A fortunate period of overlap with Prof. Haruki Nakamura

The author recounts a period of overlap with Prof. Haruki Nakamura that stretched from 2007 till the present day. Starting as a short-term research fellow in his laboratory, the author has also been a coauthor, academic colleague, and joint journal editorial board member of Prof. Nakamura.

I first met Prof. Haruki Nakamura in June of 2007 after coming to Osaka to talk with him about the possibility of taking on a short-term research position in his laboratory. At that stage, he was the Professor in charge of the Laboratory for Bioinformatics and Computational Structural Biology located within the Institute for Protein Research (IPR) at Osaka University as well as the Director of the Protein Data Bank in Japan (PDBj)—the Asian hub of the worldwide PDB. Since that time, he has been an interesting constant in my life and is someone that I have come to admire as much for his character and work ethic as for his scientific prowess, the latter of which is truly remarkable. In this Commentary, I thought I might recount some of the interesting ways my scientific career has intertwined with Prof. Nakamura’s, hopefully shining a light on some of the positive ways that scientists can interact with each other as well as highlighting some of the points that I genuinely admire about Prof. Nakamura.     

A special issue of the Australian society for Biophysics

On behalf of the Australian Society for Biophysics (ASB) and the Editors of this Special Issue, I would like to express our appreciation to Editor-in-Chief, Damien Hall, for arranging the publication of this Special Issue. The ASB is about five times smaller than our sister the Biophysical Society for Japan (BSJ) and tenfold smaller than the US Biophysical Society (USBS), but our meetings are notable because of the encouragement the Society gives to emerging biophysicists. It can be a terrifying experience for a PhD student to have to face a roomful of professors and senior academics, but invariably they appreciate the experience. Another feature of the ASB meetings is the inclusion of contributions from the Asian Pacific region. We now have formal ties with our New Zealand colleagues and our meetings with the BSJ contain joint sessions (see below). In 2020, despite the impact of COVID-19 (see Adam Hill’s Commentary), there is a joint session with the University of California Davis. This Special Issue comprises 2 Editorials, 3 Commentaries, and 25 reviews.

