AMPR/SSMI data comparisons

The AMPR was flown during CAPE and STORMFEST, during which some good data were gathered. Significant instrument noise problems were encountered in both deployments which appear to be temperature related. These are being fixed before the TOGA COARE deployment. New calibration loads have also been manufactured for the TOGA COARE configuration. Eric Smith at FSU had been analyzing the AMPR data and has written a journal article to be submitted early this summer. The emphasis of his work is on the interpretation of low resolution microwave data from space, based upon what we have learned from the high-resolution AMPR signatures

Influence of light on the infection of Aureococcus anophagefferens CCMP 1984 by a “giant virus”

The pelagophyte Aureococcus anophagefferens has caused recurrent brown tide blooms along the northeast coast of the United States since the mid-1980\u27s, and more recently spread to other regions of the globe. These blooms, due to the high cell densities, are associated with severe light attenuation that destroys the sea grass beds which provide the basis for many fisheries. Data collected by transmission electron microscopy, PCR, and metatranscriptomic studies of the blooms, support the hypothesis that large dsDNA viruses play a role in bloom dynamics. While a large (~140 nm) icosahedral virus, with a 371 kbp genome, was first isolated more than a decade ago, the constraints imposed by environmental parameters on bloom infection dynamics by Aureococcus anophagefferens Virus, (AaV) remain unknown. To investigate the role light plays in infection by this virus, we acclimated A. anophagefferens to light intensities of 30 (low), 60 (medium) or 90 μmol photons m-2 s-1 (high) and infected cultures at these irradiance levels. Moreover, we completed light shift experiments where acclimated cultures were exposed to even lower light intensities (0, 5, and 15 μmol photons m-2 s-1) consistent with irradiance found during the peak of the bloom when cell concentrations are highest. The abundance of viruses produced per lytic event (burst size) was lower in the low irradiance acclimated cultures compared to the medium and high acclimated cultures. Transferring infected cultures to more-limiting light availabilities further decreased burst size and increased the length of time it took for cultures to lyse, regardless of acclimation irradiance level. A hypothetical mechanism for the reduced efficiency of the infection cycle in low light due to ribosome biogenesis was predicted from pre-existing transcriptomes. Overall, these studies provide a framework for understanding light effects on infection dynamics over the course of the summer months when A. anophagefferens blooms occur

2010 Convocation

Prelude Music: Balaji Mani, 2006 IMSA Graduate Pledge of Allegiance and Welcome: Shawon Jackson, Student Council President; Dr. Glenn W. Max McGee, President; Dr. Eric McLaren, Principal Featured Piece: Balaji Mani, 2006 IMSA Graduate Keynote Speaker: Dr. Julie Crawford, 1998 IMSA Graduat

Alternative Fourier Expansions for Inverse Square Law Forces

Few-body problems involving Coulomb or gravitational interactions between pairs of particles, whether in classical or quantum physics, are generally handled through a standard multipole expansion of the two-body potentials. We discuss an alternative based on a compact, cylindrical Green's function expansion that should have wide applicability throughout physics. Two-electron "direct" and "exchange" integrals in many-electron quantum systems are evaluated to illustrate the procedure which is more compact than the standard one using Wigner coefficients and Slater integrals.Comment: 10 pages, latex/Revtex4, 1 figure

A Chromosome-Scale Assembly of the Garden Orach (Atriplex hortensis L.) Genome Using Oxford Nanopore Sequencing

Atriplex hortensis (2n = 2x = 18, 1C genome size 1.1 gigabases), also known as garden orach and mountain-spinach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae alliance (Chenopodiaceae sensu stricto, subfam. Chenopodioideae) that has spread in cultivation from its native primary domestication area in Eurasia to other temperate and subtropical regions worldwide. Atriplex L. is a highly complex but, as understood now, a monophyletic group of mainly halophytic and/or xerophytic plants, of which A. hortensis has been a vegetable of minor importance in some areas of Eurasia (from Central Asia to the Mediterranean) at least since antiquity. Nonetheless, it is a crop with tremendous nutritional potential due primarily to its exceptional leaf and seed protein quantities (approaching 30%) and quality (high levels of lysine). Although there is some literature describing the taxonomy and production of A. hortensis, there is a general lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic positioning, and future potential of the species. Here, we report the assembly of the first high-quality, chromosome-scale reference genome for A. hortensis cv. “Golden.” Long-read data from Oxford Nanopore’s MinION DNA sequencer was assembled with the program Canu and polished with Illumina short reads. Contigs were scaffolded to chromosome scale using chromatin-proximity maps (Hi-C) yielding a final assembly containing 1,325 scaffolds with a N50 of 98.9 Mb – with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-six percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy- (32%) and Copia-like (11%) long-terminal repeats. The annotation was completed using MAKER which identified 37,083 gene models and 2,555 tRNA genes. Completeness of the genome, assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) metric, identified 97.5% of the conserved orthologs as complete, with only 2.2% being duplicated, reflecting the diploid nature of A. hortensis. A resequencing panel of 21 wild, unimproved and cultivated A. hortensis accessions revealed three distinct populations with little variation within subpopulations. These resources provide vital information to better understand A. hortensis and facilitate future study

Effects of Three Modest Levels of Proximal Loading on Marathon Pace Running Economy

