Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution

Understanding intratumor heterogeneity is clinically important because it could cause therapeutic failure by fostering evolutionary adaptation. To this end, we profiled the genome and epigenome in multiple regions within each of nine colorectal tumors. Extensive intertumor heterogeneity is observed, from which we inferred the evolutionary history of the tumors. First, clonally shared alterations appeared, in which C>T transitions at CpG site and CpG island hypermethylation were relatively enriched. Correlation between mutation counts and patients’ ages suggests that the early-acquired alterations resulted from aging. In the late phase, a parental clone was branched into numerous subclones. Known driver alterations were observed frequently in the early-acquired alterations, but rarely in the late-acquired alterations. Consistently, our computational simulation of the branching evolution suggests that extensive intratumor heterogeneity could be generated by neutral evolution. Collectively, we propose a new model of colorectal cancer evolution, which is useful for understanding and confronting this heterogeneous disease.     

Evolution of plant shape: Design constraints

The fossil record documents the morphological and anatomical changes that have occurred over more than 400 million years of land plant evolution. Many of these changes can be interpreted, and even predicted, on the basis of standard engineering principles pertaining to mechanical stability, hydraulics, and the rescaling of form to maintain a constant level of performance or function. Theoretically based hypotheses, constructed using modern computer technology, can be compared with the major trends seen in the evolution of land plants and so provide insights into the factors motivating morphological and anatomical changes during the Phanerozoic.     

Protein Design and Evolution for Biocatalysis

Cover illustration: Soon designing proteins on demand? This is the vision expressed by the designer pencils pointing at the logo of the meeting held in September 2006 in Greifswald, Germany. This special issue was edited by Prof. Uwe Bornscheuer from Greifswald, who selected papers from keynote speakers at this meeting. With special thanks to Prof. Romas Kazlauskas, University of Minnesota, for the design of the conference logo. Pencils © FOTOLIA.     

Protein Design and Evolution for Biocatalysis

Cover illustration: Protein Design and Evolution for Biocatalysis. This special issue of Biotechnology Journal contains selected contributions from scientists participating to the ESF-EMBO Symposium which took place in October 2008 in San Feliu, Spain. Guest Editor is the chair and organizer of the meeting, Jiri Damborsky from Brno (Czech Republic). He highlights a variety of topics brought up in the meeting, ranging from new methods of rational design, directed evolution, metagenomics and single-molecule techniques, to construction of useful enzymes for industrial applications. Uwe Bornscheuer (Greifswald, Germany) authored a meeting report. Image colored pencils, © PhotoDisc, Inc.; Protein logo © ESF.     

Evolution of Design Features in the Coding of Species-Specificity

Reproductive isolation between species is the major factor responsiblefor the evolution of species-specificity in communication signals.However, the actual physical or chemical structure of signalsmay be determined by a number of factors such as the physicallaws regulating the transmission of signal energy, locatability,the functional properties of sensory organs, the physical characteristicsof the habitats in which communication occurs, and prey-predatorrelationships. This fact implies that there is some degree ofpredictability in design features of signaling systems.     

An Integrated Framework Advancing Membrane Protein Modeling and Design

Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design.     

A Multifunctional Integrated Design of Simultaneous Unity Absorption and Polarization Conversion

Plasmonics - Herein, an integrated multifunctional design for simultaneous perfect absorption and polarization conversion is proposed that worked in the Ku band: the proposed structure consisted of...     

Evolution and Design of Protein Structure by Folding Nucleus Symmetric Expansion

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Problem Concepts in Evolution Part I: Purpose and Design

In 1999, Scott suggested that evolution has existential repercussions for some students because they confuse methodological naturalism with philosophical naturalism: conflating the incapacity of scientific explanations to appeal to the supernatural with the idea that God must not exist. Unfortunately, part of the reason for the confusion involves terms that are used in a technical sense by evolutionary biologists but that also convey existential meanings to the general public. Such terms therefore should be used carefully by teachers, and their scientific meanings distinguished from their common meanings. We revisit these problem concepts, particularly in light of recent papers in cognitive psychology as they relate to understanding evolution, in a two-part series of articles. Here, in part I, we address design and purpose.     

