Synthetic Biology: Engineering Biological Systems

from: Snapshots in Research, Volume 2 (Spring 2009)

(You may also see the full spread of this article in a PDF.)

Abstract

Recent advancements in molecular biology and biochemistry allow for a new field of bioengineering known as synthetic biology. Using biological parts discovered in the last thirty years and mathematical models grounded in physical principles, synthetic biology seeks to create biological systems with user-defined behaviors. The major focus of research in this emerging field is the characterization of genetic regulation and the abstraction of biological systems to clearly defined logic circuits. With the abstraction of individual DNA sequences to known biological functions, synthetic biologists seek to create a standard list of interchangeable biological parts as the foundation of this emerging field. Through genetic manipulation, these parts are expected to be useful for programming biological machines that process information, synthesize chemicals, and fabricate complex biomaterials that improve our quality of life.

Genomic Era and Tools of the Trade

On June 26, 2000, President Bill Clinton and Prime Minister Tony Blair, along with Francis Collins, director of the Human Genome Project at the NIH, and Craig Venter, president of Celera Genomics, announced the arrival of the genomic era with the sequencing of the first draft sequence of the human genome. With this wealth of information, scientists and policy-makers alike were eager to welcome in the genomic era of genetics. Doctors dreamed of personalized medicine, where genomic information can be used to diagnose individual predispositions to cancer and disease. Politicians pondered the implications of genetic profiling, where insurance companies can potentially use genetic information to screen policyholders. The genomic era is bright with promise and unprecedented potential but also rife with social implications and practical applications.

While a sequenced genome provides a boon of new information and the scientific community is quick to emphasize the potential of this plethora of information, there are still many challenges in its interpretation and analysis. The interpretation of genomic data requires both high throughput techniques, such as microarray analysis, and heuristic algorithms in bioinformatics to analyze large amounts of data. Microarray analysis allows researchers to understand differential expression of many different proteins between different species, ages, and diseases states. With more than four billion base-pairs in the human genome and over thirty thousand open reading frames, the sheer size of the human genome requires the use of ad hoc analytical methods. The status quo approach in analyzing individual enzymes and molecules is complemented by a recent desire to understand entire systems, regulatory networks, and gene families. Exponentially increasing information on biological organisms and increasing computational power has broadened the perspective of current biological research.

Although genomic sequences provide insight into the enzymes that make up an organism, understanding of how these parts work together to produce complex phenotypes is the focus of current research. Understanding the regulation of gene expression and multicellular development will require a deeper analysis of how transcription and stability of mRNA is regulated in response to the environmental stimuli. Despite the age old debate between nature vs. nurture, it is the interplay of the environment and gene products that determine disease states and merge to create the fascinating output of life. Greater understanding of the regulation of gene products is required in determining their effects on physiology and development. Synthetic biology seeks to understand and apply understanding of biological regulation to tackle general problems.

Recombinant DNA technology laid the foundation for manipulation of biological systems on a molecular level, but recent advances in DNA sequencing and synthesis technology have greatly expanded the potential of biological engineering projects. The decreasing cost of oligonucleotide synthesis as well as improved techniques of combining oligonucleotides allows unparalleled flexibility in synthesizing long DNA sequences. From traditional methods of subcloning using restriction endonucleases and ligases to polymerase-based techniques such as gene Splicing by Overlap Extension (gene SOEing), researchers have unprecedented power in their ability to alter and characterize DNA. We can now identify new genes or regulatory sequences in diverse systems and recombine them into novel networks that attempt to recreate our understanding of existing biological systems. The rapidly expanding molecular biologist’s toolkit broadens the scope of manipulation to whole genetic systems instead of individual genes.

The current state of molecular biology has improved our understanding of the networks of biomolecular interactions that give rise to complex phenotypes and allows for unprecedented control of biological systems through clear characterization and synthetic techniques. Just as electrical engineering required increased aptness in manipulating individual circuits and transistors, biology is on the cusp of synthetic potential as new technologies overcome technical difficulties challenging previous generations of scientists.

Concept

Synthetic biology can be described as a hierarchy of fundamental biological concepts. From discrete genetic parts to whole biological circuits, each level of regulation builds upon a lower level of biological function for the ultimate goal of using biological systems to perform novel tasks or improving upon natural functions. Individual genetic parts, or particular DNA sequences with known functionality, can be integrated into genetic circuits. Genetic circuits, or new combinations of regulatory and coding sequences, can be created to produce unique behavior. Ultimately, these genetic circuits can be incorporated into biological organisms or systems.

Ongoing efforts in synthetic biology are focused on the creation of reusable, modular fragments with clearly characterized behavior and functionality in biological systems. With the discovery of the lac operon, biologists recognized the possibility for digital, discrete outputs within biological systems. Detecting the presence of lactose, the LacI repressor recognizes and binds to particular DNA sequences upstream of coding regions, regulating the transcription of the gene products in an all-or-none fashion. With clearly characterized behavior, the LacI repressor is already widely used in biotechnology applications, such as PET vectors, as integral parts of simple genetic circuits. As the biological analog of electronic circuits, researchers hope to use a growing repertoire of genetic parts to mimic logic functionalities and produce complex output.

The basic premise of synthetic biology is the ability to characterize and categorize a database of biological parts. A prominent example of this concept is the Registry of Standard Biological Parts (http://partsregistry.org/Main_Page) maintained by the BioBrick Foundation. Drawing upon the analogy of Lego bricks, synthetic biologists hope to use a standardized list of biological parts, ‘BioBricks’, to build large constructs with novel activity and unprecedented functionality. With defined activities for each component and a standardized subcloning method for combining DNA sequences, synthetic biologists hope to easily integrate ‘BioBricks’ to create novel biological circuits in a process analogous to the way computer scientists program computers. A database of DNA sequences, the Registry details the specific activity of individual sequences, the original sources and additional information necessary for synthetic biologists to integrate biological parts into particular biological systems.

