Bacterial communities of tyre monofill sites: growth on tyre shreds and leachate

Aims: To investigate bacterial communities of tyre monofill sites, colonization of tyre material by bacteria and the effect of tyre leachate on bacteria. Methods and Results: Culturable bacteria were isolated from buried tyre shreds and identified using fatty acid methyl ester analysis. Isolates belonged to taxonomic groups such as Bacilli, Actinobacteria, Clostridia, Flavobacteria, β and γ‐proteobacteria. For tyre material colonization experiments, Bacillus megatarium, Bacillus cereus, Hydrogenophaga  flava, Janthinobacterium  lividum, Cellulosimicrobium  cellulans, Arthrobacter  globiformis (isolated from tyre shreds or leachate at the study site); Escherichia  coli and Acidithiobacillus  ferrooxidans were used. Beakers containing tyre shreds and artificial rain water were inoculated with a given bacterial culture, incubated at room temperature and sampled at regular intervals. 4′,6‐diamidino‐2‐phenylindole (DAPI) staining followed by epifluorescent microscopy was used to enumerate bacteria in samples. Of the bacteria tested, B. megatarium, J. lividum, E. coli, C. cellulans and A. globiformis exhibited the most extensive colonization of the tyre shreds. However, the extent of colonization varied among bacteria. Response to tyre leachate was also examined using B. cereus and J. lividum. Both bacteria increased in abundance due to the addition of leachate. Conclusions: Bacteria associated with buried tyre shreds were identified and found to include typical soil and freshwater organisms. The majority of indigenous isolates grew on tyre material (or leachate) suggesting that they play an active role in the ecology of these sites and that their potential role in tyre degradation should be explored. Significance and Impact of the study: This study provides information on bacterial communities of tyre‐waste disposal sites, explores the interaction between tyre material and bacteria and identifies bacteria that could be involved in or employed for recycling tyre‐waste.     

Bill Arnold: Scientist, philosopher, friend

Bill Arnold is a great scientist in whose laboratory I was privileged to work during the years he discovered the thermoluminescence and the electroluminescence of green plants. I reminisce about Bill's influences on me, scientific and otherwise, during those years.     

Neutrons, magnets, and photons: a career in structural biology

The purpose of Reflections articles, it seems, is to give elderly scientists a chance to write about the "good old days," when everyone walked to school in the snow. They enjoy this activity so much that your editor, Martha Fedor, must have known that I would accept her invitation to write such an article, no matter how much I demurred at first. As everyone knows, flattery will get you everywhere. It may comfort the apprehensive reader to learn that there is not going to be much walking to school in the snow in this story. On the contrary, rather than thinking how hard I had it during my scientific career, I find it inconceivable that anyone could have had a smoother ride. At the time I began my career, science was an expanding enterprise in the United States that welcomed the young. Only in such an opportunity-rich environment would someone like me have stood a chance. The contrast between that world and the dog-eat-dog world young scientists confront today is stark.     

A letter from Professor Boysen Jensen to Professor Monsi, September 1955

Prof. P. Boysen Jensen Raadmandsgade 49 KøbenhavnN. 24 September 1955 Professor Masami Monsi Dear colleague Please allow me to reply in German. In this language, it iseasiest for me to find the right expressions. I would like to cordially thank you for your kind letter, andalso for the reprints, which I have read with great interest. Of course I am very pleased to hear that my Japanese colleagueswant to continue my investigations on productivity. I myselfhave     

(M,R)-systems, (P,M,C)-nets, hierarchical decay, and biological aging: reminiscences of Robert Rosen

I have the pleasure to present a number of personal experiences that I had with Robert Rosen, both as his student and as a research colleague, and I will describe how this affected my academic career over the past decades. As a matter of fact, Rosen's work with (M,R)-systems as well as his continuing mentorship guided me into my own research in gerontology and geriatrics. Amazingly, this still continues to affect my work in complexity theory after 30 years.     

Primate origins,human origins,and the end of higher taxa

When people learn that I study human evolution and we start talking about it, they sometimes ask me, “How long ago did the first humans live?” My answer is usually another question: “What do you mean by 'humans'?” That response seems as baffling and wrong‐headed to them as their question seems to me, and it usually takes us a while to straighten things out. © 2012 Wiley Periodicals, Inc.     

What do I want from health research and researchers when I am a patient?

I have attempted to adopt the perspective of a patient--albeit one with a rather atypical background--to explore what I want from health research and researchers. This has left me with the impression that health researchers could serve the interests of the public more effectively in a variety of ways, and that they would be helped to do so by greater lay involvement in planning and promoting health research.     

