Effects of Endothelin 3 on the Tumor-Angiogenic Response in a Novel Melanoma Mouse Model

Skin cancer is the most common form of cancer in the United States. Melanoma is a particular type of skin cancer, which arises from the malignant transformation of melanocytes and generally exhibits a high propensity to metastasize. Melanoma progression is dependent on angiogenesis to deliver the oxygen and nutrients required to maintain the altered metabolism of rapidly proliferating tumorigenic cells. Recent studies have implicated the growth factor Endothelin 3 (Edn3) in melanoma progression and metastasis. The aim of this study was to examine the role that Edn3 plays in the angiogenesis of melanocytic lesions. For this purpose, Dct-Grm1 transgenic mice, which spontaneously acquire melanocytic lesions through the aberrant expression of the metabotropic glutamate receptor 1 (mGluR1), were crossed with K5-Edn3 transgenic mice that overexpress Edn3. Tumors in the Dct-Grm1/K5-Edn3 experimental population were examined and compared to the control Dct-Grm1 population using immuno-fluorescent staining targeted against the vascular endothelial cell marker CD31. Proteomic arrays were also used and identified changes in the expression of specific angiogenic factors. CD31 antibody staining results revealed an increased vascular density in Dct-Grm1/K5-Edn3 tumors compared with tumors from the Dct-Grm1 controls. Analysis of the relative expression of angiogenic proteins showed an upregulation of various vascular factors in tumors from the Dct-Grm1/K5-Edn3 population, including VEGF-B, MMP-8, MMP-9, and Angiogenin. These results suggest that endothelin signaling promotes angiogenesis in melanocytic lesions. Targeting the factors upregulated by Edn3 signaling may prove effective in hindering melanoma progression.

Allocation of Biomass and Net Primary Productivity of Mangrove Forests along Environmental Gradients in the Florida Coastal Everglades, USA

Vegetation patterns of mangroves in the Florida Coastal Everglades (FCE) result from the interaction of environmental gradients and natural disturbances (i.e., hurricanes), creating an array of distinct riverine and scrub mangroves across the landscape. We investigated how landscape patterns of biomass and total net primary productivity (NPPT), including allocation in above- and below-ground mangrove components, vary inter-annually (2001–2004) across gradients in soil properties and hydroperiod in two distinct FCE basins: Shark River Estuary and Taylor River Slough. We propose that the allocation of belowground biomass and productivity (NPPB) relative to aboveground allocation is greater in regions with P limitation and permanent flooding. Porewater sulfide was significantly higher in Taylor River (1.2 ± 0.3 mM) compared to Shark River (0.1 ± 0.03 mM) indicating the lack of a tidal signature and more permanent flooding in this basin. There was a decrease in soil P density and corresponding increase in soil N:P from the mouth (28) to upstream locations (46–105) in Shark River that was consistent with previous results in this region. Taylor River sites showed the highest P limitation (soil N:P > 60). Average NPPT was double in higher P environments (17.0 ± 1.1 Mg ha−1 yr−1) compared to lower P regions (8.3 ± 0.3 Mg ha−1 yr−1). Root biomass to aboveground wood biomass (BGB:AWB) ratio was 17 times higher in P-limited environments demonstrating the allocation strategies of mangroves under resource limitation. Riverine mangroves allocated most of the NPPT to aboveground (69%) while scrub mangroves showed the highest allocation to belowground (58%). The total production to biomass (P:B) ratios were lower in Shark River sites (0.11 yr−1); whereas in Taylor River sites P:B ratios were higher and more variable (0.13–0.24 yr−1). Our results suggest that the interaction of lower P availability in Taylor River relative to Shark River basin, along with higher sulfide and permanent flooding account for higher allocation of belowground biomass and production, at expenses of aboveground growth and wood biomass. These distinct patterns of carbon partitioning between riverine and scrub mangroves in response to environmental stress support our hypothesis that belowground allocation is a significant contribution to soil carbon storage in forested wetlands across FCE, particularly in P-limited scrub mangroves. Elucidating these biomass strategies will improve analysis of carbon budgets (storage and production) in neotropical mangroves and understanding what conditions lead to net carbon sinks in the tropical coastal zone.

