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The article announces the winners of Development's Outstanding Paper Prize for papers published in 2023. The winning papers focus on developmental and stem cell biology. One paper demonstrates the potential of genome engineering techniques and pharmacological upregulation of the Wnt signaling pathway in treating frizzled 2-associated congenital malformations in mouse models. Another paper explores how Frizzled2 receives WntA signaling during butterfly wing pattern formation, providing insights into the complexity and evolution of signaling pathways. The article also mentions a study on the development of primordial germ cell-like cells using stem cell technologies. Additionally, the article discusses a study on the molecular functioning of WntA in butterfly wing color patterning, which involved collaboration between international teams and faced challenges in rearing and injecting butterflies in the lab. The researchers plan to further investigate butterfly color patterns. [Extracted from the article]

This article features an interview with Jingjing Sun and Angelike Stathopoulos, who conducted a study on the collective migration of caudal visceral mesoderm (CVM) cells in Drosophila embryos. They discovered that cell division coordinates two gene expression programs in migrating CVM cells. The researchers discuss their scientific backgrounds and the questions they are trying to answer in their lab. They also highlight the importance of the Drosophila system for their research. The study's key findings include the identification of two groups of genes that regulate the behaviors of CVM cells during migration, and the role of cell division in controlling gene expression programs. The researchers also discuss their motivations and future directions for their research. [Extracted from the article]

This article discusses a new study on lissencephaly, a neurodevelopmental disorder characterized by a loss of brain folds. The study identifies a new variant of the BAIAP2 gene that is associated with lissencephaly. The researchers used in utero electroporation and microscopy to investigate the cellular mechanisms of neuronal migration during brain development. They also conducted genetic screens and identified mutations in centrosomal and dynein-recruiting proteins. The study provides insights into the basic mechanisms of neurodevelopmental disorders and neuronal migration. [Extracted from the article]

This article discusses a study conducted by Yukiko Kuroda and Koichi Matsuo on the coordination of bone growth in the mouse fibula. The researchers discovered a process called "endo-forming trans-pairing," where bone resorption by osteoclasts in the outer periosteum is paired with bone formation by osteoblasts in the inner endosteum to shape the growing bone. The study used X-ray microscopy to observe the cellular level and morphology of bones. The researchers hope to further investigate the left-right symmetric morphogenesis of the skeleton and the involvement of the nervous system in trans-pairing. [Extracted from the article]

Aristotle is often named as the first zoologist or biologist because of his writings on animals. Although Aristotle's major intention in these books was to illustrate his ideas of how knowledge and understanding might advance, at least one modern biologist (C. Darwin) has recognized Aristotle's depth and breadth as being of surviving merit. Of greater surprise is the ongoing attention that his works continue to receive, including publications in contemporary scientific journals. This review identifies 38 peer-reviewed papers on various topics from Aristotle's biological writings that have been published during the last 50 years. These papers are described according to content (genetics, population biology, anatomy, brain, movement), specific creatures (fish, scorpions, elephants, insects, birds), publication outlet, distribution over the fifty year period surveyed, and visible trends in the topics studied. It is concluded that, in the highly-competitive field of peer-reviewed scientific publication and citation, Aristotle's biology continues to excite the interest of scientists and remains salient to modern science itself. [ABSTRACT FROM AUTHOR]

The article presents an interview with Jeff Mumm, an Associate Professor in Ophthalmology at Johns Hopkins University. He discusses the context-dependent genetic regulation of retinal ganglion cell regeneration in zebrafish, including the impact of specific genes on regeneration, the use of innovative techniques like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), and the collaborative effort required for the research.