THE THREE G's Meeting the Invertebrate Cell Culture Pioneers: Goldschmidt, Gaw, and Grace

It was my good fortune to meet personally the three invertebrate cell culture pioneers,Richard Goldschmidt,Zan-Yin Gaw,and Thomas D.C.Grace (Fig.1).In 1951 I met Goldschmidt at a symposium in Cold Spring Harbor,but I only knew that he was a prominent geneticist.I had no idea about his insect cell culture work at Yale University and daily contacts with Ross G.Harrison.In 1959 Zan Yin Gaw in Wuhan successfully cultured monolayers of silkworm cells for more than one year.I reported his breakthrough achievement at the 11th International Congress of Entomology in Vienna in 1960,but his work was completely ignored outside China.In 1982 Gaw invited me to Wuhan where he told me that he studied in the United States in the 1930s,working as postdoctoral scientist at the Rockefeller Institute,where he was daily meeting William Trager,and later at Yale University in the Osborn Laboratory,where he was inspired by Harrison.T.D.C.Grace worked in my laboratory at Rockefeller University during 1957 and 1958,then returned to CSIRO in Canberra,Australia.     

Epilogue: Luria's Psychological Symphony

A finely worked bronze dog has been standing on my desk for twenty years now. Aside from the books with their dedicatory signatures, it is the only material thing I have in memory of Aleksandr Romanovich Luria. A week after he died, Lana Pimenovna, his wife, asked if I could drop in to see her. I thought that the reason for her call—to ask me to enlarge, reproduce, and frame some photos she had made of Aleksandr Romanovich in various years during his lifetime—was only a pretext: the publisher's in-house photographer or any other photographer could have done this.     

Reflections on race,ethnicity, and NIH research awards

It has been a decade since “Race, Ethnicity, and NIH Research Awards” was published. Receiving the American Society for Cell Biology Public Service Award allows me to reflect on this research and its impact. In this essay, I share the story of how my research interests and professional networks provided the opportunity to do this important work. I also make the case for improved data and mentoring to address race and ethnic disparities in NIH funding.     

The Invisible Hand of Natural Selection, and Vice Versa

Building on work by Popper, Schweber, Nozick, Sober, and others in a still-growing literature, I explore here the conceptual kinship (not the hackneyed ideological association) between Adam Smith's 'invisible hand' and Darwinian natural selection. I review the historical ties, and examine Ullman-Margalit's 'constraints' on invisible-hand accounts, which I later re-apply to natural selection, bringing home the close relationship. These theories share a 'parent' principle, itself neither biological no politico-economic, that collective order and well-being can emerge parsimoniously from the dispersed (inter)action of individuals. The invisible hand operates on 'memes' the way natural selection operates on genes. Like Darwin's concept, it brings together traditional opposites, 'nature' and 'selection,' forming a saltation-mitigating transition between biological instinct and full-blown conscious design. Herschel's criterion of confirmation, which Darwin long strove to satisfy, is itself an invisible hand-like meme – a 'Midas effect' revealing and rewarding the fittest theories, Darwin's and Smith's emphatically among them.     

Author Index to Journal of Russian and East European Psychology: Volume 44 (January-December 2006)

I had occasion, in the late 1930s, to address directly the question of how to teach beginners to read. By then I was a relatively mature psychologist and a pupil of Vygotsky, and had already been teaching for several years in the primary grades. My practical work convinced me of the difficulties of teaching beginners to read and of the deep contradictions between method and the scientific data accumulated in linguistics and psychology—ideas that could be tested only many years later.     

Protocols, Toolboxes and Resource papers

In the August 2009 issue of Autophagy, I indicated that we were launching a new category of article, Protocols. At that time, I noted that we would ultimately be placing these articles on a new site online. Well, that time has finally arrived (see www.landesbioscience.com/journals/autophagy/protocols/ for links to these papers). Therefore, it seems appropriate for me to briefly distinguish among three types of community-oriented papers, Protocol, Toolbox and Resource.     

