Discriminating antigen and non-antigen using proteome dissimilarity II:viral and fungal antigens

Immunogenicity arises via many synergistic mechanisms, yet the overall dissimilarity of pathogenic proteins versus the host proteome has been proposed as a key arbiter. We have previously explored this concept in relation to Bacterial antigens; here we extend our analysis to antigens of viral and fungal origin. Sets of known viral and fungal antigenic and non-antigenic protein sequences were compared to human and mouse proteomes. Both antigenic and non-antigenic sequences lacked human or mouse homologues. Observed distributions were compared using the non-parametric Mann-Whitney test. The statistical null hypothesis was accepted, indicating that antigen and non-antigens did not differ significantly. Likewise, we could not determine a threshold able meaningfully to separate non-antigen from antigen. We conclude that viral and fungal antigens cannot be predicted from pathogen genomes based solely on their dissimilarity to mammalian genomes.

Statnote 30 : The one-way analysis of variance (ANOVA):fixed effects model

In Statnote 9, we described a one-way analysis of variance (ANOVA) ‘random effects’ model in which the objective was to estimate the degree of variation of a particular measurement and to compare different sources of variation in space and time. The illustrative scenario involved the role of computer keyboards in a University communal computer laboratory as a possible source of microbial contamination of the hands. The study estimated the aerobic colony count of ten selected keyboards with samples taken from two keys per keyboard determined at 9am and 5pm. This type of design is often referred to as a ‘nested’ or ‘hierarchical’ design and the ANOVA estimated the degree of variation: (1) between keyboards, (2) between keys within a keyboard, and (3) between sample times within a key. An alternative to this design is a 'fixed effects' model in which the objective is not to measure sources of variation per se but to estimate differences between specific groups or treatments, which are regarded as 'fixed' or discrete effects. This statnote describes two scenarios utilizing this type of analysis: (1) measuring the degree of bacterial contamination on 2p coins collected from three types of business property, viz., a butcher’s shop, a sandwich shop, and a newsagent and (2) the effectiveness of drugs in the treatment of a fungal eye infection.

Role of copper in reducing hospital environment contamination

The environment may act as a reservoir for pathogens that cause healthcare-associated infections (HCAIs). Approaches to reducing environmental microbial contamination in addition to cleaning are thus worthy of consideration. Copper is well recognised as having antimicrobial activity but this property has not been applied to the clinical setting. We explored its use in a novel cross-over study on an acute medical ward. A toilet seat, set of tap handles and a ward entrance door push plate each containing copper were sampled for the presence of micro-organisms and compared to equivalent standard, non-copper-containing items on the same ward. Items were sampled once weekly for 10 weeks at 07:00 and 17:00. After five weeks, the copper-containing and non-copper-containing items were interchanged. The total aerobic microbial counts per cm2 including the presence of ‘indicator micro-organisms’ were determined. Median numbers of microorganisms harboured by the copper-containing items were between 90% and 100% lower than their control equivalents at both 07:00 and 17:00. This reached statistical significance for each item with one exception. Based on the median total aerobic cfu counts from the study period, five out of ten control sample points and zero out of ten copper points failed proposed benchmark values of a total aerobic count of <5 cfu/cm2. All indicator micro-organisms were only isolated from control items with the exception of one item during one week. The use of copper-containing materials for surfaces in the hospital environment may therefore be a valuable adjunct for the prevention of HCAIs and requires further evaluation.

Studies in fungal biology

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT

A bio-adhesive formulation for the delivery of anti-fungal agents to the oesophagus

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT

A comparative study to evaluate surface microbial contamination associated with copper-containing and stainless steel pens used by nurses in the critical care unit

A clinical study was undertaken to compare the surface microbial contamination associated with pens constructed of either a copper alloy or stainless steel used by nurses on intensive care units. A significantly lower level of microbial contamination was found on the copper alloy pens. Copyright © 2011 by the Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Blood Lead Levels in Children and Environmental Lead Contamination in Miami Inner City, Florida

