Thoughts of a Travelling Ecologist 1 Human impacts, invasions and urbanisation

At the start of our new Journal of Biosafety, I was prompted by my Co-Editors-in-Chief, Professor Wan and Professor You, to provide regular reviews or updates on biosafety for our readers, given that I mostly reside outside China, and have many international connections. That is a very big task, and I was not sure that I could do it as the journal demands. However, I had thought that in a lighter way, I could attempt to present my thoughts on some issues that I feel are of importance today. China is very...     

In memoriam: Joep MA Lange(1954–2014)

<正>July 17,2014 marks the date of the brutal and unforgivable shooting down of Malaysian Airlines flight MH17 over the Ukraine,resulting in the death of all its passengers,including my longstanding friends and colleagues Joep Lange and Jacqueline van Tongeren.They were on their way to attend the 20th International Aids Conference,held this year in Melbourne,Australia.I myself had already arrived in Mel-     

The Value and Significance of Metagenomics of Marine Environments

<正>Microbes have played a fundamental role in the natural history of our planet,and have done so for billions of years.They have adapted to Earth’s many environments from the mild to the very extreme.Studying their diversity and their way of life is critical for understanding their full impact on the global ecology.Although the field of metagenomics is still young,it has unravelled a wider microbial diversity that had otherwise been completely overlooked by the traditional methods of     

A Preliminary Study of the Noninvasive Remote Control System for Rat Bio-Robot

<正> A system is described here that can noninvasively control the navigation of freely behaving rat via ultrasonic,epidermaland LED photic stimulators on the back.The system receives commands from a remote host computer to deliver specifiedelectrical stimulations to the hearing,pain and visual senses of the rat respectively.The results demonstrate that the three stimuliwork in groups for the rat navigation.We can control the rat to proceed and make right and left turns with great efficiency.Thisexperiment verified that the rat was able to reach a setting destination in the way of cable with the help of a person through theappropriate coordination of the three stimulators.The telemetry video camera mounted on the head of the rat also achieveddistant image acquisition and helped to adjust its navigation path over a distance of 300 m.In a word,the non-invasive motioncontrol navigation system is a good,stable and reliable bio-robot.     

Disentangling confusions in inflorescence morphology:Patterns and diversity of reproductive shoot ramification in angiosperms

Terminology of inflorescence diversity has often been used in a confusing way in the literature,partly because it was based on uncritical and outdated definitions.In particular,the terms cyme,thyrse,and panicle have been misused.Although a more critical classification worked out by several authors is available,it is unfortunately not in general use because most of the relevant publications are written in German.In addition,some terms have not been used in the same way by morphologists and developmental geneticists.The present review attempts to remedy the situation with a simple outline of a classification based on:(i)different branching patterns;(ii)differential elongation of axes of different orders;and(iii)repetition of basic ramification patterns in different ways.Racemose and cymose branching are two extreme patterns;the former with limitation of axial orders to two,the second with limitation of lateral axes of each order to two.In a branching system,a sequence of racemose→cymose and,within the cyme,of dichasial→monochasial is common,but the reverse sequence generally does not occur.Systematic and evolutionary aspects of inflorescences are briefly discussed.Branching patterns are often stable in larger clades.Inflorescences of mutants studied in developmental genetic studies are mainly altered in flower or branch numbers or relative branch length,but not in branching patterns.This is also a contribution towards the goal of a unified terminology for the different fields of biology dealing with inflorescences.     

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.     

Entire solutions in a delayed nonlocal dispersal competitive system

In this paper, we are concerned with the existence of an entire solution in a delayed nonlocal dispersal competitive system. This entire solution converges to two monotone fronts with different speeds, which approach each other from both sides of the x-axis, as t converge to-∞ and then converge to (1,0) as t converges to +∞. Its global dynamic shows the superior species invade the inferior ones from both sides of the x-axis and then the inferior ones become extinct, which is a new invading way. In fact, our conclusions extend this invading way into a more general competitive system. Furthermore, we show several properties of this entire solution.     

A General Introduction of HIV/AIDS Treatment with Traditional Chinese Medicine in China

This paper gives a general introduction of HIV/AIDS treatment with Traditional Chinese Medicine (TCM) in China during the past 20 years. Although the role of TCM in treatment of HIV/AIDS is promising,there is still a long way to go.     

Protein secondary structure prediction using dynamic programming

In the present paper, we describe how a directed graph was constructed and then searched for the optimum path using a dynamic programming approach, based on the secondary structure propensity of the protein short sequence derived from a training data set. The protein secondary structure was thus predicted in this way. The average three-state accuracy of the algorithm used was 76.70%.     

Clinical utility of whole genome sequencing for the detection of mitochondrial genome mutations

正Genetic mitochondrial disorders are a heterogenous group of multi-system disorders caused by an imbalance in mitochondrial function (Moggio et al.,2014;Wallace,2018).In contrast to the nuclear genome,each cell contains hundreds,or even thousands,of mtDNA molecules (Veltri et al.,1990;Calvo et al., 2006).Thus,a mixture of different mtDNA sequences can co-exist within the same individual,a situation referred to as he terop las my.The level of heteroplasmy in an individual often affects the penetrance and phenotypic severity of the diseases.Consequently,detection of sequence heteroplasmy is essential for the proper clinical interpretation of mitochondrial diseases (Stewart and Chinnery,2015).     

