The A.M.A. Meeting,June 25-30, 1961, New York City

This “news and comment” report on the recent annual meeting of the American Medical Association was written by Mr. Ed Clancy, director of public relations of the California Medical Association.     

Morphogenesis in Kyoto: A Confluence of Cell and Developmental Biology

Understanding morphogenesis is the ultimate multidisciplinary (ad)venture. Three-dimensional tissues are generated from the actions of genes, biochemical pathways, and cells that form multicellular networks and interact with their biomechanical environment. A comprehensive explanation of morphogenetic processes must encompass these different levels of analysis. A recent meeting in Kyoto on “Building the Body Plan: How Cell Adhesion, Signaling, and Cytoskeletal Regulation Shape Morphogenesis” highlighted recent advances in tackling this challenging problem.     

The new ParaDIgm: IgM from bench to clinic: November 15–16, 2011, Frankfurt,Germany

The inaugural IgM event entitled “The new ParaDIgm: IgM from bench to clinic” brought together the increasingly active and growing IgM antibody community to discuss recent advances and challenges facing the discovery and development of IgM antibody therapies and technologies. Researchers, clinicians and biomanufacturing experts delivered 21 talks on the basic science and isolation of IgM, upstream and downstream development, and formulation and clinical development of the molecules. Participants networked around topics aimed at exploring the full potential of IgM antibodies. The meeting was held at DECHEMA Gesellschaft für Chemische Technik und Biotechnologie e. V. (Society for Chemical Engineering and Biotechnology), a non-profit scientific and technical society based in Frankfurt am Main, Germany. The meeting was sponsored by Patrys, Laureate Biopharma, Bio-Rad Laboratories, BIA Separations, Percivia and the Bio Affinity Company (BAC). The second New ParaDIgm: IgM from bench to clinic meeting, will be held on April 23–24, 2013 in Frankfurt, Germany.     

Rethinking the Response to Emerging Microbes: Vaccines and Therapeutics in the Ebola Era—a Conference at Harvard Medical School

Harvard Medical School convened a meeting of biomedical and clinical experts on 5 March 2015 on the topic of “Rethinking the Response to Emerging Microbes: Vaccines and Therapeutics in the Ebola Era,” with the goals of discussing the lessons from the recent Ebola outbreak and using those lessons as a case study to aid preparations for future emerging infections. The speakers and audience discussed the special challenges in combatting an infectious agent that causes sporadic outbreaks in resource-poor countries. The meeting led to a call for improved basic medical care for all and continued support of basic discovery research to provide the foundation for preparedness for future outbreaks in addition to the targeted emergency response to outbreaks and targeted research programs against Ebola virus and other specific emerging pathogens.     

7th Cancer Scientific Forum of the Cancérop?le Lyon Auvergne Rh?ne-Alpes: March 20–21, 2012, Lyon,France

The Innovative Approaches in Anti-Cancer Monoclonal Antibodies meeting, held on March 20, 2012 in Lyon, was organized by Cancéropôle Lyon Auvergne-Rhône-Alps in partnership with the French competitiveness cluster Lyonbiopôle. CLARA is one of the seven cancer research clusters within France in charge of facilitating Translational Oncology Research by taking into account the objectives of the French National Cancer Plans I and II and, in coordination with the French National Cancer Institute and local authorities (mainly Grand Lyon, Rhône County and Rhône-Alpes Region), to perform economic development of research findings. The contribution of lectures by outstanding speakers as described in this report, the organization of two-round tables: “Antibody treatment in cancer: Unmet needs in solid tumors and hematological malignancies,” and “From chimeric to more than human antibodies,” together with face-to-face meetings, was shared by over 230 participants. The lectures provided an overview of the commercial pipeline of monoclonal antibody (mAb) therapeutics for cancer; discussion of the distinction between biosimilar, biobetter and next generation therapeutic antibodies for cancer; updates on obinutuzumab and the use of mAbs in lymphoma; and discussion of antibody-drug conjugates.     

Report of the 14th Genomic Standards Consortium Meeting,Oxford, UK,September 17-21, 2012.

This report summarizes the proceedings of the 14^th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The primary goal of the workshop was to work towards the launch of the Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of “champions” ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings.     