When we began to put together an editorial on the contributions to this Special Issue of the 44th meeting of the Australian Society for Biophysics (ASB), we were struck by the sheer diversity of what we call “Biophysics”. Biophysics is actually not easy to define. The glib answer is “Biophysics is what biophysicists do”, but what do they do? If we asked an Australian Minister for Science to tell us what biophysicists do, he or she could tell us what immunologists and virologists do, but would probably have no idea what a biophysicist does. So how should we explain biophysics to the Minister? The US Biophysical Society defines “biophysics” as the field that applies the theories and methods of physics to understand how biological systems work. Operationally, biophysicists analyse the structure of biological molecules like DNA and proteins, they develop computer models to understand how drugs bind to the receptors in the body, and they investigate how gene mutations change the function of proteins.We thought a good example of biophysics research is the article by Boris Martinac at the beginning of this Special Issue. Boris has worked for much of his research life on trying to figure out how a mechanosensitive ion channel works. His “babies” are molecules encoded by the MscL and MscS genes and more recently also by the Piezo1 gene. He realised that bacteria needed to have sensors embedded in their surface membrane so they can quickly produce electrical or chemical signals in response to a mechanical force which occurs in the form of osmotic pressure. This of course is what enables the bacterium to survive when exposed to a hypoosmotic shock. More recently he and his colleagues turned their attention to investigating whether Piezo1 channels are the inherently mechanosensitive channels in vertebrates (Syeda et al. 2016) like MscL and MscS channels are in bacteria. They explained how Piezo receptors respond to changes in mechanical curvature of the cell membranes that open non-specific cation channels, thereby generating an electrical signal. In 2013 Boris was elected to the Australian Academy of Science in recognition of his discovery of bacterial mechanosensitive channels and the physical principles of mechanosensitive channel gating. More recently his work has expanded into the roles of mechanosensitive channels in nerves and heart disease. While we all hope he would get the “big” prize in science, it was his colleague, Ardem Patapoutian, who was awarded a share for the 2021 Nobel Prize in Physiology or Medicine for his research on Piezo1 and Piezo2.The 44th meeting of the Australian Society for Biophysics (ASB) was notable for two other reasons. It was either despite the fact or because it was a virtual meeting that the Society concurrently ran an international symposium with our sister society in Japan the Japanese Society for Biophysics. There is a close connection between the ABS and JSB. For years they have encouraged Australian biophysicists to travel to the large JSB meetings in Japan and they regularly send a strong contingent to Australia. A lot of hard work was put in by Kumiko Hayashi and her colleagues Risa Shibuya and Emi Hibino and the meeting attracted Japanese biophysicists from Tsukuba, Osaka, Kyoto, Shinjuku, Okayama, Kawasaki and Nagoya.The Society also hosted a virtual Early Career Researcher symposium which involved ASB and the University of California Davis. This was chaired by Dr Adam Hill and we refer you to his Commentary where he writes about the challenges and successes of running a virtual meeting “Biophysics in the time of COVID”.The ASB has had a long-standing policy to encourage presentations from early career biophysicists, even as early as PhD students. These young biophysicists prepare carefully and seem to enjoy what can be a terrifying experience. Professor Jamie Vandenberg moderated a session on careers in biophysics where participants discussed the latest technology in ultrasound, the Victor Chang Innovation Centre, strategies for careers outside of traditional biophysics, the importance of scientific communication and advocacy, and the importance intellectual property law, and finally, there were some encouraging words on a career in biophysics from Boris Martinac.Our friends across the “ditch” in New Zealand had a session that discussed calcium imaging in mouse models of disease, the impact fibrosis on Ca signalling, high-content super-resolution microscopy, effects of ryanodine receptor clustering on arrhythmia, the impact of fibrosis on cardiac Ca signalling, how N-glycans affect shear force activation of Na channels, and a fascinating analysis of how insects have managed to adapt their flight muscles to achieve high-frequency flapping flight.The meeting finished with a presentation of the McAuley-Hope prize for a biophysicist who crosses boundaries in biophysics and develops new techniques and methods. It is not always presented but Dr Till Boecking at the University of New South Wales was the well-deserved winner of this much sought-after Prize.     

History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics

Prof. Haruki Nakamura, who is the former head of Protein Data Bank Japan (PDBj) and an expert in computational biology, retired from Osaka University at the end of March 2018. He founded PDBj at the Institute for Protein Research, together with other faculty members, researchers, engineers, and annotators in 2000, and subsequently established the worldwide Protein Data Bank (wwPDB) in 2003 to manage the core archive of the Protein Data Bank (PDB), collaborating with RCSB-PDB in the USA and PDBe in Europe. As the former head of PDBj and also an expert in structural bioinformatics, he has grown PDBj to become a well-known data center within the structural biology community and developed several related databases, tools and integrated with new technologies, such as the semantic web, as primary services offered by PDBj.     

Meet the IUPAB Councilor—Hans-Joachim Galla

As one of the twelve Councilors, it is my pleasure to provide a short biographical sketch for the readers of Biophys. Rev. and for the members of the Biophysical Societies. I have been a member of the council in the former election period. Moreover, I served since decades in the German Biophysical Society (DGfB) as board member, secretary, vice president, and president. I hold a diploma degree in chemistry as well as PhD from the University of Göttingen. The experimental work for both qualifications has been performed at the Max Planck Institute for Biophysical Chemistry in Göttingen under the guidance of Erich Sackmann and the late Herman Träuble. When E. Sackmann moved to the University of Ulm, I joined his group as a research assistant performing my independent research on structure and dynamics of biological and artificial membranes and qualified for the “habilitation” thesis in Biophysical Chemistry. I have spent a research year at Stanford University supported by the Deutsche Forschungsgemeinschaft (DFG) and after coming back to Germany, I was appointed as a Heisenberg Fellow by the DFG and became Professor in Biophysical Chemistry in the Chemistry Department of the University of Darmstadt. Since 1990, I spent my career at the Institute for Biochemistry of the University of Muenster as full Professor and Director of the institute. I have trained numerous undergraduate, 150 graduate, and postdoctoral students from chemistry, physics, and also pharmacy as well as biology resulting in more than 350 published papers including reviews and book articles in excellent collaboration with colleagues from different academic disciplines in our university and also internationally, e.g., as a guest professor at the Chemistry Department of the Chinese Academy of Science in Beijing.