Genetic Parts

There are three distinct levels where biological information can be regulated. In biological systems, information moves from DNA to RNA to protein. First proposed by Francis Crick in 1958, this “central dogma of molecular biology” addresses the detailed residue-by-residue transfer of sequential information. Synthetic biology utilizes regulatory elements at each level of this basic concept to create novel biological machines. On the DNA level, current understanding of genetic regulation reveals a complex system of promoters and terminators regulating transcription. The Registry contains a wide collection of parts for regulating transcription and translation, such as constitutive, inducible and repressible promoters, operator sequences, and ribosomal binding sites. Promoters, the 5’ upstream DNA sequencing before coding regions, determine the amount, duration, and timing of the translation. In the Registry, there is a large catalogue of terminator sequences. The 3’ region after coding regions, which form hairpin loops at the end of mRNA transcripts, cause RNA polymerase to dissociate from the template strand and end transcription. This compilation of a wide body of knowledge and literature about genetic regulation chronicles the behavior of many DNA sequences found in native systems.

Knowledge of regulation on the RNA level is applied to synthetic biology and builds upon a deep understanding of the regulation of protein production through mRNA stability and translation efficiency. Native systems display a wide range of RNA regulation that help modulate where and when particular proteins are translated. Transcribed RNA has the unique characteristic of being able to form diverse forms of secondary structure. Hairpin looping, which is intramolecular basepairing of palindromic sequences of RNA, is the basis of RNA secondary structure and can be used to create complex three dimensional structures. With the additional complexity of secondary structures, engineered RNAs function in RNA interference, as riboregulators, and catalyze key reactions. These RNA structures have been shown to mediate ligand binding and show temperature dependent activity. With temperature mediated stability, RNA sequences with designed hairpin loops can function as biological thermometers, regulating temperature sensitive expression.

The use of riboregulators is a prominent example of applying understanding of RNA behavior to regulate the expression of gene products in biological systems. Collins et al designed a system of RNA molecules that requires cooperative function of multiple RNA molecules for translation to occur. An mRNA transcript has an additional 5’ sequence complementary to the ribosomal binding site, prevent binding to the ribosome from binding to and translating the gene product. This ‘lock’ sequence can be unlocked by the regulated production of another mRNA molecule with similar homology and tighter binding affinity; allowing translation. Riboregulators with ligand mediated activity can bind to specific mRNA transcripts, silencing translation of particular genes as the result of exogenous stimuli. Both as sensors of environmental stimuli and in mediating translation, RNA has a distinct regulatory role allowing for programmable cellular behavior.

Genetic Circuits

In synthetic biology, identified regulatory components are recombined into novel networks that behave in predictable ways. An early example of a genetic circuit is the AND gate. Mimicking the functionality of digital logic of AND gates in which two unique inputs must combine to produce a positive output, Arkin and coworkers designed and modeled a genetic part to synthesize a marker protein in the presence of both salicylate and arabinose. Salicylate and arabinose are two naturally occuring, freely diffusible metabolites that bacteria normally react to; this proof of principle construct showed the ability to produce a novel reaction to simultaneous induction of both metabolites. Using two inducible promoters (NahR induced by salicylate and AraC induced by arabinose), this particular genetic part transcribed a unique T7 polymerase and the SupD amber suppressor terminator. The SupD tRNA allows translational read through at the amber stop codon, while the mutant T7 polymerase transcript includes two internal amber codons. Without the transcription of the SupD tRNA, the mutant T7 polymerase transcript would only create a nonfunctional protein product, while the SupD itself cannot induce transcription after the T7 promoter. With the combination of both gene products, a functional T7 polymerase can be expressed, which will synthesize any gene products behind the T7 promoter.

An ultimate goal of genetic manipulation is the creation of unique genetic devices or systems that can display unique characteristics or output not found in natural systems. An example of such a biological device is the repressilator, a biological device emulating the functionality of a digital oscillator which oscillates in its production of three different protein products. A system of inter-regulating gene products, the repressilator allows for sequential expression of three individual elements. Mimicking time dependent processes commonly found natural organisms, such as the KaiABC system and the circadian rhythm in photosynthetic organisms, this genetic circuit indicates the ability of simple DNA sequences to produce complex behaviors. Although this proof-of-concept constructare not as robust as natural systems, this biological device demonstrates the potential of deliberate genetic engineering to create novel output and emulate natural organisms.

A LacI repressible promoter regulates a tn10 transposon gene product which can repress another tn10 transposon promoter. This pTet promoter regulates the cI gene. A regulatory unit originally found in lambda phage, the cI protein regulates a lambda promoter that natively regulates switching between lytic and lysogenic phages in the lambda phage lifecycle. In a time dependent manner, the repressilator mimics the circadian clock found in most eukaryotic and many prokaryotic organisms.

Applications and Conclusions

In the last one hundred years, electrical systems have changed the face of the earth. Since the invention of the transistors, computers, phones, and other electronic systems have encroached upon all aspects of daily life. One can barely go through one day without use of e-mails, televisions, or cameras. Synthetic biologists dream of another world-changing revolution. Through modular parts and deliberate design, synthetic biology hopes to design biological systems to tackle challenging problems. From smart, self-regulating treatments for cancer to new solutions to the global energy crisis, the ability to engineer biological organisms has the potential to address many status quo questions. The vast natural diversity of life is a testament to the potential and opportunities available in synthetic biology.

