The Association of Outer Ear Commensal Bacteria with Otitis Media in Children

Background: Middle ear infections (otitis media) are a significant burden on children’s health. They are one of the more common childhood ailments and are responsible for about a third of children’s general practitioner visits. Three bacteria of the nasopharynx have been well documented as true pathogens of otitis media. These are Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis. A newer bacterium, Alloiococcus otitidis, which is more difficult to culture than the initial three pathogens, was discovered in 1989 by Faden & Dryja. The pathogenicity of A. otitidis in otitis media is controversial, as is the association of two other bacteria, Turicella otitidis and Corynebacterium auris. These three bacteria are regarded as commensals of the outer ear canal, and how they move into the middle ear is subject to much debate. My hypothesis is that during a primary middle ear infection, commensal bacteria of the external ear canal may be able to move through the inflamed tympanic membrane and into the middle ear where they act as opportunistic pathogens. This may create a more persistent bacterial infection, with greater resistance to antibiotic therapies. Methods: DNA was extracted directly from swabs of the outer ear canal and nasopharynx of children with otitis media and otitis-free controls, and from the middle ear exudates of the otitis media study group. This DNA was then amplified using primers specific for each of the organisms of interest. The presence of a specific PCR product, confirmed by DNA sequencing, indicated a positive result. Swabs from each of the sites of interest were also grown on 10% Columbia blood agar, 10% Columbia chocolate agar and in BHI broth supplemented with foetal calf serum. These results gave further information on bacterial presence in New Zealand children beyond the six studied. Sau-PCR microbial community profiling was used to demonstrate the diversity of species present in the polymicrobial samples. DNA was restriction digested and the resulting banding patterns were compared between study sites, and study groups. Results and Conclusions: Moraxella species colonised the outer ear canal of control participants more regularly than the outer ear canal of otitis media patients (58% vs. 33%). This difference was found to be statistically significant (p= 0.0023). Differences between the colonisation of the outer ear canal and nasopharyngeal body sites were found at a statistically significant level in control participants with A. otitidis (p=0.0433), C. auris (p=0.0000), T. otitidis (p=0.0050) and Moraxella spp. (p=0.0005). Of the same body sites in otitis media patients, only the colonisation of C. auris (p=0.0002) and T. otitidis (p=0.0004) were found to be statistically significant. This shows that four of the six studied bacteria colonise both anatomical sites in otitis media patients in a similar manner (without statistical significance), as opposed to only two in the control participants. Of the six bacterial species analysed using non-culture techniques, S. pneumoniae, H. influenzae and C. auris failed to be cultured. This may show that storage prior to analysis made samples less suitable for culture based research. A number of other species were cultured, with subsequent sequencing identifying them. This included species thought to be associated with a decreased risk of developing otitis media, found in both of the control participant nasopharynxes that were studied, and in only one nasopharynx from the otitis media group. A. otitidis was cultured regularly in outer ear samples, and one middle ear effusion. Sau-PCR microbial profiling was an effective but crude indication of microbial diversity. Otitis media patient nasopharyngeal profiles resembled each other, with resemblance extending to the middle ear effusion profile. Control participant banding patterns within sites were similar, but this resemblance did not extend to the otitis media group profiles. Comparisons between the banding patterns from known bacterial species to those of unknown polymicrobial species were useful if the identifying species had a unique banding pattern, as with A. otitidis. Sau-PCR therefore proved useful in analysing the complexities that are polymicrobial samples, however identifications of these species by cloning proved unsuccessful. Further research using all the techniques above with increased numbers of participants is necessary to substantiate results of this study. Information on antibiotic resistance, viral presence, and biofilm status could prove useful information in helping treat infection

VALUE OF BEEF STEAK BRANDING: HEDONIC ANALYSIS OF RETAIL SCANNER DATA

Replaced with revised version of paper 07/18/10.beef steak, brand premium, hedonic modeling, Food Consumption/Nutrition/Food Safety, Livestock Production/Industries, Marketing,

Hordes of mandrills (Mandrillus sphinx): extreme group size and seasonal male presence

