Teaming up: from motors to people

When I reflect on how I became a cell biologist and why I love being one today, one thing that comes to mind is the many terrific collaborations I have had. The science I am most proud of from my graduate and postdoctoral training would not have been possible without working in teams with other scientists. Now, in my own group, much of our best work is being done collaboratively, both within the lab and with other labs. In this essay, I will highlight my experiences working in teams as a trainee, the role teamwork has played in my own research group, and how important I think collaborative science is for the future of biological research.     

Establishing an academic laboratory: mentoring as a business model

It is a tremendous honor for my group and me to receive the recognition of the 2014 Women in Cell Biology Junior Award. I would like to take the opportunity of this essay to describe my scientific journey, discuss my philosophy about running a group, and propose what I think is a generalizable model to efficiently establish an academic laboratory. This essay is about my view on the critical components that go into establishing a highly functional academic laboratory during the current tough, competitive times.     

Towards the analysis of vegetation succession

Attention is drawn to canonical analysis as a plausible model for analyzing vegetation succession. An assessment of the opportunities afforded by canonical analysis for this purpose is then made by reference to two applications of the method. The applications deal with characteristics of hydroseral processes and with the dynamic status of an area of lowland tropical rain forest. On the basis of these and other studies the conclusion is drawn that canonical analysis could contribute usefully in efforts to place the study of dynamic ecosystem processes on a more analytic footing.This work was supported by a Natural Sciences and Engineering Research Council award to L. Orlóci. It is a pleasure to acknowledge my indebtedness both to Dr. Orlóci for his support and encouragement and to the Department of Plant Sciences at the University of Western Ontario for hospitality and help. Appreciation is expressed also to Dr. John Ogden, Research School of Pacific Studies, The Australian National University, Canberra for kindly placing his rain forest data at my disposal and for his invaluable help in interpreting the results of analyses of these data.     

A Reminiscence

Leslie Orgel and Francis Crick with Gobind Khorana in Madison, Wisconsin (December 1965). I first met Leslie at the Endicott House (MIT) in February 1964. Leslie was then spending a period of time at MIT and the occasion was a party for him. During our conversation, Leslie talked about starting some experimental work. He seemed to be particularly interested in polyphosphates and the chemical activation of small molecules (building blocks).Shortly after his move to the Salk Institute in the Fall of 1964 I visited him in January 1965. He already had a lab going. I remember meeting Jim Ferris, in particular, and John Sulston sometime later. That particular time was exciting for my research as well. We had the first results on the Genetic Code using the chemical-biochemical approach that my lab had developed. Francis Crick was also at the Salk Institute during the time of my visit. Both Leslie and Francis were very excited by my results and they began to ask a lot of questions and gave me a whole lot of suggestions about further experiments. In fact, my thinking and planning of things that we were doing were so scrutinized and clarified during these discussions that, it seemed to me, my own group had only to turn out all the experiments that were needed. These interactions with Francis and Leslie continued intensively throughout that year and later. In fact, both Leslie and Francis accepted my invitation to Madison in December 1965 for more discussions.Since those early days of the Salk Institute, I have made numerous visits over the years to Leslie and his research group. It has always been very exciting to learn about the many discoveries bearing on chemical evolution that have unfolded from Leslie's research group. In addition, I have always benefitted from the insightful comments that Leslie invariably provided on my own research. I look forward to our continued interactions and friendship in the future.Leslie, A Happy Birthday!     

My Journey to DNA Repair

I completed my medical studies at the Karolinska Institute in Stockholm but have always been devoted to basic research. My longstanding interest is to understand fundamental DNA repair mechanisms in the fields of cancer therapy, inherited human genetic disorders and ancient DNA. I initially measured DNA decay, including rates of base loss and cytosine deamination. I have discovered several important DNA repair proteins and determined their mechanisms of action. The discovery of uracil-DNA glycosylase defined a new category of repair enzymes with each specialized for different types of DNA damage. The base excision repair pathway was first reconstituted with human proteins in my group. Cell-free analysis for mammalian nucleotide excision repair of DNA was also developed in my laboratory. I found multiple distinct DNA ligases in mammalian cells, and led the first genetic and biochemical work on DNA ligases Ⅰ, and Ⅳ. I discovered the mammalian exonucleases DNase Ⅲ (TREX1) and IV (FEN1). Interestingly, expression of TREX1 was altered in some human autoimmune diseases. I also showed that the mutagenic DNA adduct O6-methylguanine (O6 mG) is repaired without removing the guanine from DNA, identifying a surprising mechanism by which the methyl group is transferred to a residue in the repair protein itself. A further novel process of DNA repair discovered by my research group is the action of AlkB as an iron-dependent enzyme carrying out oxidative demethylation.     