     

Biophysical Reviews: 2020—looking back,going forward

After first describing the issue contents (Biophysical Reviews—Volume 12 Issue 6), this Editorial goes on to provide a short round-up of the activities of the journal in 2020. Directly following this Editorial are two obituaries marking the recent deaths of Prof. Fumio Oosawa (Japan) and Dr. Herbert Tabor (USA)—two major figures in Biophysical/Biochemical science from the last 100 years.

With the outbreak of the COVID-19 pandemic, 2020 has been a testing year for all. Filled with a myriad combination of personal tragedies and work/life inconveniences, circumstances have required many difficult decisions to be made at the personal, family, organizational and society levels with the results of these difficult choices amplifying the general level of stress within communities. Scientists have certainly not been immune from such pressures. For working scientists, this year has presented a number of challenges. Those scientists heavily involved in teaching have had to engage with remote teaching methodologies and the necessarily rapid preparation of additional online teaching materials. Research-focused scientists have had to cope with the closing or restriction of work facilities and the loss of personnel, which has certainly impacted (and often disrupted) scientific progress. For the many itinerant working scientists living away from home and family, the restrictions on worldwide travel have caused additional dilemmas and necessitated difficult career decisions. Student scientists have had to deal with other problems. Oftentimes educational institutions have maintained the steep fee requirements associated with enrolment despite the year being a virtual write-off in terms of focusing on academic performance. Overseas students have also faced problems related to maintaining interdependent attendance and residence requirements.Irrespective of the stage of their career progression, scientists (like all members of society) have tried their best to make the most of a bad situation. In 2020, the Biophysical Reviews’ Editorial Board and the specifically dedicated professional officers from Springer-Nature have similarly pushed on with our journal related duties. From 2018, Biophysical Reviews moved to a six Issue per year format. The current Issue (Issue 6) is the last for 2020, and as such, the first duty of this Editorial is to describe the contents of the twelve articles appearing within it. After providing a precis of these articles, we then move on to describe some of the highlights of this year and finish by welcoming some new members to the Editorial Board.     

Obituary Fumio Oosawa 1922–2019

Prof. Fumio Oosawa passed away in Nagoya on March 4, 2019, at the age of 96. As two of his former students we, like a great many scientists both in Japan and around the world, were much inspired and influenced by him. We have, at the request of the journal, penned this note to describe some of his major scientific contributions and also provide the readers of Biophysical Reviews with an idea of the remarkable personality and character traits that he displayed throughout his life. Fumio Oosawa (or Oosawa-san as he preferred to be called) was a physicist who initially entered the area of biophysics through studies in the field of condensed matter phenomena. Although a remarkable human being, he was, first and foremost, one of the leading scientists of his generation, making many original contributions that could, by any measure, be described as scientific breakthroughs. Therefore, before providing a short biography of his life in and around science, we thought it most appropriate to begin this Letter by first summarizing his major scientific contributions.     

Announcing the call for the Special Issue on “The Australian Society for Biophysics (ASB) – 2021 Meeting”

This Commentary describes a call for submissions for the upcoming Special Issue focused on the research topics presented at the Australian Society of Biophysics (ASB) in 2020 and 2021. Submissions from past and present ASB members who could not attend these meetings are also welcome as contributions to this special issue.

