Trophic Shifts Introduced To The Saco River Estuary By A Central Secondary Consumer, The Invasive European Green Crab (Carcinus Maenas)

The European green crab (Carcinus maenus) is one of the most notorious invasive species found along the East coast of the United States. Green crabs were introduced to the US in the 1800s when they supposedly rode in ballast water across the Atlantic Ocean. Green crabs are native to the Atlantic coasts of Europe and Northern Africa. Once established on the Atlantic coast of North America, they started to migrate mostly north, and will continue to do so with warming waters due to climate change. (Glude 1955). Warmer winters will lead to greater crab egg survival, increasing the green crabs’ reproductive success. Green crabs have become one of the main and most dangerous predators of bivalve mollusks on the East coast and have become a major problem for soft shell clam harvesters. Not only are green crabs decimating soft shell clam flats, they also have greatly reduced populations of blue mussels (Mytulis edulis), and recent work in Newfoundland has shown that they are also starting to target shallow water scallop populations (Matheson and Mckenzie, 2014). Larger crabs also tend to choose soft shell clams and mussels over scallops, but crabs of all sizes will eat scallops, if presented to them. Green crabs range from 6 to 10 cm, but some are larger (Perry, 2017). Green crab populations are able to access to a wide variety of types and sizes of prey ranging from bivalves to native crabs, due to their scavenger lifestyle. While many of these consequences of the invasive are regularly observed by fishermen, beachcomber, and researchers, not much is known about the true quantifiable and qualitative results of these crabs. This thesis aims to gain an understanding of the fallouts of the green crab invasion by analyzing the trophic interactions in which the green crab acts as a predator and in which it is the prey. The first chapter found in this thesis is the paper titled Stable Isotope Signatures Reflected in Habitat Affinities: Saltwater, Estuarine, and Freshwater Fish in Saco Bay. Utilizing stable isotope analysis of muscle samples from marine species found in Saco Bay, a biplot was created in which these marine species were characterized by their δ13C and δ15N values. Some of the species included in these samples were striped bass (Morone saxatilis), sand eels (Ammodyes americanus), green crabs, and Atlantic herring (Clupea harengus). Studying species like this is incredibly important due to their high recreational and commercial values. The results from this analytical paper allowed for conclusions to be made about the trophic level of organisms and the geographic location of where that organism was caught, simply based on their δ13C and δ15N signatures. Where each organism was captured was reflected by the δ13C value on the graph, supporting that geographic location, even if it is a within a small area, can be determined using carbon stable isotope analysis. Green crabs were the only species on the list of those sampled that are labelled as invasive and based on the biplot, green crabs seemed to have an impact on other species interactions with each other. Discerning the top-down and bottom up effects of the green crab presence on the Atlantic coast of North America is significant in protecting native resources and coastal livelihoods. The soft shell clam (Mya arenaria), has experienced dramatic population shifts with the introduction of green crabs and is currently being studied to determine the true impacts of this invasive predations. The crabs’ direct effects on economically important species like the soft shell clam are felt by the clammers who rely on soft shell clams as a portion of their annual income. Reduced juvenile soft shell recruitment and reduced seeded clam survivorship are two of the most observed changes in the clam flat communities in recent times. Clammers have started to use landscape mesh to cover their juvenile clams in order to increase the clams’ survivorship and the profit margins for the clammers. With soft shell clams holding 4% of the seafood market value in Maine, it is critical that the true impacts of predation are understood in order to try an reduce the effects and increase both the clammers’ yields and also help to maintain this incredibly important ecosystem found within the mudflats. It is estimated that commercial fisheries have experienced upwards of $44 million in losses from green crabs (Perry, 2011). Chapter 2 titled, The relative impacts of both native predators and the invasive European green crab (Carcinus maenas) on seeded soft shell clams (Mya arenaria) in Southern Maine tidal mudflats, aimed to quantify the predation of green crabs on soft shell clams by utilizing various predator exclusion methods, one of which was the landscape mesh that clammers already use. Green crabs are not only an efficient and deadly predator on the mudflats, but they also pose another ecological role: as a food source. Striped bass are well known as having an extremely varied diet throughout each migratory season. Squid, mackerel, lobsters, and herring are just a few of the notable prey items of the striped bass, but their diet changes as they travel south to north and north to south during the spring and fall (Nelson et al, 2003). Green crabs happen to live within the same range that the striped bass do and are regularly found in the mouths and stomachs of striped bass of all sizes. Striped bass constantly move in search of bait, scouring boulder field, sandflats, and river mouths, among other locations along the Atlantic Coast of North America (Walbaum, 1792). Green crabs also habit the same areas that striped bass do, presenting themselves as a potential food source for striped bass. While many of the striped bass’ preferred food sources (i.e. baitfish) are constantly travelling to find food and avoid predators, green crabs tend to congregate in the same areas, as they are weak swimmers and do not migrate any more than within the intertidal zone (Green Crab, Washington). Striped bass find themselves in the presence of green crabs on a near day to day basis, due to their high abundance. As striped bass are opportunistic feeders, green crabs pose a potential to be a supplement to the striped bass’s diet, especially when other food sources are scarce. Chapter 3, Trophic shifts in the Saco River Estuary that occur with the arrival and summer residence of the striped bass (Morone saxatilis), aimed to determine the importance of green crabs in the striped bass diet, and compare its stable isotope signatures with signatures from other prey items of the striped bass. Invasive species are of utmost concern when it comes to environmental protection as they can dominate important native species and cause major damage to essential ecological processes, like the cycling of nutrients. Green crabs have been established on the Atlantic coast of North America for 200 years now, and the progressive effects of these invaders on native populations is being observed and analyzed in the field and in the lab. This thesis aims to evaluate the top-down and bottom-up effects caused by the green crab in the Saco River Estuary