Environmental Dynamics of Dissolved Black Carbon in Wetlands

Wetlands are ecosystems commonly characterized by elevated levels of dissolved organic carbon (DOC), and although they cover a surface area less than 2 % worldwide, they are an important carbon source representing an estimated 15 % of global annual DOC flux to the oceans. Because of their unique hydrological characteristics, fire can be an important ecological driver in pulsed wetland systems. Consequently, wetlands may be important sources not only of DOC but also of products derived from biomass burning, such as dissolved black carbon (DBC). However, the biogeochemistry of DBC in wetlands has not been studied in detail. The objective of this study is to determine the environmental dynamics of DBC in different fire-impacted wetlands. An intensive, 2-year spatial and temporal dynamics study of DBC in a coastal wetland, the Everglades (Florida) system, as well as one-time sampling surveys for the other two inland wetlands, Okavango Delta (Botswana) and the Pantanal (Brazil), were reported. Our data reveal that DBC dynamics are strongly coupled with the DOC dynamics regardless of location, season or recent fire history. The statistically significant linear regression between DOC and DBC was applied to estimate DBC fluxes to the coastal zone through two main riverine DOC export routes in the Everglades ecosystem. The presence of significant amounts of DBC in these three fire-impacted ecosystems suggests that sub-tropical wetlands could represent an important continental-ocean carrier of combustion products from biomass burning. The discrimination of DBC molecular structure (i.e. aromaticity) between coastal and terrestrial samples, and between samples collected in wet and dry season, suggests that spatially-significant variation in DBC source strength and/or degree of degradation may also influence DBC dynamics.

Connectivity of fragmented amphibian populations in a neotropical landscape

A high proportion of amphibian species are threatened with extinction globally, and habitat loss and degradation are the most frequently implicated causes. Rapid deforestation for the establishment of agricultural production is a primary driver of habitat loss in tropical zones where amphibian diversity is highest. Land-cover change affects native assemblages, in part, through the reduction of habitat area and the reduction of movement among remnant populations. Decreased gene flow contributes to loss of genetic diversity, which limits the ability of local populations to respond to further environmental changes. The focus of this dissertation is on the degree to which common land uses in Sarapiquí, Costa Rica impede the movement of two common amphibian species. First, I used field experiments, including displacement trials, and a behavioral landscape ecology framework to investigate the resistance of pastures to movement of Oophaga pumilio. Results from experiments demonstrate that pastures do impede movement of O. pumilio relative to forest. Microclimatic effects on movement performance as well as limited perceptual ranges likely contribute to reduced return rates through pastures. Next, I linked local processes to landscape scale estimates of resistance. I conducted experiments to measure habitat-specific costs to movement for O. pumilio and Craugastor bransfodrii, and then used experimental results to parameterize connectivity models. Model validation indicated highest support for resistance estimates generated from responses to land-use specific microclimates for both species and to predator encounters for O. pumilio. Finally, I used abundance and experiment-derived resistance estimates to analyze the effects of prevalent land uses on population genetic structure of the two focal species. While O. pumilio did not exhibit a strong response to landscape heterogeneity and was primarily structured by distances among sites, C. bransfordii genetic variation was explained by resistance estimates from abundance and experiment data. Collectivity, this work demonstrates that common land uses can offer different levels of resistance to amphibian movements in Sarapiquí and illustrates the value of investigating local scales processes to inform interpretation of landscape-scale patterns.^

Managing small-scale commercial fisheries for adaptive capacity: Insights from dynamic social-ecological drivers of change in Monterey Bay

Globally, small-scale fisheries (SSFs) are driven by climate, governance, and market factors of social-ecological change, presenting both challenges and opportunities. The ability of small-scale fishermen and buyers to adapt to changing conditions allows participants to survive economic or environmental disturbances and to benefit from optimal conditions. This study presented here identifies key large-scale factors that drive SSFs in California to shift focus among targets and that dictate long-term trends in landings. We use Elinor Ostrom’s Social-Ecological System (SES) framework to apply an interdisciplinary approach when identifying potential factors and when understanding the complex dynamics of these fisheries. We analyzed the interactions among Monterey Bay SSFs over the past four decades since the passage of the Magnuson Stevens Fisheries Conservation and Management Act of 1976. In this region, the Pacific sardine (Sardinops sagax), northern anchovy (Engraulis mordax), and market squid (Loligo opalescens) fisheries comprise a tightly linked system where shifting focus among fisheries is a key element to adaptive capacity and reduced social and ecological vulnerability. Using a cluster analysis of landings, we identified four modes from 1974 to 2012 that were dominated by squid, sardine, anchovy, or lacked any dominance, enabling us to identify external drivers attributed to a change in fishery dominance during seven distinct transition points. Overall, we show that market and climate factors drive the transitions among dominance modes. Governance phases most dictated long-term trends in landings and are best viewed as a response to changes in perceived biomass and thus a proxy for biomass. Our findings suggest that globally, small-scale fishery managers should consider enabling shifts in effort among fisheries and retaining existing flexibility, as adaptive capacity is a critical determinant for social and ecological resilience.