Many different native biological organisms, such as E. coli and S. cerevesiae, are already used in many pharmaceutical and biotechnology applications. With a goal of standardization and optimization, synthetic biology allows for novel possibilities as well as improvement upon existing engineered systems. Regulating the interaction of bacteria, bacteriophage, and mammalian cells can allow for applications in medical diagnosis and treatment. The feasibility of using bacteria in biofabrication and energy generation requires designed logic functions in biological systems and biological computation. One interesting area of investigation is the removal of non-essential genes from the genome E. coli to produce an idealized minimal cell. With less chance of interfering regulatory sequences and gene products, such a minimal “cell chassis” could be the optimal shuttles for synthetic gene networks. A simplification of the cellular environment allows for greater ease in characterizing and modeling biomolecular interactions.

Utilizing the modularity of many biological systems, researchers hope to eventually produce complex behaviors through the simple combination of different biological parts. However, important considerations and research into the modularity of biological parts must still be made. In an idealized world, biological parts and coding regions could work equally well in all different cell types and organisms. Unfortunately, due to the inherent complexity of cells and intrinsically noisy nature of molecular systems, different modules might not work in different cellular environments or might not be optimized for maximum efficacy. The stochastic nature of biochemical interactions requires more work to build synthetic models and thereby understand both natural biological systems.

As genomic sequencing costs continue to decrease, the number of characterized native biological parts and unique designed parts will increase exponentially. Ultimately, synthetic biology introduces novel biological architectures not present in nature. As synthetic biology seeks to stretch the boundary of biological limits and go beyond what currently exists, questions of ethics and morality need to be addressed. What should be the limitations of investigation in this powerful field? With projects like the Venter Synthetic Genome Project, will the threshold between aggregates of molecules and life be more blurred? Should there be manipulation of the human genome, both for medicinal treatments as well as non-life threatening situations? How will intellectual property be handled, as the objects in question are inherent in natural systems? This author does not have the answers to these difficult questions, but feels that one needs to balance the potential benefits with the putative risks in this potent area of research. With great power comes great responsibility; a critical and diligent eye must be maintained in this area of active research. In addition to advancing current knowledge, it is the responsibility of the scientific community to educate the public to the potential and the risks of synthetic biology. Both to prevent Luddite reactions and to address legitimate concerns, dialogue and education are required of a field that seeks to make broad impacts on society at large.

Applying the tools and understanding of molecular biology and biochemistry, synthetic biology focuses on using current molecular tools to engineer unique biological parts and systems. Through such an engineering approach, synthetic biology also seeks to augment current approaches toward understanding regulation. Designed structures and sequences, not unique to natural systems, can be used to understand the finer details of regulation down to the very last nucleotide. As we continue to increase our knowledge of both prokaryotic and eukaryotic regulation, synthetic biologists continue to increase their repertoire of biological parts. Synthetic genome projects are currently underway and new applications such as biological computation, biological chemical fabrication, and disease treatments are being unveiled. Coupled with selection and refinement of genetic devices, deliberate genetic engineering has the potential to tackle many challenges in the near future.

David Ouyang is a sophomore Biochemistry & Cell Biology major at Baker College.

Acknowledgements

I would like to thank Dr. Jonathan Silberg for introducing me to this fascinating field of research and Dr. Daniel Wagner for his keen eye and constructive feedback. Their advice, encouragement, and support greatly aided in the writing process. I would also like to thank Erol Bakkalbasi for editing my paper.

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It’s a Coyote Eat Deer Feed Tick World: A Deterministic Model of Predator-Prey Interaction in the Northeast

from: Snapshots in Research, Volume 2 (Spring 2009)

For the full article complete with figures, please see the pdf of this article from the magazine.

Abstract

Occurrences of Lyme Disease have dramatically increased since the disease was named in the 1970’s. Much research now focuses on controlling Lyme through ticks (the vector for the disease), or White Tailed Deer (the host for ticks). Deer have recently reached surprisingly high numbers in the Northeast and it is thought that reducing deer populations will effectively decrease tick populations and thus the threat of Lyme. Consequently many towns have considered implementing ambitious yet controversial deer culling programs. As an alternative, we look at the potential for coyotes to biologically control deer populations through predation.

Coyotes, who prey on deer, have recently migrated into the Northeast from the Plains and may have been attracted to their new territory by the abundant prey supply. It is questioned whether the coyotes will act to replace the wolf as a natural control on deer population, thereby reducing Lyme Disease.

We construct a deterministic model to represent the current deer and coyote population dynamics and use this model to investigate the long term interaction of coyotes and deer. We explore the potential for coyotes to either solely act as a biological control on the deer populations or aid deer culling programs. The model is explored analytically and numerically and predicts that significant human intervention is needed to successfully control deer. Thus numerical simulations of the model and possible culling programs are provided to help highlight the system dynamics and guide culling policies.

Introduction

Recently the northeastern region of the United States has suffered an explosion of both White-Tailed Deer and cases of Lyme Disease. These two explosions are not considered to be independent and both issues greatly concern residents and policy makers of the area.

