Physical and functional characterisation of apoptotic cell-derived extracellular vesicles

Damaged, aged or unwanted cells are removed from the body by an active process known as apoptosis. This highly orchestrated programme results in the exposure of 'flags' at the dying cell surface and the release of attractive signals to recruit phagocytes. Together these changes ensure efficient phagocytic removal of dying cells and prevention of inflammatory and autoimmune disorders. Extracellular vesicles (EV) are released from a variety of cells (both viable and apoptotic) and they serve as a novel means of intercellular communication. They range in size: 70-100nm ('exosomes') through 100-1000nm ('microparticles') to large vesicles released from dying cells ('apoptotic bodies'). Release of apoptotic cell-derived extracellular vesicles (acdEV) of less than 1000nm is an important mechanism by which phagocytes are attracted to sites of cell death. Using a variety of approaches we characterize the release, physical characteristics and function of acdEV. Using fluorescence microscopy we demonstrate release of ICAM-3 on acdEV from dying leukocytes and, through the use of resistive pulse technology (qNano, IZON Science), we accurately size and quantitate acdEV release. The function of acdEV is revealed through the use of both horizontal chemotaxis assays (Dunn chambers) and vertical transwell migration assays (Cell-IQ, CM Technologies). These assays reveal potent chemoattractive capacity of acdEV and associated ICAM-3. Additionally we demonstrate an additional novel function of acdEV as anti-inflammatory immune-modulators. These data support an integrated approach to the physical and functional analyses of EV.

Experimental and theoretical study of longitudinal power distribution in a random DFB fiber laser

We have measured the longitudinal power distribution inside a random distributed feedback Raman fiber laser. The observed distribution has a sharp maximum whose position depends on pump power. The spatial distribution profiles are different for the first and the second Stokes waves. Both analytic solution and results of direct numerical modeling are in excellent agreement with experimental observations. © 2012 Optical Society of America.

Physical and ultrastructural basis of blue leaf iridescence in four Malaysian understory plants

Iridescent blue leaf coloration in four Malaysian rain forest understory plants, Diplazium tomentosum Bl. (Athyriaceae), Lindsaea lucida Bl. (Lindsaeaceae), Begonia pavonina Ridl. (Begoniaceae), and Phyllagathis rotundifolia Bl. (Melastomataceae) is caused by a physical effect, constructive interference of reflected blue light. The ultrastructural basis for this in D. tomentosum and L. lucida is multiple layers of cellulose microfibrils in the uppermost cell walls of the adaxial epidermis. The helicoidal arrangement of these fibrils is analogous to that which produces a similar color in arthropods. In B. pavonina and P. rotundifolia the blue-green coloration is caused by parallel lamellae in specialized plastids adjacent to the abaxial wall of the adaxial epidermis. The selective advantage of this color production, if any, is unknown.

Physical and ultrastructural basis of blue leaf iridescence in two neotropical ferns.

Iridescent blue leaf coloration in two neotropical ferns, Danaea nodosa (L.) Sm. (Marattiaceae) and Trichomanes elegans L. C. Rich. (Hymenophyllaceae), is caused by thin film constructive interference. The ultrastructural basis for the film in D. nodosa is multiple layers of cellulose microfibrils in the adaxial cell walls of the adaxial epidermis. The apparent helicoidal arrangement of the fibrils is analogous to similar color production in arthropods. In T. elegans the blue-green coloration is caused by the remarkably uniform thickness and arrangement of grana in specialized chloroplasts adjacent to the adaxial wall of the adaxial epidermis. The selective advantage of this color production, if any, is unknown but apparently different from that previously studied in Selaginella.