Mandrill Mandrillus sphinx hordes in the Lopé Reserve, Gabon, the approximate centre of the mandrill species range, were studied over 3 years from 1996 to 1999. Part of the study site included gallery forests within savanna areas, allowing observation of entire hordes, hitherto impossible in dense forest habitat. Horde size and composition (sex and age classes) were documented using exact records on video film whenever a horde or subgroup crossed an open space. Mean horde size was 620, and hordes of up to 845 individuals were documented, probably the largest stable group size found in any wild, unprovisioned primate population. Hordes were cohesive throughout the study period and did not seem to be aggregations of smaller units. Mandrill societies seem to be quite different from the baboon societies, to which they have been compared to date. Mature, breeding-age males were not resident members of hordes, but entered at the onset of seasonal cycles in the females (as deduced by the presence of sexual tumescence) and emigrated once female sexual cycles ceased. The number of breeding males present in the horde at any one time is best explained by the number of sexually attractive females. It is postulated that the extreme coloration of males and strong sexual dimorphism in mandrills may have evolved through an enhanced need for competitive signals in a situation where no long-term social bonds between breeding partners exist

Rational design and directed evolution of probe ligases for site-specific protein labeling and live-cell imaging

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012.Cataloged from PDF version of thesis.Includes bibliographical references.Chemical fluorophores have superior photophysical properties to fluorescent proteins and are much smaller. However, in order to use these probes for live-cell protein imaging, highly specific labeling methods are required. Here, we will describe three efforts to re-engineer the E. coli enzyme, lipoic acid ligase (LplA), to catalyze the ligation of small-molecule probes onto recombinant proteins. We call this collection of methods the PRIME (PRobe Incorporation Mediated by Enzymes) methodologies. First, we describe the structure-guided mutagenesis of LplA and the identification of an LplA variant that can ligate a blue coumarin fluorophore onto a 13-amino acid LplA acceptor peptide (LAP2). This "coumarin ligase" can be used to image cellular proteins with high specificity, sensitivity, and minimal perturbation of the biology of the protein of interest. We also demonstrate how subpopulations of a protein of interest can be labeled using genetically targeted coumarin ligase. Second, we describe our attempts to use yeast display evolution and fluorescence activated cell sorting (FACS) to evolve a truncated LplA enzyme. The original truncated enzyme had severely decreased activity for LplA's natural substrate, lipoic acid. We created a 107 library of LplA mutants and, after four rounds of selection, produced a truncated LplA mutant with lipoylation activity equivalent to full-length LplA. We next sought to evolve activity for an unnatural small molecule probe, but found that this strategy was limited by both increased hydrophobic probe sticking when using the truncated enzyme and some enzyme-dependent nonspecificity. Finally, from a library of 107 LplA mutants, we evolved a full-length LplA capable of ligating an unnatural picolyl azide (pAz) substrate. We demonstrated improved activity of the "pAz ligase" in the secretory pathway and cell surface, two regions where coumarin ligase is inactive. This enzyme can also be used to image cell surface protein-protein interactions as well as label proteins as they are trafficked through the endoplasmic reticulum. These probe ligases will be useful tools for cell biologists interested in studying protein function or protein-protein interactions in the context of living cells.by Katharine Alice White.Ph.D

Value of Beef Steak Branding: Hedonic Analysis of Retail Scanner Data

Consumers rely on experience and credence attributes when purchasing beef from retailers. It is essential for all beef industry sectors to recognize the complexity of consumer buying behavior. A hedonic model is estimated to determine if there are incentives to brand beef steaks, the types of brands that entertain price premiums, and the level of existing premiums. Most branded steaks garnered premiums along with organic claims, religious processing claims, and premium cuts. Factors influencing brand value were new brands targeting emerging consumer trends, brands with regional prominence, and brands positioned as special label, program/breed specific production, and store labels

Underidentification of Autism Spectrum Disorder in Females: A Case Series Illustrating the Unique Presentation of this Disorder in Young Women

Autism spectrum disorder (ASD) is diagnosed more often in males than females, with the male-to-female gender ratio reported to be around 4.3:1 to 5:1. It is possible that the underrecognition of ASD in females partially contributes to this uneven ratio. Recent attention has been placed on understanding the processes that give rise to this gender difference in ASD prevalence. Socialization may contribute to the unique presentation of ASD in females, which may underlie this condition's subsequent underidentification in this group.The purpose of this case series is to demonstrate how symptoms of ASD may uniquely manifest in females without co-occurring intellectual impairment.An examination of three case examples of young women diagnosed with ASD will illustrate the processes that contribute to the atypical manifestation and underidentification of ASD in females.Across cases, the females in this study demonstrated shared symptom presentations within three domains: 1) unique core symptom manifestation (insistence on sameness, lack of social engagement, and social processing difficulties); 2) heightened psychiatric comorbidities with internalizing disorders (anxiety, depression, and borderline personality traits); and 3) emotional dysregulation. These three domains reflect specific processes that may help to explain the underidentification of ASD in females via diagnostic overshadowing.Consideration of atypical symptom presentations, heightened comorbidities, and emotion regulation difficulties may help with the understanding of why ASD symptoms in females are commonly underidentified or identified later than they are in males. Social difficulties in combination with internalizing psychiatric disorders and emotional dysregulation may lead to the development of a specific symptom presentation in females that obscures the detection of ASD symptoms. Suggestions for clinical practice are made to promote the accurate identification of ASD and to inform case formulation and treatment planning