It is thought the deer explosion is a result of an increase in human population density. As humans developed the area, they created more disturbed landscapes that favor the growth of grasses, a major deer food source. Human development also conflicted with large carnivores and resulted in humans effectively killing wolves and natural ungulate predators in the region. Without predation, deer populations burgeoned in the last century [5]. Populations have gotten so large that deer have been reported in some areas at population densities as high as ten times what is thought to be healthy deer densities (20 deer per square mile vs. 200 deer per square mile) [5, 22]. Having such dense deer populations is dangerous; it leads to increased deer-car collisions [11, 24], over-grazing that can destroy natural forests, and endangerment of indigenous species [15, 4]. Possibly the greatest danger of a dense deer population, (though), is that it increases the risk of contracting Lyme disease [11, 26, 25, 22].
Lyme Disease is caused by at least three spirochetal bacteria in the genus Borrealia, but most commonly by Borrealia burgforferi. The spirochete is transmitted to individuals by ticks of the genus Ixodes. When a tick bites a host to feed on their blood, the tick transmits the spirochete to the host through its saliva and thus infects the host. Because adult Ixodes ticks frequently feed on the blood of White Tailed Deer, it is thought that more deer mean more tick and thus more Lyme. Municipalities have thus begun to explore the possibility of protecting their citizens from Lyme disease and dangers of deer overpopulation with deer control programs [5]. These programs usually propose periodically culling a portion of the deer population. Such programs have many drawbacks.

Culling is expensive and diffiult to practice as annual surveys are needed to count and monitor deer populations. Further difficulties arise with residents as the majority of land is privately owned and not all citizens morally agree with killing deer or bringing the dangers of hunting close to their homes.

We want to look for another way to potentially control deer without having to cull seasonally. We look for a biological control in the area that could act to control deer in adequate time. Specifically, we investigate if the effect of the emergent Eastern Coyote would be enough to act as this biological control.

In addition to allowing explosive deer growth, the extinction of wolves in the region has opened a niche for larger carnivores. As the emergence of a resident coyote population has occurred simultaneously, some suggest the coyote, which preys on ungulates, may be filling the wolf niche [14, 2]. Coyotes indigenous to the Great Plains and Southwest United States began migrating east and have successfully established populations in areas as far as New Brunswick and Nova Scotia [17, 2]. The eastern migration of the coyote has happened rather quickly and is thought to have resulted in a population of coyotes that is drastically different from the western coyote. The eastern coyote is physically larger [23, 13, 18, 8, 12] and has a larger home range than its western counterpart [27]. It is unknown why coyotes have moved so quickly to the Northeast, but it is believed that coyotes were attracted by abundant prey [23].

Very little is known about New England’s newest resident carnivore. It is necessary to learn about coyotes in the Northeast, as their new habitats of suburbia and New England deciduous forest differ greatly from their original home of expansive plains or the arid Southwest and puts coyotes in close proximity to humans. However, mammals with large home ranges are incredibly diffcult to track and study, so other methods of study are needed to investigate and understand coyotes on a broad scale in the Northeast [9]. These studies are especially needed if coyotes present a possible predator for deer and municipalities are looking for a method to control deer. Currently there seems to be no literature that looks at potential impact from the growth of the coyote population on Lyme. Further it appears no research has looked at exploiting coyotes as a new natural predator and control on deer populations.

We hope that employing a mathematical model might be a good way to study coyote dynamics and overcome the problems of tracking coyotes. We hope to gain insight into whether coyotes will have a significant impact on bringing deer down to acceptable densities and if the coyotes can achieve this feat within some reasonable time frame. As humans have a low tolerance of coyotes, we are also interested in if the coyotes can accomplish deer reduction with low coyote densities. Since we find mathematically that coyotes alone will not successfully control deer, we want to investigate the different types, impacts, and efficiencies of culling programs that towns might pursue. We hope to find a program that will allow us to suggest a minimally invasive cull to minimize expenses by only culling the minimum number of deer.

Modeling

Preliminary Assumptions and Notations
For simplicity, we ignore spatial variation and focus on a one square mile spatially homogeneous closed system. While this prevents modeling the varied distribution of fauna across the landscape, it will allow us to make estimates for larger scales such as multi-state domains. We also use similar assumptions to average predation and growth over a year. There is naturally some annual variability in growth and predation as birth rates and deer vulnerability vary on seasonal conditions such as snow depth [16, 17]. However this assumption is necessary to maintain an autonomous system of equations for analysis; it will also not inhibit our goal of studying the long term population dynamics.

We wish to model the density of deer D(t) and coyote C(t) populations with respect to time t in months. We begin with a classical Lotka-Volterra predator prey system,

where r is deer growth rate, a is the proportion of deer \that die in coyote-deer interactions, e is the energy that coyotes get from each killed deer, and d is the death rate for coyotes. Note this model is too simplistic, as in the absence of coyote predation, this model assumes exponential growth for deer and, in the absence of deer prey, exponential decay for coyotes. Therefore we introduce terms to more realistically portray coyote and deer interaction and reliance on the environment.

Predation
As in the classical model, we assume that at reasonable densities, deer die only as a result of coyote-deer interactions. In our sample area, this assumption is nearly reasonable as other natural predators of deer (wolves and large cats) are virtually extinct in the area. To represent this density-dependent predation, we use a Holling type II functional response term [10].

Classical mass-action predation terms such as aDC show that as prey increase, the number of prey killed by each predator increases. This is accurate if prey populations are relatively small. If prey become dense, mass action says that each coyote will kill proportionally large numbers of deer. It is more realistic that each coyote will have a maximum number of deer it can eat each month, regardless of how gigantic a population may be. Whether each coyote’s predation is maximized depends on if there are ample deer.

Holling type terms allow us to model such a cap for individual coyote predation (see Figure 1). A Holling type III term is frequently used to model mammal predation as it shows prey switching and lower predation rates if primary prey abundance is low [1]. However as studies carried out by Patterson (2000) indicate, the coyote-deer interactions better resembles a type II response

where α is the maximum deer that a single coyote will consume in one month and β controls how quickly the predation reaches α.