Food customs of rural and urban Inupiaq elders and their relationships to select nutrition parameters, food insecurity, health, and physical and mental functioning

The Inupiaq Tribe resides north of the Arctic Circle in northwestern Alaska. The people are characterized by their continued dependence on harvested fish, game and plants, known as a subsistence lifestyle (Lee 2000:35-45). Many are suggesting that they leave their historical home and move to urban communities, places believed to be more comfortable as they age. Tribal Elders disagree and have stated, "Elders need to be near the river where they were raised" (Branch 2005:1). The research questions focused on differences that location had on four groups of variables: nutrition parameters, community support, physical functioning and health. A total of 101 Inupiaq Elders ≥ 50 years were surveyed: 52 from two rural villages, and 49 in Anchorage. Location did not influence energy intake or intake of protein; levels of nutrition risk and food insecurity; all had similar rates between the two groups. Both rural and urban Elders reported few limitations of ADLs and IADLs. Self-reported general health scores (SF-12.v2 GH) were also similar by location. Differences were found with rural Elders reporting higher physical functioning summary scores (SF-12.v2 PCS), higher mental health scores (SF-12.v2 MH), higher vitality and less pain even though the rural mean ages were five years older than the urban Elders. Traditional food customs appear to support the overall health and well being of the rural Inupiaq Elders as demonstrated by higher intakes of Native foods, stronger food sharing networks and higher family activity scores than did urban Elders. The rural community appeared to foster continued physical activity. It has been said that when Elders are in the rural setting they are near "people they know" and it is a place "where they can get their Native food" (NRC 2005). These factors appear to be important as Inupiaq Elders age, as rural Inupiaq Elders fared as well or better than Inupiaq Elders in terms of diet, mental and physical health.

An experimental and theoretical analysis of nitric oxide availability in the microcirculation

Nitric Oxide (NO) is produced in the vascular endothelium where it then diffuses to the adjacent smooth muscle cells (SMC) activating agents known to regulate vascular tone. The close proximity of the site of NO production to the red blood cells (RBC) and its known fast consumption by hemoglobin, suggests that the blood will scavenge most of the NO produced. Therefore, it is unclear how NO is able to play its role in accomplishing vasodilation. Investigation of NO production and consumption rates will allow insight into this paradox. DAF-FM is a sensitive NO fluorescence probe widely used for qualitative assessment of cellular NO production. With the aid of a mathematical model of NO/DAF-FM reaction kinetics, experimental studies were conducted to calibrate the fluorescence signal showing that the slope of fluorescent intensity is proportional to [NO]2 and exhibits a saturation dependence on [DAF-FM]. In addition, experimental data exhibited a Km dependence on [NO]. This finding was incorporated into the model elucidating NO 2 as the possible activating agent of DAF-FM. A calibration procedure was formed and applied to agonist stimulated cells, providing an estimated NO release rate of 0.418 ± 0.18 pmol/cm2s. To assess NO consumption by RBCs, measurements of the rate of NO consumption in a gas stream flowing on top of an RBC solution of specified Hematocrit (Hct) was performed. The consumption rate constant (kbl)in porcine RBCs at 25°C and 45% Hct was estimated to be 3500 + 700 s-1. kbl is highly dependent on Hct and can reach up to 9900 + 4000 s-1 for 60% Hct. The nonlinear dependence of kbl on Hct suggests a predominant role for extracellular diffusion in limiting NO uptake. Further simulations showed a linear relationship between varying NO production rates and NO availability in the SMCs utilizing the estimated NO consumption rate. The corresponding SMC [NO] level for the average NO production rate estimated was approximately 15.1 nM. With the aid of experimental and theoretical methods we were able to examine the NO paradox and exhibit that endothelial derived NO is able to escape scavenging by RBCs to diffuse to the SMCs.

Norm-based comparison of SF -12 physical and mental health scale scores for a sample of employees of Broward County

In the new health paradigm, the connotation of health has extended beyond the measures of morbidity and mortality to include wellness and quality of life. Comprehensive assessments of health go beyond traditional biological indicators to include measures of physical and mental health status, social role-functioning, and general health perceptions. To meet these challenges, tools for assessment and outcome evaluation are being designed to collect information about functioning and well-being from the individual's point of view.^ The purpose of this study was to profile the physical and mental health status of a sample of county government employees against U.S. population norms. A second purpose of the study was to determine if significant relationships existed between respondent characteristics and personal health practices, lifestyle and other health how the tools and methods used in this investigation can be used to guide program development and facilitate monitoring of health promotion initiatives.^ The SF-12 Health Survey (Ware, Kosinski, & Keller, 1995), a validated measure of health status, was administered to a convenience sample of 450 employees attending one of nine health fairs at an urban worksite. The instrument has been utilized nationally which enabled a comparative analysis of findings of this study with national results.^ Results from this study demonstrated that several respondent characteristics and personal health practices were associated with a greater percentage of physical and/or mental scale scores that were significantly "worse" or significantly "better" than the general population. Respondent characteristics that were significantly related to the SF-12 physical and/or mental health scale scores were gender, age, education, ethnicity, and income status. Personal health practices that were significantly related to SF-12 physical and/or mental scale scores were frequency of vigorous exercise, presence of chronic illness, being at one's prescribed height and weight, eating breakfast, smoking and drinking status. This study provides an illustration of the methods used to analyze and interpret SF-12 Health Survey data, using norm-based interpretation guidelines which are useful for purposes of program development and collecting information on health at the community level. ^

