Identification of diagnostic biomarkers for infection in premature neonates

Infection is a leading cause of neonatal morbidity and mortality worldwide. Premature neonates are particularly susceptible to infection because of physiologic immaturity, comorbidity, and extraneous medical interventions. Additionally premature infants are at higher risk of progression to sepsis or severe sepsis, adverse outcomes, and antimicrobial toxicity. Currently initial diagnosis is based upon clinical suspicion accompanied by nonspecific clinical signs and is confirmed upon positive microbiologic culture results several days after institution of empiric therapy. There exists a significant need for rapid, objective, in vitro tests for diagnosis of infection in neonates who are experiencing clinical instability. We used immunoassays multiplexed on microarrays to identify differentially expressed serum proteins in clinically infected and non-infected neonates. Immunoassay arrays were effective for measurement of more than 100 cytokines in small volumes of serum available from neonates. Our analyses revealed significant alterations in levels of eight serum proteins in infected neonates that are associated with inflammation, coagulation, and fibrinolysis. Specifically P- and E-selectins, interleukin 2 soluble receptor alpha, interleukin 18, neutrophil elastase, urokinase plasminogen activator and its cognate receptor, and C-reactive protein were observed at statistically significant increased levels. Multivariate classifiers based on combinations of serum analytes exhibited better diagnostic specificity and sensitivity than single analytes. Multiplexed immunoassays of serum cytokines may have clinical utility as an adjunct for rapid diagnosis of infection and differentiation of etiologic agent in neonates with clinical decompensation.     

Development and standardization of multiplexed antibody microarrays for use in quantitative proteomics

BACKGROUND: Quantitative proteomics is an emerging field that encompasses multiplexed measurement of many known proteins in groups of experimental samples in order to identify differences between groups. Antibody arrays are a novel technology that is increasingly being used for quantitative proteomics studies due to highly multiplexed content, scalability, matrix flexibility and economy of sample consumption. Key applications of antibody arrays in quantitative proteomics studies are identification of novel diagnostic assays, biomarker discovery in trials of new drugs, and validation of qualitative proteomics discoveries. These applications require performance benchmarking, standardization and specification. RESULTS: Six dual-antibody, sandwich immunoassay arrays that measure 170 serum or plasma proteins were developed and experimental procedures refined in more than thirty quantitative proteomics studies. This report provides detailed information and specification for manufacture, qualification, assay automation, performance, assay validation and data processing for antibody arrays in large scale quantitative proteomics studies. CONCLUSION: The present report describes development of first generation standards for antibody arrays in quantitative proteomics. Specifically, it describes the requirements of a comprehensive validation program to identify and minimize antibody cross reaction under highly multiplexed conditions; provides the rationale for the application of standardized statistical approaches to manage the data output of highly replicated assays; defines design requirements for controls to normalize sample replicate measurements; emphasizes the importance of stringent quality control testing of reagents and antibody microarrays; recommends the use of real-time monitors to evaluate sensitivity, dynamic range and platform precision; and presents survey procedures to reveal the significance of biomarker findings.     

Diurnal and Seasonal Cortisol,Testosterone, and DHEA Rhythms in Boys and Girls during Puberty

Diurnal and seasonal rhythms of cortisol, testosterone, and DHEA were examined, as little is known about the relationship between these rhythmicities and pubertal development. Salivary samples were obtained from 60 boys and 60 girls at approximately 07∶45, 08∶00, 08∶30, 12∶00, 16∶50, and 21∶00 h. The participants' ages ranged from 8–14 yrs, and each participant was tested three times at six‐month intervals. The study was conducted at a General Clinical Research Center (GCRC) and at the homes of the participants. All hormones showed diurnal fluctuations. The acrophase (peak time) of cortisol occurred earlier than for testosterone or DHEA and showed a seasonal effect, with the acrophase occurring earlier in spring than in summer. The cortisol acrophase also occurred later in the day for boys than for girls during later puberty. Seasonal effects were found only for cortisol with higher concentrations in the spring and summer. Cortisol concentrations were relatively stable across pubertal maturation, but significantly lower concentrations were observed at pubertal stage 3 compared to the other stages. Morning cortisol levels were also higher in boys at pubertal stage 2. Testosterone concentrations were higher in boys at pubertal stages 3 and 4, and DHEA was lower at pubertal stage 1 than 3 and 4 for both boys and girls. For the total sample, there was a positive correlation between DHEA and testosterone during early puberty (stages 1–3) but not later puberty (stages 4–5). Awakening secretory activity correlated with daytime secretory activity for testosterone and DHEA, but not for cortisol. These data provide novel chronobiological information on cortisol, testosterone, and DHEA as it relates to sexual maturation and encourage further study on both normal and abnormal endocrine rhythms.     