In 2020, the ASB held its 44^th Annual Conference virtually, enabling joint sessions with the University of California Davis Early Career Researchers, Biophysical Society of Japan, and the New Zealand Section of ASB to take place despite the ongoing COVID-19 pandemic. To complement these ASB joint meetings, Biophysical Reviews in partnership with the Australian Society for Biophysics (ASB) will present the second of a series of Special Issues highlighting the activities of a National Biophysical Society. This National Biophysical Society Special Issue series will highlight the activities and showcase the areas of research carried out by its members.Review articles are solicited from speakers and poster presenters of the 44^th and participants at the 45^th ASB annual conferences. Commentaries from session chairs and meeting organisers are also requested. Submissions from those who have had long-standing association with ASB or with knowledge of its history are also most welcome. This Special Issue will be prepared and edited by the above authors.     

The view from Awaji island: past, present, and future of RCC1 and the Ran GTPase system

The International Symposium on Ran and the Cell Cycle was held on October 1-4, 2005, at the Awaji Island Resort near Osaka, to celebrate the career and scientific achievements of Professor Takeharu Nishimoto. One hundred of his former lab members, collaborators and other scientific colleagues from around the world attended the symposium organized by Mary Dasso (National Institutes of Health) and Yoshihiro Yoneda (Osaka University). The program was divided into sessions on cell cycle and chromosomes, nuclear import and export of proteins and RNA, nuclear envelope and the nuclear pore complex, and RCC1 and chromatin. Dr. Nishimoto's retirement from Kyushu University is a perfect time to look back at the history of Ran and RCC1, assess the current state of the field, and discuss the challenges that remain in order to unravel the complexities of the Ran GTPase system.     

Biophysical Reviews— 2021, the year that was

The current issue (volume 13 issue 6, 2021) is a Special Issue jointly dedicated to scientific content presented at the 20th triennial IUPAB Congress that was held in conjunction with both the 45th Annual Meeting of the Brazilian Biophysical Society (Sociedade Brasileira de Biofísica - SBBf) and the 50th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology (Sociedade Brasileira de Bioquímica e Biologia Molecular – SBBq). In addition to describing the scientific and nonscientific content arising from the meeting this sub-editorial also provides a look back at some of the high points for Biophysical Reviews in the year 2021 before going on to describe a number of matters of interest to readers of the journal in relation to the coming year of 2022.

This Editorial marks the last issue for the journal to be published in 2021 – a year that has been characterized by a mixture of hardship, frustration, and of late, (possibly) a slowly developing cautious optimism in relation to the COVID-19 pandemic. Over the last 2 years, the journal has had to rapidly adapt to suddenly altered plans of contributors, as the publication of scientific reviews and organization of conference-based special issues has necessarily taken a back seat to the realities of altered work practices and, in some cases, changed life and career plans. One such major change was directly concerned with the subject of this special issue (SI) on the scientific content associated with the 20th Congress of the IUPAB (International Union for Pure and Applied Biophysics) conducted in concert with the 45th Annual Meeting of the Brazilian Biophysical Society (SBBf) and the 50th Annual Meeting of the Brazilian Biochemical and Molecular Biology Society (SBBq) (Itri et al. 2021). After discussing a few notable features of the SI, this editorial will introduce important developments occurring with the journal that relate to new feature commentaries and Institutional access arrangements. This Editorial will then close with a look back at some of the standout articles of 2021.     

Foreword to ‘Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines’, a special issue in Honour of Fumio Arisaka’s 70th birthday

This issue of Biophysical Reviews, titled ‘Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines’, is a collection of articles dedicated in honour of Professor Fumio Arisaka’s 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.     

Announcing the call for the Special Issue on the 20th International Congress of the International Union of Pure and Applied Biophysics (IUPAB)—virtual meeting,October 2021

This Commentary describes a call for submissions for the upcoming Special Issue focused on the science presented at the 20^th IUPAB Congress to be held in conjunction with the 45^th Annual Meeting of the Brazilian Biophysical Society and the 49^th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology.