Neodymium and Strontium chemistry of Arctic Ocean sediments

The early oceanographic history of the Arctic Ocean is important in regulating, and responding to, climatic changes. However, constraints on its oceanographic history preceding the Quaternary (the past 1.8 Myr) have become available only recently, because of the difficulties associated with obtaining continuous sediment records in such a hostile setting. Here, we use the neodymium isotope compositions of two sediment cores recovered near the North Pole to reconstruct over the past ~5 Myr the sources contributing to Arctic Intermediate Water, a water mass found today at depths of 200 to 1,500 m. We interpret high neodymium ratios for the period between 15 and 2 Myr ago, and for the glacial periods thereafter, as indicative of weathering input from the Siberian Putoranan basalts into the Arctic Ocean. Arctic Intermediate Water was then derived from brine formation in the Eurasian shelf regions, with only a limited contribution of intermediate water from the North Atlantic. In contrast, the modern circulation pattern, with relatively high contributions of North Atlantic Intermediate Water and negligible input from brine formation, exhibits low neodymium isotope ratios and is typical for the interglacial periods of the past 2 Myr. We suggest that changes in climatic conditions and the tectonic setting were responsible for switches between these two modes.

Photocatalytic Concretes – The interface between photocatalysis and cement chemistry

We thank the European Commission for financial support through the European Project Light2CAT, funded by the European Union’s Seventh Framework Programme (FP7) under the grant agreement no. 283062 Eco-Innovation, Theme Environment

Physical and Genetic Analysis of the CUP1 Tandem Array in the Yeast Saccharomyces cerevisiae

The genomes of many strains of baker’s yeast, Saccharomyces cerevisiae, contain multiple repeats of the copper-binding protein Cup1. Cup1 is a member of the metallothionein family, and is found in a tandem array on chromosome VIII. In this thesis, I describe studies that characterized these tandem arrays and their mechanism of formation across diverse strains of yeast. I show that CUP1 arrays are an illuminating model system for observing recombination in eukaryotes, and describe insights derived from these observations.

In our first study, we analyzed 101 natural isolates of S. cerevisiae in order to examine the diversity of CUP1-containing repeats across different strains. We identified five distinct classes of repeats that contain CUP1. We also showed that some strains have only a single copy of CUP1. By comparing the sequences of all the strains, we were able to elucidate the mechanism of formation of the CUP1 tandem arrays, which involved unequal non-homologous recombination events starting from a strain that had only a single CUP1 gene. Our observation of CUP1 repeat formation allows more general insights about the formation of tandem repeats from single-copy genes in eukaryotes, which is one of the most important mechanisms by which organisms evolve.

In our second study, we delved deeper into our mechanistic investigations by measuring the relative rates of inter-homolog and intra-/inter-sister chromatid recombination in CUP1 tandem arrays. We used a diploid strain that is heterozygous both for insertion of a selectable marker (URA3) inside the tandem array, and also for markers at either end of the array. The intra-/inter-sister chromatid recombination rate turned out to be more than ten-fold greater than the inter-homolog rate. Moreover, we found that loss of the proteins Rad51 and Rad52, which are required for most inter-homolog recombination, did not greatly reduce recombination in the CUP1 tandem repeats. Additionally, we investigated the effects of elevated copper levels on the rate of each type of recombination at the CUP1 locus. Both types of recombination are increased at high concentrations of copper (as is known to be the case for CUP1 transcription). Furthermore, the inter-homolog recombination rate at the CUP1 locus is higher than the average over the genome during mitosis, but is lower than the average during meiosis.

The research described in Chapter 2 is published in 2014.