Studies have shown that the environmental conditions of the home are important predictors of health, especially in low-income communities. Understanding the relationship between the environment and health is crucial in the management of certain diseases. One health outcome related to the home environment among urban, minority, and low-income children is childhood lead poisoning. The most common sources of lead exposure for children are lead paint in older, dilapidated housing and contaminated dust and soil produced by accumulated residue of leaded gasoline. Blood lead levels (BLL) as low as 10 μg/dL in children are associated with impaired cognitive function, behavior difficulties, and reduced intelligence. Recently, it is suggested that the standard for intervention be lowered to BLL of 5 μg /dl. The objectives of our report were to assess the prevalence of lead poisoning among children under six years of age and to quantify and test the correlations between BLL in children and lead exposure levels in their environment. This cross-sectional analysis was restricted to 75 children under six years of age who lived in 6 zip code areas of inner city Miami. These locations exhibited unacceptably high levels of lead dust and soil in areas where children live and play. Using the 5 μg/dL as the cutoff point, the prevalence of lead poisoning among the study sample was 13.33%. The study revealed that lead levels in floor dust and window sill samples were positively and significantly correlated with BLL among children (p < 0.05). However, the correlations between BLL and the soil, air, and water samples were not significant. Based on this pilot study, a more comprehensive environmental study in surrounding inner city areas is warranted. Parental education on proper housecleaning techniques may also benefit those living in the high lead-exposed communities of inner city Miami.

Environmental lead contamination in Miami inner-city area

The purpose of the study was to evaluate the magnitude of environmental lead contamination in the downtown area of Miami. Lead inspections took place at 121 homes in Little Haiti and Liberty City and involved the collection ofrepresentative samples from floors, window wells, tap water, soil and air. Community health workers (CHWs) trained in interview and safety techniques went from door to door to enlist participation. On-site investigations were tailored to areas most utilized by children underthe age of6 years. The presence of lead-containing paint was also investigated in situ via X-ray fluorescence (XRF) analysis. Results: Of the sampling areas, the window wells area had the most abundant occurrence of lead. On analysis, 24% of sites returned window well samples with lead levels above Department of Housing and Urban Development (HUD) guidelines. Of the soil samples, the playgrounds around the house had the highest concentration of lead. Soil sampling demonstrated that 27.5% of sites returned samples with lead levels (400 to 1600 ppm) inexcess of HUD/Environmental Protection Agency (EPA) standards. Positive XRF readings in one or more components were returned by 18% of sites. Conclusions: More than half of the houses in these two neighborhoods exhibited unacceptably high levels of lead dust and soil in areas where children live and play. Limitations of this study did not allow the assessment of how many children in this area are affected. A more comprehensive study including other areas of Miami-Dade County with older housing stock is recommended.

Human impacts on pig frog (Rana grylio) populations in south Florida wetlands: Harvest, water management and mercury contamination

This study investigated how harvest and water management affected the ecology of the Pig Frog, Rana grylio. It also examined how mercury levels in leg muscle tissue vary spatially across the Everglades. Rana grylio is an intermediate link in the Everglades food web. Although common, this inconspicuous species can be affected by three forms of anthropogenic disturbance: harvest, water management and mercury contamination. This frog is harvested both commercially and recreationally for its legs, is aquatic and thus may be susceptible to water management practices, and can transfer mercury throughout the Everglades food web. ^ This two-year study took place in three major regions: Everglades National Park (ENP), Water Conservation Areas 3A (A), and Water Conservation Area 3B (B). The study categorized the three sites by their relative harvest level and hydroperiod. During the spring of 2001, areas of the Everglades dried completely. On a regional and local scale Pig Frog abundance was highest in Site A, the longest hydroperiod, heavily harvested site, followed by ENP and B. More frogs were found along survey transects and in capture-recapture plots before the dry-down than after the dry-down in Sites ENP and B. Individual growth patterns were similar across all sites, suggesting differences in body size may be due to selective harvest. Frogs from Site A, the flooded and harvested site, had no differences in survival rates between adults and juveniles. Site B populations shifted from a juvenile to adult dominated population after the dry-down. Dry-downs appeared to affect survival rates more than harvest. ^ Total mercury in frog leg tissue was highest in protected areas of Everglades National Park with a maximum concentration of 2.3 mg/kg wet mass where harvesting is prohibited. Similar spatial patterns in mercury levels were found among pig frogs and other wildlife throughout parts of the Everglades. Pig Frogs may be transferring substantial levels of mercury to other wildlife species in ENP. ^ In summary, although it was found that abundance and survival were reduced by dry-down, lack of adult size classes in Site A, suggest harvest also plays a role in regulating population structure. ^