Due to the COVID-19 pandemic, the 20^th International IUPAB Congress will take place as a virtual meeting this year from October 4 to 8, 2021. This triennial IUPAB Congress will be held in loose conjunction with the 45^th Annual Meeting of the Brazilian Biophysical Society and the 49^th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology. To act as a complement to this virtual meeting, the Biophysical Reviews journal will base a Special Issue on the scientific topics of the meeting contributors selected from the range of invited speakers and poster presenters. This Special Issue will also work to highlight the host country’s (Brazil) National Biophysical Society. Finally, this Special Issue will also serve to publish the meeting abstracts in supplemental form.Review articles from IUPAB Congress speakers and poster presenters to the IUPAB Congress and associated conferences (the 45^th Annual Meeting of the Brazilian Biophysical Society and the 49^th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology) are solicited. Similar to the SI based on the 19^th IUPAB Congress held in Edinburgh summarizing Commentaries from session chairs are also requested (Hall and dos Remedios 2017). The Special Issue for the 20^th IUPAB International Congress will be prepared and edited by the current authors (Rosangela Itri, Mauricio Baptista, Richard Garratt, and Antonio Jose Costa-Filho).     

Hans Zinsser: a tale of two cultures

Hans Zinsser, president of the Society of American Bacteriologists in 1926, was known as much for his literary and textbook writing as for his scientific contributions. He was a widely known scientist and person of letters. His early interests in poetry and other forms of literature were maintained and developed during his career as a microbiologist, and his most enduring legacy is based on his writing about microbiology for a general readership as well as his reflective and philosophical autobiography.     

Biophysical Reviews’ “Meet the Councilor”—a profile of Anastasia A. Anashkina

As one of the twelve Councilors of the International Union of Pure and Applied Biophysics elected in summer 2021, I have been asked to provide this short biographical sketch for the journal readers. I am a new member of the IUPAB Council. I hold a specialist degree in Applied Physics and Mathematics from the Moscow Institute of Physics and Technology and PhD in Biophysics from Moscow State University. I have spent my entire professional career at Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences in Moscow, where I am currently a senior researcher. I am Associate Professor at the Digital Health Institute of the I.M. Sechenov First Moscow State Medical University since 2018, and have trained undergraduate students in structural biology, biophysics, and bioinformatics. In addition, I serve as the Guest Editor of special journal issues of International Journal of Molecular Sciences and Frontiers in Genetics BMC genomics. Now I joined Biophysical Reviews Editorial Board as IUPAB Councilor. I am a Secretary of National Committee of Russian Biophysicists, and have helped to organize scientific conferences and workshops, such as the VI Congress of Russian Biophysicists.

     

The evolution of structural genomics

Structural genomics began as a global effort in the 1990s to determine the tertiary structures of all protein families as a response to large-scale genome sequencing projects. The immediate outcome was an influx of tens of thousands of protein structures, many of which had unknown functions. At the time, the value of structural genomics was controversial. However, the structures themselves were only the most obvious output. In addition, these newly solved structures motivated the emergence of huge data science and infrastructure efforts, which, together with advances in Deep Learning, have brought about a revolution in computational molecular biology. Here, we review some of the computational research carried out at the Protein Data Bank Japan (PDBj) during the Protein 3000 project under the leadership of Haruki Nakamura, much of which continues to flourish today.     

Scientific research at the Laboratoire Arago (Banyuls, France) in the twentieth Century: Edouard Chatton, the "master", and André Lwoff, the "pupil"

