Color variation in museum specimens of birds: effects of stress, pigmentation, and duration of storage

Animal coloration often serves as a signal to others that may communicate traits about the individual such as toxicity, status, or quality. Colorful ornaments in many animals are often honest signals of quality assessed by mates, and different colors may beproduced by different biochemical pigments. Investigations of the mechanisms responsible for variation in color expression among birds are best when including a geographically and temporally broad sample. In order to obtain such a sample, studies such as this often use museum specimens; however, in order for museum specimens toserve as an accurate replacement, they must accurately represent living birds, or we must understand the ways in which they differ. In this thesis, I investigated the link between feather corticosterone, a hormone secreted in response to stress, and carotenoid-basedcoloration in the Red-winged Blackbird (Agelaius phoeniceus) in order to explore a mechanistic link between physiological state and color expression. Male Red-winged Blackbirds with lower feather corticosterone had significantly brighter red epaulets than birds with higher feather corticosterone, while I found no significant changes in red chroma. I also performed a methodological comparison of color change in museum specimens among different pigment types (carotenoid and psittacofulvin) and pigments in different locations in the body (feather and bill carotenoids) in order to quantify colorchange over time. Carotenoids and psittacofulvins showed significant reductions in red brightness and chroma over time in the collection, and carotenoid color changed significantly faster than psittacofulvin color. Both bill and feather carotenoids showed significant reductions in red brightness and red chroma over time, but change of both red chroma and red brightness occurred at a similar rate in feathers and bills. In order to use museum specimens of ecological research on bird coloration specimen age must be accounted for before the data can be used; however, once this is accomplished, museum- based color data may be used to draw conclusions about wild populations.

Kinetic assessment of persistent halogenated xenobiotics in cell culture models: comparison of mono- and poly-halogenated compounds

We evaluated the suitability of single and multiple cell type cultures as model systems to characterise cellular kinetics of highly lipophilic compounds with potential ecotoxicological impact. Confluent mono-layers of human skin fibroblasts, rat astrocytoma C6 cells, non-differentiated and differentiated mouse 3T3 cells were kept in culture medium supplemented with 10% foetal calf serum. For competitive uptake experiments up to four different cell types, grown on glass sectors, were exposed for 3h to (14)C-labelled model compounds, dissolved either in organic solvents or incorporated into unilamellar lecithin liposomes. Bromo-, or chloro-benzenes, decabromodiphenylether (DBP), and dichlorodiphenyl ethylene (DDE) were tested in rather high concentration of 20 microM. Cellular toxicity was low. Compound levels were related to protein, DNA, and triglyceride contents. Cellular uptake was fast and dependent on physico-chemical properties of the compounds (lipophilicity, molecular size), formulation, and cell type. Mono-halogenated benzenes showed low and similar uptake levels (=low accumulation compounds). DBP and DDE showed much higher cellular accumulations (=high accumulation compounds) except for DBP in 3T3 cells. Uptake from liposomal formulations was mostly higher than if compounds were dissolved in organic solvents. The extent of uptake correlated with the cellular content of triglycerides, except for DBP. Uptake competition between different cell types was studied in a sectorial multi-cell culture model. For low accumulation compounds negligible differences were found among C6 cells and fibroblasts. Uptake of DDE was slightly and that of DBP highly increased in fibroblasts. Well-defined cell culture systems, especially the sectorial model, are appropriate to screen for bioaccumulation and cytotoxicity of (unknown) chemical entities in vitro.