Ueber die Hutchinsonschen Zähne 1 )

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A Method for Fast, High-Precision Characterization of Synthetic Biology Devices

Engineering biological systems with predictable behavior is a foundational goal of synthetic biology. To accomplish this, it is important to accurately characterize the behavior of biological devices. Prior characterization efforts, however, have generally not yielded enough high-quality information to enable compositional design. In the TASBE (A Tool-Chain to Accelerate Synthetic Biological Engineering) project we have developed a new characterization technique capable of producing such data. This document describes the techniques we have developed, along with examples of their application, so that the techniques can be accurately used by others

Zur Lehre von der "Mola haematomatosa"

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Foundational platform for mammalian synthetic biology

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, February 2013Cataloged from PDF version of thesis.Includes bibliographical references (p. 116-129).The emergent field of synthetic biology is different from many other biological engineering efforts, in that its roots, design principles, and forward engineering perspective have been adopted from electrical engineering and computer science. Synthetic biology is uniquely poised to make great contributions to numerous fields such as bio-fuel, energy production, agriculture and eco-remediation, national defense, and biomedical and tissue engineering. Considerable progress has been made in engineering novel genetic circuits in many different organisms. However, not much progress has been made toward developing a formal methodology to engineer complex genetic systems in mammalian cells. One of the most promising areas of research is the study of embryonic and adult stem cells. Synthetic biology has the potential to greatly impact the progression and development of research in this area of study. A critical impediment to the development of stem cell engineering is the innate complexity, little to no characterization of parts, and limited compositional predictive capabilities. In this thesis, I discuss the strategies used for constructing and optimizing the performance of signaling pathways, the development of a large mammalian genetic part and circuit library, and the characterization and implementation of novel genetic parts and components aimed at developing a foundation for mammalian synthetic biology. I have designed and tested several orthogonal strategies aimed at cell-cell communication in mammalian cells. I have designed a characterization framework for the complete and proper characterization of genetic parts that allows for modular predictive composition of genetic circuits. With this characterization framework I have generated a small library of characterized parts and composite circuits that have well defined input-output relationships that can be used in novel genetic architectures. I also aided in the development of novel analysis and computational tools necessary for accurate predictive composition of these novel circuits. This work collectively provides a foundation for engineering complex intracellular transcriptional networks and intercellular signaling systems in mammalian cells.by Noah Davidsohn.Ph.D