Ten simple rules for creating a brand-new virtual academic meeting (even amid a pandemic)

The increased democratization of the creation, implementation, and attendance of academic conferences has been a serendipitous benefit of the movement toward virtual meetings. The Coronavirus Disease 2019 (COVID-19) pandemic has accelerated the transition to online conferences and, in parallel, their democratization, by necessity. This manifests not just in the mitigation of barriers to attending traditional physical conferences but also in the presentation of new, and more importantly attainable, opportunities for young scientists to carve out a niche in the landscape of academic meetings. Here, we describe an early “proof of principle” of this democratizing power via our experience organizing the Canadian Computational Neuroscience Spotlight (CCNS; crowdcast.io/e/CCNS), a free 2-day virtual meeting that was built entirely amid the pandemic using only virtual tools. While our experience was unique considering the obstacles faced in creating a conference during a pandemic, this was not the only factor differentiating both our experience and the resulting meeting from other contemporary online conferences. Specifically, CCNS was crafted entirely by early career researchers (ECRs) without any sponsors or partners, advertised primarily using social media and “word of mouth,” and designed specifically to highlight and engage trainees. From this experience, we have distilled “10 simple rules” as a blueprint for the design of new virtual academic meetings, especially in the absence of institutional support or partnerships, in this unprecedented environment. By highlighting the lessons learned in implementing our meeting under these arduous circumstances, we hope to encourage other young scientists to embrace this challenge, which would serve as a critical next step in further democratizing academic meetings.     

Epigenetics: Judge,jury and executioner of stem cell fate

Emerging evidence is shedding light on a large and complex network of epigenetic modifications at play in human stem cells. This “epigenetic landscape” governs the fine-tuning and precision of gene expression programs that define the molecular basis of stem cell pluripotency, differentiation and reprogramming. This review will focus on recent progress in our understanding of the processes that govern this landscape in stem cells, such as histone modification, DNA methylation, alterations of chromatin structure due to chromatin remodeling and non-coding RNA activity. Further investigation into stem cell epigenetics promises to provide novel advances in the diagnosis and treatment of a wide array of human diseases.     

Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute,Walnut Creek,CA, March 27, 2013

The Prokaryotic Super Program Advisory Committee met on March 27, 2013 for their annual review the Prokaryotic Super Program at the DOE Joint Genome Institute. As is the case with any site visit or program review, the objective is to evaluate progress in meeting organizational objectives, provide feedback to from the user-community and to assist the JGI in formulating plans for the coming year. The advisors want to commend the JGI for its central role in developing new technologies and capabilities, and for catalyzing the formation of new collaborative user communities. Highlights of the post-meeting exchanges among the advisors focused on the importance of programmatic initiatives including:• GEBA, which serves as a phylogenetic “base-map” on which our knowledge of functional diversity can be layered.• FEBA, which promises to provide new insights into the physiological capabilities of prokaryotes under highly standardized conditions.• Single-cell genomics technology, which is seen to significantly enhance our ability to interpret genomic and metagenomic data and broaden the scope of the GEBA program to encompass at least a part of the microbial “dark-matter”.• IMG, which is seen to play a central role in JGI programs and is viewed as a strategically important asset in the JGI portfolio.On this latter point, the committee encourages the formation of a strategic relationship between IMG and the Kbase to ensure that the intelligence, deep knowledge and experience captured in the former is not lost. The committee strongly urges the DOE to continue its support for maintaining this critical resource.     

Epithelial cell plasticity: breaking boundaries and changing landscapes

Epithelial tissues respond to a wide variety of environmental and genotoxic stresses. As an adaptive mechanism, cells can deviate from their natural paths to acquire new identities, both within and across lineages. Under extreme conditions, epithelial tissues can utilize “shape‐shifting” mechanisms whereby they alter their form and function at a tissue‐wide scale. Mounting evidence suggests that in order to acquire these alternate tissue identities, cells follow a core set of “tissue logic” principles based on developmental paradigms. Here, we review the terminology and the concepts that have been put forward to describe cell plasticity. We also provide insights into various cell intrinsic and extrinsic factors, including genetic mutations, inflammation, microbiota, and therapeutic agents that contribute to cell plasticity. Additionally, we discuss recent studies that have sought to decode the “syntax” of plasticity—i.e., the cellular and molecular principles through which cells acquire new identities in both homeostatic and malignant epithelial tissues—and how these processes can be manipulated for developing novel cancer therapeutics.     

Nucleosomes,transcription, and probability

Speaking of current measurements on single ion channel molecules, David Colquhoun wrote in 2006, “Individual molecules behave randomly, so suddenly we had to learn how to deal with stochastic processes.” Here I describe theoretical efforts to understand recent experimental observations on the chromatin structure of single gene molecules, a molecular biologist''s path toward probabilistic theories.     