Note that a problem with Holling predation is that it does assume deer must reach an infinite population before individual coyotes maximize their prey consumption. Finally, we modify the Holling term to take into account the density of predators, to include C in coyote-deer interaction term.

Prey Growth
To model deer growth, we choose to use a logistic term:

where Rd is a natural growth rate for the deer population and Kd is a carrying capacity for deer. (The issue of how to chose the carrying capacity is extremely difficult, important to both coyotes and deer, and discussed later.) While the deer populations have exploded in a relatively short time, it does not seem reasonable to assume that deer continually reproduce exponentially. Furthermore, if we were to assume exponential growth and run our model with initial values as large as current population estimates, then the D(t) would quickly overrun the model and inhibit any sort of reasonable study. Recent field surveys also show that deer populations seem to be stabilizing, though only at extremely high densities [7].

Predator Growth
We want the coyote population to be correlated with deer and to grow with increased deer, which the Holling term allows. However if we use the Holling term with the extremely high populations of deer that have been observed in the Northeast, then the model will predict exploding coyote population. As there are reports of human-coyote encounters and coyotes killing pets, coyotes are often seen as a threat by humans and it is reasonable to assume that humans will control coyotes [3, 27]. If the coyote population gets too large, humans will begin killing coyotes. It is reasonable to assume that the density of coyotes that humans will tolerate is below the density of the coyotes that the current prey population could support. To impose this anthropogenic growth barrier, we multiply predation by a logistic growth term with carrying capacity Kc. The importance of Kc will become apparent later.

We also want to consider that coyotes prey on a variety of forest creatures and fruit: they are not solely dependent on the presence of deer [21, 16]. Hence we introduced a term for coyote growth independent of deer:

This term allows Rc to represent the growth from coyotes preying on species other than deer. Multiplying by a logistic term (1 − Kc ) represents the human barrier imposed on this term too. Then in the absence of deer, the coyote population will grow extremely slowly.

Carrying Capacity
The issue of carrying capacity is a delicate issue that arises quite frequently in biological problems. Mathematically, the carrying capacity represents a value which, if the density exceeds this value, growth becomes negative and the population decays back to the carrying capacity. Biologically, carrying capacity is the maximum density of a species that a given habitat can support long-term in ideal conditions.
Mathematically, carrying capacities are typically constants because they approximate long term dynamics. However, many factors affect biological carrying capacity such as food supply, climate, and over crowding. Carrying capacities can vary with respect to what is considered an external factor, such as human development, or an internal factor, such as overabundant inhabitants overgrazing and damaging the environment, thus diminishing their food source. Due to different factors, carrying capacities are an extremely delicate matter; we take Kd, Kc to be constant within our model, however, and find reasonable values from literature that predict maximum population levels.

Specialized Coyote-Deer Model
Taking into consideration all of the terms developed above, we end up with the following model:

To aid our analysis, we nondiminsionalize the system with the following substitutions:

These substitutions give us a system that behaves in the same manner and has the same equilibria as (1) but has fewer visible constants and simpler computations. The nondimensionalized system is

The reader must be cautious and recall while looking at our results that we will work with a dimensionless system. Results are dimensionless and should be analyzed as such.

Analysis

Equilibrium
We are interested in the long term interaction of coyotes and deer, so we look for points of equilibrium. More specifically, we are interested in whether the coyotes can control the deer, i.e. the existence of an equilibrium below the deer carrying capacity that has neither coyotes nor deer extinct. Equilibria occur at the intersections of the nullclines

There are six intersections and thus equilibria for our system. Given as (x, y) they are

Mathematically, coyotes controlling deer translates to an equilibrium with 0 < x< 1 and 0

Stability
To show stability of equilibria (3) -(7), we evaluate the Jacobian at each equi-librium and examine the signs of eigenvalues. The 2 × 2 jacobian matrix is

At (3) and (5) the eigenvalues are positive and therefore equilibrium (3) and (5) (mutual extinction and coyote extinction, respectively) are unstable.
Evaluating the Jacobian at (4), we obtain

As the eigenvalues of the above matrix are negative, depending upon parameter values, we see that this equilibrium is conditionally unstable. As (4) represents coyotes at carrying capacity and deer extinct, we assume this equilibrium is unstable. Thus we force one negative and one positive eigenvalue and we obtain the parameter restriction

It can easily be shown that this restriction forces equilibrium (6) and (7) to have positive and negative x-values, respectively. We discard equilibrium (7), as biologically meaningless and concentrate on equilibrium (6), the only equilibrium with positive values for both x and y. We expect this equilibrium to be stable. Evaluating the Jacobian yields an upper triangular matrix

Therefore, J11 and J22 are the eigenvalues and must both be negative for the equilibrium to be stable.

where

Squaring the both sides of the above equation we obtain

where the rst inequality uses the restriction 9.

The above inequality is equivalent to

The three coecients of delta in the numerator of J11 can be written as

Hence,

Consider the six terms in the numerator of J11 that are independent of delta. Further, consider that due to energy transfer through tropic levels, ecosystems support more herbivores than carnivores; thus, it is reasonable that Kc < Kd.With this assumption two of the terms in the numerator are

The remaining four terms can be written as

By noting that and combining (11) and (12), we obtain

Therefore, J11 is negative and one of the eigenvalues is negative.

Now we check the sign of the other eigenvalue

Again as parameters are positive, the denominator is positive. Due to the negative sign in front, it only remains to show the sum of terms in the numerator of J22 is positive. Since there is only one negative term in the numerator, we simply show that combined with the other positive terms, the result is positive. Looking at the last three terms in the numerator and using (10) from above, we have

As the last three terms in the numerator of J22 are nonnegative, the entire numerator is positive and J22 is negative.