Experimental and Theoretical Models to Probe Mechanisms of Biological Charge Flow

Nature is challenged to move charge efficiently over many length scales. From sub-nm to μm distances, electron-transfer proteins orchestrate energy conversion, storage, and release both inside and outside the cell. Uncovering the detailed mechanisms of biological electron-transfer reactions, which are often coupled to bond-breaking and bond-making events, is essential to designing durable, artificial energy conversion systems that mimic the specificity and efficiency of their natural counterparts. Here, we use theoretical modeling of long-distance charge hopping (Chapter 3), synthetic donor-bridge-acceptor molecules (Chapters 4, 5, and 6), and de novo protein design (Chapters 5 and 6) to investigate general principles that govern light-driven and electrochemically driven electron-transfer reactions in biology. We show that fast, μm-distance charge hopping along bacterial nanowires requires closely packed charge carriers with low reorganization energies (Chapter 3); singlet excited-state electronic polarization of supermolecular electron donors can attenuate intersystem crossing yields to lower-energy, oppositely polarized, donor triplet states (Chapter 4); the effective static dielectric constant of a small (~100 residue) de novo designed 4-helical protein bundle can change upon phototriggering an electron transfer event in the protein interior, providing a means to slow the charge-recombination reaction (Chapter 5); and a tightly-packed de novo designed 4-helix protein bundle can drastically alter charge-transfer driving forces of photo-induced amino acid radical formation in the bundle interior, effectively turning off a light-driven oxidation reaction that occurs in organic solvent (Chapter 6). This work leverages unique insights gleaned from proteins designed from scratch that bind synthetic donor-bridge-acceptor molecules that can also be studied in organic solvents, opening new avenues of exploration into the factors critical for protein control of charge flow in biology.

(Table 1) Determined and theoretical chemical composition of thaumasite of ODP Hole 135-841B

Hole 841B was drilled in the forearc region of the Lau Basin at a water depth of 4810 m. The hole penetrated a roughly 500-m-thick series of Miocene volcanic sediments with a number of basaltic to andesitic units (sills?) varying in thickness between 7 cm and 17 m. The volcanics are slightly to moderately altered and contain analcite, chabazite, natrolite-thompsonite, heulandite (?), prehnite, and quartz as secondary phases. In addition, thaumasite [Ca3Si(OH)6 * 12H2O](SO4)(CO3) was identified in the altered sequence. Sulfur isotope data of two thaumasite separates (+23.5 per mil and +21.1 per mil d34S) indicate a seawater origin of the sulfate sulfur. It is suggested that thaumasite is a product of low-temperature (<60 °C), seawater-derived CaCl2-rich fluids that were almost identical in composition to those presently circulating in the sub-seafloor.

Seawater carbonate chemistry and hydrogen ions and carbonate chemistry in calcifying fluid of coral Astrangia poculata during experiments, 2011

A generalized physicochemical model of the response of marine organisms' calcifying fluids to CO2-induced ocean acidification is proposed. The model is based upon the hypothesis that some marine calcifiers induce calcification by elevating pH, and thus Omega aragonite, of their calcifying fluid by removing protons (H+). The model is explored through two end-member scenarios: one in which a fixed number of H+ is removed from their calcifying fluid, regardless of atmospheric pCO2, and another in which a fixed external-internal proton ratio ([H+]E/[H+]I) is maintained. The model is able to generate the full range of calcification response patterns observed in prior ocean acidification experiments and is consistent with the assertion that organisms' calcification response to ocean acidification is more negative for marine calcifiers that exert weaker control over their calcifying fluid pH. The model is empirically evaluated for the temperate scleractinian coral Astrangia poculata with in situ pH microelectrode measurements of the coral's calcifying fluid under control and acidified conditions. These measurements reveal that (1) the pH of the coral's calcifying fluid is substantially elevated relative to its external seawater under both control and acidified conditions, (2) the coral's [H+]E/[H+]I remains constant under control and acidified conditions, and (3) the coral removes fewer H+ from its calcifying fluid under acidified conditions than under control conditions. Thus, the carbonate system dynamics of A. poculata's calcifying fluid appear to be most consistent with the fixed [H+]E/[H+]I end-member scenario. Similar microelectrode experiments performed on additional taxa are required to assess the model's general applicability.