Theory and Application of Dissociative Electron Capture in Molecular Identification

The coupling of an electron monochromator (EM) to a mass spectrometer (MS) has created a new analytical technique, EM-MS, for the investigation of electrophilic compounds. This method provides a powerful tool for molecular identification of compounds contained in complex matrices, such as environmental samples. EM-MS expands the application and selectivity of traditional MS through the inclusion of a new dimension in the space of molecular characteristics--the electron resonance energy spectrum. However, before this tool can realize its full potential, it will be necessary to create a library of resonance energy scans from standards of the molecules for which EM-MS offers a practical means of detection. Here, an approach supplementing direct measurement with chemical inference and quantum scattering theory is presented to demonstrate the feasibility of directly calculating resonance energy spectra. This approach makes use of the symmetry of the transition-matrix element of the captured electron to discriminate between the spectra of isomers. As a way of validating this approach, the resonance values for twenty-five nitrated aromatic compounds were measured along with their relative abundance. Subsequently, the spectra for the isomers of nitrotoluene were shown to be consistent with the symmetry-based model. The initial success of this treatment suggests that it might be possible to predict negative ion resonances and thus create a library of EM-MS standards.Comment: 18 pages, 7 figure

Virulence Factors of Aeromonas hydrophila: In the Wake of Reclassification

The ubiquitous “jack-of-all-trades,” Aeromonas hydrophila, is a freshwater, Gram-negative bacterial pathogen under revision in regard to its phylogenetic and functional affiliation with other aeromonads. While virulence factors are expectedly diverse across A. hydrophila strains and closely related species, our mechanistic knowledge of the vast majority of these factors is based on the molecular characterization of the strains A. hydrophila AH-3 and SSU, which were reclassified as A. piscicola AH-3 in 2009 and A. dhakensis SSU in 2013. Individually, these reclassifications raise important questions involving the applicability of previous research on A. hydrophila virulence mechanisms; however, this issue is exacerbated by a lack of genomic data on other research strains. Collectively, these changes represent a fundamental gap in the literature on A. hydrophila and confirm the necessity of biochemical, molecular, and morphological techniques in the classification of research strains that are used as a foundation for future research. This review revisits what is known about virulence in A. hydrophila and the feasibility of using comparative genomics in light of this phylogenetic revision. Conflicting data between virulence factors, secretion systems, quorum sensing, and their effect on A. hydrophila pathogenicity appears to be an artifact of inappropriate taxonomic comparisons and/or be due to the fact that these properties are strain-specific. This review audits emerging data on dominant virulence factors that are present in both A. dhakensis and A. hydrophila in order to synthesize existing data with the aim of locating where future research is needed

Impact of alternative footwear on human energy expenditure

Purpose: Use of alternative footwear options such as flip-flop style sandals and minimalist athletic shoes are becoming increasingly popular footwear choices. The purpose of the investigation was to analyze the energy expenditure and oxygen consumption requirements of walking at preferred pace while wearing flip-flops, slip-on style shoes, and minimalist athletic shoes. Methods: Eighteen healthy male adults participated in this study. In addition to an initial familiarization session, participants were tested in three different footwear conditions [thong-style flip-flops (FF), Croc® slip on shoes (CROC), and Vibram Fivefingers® minimalist shoes (MIN)]. Then after a brief warm-up, participants walked a one-mile distance at their preferred pace. Immediately following completion of the one-mile walk, participants stood quietly on the treadmill for an additional period to assess excess post-exercise oxygen consumption (EPOC). Results: A repeated-measures ANOVA that the following variables did not show evidence of a significant differently value between conditions: preferred pace (p = 0.392), average oxygen consumption (p = 0.804), energy expenditure per mile (p = 0.306), or EPOC (p = 0.088). There was shown to be a significantly higher RER during exercise in CROC compared to MIN (p = 0.031) with no significant differences observed when comparing CROC to FF (p = 0.106) or FF to MIN (p = 0.827). Conclusion: Based on the results of the current study, it appears that the alternative footwear selected for evaluation do not lead to a substantial alteration of walking pace or overall EE. However, the significant difference in RER suggesting a slightly elevated exercise intensity while wearing the CROC could perhaps be related to the softer sole, influencing overall mechanical efficiency.The study was funded by a grant awarded by the Graduate Student Council at the author’s University

Expression profiling of human renal carcinomas with functional taxonomic analysis

BACKGROUND: Molecular characterization has contributed to the understanding of the inception, progression, treatment and prognosis of cancer. Nucleic acid array-based technologies extend molecular characterization of tumors to thousands of gene products. To effectively discriminate between tumor sub-types, reliable laboratory techniques and analytic methods are required. RESULTS: We derived mRNA expression profiles from 21 human tissue samples (eight normal kidneys and 13 kidney tumors) and two pooled samples using the Affymetrix GeneChip platform. A panel of ten clustering algorithms combined with four data pre-processing methods identified a consensus cluster dendrogram in 18 of 40 analyses and of these 16 used a logarithmic transformation. Within the consensus dendrogram the expression profiles of the samples grouped according to tissue type; clear cell and chromophobe carcinomas displayed distinctly different gene expression patterns. By using a rigorous statistical selection based method we identified 355 genes that showed significant (p < 0.001) gene expression changes in clear cell renal carcinomas compared to normal kidney. These genes were classified with a tool to conceptualize expression patterns called "Functional Taxonomy". Each tumor type had a distinct "signature," with a high number of genes in the categories of Metabolism, Signal Transduction, and Cellular and Matrix Organization and Adhesion. CONCLUSIONS: Affymetrix GeneChip profiling differentiated clear cell and chromophobe carcinomas from one another and from normal kidney cortex. Clustering methods that used logarithmic transformation of data sets produced dendrograms consistent with the sample biology. Functional taxonomy provided a practical approach to the interpretation of gene expression data

