Mapping the Space of Genomic Signatures

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to $k$ (herein $k=9$) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence homology and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information.Comment: 14 pages, 7 figures. arXiv admin note: substantial text overlap with arXiv:1307.375

Transcript abundance of photorhabdus insect-related (Pir) toxin in Manduca sexta and Galleria mellonella infections

In this study, we assessed pirAB toxin transcription in Photorhabdus luminescens laumondii (strain TT01) (Enterobacteriaceae) by comparing mRNA abundance under in vivo and in vitro conditions. In vivo assays considered both natural and forced infections with two lepidopteran hosts: Galleria mellonella and Manduca sexta. Three portals of entry were utilized for the forced infection assays: (a) integument; (b) the digestive route (via mouth and anus); and (c) the tracheal route (via spiracles). We also assessed plu4093-2 transcription during the course of a natural infection; this is when the bacteria are delivered by Heterorhabditis bacteriophora nematodes. Transcript abundance in G. mellonella was higher than in M. sexta at two of the observed time points: 15 and 18 h. Expression of pirAB plu4093-2 reached above endogenous control levels at 22 h in G. mellonella but not in M. sexta. Overall, pirAB plu4093-2 transcripts were not as highly expressed in M. sexta as in G. mellonella, from 15 to 22 h. This is the first study to directly compare pirAB plu4093-2 toxin transcript production considering different portals of entry

Deep ACS Imaging in the Globular Cluster NGC 6397: The Cluster Color Magnitude Diagram and Luminosity Function

We present the CMD from deep HST imaging in the globular cluster NGC 6397. The ACS was used for 126 orbits to image a single field in two colors (F814W, F606W) 5 arcmin SE of the cluster center. The field observed overlaps that of archival WFPC2 data from 1994 and 1997 which were used to proper motion (PM) clean the data. Applying the PM corrections produces a remarkably clean CMD which reveals a number of features never seen before in a globular cluster CMD. In our field, the main sequence stars appeared to terminate close to the location in the CMD of the hydrogen-burning limit predicted by two independent sets of stellar evolution models. The faintest observed main sequence stars are about a magnitude fainter than the least luminous metal-poor field halo stars known, suggesting that the lowest luminosity halo stars still await discovery. At the bright end the data extend beyond the main sequence turnoff to well up the giant branch. A populous white dwarf cooling sequence is also seen in the cluster CMD. The most dramatic features of the cooling sequence are its turn to the blue at faint magnitudes as well as an apparent truncation near F814W = 28. The cluster luminosity and mass functions were derived, stretching from the turn off down to the hydrogen-burning limit. It was well modeled with either a very flat power-law or a lognormal function. In order to interpret these fits more fully we compared them with similar functions in the cluster core and with a full N-body model of NGC 6397 finding satisfactory agreement between the model predictions and the data. This exercise demonstrates the important role and the effect that dynamics has played in altering the cluster IMF.Comment: 43 pages including 4 tables and 12 diagrams. Figures 2 and 3 have been bitmapped. Accepted for publication in the Astronomical Journa

The Limits of Literary Language: Linguistic Skepticism and Literary Experiment in Postwar Germany and Austria

This dissertation addresses the concurrent revival of experimental writing and linguistic skepticism in West Germany and Austria after 1945, concentrating on the work of Helmut HeiÃ?enbüttel, Konrad Bayer, Peter Handke, and Rolf Dieter Brinkmann. While the immediate postwar years gave rise to a germanophone literature that was largely intolerant of formal experimentation--due to widespread adherence to a neo-Sartrean model of littérature engagée and a restorationist return to classical form--certain writers began to oppose this aesthetic conservatism in the early fifties. Influenced by international avant-garde developments--from concrete poetry to the nouveau roman--they developed a new form of German writing that actively experimented with literary and linguistic form. Their work was often accompanied by a sophisticated theoretical critique of language, connecting back via Wittgenstein and Whorf to the turn-of-the-century Sprachkrise and the writings of Mauthner and Hofmannsthal. I aim to offer an analysis of this language-skeptical approach to writing, showing how it was employed to create a cultural space for avant-garde literature in the postwar period--presenting experimental writing as a legitimate intellectual endeavor with tangible social value, despite its running contrary to prevalent models of politically engaged or formally conservative writing. Against the common literary-historical view of the sixties as the decade of the politicization of literature, I aim to show the existence of an alternate track of linguistic aesthetics propagated almost exclusively by writers of experimental literature, developing in the fifties and extending through the sixties and beyond. For these writers, a skeptical and analytical treatment of language became the necessary starting point for any progressive literature. I also aim to show how later writers like Handke and Brinkmann came to see this linguistic skepticism as en encumbering limitation of literary possibility. In their early-seventies work, which is often grouped with the movement of New Subjectivity, these writers adopt a pragmatic model of language as a flawed but functional tool for the communication of subjective experience, resulting in a writing that continues to explore the ambiguous link between word and world