This article features an interview with Margaret Hung and Robert Krauss, who discuss their research on the adhesion of muscle stem cells to their niche. They explore the role of catenin/cadherin-based adhesion interactions in maintaining niche localization. The researchers found that cadherin-based adhesion is necessary for muscle stem cells to return to the niche after injury and regeneration. They also discuss their scientific backgrounds and the questions driving their current work. Margaret Hung has since moved into the biotech sector, while Robert Krauss's lab aims to identify additional niche factors that promote muscle stem cell quiescence. [Extracted from the article]

This document, published in Science Advances, discusses the challenges of multidisciplinary research in the field of neuroscience. The author emphasizes the importance of drawing on various disciplines to understand the mind and brain. However, the review process can be challenging due to different norms, philosophies, and standards of assessment in different fields. The author suggests tools such as cross-review and involving authors in the editorial process to address these challenges. The document also highlights the importance of collaboration across disciplines in advancing neuroscience knowledge. [Extracted from the article]

This article features an interview with Emily Bulger and Benoit Bruneau, discussing their study on the role of the transcription factor brachyury (TBXT) in early human gastrulation. They found that TBXT dosage directly correlates with the timing of the epithelial-mesenchymal transition (EMT), a process that enables cells to become more migratory. The study used in vitro models and single-nucleus sequencing to gain more precise insights into gene regulation and embryonic development. The researchers hope to further investigate transcription factor haploinsufficiency in human systems and understand its mechanisms. Outside of their work, Bruneau enjoys catching live music shows and eating spicy food, while Bulger is passionate about art and spending time outdoors. [Extracted from the article]

We investigate a tritrophic system whose cyclic dominance is modelled by the rock–paper–scissors game. We consider that organisms of one or two species are affected by movement limitations, which unbalances the cyclic spatial game. Performing stochastic simulations, we show that mobility unevenness controls the population dynamics. In the case of one slow species, the predominant species depends on the level of mobility restriction, with the slow species being preponderant if the mobility limitations are substantial. If two species face mobility limitations, our outcomes show that being higher dispersive does not constitute an advantage in terms of population growth. On the contrary, if organisms move with higher mobility, they expose themselves to enemies more frequently, being more vulnerable to being eliminated. Finally, our findings show that biodiversity benefits in regions where species are slowed. Biodiversity loss for high mobility organisms, common to cyclic systems, may be avoided with coexistence probability being higher for robust mobility limitations. Our results may help biologists understand the dynamics of unbalanced spatial systems where organisms' dispersal is fundamental to biodiversity conservation. • Stochastic simulations of the rock–paper–scissors model with organisms facing mobility limitations were performed. • The pattern formation is investigated in the case of one or two species slowed by environmental mobility restrictions. • Species predominance is studied in terms of mobility unevenness in the cyclic spatial game. • The benefits of the mobility limitations for avoiding biodiversity loss are quantified. [ABSTRACT FROM AUTHOR]

We study a nonhierarchical tritrophic system, whose predator-prey interactions are described by the rock-paper-scissors game rules. In our stochastic simulations, individuals may move strategically towards the direction with more conspecifics to form clumps instead of moving aimlessly on the lattice. Considering that the conditioning to move gregariously depends on the organism's physical and cognitive abilities, we introduce a maximum distance an individual can perceive the environment and a minimum conditioning level to perform the gregarious movement. We investigate the pattern formation and compute the average size of the single-species spatial domains emerging from the grouping behaviour. The results reveal that the defence tactic reduces the predation risk significantly, being more profitable if individuals perceive further distances, thus creating bigger groups. Our outcomes show that the species with more conditioned organisms dominate the cyclic spatial game, controlling most of the territory. On the other hand, the species with fewer individuals ready to perform aggregation strategy gives its predator the chance to fill the more significant fraction of the grid. The spatial interactions assumed in our numerical experiments constitute a data set that may help biologists and data scientists understand how local interactions influence ecosystem dynamics. • Stochastic simulations of the spatial rock-paper-scissors model with behavioural movement of aggregation were performed. • The emergence of single-species spatial domains caused by gregarious movement is demonstrated. • The benefits of the aggregation strategy in reducing predation risk are calculated. • The impact of the organisms' conditioning in the dynamics of species densities is quantified. [ABSTRACT FROM AUTHOR]