Academic genealogy and direct calorimetry: a personal account

Each of us as a scientist has an academic legacy that consists of our mentors and their mentors continuing back for many generations. Here, I describe two genealogies of my own: one through my PhD advisor, H. T. (Ted) Hammel, and the other through my postdoctoral mentor, Knut Schmidt-Nielsen. Each of these pathways includes distingished scientists who were all major figures in their day. The striking aspect, however, is that of the 14 individuals discussed, including myself, 10 individuals used the technique of direct calorimetry to study metabolic heat production in humans or other animals. Indeed, the patriarchs of my PhD genealogy, Antoine Lavoisier and Pierre Simon Laplace, were the inventors of this technique and the first to use it in animal studies. Brief summaries of the major accomplishments of each my scientific ancestors are given followed by a discussion of the variety of calorimeters and the scientific studies in which they were used. Finally, readers are encouraged to explore their own academic legacies as a way of honoring those who prepared the way for us.     

Analogies and resonances in the process of ethnographic understanding

In this paper I explore the way in which anthropological understanding is engendered through analogies with an ethnographers experiential knowledge. This theme is addressed via an account of the development of my friendship with my ‘key informant,’ employing what Riesman (1977) calls a ‘disciplined introspection’ of what I as an ethnographer brought to the ethnographic encounter.     

A path to the powerhouse: systems‐to‐structure approaches for studying mitochondrial proteins

The young investigator award from the Protein Society was a special honor for me because, at its essence, the goal of my laboratory is to define what obscure proteins do. Years ago, I stumbled into mitochondria as a venue for this work, and these organelles continue to define the biological theme of my laboratory. Our approaches are fairly broad, reflecting my own somewhat unorthodox training among diverse scientific fields spanning organic synthesis, chemical biology, mechanistic biochemistry, signal transduction, and systems biology. Yet, whatever the theme or the discipline, we aim to understand how proteins work—especially those that hide in the dark corners of mitochondria. Below, I recount my own path into this arena of protein science, and describe how my experiences along the way have shaped our current multi‐disciplinary efforts to define the inner workings of this complex biological system.     

Why do we need autophagy? A cartoon depiction

In my role as an instructor I am constantly looking for ways to more effectively convey information to my audience, which is typically the students in my class. However, the same concerns apply to most of the people who attend a seminar. The approach you take to making the material easier to understand is likely to be influenced by the course you teach. That is, the same instructor may use different examples when teaching an upper division vs. a lower division course. I teach introductory biology, and my students may have little familiarity with cell biology, let alone autophagy. Accordingly, I have tried to consider how to illustrate the importance of autophagy in a way that can be comprehended by people who may not even be familiar with the term.     

Alterations in hypertensive arteries

Mentoring in academia is often carried out in an informal way depending on individuals and circumstances. I was quite fortunate to make the acquaintance of Professor E.E. Daniel when I was making a transition from my research in entomology to biomedical sciences. Here I recount some of that experience, and describe some of the lessons I have learned from this experience, as my tribute to Dr. Daniel on the occasion of his 80th birthday.     

The wanderings of a free radical

In my career I have moved from chemistry to biochemistry to plant science to clinical chemistry and back again (in a partial way) to plants. This review presents a brief history of my research achievements (ascorbate–glutathione cycle, role of iron in oxidative damage and human disease, biomarkers of free radical damage, and studies on atherosclerosis and neurodegeneration) and how they relate to my research activities today. The field of free radicals/other reactive species/antioxidants underpins all of modern Biology. These agents helped to drive human evolution and the basic principles of the field are repeatedly found to be relevant in other research areas. It was an exciting field when I started some 40 years ago, and it still is today, but some major challenges must be faced.     

Life in a Three-dimensional Grid

There have been two sharp demarcations in my life in science: the transition from fine arts to chemistry, which happened early in my career, and the move from New York to Stanford University, which initiated an ongoing collaboration with the physicist Harley McAdams. Both had a profound effect on the kinds of questions I posed and the means I used to arrive at answers. The outcome of these experiences, together with the extraordinary scientists I came to know along the way, was and is an abiding passion to fully understand a simple cell in all its complexity and beauty.     

Advice to a young scientist (by someone who doesn’t know how to give it)

While trying to extract original and general advice from the details of my career, I realized this might not be possible. My path, like those of so many others, had too many idiosyncratic twists and turns that had to work out just the way they did to be mined for generally useful strategies. So I abandon the conceit of advice and simply give you my story. There are many like it, but this one is mine. Take what you wish from it.     

Sociobiology and the Comparative Approach: One Way to Study Ourselves

This paper is based on my lecture in a macroevolution course I team-teach with Profs. Daniel Brooks and David Evans at the University of Toronto. The lecture has undergone many revisions over the years as I grappled with problems discussing certain areas (e.g., rape as an adaptive strategy, gender “roles”). Eventually, I realized that the problem areas said more about my personal conflicts than they did about the science. This was one of those epiphany moments, a time when I recognized that I was less likely to accept hypotheses that contradicted the way I wanted the world to be and more likely to uncritically accept hypotheses that confirmed my world view. That epiphany, in turn, led me to realize that science is never separate from the personal biases/demons of its practitioners, especially when we are asking questions about the evolution of human behavior. That realization was not novel within the vast literature of sociology and philosophy. But it was novel for me. I was aware of discussions about personal biases clouding scientific interpretation; I just didn’t think it applied to me (I absorbed the philosophical discussions without making the connection to “my world”). So, on the heels of that epiphany, the following is a very personal take on the question of teaching sociobiology, based on where my journey, aided by my experience as an ethologist and phylogeneticist and colored by my own history, has taken me.