Shedding light on proteins, nucleic acids, cells, humans and fish

I was trained as a physicist in graduate school. Hence, when I decided to go into the field of biophysics, it was natural that I concentrated on the effects of light on relatively simple biological systems, such as proteins. The wavelengths absorbed by the amino acid subunits of proteins are in the ultraviolet (UV). The wavelengths that affect the biological activities, the action spectra, also are in the UV, but are not necessarily parallel to the absorption spectra. Understanding these differences led me to investigate the action spectra for affecting nucleic acids, and the effects of UV on viruses and cells. The latter studies led me to the discovery of the important molecular nature of the damages affecting DNA (cyclobutane pyrimidine dimers) and to the discovery of nucleotide excision repair. Individuals with the genetic disease xeroderma pigmentosum (XP) are extraordinarily sensitive to sunlight-induced skin cancer. The finding, by James Cleaver, that their skin cells were defective in DNA repair strongly suggested that DNA damage was a key step in carcinogenesis. Such information was important for estimating the wavelengths in sunlight responsible for human skin cancer and for predicting the effects of ozone depletion on the incidence of non-melanoma skin cancer. It took experiments with backcross hybrid fish to call attention to the probable role of the longer UV wavelengths not absorbed by DNA in the induction of melanoma. These reflections trace the biophysicist's path from molecules to melanoma.     

You are the most valuable reagent in the lab: mental health before and during the pandemic

No one maps out their tenure as a postdoc anticipating a life-altering tragedy. But mental health crises of all kinds affect academic trainees and staff at similar or higher levels than the general public. While the mental health resources available to trainees are often set by healthcare providers, all levels of university leadership can work to remove material and immaterial obstacles that render such resources out of reach. I describe how access to care via telemedicine helped me following a loss in my family.