We study a three-species cyclic game system where organisms face a contagious disease whose virulence may change by a pathogen mutation. As a responsive defence strategy, organisms' mobility is restricted to reduce disease dissemination in the system. The impact of the collective self-preservation strategy on the disease infection risk is investigated by performing stochastic simulations of the spatial version of the rock–paper–scissors game. Our outcomes show that the mobility control strategy induces plasticity in the spatial patterns with groups of organisms of the same species inhabiting spatial domains whose characteristic length scales depend on the level of dispersal restrictions. The spatial organisation plasticity allows the ecosystems to adapt to minimise the individuals' disease contamination risk if an eventual pathogen alters the disease virulence. We discover that if a pathogen mutation makes the disease more transmissible or less lethal, the organisms benefit more if the mobility is not strongly restricted, thus forming large spatial domains. Conversely, the benefits of protecting against a pathogen causing a less contagious or deadlier disease are maximised if the average size of groups of individuals of the same species is significantly limited, reducing the dimensions of groups of organisms significantly. Our findings may help biologists understand the effects of dispersal control as a conservation strategy in ecosystems affected by epidemic outbreaks. • Stochastic simulations of the rock–paper–scissors model with organisms facing a disease spreading are performed. • The effects of individuals' mobility restrictions on the spatial organisation scale are quantified. • The impact of changes in the disease virulence on population dynamics is studied. • The benefits of the spatial organisation plasticity induced by the adaptation of the mobility restrictions in response to changes in the disease virulence are calculated. [ABSTRACT FROM AUTHOR]

An introduction, overview and discussion are provided for this special issue of the Biological Journal of the Linnean Society , entitled 'Teleonomy in Living Systems'. The introduction offers a brief account of the origin of Colin Pittendrigh's notion of teleonomy, in many ways comparable to Dobzhansky's later proposal of 'internal teleology', and a subsequent externalist interpretation of the concept by Ernst Mayr which, unfortunately, has remained influential. As part of the growing movement that places organismic purpose, goal-directedness and agency back at the centre of biology, in June 2021 a 2-day online international meeting was organized by the authors through the Linnean Society of London, under the title Evolution 'On Purpose': Teleonomy in Living Systems. Our overview provides a summary, with some commentary, for each of 15 papers presented here. Together with a complementary volume of 18 papers published by MIT Press, they form a selected and extended proceedings. These papers represent scientifically founded views of evolutionary biologists and philosophers of science who seriously question the adequacy of the neo-Darwinian Modern Synthesis to account for the purposive nature of living systems. Like any other phenomena associated with life, purposive and teleonomic behaviours demand evolutionary explanations and context. Without any recourse to supernatural or non-material processes, various approaches to trying to understand how this goal-directed, teleonomic property of life has influenced the course of evolution are explored. [ABSTRACT FROM AUTHOR]

The article features an interview with Ke Shan and Trieu Le, co-first authors of a paper titled "TMEM16F scramblase regulates angiogenesis via endothelial intracellular signaling" published in the Journal of Cell Science. The study focuses on the protein TMEM16F and its role in disrupting the arrangement of components in the cell membrane, affecting processes such as blood clotting, fighting infections, and placenta formation. The researchers discovered that TMEM16F also plays a crucial role in forming new blood vessels by affecting proteins and signals that control connections between endothelial cells. They overcame challenges by seeking advice from other labs and integrating various perspectives. The researchers chose the Journal of Cell Science for their paper due to its previous publication on a similar topic and positive experiences from collaborators. They also discuss their mentors and motivations for pursuing a career in science. Ke Shan plans to transition to an R&D role in the biotechnology industry, while Trieu Le is looking for new opportunities in the biotech and pharmaceutical industry. [Extracted from the article]

The article features an interview with Ana Julia Fernández-Alvarez and María Gabriela Thomas, the co-first authors of a paper titled "Smaug1 membrane-less organelles respond to AMPK and mTOR and affect mitochondrial function." The researchers discuss their findings on the protein Smaug1 and its role in regulating mitochondrial respiration. They explain that Smaug1 forms membrane-less organelles called biocondensates, which play a crucial role in coordinating the biogenesis of the respiratory machinery. The disruption of Smaug1 organelles has significant effects on mitochondrial morphology and function. The researchers express their admiration for the Journal of Cell Science and their excitement to continue their work in expanding their findings to different physiological systems. [Extracted from the article]