Evidence for Evolution Versus Evidence for Intelligent Design: Parallel Confusions

The popular defense of intelligent design/creationism (ID) theories, as well as theories in evolutionary biology, especially from the perspective that both are worthy of scientific consideration, is that empirical evidence has been presented that supports both. Both schools of thought have had a tendency to rely on the same class of evidence, namely, the observations of organisms that are in need of being explained by those theories. The result is conflation of the evidence that prompts one to infer hypotheses applying ID or evolutionary theories with the evidence that would be required to critically test those theories. Evidence is discussed in the contexts of inferring theories/hypotheses, suggesting what would be possible tests, and actual testing. These three classes of inference being abduction, deduction, and induction, respectively. Identifying these different inferential processes in evolutionary biology and ID allow for showing that the evidence to which theories and hypotheses provide understanding cannot be the same evidence supporting those theories and hypotheses. This clarification provides a strong criterion for showing the inability of an ID theory to be of utility in the ongoing process of acquiring causal understanding, that is the hallmark of science.     

A Biotic Game Design Project for Integrated Life Science and Engineering Education

Engaging, hands-on design experiences are key for formal and informal Science, Technology, Engineering, and Mathematics (STEM) education. Robotic and video game design challenges have been particularly effective in stimulating student interest, but equivalent experiences for the life sciences are not as developed. Here we present the concept of a "biotic game design project" to motivate student learning at the interface of life sciences and device engineering (as part of a cornerstone bioengineering devices course). We provide all course material and also present efforts in adapting the project''s complexity to serve other time frames, age groups, learning focuses, and budgets. Students self-reported that they found the biotic game project fun and motivating, resulting in increased effort. Hence this type of design project could generate excitement and educational impact similar to robotics and video games.

This Education article is part of the Education Series.