Biodegradation of Trichloroethylene and Its Anaerobic Daughter Products in Freshwater Wetland Sediments

The wide range of redox conditions and diversity of microbial populations in organic-rich wetland sediments could enhance biodegradation of chlorinated solvents. To evaluate potential biodegradation rates of trichloroethylene (TCE) and its anaerobic daughter products (cis-1,2-dichloroethylene; trans-1,2-dichloroethylene; and vinyl chloride), laboratory microcosms were prepared under methanogenic, sulfate-reducing, and aerobic conditions using sediment and groundwater from a freshwater wetland that is a discharge area for a TCE contaminant plume. Under methanogenic conditions, biodegradation rates of TCE were extremely rapid at 0.30 to 0.37 d^-1 (half-life of about 2 days). Although the TCE biodegradation rate was slower under sulfate-reducing conditions (0.032 d^-1) than under methanogenic conditions, the rate was still two orders of magnitude higher than those reported in the literature for microcosms constructed with sandy aquifer sediments. In the aerobic microcosm experiments, biodegradation occurred only if methane consumption occurred, indicating that methanotrophs were involved. Comparison of laboratory-measured rates indicates that production of the 1,2-dichloroethylene isomers and vinyl chloride by anaerobic TCE biodegradation could be balanced by their consumption through aerobic degradation where methanotrophs are active in wetland sediment. TCE degradation rates estimated using field data (0.009 to 0.016 d^-1) agree with the laboratory-measured rates within a factor of 3 to 22, supporting the feasibility of natural attenuation as a remediation method for contaminated groundwater discharging in this wetland and other similar environments.     

Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data

Four different immunoassay and antibody microarray methods performed at four different sites were used to measure the levels of a broad range of proteins (N = 323 assays; 39, 88, 168, and 28 assays at the respective sites; 237 unique analytes) in the human serum and plasma reference specimens distributed by the Plasma Proteome Project (PPP) of the HUPO. The methods provided a means to (1) assess the level of systematic variation in protein abundances associated with blood preparation methods (serum, citrate-anticoagulated-plasma, EDTA-anticoagulated-plasma, or heparin-anticoagulated-plasma) and (2) evaluate the dependence on concentration of MS-based protein identifications from data sets using the HUPO specimens. Some proteins, particularly cytokines, had highly variable concentrations between the different sample preparations, suggesting specific effects of certain anticoagulants on the stability or availability of these proteins. The linkage of antibody-based measurements from 66 different analytes with the combined MS/MS data from 18 different laboratories showed that protein detection and the quality of MS data increased with analyte concentration. The conclusions from these initial analyses are that the optimal blood preparation method is variable between analytes and that the discovery of blood proteins by MS can be extended to concentrations below the ng/mL range under certain circumstances. Continued developments in antibody-based methods will further advance the scientific goals of the PPP.     

Characterization of a Microbial Consortium Capable of Rapid and Simultaneous Dechlorination of 1,1,2,2-Tetrachloroethane and Chlorinated Ethane and Ethene Intermediates

Mixed cultures capable of dechlorinating chlorinated ethanes and ethenes were enriched from contaminated wetland sediment at Aberdeen Proving Ground (APG) Maryland. The “West Branch Consortium” (WBC-2) was capable of degrading 1,1,2,2-tetrachloroethane (TeCA), trichloroethene (TCE), cis and trans 1,2-dichloroethene (DCE), 1,1,2-trichloroethane (TCA), 1,2-dichloroethane, and vinyl chloride to nonchlorinated end products ethene and ethane. WBC-2 dechlorinated TeCA, TCA, and cisDCE rapidly and simultaneously. A Clostridium sp. phylogenetically closely related to an uncultured member of a TCE-degrading consortium was numerically dominant in the WBC-2 clone library after 11 months of enrichment in culture. Clostridiales, including Acetobacteria, comprised 65% of the bacterial clones in WBC-2, with Bacteroides (14%), and epsilon Proteobacteria (14%) also numerically important. Methanogens identified in the consortium were members of the class Methanomicrobia, which includes acetoclastic methanogens. Dehalococcoides did not become dominant in the culture, although it was present at about 1% in the microbial population. The WBC-2 consortium provides opportunities for the in situ bioremediation of sites contaminated with mixtures of chlorinated ethenes and ethanes.     