Socioecological Determinants of Drought Impacts and Coping Strategies for Ranching Operations in the Great Plains

In Great Plains rangelands, drought is a recurring disturbance. Ranchers in this region expect to encounter drought but may not be adequately prepared for it. Efforts to encourage drought preparednesswould benefit froma better understanding of the conditions under which managers make decisions to minimize the impacts of drought.We tested the direct andmoderating roles of the drought hazard and the social-ecological context on drought impacts and response. This study was conducted with ranchers in western and central South Dakota and Nebraska following the drought that began in 2012. We surveyed ranchers regarding the effects of the drought and their responses and used multimodel analysis to explore the relationships among measures of drought preparedness, drought response, and drought impacts. Drought severity was the primary predictor of all impacts, but specific types of impacts were varied depending on the operation’s enterprisemix, resources, and management. The socioecological characteristics of the ranch system predicted drought response actions taken, by either providing the necessary resources and capacity to take action or creating sensitivity in the system that required action to be taken. We conclude with recommendations for learning from current drought experiences in order to better adapt to future drought events

SPIRITS 15c and SPIRITS 14buu: Two Obscured Supernovae in the Nearby Star-Forming Galaxy IC 2163

SPIRITS---SPitzer InfraRed Intensive Transients Survey---is an ongoing survey of nearby galaxies searching for infrared (IR) transients with Spitzer/IRAC. We present the discovery and follow-up observations of one of our most luminous ($M_{[4.5]} = -17.1\pm0.4$ mag, Vega) and red ($[3.6] - [4.5] = 3.0 \pm 0.2$ mag) transients, SPIRITS 15c. The transient was detected in a dusty spiral arm of IC 2163 ($D\approx35.5$ Mpc). Pre-discovery ground-based imaging revealed an associated, shorter-duration transient in the optical and near-IR (NIR). NIR spectroscopy showed a broad ($\approx 8400$ km s$^{-1}$), double-peaked emission line of He I at $1.083 \mu$m, indicating an explosive origin. The NIR spectrum of SPIRITS 15c is similar to that of the Type IIb SN 2011dh at a phase of $\approx 200$ days. Assuming $A_V = 2.2$ mag of extinction in SPIRITS 15c provides a good match between their optical light curves. The IR light curves and the extreme $[3.6]-[4.5]$ color cannot be explained using only a standard extinction law. Another luminous ($M_{4.5} = -16.1\pm0.4$ mag) event, SPIRITS 14buu, was serendipitously discovered in the same galaxy. The source displays an optical plateau lasting $\gtrsim 80$ days, and we suggest a scenario similar to the low-luminosity Type IIP SN 2005cs obscured by $A_V \approx 1.5$ mag. Other classes of IR-luminous transients can likely be ruled out in both cases. If both events are indeed SNe, this may suggest $\gtrsim 18\%$ of nearby core-collapse SNe are missed by currently operating optical surveys.Comment: 19 pages, 7 Figures, 4 Table

Long-term Declines in the Size of Northern Fulmar (Fulmarus glacialis) Colonies on Eastern Baffin Island, Canada

We censused three colonies of Northern Fulmars (Fulmarus glacialis) along eastern Baffin Island, Canada, that&nbsp;were estimated to support 155 000 breeding pairs in 1973, but had not been adequately counted since then. The colonies were surveyed in July and August 2018 using photographs taken from a helicopter or a drone. The combined estimated colony sizes were 36 500 pairs, much smaller than historical estimates. Although the 1973 estimates were coarse, this difference represents an apparent 3+% annual decline in numbers at each colony over approximately four decades or more than 87% over three generations (66 years). Several factors may be contributing to these declines, including changes in winter food supplies and the susceptibility of fulmars to fisheries bycatch. We recommend efforts to survey the remaining major fulmar colonies in Arctic&nbsp;Canada to assess the overall population size and trends, and allow for further analyses of potential population drivers.Nous avons recensé trois colonies de fulmars boréaux (Fulmarus glacialis) sur la côte est de l’île de Baffin, au&nbsp;Canada. Selon des estimations réalisées en 1973, 155 000 couples reproducteurs y nichaient, mais aucun dénombrement adéquat n’avait été effectué depuis. Les colonies ont été recensées en juillet et en août 2018 au moyen de photographies prises à partir d’un hélicoptère ou d’un drone. La taille combinée des colonies a été estimée à 36500 couples, soit un nombre beaucoup moins élevé que les estimations précédentes. Bien que les estimations de 1973 étaient des estimations grossières, cette différence représente une baisse annuelle apparente de plus de 3 % à chacune des colonies sur environ quatre décennies, soit plus de 87 % sur trois générations (66 ans). Ces diminutions peuvent être attribuables à plusieurs facteurs, dont les changements caractérisant les approvisionnements en nourriture pendant l’hiver et la susceptibilité des fulmars à faire l’objet de captures accessoires. Nous recommandons que des efforts soient faits pour recenser les grandes colonies de fulmars qui restent dans l’Arctique canadien afin d’évaluer la taille globale de la population et les tendances la caractérisant, ainsi que pour&nbsp;pousser plus loin l’analyse des facteurs susceptibles d’avoir un effet sur leurs populations

Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum

To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that gene family similarity among Bacillus genomes ranges from 32- 90%, with 2,839 genes within the core genome of B. amyloliquefaciens subsp. plantarum. Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization. Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies. To evaluate their role in plant pathogen biocontrol, genes involved in secondary metabolite biosynthesis were deleted in B. amyloliquefaciens subsp. plantarum strain, revealing that difficidin expression is critical in reducing the severity of disease, caused by Xanthomonas axonopodis pv. vesicatoria in tomato plants. This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization