Company Of Biologists Research Articles

Interview with Laura Machesky – President of the British Society for Cell Biology

ABSTRACT Laura Machesky is the Sir William Dunn Professor of Biochemistry in the Department of Biochemistry at The University of Cambridge, and the current president of the British Society for Cell Biology (BSCB). She also serves on the Board of Directors at The Company of Biologists. Originally from Michigan, USA, Laura carried out her PhD research at Johns Hopkins University in Baltimore, before moving to the UK for her postdoctoral research. In 1998, Laura set up her research group at The University of Birmingham, and then moved on to a position at The Beatson Institute in Glasgow, before returning to Cambridge in 2023. Laura's research focuses on cancer cell migration, invasion and metastasis, and how the extracellular environment of a cell can shape its responses. We spoke to Laura to find out more about her career, her research and roles in the BSCB and The Company of Biologists.

Interview with FocalPlane Scientific Advisory Board member Jennifer Waters

ABSTRACT Jennifer Waters is Director of the Nikon Imaging Center and Lecturer in Cell Biology at Harvard Medical School, USA. Jennifer started using microscopes during her undergraduate studies and continued developing her technical skills during her PhD at University of North Carolina (UNC) at Chapel Hill. After completing her PhD, Jennifer was appointed to a faculty position teaching microscopy at Wake Forest before she moved to her current position at Harvard Medical School. We caught up with Jennifer to discuss her career, her passion for microscopy education, and the merger of Microlist and FocalPlane, the microscopy community site hosted by The Company of Biologists (https://focalplane.biologists.com/).

Programming human cell fate: overcoming challenges and unlocking potential through technological breakthroughs.

In recent years, there have been notable advancements in the ability to programme human cell identity, enabling us to design and manipulate cell function in a Petri dish. However, current protocols for generating target cell types often lack efficiency and precision, resulting in engineered cells that do not fully replicate the desired identity or functional output. This applies to different methods of cell programming, which face similar challenges that hinder progress and delay the achievement of a more favourable outcome. However, recent technological and analytical breakthroughs have provided us with unprecedented opportunities to advance the way we programme cell fate. The Company of Biologists' 2023 workshop on 'Novel Technologies for Programming Human Cell Fate' brought together experts in human cell fate engineering and experts in single-cell genomics, manipulation and characterisation of cells on a single (sub)cellular level. Here, we summarise the main points that emerged during the workshop's themed discussions. Furthermore, we provide specific examples highlighting the current state of the field as well as its trajectory, offering insights into the potential outcomes resulting from the application of these breakthrough technologies in precisely engineering the identity and function of clinically valuable human cells.

Neuronal actin cytoskeleton gain of function in the human brain

While advancements in imaging techniques have led to major strides in deciphering the human brain, successful interventions are elusive and represent some of the most persistent translational gaps in medicine. Human restricted CHRFAM7A has been associated with neuropsychiatric disorders. The physiological role of CHRFAM7A in human brain is explored using multiomics approach on 600 post mortem human brain tissue samples. The emerging pathways and mechanistic hypotheses are tested and validated in an isogenic hiPSC model of CHRFAM7A knock-in medial ganglionic eminence progenitors and neurons. CHRFAM7A is identified as a modulator of intracellular calcium dynamics and an upstream regulator of Rac1. Rac1 activation re-designs the actin cytoskeleton leading to dynamic actin driven remodeling of membrane protrusion and a switch from filopodia to lamellipodia. The reinforced cytoskeleton leads to an advantage to tolerate stiffer mechanical properties of the extracellular environment. CHRFAM7A modifies the actin cytoskeleton to a more dynamic and stiffness resistant state in an α7nAChR dependent manner. CHRFAM7A may facilitate neuronal adaptation to changes in the brain environment in physiological and pathological conditions contributing to risk or recovery. Understanding how CHRFAM7A affects human brain requires human studies in the areas of memory formation and erasure, cognitive reserve, and neuronal plasticity. This work is supported in part by the Community Foundation for Greater Buffalo (Kinga Szigeti). Also, in part by the International Society for Neurochemistry (ISN) and The Company of Biologists (Nicolas Rosas). ROSMAP is supported by NIA grants P30AG10161, P30AG72975, R01AG15819, R01AG17917. U01AG46152, and U01AG61356.

The Forest of Biologists - for biologists, for biology.

The Forest of Biologists - for biologists, for biology.

The Forest of Biologists - for biologists, for biology.

The Forest of Biologists - for biologists, for biology.

The Forest of Biologists – for biologists, for biology

The Forest of Biologists – for biologists, for biology

Turning a page: remaining a top competitor in an evolving publication ecosystem.

Journal of Experimental Biology (JEB) is celebrating its first 100 years this year. My own relationship with the journal spans over six decades and encompasses a variety of roles: reader, author, Editor (1995-2000), Editorial Advisory Board member (2000 to present) and Director on the board of its publisher, The Company of Biologists (2003-2009). I was therefore delighted when the journal Editors asked me to write a Perspective to reflect on how the journal and the publishing environment in which it competes have evolved over this long period, and to peek into my crystal ball and comment on what the future might hold for the journal and the primary fields it covers: comparative-environmental-evolutionary physiology, neuroethology and biomechanics.

Simon Hugh Piper Maddrell. 11 December 1937—10 September 2020

Simon Maddrell transformed our understanding of how insects regulate their internal environments, a major determinant of their extraordinary success. Raised during wartime on his family's farm, Simon was a grammar school scholar at St Catharine's College, Cambridge, where he obtained the top first of his year in zoology. A keen sportsman, he combined his studies with half-Blues in table tennis and athletics. After a PhD under the supervision of Sir Vincent Wigglesworth FRS, he took a fellowship at Dalhousie University in Canada. He returned to Cambridge as a fellow of Gonville and Caius College, and took up a post in the AFRC Unit housed in the Department of Zoology. His academic work focused on the insect kidney, or Malpighian tubule. He unravelled details both of the mechanisms of secretion of fluids, ions and toxins, and of their control by the nervous system. His favoured organism was the blood-sucking ‘kissing bug’, Rhodnius prolixus , which demonstrated remarkable adaptations to handle massive (but irregular) blood meals. Later he also studied the classic genetic model insect Drosophila melanogaster , helping to lay the framework for combined physiological and genetic approaches in the same organism. Outside the lab, his massive energy and financial skills were potent influences on the Company of Biologists, a charity publishing scientific journals. Living increasingly in the family seat on the Isle of Man, he also brought his perfectionism to bear on daffodil shows and woodland tree planting. He is survived by his wife and four children.

Meeting report: Salamander models in cross‐disciplinary biological research meeting

The third annual meeting on "Salamander Models in Cross-disciplinary Biological Research" took place online on August 2021, bringing together over 200 international researchers using salamanders as research models and encompassing diverse fields, ranging from Development and Regeneration through to Immunology, Pathogenesis, and Evolution. The event was organized by Maximina H. Yun (Center for Regenerative Therapies Dresden, Germany) and Tatiana Sandoval-Guzmán (TU Dresden, Germany) with the generous support of the Deutsche Forschungsgemeinschaft, the Center for Regenerative Therapies Dresden, Technische Universität Dresden, and the Company of Biologists. Showcasing a number of emerging salamander models, innovative techniques and resources, and providing a platform for sharing both published and ongoing research, this meeting proved to be an excellent forum for exchanging ideas and moving research forwards. Here, we discuss the highlights stemming from this exciting scientific event.

Farewell Julian and welcome John

Farewell Julian and welcome John

Essay series on equity, diversity and inclusion in cell biology.

The topic of equity, diversity and inclusion is a strong focus for all five of the journals published by The Company of Biologists. We have been scrutinising our own processes over the past couple of years to try to minimise the biases that exist in scholarly publishing – you can read more about the different ways in which we are tackling this issue in this editorial: https://journals.biologists.com/jcs/article/doi/10.1242/jcs.259829. But as a community journal, we also wanted to think more broadly about the issue and how we can contribute to a cell biology community that is equitable, diverse and inclusive. We realised that a great starting point was to ask the community to share their experiences of how equity, diversity and/or inclusion have shaped their journeys as cell biologists. We launched our essay series in September, inviting submissions on the theme of ‘Equity, diversity and inclusion in cell biology’.We were delighted with the response and were honoured that so many people were willing to share their experiences. The essays cover an array of perspectives and include submissions from groups who are actively trying to address these issues themselves. Members of the Journal of Cell Science Editorial Advisory Board had a very difficult time choosing a single winning essay from the shortlist, so in the end, we chose three, each of which is published in this issue: “Biased in favour” by Swetha Gopalakrishnan, “Autism in science – ‘through the looking glass’ and the role of empathy in the equation” by Mariana De Niz, and “Uniting diversity to create a more inclusive academic environment” by Lucie Delemotte, Sarahi L. Garcia, Alejandro Rodríguez-Gijón, Erdinc Sezgin and Anniina Vihervaara. We all felt strongly, however, that all the shortlisted essays told compelling and important stories, so we will be publishing them as well in upcoming issues.We hope you enjoy reading the essays as much as we did. We sincerely thank each and every entrant for sharing their experiences so generously.

The 2021 FASEB Virtual Science Research Conference on Protein Aggregation: Function, Dysfunction, and Disease, June 23-25, 2021.

The 2021 FASEB Virtual Science Research Conference on Protein Aggregation: Function, Dysfunction, and Disease, June 23-25, 2021.

William "Bill" Joseph Whelan, D.Sc., FRS November 14, 1924 to June 5, 2021.

William "Bill" Joseph Whelan, D.Sc., FRS November 14, 1924 to June 5, 2021.

Shifting away from the business-as-usual approach to research conferences.

ABSTRACTTo combat the climate crisis, we need rapid, unprecedented social change. Scientists can play a lead role by signaling to society that we recognize the critical importance of redesigning our business-as-usual approach to research conferences. Traditional research conferences have high CO2 emissions as well as significant financial and travel time costs for participants. Using available technology, early career scientists Chelsie Counsell and Franziska Elmer created a global, virtual, coral reef research conference with live talks, recorded contributions, and networking events. Funding from The Company of Biologists allowed this event to be free, supporting attendance of 2700 subscribers and content contributions from 165 participants from diverse backgrounds and career stages. We provide metrics on content viewership and participation in networking activities, note the success of incorporating regionally focused sub-events, and discuss the emergence of a collaborative research project. We highlight the broad accessibility of virtual conferences as well as their increased flexibility in programming, health benefits, and cost savings. Our approach to organizing and hosting a global, low-carbon emission research conference is documented. Finally, we propose a hybrid approach to future conferences with virtually connected remote (sub-regional or local) hubs.

Author choices on JEB: how ‘open’ are we to Open Access?

The past decade has seen a proliferation of publishing models from both commercial and not-for-profit organisations, and authors now have a multitude of choices to make when deciding where to submit their paper. One aspect of this is Open Access. As a ‘hybrid’ journal – a primarily

Expression of Concern: Mechanisms underlying p53 regulation of PIK3CA transcription in ovarian surface epithelium and in ovarian cancer.

This Expression of Concern relates to J. Cell Sci. (2008) 121, 664-674 (doi:10.1242/jcs.013029)A reader informed the journal that there were several potential issues with the blots in this paper, which were also highlighted on the PubPeer website. Possible band duplications were highlighted in: p21 and actin blots in OSE457 and MCF7 panels in Fig. 1A; actin blots in A2780 and OVCAR5 panels in Fig. 1B; actin blots in IOSE 166 h and WI38 panels in Fig. 2A; T-AKT blot in IOSE 166a panel in Fig. 3A; T-AKT blots in OSEC2 and IOSE166a panels in Fig. 3B.Journal of Cell Science contacted Dr Auersperg, the corresponding author, to request the original blots, but unfortunately the blots were no longer available. As is our standard practice in such cases, without the original full blots to support the results shown in these figures, the journal referred the matter to the Vice-President, Research and Innovation at The University of British Columbia (UBC), asking them to provide further information and a recommendation as to the next steps.As part of the case summary provided to UBC, the journal included a visual demonstration of the similarities between the blots in question using the open-source software ‘Forensically’. It is important to note that the software was not used to detect similarities between blots, but rather to highlight them.UBC contacted the journal upon conclusion of its investigation and stated that no misconduct had occurred. The journal requested the report to understand how the committee arrived at this conclusion, stating that we would have expected the report to comment on the soundness of the conclusions in the paper. UBC provided the report, which showed that the committee had focused its investigation on the use of the Forensically software tool. The report concluded that “…there is no basis for concluding that the blots in question were duplicated or improperly altered.” Their recommendation was: “Care should be taken whenever a report of duplication has resulted from analysis using the current version of the Forensically software.” Furthermore, UBC stated: “It is not the University's place to comment on [the soundness and trustworthiness of the data] – we leave those determinations to the expertise of peer reviewers, editorial boards and the academic community more generally.”The journal clarified that Forensically was not used to detect any potential duplications, and reiterated its expectations that an institutional investigation would indeed comment on the validity of the data, highlighting relevant sections from the COPE (Committee on Publication Ethics) website; Journal of Cell Science and its publisher, The Company of Biologists, are members of COPE. The journal requested that UBC conduct a more-detailed investigation into the issues raised about this paper, but UBC declined.The journal therefore referred the matter to an external expert, requesting an opinion on the soundness of the conclusions of the paper by Astanahe et al., considering that the blots in question are unreliable. Our expert advisor expressed the opinion that the conclusions are possibly still sound, noting two additional papers published subsequently that report results similar to those of the paper in question.The journal also contacted all of the co-authors of the paper, and although there was some initial correspondence, further attempts to communicate with them went unanswered.The journal is therefore publishing this Expression of Concern to make readers aware of these issues and our efforts to resolve them.

The 2019 FASEB Science Research Conference on Matricellular Proteins in Inflammation and Tissue Remodeling, July 14-19, 2019, Lisbon, Portugal.

The 2019 FASEB Science Research Conference on Matricellular Proteins in Inflammation and Tissue Remodeling, July 14-19, 2019, Lisbon, Portugal.

An interview with Sally Lowell.

Sally Lowell is a Wellcome Trust Senior Research Fellow at the University of Edinburgh, UK. Her research group, which is based in the Centre for Regenerative Medicine, studies cell fate decisions in stem cells, focussing on how communication and interactions between cells can influence these decisions. Sally, who has been a long-serving committee member of the British Society for Developmental Biology, recently joined the Board of Directors at The Company of Biologists. We caught up with Sally to find out more about her career and her research, and why she's excited about her role at the Company.

Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

In the past decade, two major advances in our understanding of nuclear organization have taken the field of gene regulation by storm. First, technologies that can analyze the three-dimensional conformation of chromatin have revealed how the genome is organized and have provided novel insights into how regulatory regions in the genome interact. Second, the recognition that many proteins can form membraneless compartments through liquid-liquid phase separation (LLPS) has challenged long-standing notions of how proteins within the nucleus are organized and has offered a tantalizing general mechanism by which many aspects of nuclear function may be regulated. However, the functional roles of chromatin topology and LLPS in regulating gene expression remain poorly understood. These topics were discussed with great fervor during an open discussion held at a recent workshop titled 'Chromatin-based regulation of development' organized by The Company of Biologists. Here, we summarize the major points covered during this debate and discuss how they tie into current thinking in the field of gene regulation.