Effects of invasive Africanized honey bees (Apis mellifera scutellata) on native stingless bee populations (Meliponinae) and traditional Mayan beekeeping in central Quintana Roo, Mexico

The Maya of the Yucatan region have a long history of keeping the native stingless bees (subfamily Meliponinae). However, market forces in the last few decades have driven the Maya to favor the use of invasive Africanized honey bees (Apis mellifera scutellata) for producing large quantities of high quality honey that has an international market. Furthermore, the native bees traditionally used by the Maya are now disappearing, along with the practice of keeping them. ^ An interdisciplinary approach was taken in order to determine the social factors behind the decrease in stingless beekeeping and the ecological driving forces behind their disappearance from the wild. Social research methods included participant observation with stingless beekeepers, Apis beekeepers, and marketing intermediaries. Ecological research methods included point observations of commonly known melliferous and polliniferous plants along transects in three communities with different degrees of human induced ecosystem disturbance. ^ The stingless bee species most important to the Maya, Melipona beecheii, has become extremely rare, and this has caused a breakdown of stingless beekeeping tradition, compounded with the pressure of the market economy, which fuels Apis beekeeping and has lessened the influence of traditional practices. The community with the heaviest amount of human induced ecosystem disturbance also had the highest degree of dominance of Apis mellifera, while the area with the most intact ecosystem had the highest diversity of stingless bees, though Apis mellifera was still the dominant species. Aggressive competitive behavior involving physical attacks by Apis mellifera against stingless bees was observed on several occasions, and this is a new observation previously unreported by science. ^

An overview on Human Leukocyte Antigen (HLA) region gene expression during Pseudomonas aeruginosa infection

The human leukocyte antigen (HLA) complex is an extensively studied cluster of genes with immunoregulatory function. Pseudomonas aeruginosa is capable of infecting individuals with weakened immune systems, and is associated with a high mortality rate. Previous genetic studies of the HLA region have found correlations between bacterial infection and its effect on regulating HLA gene expressions to establish their infection. This project analyzes the expression of classical HLA loci (A, B, C, DR, DQ, DP) in human B cells and macrophage cells during the infection of virulent strains of P. aeruginosa. Cells were cultured and infected with different virulent live, and heat-killed strains of P. aeruginosa for different time periods. The mRNA was extracted and converted into cDNA followed by real-time quantitative PCR and data analysis. The Western Blot technique was used to identify the targeted protein’s cell surface expression. Infection with P. aeruginosa was found to inhibit the expression of HLA proteins. The PA14 strain inhibited expression of all targeted genes in all experiments. Infections with PA01 and PA103 showed different patterns depending on the incubation time and the targeted gene. These differences suggest that the three strains use various mechanisms to inhibit HLA protein expression.

Evaluation of Some Statistical Methods for the Identification of Differentially Expressed Genes

Microarray platforms have been around for many years and while there is a rise of new technologies in laboratories, microarrays are still prevalent. When it comes to the analysis of microarray data to identify differentially expressed (DE) genes, many methods have been proposed and modified for improvement. However, the most popular methods such as Significance Analysis of Microarrays (SAM), samroc, fold change, and rank product are far from perfect. When it comes down to choosing which method is most powerful, it comes down to the characteristics of the sample and distribution of the gene expressions. The most practiced method is usually SAM or samroc but when the data tends to be skewed, the power of these methods decrease. With the concept that the median becomes a better measure of central tendency than the mean when the data is skewed, the tests statistics of the SAM and fold change methods are modified in this thesis. This study shows that the median modified fold change method improves the power for many cases when identifying DE genes if the data follows a lognormal distribution.

Evaluation of the use and management of fish resources in the pachitea river basin, Peruvian Amazon

The purpose of this study was to analyze the interrelations between the needs of local people and their usage and management of natural fisheries. Between June and August 2001, 177 households in the basin were interviewed regarding their fishing customs. The results were analyzed with parametric and nonparametric statistics considering a cultural and a geographic comparison. Results confirm that indigenous households rely more on fisheries as a resource than colonists. Fishing takes place throughout the year but is more common in the dry season. Fishing is commonly practiced using hooks and cast nets. More destructive techniques such as dynamite and "barbasco" (poisonous plant) were also used. Indigenous people use a greater array of techniques and they fish at a greater diversity of sites. Respondents also reported that fishing yields have decreased recently. Some of the most common fish genera captured are Pimelodus and Leporinus.