Polychlorinated biphenyl-induced alteration of biologic parameters in the rat,

Aroclor 1242, a commercial polychlorinated biphenyl (PCB) mixture, was administered ip to rats for 10 weeks. Principal findings included: loss of body weight; hepatic and renal damage, with some animals exhibiting renal papillary epithelial hyperplasia; slight reduction in erythrocyte count, diameter, and hemoglobin content, with an elevation in serum iron; diminished plasma corticosteroid and glucose concentrations; increased urinary excretion of protein, sugars, and coproporphyrin.The effect of PCBs on several hepatic microsomal enzymatic parameters was also evaluated. Maximal hydroxylation and N-demethylation activities were observed 3-10 days following a single ip injection (100 mg/kg). Each remained significantly higher than control values after 20 days, with hydroxylation activity still 150% of controls after 40 days. The minimal effective single dose for induction of hydroxylation activity was approximately 5 mg/kg. Induction of hydroxylation activity was found to be dose-dependent; however, a smaller degree of correlation was noted between N-demethylation activity and dose. Values for cytochromes P450 and b5 and NADPH-cytochrome c reductase activity were observed to roughly parallel hydroxylation and N-demethylation activities, the highest degree of correlation was manifest between enzymatic activity and cytochrome P450 values.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22359/1/0000805.pd

Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity

Synthetic biology efforts have largely focused on small engineered gene networks, yet understanding how to integrate multiple synthetic modules and interface them with endogenous pathways remains a challenge. Here we present the design, system integration, and analysis of several large scale synthetic gene circuits for artificial tissue homeostasis. Diabetes therapy represents a possible application for engineered homeostasis, where genetically programmed stem cells maintain a steady population of β-cells despite continuous turnover. We develop a new iterative process that incorporates modular design principles with hierarchical performance optimization targeted for environments with uncertainty and incomplete information. We employ theoretical analysis and computational simulations of multicellular reaction/diffusion models to design and understand system behavior, and find that certain features often associated with robustness (e.g., multicellular synchronization and noise attenuation) are actually detrimental for tissue homeostasis. We overcome these problems by engineering a new class of genetic modules for ‘synthetic cellular heterogeneity’ that function to generate beneficial population diversity. We design two such modules (an asynchronous genetic oscillator and a signaling throttle mechanism), demonstrate their capacity for enhancing robust control, and provide guidance for experimental implementation with various computational techniques. We found that designing modules for synthetic heterogeneity can be complex, and in general requires a framework for non-linear and multifactorial analysis. Consequently, we adapt a ‘phenotypic sensitivity analysis’ method to determine how functional module behaviors combine to achieve optimal system performance. We ultimately combine this analysis with Bayesian network inference to extract critical, causal relationships between a module's biochemical rate-constants, its high level functional behavior in isolation, and its impact on overall system performance once integrated.National Institutes of Health (U.S.) (NIH NIGMS grant R01GM086881)National Science Foundation (U.S.) (NSF Award #1001092)National Science Foundation (U.S.) (NSF Graduate Research Fellowship Program)Swiss National Science Foundation (SystemsX.ch grant

An enhanced CRISPR repressor for targeted mammalian gene regulation.

The RNA-guided endonuclease Cas9 can be converted into a programmable transcriptional repressor, but inefficiencies in target-gene silencing have limited its utility. Here we describe an improved Cas9 repressor based on the C-terminal fusion of a rationally designed bipartite repressor domain, KRAB-MeCP2, to nuclease-dead Cas9. We demonstrate the system's superiority in silencing coding and noncoding genes, simultaneously repressing a series of target genes, improving the results of single and dual guide RNA library screens, and enabling new architectures of synthetic genetic circuits