Annexins as cell-type-specific markers in the developing chicken chorionallantoic membrane

Between day E8 and E12 of embryonic development, the chicken chorioallantoic membrane (CAM) undergoes massive structural rearrangement enabling calcium-uptake from the eggshell to supply the growing embryo. However, the contribution of the various cell types of the chorionic epithelium including the capillary covering (CC) cells, villus cavity (VC) cells, endothelial-like cells, and basal cells to this developmental program is largely unknown. In order to obtain markers for the different cell types in the chorionic epithelium, we determined the expression patterns of various calcium-binding annexins in the developing chicken CAM. By reverse transcription/polymerase chain reaction with primers deduced from nucleotide sequences available in various databases, the presence of annexin (anx)-1, anx-2, anx-5, and anx-6 was demonstrated at days E8 and E12. Quantitative immunoblotting with novel antibodies raised against the recombinant proteins revealed that anx-1 and anx-5 were significantly up-regulated at day E12, whereas anx-2 and anx-6 expression remained almost unchanged in comparison to levels at day E8. Immunohistochemistry of paraffin-embedded sections of E12 CAM revealed anx-1 in CC cells and VC cells. Anx-2 was localized in capillaries in the chorionic epithelium and in basal cells of the allantoic epithelium, whereas anx-6 was detected in basal cells or endothelial-like cells of the chorionic epithelium and in the media of larger vessels in the mesenchyme. A 2-day exposure of the CAM to a tumor cell spheroid resulted in strong proliferation of anx-1-expressing CC cells suggesting that these cells participate in the embryonic response to experimental intervention. Thus, annexins exhibit complementary expression patterns and represent appropriate cell markers for the further characterization of CAM development and the interpretation of results obtained when using CAM as an experimental model.

Response to Innes and Mattsson: Neospora caninum emerges from the shadow of Toxoplasma gondii

It is tempting to extrapolate research findings regarding the intensively studied Toxoplasma gondii to Neospora caninum. This is based on morphological and ultrastructural studies, the molecular phylogeny of both parasites, their wide host ranges in nature, their ability to invade many different cell types in vitro and the occurrence of homologous proteins in both species. However, as Innes and Mattsson point out, T. gondii is the most successful parasite worldwide, whereas N. caninum has a more limited host range. Thus, some of the most challenging questions are: (i) what is T. gondii doing that N. caninum is not doing, or is doing differently, that renders the former so much more successful? And (ii) can some of these features be exploited for the development of interventional tools to limit infection and pathology caused by N. caninum?

Imaging of salivary gland tumours

Imaging of salivary gland tumours is a major challenge for radiologists due to the great variety of differential diagnoses. This article gives a short overview on the anatomy of the salivary glands, the epidemiology of salivary gland tumours as well as the clinical presentation and the different imaging modalities including new magnetic resonance techniques such as diffusion-weighted magnetic resonance imaging, dynamic contrast-enhanced magnetic resonance imaging and magnetic resonance spectroscopy applied in the work-up of salivary gland masses. The imaging features of different tumour types and their differential diagnoses are also discussed. Finally, staging classification and treatment options are presented.

Large deletions in the CFTR gene: clinics and genetics in Swiss patients with CF

Cystic fibrosis (CF) is the most common life-shortening autosomal recessive disorder in Caucasians, and is associated with at least one mutation on each CF transmembrane conductance regulator (CFTR) allele. Some patients, however, with only one identifiable point mutation carry on the other allele, a large deletion that is not detected by conventional screening methods. The overall frequency of large deletions in patients with CF is estimated to be 1-3%. Using the CFTR Multiplex Ligation dependent Probe Amplification Kit (MRC-Holland, Amsterdam, Netherlands) that allows the exact detection of copy numbers from all 27 exons in the CFTR gene, we screened 50 patients with only one identified mutation for large deletions in the CFTR gene. Each detected deletion was confirmed using our real-time polymerase chain reaction (PCR) assay and deletion-specific PCR reactions using junction fragment primers. We detected large deletions in eight patients (16%). These eight CF alleles belong to four different deletion types (CFTRindel2, CFTRdele14b-17b, CFTRdele17a-17b and CFTRdele 2-9) whereof the last is novel. Comparing detailed clinical data of all these patients with CF and the molecular genetic findings, we were able to elaborate criteria for deletion screenings and possible genotype-phenotype associations. In conclusion, we agree with other authors that deletion screenings should be implemented in routine genetic diagnostics of CF.