Sampling phylogenetic tree space with the generalized Gibbs sampler

A recent article published in Cladistics is critical of a number of heuristic methods for phylogenetic inference based on parsimony scores. One of my papers is among those criticized, and I would appreciate the opportunity to make a public response. The specific criticism is that I have re‐invented an algorithm for economizing parsimony calculations on trees that differ by a subtree pruning and regrafting (SPR) rearrangement. This criticism is justified, and I apologize for incorrectly claiming originality for my presentation of this algorithm. However, I would like to clarify the intent of my paper, if I can do so without detracting from the sincerity of my apology. My paper is not about that algorithm, nor even primarily about parsimony. Rather, it is about a novel strategy for Markov chain Monte Carlo (MCMC) sampling in a state space consisting of trees. The sampler involves drawing from conditional distributions over sets of trees: a Gibbs‐like strategy that had not previously been used to sample tree‐space. I would like to see this technique incorporated into MCMC samplers for phylogenetics, as it may have advantages over commonly used Metropolis‐like strategies. I have recently used it to sample phylogenies of a biological invasion, and I am finding many applications for it in agent‐based Bayesian ecological modelling. It is thus my contention that my 2005 paper retains substantial value.     

Anglo-Canadian Exchange in General Practice: Canadian View of British General Practice

Before embarking on this exchange venture in British general practice I had many preconceived impressions of what it might be like to be an English family physician. Early in my five months of group practice it became apparent that many of my attitudes had no real basis and in fact I had to admit many aspects of the British health system were indeed superior. It has been my impression that a group general practice in Great Britain can certainly afford the practising family doctor a stimulating and rewarding professional and social life.     

Prediction and design of macromolecular structures and interactions

In this article, I summarize recent work from my group directed towards developing an improved model of intra and intermolecular interactions and applying this improved model to the prediction and design of macromolecular structures and interactions. Prediction and design applications can be of great biological interest in their own right, and also provide very stringent and objective tests which drive the improvement of the model and increases in fundamental understanding. I emphasize the results from the prediction and design tests that suggest progress is being made in high-resolution modelling, and that there is hope for reliably and accurately computing structural biology.     

Reply to the Comment by S. Harvey on “Entropy,Energy, and Bending of DNA in Viral Capsids”

The comment by Stephen Harvey in this issue of the Biophysical Journal concludes with two statements regarding my recent letter about DNA packaging into viral capsids. Harvey agrees with my interpretation of the origin of the large confinement entropy predicted by the molecular-dynamics simulations of his group, and its sensitive dependence on the molecular parameters of their wormlike chain model of double-stranded DNA. On the other hand, he doubts my assertion that the confinement entropy is already included in the interstrand repulsion free energy derived from osmotic stress measurements, which constitutes the major contribution to the packaging free energy used in recent continuum theories of this process. Harvey suggests instead that the confinement entropy should be added to this free energy as a separate term (using, for instance, the method described in my letter). I will argue that this addition is redundant, and, in a brief discussion of continuum theories, will also discuss his comments as relates to the work of other researchers.     