Modeling the impact of single-cell stochasticity and size control on the population growth rate in asymmetrically dividing cells

Microbial populations show striking diversity in cell growth morphology and lifecycle; however, our understanding of how these factors influence the growth rate of cell populations remains limited. We use theory and simulations to predict the impact of asymmetric cell division, cell size regulation and single-cell stochasticity on the population growth rate. Our model predicts that coarse-grained noise in the single-cell growth rate λ decreases the population growth rate, as previously seen for symmetrically dividing cells. However, for a given noise in λ we find that dividing asymmetrically can enhance the population growth rate for cells with strong size control (between a “sizer” and an “adder”). To reconcile this finding with the abundance of symmetrically dividing organisms in nature, we propose that additional constraints on cell growth and division must be present which are not included in our model, and we explore the effects of selected extensions thereof. Further, we find that within our model, epigenetically inherited generation times may arise due to size control in asymmetrically dividing cells, providing a possible explanation for recent experimental observations in budding yeast. Taken together, our findings provide insight into the complex effects generated by non-canonical growth morphologies.     

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.     

Morphology,Classification, and Distribution of the Projection Neurons in the Dorsal Lateral Geniculate Nucleus of the Rat

The morphology of confirmed projection neurons in the dorsal lateral geniculate nucleus (dLGN) of the rat was examined by filling these cells retrogradely with biotinylated dextran amine (BDA) injected into the visual cortex. BDA-labeled projection neurons varied widely in the shape and size of their cell somas, with mean cross-sectional areas ranging from 60–340 µm². Labeled projection neurons supported 7–55 dendrites that spanned up to 300 µm in length and formed dendritic arbors with cross-sectional areas of up to 7.0×10⁴ µm². Primary dendrites emerged from cell somas in three broad patterns. In some dLGN projection neurons, primary dendrites arise from the cell soma at two poles spaced approximately 180° apart. In other projection neurons, dendrites emerge principally from one side of the cell soma, while in a third group of projection neurons primary dendrites emerge from the entire perimeter of the cell soma. Based on these three distinct patterns in the distribution of primary dendrites from cell somas, we have grouped dLGN projection neurons into three classes: bipolar cells, basket cells and radial cells, respectively. The appendages seen on dendrites also can be grouped into three classes according to differences in their structure. Short “tufted” appendages arise mainly from the distal branches of dendrites; “spine-like” appendages, fine stalks with ovoid heads, typically are seen along the middle segments of dendrites; and “grape-like” appendages, short stalks that terminate in a cluster of ovoid bulbs, appear most often along the proximal segments of secondary dendrites of neurons with medium or large cell somas. While morphologically diverse dLGN projection neurons are intermingled uniformly throughout the nucleus, the caudal pole of the dLGN contains more small projection neurons of all classes than the rostral pole.     

Tailored Immune Responses: Novel Effector Helper T Cell Subsets in Protective Immunity

Differentiation of naïve CD4⁺ cells into functionally distinct effector helper T cell subsets, characterised by distinct “cytokine signatures,” is a cardinal strategy employed by the mammalian immune system to efficiently deal with the rapidly evolving array of pathogenic microorganisms encountered by the host. Since the T_H1/T_H2 paradigm was first described by Mosmann and Coffman, research in the field of helper T cell biology has grown exponentially with seven functionally unique subsets having now been described. In this review, recent insights into the molecular mechanisms that govern differentiation and function of effector helper T cell subsets will be discussed in the context of microbial infections, with a focus on how these different helper T cell subsets orchestrate immune responses tailored to combat the nature of the pathogenic threat encountered.     

The serine threonine kinase RIP3: lost and found

Receptor-interacting protein kinase-3 (RIP3, or RIPK3) is an essential protein in the “programmed”, or “regulated” necrosis cell death pathway that is activated in response to death receptor ligands and other types of cellular stress. Programmed necrotic cell death is distinguished from its apoptotic counterpart in that it is not characterized by the activation of caspases; unlike apoptosis, programmed necrosis results in plasma membrane rupture, thus spilling the contents of the cell and triggering the activation of the immune system and inflammation. Here we discuss findings, including our own recent data, which show that RIP3 protein expression is absent in many cancer cell lines. The recent data suggests that the lack of RIP3 expression in a majority of these deficient cell lines is due to methylation-dependent silencing, which limits the responses of these cells to pro-necrotic stimuli. Importantly, RIP3 expression may be restored in many cancer cells through the use of hypomethylating agents, such as decitabine. The potential implications of loss of RIP3 expression in cancer are explored, along with possible consequences for chemotherapeutic response. [BMB Reports 2015; 48(6): 303-312]     