Translocation of particles and inflammatory responses after exposure to fine particles and nanoparticles in an epithelial airway model

ABSTRACT: BACKGROUND: Experimental studies provide evidence that inhaled nanoparticles may translocate over the airspace epithelium and cause increased cellular inflammation. Little is known, however, about the dependence of particle size or material on translocation characteristics, inflammatory response and intracellular localization. RESULTS: Using a triple cell co-culture model of the human airway wall composed of epithelial cells, macrophages and dendritic cells we quantified the entering of fine (1 mum) and nano-sized (0.078 mum) polystyrene particles by laser scanning microscopy. The number distribution of particles within the cell types was significantly different between fine and nano-sized particles suggesting different translocation characteristics. Analysis of the intracellular localization of gold (0.025 mum) and titanium dioxide (0.02-0.03 mum) nanoparticles by energy filtering transmission electron microscopy showed differences in intracellular localization depending on particle composition. Titanium dioxide nanoparticles were detected as single particles without membranes as well as in membrane-bound agglomerations. Gold nanoparticles were found inside the cells as free particles only. The potential of the different particle types (different sizes and different materials) to induce a cellular response was determined by measurements of the tumour necrosis factor-alpha in the supernatants. We measured a 2-3 fold increase of tumour necrosis factor-alpha in the supernatants after applying 1 mum polystyrene particles, gold nanoparticles, but not with polystyrene and titanium dioxide nanoparticles. CONCLUSION: Quantitative laser scanning microscopy provided evidence that the translocation and entering characteristics of particles are size-dependent. Energy filtering transmission electron microscopy showed that the intracellular localization of nanoparticles depends on the particle material. Both particle size and material affect the cellular responses to particle exposure as measured by the generation of tumour necrosis factor-alpha.

Gunshot-related displacement of skin particles and bacteria from the exit region back into the bullet path

In previous studies, it was shown that there is a gunshot-related transport of skin particles and microorganisms from the entrance region into the depth of the bullet path. The present study deals with the question of whether gunshots may also cause a retrograde transport of skin particles and microorganisms from the bullet exit region back into the bullet path. For this purpose, we used a composite model consisting of rectangular gelatin blocks and pig skin. The skin pieces were firmly attached to the gelatin blocks on the side where the bullet was to exit. Prior to the test shots, the outer surface of the pig skin was contaminated with a thin layer of a defined bacterial suspension. After drying the skin, test shots were fired from a distance of 10 m using cartridges calibre .38 spec. with different bullet types. Subsequent analyses showed that in all shots with full penetration of the composite model, the bullet path contained displaced skin particles and microorganisms from the skin surface at the exit site. These could be regularly detected in the distal 6-8 cm of the track, occasionally up to a distance of 18 cm from the exit hole. The distribution of skin particles and microorganisms is presented and the possible mechanism of this retrograde transport is discussed.

Biological mediators and periodontal regeneration: a review of enamel matrix proteins at the cellular and molecular levels

BACKGROUND: Despite a large body of clinical and histological data demonstrating beneficial effects of enamel matrix proteins (EMPs) for regenerative periodontal therapy, it is less clear how the available biological data can explain the mechanisms underlying the supportive effects of EMPs. OBJECTIVE: To analyse all available biological data of EMPs at the cellular and molecular levels that are relevant in the context of periodontal wound healing and tissue formation. METHODS: A stringent systematic approach was applied using the key words "enamel matrix proteins" OR "enamel matrix derivative" OR "emdogain" OR "amelogenin". The literature search was performed separately for epithelial cells, gingival fibroblasts, periodontal ligament cells, cementoblasts, osteogenic/chondrogenic/bone marrow cells, wound healing, and bacteria. RESULTS: A total of 103 papers met the inclusion criteria. EMPs affect many different cell types. Overall, the available data show that EMPs have effects on: (1) cell attachment, spreading, and chemotaxis; (2) cell proliferation and survival; (3) expression of transcription factors; (4) expression of growth factors, cytokines, extracellular matrix constituents, and other macromolecules; and (5) expression of molecules involved in the regulation of bone remodelling. CONCLUSION: All together, the data analysis provides strong evidence for EMPs to support wound healing and new periodontal tissue formation.

