Spectroscopic Studies of Fluoranthene and 3-Nitrofluoranthene

Polycyclic aromatic hydrocarbons (PAHs) are known byproducts of anthropogenic sources including incomplete combustion of fossil fuels. They are known to be teratogenic, mutagenic and carcinogenic. This study investigated the spectral properties of fluoranthene and 3- nitrofluoranthene using NMR, UV-Vis and infrared techniques. The acquisition of spectral data provides a means to identify these compounds in mixtures and can be used which to develop model formulae for quantitation. A 2-D NMR method (HMQC ) was used for assigning 13C peaks. The infrared spectrum for 3-nitrofluoranthene showed characteristic strong absorption peaks at 1323 and 1516 cm-1 assigned to symmetric/asymmetric nitro stretches, respectively. UV– vis characterization showed a bathochromic shift. This finding supports a degree of nitro group planarity with the fluoranthene moiety; in agreement with the finding that planar molecules exhibit greater mutagenicity when introduced into biological systems. The structure, then, is of paramount importance in understanding the molecule’s biological effects on cells

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

<p>Abstract</p> <p>Background</p> <p>Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels?</p> <p>Results</p> <p>We reconstruct the infrageneric phylogeny of <it>Pinus </it>from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve <it>Pinus</it>, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (<it>ycf</it>1, <it>ycf</it>2), highlighting their unusual evolutionary properties.</p> <p>Conclusion</p> <p>Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling, such as phylogeographic analyses and species-level DNA barcoding.</p

A Choice of Weapons : The X-Men and the Metaphor for Approaches to Racial Equality

The authors explore The X-Men comic as a metaphor for both racial discrimination in the United States and strategies for addressing such discrimination. In consideration of the recent rise in the shooting of people of color, particular African American men and women, at the hands of law enforcement officers, an increasingly vocal and aggrieved segment of the white populace in the form of the “alt right,” and a presidential candidate that both implicitly and explicitly deploys “law and order” and racist appeals for particular social and political changes, we appear to once again stand at an important crossroads in American history. In consideration of the social upheavals of the 1960s, these choices are, however, not new and have been well-detailed in graphic novels and comic books, such as The X-Men. These popular representations gesture toward an important question: Which approach (peace or violence) is best, particularly in light of the current struggle for racial equality in the United States? In Part I, the authors provide a basic analysis of how The X-Men deliver a metaphor for race, bias, and discrimination. In Part II, the authors parse the ideology and methods of Magneto, chief antagonist in the X-Men, as a metaphor for Malcolm X and the Black Power/Black Nationalist approach. In Part III, the authors parse the ideology and methods of Professor Xavier, chief protagonist in the X-Men, as a metaphor for Martin Luther King, Jr. and the civil rights movement approach. The authors conclude by speculating as to which approach would be best for African American advancement today

Design Memo 16-04: Designer Summary of Required Utility Relocations - Project Design and Utility Summary

This session covers the effective use of all the tools necessary to understand the intent and application of the design memo requirement for designers, utility coordinators, and project managers. We will share candid experiences from consultant and project-owner perspectives. Understanding who owns the real risk of utility location data, going beyond 811, design flexibility options, subsurface utility engineering (SUE), constructability, and developing partnerships with each utility are essential elements in meeting this requirement

Plastome phylogenomics in the genus Pinus using massively parallel sequencing technology