Hands-on robotic and video game design projects and competitions are widespread and have proven particularly effective at sparking interest and teaching K–12 and college students in mechatronics, computer science, and Science, Technology, Engineering, and Mathematics (STEM). Furthermore, these projects foster teamwork, self-learning, design, and presentation skills [1,2]. Such playful and interactive media that provide fun, creative, open-ended learning experiences for all ages are arguably underdeveloped in the life sciences. Most hands-on education occurs in traditionally structured laboratory courses with a few exceptions like the International Genetically Engineered Machine (iGEM) competition [3]. Furthermore, there is an increasing need to bring the traditional engineering and life science disciplines together. In order to fill these gaps, we present the concept of a biotic game design project to foster student development in a broad set of engineering and life science skills in an integrated manner (Fig. 1). Though we primarily discuss our specific implementation as a cornerstone project-based class [4], alternative implementations are possible to motivate a variety of learning goals under various constraints such as student age and cost (see supplements for all course material).Open in a separate windowFig 1We developed a bioengineering devices course that employed biotic game design as a motivating project scheme. A: Biotic games enable human players to interact with cells. B: Conceptual overview of a biotic game setup. C: Students built and played biotic games. Image credits: A C64 joystick by Speed-link, 1984 (http://commons.wikimedia.org/wiki/File:Joystick_black_red_petri_01.svg); Euglena viridis by C. G. Ehrenberg, 1838; C Photo, N. J. C.Biotic games are games that operate on biological processes (Fig. 1) [5]. The biotic games we present here involve the single-celled phototactic eukaryote, Euglena gracilis. These microscopic organisms are housed in a microfluidic chip and are displayed in a magnified image on a video screen. Players interact with these cells by modulating the intensity and direction of light perpendicular to the microfluidic chip via a joystick, thereby influencing the cells’ phototactic motion. Software tracks the position of individual euglena with respect to virtual objects overlaid on the screen, creating myriad opportunities for creative game design and play. For example, in a simple game, points might be scored when a cell hits a virtual box (see S1 Video).The biotic game design project we developed was intended to motivate all the broad categories of theoretical and hands-on skills for creating any integrated instrument intended to house and to interface with biological materials, i.e., optics, electronics, sensing, actuation, microfluidics, fabrication, image processing, programming, and creative design. We termed the synthesis of these skills “biotics” in analogy to mechatronics. Our intended audience for this course was bioengineering undergraduate students at Stanford University who already had some programming experience but little to no experience in device design, fabrication, and integration. We also incorporated bioethics into the curriculum to emphasize the social responsibility of every engineer and demonstrate the potential for the biotic game project to motivate multiple fields. The course we taught spanned ten weeks, divided roughly equally into a set of technical units and the biotic game project, with two 4-hour lab sections and a single 1.5-hour lecture each week. For details and all course documents, please refer to the supplemental material.The technical section of the course focused on developing hands-on skills and theoretical understanding related to devices in a conventionally structured laboratory setting. We introduced students to fundamental electronics concepts and components such as voltage, current, resistors, capacitors, LEDs, filters, operational amplifiers, motors, microcontrollers (Arduino Uno), and breadboards. We followed a similar traditional approach in introducing optics, presenting the thin lens equation, ray tracing, conjugate planes, basic optical system design, and Köhler illumination. We covered additional topics in less detail: MATLAB programming, particle tracking, computer-aided design (CAD), fabrication, and microfluidics (learning objectives are provided at the beginning of each unit in the supplemental material).During the project-based section, students built their own biotic games. We left specific choices of implementation, architecture, and design to the students to encourage creativity and exploration but required students to revisit the technical skills they learned in the first section by integrating some specific requirements into their games (Fig. 2). Students built a bright field microscope with Köhler illumination and projected their images onto a webcam (optics). Glass and polydimethylsiloxane (PDMS) components comprised the microfluidic chip (microfluidics) and housed the euglena (microbiology). The holder for the chip and euglena-steering LEDs was designed in Solidworks (CAD) and 3-D printed (fabrication). The students constructed a polycarbonate housing for the game controller using a band saw and drill press (fabrication). The students revisited electronic breadboarding and soldering when creating the electronic circuits to communicate between the LEDs, joystick, microcontroller, and computer. Finally, they used MATLAB to program the microcontroller, implement real time image recognition, and provide the user interface for the game experience (image processing and programming).Open in a separate windowFig 2Biotic game-based courses encourage students to integrate a versatile set of relevant STEM topics.Image credits: Taken by N. J. C. (credit for the work and artifacts to the students who took the course).We challenged students to consider the ethical implications [6] of manipulating life in a game context before building their projects. Although phototaxis experiments with euglena are commonplace in education, and have hitherto raised no ethical concerns, the equivalent manipulation in the form of a game warrants its own ethical analysis as provided by Harvey et al. [7]. The students read and discussed this paper, then wrote a 200-word essay on whether they found it permissible or not to make and play biotic games. Students had the choice to switch to a nongame project of equivalent complexity. All students found euglena-based games permissible, pointing out that “they are nonsentient and cannot feel pain,” followed by a diverse range of considerations such as “the euglena are still free to act as they please,” “there needs to be an educational intention,” or “a pet…provides a way…to work on responsibility and caring.” Based on further student-initiated discussions that spontaneously emerged throughout the course, we believe that biotic games are effective in providing a stimulating, student-relevant, in-class context for bioethics.We motivated the game design project to the students as having educational potential at two levels, i.e., learning by building and learning by playing; we lectured them about the needs and opportunities for new approaches to K–12 STEM education [8,9]. The students were then asked to consider building a game that had educational value for the player. Educational value has many aspects, which was reflected in students’ statements regarding their intended educational outcomes for their games on their course project websites. These ranged from more factual learning objectives (“learn about…” “…inner working,” “…structural detail,” “… light responses,” “…euglena behavior”) to objectives affecting attitude (“spark interest,” “generate fascination,” “encourage to explore,” “respect for life”). We also had a game designer give a guest lecture to the students. For pragmatic reasons, we requested the students keep games very simple (ideally having just a single in-game objective) and cap game duration at one minute. Before, during, and after their projects, students received feedback from instructors as well as from their peers on their games from technical and user perspectives.The games that the students ultimately produced were diverse and creative (Fig. 2 and S1 Video), including single and multiplayer scenarios, games where euglena hit virtual targets, and games where euglena pushed virtual objects. Games that involved pushing objects across the screen (relying on collective motion of many organisms) were generally more consistent at correlating player strategy to scored points than those that involved hitting target objects. The quality and robustness of these integrated projects naturally varied, and individual groups placed more or less emphasis on different aspects based on personal preferences and learning goals (for example, fabricating a more elaborate housing for the game controller versus programming more complex game mechanics). A key point was that the students did not rely on prepared materials or platforms to develop their games but rather had to design, build, and test their game setups from scratch, thereby revisiting and deepening the primary learning goals of the course with some freedom to follow their own learning aspirations (Fig. 2). The final project deliverables were a two-minute project demonstration video, a website describing the elements of the project, and a game that all instructors and students played on the final day (Fig. 1B), which led to lots of laughter as well as in-depth discussions on technical details.Many students self-reported that they enjoyed the project and that it led to increased motivation and effort during the course. In response to the question “Do you think you were motivated to try harder or had more fun (and thereby learned more) during your final project because you were making a game (rather than just building a technical instrument, for example)? If so—please give some examples:” 15 out of 17 students responded “Very/definitely” on a five point scale. As examples, students listed: “wanted to make the best game,” “want to make it clever and cool in the eyes of classmates who are play testing,” “motivated during final push,” “willing to put in more time,” “was fun”/”made it fun,” “create a game that actually works,” “reinforced what was learned before,” and “provided room for creativity.” These comments reflect the overall excitement we saw for the biotic game project. While these responses do not constitute rigorous proof regarding course effectiveness (which will require more detailed and controlled assessments in the future), we consider this course a success based on our teaching experiences.45 students have now taken this class over the past three years, with 18 students in our most recent offering. We used each year to iterate and improve our implementation. For example, we changed the organism and stimulus from Paramecia galvanotaxis [5] to Euglena phototaxis, which gave more reliable long-term responses. We also added a simple microfluidics unit enabling students to build more robust organism housing chambers. We changed the microscope structure from LEGO to Thorlabs parts (essentially trading the emphasis on 3-D structural design, flexibility, and cost for a more in-depth focus on high-end optics and their alignment). Finally, we explicitly asked the students to design and fabricate a housing for the game controller to better incorporate fabrication skills like using a band saw and tapping screw threads. So far, we primarily used MATLAB as the programming component given its widespread use in education and research and the available Arduino interface. However, MATLAB is not particularly well-suited to support game design and is also not free, making translation into lower resource settings challenging. For the future, we are considering moving to smartphone-based control (such as Android) given that these mobile environments are very flexible and increasingly used for control of scientific and consumer instruments and are becoming more widespread in education. We also see the opportunity to better emphasize and teach the approach of iterative design; for example, by letting students prototype and test their game ideas on paper [10] and simple programming environments like Scratch [11] first, before attempting the full implementation. It would likely also be very rewarding for the students to be able to take their project home at the end of the course. In summary, many different course design decisions can be made based on specific intended educational outcomes. Not all of these can be fit into one course at the same time, and clear decisions should be made on how to balance covering a breadth of topics with depth on a selected few.As a preliminary test of another age range, time frame, and budget, we taught a greatly simplified 3-hour workshop where high school and middle school students assembled a low-cost microscope and microfluidics chamber, attached it to a smartphone, and stimulated euglena using a preprogrammed Arduino-based controller (see supplements). We had no game interface implemented yet on the phone, but the students could observe the euglena responses to the light stimuli. All students were able to complete the project and take their microscopes home. Over half of our undergraduate student teams also volunteered to present their game projects for this outreach event which took place multiple weeks after their class had ended. This separate experience suggests that the biotic game concept holds promise for reaching a wider age range in a shortened timespan and at a greatly reduced budget, and that completed games can be used in outreach activities. We are currently developing a kit modeled after this unit.In conclusion, we consider biotic games promising in motivating integrated, hands-on learning at the interface of life science and engineering. Our efforts so far indicate that this concept could be adapted to various age groups and learning goals with the potential for wider future impacts on education. We draw upon the analogy to robotics, where microcontrollers went from initially unfathomable as an educational tool to the vision of Papert and collaborators and their use of programmable robotics with children [12], eventually leading to multiple commercial realizations (LEGO mindstorm, Arduino, etc.), a large public following, and a major role in education both in the classroom and through competitions such as First Robotics [1]. We also see additional potential for integrating more creative and artistic aspects into STEM, i.e., leading to generalized Science, Technology, Engineering, Arts, and Mathematics (STEAM) disciplines [13]. We invite others to join us in these endeavors—all instructional materials are available in the appendix for further adaptations and educational use.     