Translocation and cellular entering mechanisms of nanoparticles in the respiratory tract

Anthropogenic nano-sized particles (NSP), ie, particles with a diameter of less than 100 nm, are generated with or without purpose as chemically and physically well-defined materials or as a consequence of combustion processes respectively. Inhalation of NSP occurs on a regular basis due to air pollution and is associated with an increase in respiratory and cardiovascular morbidity and mortality. Manufactured NSP may intentionally be inhaled as pharmaceuticals or unintentionally during production at the workplace. Hence the interactions of NSP with the respiratory tract are currently under intensive investigation. Due to special physicochemical features of NSP, its biological behaviour may differ from that of larger sized particles. Here we review two important themes of current research into the effects of NSP on the lungs: 1) The potential of NSP to cross the blood-air barrier of the lungs, thus gaining access to the circulation and extrapulmonary organs. It is currently accepted that a small fraction of inhaled NSP may translocate to the circulation. The significance of this translocation requires further research. 2) The entering mechanisms of NSP into different cell types. There is evidence that NSP are taken up by cells via well-known pathways of endocytosis but also via different mechanisms not well understood so far. Knowledge of the quantitative relationship between the different entering mechanisms and cellular responses is not yet available but is urgently needed in order to understand the effects of intentionally or unintentionally inhaled NSP on the respiratory tract.

Structural capacity of steel tubular cast-in-place piling

Steel tubular cast-in-place pilings are used throughout the country for many different project types. These piles are a closed-end pipe with varying wall thicknesses and outer diameters, that are driven to depth and then the core is filled with concrete. These piles are typically used for smaller bridges, or secondary structures. Mostly the piling is designed based on a resistance based method which is a function of the soil properties of which the pile is driven through, however there is a structural capacity of these members that is considered to be the upper bound on the loading of the member. This structural capacity is given by the AASHTO LRFD (2010), with two methods. These two methods are based on a composite or non-composite section. Many state agencies and corporations use the non-composite equation because it is requires much less computation and is known to be conservative. However with the trends of the time, more and more structural elements are being investigated to determine ways to better understand the mechanics of the members, which could lead to more efficient and safer designs. In this project, a set of these piling are investigated. The way the cross section reacts to several different loading conditions, along with a more detailed observation of the material properties is considered as part of this research. The evaluation consisted of testing stub sections of pile with varying sizes (10-¾”, 12-¾”), wall thicknesses (0.375”, 0.5”), and testing methods (whole compression, composite compression, push through, core sampling). These stub sections were chosen as they would represent a similar bracing length to many different soils. In addition, a finite element model was developed using ANSYS to predict the strains from the testing of the pile cross sections. This model was able to simulate the strains from most of the loading conditions and sizes that were tested. The bond between the steel shell and the concrete core, along with the concrete strength through the depth of the cross section were some of the material properties of these sections that were investigated.

