Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.U.S. National Institutes of Health R00-GM087550U.S. National Science Foundation (NSF) DEB-0515729NSF BEACON Center for the Study of Evolution in Action DBI-0939454Cancer Prevention & Research Institute of Texas (CPRIT) RP130124University of Texas at Austin startup fundsUniversity of Texas at AustinCPRIT Cancer Research TraineeshipMolecular Bioscience

Retesting personality in employee selection: Implications of the context, sample, and setting

The present study sought to assess when and how actual job applicants change their responses when filling out an unproctored personality selection assessment for a second time. It was predicted feedback would be a key contextual motivator associated with how much applicants change their answers during the second administration. Mediation results showed that individuals receiving feedback that showed a low score on the personality assessment was the reason they did not get the job were more likely to employ faking response strategies in the second testing session, predicting the highest change in scores between the first and second testing sessions. Individuals receiving no feedback and those not experimentally motivated to fake (i.e., a comparison group of students) showed less change in responses across administrations. © Psychological Reports 2013

Pennsylvania Folklife Vol. 34, No. 3

• Johann Adam Eyer: Lost Fraktur Writer of Hamilton Square • Aunt Lydia • The Image of the Jew in South-Central Pennsylvania • Gertrude Rapp: Harmony Society Abbess • Aldes un Neieshttps://digitalcommons.ursinus.edu/pafolklifemag/1107/thumbnail.jp

An assessment of ozone photochemistry in the extratropical western North Pacific: Impact of continental outflow during the late winter/early spring

This study examines the influence of photochemical processes on tropospheric ozone distributions over the extratropical western North Pacific. The analysis presented ere is based on data collected during the Pacific Exploratory Mission-West Phase B (PEM-West B) field study conducted in February-March 1994. Sampling in the study region involved altitudes of 0-12 km and latitudes of 10°S to 50°N. The extratropical component of the data set (i.e., 20-50°N) was defined by markedly different photochemical environments north and south of 30°N. This separation was clearly defined by an abrupt decrease in the tropopause height near 30°N and a concomitant increase in total O3 column density. This shift in overhead O3 led to highly reduced rates of O3 formation and destruction for the 30-50°N latitude regime. Both latitude ranges, however, stili exhibited net O3 production at all altitudes. Of special significance was the finding that net O3 production prevailed even at boundary layer and lower free tropospheric altitudes (e.g., < 4 km), a condition uncommon to Pacific marine environments. These results reflect the strong impact of continental outflow of O3 precursors (e.g., NO and NMHCs) into the northwestern Pacific Basin. Comparisons with PEM-West A, which sampled the same region in a different season (September-October), revealed major differences at altitudes below 4 km, the altitude range most influenced by continental outflow. The resulting net rate of increase in the tropospheric O3 column for PEM-West B was 1-3% per day, while for PEM-West A it was approximately zero. Unique to the PEM-West B study is the finding that even under wintertime conditions substantial column production of tropospheric O3 can occur at subtropical and mid-latitudes. While such impacts may not be totally unexpected at near coast locations, the present study suggests that the impact from continental outflow on the marine BL could extend out to distances of more than 2000 km from the Asian Pacific Rim

Implications of large scale shifts in tropospheric NOx levels in the remote tropical Pacific

A major observation recorded during NASA's western Pacific Exploratory Mission (PEM-West B) was the large shift in tropical NO levels as a function of geographical location. High-altitude NO levels exceeding 100 pptv were observed during portions of tropical flights 5-8, while values almost never exceeded 20 pptv during tropical flights 9 and 10. The geographical regions encompassing these two flight groupings are here labeled "high" and "low" NOx regimes. A comparison of these two regimes, based on back trajectories and chemical tracers, suggests that air parcels in both were strongly influenced by deep convection. The low NOx regime appears to have been predominantly impacted by marine convection, whereas the high NOx regime shows evidence of having been more influenced by deep convection over a continental land mass. DMSP satellite observations point strongly toward lightning as the major source of NOx in the latter regime. Photochemical ozone formation in the high NOx regime exceeded that for low NOx by factors of 2 to 6, whereas O3 destruction in the low NOx regime exceeded that for high NOx by factors of up to 3. Taking the tropopause height to be 17 km, estimates of the net photochemical effect on the O3 column revealed that the high NOx regime led to a small net production. By contrast, the low NOx regime was shown to destroy O3 at the rate of 3.4% per day. One proposed mechanism for off-setting this projected large deficit would involve the transport of O3 rich midlatitude air into the tropics. Alternatively, it is suggested that O3 within the tropics may be overall near self-sustaining with respect to photochemical activity. This scenario would require that some tropical regions, unsampled at the time of PEM-B, display significant net column O3 production, leading to an overall balanced budget for the "greater" tropical Pacific basin. Details concerning the chemical nature of such regimes are discussed

Assessment of ozone photochemistry in the western North Pacific as inferred from PEM-West A observations during the fall 1991