Fibonacci Series, Golden Proportions, and the Human Biology

Pythagoras, Plato and Euclid’s paved the way for Classical Geometry. The idea of shapes that can be mathematically defined by equations led to the creation of great structures of modern and ancient civilizations, and milestones in mathematics and science. However, classical geometry fails to explain the complexity of non-linear shapes replete in nature such as the curvature of a flower or the wings of a Butterfly. Such non-linearity can be explained by fractal geometry which creates shapes that emulate those found in nature with remarkable accuracy. Such phenomenon begs the question of architectural origin for biological existence within the universe. While the concept of a unifying equation of life has yet to be discovered, the Fibonacci sequence may establish an origin for such a development. The observation of the Fibonacci sequence is existent in almost all aspects of life ranging from the leaves of a fern tree, architecture, and even paintings, makes it highly unlikely to be a stochastic phenomenon. Despite its wide-spread occurrence and existence, the Fibonacci series and the Rule of Golden Proportions has not been widely documented in the human body. This paper serves to review the observed documentation of the Fibonacci sequence in the human body.

Environmental analysis of polar herbicides in complex organic-rich matrices by high performance liquid chromatography atmospheric pressure ionization mass spectrometry (HPLC-API-MS)

A comprehensive forensic investigation of sensitive ecosystems in the Everglades Area is presented. Assessing the background levels of contamination in these ecosystems represents a vital resource to build up forensic evidence required to enforce future environmental crimes within the studied areas. This investigation presents the development and validation of a fractionation and isolation method for two families of herbicides commonly applied in the vicinity of the study area, including phenoxy acids like 2,4-D, MCPA, and silvex; as well as the most common triazine-based herbicides like atrazine, prometyne, simazine and related metabolites like DIA and DEA. Accelerated solvent extraction (ASE) and solid phase extraction (SPE) were used to isolate the analytes from abiotic matrices containing large amounts of organic material. Atmospheric-pressure ionization (API) with electrospray ionization in negative mode (ESP-), and Chemical Ionization in the positive mode (APCI+) were used to perform the characterization of the herbicides of interest.

Stream drying drives microbial ammonia oxidation and first-flush nitrate export

Funded by Spanish National Research Council (CSIC). Grant Number: CGL2012-32747 MINECO. Grant Numbers: CGL2012-32747, CGL2011-30590-CO2-02 EU Commission. Grant Number: 244121 FP7

Decoupling of Greenhouse Gas Emissions from Global Agricultural Production : 1970 - 2050

This article is protected by copyright. All rights reserved. Acknowledgements We thank Tamara Ben-Ari and Jean-Francois Soussana, from INRA in France, for their valuable contributions to the early development stage of this project. We also owe great acknowledge to Prof. Ib Skovgaard, University of Copenhagen, for giving essential assistance in developing the methods for decomposing emission changes. We also thank the Centre for Regional Change in the Earth System (CRES, www.cres-centre.dk) and the Department of Plant- and Environmental Sciences, University of Copenhagen, for funding the work.

Assessing consistency of fish survey data : uncertainties in the estimation of mackerel icefish (Champsocephalus gunnari) abundance at South Georgia

Acknowledgments The authors wish to thank the crews, fishermen and scientists who conducted the various surveys from which data were obtained, and Mark Belchier and Simeon Hill for their contributions. This work was supported by the Government of South Georgia and South Sandwich Islands. Additional logistical support provided by The South Atlantic Environmental Research Institute with thanks to Paul Brickle. Thanks to Stephen Smith of Fisheries and Oceans Canada (DFO) for help in constructing bootstrap confidence limits. Paul Fernandes receives funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland), and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. We also wish to thank two anonymous referees for their helpful suggestions on earlier versions of this manuscript.

Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line

This project was carried out during CD’s BBSRC Eastbio PIPS placement at Marine Scotland. The authors are grateful to Dr Milena Monte (University of Aberdeen) for help with the FACS analysis. The authors wish to thank Dr Filippo Del Bene (Neuronal Circuit Development, Institut Curie) and Dr Wenbiao Chen (School of Medicine, Vanderbilt University) for the Addgene plasmids, #61051 and #47929, respectively, and Prof. Nancy C. Reich Marshall (Department of Molecular Genetics and Microbiology, Stony Brooks University) for the plasmid pmEGFP-N1.