Promoting Biodiversity in Forest Ecosystems Using Ecological Forestry

A subset of forest management techniques, termed ecological forestry, have been developed in order to produce timber and maintain the ecological integrity of forest communities through practices that more closely mirror natural disturbance regimes. Even though alternative methods have been described and tested, these approaches still need to be established and analyzed in a variety of geographic regions in order to calibrate and measure effectiveness across different forest types. The primary objective of this research project was to assess whether group selection combined with legacy-tree retention could enhance mid-tolerant tree recruitment in a late-successional northern hardwood forest. In order to evaluate a novel alternative regeneration technique, 49 group-selection openings in three size classes were created in 2003 with a biological legacy tree retained in the center of each opening. Twenty reference sites, managed using single-tree selection, were also analyzed for comparison. The specific goals of the project were to: 1) determine the fate and persistence of the openings and legacy trees 2) assess the understory response of the group-selection openings versus the single-tree selection reference sites, and 3) evaluate the spatial patterns of yellow birch (Betula alleghaniensis Britt.) and eastern hemlock (Tsuga canadensis (L.) Carr.) in the group-selection openings. The results from 8-9 years post-study implementation and the changes that have occurred between 2004/5 and 2011/12 are discussed. The alternative regeneration technique developed and assessed in this study has the potential to enrich biodiversity in a range of forest types. Projected group-selection opening persistence rates ranged from 41-91 years. Openings from 500-1500 m2 are predicted to persist long enough for mid-tolerant tree recruitment. The legacy trees responded well to release and experienced a low mortality rate. Yellow birch (the primary shade mid-tolerant tree in the study area) densities increased with opening size. Maples surpassed all other species in abundance. In the sapling layer, sugar maple (Acer saccharum Marsh.) was 2 to over 300 times more abundant in the group-selection openings and 2 to 3 times more abundant in the references sites than all other species present. Red maple (Acer rubrum L.) was the second most abundant species present in the openings and reference sites. Spatial patterns of yellow birch and eastern hemlock in the openings were mostly aggregated. The southern edges of the largest openings contained the highest magnitude of yellow birch and eastern hemlock per unit area. Continued monitoring and additional treatments will likely be necessary in order to ensure underrepresented species successfully reach maturity.

EVALUATING INFRASTRUCTURE PERFORMANCE TO ASSIST FACILITY MANAGEMENT TOWARD SUSTAINABLE SYSTEMS

Civil infrastructure provides essential services for the development of both society and economy. It is very important to manage systems efficiently to ensure sound performance. However, there are challenges in information extraction from available data, which also necessitates the establishment of methodologies and frameworks to assist stakeholders in the decision making process. This research proposes methodologies to evaluate systems performance by maximizing the use of available information, in an effort to build and maintain sustainable systems. Under the guidance of problem formulation from a holistic view proposed by Mukherjee and Muga, this research specifically investigates problem solving methods that measure and analyze metrics to support decision making. Failures are inevitable in system management. A methodology is developed to describe arrival pattern of failures in order to assist engineers in failure rescues and budget prioritization especially when funding is limited. It reveals that blockage arrivals are not totally random. Smaller meaningful subsets show good random behavior. Additional overtime failure rate is analyzed by applying existing reliability models and non-parametric approaches. A scheme is further proposed to depict rates over the lifetime of a given facility system. Further analysis of sub-data sets is also performed with the discussion of context reduction. Infrastructure condition is another important indicator of systems performance. The challenges in predicting facility condition are the transition probability estimates and model sensitivity analysis. Methods are proposed to estimate transition probabilities by investigating long term behavior of the model and the relationship between transition rates and probabilities. To integrate heterogeneities, model sensitivity is performed for the application of non-homogeneous Markov chains model. Scenarios are investigated by assuming transition probabilities follow a Weibull regressed function and fall within an interval estimate. For each scenario, multiple cases are simulated using a Monte Carlo simulation. Results show that variations on the outputs are sensitive to the probability regression. While for the interval estimate, outputs have similar variations to the inputs. Life cycle cost analysis and life cycle assessment of a sewer system are performed comparing three different pipe types, which are reinforced concrete pipe (RCP) and non-reinforced concrete pipe (NRCP), and vitrified clay pipe (VCP). Life cycle cost analysis is performed for material extraction, construction and rehabilitation phases. In the rehabilitation phase, Markov chains model is applied in the support of rehabilitation strategy. In the life cycle assessment, the Economic Input-Output Life Cycle Assessment (EIO-LCA) tools are used in estimating environmental emissions for all three phases. Emissions are then compared quantitatively among alternatives to support decision making.

