Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits

Synthetic biology combines biological parts from different sources in order to engineer non-native, functional systems. While there is a lot of potential for synthetic biology to revolutionize processes, such as the production of pharmaceuticals, engineering synthetic systems has been challenging. It is oftentimes necessary to explore a large design space to balance the levels of interacting components in the circuit. There are also times where it is desirable to incorporate enzymes that have non-biological functions into a synthetic circuit. Tuning the levels of different components, however, is often restricted to a fixed operating point, and this makes synthetic systems sensitive to changes in the environment. Natural systems are able to respond dynamically to a changing environment by obtaining information relevant to the function of the circuit. This work addresses these problems by establishing frameworks and mechanisms that allow synthetic circuits to communicate with the environment, maintain fixed ratios between components, and potentially add new parts that are outside the realm of current biological function. These frameworks provide a way for synthetic circuits to behave more like natural circuits by enabling a dynamic response, and provide a systematic and rational way to search design space to an experimentally tractable size where likely solutions exist. We hope that the contributions described below will aid in allowing synthetic biology to realize its potential.

Physiological Determinants of Invasive Success Linking Distribution Patterns to Metabolic Physiology in Native and Invasive Blue Mussels (genus Mytilus)

In the early 20th century, a blue mussel species from the Mediterranean invaded the California coast and subsequently out-competed the native species south of Monterey Bay. Like other invasive species, Mytilus galloprovincialis has physiological traits that make it successful in habitats formerly occupied by the native M. trossulus, namely its adaptation to warm sea surface temperatures. This study looks at the current genotype distributions and enzymatic activities of field-acclimatized mussels within the hybrid zone where the species co-occur as well as mussels that have been acclimated for four weeks to different temperature and salinity conditions. In the field-acclimatized and laboratory-acclimated mussels, the native species exhibited significantly higher enzyme rates, which may reflect an evolutionary adaptation to compensate to low habitat temperatures. Indeed, the results of the laboratory acclimation indicate that these differences are genetically based. Whether an acclimation capacity exists may require even longer-term acclimation to different temperatures. Current findings suggest that the further spread of the invasive species is likely to be governed in large measure by the potentially counteracting effects of rising temperatures, which would favor the northerly spread of M. galloprovincialis, and increased winter precipitation, which would favor the persistence of M. trossulus. However, the success of M. galloprovincialis during acclimation to ‘dilute’ salinity (25 ppt) suggests that the invasive species can tolerate a greater salinity range than previously thought. Thus, further investigation is needed to build a comprehensive predictive model of the movement of M. galloprovincialis and the hybrid zone along the California coast.

Developing aquaculture of Small Native Species (SNS) in Bangladesh: village level agroecological change and the availability of SNS

Small native species (SNS) of fish are important source of protein and income for rural people in Bangladesh. A rapid rural appraisal study was carried out to explore the recent changes in the availability of SNS in relation to agroecology and related issues. Village residents noted that the availability of SNS had declined drastically due to habitat loss related to agricultural intensification and due to the restriction of access to the remaining habitats in the course of aquaculture development. Their perception was that poor people had gained from the intensification of agriculture in terms of rice consumption but had lost in terms of reduced access to fish and other animal products.

Deleterious effects of non-native species introduced into Lake Victoria, East Africa

Lake Victoria, in East Africa, has suffered from introductions and invasions of non-native species such as Lates niloticus, various tilapiine species, and Eichornia crassipes since the 1950s. These have had a devastating effect on the natural biological communities. This paper reviews the effects of the introductions on ecology, environment, fisheries and the local human population.

Quahogs in Eastern North America: Part II, History by Province and State

The northern quahog, Mercenaria mercenaria, ranges along the Atlantic Coast of North America from the Canadian Maritimes to Florida, while the southern quahog, M. campechiensis, ranges mostly from Florida to southern Mexico. The northern quahog was fished by native North Americans during prehistoric periods. They used the meats as food and the shells as scrapers and as utensils. The European colonists copied the Indians treading method, and they also used short rakes for harvesting quahogs. The Indians of southern New England and Long Island, N.Y., made wampum from quahog shells, used it for ornaments and sold it to the colonists, who, in turn, traded it to other Indians for furs. During the late 1600’s, 1700’s, and 1800’s, wampum was made in small factories for eventual trading with Indians farther west for furs. The quahoging industry has provided people in many coastal communities with a means of earning a livelihood and has given consumers a tasty, wholesome food whether eaten raw, steamed, cooked in chowders, or as stuffed quahogs. More than a dozen methods and types of gear have been used in the last two centuries for harvesting quahogs. They include treading and using various types of rakes and dredges, both of which have undergone continuous improvements in design. Modern dredges are equipped with hydraulic jets and one type has an escalator to bring the quahogs continuously to the boats. In the early 1900’s, most provinces and states established regulations to conserve and maximize yields of their quahog stocks. They include a minimum size, now almost universally a 38-mm shell width, and can include gear limitations and daily quotas. The United States produces far more quahogs than either Canada or Mexico. The leading producer in Canada is Prince Edward Island. In the United States, New York, New Jersey, and Rhode Island lead in quahog production in the north, while Virginia and North Carolina lead in the south. Connecticut and Florida were large producers in the 1990’s. The State of Tabasco leads in Mexican production. In the northeastern United States, the bays with large openings, and thus large exchanges of bay waters with ocean waters, have much larger stocks of quahogs and fisheries than bays with small openings and water exchanges. Quahog stocks in certified beds have been enhanced by transplanting stocks to them from stocks in uncertified waters and by planting seed grown in hatcheries, which grew in number from Massachusetts to Florida in the 1980’s and 1990’s.