Anaerobic Biodegradation and Hydrogeochemical Controls on Natural Attenuation of Trichloroethene in an Inland Forested Wetland

A field and laboratory investigation of natural attenuation, focusing on anaerobic biodegradation, was conducted in a forested wetland where a plume of trichloroethene discharges from a sand aquifer through organic-rich wetland and stream-bottom sediments. The rapid response of the wetland hydrology to precipitation events altered groundwater flow and geochemistry during wet conditions in the spring compared to the drier conditions in the summer and fall. During dry conditions, partial reductive dechlorination of trichloroethene to cis-1,2-dichloroethene occurred in methanogenic wetland porewater. Influx of oxygenated recharge during wet conditions resulted in a change from methanogenic to iron-reducing conditions and a lack of 1,2-dichloroethene production in the wet spring conditions. During these wet conditions, dilution was the primary attenuation mechanism evident for trichloroethene in the wetland porewater. Trichloroethene degradation was insignificant in anaerobic microcosms constructed with the shallow wetland sediment, and microbiological analyses showed a low microbial biomass and absence of known dehalorespiring microorganisms. Despite the typically organic-rich characteristic of wetland sediments, natural attenuation by anaerobic degradation may not be an effective groundwater remediation for chlorinated solvents at all sites.     

The Impact of Therapeutic Riding for People with Disabilities on Variables Related to Mental Health

Substantial anecdotal evidence and some research indicate that therapeutic riding for people with disabilities has a positive impact on mental health. There is similar evidence showing that equine programs that include a psychotherapeutic component also have a positive impact. However, much of the existing research has many methodological problems, the most common being the absence of a comparison or control group. Therefore the present study investigated the mental health benefits of therapeutic riding for people with disabilities in comparison to therapeutic skiing for people with disabilities. The age range of participants was 16 to 70 years. They had a wide range of physical disabilities. In a quasi-experimental pre-test post-test design, all participants completed The Beck Depression Inventory, The Beck Anxiety Inventory, and The Rosenberg Self-Esteem Scale. They also completed an adjective checklist, consisting of 26 items that focused on mood, emotion, and sense of self. Open-ended interviews were conducted with a subset of riders. In addition, the riders completed the Pet Attitude Scale (PAS-M). Scores on the PAS-M were not related to the three psychometric measures. Both groups improved on the three psychometric measures during the course of their respective programs. Although the improvement was statistically significant, it was not clinically significant. Contrary to the hypothesis, there was no difference in improvement between riders and skiers on these measures. However, on the adjective checklist riders felt more positive regarding 21 of the 26 items, and of those 21, eight were statistically significant. The interview data suggest that the riding program improves motivation, relationship building, and self-esteem. Although these results must be interpreted with caution, due to the exploratory nature of the checklist and the interviews, they suggest that equine activities have a positive impact for people with disabilities and may have a greater impact than other activities for some aspects of mental health. However, the positive impact may be related to general wellbeing rather than psychopathology per se.     

Effect of Fe(III) on 1,1,2,2-Tetrachloroethane Degradation and Vinyl Chloride Accumulation in Wetland Sediments of the Aberdeen Proving Ground

1,1,2,2-Tetrachloroethane (TeCA) contaminated groundwater at the Aberdeen Proving Ground discharges through an anaerobic wetland in West Branch Canal Creek (MD), where dechlorination occurs. Two microbially mediated pathways, dichloroelimination and hydrogenolysis, account for most of the TeCA degradation at this site. The dichloroelimination pathways lead to the formation of vinyl chloride (VC), a recalcitrant carcinogen of great concern. The goal of this investigation was to determine whether microbially-available Fe(III) in the wetland surface sediment influenced the fate of TeCA and its daughter products. Differences were identified in the TeCA degradation pathway between microcosms treated with amorphous ferric oxyhydroxide (AFO-treated) and untreated (no AFO) microcosms. TeCA degradation was accompanied by a lower accumulation of VC in AFO-treated microcosms than untreated microcosms. The microcosm incubations and subsequent experiments with the microcosm materials showed that AFO treatment resulted in lower production of VC by (1) shifting TeCA degradation from dichloroelimination pathways to production of a greater proportion of chlorinated ethane products, and (2) decreasing the microbial capability to produce VC from 1,2-dichloroethene (DCE). VC degradation was not stimulated in the presence of Fe(III). Rather, VC degradation occurred readily under methanogenic conditions and was inhibited under Fe(III)-reducing conditions.