A PETROPHYSICAL EVALUATION OF THE TRENTON-BLACK RIVER FORMATION OF THE MICHIGAN BASIN

This work is conducted to study the geological and petrophysical features of the Trenton- Black River limestone formation. Log curves, crossplots and mineral identification methods using well-log data are used to determine the components and analyze changes in lithology. Thirty-five wells from the Michigan Basin are used to define the mineralogy of Trenton-Black River limestone. Using the different responses of a few log curves, especially gamma-ray, resistivity and neutron porosity, the formation tops for the Utica shale, the Trenton limestone, the Black River limestone and the Prairie du Chien sandstone are identified to confirm earlier authors’ work and provide a basis for my further work. From these, an isopach map showing the thickness of Trenton-Black River formation is created, indicating that its maximum thickness lies in the eastern basin and decreases gradually to the west. In order to obtain more detailed lithological information about the limestone formations at the thirty-five wells, (a) neutron-density and neutron-sonic crossplots, (b) mineral identification methods, including the M-N plot, MID plot, ϱmaa vs. Umaa MID plot, and the PEF plot, and (c) a modified mineral identification technique are applied to these wells. From this, compositions of the Trenton-Black River formation can be divided into three different rock types: pure limestone, partially dolomitized limestone, and shaly limestone. Maps showing the fraction of dolomite and shale indicate their geographic distribution, with dolomite present more in the western and southwestern basin, and shale more common in the north-central basin. Mineral identification is an independent check on the distribution found from other authors, who found similar distributions based on core descriptions. The Thomas Stieber method of analysis is best suited to sand-shale sequences, interpreting hree different distributions of shale within sand, including dispersed, laminated and structural. Since this method is commonly applied in clastic rocks, my work using the Thomas Stieber method is new, as an attempt to apply this technique, developed for clastics, to carbonate rocks. Based on the original assumption and equations with a corresponding change to the Trenton-Black River formation, feasibility of using the Thomas Stieber method in carbonates is tested. A graphical display of gamma-ray versus density porosity, using the properties of clean carbonate and pure shale, suggests the presence of laminated shale in fourteen wells in this study. Combined with Wilson’s study (2001), it is safe to conclude that when shale occurs in the Trenton-Black River formation, it tends to be laminated shale.

Carbon in the Peatlands in the Great Lakes Region

Peatlands cover only ~3% of the global land area, but store ~30% of the worlds' soil carbon. There are many different peat types that store different amounts of carbon. Most inventories of carbon storage in northern peatlands have been conducted in the expansive Sphagnum dominated peatlands. Although, northern white cedar peatlands (NW cedar, Thuja occidentalis L.) are also one of the most common peatland types in the Great Lakes Region, occupying more than 2 million hectares. NW cedar swamps are understudied, due in part to the difficulties in collection methods. General lack of rapid and consistent sampling methods has also contributed in a lack of carbon stock quantification for many peatlands. The main objective of this thesis is to quantify: 1) to evaluate peat sampling methods 2) the amount of C-stored and the rates of long-term carbon accumulation in NW cedar peatlands. We sampled 38 peatlands separated into four categories (black ash, NW cedar swamp, sedge, and Sphagnum) during the summers of 2011/2012 across northern MN and the Upper Peninsula of MI. Basal dates of peat indicate that cedar peatlands were between 1970-7790 years old. Cedar peatlands are generally shallower than Sphagnum peat, but due to their higher bulk density, hold similar amounts of carbon with our sites averaging ~800 MgC ha-1. We estimate that NW cedar peatlands store over 1.7 Gt of carbon in the Great Lakes Region. Each of the six methods evaluated had a different level of accuracy and requires varying levels of effort and resources. The depth only method and intermittent sampling method were the most accurate methods of peatland sampling.