This paper aims to propose an quantitative engineering approach to study and compare the jaw mechanisms of different marine species, considering essential mechanical parameters generally used to evaluate the performance of industrial linkage mechanisms. By leveraging these parameters, the paper demonstrates how the species' characteristics and behaviors align with the findings of biologists, enabling a meaningful comparison that was not previously possible. Seven fish species from various families are chosen to maintain a generic approach. [ABSTRACT FROM AUTHOR]

Many current reports in the scientific literature describe novel fluorescent probes intended to provide information on various structures or properties of live cells by using microscopic imaging. Unfortunately, many such reports fail to provide key information regarding the staining process. It is often the case that neither the necessary minimum technical detail (probe concentration, solvent and cosolute, temperature and time of staining, and details of post-staining washes) nor a discussion of the proposed staining mechanism are provided. Such omissions make it unnecessarily difficult for biomedical end-users to try out reported novel probes in their own laboratories. The validity of these criticisms is explored and demonstrated by a detailed analysis of 75 non-cherry-picked articles describing novel fluorescent probes for the detection of lipid droplets in live cells. This dataset also suggests that papers from journals with high journal impact factors or from better-known research groups are no more likely to provide better protocol information or discussion of the mechanism than papers from less prestigious sources. Comments on possible reasons for this suboptimal reporting are offered. The use of a suitable information/feature checklist, following best practice in many leading chemical and biological journals, is suggested as a mechanism for ameliorating this situation, with a draft checklist being provided. [ABSTRACT FROM AUTHOR]

This document is an interview with Alexandra Fletcher-Jones, the first author of a paper titled "SGIP1 binding to the α-helical H9 domain of cannabinoid receptor 1 promotes axonal surface expression." The paper explores the role of the endocannabinoid signaling system (ECS) in the brain and how it is regulated. The study found that a protein called SGIP1 binds to cannabinoid receptor 1 (CB1R) to keep it in the correct place, and when SGIP1 is removed, CB1R is less stable and its effects are reduced. Understanding the regulation of CB1R could help in the development of cannabinoid-based drugs for various diseases. The interview also discusses the challenges faced during the project and the author's motivations and future plans in science. [Extracted from the article]

This paper deals in detail with a fairly recent philosophical debate centered around the ability of the theory of natural selection to account for those phenotypical changes which can be argued to make organisms better adapted to their environments. The philosopher and cognitive scientist Jerry Fodor started the debate by claiming that natural selection cannot do the job. He follows two main lines of argumentation. One is based on an alleged conceptual defect in the theory, the other on alleged empirical problems in it as well as empirical alternatives to it. Four philosophers and two biologists respond in a way that displays what might easily be described as fallacious. The paper relies on the ideal model of critical discussion of pragma-dialectics to offer a step-by-step analysis of the whole debate, which extended for four issues of the London Review of Books, from October 2007 through January 2008. This pragma-dialectical analysis is carried out by constant reference to the various questions (problems, issues) that arise in the debate. The analysis includes as much detail as possible both in Fodor's original argument and in the critics' various comments as well as Fodor's replies along two rounds of debate. Since a simple negative evaluation in terms of fallacies is out of the question in view of the proved argumentative accomplishments of the participants, an alternative explanation is offered: the undeniable derailments in strategic maneuvering are due to the fact that, whilst ostensibly discussing the theory of natural selection, Fodor's detractors are worried by an underlying issue, namely, the dangers of discussing the merits and demerits of natural selection as a theory of evolution in a venue as exposed to the general public as the London Review of Books, given the religiously inspired movements that threaten the teaching of evolutionary biology in schools. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "DIS3 ribonuclease is essential for spermatogenesis and male fertility in mice." The correction addresses errors in the supplementary file of the article, specifically in the legends and figures. The corrected versions of the legends and figures are provided. The errors do not affect the results and conclusions of the paper. [Extracted from the article]

