting Dates and Methods on Snap Bean (Phaseolus Vulgaris) Production in a Tunnel House

The study was conducted to evaluate the impact of two planting dates and methods on snap bean yields in a tunnel house. The main plots included planting dates March 17 and 31, 2016 for first and second plantings. The sub-plots consisted of planting Method 1 where one seed per hill was planted every 4” apart, and planting Method 2 where three seeds per hill were planted every 12” apart; each treatment combination was replicated four times. The results of the study showed that it took 55 days for the snap beans to be ready for harvest for both planting dates. Also, there were no significant differences in yields between planting dates, and there were no significant differences in yields between planting methods. This notwithstanding, it may appear that Method 2 would better for weed control because the plants will be well spaced compared to Method 1. Keywords: Tunnel House, Snap bean Planting Dates, Snap bean Planting Methods, Snap bean Yield

Higher body weight is associated with lower concentrations of progesterone and estrogen in early pregnancy following in vitro fertilization

To evaluate if body weight impacts progesterone and estradiol concentration levels in early pregnancy in women conceiving following single embryo transfer

Detection of Ocean Glint and Ozone Absorption Using LCROSS Earth Observations

The Lunar CRater Observation and Sensing Satellite (LCROSS) observed the distant Earth on three occasions in 2009. These data span a range of phase angles, including a rare crescent phase view. For each epoch, the satellite acquired near-infrared and mid-infrared full-disk images, and partial-disk spectra at 0.26-0.65 microns (R~500) and 1.17-2.48 microns (R~50). Spectra show strong absorption features due to water vapor and ozone, which is a biosignature gas. We perform a significant recalibration of the UV-visible spectra and provide the first comparison of high-resolution visible Earth spectra to the NASA Astrobiology Institute's Virtual Planetary Laboratory three-dimensional spectral Earth model. We find good agreement with the observations, reproducing the absolute brightness and dynamic range at all wavelengths for all observation epochs, thus validating the model to within the ~10% data calibration uncertainty. Data-model comparisons reveal a strong ocean glint signature in the crescent phase dataset, which is well matched by our model predictions throughout the observed wavelength range. This provides the first observational test of a technique that could be used to determine exoplanet habitability from disk-integrated observations at visible and near-infrared wavelengths, where the glint signal is strongest. We examine the detection of the ozone 255 nm Hartley and 400-700 nm Chappuis bands. While the Hartley band is the strongest ozone feature in Earth's spectrum, false positives for its detection could exist. Finally, we discuss the implications of these findings for future exoplanet characterization missions.Comment: Accepted to The Astrophysical Journal; recalibration data for LCROSS VSP can be found at: https://sites.google.com/site/tdrobinsonscience/science/moo

Sidestream Smoke Extracts from Harm-Reduction and Conventional Camel Cigarettes Inhibit Osteogenic Differentiation via Oxidative Stress and Differential Activation of intrinsic Apoptotic Pathways

Epidemiological studies suggest cigarette smoking as a probable environmental factor for a variety of congenital anomalies, including low bone mass, increased fracture risk and poor skeletal health. Human and animal in vitro models have confirmed hypomineralization of differentiating cell lines with sidestream smoke being more harmful to developing cells than mainstream smoke. Furthermore, first reports are emerging to suggest a differential impact of conventional versus harm-reduction tobacco products on bone tissue as it develops in the embryo or in vitro. To gather first insight into the molecular mechanism of such differences, we assessed the effect of sidestream smoke solutions from Camel (conventional) and Camel Blue (harm-reduction) cigarettes using a human embryonic stem cell osteogenic differentiation model. Sidestream smoke from the conventional Camel cigarettes concentration-dependently inhibited in vitro calcification triggered by high levels of mitochondrially generated oxidative stress, loss of mitochondrial membrane potential, and reduced ATP production. Camel sidestream smoke also induced DNA damage and caspase 9-dependent apoptosis. Camel Blue-exposed cells, in contrast, invoked only intermediate levels of reactive oxygen species insufficient to activate caspase 3/7. Despite the absence of apoptotic gene activation, damage to the mitochondrial phenotype was still noted concomitant with activation of an anti-inflammatory gene signature and inhibited mineralization. Collectively, the presented findings in differentiating pluripotent stem cells imply that embryos may exhibit low bone mineral density if exposed to environmental smoke during development

Functional and morphological plasticity of crocodile (Crocodylus porosus) salt glands

The estuarine crocodile, Crocodylus porosus, inhabits both freshwater and hypersaline waterways and maintains ionic homeostasis by excreting excess sodium and chloride ions via lingual salt glands. In the present study, we sought to investigate the phenotypic plasticity, both morphological and functional, in the lingual salt glands of the estuarine crocodile associated with chronic exposure to freshwater (FW) and saltwater (SW) environments. Examination of haematological parameters indicated that there were no long-term disruptions to ionic homeostasis with prolonged exposure to SW. Maximal secretory rates from the salt glands of SW-acclimated animals (100.8±14.7 µmol 100 g–0.7 body mass h–1) were almost three times greater than those of FW-acclimated animals (31.6±6.2 µmol 100 g–0.7 body mass h–1). There were no differences in the mass-specific metabolic rate of salt gland tissue slices from FW- and SW-acclimated animals (558.9±49.6 and 527.3±142.8 µl O2 g–1 h–1, respectively). Stimulation of the tissue slices from SW-acclimated animals by methacholine resulted in a 33% increase in oxygen consumption rate. There was no significant increase in the metabolic rate of tissues from FW-acclimated animals in response to methacholine. Morphologically, the secretory cells from the salt glands of SW-acclimated animals were larger than those of FW-acclimated animals. In addition, there were significantly more mitochondria per unit volume in secretory tissue from SW-acclimated animals. The results from this study demonstrate that the salt glands of C. porosus are phenotypically plastic, both morphologically and functionally and acclimate to changes in environmental salinity