Combining Information from Two Surveys to Estimate County-Level Prevalence Rates of Cancer Risk Factors and Screening

Cancer surveillance requires estimates of the prevalence of cancer risk factors and screening for small areas such as counties. Two popular data sources are the Behavioral Risk Factor Surveillance System (BRFSS), a telephone survey conducted by state agencies, and the National Health Interview Survey (NHIS), an area probability sample survey conducted through face-to-face interviews. Both data sources have advantages and disadvantages. The BRFSS is a larger survey, and almost every county is included in the survey; but it has lower response rates as is typical with telephone surveys, and it does not include subjects who live in households with no telephones. On the other hand, the NHIS is a smaller survey, with the majority of counties not included; but it includes both telephone and non-telephone households and has higher response rates. A preliminary analysis shows that the distributions of cancer screening and risk factors are different for telephone and non-telephone households. Thus, information from the two surveys may be combined to address both nonresponse and noncoverage errors. A hierarchical Bayesian approach that combines information from both surveys is used to construct county-level estimates. The proposed model incorporates potential noncoverage and nonresponse biases in the BRFSS as well as complex sample design features of both surveys. A Markov Chain Monte Carlo method is used to simulate draws from the joint posterior distribution of unknown quantities in the model based on the design-based direct estimates and county-level covariates. Yearly prevalence estimates at the county level for 49 states, as well as for the entire state of Alaska and the District of Columbia, are developed for six outcomes using BRFSS and NHIS data from the years 1997-2000. The outcomes include smoking and use of common cancer screening procedures. The NHIS/BRFSS combined county-level estimates are substantially different from those based on BRFSS alone

HISTORY FROM THE MIDDLE: THE STUDENT INTERPRETERS CORPS AND IMAGINED AMERICAN ECONOMIC IMPERIALISM IN CHINA, 1902-1941

The project of American economic imperialism in China during the first half of the twentieth century was first and foremost an imagined enterprise. This dissertation examines the role of the Student Interpreters Corps (SIC) in this endeavor. Studying language-trained intermediaries, this treatment is a first step towards studying history with an approach that is neither top-down nor bottom-up but rather middle-outward. Examining hitherto neglected personnel records and State Department correspondence, this study reveals the SIC as part of an imagined but unsuccessful program of economic imperialism. Although effective in garnering American business interest and support for Foreign Service reform and expansion, efforts to entice American merchants and companies to enter Asian markets (particularly in China) failed to yield a coherent, successful trade empire. However, the largely unstated goal of increased American power was achieved as the result of a bureaucratic imperative for specialization, professionalization, and institutional expansion set in motion during the establishment of the SIC. Examining the evolving roles and views of SIC-trained intermediaries, this dissertation finds that while the imagined trade empire failed to materialize, the SIC contributed to a developing American perception of China that envisioned increasingly greater American intervention in East Asia. In this millieu, a “Peking” order emerged by the mid-1920s that became influential in American East Asia policy towards the eve of Word War II that saw China as vital to American interests. Established as precursor of American economic empire in China, the SIC was instrumental in shifting discourse away from economic empire towards an interventionist American Orientalism. Trade expansion rhetoric waned and Orientalist language solidified as Japanese aggression became more blatant and the ascendance of Communism in China ever more certain. Highlighting the bureaucratic intermediaries as new method of studying history, this study indicates that the project of American economic imperialism was largely imagined, but one that transformed to accommodate evolving visions of expanding American power in East Asia. These conclusions offer new challenges to and opportunities for scholars of American foreign relations

Thus Saith the Lord : The Theological Rhetoric of Dr. Martin Luther King, Jr.

This text seeks to explain the rhetorical appeals that Martin Luther King, Jr. used to persuade his audience of the fundamental truths of human dignity, sin, justice, and hope