Edouard Chatton (1883–1947) began his scientific career in the Pasteur Institute, where he made several important discoveries regarding pathogenic protists (trypanosomids, Plasmodium, toxoplasms, Leishmania). In 1908 he married a "Banyulencque", Marie Herre; from 1920, he focused his research on marine protists. He finished his career as Professor at the Sorbonne (Paris) and director of the Laboratoire Arago in Banyuls-sur-mer, where he died in 1947. André Lwoff (1902–1994) lived several scientific lives in addition to his artistic and family life. But it is the study of protists that filled his first life after he encountered the exceptional Master who was Chatton. Lwoff's father was a psychiatrist and his mother an artist sculptor. He became a Doctor of Medicine in 1927 and then a Doctor of Sciences in 1932, his thesis dealing with biochemical aspects of protozoa nutrition. He met Chatton in 1921 and – until Chatton's death – their meetings, first in Roscoff and then in Banyuls-sur-mer, were numerous and their collaboration very close. Their monograph on apostome ciliates was one of the peaks of this collaboration. In 1938, Lwoff was made director of the Microbial Physiology Department at the Pasteur Institute in Paris, where he began a new life devoted to bacteria, and then to viruses, before pursuing his career as director of the Cancer Research Institute in Villejuif (France). Lwoff was awarded the Nobel Prize in Physiology or Medicine in 1965. He died in Banyuls in 1994. "Master" and "pupil" had in common perseverance in their scientific work, conception and observation, a critical sense and rigor but also a great artistic sensibility that painting and drawing in the exceptional surroundings of Banyuls-sur-mer had fulfilled. Electronic Publication     

The costs of being a restless intellect: Julian Huxley’s popular and scientific career in the 1920s

Julian Huxley’s (1887–1975) contribution to twentieth-century biology and science popularisation is well documented. What has not been appreciated so far is that despite Huxley’s eminence as a public scientific figure and the part that he played in the rise of experimental zoology in Britain in the 1920s, his own research was often heavily criticised in this period by his colleagues. This resulted in numerous difficulties in getting his scientific research published in the early 1920s. At this time, Huxley started his popular science career. Huxley’s friends criticised him for engaging in this actively and attributed the publication difficulties to the time that he allocated to popular science. The cause might also have its roots in his self-professed inability to delve deeply into the particularities of research. This affected Huxley’s standing in the scientific community and seems to have contributed to the fact that Huxley failed twice in the late 1920s to be elected to the Royal Society. This picture undermines to some extent Peter J. Bowler’s recent portrayal of Huxley as a science populariser.     

Q & A. [interview

George Oster is Professor of Biophysics, University of California, Berkeley. He received his B.S. at the U.S. Merchant Marine Academy and his Ph.D. at Columbia University. He began his career in biophysics as a postdoc at the Weizmann Institute under Aharon Katchalsky, where his research involved membrane biophysics and irreversible thermodynamics. His concern for environmental issues led him into population biology, which shaded into evolutionary biology and thence to developmental biology, cell biology and, most recently, protein motors and bacterial motility and pattern formation. His tools are mathematics, physics and computer simulation. He is currently a faculty member in the Departments of Molecular and Cellular Biology and the College of Natural Resources at Berkeley.     

Henk van den Bosch: chemist and biochemist

Henk van den Bosch is a native of The Netherlands and recently retired from his position as Professor at Utrecht University. This article summarizes the many scientific achievements of Dr. van den Bosch. He enjoys an international reputation for his research on phospholipases A, cardiolipin biosynthesis in eukaryotes, lysophospholipases, phosphatidylcholine biosynthesis for lung surfactant, plasmalogen biosynthesis in peroxisomes, diagnosis of peroxisomal disorders and most recently his work on alkyl-dihydroxyacetone phosphate synthase. During his research career Henk van den Bosch published approximately 280 articles and presented 110 invited lectures.     

Foreword to ‘Quantitative and analytical relations in biochemistry’—a special issue in honour of Donald J. Winzor’s 80th birthday

The purpose of this special issue is to honour Professor Donald J. Winzor’s long career as a researcher and scientific mentor, and to celebrate the milestone of his 80th birthday. Throughout his career, Don has been renowned for his development of clever approximations to difficult quantitative relations governing a range of biophysical measurements. The theme of this special issue, ‘Quantitative and analytical relations in biochemistry’, was chosen to reflect this aspect of Don’s scientific approach.