Assessing the sources, quantities, and trends on human waste contamination along protected south Florida ecosystem: A chemical tracer based study

The common occurrence of human derived contaminants like pharmaceuticals, steroids and hormones in surface waters has raised the awareness of the role played by the release of treated or untreated sewage in the water quality along sensitive coastal ecosystems. South Florida is home to many important protected environments ranging from wetlands to coral reefs which are in close proximity to large metropolitan cities. Since large portions of South Florida and most of the Florida Keys population are not served by modern sewage treatment plants and rely heavily on the use of inefficient septic systems; a comprehensive survey of selected human waste contamination markers is needed in these areas to assess water quality with respect to non-traditional micro-constituents. ^ This study reports the development and application of new sensitive and selective analytical methods for the fast screening of multiple wastewater tracers, classified as Emergent Pollutants of Concern (EPOC). Novel methods for the trace analysis of non-traditional markers of human-specific contamination such as aminopropanone were developed and used to assess the potential of non-traditional markers as wastewater tracers. ^ During our investigation, surface water samples collected from near shore environments along the South Florida were analyzed for fifteen hormones and steroids, and five commonly detected pharmaceuticals. The compounds most frequently detected were: coprostanol, cholesterol, estrone, β-estradiol, caffeine, triclosan and DEET. Concentrations of caffeine, bisphenol A and DEET were usually higher and more prevalent than the hormonal steroids. In general, it was found that common pharmaceuticals and steroids are widely present in major coastal environments in South Florida. It is also evident that aquatic bodies in heavily urbanized sectors such as the Miami River and Key Largo Harbor contain higher concentrations of several compounds while relatively open bay waters and agricultural areas show reduced chemical signatures. Concentrations of hormones in the Little Venice area of Marathon Key were above the Lowest Observable Effect Levels (LOELs) for several species, indicating that biological resources in this area are at risk. Water quality issues in some of these coastal water environments go beyond eutrophication, thus EPOC should be the target goal for future mitigation projects. ^

Presumptive Identification of the Fungal Communities in Cystic Fibrosis Patients' Sputum Using Amplicon Length Heterogeneity Polymerase Chain Reaction

This thesis would not have been possible without the aid of my family, friends, laboratory members, and professors. First and foremost, I would like to thank Dr. Kalai Mathee for allowing me to enter her lab in August 2007 and enabling to embark on this journey. This experience has transformed me into more mature scientist, teaching me how to ask the right questions and the process needed to solve them. I would also like to acknowledge Dr. Lisa Schneper. She has helped me throughout the whole process, by graciously giving me input at every step of the way. I would like to express gratitude to Dr. Jennifer Richards for all her input in writing the thesis. She has been a great teacher and being in her class has been a pleasure. Moreover, I would like to thank all the committee members for their constructive criticism throughout the process. When I entered the lab in August, there was one person who literally was by my side, Melissa Doud. Without your input and guidance I would not have even been able to do these experiments. I would also like to thank you and Dr. Light for allowing me to meet some cystic fibrosis patients. It has allowed me to put a face on the disease, and help the patients' fight. For a period before I had entered the lab, Ms. Doud had an apprentice, who started the fungal aspect of the project, Caroline Veronese. Her initial work has enabled me to prefect the protocols and complete the ITS 1 region.One very unique aspect about Dr. Mathee's lab is the camaraderie. I would like to thank all the lab members for the good times in and out of the lab. These individuals have been able to make smile and laugh in parties and lab meetings. I would like to individually thank Balachandar Dananjeyan, Deepak Balasubramanian, and V arinderpal Singh Pannu for all the PCR help and Natalie Maricic for the laughs and being a great classmate. Last, but not least, I would like to acknowledge my family and friends for their support and keeping me sane: Cecilia, my mother, Mohammad, my father, Amir, my older brother, Billal, my younger brother, Ouday Akkari and Stephanie De Bedout, my best friends.