International Journal of Exercise Science 13(7): 1120-1131, 2020. This study examined the effect of modest increases in proximal body mass on running economy expressed as metabolic cost (MC). External loads of 1.6 (L), 2.4 (M), and 3.2 kg (H) were added to the anterior and posterior torso region of male (n = 18) and female (n = 18) runners using a double-layered compression garment with gel inserts. MC was evaluated using stoichiometry equations of data collected via indirect calorimetry. Data was collected during four, 5-min running bouts at marathon pace for the 3 load levels and an unloaded state (CON). When data from both sexes were combined, MC for CON (13.2 ± 2.7) was lower (p \u3c 0.05) versus L (13.5 ± 2.6), M (13.6 ± 2.6), and H (13.7 ± 2.6 kcal/min), but L did not differ from CON when data was analyzed for each sex. Male runners exhibited stepped increases in MC across loads and a weak-moderate relationship (r = 0.37; p \u3c 0.01) between percentage change in absolute MC and increased percent body mass. A prediction model for MC (∆% kcal/min = 0.98(∆% body mass) – 0.91; SEE = ± 2.5%) was developed. For female runners, L increased MC by ~3.5% above CON, but no differentiation was found among L, M, and H, limiting the development of a prediction equation for females. Modest increases in body mass can produce detectable and potentially important levels of running economy impairment, but the relationship between changes in body mass and RE are complex, particularly in regards to sex

On the Nature of Small Planets around the Coolest Kepler Stars

We constrain the densities of Earth- to Neptune-size planets around very cool (Te =3660-4660K) Kepler stars by comparing 1202 Keck/HIRES radial velocity measurements of 150 nearby stars to a model based on Kepler candidate planet radii and a power-law mass-radius relation. Our analysis is based on the presumption that the planet populations around the two sets of stars are the same. The model can reproduce the observed distribution of radial velocity variation over a range of parameter values, but, for the expected level of Doppler systematic error, the highest Kolmogorov-Smirnov probabilities occur for a power-law index alpha ~ 4, indicating that rocky-metal planets dominate the planet population in this size range. A single population of gas-rich, low-density planets with alpha = 2 is ruled out unless our Doppler errors are >= 5m/s, i.e., much larger than expected based on observations and stellar chromospheric emission. If small planets are a mix of gamma rocky planets (alpha = 3.85) and 1-gamma gas-rich planets (alpha = 2), then gamma > 0.5 unless Doppler errors are >=4 m/s. Our comparison also suggests that Kepler's detection efficiency relative to ideal calculations is less than unity. One possible source of incompleteness is target stars that are misclassified subgiants or giants, for which the transits of small planets would be impossible to detect. Our results are robust to systematic effects, and plausible errors in the estimated radii of Kepler stars have only moderate impact.Comment: Accepted to the Astrophysical Journa

An Economic Analysis of the Appalachian Coal Industry Ecosystem: Summary Report

The decline in the demand for coal has led to significant negative impacts in areas throughout Appalachia. Consider the integrated effects across components of the coal industry ecosystem (CIE). As extraction activity is diminished, there are ripples through the industry supply chain that extends to a wide number of sectors, occupations, and county and multi-county regions of the Appalachian economy. As these suppliers are impacted, jobs are imperiled, and the fiscal health of communities i s weakened. Displaced workers will need to seek alternative employment opportunities that may entail investments in formal education and training, and this takes both time and resources. As the economic base suffers, state and local governments will see their capacity to fund education weaken as well. The decline in natural gas prices and increasing environmental concerns, along with the age of the capital stock, has affected coal-fired power generation in the Appalachian Region. When capacity is replaced by natural gas, the demand for the Region’s coal is further distressed. The shifting structure and spatial location of power generation creates additional impacts on the economic base, tax base, and employment prospects. A vibrant rail transportation infrastructure has developed to support coal-related commerce and this regional asset is now at risk. Retirement of portions of the railroad capital stock may translate into higher transportation costs and diminished opportunities for economic development tied to the movement of bulk commodities, inputs, and final products

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

There is a great need for quantitative assays in measuring proteins. Traditional sandwich immunoassays, largely considered the gold standard in quantitation, are associated with a high cost, long lead time, and are fraught with drawbacks (e.g. heterophilic antibodies, autoantibody interference, 'hook-effect').1 An alternative technique is affinity enrichment of peptides coupled with quantitative mass spectrometry, commonly referred to as SISCAPA (Stable Isotope Standards and Capture by Anti-Peptide Antibodies).2 In this technique, affinity enrichment of peptides with stable isotope dilution and detection by selected/multiple reaction monitoring mass spectrometry (SRM/MRM-MS) provides quantitative measurement of peptides as surrogates for their respective proteins. SRM/MRM-MS is well established for accurate quantitation of small molecules 3, 4 and more recently has been adapted to measure the concentrations of proteins in plasma and cell lysates.5-7 To achieve quantitation of proteins, these larger molecules are digested to component peptides using an enzyme such as trypsin. One or more selected peptides whose sequence is unique to the target protein in that species (i.e. "proteotypic" peptides) are then enriched from the sample using anti-peptide antibodies and measured as quantitative stoichiometric surrogates for protein concentration in the sample. Hence, coupled to stable isotope dilution (SID) methods (i.e. a spiked-in stable isotope labeled peptide standard), SRM/MRM can be used to measure concentrations of proteotypic peptides as surrogates for quantification of proteins in complex biological matrices. The assays have several advantages compared to traditional immunoassays. The reagents are relatively less expensive to generate, the specificity for the analyte is excellent, the assays can be highly multiplexed, enrichment can be performed from neat plasma (no depletion required), and the technique is amenable to a wide array of proteins or modifications of interest.8-13 In this video we demonstrate the basic protocol as adapted to a magnetic bead platform