In conclusion, both eigenvalues J11 and J22 are negative and equilibrium (6) is stable. This means that our coyote-deer system has a stable equilibrium below the maximum number of deer and thus predicts that coyotes will have some controlling effect. Now we numerically examine the extent of this effect.

Numerical Investigation

Setting Parameters
We consider ranges of the parameters which have been gathered from the liter-ature and refine these ranges by choosing values which best model the historical growth of the two populations. The values

gave us results which best correlated with the historical dynamics described: deer population suffered until the 1950’s but exploded by the 1990’s [22] and coyote observations were sparse in the late 1950’s but more common around the 1970’s [6, 19]. This can be seen in Figure (2).

Model Results
We start the model with deer and coyotes at their respective carrying capacities, as these are the presumed current levels, and use MapleTMsoftware to numeri¬cally solve and plot our system. We consider evolution of the system over the next fifty years in Figure 3. We see that without predation, deer stay at their carrying capacity but with coyote predation, deer population drop to the level of (6), the previously found equilibrium. This shows us that coyotes do and will have an effect on deer populations.

The thin horizontal line in Figure 3 represents 20 deer per square mile which is a third of the current deer population levels and is thought to be a natural, healthy level that deer existed at in the presence of the wolf and that deer can continue to exist at without overpopulating the area [15, 4]. This is a level that is recommended by state officials for deer control programs [22, 11]. To begin to control Lyme Disease, municipalities would even like to see deer below this recommended level [5].

Deer Carrying Capactity Kd
As previously discussed, we take carrying capacity to be constant. In Figure 3 Kd is set to current level of deer populations, 60 deer per square mile. However, we can also set Kd to what the literature suggests is a healthy environmen¬tal carrying capacity, 20 deer per square mile. At this level, the logistic term causes the deer population to naturally fall to the healthy environmental carrying capacity of 20 deer per square mile within 300 months without any human intervention or predation. Even with an artificially high initial condition of 10 times the natural carrying capacity or 200 deer per square mile and no coyote predation, the deer fall to reasonable densities fairly quickly as see in Figure 4. This does not reflect reality as deer populations have remained well above the healthy carrying capacity of 20 deer per square mile and have not fallen nor are they showing signs of steep decline. Thus clearly, we cannot use the theoretical carrying capacity but must use the current population levels and let Kd=60.

Additional Coyotes
It is evident from Figure 3 that at their current densities of .2 coyotes per square mile, coyotes will not be able to control deer population to the desired levels. If we are correct in assuming that humans control coyote population size to a certain density Kc, then we can consider what would happen if humans would allow more coyotes to inhabit the area. Perhaps, if coyotes were fostered in the area to act as biological control on deer, we would see reduced numbers of deer.

We study this scenario by raising the value of Kc from .2 to .38, a doubling of the population from current levels in Massachusetts [27]. Figure 5 shows that even doubling the coyote population, while having a larger effect on the deer, will not effectively get deer to or maintain deer at desired levels.

We see that on their own, and at higher levels, coyotes will not control deer population. Even with larger populations (which are unrealistic due to the dense population in the area who are already reluctant to share the landscape with the carnivore), coyotes cannot control the deer. Hence, we now consider other efforts that would have to be taken to control deer and add the effect of culling to our model.

Culling

Analytically, we found that coyotes would indeed control the deer population to some extent. The level that coyotes could keep the deer at are below the observed densities of 60 deer per square mile as illustrated in Figure 4. However, within the range of realistic parameters, our model does not show that coyotes are capable of controlling deer to or below the 10 deer per square mile densities that are presumed optimal for controlling Lyme disease or reducing the nuisance of deer. Thus, we establish that external forces, such as active culling, will be needed to control deer and we look at some of the types of culling.

We begin our study by reconsidering deer growth and modifying our original equation to take into account a loss of deer due to an external active cull. We consider two types of culling: proportional and lump.

We consider the culling strategy that takes a proportion of the population by introducing μ, the proportion of deer killed. Frequently this sort of culling is used for modeling, as it allows for simpler analysis than the more realistic constant value or lump culling.

Continuous Proportional Culling
We consider the culling strategy that takes a proportion of the population by introducing μ, the proportion of deer killed. Frequently this sort of culling is used for modeling, as it allows for simpler analysis than the more realistic constant value or lump culling. The dimensionless culling model is

Figure 6 shows the sensitivity of the model to coyote predation. Killing only 1.2% of the deer population has a drastic effect of reducing deer. However this model also illuminates the importance of coyotes. With the increased pressure of culling, deer are more susceptible to the effect of coyote predation.

However this model seems unrealistic as culling 1.2% of deer is an extremely small portion of the deer. It is projected that much larger culls will be needed to control deer populations. We propose that the fallacy of this model is due to it assuming that the culling is continuous. This means the model is continuously taking 1.2% of the deer which is clearly unrealistic. Culling programs tend to be administered through seasonal culls or taking deer at only one period in the year and not continuously. We would like to take this seasonal culling into consideration, and thus we need a way to make the effect of culling on our model discrete.

Discrete (Seasonal) Culling
To study a realistic seasonal, proportional culling model, we utilize numerical approximating packages in MapleTM . We write a simple program which runs the system for a year, stops and subtracts a proportion μ of the deer population, and then uses that value as an initial condition for the next year. This program outputs a plot of projected yearly deer population values.
We see that with discrete culling much larger proportions of deer need to be killed in order to control populations (Figure 6). This is the more realistic result that we hoped to achieve with our MapleTMprogram. However one problem remains: time. Looking at the horizontal axis we see that culling a set proportion takes too long to get deer to or below desired levels.