Over most of the 20th century, evolutionary biologists predominantly subscribed to a strong form of "micro‐mutationism," in which adaptive phenotypic divergence arises from allele frequency changes at many loci, each with a small effect on the phenotype. To be sure, there were well‐known examples of large‐effect alleles contributing to adaptation, yet such cases were generally regarded as atypical and unrepresentative of evolutionary change in general. In 1998, Allen Orr published a landmark theoretical paper in Evolution, which showed that both small‐ and large‐effect mutations are likely to contribute to "adaptive walks" of a population to an optimum. Coupled with a growing set of empirical examples of large‐effect alleles contributing to divergence (e.g., from QTL studies), Orr's paper provided a mathematical formalism that converted many evolutionary biologists from micro‐mutationism to a more pluralistic perspective on the genetic basis of evolutionary change. We revisit the theoretical insights emerging from Orr's paper within the historical context leading up to 1998, and track the influence of this paper on the field of evolutionary biology through an examination of its citations over the last two decades and an analysis of the extensive body of theoretical and empirical research that Orr's pioneering paper inspired. [ABSTRACT FROM AUTHOR]

The debate about what causes the generation of form and structure in embryological development goes back to antiquity. Most recently, it has focused on the divergent views as to whether the generation of patterns and form in development is a largely self-organized process or is mainly determined by the genome, in particular, complex developmental gene regulatory processes. This paper presents and analyzes pertinent models of pattern formation and form generation in a developing organism in the past and the present, with a special emphasis on Alan Turing's 1952 reaction–diffusion model. I first draw attention to the fact that Turing's paper remained, at first, without a noticeable impact on the community of biologists because purely physical–chemical models were unable to explain embryological development and often also simple repetitive patterns. I then show that from the year 2000 and onwards, Turing's 1952 paper was increasingly cited also by biologists. The model was updated to include gene products and now seemed able to account for the generation of biological patterns, though discrepancies between models and biological reality remained. I then point out Eric Davidson's successful theory of early embryogenesis based on gene-regulatory network analysis and its mathematical modeling that not only was able to provide a mechanistic and causal explanation for gene regulatory events controlling developmental cell fate specification but, unlike reaction–diffusion models, also addressed the effects of evolution and organisms' longstanding developmental and species stability. The paper concludes with an outlook on further developments of the gene regulatory network model. [ABSTRACT FROM AUTHOR]

This document is a first-person interview with Liheng Yang, the first author of a paper titled "Trophoblast organoids with physiological polarity model placental structure and function" published in the Journal of Cell Science. Yang is a Senior Research Associate at Duke University School of Medicine, investigating the use of human placenta organoids to study the innate immune defense against pathogen infection at the maternal-fetal interface. The paper describes a method to generate human trophoblast organoids that accurately reflect the physiological polarity of the human placenta, providing a useful tool for research in this area. Yang also discusses the challenges faced during the project and the mentors who have guided and inspired their work. [Extracted from the article]

This document is an interview with Artem Fokin, the first author of a paper titled "Inactivating negative regulators of cortical branched actin enhances persistence of single cell migration" published in the Journal of Cell Science. Fokin conducted the research while working as a postdoc in Alexis Gautreau's lab at Ecole Polytechnique in France. The paper explores the role of cortical branched actin in cell migration and the effects of inhibiting its antagonists. The research found that depleting these inhibitors resulted in increased cell migration, and combining three knockouts produced a significant gain in migration. The study also identified a checkpoint downstream of cortical branched actin that regulates an epithelial cell state and the role of vimentin in regulating migration persistence. Fokin chose the Journal of Cell Science for publication because it aligns with the focus of the research. [Extracted from the article]

Molecular genetics has taken the preeminent position in the search for the ancestors of modern humans in sub-Saharan Africa. The usefulness of DNA in identifying lineage and familial relatedness is unquestioned but lost in this rush to use genetics to sort out human ancestry is the large body of recent and current research in skeletal biology. This has become particularly important as molecular genetics moves away from identifying the ancestry of living individuals to extracting DNA directly from archaeological skeletons. Skeletal biology provides a range of data that genetics cannot access, including life history and events at death. Skeletal biology also provides testable hypotheses about the past because of its close association with archaeology. This paper reviews the non-genetics literature published since the 1970's which discusses analyses of human skeletal material from sub-Saharan Africa. It is aimed at genetics researchers who are generally unfamiliar with the publication vehicles frequented by skeletal biologists and archaeologists. [ABSTRACT FROM AUTHOR]