Charting a new frontier of science by integrating mathematical modeling to understand and predict complex biological systems

Biological systems are staggeringly complex. To untangle this complexity and make predictions about biological systems is a continuous goal of biological research. One approach to achieve these goals is to emphasize the use of quantitative measures of biological processes. Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, ecological) has transformed how we understand, categorize, and predict complex biological systems. Simultaneously, thanks to increased computational power, mathematicians, engineers and physical scientists -- collectively termed theoreticians -- have developed sophisticated models of biological systems at different scales. But there is still a disconnect between the two fields. This surge of quantitative data creates an opportunity to apply, develop, and evaluate mathematical models of biological systems and explore novel methods of analysis. The novel modeling schemes can also offer deeper understanding of principles in biology. In the context of this paper, we use “models” to refer to mathematical representations of biological systems. This data revolution puts scientists in a unique position to leverage information-rich datasets to improve descriptive modeling. Moreover, advances in technology allow inclusion of heterogeneity and variability within these datasets and mathematical models. This inclusion may lead to identifying previously undetermined variables driving or maintaining heterogeneity and diversity. Improved inclusion of variation may even improve biologically meaningful predictions about how systems will respond to perturbations. Although some of these practices are mainstream in specific sub-fields of biology, such practices are not widespread across all fields of biological sciences. With resources dedicated to better integrating biology and mathematical modeling, we envision a transformational improvement in the ability to describe and predict complex biological systems

E.B. White Correspondence

Entries include a brief biography, a typed and a hand written letter on personal stationery, and a copy of a review articl

Fire management in a changing landscape: a case study from Lopé National Park, Gabon

A key management goal in Lopé National Park, Gabon, is to protect regionally-rare savannah ecosystems within the continuous rainforest block. In order to evaluate the impact of existing protection efforts, data on burning season environmental conditions, burning effort and current woody values for savannahs were examined between 1995 and 2008. Results showed (a) spatial heterogeneity in woody values to be correlated with grassy vegetation type (b) a negative relationship between woody vegetation and fire return frequency over the study, suggesting that decreased fire return frequency may favour savannah thickening and (c) that inconsistent burn effort by Park staff, and burns designed for reduced heat, may limit the efficiency of fire to prevent savannah thickening or forest expansion. Optimal humidity and fuel moisture conditions for burning are identified and recommendations made for improving the existing fire plan to achieve the management goal. Modifications will require significant investment of resources and training and require urgent experimental work to disentangle the direct impacts of fire from other processes of vegetation change. Lopé's fire policy should ultimately be a dynamic response to change in the local landscape driven by direct fire impacts or by global climate change

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient.

While it is well established that microbial composition and diversity shift along environmental gradients, how interactions among microbes change is poorly understood. Here, we tested how community structure and species interactions among diverse groups of soil microbes (bacteria, fungi, non-fungal eukaryotes) change across a fundamental ecological gradient, succession. Our study system is a high-elevation alpine ecosystem that exhibits variability in successional stage due to topography and harsh environmental conditions. We used hierarchical Bayesian joint distribution modeling to remove the influence of environmental covariates on species distributions and generated interaction networks using the residual species-to-species variance-covariance matrix. We hypothesized that as ecological succession proceeds, diversity will increase, species composition will change, and soil microbial networks will become more complex. As expected, we found that diversity of most taxonomic groups increased over succession, and species composition changed considerably. Interestingly, and contrary to our hypothesis, interaction networks became less complex over succession (fewer interactions per taxon). Interactions between photosynthetic microbes and any other organism became less frequent over the gradient, whereas interactions between plants or soil microfauna and any other organism were more abundant in late succession. Results demonstrate that patterns in diversity and composition do not necessarily relate to patterns in network complexity and suggest that network analyses provide new insight into the ecology of highly diverse, microscopic communities