This study examines the influence of photochemical processes on ozone distributions in the western North Pacific. The analysis is based on data generated during NASA's western Pacific Exploratory Mission (PEM-West A) during the fall of 1991. Ozone trends were best described in terms of two geographical domains: the western North Pacific rim (WNPR) and the western tropical North Pacific (WTNP). For both geographical regions, ozone photochemical destruction, D(O3), decreased more rapidly with altitude than did photochemical formation, F(O3). Thus the ozone tendency, P(O3), was typically found to be negative for z <6 km and positive for z > 6-8 km. For nearly all altitudes and latitudes, observed nonmethane hydrocarbon (NMHC) levels were shown to be of minor importance as ozone precursor species. Air parcel types producing the largest positive values of P(O3) included fresh continental boundary layer (BL) air and high-altitude (z > 7 km) parcels influenced by deep convection/lightning. Significant negative P(O3) values were found when encountering clean marine BL air or relatively clean lower free-tropospheric air. Photochemical destruction and formation fluxes for the Pacific rim region were found to exceed average values cited for marine dry deposition and stratospheric injection in the northern hemisphere by nearly a factor of 6. This region was also found to be in near balance with respect to column-integrated O3 photochemical production and destruction. By contrast, for the tropical regime column-integrated O3 showed photochemical destruction exceeding production by nearly 80%. Both transport of O3 rich midlatitude air into the tropics as well as very high-altitude (10-17 km) photochemical O3 production were proposed as possible additional sources that might explain this estimated deficit. Results from this study further suggest that during the fall time period, deep convection over Asia and Malaysia/Indonesia provided a significant source of high-altitude NOx to the western Pacific. Given that the high-altitude NOx lifetime is estimated at between 3 and 9 days, one would predict that this source added significantly to high altitude photochemical O3 formation over large areas of the western Pacific. When viewed in terms of strong seasonal westerly flow, its influence would potentially span a large part of the Pacific. Copyright 1996 by the American Geophysical Union

Pennsylvania Folklife Vol. 26, No. 2

• Battalion Day: Militia Exercise and Frolic in Pennsylvania Before the Civil War • Folklore in the Library: Cherished Memories of Old Lancaster • Widows\u27 Wills for Philadelphia County, 1750-1784: A Study of Pennsylvania German Folklife • Forest County Lore • The Big Valley Amish of Central Pennsylvania: A Community of Cultural Contrasts • Maurice A. Mook (1904-1973): An Appreciation • Collectanea: Ore-Mining and Basket-Making in Maxatawny ; The Sharadin Tannery at Kutztown ; Occult Lore Recorded in Cumberland County • German Immigrants in America as Presented in Travel Accounts • The Pie and Related Forms in Pennsylvania Cuisine: Folk-Cultural Questionnaire No. 46https://digitalcommons.ursinus.edu/pafolklifemag/1071/thumbnail.jp

Regional-scale chemical transport modeling in support of the analysis of observations obtained during the TRACE-P experiment

Data obtained during the TRACE-P experiment is used to evaluate how well the CFORS/STEM-2K1 regional-scale chemical transport model is able to represent the aircraft observations. Thirty-one calculated trace gas and aerosol parameters are presented and compared to the in situ data. The regional model is shown to accurately predict many of the important features observed. The mean values of all the model parameters in the lowest 1 km are predicted within ±30% of the observed values. The correlation coefficients (R) for the meteorological parameters are found to be higher than those for the trace species. For example, for temperature, R \u3e 0.98. Among the trace species, ethane, propane, and ozone show the highest values (0.8 \u3c R \u3c 0.9), followed by CO, SO2, and NOy, NO and NO2 had the lowest values (R \u3c 0.4). Analyses of pollutant transport into the Yellow Sea by frontal events are presented and illustrate the complex nature of outflow. Biomass burning from SE Asia is transported in the warm conveyor belt at altitudes above ∼2 km and at latitudes below 30N. Outflow of pollution emitted along the east coast of China in the postfrontal regions is typically confined to the lower ∼2 km and results in high concentrations with plume-like features in the Yellow Sea. During these situations the model underpredicts CO and black carbon (among other species). An analysis of ozone production in this region is also presented. In and around the highly industrialized regions of East Asia, where fossil fuel usage dominates, ozone is NMHC-limited. South of ∼30-35N, ozone production is NOx-limited, reflecting the high NMHC/NOx ratios due to the large contributions to the emissions from biomass burning, biogenics sources, and biofuel usage in central China and SE Asia. Copyright 2003 by the American Geophysical Union

Pennsylvania Folklife Vol. 19, No. 1

• The Moravian Settlements of Pennsylvania in 1757: The Nicholas Garrison Views • The San Rocco Festival at Aliquippa, Pennsylvania: A Transplanted Tradition • Amish Genealogy: A Progress Report • Pulpit Humor in Central Pennsylvania • The Pre-Metric Foot and its Use in Pennsylvania German Architecture • Mennonite Contacts Across the Atlantic: The Van der Smissen Letter of 1838 • Bread, Baking, and the Bakeoven: Folk-Cultural Questionnaire No. 13https://digitalcommons.ursinus.edu/pafolklifemag/1037/thumbnail.jp