This thesis summarizes work completed over the previous four years primarily focusing on chloroplast phylogenomic inquiry into the genus Pinus and related Pinaceae outgroups using next-generation sequencing on Illumina platforms. During the time of our work, Illumina sequence read lengths have essentially been limited to 25 to 100 base pairs, presenting challenges when trying to assemble genomic space featuring repetitive regions or regions divergent from established reference genomes. Our assemblies initially relied on previously constructed high quality plastome sequences for each of the two Pinus subgenera, yet we were able to show clear negative trends in assembly success as divergence from reference sequences. This was most evident in assemblies of Pinaceae outgroups, but the trend was also apparent within Pinus subgenera. To counter this problem, we used a combination of de novo and reference-guided assembly approaches, which allowed us to more effectively assemble highly divergent regions. From a biological standpoint, our initial focus was on increasing phylogenetic resolution by using nearly complete plastome sequences from select Pinus and Pinaceae outgroup species. This effort indeed resulted in greatly increased phylogenetic resolution as evidenced by a nearly 60-fold increase in parsimony informative positions in our dataset as compared to previous datasets comprised of only several chloroplast loci. In addition, bootstrap support levels across the resulting phylogenetic tree were consistently high, with ≥95% bootstrap support at 30/33 ingroup nodes in maximum likelihood analysis. A positive correlation between the length/amount of sequence data applied to our phylogeny and overall bootstrap support values was also supported, although trends indicated some nodes would likely remain recalcitrant even with the application of complete plastomes. This correlation was important to demonstrate, as it was reflective of trends seen in a meta-analysis of contemporary, infrageneric chloroplast-based phylogenies. In addition, our meta-analysis indicated that most researchers rely on relatively small regions of the chloroplast genome in these studies and obtain relatively little in resolution and support in resulting phylogenies. Clearly, the application of plastome sequences to these types of analyses has great potential for increasing our understanding of evolutionary relationships at low taxonomic levels. An unexpected finding of this work involved two putative protein-coding regions in the chloroplast, ycf1 and ycf2, which featured strongly elevated rates of mutation, and together accounted for over half of exon parsimony informative sites although making up only 22% of exon sequence length. Of these two loci, clearly ycf1 was more problematic to assemble from short read data, as it featured numerous indels as well as several repetitive regions. We designed primers based on conserved regions allowing essentially complete amplification of this locus and sequenced the ycf1 locus (with Sanger technology) for a representative of each of the 11 Pinus subsections, using accessions from the previous study. Importantly, these primers were also effective across Pinaceae and should facilitate future work throughout the family. Accessions with full ycf1 sequences were in turn utilized as subsectional references as we sequenced and assembled plastomes for most of the remaining Pinus species. To efficiently produce these sequences, we relied on a solution-based hybridization strategy developed by Richard Cronn to enrich preparations of total genomic DNA for chloroplast-specific DNA. While the phylogenetic results of a full-plastome, full-genus analysis were certainly of interest, our final focus was on the investigation of ‘noise’ in our dataset, and whether it affected phylogenetic conclusions drawn from the plastome. To determine this, we explored the removal of variable sites from our alignment and the resultant effect on topology and resolution. This allowed us to identify a window of alignment partitions in which nodal bootstrap support remained high across the genus, yet sufficient noise was removed to identify important patterns in the positioning of three clades with historically problematic phylogenetic positioning

Netrin-3 Peptide (C-19) is a Chemorepellent and a Growth Inhibitor in \u3cem\u3eTetrahymena thermophila\u3c/em\u3e

The netrins are a family of signaling proteins expressed throughout the animal kingdom. Netrins play important roles in developmental processes such as axonal guidance and angiogenesis. Netrin-1, for example, can act as either a chemoattractant or a chemorepellent for axonal growth cones depending upon the concentration of the protein as well as the cell type. Netrin-1 acts as a growth factor in some cell types and is expressed by some tumor cells. Netrin-3 appears to share some signaling apparatus with netrin-1, but is less widely expressed, and its physiological roles are much less understood. Tetrahymena thermophila are free-living, eukaryotic, ciliated protozoa used as a model system for studying chemorepellents and chemoattractants because their swimming behavior is readily observable under a microscope. We have previously found that netrin-1 peptide acts as a chemorepellent in Tetrahymena thermophila at concentrations ranging from micromolar to nanomolar. However, netrin-1 peptide does not affect growth in Tetrahymena at these concentrations. In our current study, we have found that related peptides, netrin-3 peptide (H-19 and C-19; Santa Cruz Biotechnology), act as chemorepellents in Tetrahymena thermophila at concentrations at or below 1 μg/ml. The same concentration of netrin-3 peptide reduces growth of Tetrahymena cultures by approximately 75%. We are currently conducting further studies to determine the mechanism through which these peptides are signaling