Over the years, my siblings and close friends have sought mental health resources like therapy, psychoanalysis, or psychiatry, so I loosely understood their benefits. When I was a PhD student I went to therapy briefly, but my counselor and I decided I could do without it. Since I started my postdoc, stress manifested in some new ways but I managed it well with my usual coping strategies and support. That changed one bright December morning in 2019 while I was preparing for our weekly lab meeting. My phone rang indicating a call from my father, whom I had spoken to the night before to celebrate the news of my nephew’s birth. But the voice on the phone was that of a family friend, telling me that my father had died overnight of an undiagnosed heart condition. In the moment I couldn’t even understand what was happening, saying over and over, “but I talked to him last night.” Soon I was sitting at home, dazed, on a string of tearful calls with family and friends.I often read words like “lifted” or “buoyed” to describe the stabilizing support of a network of loved ones. In my case this network was tethering me to reality over the next few weeks, preventing me from spinning off the Earth’s surface in a storm of sorrow and anxiety. The trauma also took a strange physical form and convinced me that I was suffering from a cardiac condition of my own. I had a panic attack during which I went to urgent care convinced my own heart was about to give way. Night after night these physical symptoms prevented me from sleeping.Graced by many loving connections with my siblings, my boyfriend, and close friends, I was actually weathering the process as well as one can. My PI gave me a firm directive to take as much time off as I needed. These were two key elements early in my healing process: a supportive network and an understanding advisor. The third was getting professional help, which I soon realized I needed. Even if I felt OK one day, I didn’t trust that I’d be OK the next. My grief formed too thick and too broad a landscape for me to navigate without help.Deciding to seek mental health resources and realizing that one needs them are often the hardest parts. Connecting with those resources once the decision has been made should be as simple as possible. I called a mental health number, and a triage counselor noted my therapy needs and verified my insurance. She asked what times and locations I preferred and then searched for an open appointment with a therapist who accepted my insurance. She also informed me that my coverage allowed 12 sessions with no copay, which was a pleasant surprise. The therapist who agreed to see me had very few openings, in part because this all happened in December—the holidays are especially busy for therapists. I was aiming for a time after normal working hours, or in the morning before I would head to lab, but none of those times were available. I didn’t like interrupting my workday to trot off to therapy. Taking a long break once a week meant I couldn’t run experiments or mentor my student during that time. But I made the sacrifice because my highest priority was getting the help I needed. There was no shortcut. Prioritizing mental health over lab work is tough for researchers, and I would never have accepted that kind of weekly disruption before my dad’s passing. But as a wonderful mentor of mine used to say, “You are the most valuable reagent in the lab.” She wasn’t describing mental health at the time, but the phrase now provided a guiding principle for my recovery. My first few sessions were on Tuesdays at 2:00 pm.The afternoon break turned out to be less disruptive than I had feared, because I had recently come back to the lab and was working short days. Had she asked, I would have told my PI where I was on Tuesday afternoons, but she wasn’t normally abreast of my daily schedule, so I didn’t seek her approval beforehand. Coordinating experiments with lab members thankfully wasn’t an issue because my work was largely independent; I simply let lab members know that I’d would be out of the lab for a bit on those days.The weeks went by, and the benefits of therapy accrued, helping me in large and small ways as I grieved. In mid-March of 2020, my therapist followed public health guidelines and asked all her clients to transition to remote sessions. While this was easy and sensible, it was still a little disappointing. Therapists are professional empaths, among many other things, and doing away with the physical presence and exchange with her was a blow. Yet therapy via video felt less odd simply because most of my social interactions were now virtual. Thankfully I didn’t have to move out of state for the lockdown (as did many students living in campus housing), which meant I could stay with the same therapist without any insurance complications.A few weeks into lockdown, I asked my therapist whether we had reached the limit of my 12 sessions without a copay. She replied with the good news that my insurance provider had waived all copays for mental health costs due to the pandemic. By that time therapy had generated a platform and an outlet to explore areas of my grief beyond the trauma of my father’s passing. Without needing to weigh the costs and benefits of this resource, I saw my therapist for another 4 months. I slowly took stock of my upbringing in an unconventional family and the loss of my mother when I was 25 and waded through a series of difficult decisions regarding my father’s estate. My father’s death changed me at a depth that is untouched by any amount of therapy or treatment. I’m not “healed”: I feel aged, more brittle, and a little ground down compared with who I had been. But therapy guided me through the worst of my grief, past the acute trauma to help me grasp what I was going through.Since the pandemic began, the number of people reporting increased stress or mental health issues has steadily increased (information on the impact of COVID-19 measures on mental health: https://www.apa.org/workforce/publications/depression-anxiety-coronavirus.pdf) (also see Mental health resources for trainees). I am fortunate to have affordable health insurance and the support from my lab and my department. The ease of finding my institution’s phone number for mental health resources was itself an important benefit. I share these pieces of my story with humility and understanding that not everyone enjoys the privileges that I do and the knowledge that everyone weathers life’s tragedies in their own way. It is not lost on me that some benefits stemmed from a policy change made by a private insurance provider. The provider made the right decision to waive copays, freeing me from having to choose between cost and my mental health needs. Yet had I been a student who had to move out of state due to COVID-19, access to mental health resources might have been disrupted or cut off. The need for reduced out-of-pocket costs for healthcare is known and needs no repetition, but the benefits of telehealth should be a low-cost component of health plans offered to students and staff (information on telehealth recommendations: https://www.apaservices.org/advocacy/news/congress-patient-telehealth?_ga=2.231013471.1538013741.1619359426-1228006513.1619359425 and http://www.apaservices.org/practice/advocacy/state/leadership/telebehavioral-health-policies.pdf?_ga=2.3385904.1067518037.1620039082-1228006513.1619359425.I’m not a cloud of emotions attached to a pair of good pipetting hands, I’m a human who is choosing to spend my time doing research. This observation is easy to repeat, by trainees as much as by faculty and administrators, but much harder to act upon in the midst of conflicting priorities. Consider my story a success: Because I could access the resources I needed, I was able to prioritize my mental health in the midst of my ambitious research program even during the lockdown.MEET THE AUTHORI have been a postdoc in Stefani Spranger’s lab at MIT for 4 years. Supported by an Irvington Fellowship from the Cancer Research Institute, my work examines the behaviors of dendritic cells in tumors that contribute to productive or unproductive anti-tumor immune responses. My doctoral work examined modes of multicellular invasion controlled by the actin cytoskeleton with Margaret Gardel at the University of Chicago. Earlier I was a lab technician with Thea Tlsty at the University of California, San Francisco, which followed a bachelor’s degree in biology at the University of California, Santa Cruz. I serve on the Committee for Students and Postdocs at the American Society for Cell Biology, where I chair the Outreach Subcommittee.     

The Natural Experiment

Many of you, reading the title of this report, probably felt a certain confusion about this new, unusual term natural experiment. To dispel this quite natural confusion, let me say immediately that I am proposing this term to designate special investigatory techniques situated somewhere between external, objective observation, on the one hand, and a man-devised laboratory experiment (at present referred to as a psychological experiment), on the other. These original techniques, different from both the first and the second, are actually not completely new and unusual but, on the contrary, are well known to every one of you in their rudimentary form. Considered in more detail, they might perhaps be of considerable interest both theoretically and practically. It is for this reason that I decided to propose a new term to designate them. One cannot, of course, in such a brief report attempt to outline all the possible applications of this method to all the phenomena to which it could be applied; hence, I shall focus on an area that is more familiar to me and, moreover, seems to be especially suited for conducting a natural experiment, namely, research on personality or individuality.     

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.