Conclusion

We looked at the potential of the eastern coyote as a natural biological control on deer populations. Analytically, we found one interesting stable equilibrium in which the coyotes control the deer. Numerically analyzing this equilibrium for reasonable parameters, we find that although the coyote do have some effect on controlling deer populations, it is not enough to keep deer populations below the desired levels (20 deer per square mile). Therefore, we investigated potential anthropogenic control through culling strategies. We found that modeling continuous culling was unrealistic so we wrote a program to represent seasonal culling. This annual culling model gave far more realistic predictions yet still showed that it would take too long to control the deer if the proportion culled each year was kept constant. In conclusion, we proposed the following plan: Cull deer at high rates for a short time period, say five years, and then at more modest rates to maintain healthy populations. The predictions for such a strategy can be see in Figure 7.

Acknowledgements

The authors acknowledge with gratitude support for this work provided by the NSF REU Site Grant at Texas A&M University DMS-0552610 as well as their advisors Dr. Jay R. Walton and Dr. Yuliya Gorb.

Orianna DeMasi is a senior majoring in mathematics at McGill University. Kathy Li is a sophomore majoring in Mathematical Economic Analysis at Brown College.

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Characterization of a Recently-Discovered Mutant Fetal Hemoglobin

from: Snapshots in Research, Volume 2 (Spring 2009)

For the full article complete with figures, please see the pdf of this article from the magazine.

Abstract

Last summer, Dr. Mitchell Weiss and his colleagues at Children’s Hospital of Philadelphia discovered a new hemoglobinopathy in a baby from Toms River, New Jersey, who was born cyanotic and with enlarged spleen and liver tissues. Sequencing of the baby’s hemoglobin alleles revealed a missense mutation in a segment of DNA that codes for the gamma chains of fetal hemoglobin (HbF), the oxygen-carrying protein in red blood cells of human fetuses. The objective of our work is to use recombinant DNA technology to construct the Hb Toms River mutation, γ Valine 67 (E11) Methionine, in plasmid DNA which can then be used to express and purify mutant protein using E. coli. We plan to characterize the mutant HbF in order to understand its clinical manifestations and, perhaps, to develop treatments options. This paper provides an overview of HbF developmental biology, our initial hypothesis of how the Hb Toms River mutation might lead to cyanosis, and our strategy for expressing and characterizing the γ Val67 to Met mutation in recombinant HbF.

Introduction

During a consultation with pediatricians at Children’s Hospital of Philadelphia, Dr. Mitchell Weiss discovered a new blood disorder in a child who was born cyanotic and with an enlarged spleen and liver. These symptoms resolved roughly two months after her birth, and she was normal and healthy by six months. Based on their initial clinical observations, Dr. Weiss and the treating physicians suspected that a mutant fetal hemoglobin might be the cause of the baby’s symptoms, so they drew small amounts blood samples for analysis from the baby several days after birth. They discovered that her condition appears to fall into a class of hematological disorders known as hemoglobinopathies, which are genetic defects in the DNA sequences that produce hemoglobin. Hemoglobin is the primary oxygen transport protein in humans, and when the baby’s DNA was analyzed, it was discovered that a Val67 to Met (V67M) mutation was present in one of the child’s γ chain alleles. This mutation occurs in a region of DNA that gives rise to the eleventh amino acid along the E helix of the γ globin chain, which is called Val (E11) for its spatial location in the three dimensional structure of hemoglobin subunits (Figure 1).

The original mutant fetal protein could not be studied directly because of physical and clinical limitations which prevent the withdrawal of significant amounts blood from an anemic infant. Another problem was that fetal hemoglobin production switches to adult hemoglobin production shortly after birth as part of normal developmental processes. Thus, resolution of the cyanotic condition occurred when the γ gene (characteristic of HbF) was silenced, and only normal adult hemoglobin was present in the baby’s red blood cells, which occurred 6 to 8 weeks after birth. To obtain enough starting materials for study, we chose to produce mutant HbF in our laboratory using recombinant technology. The objective of our work is to use structural biology to characterize the γ V67M mutation in HbF, examine the role of the E11 position in O2 binding in γ chains, and then understand why the mutation caused cyanosis and spleen enlargement.

Hemoglobin Development

Hemoglobin is a complex iron-containing protein in the blood that picks up oxygen from the lungs and carries it to respiring cells; at the same time, it assists in transporting carbon dioxide away from the peripheral tissues. Mammalian red cell hemoglobins are tetramers consisting of four polypeptide chains and four planar prosthetic groups known as heme molecules [2, 3, 9]. Each red blood cell contains about 280 million hemoglobin molecules [7].

Different kinds of hemoglobins are commonly identified by the specific combination of polypeptide chains or subunits within each tetramer. During development and birth, three main types of hemoglobin are expressed (Figure 2). The first type is known as embryonic hemoglobin, which consists of two α and two γ globin chains. The low oxygen conditions of the uterine wall demand a higher oxygen affinity than either HbF or adult hemoglobin confer, but embryonic hemoglobin functions well in this environment. After 10 to 12 weeks of development, the primary form of hemoglobin switches from embryonic hemoglobin to fetal hemoglobin HbF (α2γ2). At this point, the fetus’s red blood cells have access to the oxygen passing though the placenta and umbilical cord. Like embryonic hemoglobin, HbF has a higher oxygen affinity than adult hemoglobin, thus allowing the fetus to extract oxygen from the mother’s blood in the placenta.