The use of quantitative polymerase chain reaction amplification method to determine sex ratio of human spermatozoa in semen and to determine maternal contamination of amniotic fluid samples

We have modified a technique which uses a single pair of primer sets directed against homologous but distinct genes on the X and Y chromosomes, all of which are coamplified in the same reaction tube with trace amounts of radioactivity. The resulting bands are equal in length, yet distinguishable by restriction enzyme sites generating two independent bands, a 364 bp X-specific band and a 280 bp Y-specific band. A standard curve was generated to show the linear relationship between X/Y ratio average vs. %Y or %X chromosomal content. Of the 51 purified amniocyte DNA samples analyzed, 16 samples showed evidence of high % X contamination while 2 samples demonstrated higher % Y than the expected 50% X and 50% Y chromosomal content. With regards to the 25 processed sperm samples analyzed, X-sperm enrichment was evident when compared to the primary sex ratio whereas Y-sperm was enriched when we compared before and after selection samples.

Multi-media filtration for removal of petroleum contamination

A pilot scale multi-media filtration system was used to evaluate the effectiveness of filtration in removing petroleum hydrocarbons from a source water contaminated with diesel fuel. Source water was artificially prepared by mixing bentonite clay and tap water to produce a turbidity range of 10-15 NTU. Diesel fuel concentrations of 150 ppm or 750 ppm were used to contaminate the source water. The coagulants used included Cat Floc K-10 and Cat Floc T-2. The experimental phase was conducted under direct filtration conditions at constant head and constant rate filtration at 8.0 gpm. Filtration experiments were run until the filter reached its clogging point as noted by a measured peak pressure loss of 10 psi. The experimental variables include type of coagulant, oil concentration and source water. Filtration results were evaluated based on turbidity removal and petroleum hydrocarbon (PHC) removal efficiency as measured by gas chromatography. Experiments indicated that clogging was controlled by the clay loading on the filter and that inadequate destabilization of the contaminated water by the coagulant limited the PHC removal. ^

Far-infrared constraints on the contamination by dust-obscured galaxies of high-z dropout searches

The spectral energy distributions (SED) of dusty galaxies at intermediate redshift may look similar to very high-redshift galaxies in the optical/near infrared (NIR) domain. This can lead to the contamination of high-redshift galaxy searches based on broad-band optical/NIR photometry by lower redshift dusty galaxies because both kind of galaxies cannot be distinguished. The contamination rate could be as high as 50%. This work shows how the far-infrared (FIR) domain can help to recognize likely low-z interlopers in an optical/NIR search for high-z galaxies. We analyze the FIR SEDs of two galaxies that are proposed to be very high-redshift (z > 7) dropout candidates based on deep Hawk-I/VLT observations. The FIR SEDs are sampled with PACS/Herschel at 100 and 160 μm, with SPIRE/Herschel at 250, 350 and 500 μm and with LABOCA/APEX at 870 μm. We find that redshifts > 7 would imply extreme FIR SEDs (with dust temperatures >100 K and FIR luminosities >10^13 L_⊙). At z ~ 2, instead, the SEDs of both sources would be compatible with those of typical ultra luminous infrared galaxies or submillimeter galaxies. Considering all available data for these sources from visible to FIR we re-estimate the redshifts and find z ~ 1.6–2.5. Owing to the strong spectral breaks observed in these galaxies, standard templates from the literature fail to reproduce the visible-to-near-IR part of the SEDs even when additional extinction is included. These sources strongly resemble dust-obscured galaxies selected in Spitzer observations with extreme visible-to-FIR colors, and the galaxy GN10 at z = 4. Galaxies with similar SEDs could contaminate other high-redshift surveys.

Medical mycology and fungal immunology : new research perspectives addressing a major world health challenge

Peer reviewed