Evaluation of "shotgun" proteomics for identification of biological threat agents in complex environmental matrixes: experimental simulations

There is currently a great need for rapid detection and positive identification of biological threat agents, as well as microbial species in general, directly from complex environmental samples. This need is most urgent in the area of homeland security, but also extends into medical, environmental, and agricultural sciences. Mass-spectrometry-based analysis is one of the leading technologies in the field with a diversity of different methodologies for biothreat detection. Over the past few years, "shotgun"proteomics has become one method of choice for the rapid analysis of complex protein mixtures by mass spectrometry. Recently, it was demonstrated that this methodology is capable of distinguishing a target species against a large database of background species from a single-component sample or dual-component mixtures with relatively the same concentration. Here, we examine the potential of shotgun proteomics to analyze a target species in a background of four contaminant species. We tested the capability of a common commercial mass-spectrometry-based shotgun proteomics platform for the detection of the target species (Escherichia coli) at four different concentrations and four different time points of analysis. We also tested the effect of database size on positive identification of the four microbes used in this study by testing a small (13-species) database and a large (261-species) database. The results clearly indicated that this technology could easily identify the target species at 20% in the background mixture at a 60, 120, 180, or 240 min analysis time with the small database. The results also indicated that the target species could easily be identified at 20% or 6% but could not be identified at 0.6% or 0.06% in either a 240 min analysis or a 30 h analysis with the small database. The effects of the large database were severe on the target species where detection above the background at any concentration used in this study was impossible, though the three other microbes used in this study were clearly identified above the background when analyzed with the large database. This study points to the potential application of this technology for biological threat agent detection but highlights many areas of needed research before the technology will be useful in real world samples.     

Subject Index of Volume 32

Subject Index

Subject Index of Volume 32     

Application of the multimedia urban model to compare the fate of SOCs in an urban and forested watershed

A multimedia model has been developed to estimate the dynamics of semivolatile organic compounds (SOCs) in urban areas. The model is based on a Level III fugacity model of Mackay and consists of six compartments: air, surface water, sediment, soil, vegetation, and an organic film that coats impervious surfaces. The model was used to illustrate the effect of impervious surfaces in urban areas by parametrization for downtown, Toronto, Canada, and modification of the same area to simulate forested conditions. With illustrative emissions of PCB homologues to air, the model indicates that most chemicals are lost by advection, with the remainder undergoing air-to-surface (organic film or vegetation) transfer. Under urban conditions chemicals with Log[K(OA)] < 7.5 volatilize from the film into air where they are susceptible to advection and photolytic degradation. Chemicals with Log[K(OA)] > 7.5 are washed off the film to surface waters where they may undergo volatilization, advection, sedimentation, and degradation. Both loss mechanisms from the film increase the overall mobility of SOCs in the urban relative to the forested environment. In forested areas, vegetation more efficiently accumulates gas- and particle-phase SOCs and subsequently transfers them to surface soils, the greatest chemical reservoir, where they are relatively immobile.     

Gene expression of Interleukin 1 in vitamin A and proteins deficiency

The influence of low levels of protein and vitamin A on indicators of the immune response was assayed in rats. The levels of protein and vitamin A intake of the Cuban population affected by epidemic neuropathy in 1993 was reproduced in 4 diets: control, protein deficiency (DP), vitamin A deficiency (DA), protein and vitamin A deficiency (DAP). The Peyer's patches evaluated the Interleukin 1 expression gene and was related with corporal weight, food intake, serum protein, vitamin A, immunology indicators and histology evaluation (spleen, thymus and liver). Protein deficiency generated a significant decrease of the expression gene of Interleukin 1. Atrophy signs in lymphoid tissues and morphologic changes in the liver were associated with the dietary protein utilization. Protein and vitamin A deficiency generated significant stimulation of the Interleukin 1 expression gene with increase of the level of the inflammatory state indicators as serum alpha protein, total complement and neutrophils. This stimulation could be generated by a deficient retinol mobilization to tissues. These results support the hypothesis of the function of cytokines as mediators of subclinical symptoms of the immune system during the nutritional affectations.     

A statistical method for predicting automobile driving posture

A new model for predicting automobile driving posture is presented. The model, based on data from a study of 68 men and women in 18 vehicle package and seat conditions, is designed for use in posturing the human figure models that are increasingly used for vehicle interior design. The model uses a series of independent regression models, coupled with data-guided inverse kinematics, to fit a whole-body linkage. An important characteristic of the new model is that it places greatest importance on prediction accuracy for the body locations that are most important for vehicle interior design: eye location and hip location. The model predictions were compared with the driving postures of 120 men and women in five vehicles. Errors in mean eye location predictions in the vehicles were typically less than 10 mm. Prediction errors were largely independent of anthropometric variables and vehicle layout. Although the average posture of a group of people can be predicted accurately, individuals' postures cannot be predicted precisely because of interindividual posture variance that is unrelated to key anthropometric variables. The posture prediction models developed in this research can be applied to posturing computer-rendered human models to improve the accuracy of ergonomic assessments of vehicle interiors.     