Fibers with Integrated Mechanochemical Switches: Minimalistic Design Principles Derived from Fibronectin

Inspired by molecular mechanisms that cells exploit to sense mechanical forces and convert them into biochemical signals, chemists dream of designing mechanochemical switches integrated into materials. Using the adhesion protein fibronectin, whose multiple repeats essentially display distinct molecular recognition motifs, we derived a computational model to explain how minimalistic designs of repeats translate into the mechanical characteristics of their fibrillar assemblies. The hierarchy of repeat-unfolding within fibrils is controlled not only by their relative mechanical stabilities, as found for single molecules, but also by the strength of cryptic interactions between adjacent molecules that become activated by stretching. The force-induced exposure of cryptic sites furthermore regulates the nonlinearity of stress-strain curves, the strain at which such fibers break, and the refolding kinetics and fraction of misfolded repeats. Gaining such computational insights at the mesoscale is important because translating protein-based concepts into novel polymer designs has proven difficult.     

Aminoacylation of RNA Minihelices: Implications for tRNA Synthetase Structural Design and Evolution

Abstract

The genetic code is based on the aminoacylation of tRNA with amino acids catalyzed by the aminoacyl-tRNA synthetases. The synthetases are constructed from discrete domains and all synthetases possess a core catalytic domain that catalyzes amino acid activation, binds the acceptor stem of tRNA, and transfers the amino acid to tRNA. Fused to the core domain are additional domains that mediate RNA interactions distal to the acceptor stem. Several synthetases catalyze the aminoacylation of RNA oligonucleotide substrates that recreate only the tRNA acceptor stems. In one case, a relatively small catalytic domain catalyzes the aminoacylation of these substrates independent of the rest of the protein. Thus, the active site domain may represent a primordial synthetase in which polypeptide insertions that mediate RNA acceptor stem interactions are tightly integrated with determinants for aminoacyl adenylate synthesis. The relationship between nucleotide sequences in small RNA oligonucleotides and the specific amino acids that are attached to these oligonucleotides could constitute a second genetic code.     

It's Not All Sex and Violence: Integrated Anthropology and the Role of Cooperation and Social Complexity in Human Evolution

Social scientists, especially anthropologists, have long endeavored to understand the evolution of "human nature." This investigation frequently focuses on the relative importance of competition versus cooperation in human evolutionary trajectories and usually results in a primary emphasis on competition, aggression, and even war in attempting to understand humanity. This perspective conflicts with long-standing perspectives in anthropology and some emerging trends and theory in evolutionary biology and ecology. Cooperation and competition are not mutually exclusive in an evolutionary context. As anthropologists, we have demonstrated that humans can–and usually do–get along. Evolution is complex with multiple processes and patterns, not all of which involve competition and conflict. In this article, I summarize elements of modern ecological and evolutionary theory in the context of human cooperative patterns in an attempt to illustrate the valuable role of evolutionary theory and cooperative patterns in integrative anthropological approaches to the human condition.     

Structural Evolution Design and Optimization for the Metamaterials with Broadband Frequency-Independent Negative Permeability

Plasmonics - Broadband frequency-independent operations are strongly desired in metamaterial applications. In this work, we unveil the roles of each element acting in the metamaterial unit with a...