Clearing the Dead: Apoptotic Cell Sensing,Recognition, Engulfment,and Digestion

Clearance of apoptotic cells is the final stage of programmed cell death. Uncleared corpses can become secondarily necrotic, promoting inflammation and autoimmunity. Remarkably, even in tissues with high cellular turnover, apoptotic cells are rarely seen because of efficient clearance mechanisms in healthy individuals. Recently, significant progress has been made in understanding the steps involved in prompt cell clearance in vivo. These include the sensing of corpses via “find me” signals, the recognition of corpses via “eat me” signals and their cognate receptors, the signaling pathways that regulate cytoskeletal rearrangement necessary for engulfment, and the responses of the phagocyte that keep cell clearance events “immunologically silent.” This study focuses on our understanding of these steps.Multicellular organisms execute the majority of unwanted cell populations in a regulated fashion via the process of apoptosis (Henson and Hume 2006; Nagata et al. 2010). Examples of unwanted cells include excess cells generated during development, cells infected with intracellular bacteria or viruses, transformed or malignant cells capable of tumorigenesis, and cells irreparably damaged by cytotoxic agents. Swift removal of these cells is necessary for maintenance of overall health and homeostasis and prevention of autoimmunity, pathogen burden, or cancer. Quick removal of dying cells is a key final step, if not the ultimate goal of the apoptotic program.The term “phagocytosis” refers to an internalization process by which larger particles, such as bacteria and dead/dying cells, are engulfed and processed within a membrane-bound vesicle called the phagosome (Ravichandran and Lorenz 2007). A phagocyte is any cell that is capable of engulfment, including “professional” phagocytes such as macrophages, immature dendritic cells, and neutrophils. Metazoa have multiple mechanisms for clearing apoptotic cells, often depending on the tissue and apoptotic cell type (Gregory 2009). Macrophages and immature dendritic cells readily engulf dead or dying cells in tissues such as bone marrow (where a large number of new hematopoietic cells are generated), spleen (during or after an immune response), and the thymus (in young animals during T-lymphocyte development). In other tissues, neighboring “nonprofessional” phagocytes can also mediate the clearance of apoptotic targets. For example, in the mammary epithelium, viable mammary epithelial cells engulf apoptotic mammary epithelial cells after cessation of lactation (Monks et al. 2005, 2008). What distinguishes the phagocytosis of apoptotic cells from the phagocytosis of most bacteria or necrotic cells is the lack of a pro-inflammatory immune response (Henson 2005). This article discusses apoptotic cell engulfment, specifically the recruitment of phagocytes, through “find me” signals, the recognition of apoptotic cells by phagocytes via “eat me” signals, the internalization process and signaling pathways used for cytoskeletal rearrangement, and finally the digestion of apoptotic cells and phagocytic response to this process (Fig. 1).Open in a separate windowFigure 1.The steps of efficient apoptotic cell clearance. First, “find me” signals released by apoptotic cells are recognized via their cognate receptors on the surface of phagocytes. This is the sensing stage and stimulates phagocyte migration to the location of apoptotic cells. Second, phagocytes recognize exposed “eat me” signals on the surface of apoptotic cells via their phagocytic receptors, which leads to downstream signaling events culminating in Rac activation. Finally, further signaling events within the phagocyte regulate the digestion and processing of the apoptotic cell meal and the secretion of anti-inflammatory cytokines.     

Polysaccharide-degrading Enzymes are Unable to Attack Plant Cell Walls without Prior Action by a "Wall-modifying Enzyme"

A study of the degradation of plant cell walls by the mixture of enzymes present in Pectinol R-10 is described. A “wall-modifying enzyme” has been purified from this mixture by a combination of diethylaminoethyl cellulose, Bio Gel P-100, and carboxymethyl cellulose chromatography. Treatment of cell walls with the “wall-modifying enzyme” is shown to be a necessary prerequisite to wall degradation catalyzed by a mixture of polysaccharide-degrading enzymes prepared from Pectinol R-10 or by an α-galactosidase secreted by the pathogenic fungus Colletotrichum lindemuthianum. The action of the “wall-modifying enzyme” on cell walls is shown to result in both a release of water-soluble, 70% ethanol-insoluble polymers and an alteration of the residual cell wall. A purified preparation of the “wall-modifying enzyme” is unable to degrade a wide variety of polysaccharide, glycoside, and peptide substrates. However, the purified preparation of wall-modifying enzyme has a limited ability to degrade polygalacturonic acid. The fact that polygalacturonic acid inhibits the ability of the “wall-modifying enzyme” to affect cell walls suggests that the “wall-modifying enzyme” may be responsible for the limited polygalacturonic acid-degrading activity present in the purified preparation. The importance of a wall-modifying enzyme in developmental processes and in pathogenesis is discussed.