Quahogs in Eastern North America: Part I, Biology, Ecology, and Historical Uses

The northern quahog, Mercenaria mercenaria, ranges along the Atlantic Coast of North America from the Canadian Maritimes to Florida, while the southern quahog, M. campechiensis, ranges mostly from Florida to southern Mexico. The northern quahog was fished by native North Americans during prehistoric periods. They used the meats as food and the shells as scrapers and as utensils. The European colonists copied the Indians treading method, and they also used short rakes for harvesting quahogs. The Indians of southern New England made wampum from quahog shells, used it for ornaments and sold it to the colonists, who, in turn, traded it to other Indians for furs. During the late 1600’s, 1700’s, and 1800’s, wampum was made in small factories for eventual trading with Indians farther west for furs. The quahoging industry has provided people in many coastal communities with a means of earning a livelihood and has provided consumers with a tasty, wholesome food whether eaten raw, steamed, cooked in chowders, or as stuffed quahogs. More than a dozen methods and types of gear have been used in the last two centuries for harvesting quahogs. They include treading and using various types of rakes and dredges, both of which have undergone continuous improvements in design. Modern dredges are equipped with hydraulic jets and one type has an escalator to bring the quahogs continuously to the boats. In the early 1900’s, most provinces and states established regulations to conserve and maximize yields of their quahog stocks. They include a minimum size, now almost universally a 38-mm shell width, and can include gear limitations and daily quotas. The United States produces far more quahogs than either Canada or Mexico. The leading producer in Canada is Prince Edward Island. In the United States, New York, New Jersey, and Rhode Island lead in quahog production in the north, while Virginia and North Carolina lead in the south. Connecticut and Florida were large producers in the 1990’s. The State of Campeche leads in Mexican production. In the northeastern United States, the bays with large openings, and thus large exchanges of bay waters with ocean waters, have much larger stocks of quahogs and fisheries than bays with small openings and water exchanges. Quahog stocks in certifi ed beds have been enhanced by transplanting stocks to them from stocks in uncertified waters and by planting seed grown in hatcheries, which grew in number from Massachusetts to Florida in the 1980’s and 1990’s.

Modeling the Potential Spread of the Recently Identified Non-Native Panther Grouper (Chromileptes altivelis)in the Atlantic Using a Cellular Automaton Approach

The Indo-pacific panther grouper (Chromileptes altiveli) is a predatory fish species and popular imported aquarium fish in the United States which has been recently documented residing in western Atlantic waters. To date, the most successful marine invasive species in the Atlantic is the lionfish (Pterois volitans/miles), which, as for the panther grouper, is assumed to have been introduced to the wild through aquarium releases. However, unlike lionfish, the panther grouper is not yet thought to have an established breeding population in the Atlantic. Using a proven modeling technique developed to track the lionfish invasion, presented is the first known estimation of the potential spread of panther grouper in the Atlantic. The employed cellular automaton-based computer model examines the life history of the subject species including fecundity, mortality, and reproductive potential and combines this with habitat preferences and physical oceanic parameters to forecast the distribution and periodicity of spread of this potential new invasive species. Simulations were examined for origination points within one degree of capture locations of panther grouper from the United States Geological Survey Nonindigenous Aquatic Species Database to eliminate introduction location bias, and two detailed case studies were scrutinized. The model indicates three primary locations where settlement is likely given the inputs and limits of the model; Jupiter Florida/Vero Beach, the Cape Hatteras Tropical Limit/Myrtle Beach South Carolina, and Florida Keys/Ten Thousand Islands locations. Of these locations, Jupiter Florida/Vero Beach has the highest settlement rate in the model and is indicated as the area in which the panther grouper is most likely to become established. This insight is valuable if attempts are to be made to halt this potential marine invasive species