Reply to the Comment by S. Harvey on “Entropy,Energy, and Bending of DNA in Viral Capsids”

The comment by Stephen Harvey in this issue of the Biophysical Journal concludes with two statements regarding my recent letter about DNA packaging into viral capsids. Harvey agrees with my interpretation of the origin of the large confinement entropy predicted by the molecular-dynamics simulations of his group, and its sensitive dependence on the molecular parameters of their wormlike chain model of double-stranded DNA. On the other hand, he doubts my assertion that the confinement entropy is already included in the interstrand repulsion free energy derived from osmotic stress measurements, which constitutes the major contribution to the packaging free energy used in recent continuum theories of this process. Harvey suggests instead that the confinement entropy should be added to this free energy as a separate term (using, for instance, the method described in my letter). I will argue that this addition is redundant, and, in a brief discussion of continuum theories, will also discuss his comments as relates to the work of other researchers.     

In pursuit of influenza: Fort monmouth to valhalla (and back)

In reviewing 50 years of personal research on influenza, I have journeyed, literally and figuratively, from an army camp epidemic in Fort Monmouth NJ in 1947 to a (literal and figurative) Valhalla, where I now conduct my research. Having entered the field as a physician, I have always sought practical applications of my work, yet in every instance, such applications have led me to seek further answers in basic research as new questions arose. I entered the area of influenza virus genetics by the back door through an interest in the effects of corticosteroid hormones on viral replication, used the genetic approach in analyzing the morphological variation of the virus and, in so doing, exploited the finding of a linkage of high-yield growth to spherical morphology. Today, all influenza vaccine viruses are high-yield genetic reassortants. Subsequent study of reassortant viruses facilitated the identification and isolation of the two major antigens of the virus in antigenic hybrids and showed their differing functions in the induction of immunity. In turn, a new approach to influenza vaccination has been discovered and is presently under clinical investigation.     

From fundamentals to applications of bioelectrocatalysis: bioelectrocatalytic reactions of FAD-dependent glucose dehydrogenase and bilirubin oxidase

In this review, I present the main highlights of my works in the development of bioelectrocatalysis, which can be used in widespread applications, particularly for the design of biosensor and biofuel cells. In particular, I focus on research progress made in two key bioelectrocatalytic reactions: glucose oxidation by flavin adenine dinucleotide-dependent glucose dehydrogenase and oxygen reduction by bilirubin oxidase. I demonstrate the fundamental principles of bioelectrocatalysis and the requirements for enhancing the catalytic performance, including the choice of a mediator of redox reactions, immobilization, and electrode materials. These methods can allow for achieving control of the bioelectrocatalytic reaction, thereby overcoming obstacles toward their industrial applications.     

A more cost-effective method of preoperative computerized imaging

Stimulated by the explosive expansion of the computerized desk top publishing industry during the past few years, microcomputer hardware and software are evolving at a staggering rate. Memory is rapidly increasing, and prices are declining. I have found that with the hardware and software described in this paper, I was able to obtain, in a much more cost-effective manner, as useful preoperative information for my practice as I could obtain with more expensive "turnkey" (only one use) computerized imaging systems. This type of microcomputer, of course, is not limited to just the imaging system, but can be used for a variety of other programs as well, such as word processing, slide labeling and production, spreadsheet functions, billing and filing, and numerous business and other applications. The ease of use with readily available 35-mm slides of my patients has greatly enhanced the appeal of this system. Computerized imaging, when used as an educational tool, can be very helpful in preoperative planning, resident teaching, and for illustration and discussion of a patient's proposed surgery. The electronic imaging disclaimer compiled by the American Society of Plastic and Reconstructive Surgeons has been extremely helpful in clarifying the limits of computerized imaging and reducing any false expectations that my patients might have. All of us are experiencing the dawn of a very exciting evolution.     

Design-driven, multi-use research agendas to enable applied synthetic biology for global health

Many of the synthetic biological devices, pathways and systems that can be engineered are multi-use, in the sense that they could be used both for commercially-important applications and to help meet global health needs. The on-going development of models and simulation tools for assembling component parts into functionally-complex devices and systems will enable successful engineering with much less trial-and-error experimentation and laboratory infrastructure. As illustrations, I draw upon recent examples from my own work and the broader Keasling research group at the University of California Berkeley and the Joint BioEnergy Institute, of which I was formerly a part. By combining multi-use synthetic biology research agendas with advanced computer-aided design tool creation, it may be possible to more rapidly engineer safe and effective synthetic biology technologies that help address a wide range of global health problems.