Relationship between classroom behavior and academic achievement.

To investigate the relationship between classroom behavior patterns and academic achievement, multiple regression procedures were carried out in which the frequencies of 12 behaviors were used to predict the achievement scores of 90 2nd graders. Ss, with an average IQ of 98.69, were observed for 5-min periods on each of 4 days during language arts in the fall of the school year and again in the spring. The final multiple R between fall behavior patterns and fall achievement was .63, and that between spring behavior patterns and spring achievement was .51. The final multiple R for predicting spring achievement from fall behavior was .60. Of particular interest was the finding that the predictive value of combinations of discrete behaviors compared favorably to that obtained from IQ tests (r = .70), and that the addition of behavioral information to test information provided a more accurate prediction of achievement over the school year than that obtained by either alone. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Expression and proteasomal degradation of the major vault protein (MVP) in mammalian oocytes and zygotes

Major vault protein (MVP), also called lung resistance-related protein is a ribonucleoprotein comprising a major part (>70%) of the vault particle. The function of vault particle is not known, although it appears to be involved in multi-drug resistance and cellular signaling. Here we show that MVP is expressed in mammalian, porcine, and human ova and in the porcine preimplantation embryo. MVP was identified by matrix-assisted laser-desorption ionization-time-of-flight (MALDI-TOF) peptide sequencing and Western blotting as a protein accumulating in porcine zygotes cultured in the presence of specific proteasomal inhibitor MG132. MVP also accumulated in poor-quality human oocytes donated by infertile couples and porcine embryos that failed to develop normally after in vitro fertilization or somatic cell nuclear transfer. Normal porcine oocytes and embryos at various stages of preimplantation development showed mostly cytoplasmic labeling, with increased accumulation of vault particles around large cytoplasmic lipid inclusions and membrane vesicles. Occasionally, MVP was associated with the nuclear envelope and nucleolus precursor bodies. Nucleotide sequences with a high degree of homology to human MVP gene sequence were identified in porcine oocyte and endometrial cell cDNA libraries. We interpret these data as the evidence for the expression and ubiquitin-proteasome-dependent turnover of MVP in the mammalian ovum. Similar to carcinoma cells, MVP could fulfill a cell-protecting function during early embryonic development.     

Polychlorinated dioxins and furans from the World Trade Center attacks in exterior window films from lower Manhattan in New York City

Samples of ambient organic films deposited on exterior window surfaces from lower Manhattan and Brooklyn in New York City were collected six weeks after the terrorist attacks at the World Trade Center (WTC) on September 11, 2001 and analyzed for polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs). Total tetra- through octa-CDD/F concentrations in window films within 1 km of the WTC site in lower Manhattan ranged up to 630,000 pg/m2 (estimated as a mass concentration of ca. 1,300,000 pg/ g) and a maximum toxic equivalent (TEQ) concentration of 4700 TEQ/m2 (ca. 10 000 pg TEQ/g). Measurements at a background site 3.5 km away in Brooklyn showed lower concentrations at 130 pg TEQ/m2 (260 pg TEQ/g). Ambient gas-phase PCDD/F concentrations estimated for each site using an equilibrium partitioning model suggested concentrations ranging from ca. 2700 fg-TEQ/m3 near the WTC site to the more typical urban concentration of 20 fg-TEQ/m3 atthe Brooklyn site. Multivariate analyses of 2,3,7,8-substitued congeners and homologue group profiles suggested unique patterns in films near the WTC site compared to that observed at background sites in the study area and in other literature-derived combustion source profiles. Homologue profiles near the WTC site were dominated by tetra-, penta-, and Hexa-CDD/Fs, and 2,3,7,8-substituted profiles contained mostly octa- and hexachlorinated congeners. In comparison, profiles in Brooklyn and near mid-Manhattan exhibited congener and homologue patterns comprised mainly of hepta- and octa-CDDs, similar to that commonly reported in background air and soil.     

Index to Volume 31 (2001)

Subject Index

Index to Volume 31 (2001)     

Ethanol and pentobarbital: Comparison of behavioral and subjective effects in sedative drug abusers.

The behavioral and subjective effects of acute oral doses of placebo, ethanol (0.5, 1.0, and 2.0 g/kg), and pentobarbital (150, 300, 600, and 750 mg/70 kg) were compared in 8 male volunteers with histories of sedative drug abuse using a double-blind, double-dummy, cross-over design. Ethanol and pentobarbital produced similar dose-related decrements in psychomotor and cognitive performance and exhibited a similar profile of effects on staff- and participant-rated measures. There was some evidence indicating that, at the highest dose, pentobarbital was perceived by participants as being more sedating than ethanol and that pentobarbital has a greater abuse liability than ethanol. In conjunction with the results of previous human laboratory studies comparing the effects of different types of sedative-hypnotic drugs, these results support a mostly barbituratelike rather than benzodiazepinelike profile of effects for ethanol. (PsycINFO Database Record (c) 2010 APA, all rights reserved)