When a baby is born and begins to breathe air, γ chain production ceases and β chains are produced which result in adult hemoglobin HbA (α2β2) production. At birth, HbF comprises 50-95% of the child’s hemoglobin. These levels decline to almost zero after six months as adult hemoglobin synthesis is completely activated. Hemoglobin genes exist on Chromosomes 11 and 16 (Figure 3).

Genetic abnormalities can suppress the switch to adult hemoglobin synthesis, resulting in a condition known as hereditary persistence of fetal hemoglobin [6]. In adults, HbF production can be rekindled pharmacologically, which is one of the main treatment options for sickle-cell disease [5]. The mechanisms by which erythroid cells switched from the synthesis of HbF to that of HbA during the neonatal period appeared normal for the patient with HbF Toms River. As a result, this genetic disorder did not persist as a threat to the child.

Analysis of the V67M Mutation

A necessary stage for understanding the Hb Toms River disorder will be acquiring large amounts of the cyanotic child’s mutated fetal hemoglobin. In this case, our only choice was to construct the mutation in vitro with recombinant DNA techniques and then express the mutant γ chain with wild-type α chains in bacteria. The intestinal bacterium, Escherichia coli, is an excellent choice for expressing recombinant proteins because of its high tolerance for synthesizing large amounts of heterologous proteins and the ease of performing site-directed mutagenesis on plasmids that can be taken up by this bacterium. The plasmid system pHE2 was originally developed by Chien Ho’s group at Carnegie Mellon University (Shen et al., 1993) to produce adult hemoglobin, and we obtained the pHE2 expression system for HbF from Professor Kazuhiko Adachi at Children’s Hospital of Pennsylvania (Adachi, 2002). This vector contains one wild-type α gene, along with one wild-type γG gene from human HbF. We created the single-site V67M mutation using the Stratagene QuikChange Site-Directed Mutagenesis Kit. The plasmids for expression of hemoglobins were transformed into E. coli JM109 cells. E. coli cells were grown in 2x YT medium. Expression was induced by adding isopropyl-β-thiogalactopyranoside (IPTG) at 0.1 mM at 37oC and then supplemented with hemin (30 μg/ml). The harvested cell lysate was passed through a Zn2+ binding column, Fast Flow Q-Sepharose column, and finally a Fast Flow S-Sepharose column using an FPLC.

We are currently evaluating the purity and authenticity of our HbF mutant by performing gel electrophoresis and protein sequencing reactions from aliquots of the purified protein. Our long-term goal is to characterize HbF Toms River in terms of its relative stability and O2 affinity with the hope that recombinant technology can help us understand the clinical symptoms of the hemoglobinopathy and perhaps suggest a treatment.

For the past twenty years Dr. John Olson’s laboratory in the Department of Biochemistry & Cell biology at Rice has been examining O2 binding to mutants of mammalian myoglobin and the α and β subunits of HbA. Much of this work has focused on amino acid substitutions within the oxygen binding pocket, including at the valine E11 position. In 1995, an undergraduate honors research student in Dr. Olson’s laboratory, Joshua Warren (Rice BA 1996; Yale PhD 2002), used sperm whale myoglobin (Mb) as a model system to examine the effects of valine E11 to methionine, phenylalanine, tyrosine, and tryptophan mutations on oxygen binding. All four of these amino acids have much larger side chains which fill up the interior portion of the pocket which captures diatomic gases, including O2, CO, and NO. Warren observed dramatic decreases in the rates of O2 uptake and release due to the valine E11 to methionine replacement. Similar marked decreases compared to wild-type Mb were observed for the Phe, Tyr, and Trp mutations, which also decrease the size of the binding pocket [4].

The mechanism of O2 binding to either Mb or a Hb subunit is analogous to catching a baseball in a fielder’s glove. As the thumb opens, by upward and outward movement of the histidine E7 side chain (Figure 4), incoming oxygen can be “caught” in the pocket of the glove. If the available space of the glove is made too small by limiting it with a large amino acid like methionine, the ball or O2 will “bounce” back out of the globin requiring that multiple tries be made until it is finally captured and bound to the iron atom. Thus, we expect the valine E11 to methionine mutation to appreciably slow O2 binding.

At the moment, a structure of the γ valine E11 to methionine mutant has only been simulated (Figure 4) and recombinant HbF Toms River not been characterized. However, based on Warren’s results with Mb, we predict that O2 binding may be slowed so much that red blood cells containing the HbF mutant cannot uptake oxygen quickly enough during passage through the placenta or new born lungs. Consequently, the blood will only be partially saturated with O2 and appear a purplish or cyan color associated with cyanosis. We are currently setting up the HbF expression system and, as a control, show that wild-type γ subunits have kinetic and stability parameters very similar to those of HbA β subunits.

With luck this system will allow complete characterization of the HbF Toms River mutation, and recombinant DNA technology will allow us to study the clinical disorder associated with this hemoglobinopathy without having to obtain the infant’s blood. This in vitro approach represents an important advance in characterizing genetic defects in hemoglobins and will provide a general approach for determining the underlying mechanisms for the phenotype associated with the hemoglobin mutations and possible treatments to restore normal physiological function.

Arindam Sarkar is a sophomore double-majoring in Biochemistry & Cell Biology and Policy Studies at Lovett College.

Acknowledgements

I thank Dr. John S. Olson and Todd Mollan for their useful comments, Ivan Birukou for a helpful discussion on the purification of recombinant hemoglobin, Dr. Jayashree Soman for her expedient provision of images, and once again Todd Mollan for his tireless support and tutelage.

References

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