Biologists routinely fit novel and complex statistical models to push the limits of our understanding. Examples include, but are not limited to, flexible Bayesian approaches (e.g. BUGS, stan), frequentist and likelihood‐based approaches (e.g. packages lme4) and machine learning methods.These software and programs afford the user greater control and flexibility in tailoring complex hierarchical models. However, this level of control and flexibility places a higher degree of responsibility on the user to evaluate the robustness of their statistical inference. To determine how often biologists are running model diagnostics on hierarchical models, we reviewed 50 recently published papers in 2021 in the journal Nature Ecology & Evolution, and we found that the majority of published papers did not report any validation of their hierarchical models, making it difficult for the reader to assess the robustness of their inference. This lack of reporting likely stems from a lack of standardized guidance for best practices and standard methods.Here, we provide a guide to understanding and validating complex models using data simulations. To determine how often biologists use data simulation techniques, we also reviewed 50 recently published papers in 2021 in the journal Methods Ecology & Evolution. We found that 78% of the papers that proposed a new estimation technique, package or model used simulations or generated data in some capacity (18 of 23 papers); but very few of those papers (5 of 23 papers) included either a demonstration that the code could recover realistic estimates for a dataset with known parameters or a demonstration of the statistical properties of the approach. To distil the variety of simulations techniques and their uses, we provide a taxonomy of simulation studies based on the intended inference. We also encourage authors to include a basic validation study whenever novel statistical models are used, which in general, is easy to implement.Simulating data helps a researcher gain a deeper understanding of the models and their assumptions and establish the reliability of their estimation approaches. Wider adoption of data simulations by biologists can improve statistical inference, reliability and open science practices. [ABSTRACT FROM AUTHOR]

With respect to other fields, bone tissue engineering has significantly expanded in recent years, leading not only to relevant advances in biomedical applications but also to innovative perspectives. Polycaprolactone (PCL), produced in the beginning of the 1930s, is a biocompatible and biodegradable polymer. Due to its mechanical and physicochemical features, as well as being easily shapeable, PCL-based constructs can be produced with different shapes and degradation kinetics. Moreover, due to various development processes, PCL can be made as 3D scaffolds or fibres for bone tissue regeneration applications. This outstanding biopolymer is versatile because it can be modified by adding agents with antimicrobial properties, not only antibiotics/antifungals, but also metal ions or natural compounds. In addition, to ameliorate its osteoproliferative features, it can be blended with calcium phosphates. This review is an overview of the current state of our recent investigation into PCL modifications designed to impair microbial adhesive capability and, in parallel, to allow eukaryotic cell viability and integration, in comparison with previous reviews and excellent research papers. Our recent results demonstrated that the developed 3D constructs had a high interconnected porosity, and the addition of biphasic calcium phosphate improved human cell attachment and proliferation. The incorporation of alternative antimicrobials—for instance, silver and essential oils—at tuneable concentrations counteracted microbial growth and biofilm formation, without affecting eukaryotic cells' viability. Notably, this challenging research area needs the multidisciplinary work of material scientists, biologists, and orthopaedic surgeons to determine the most suitable modifications on biomaterials to design favourable 3D scaffolds based on PCL for the targeted healing of damaged bone tissue. [ABSTRACT FROM AUTHOR]

This paper forges a strong connection between two well known computational frameworks for representing biological systems, in order to facilitate the seamless transfer of techniques between them. Boolean networks are a well established formalism employed from biologists. They have been studied under different (synchronous and asynchronous) update semantics, enabling the observation and characterisation of distinct facets of system behaviour. Recently, a new semantics for Boolean networks has been proposed, called most permissive semantics, that enables a more faithful representation of biological phenomena. Reaction systems offer a streamlined formalism inspired by biochemical reactions in living cells. Reaction systems support a full range of analysis techniques that can help for gaining deeper insights into the underlying biological phenomena. Our goal is to leverage the available toolkit for predicting and comprehending the behaviour of reaction systems within the realm of Boolean networks. In this paper, we first extend the behaviour of reaction systems to several asynchronous semantics, including the most permissive one, and then we demonstrate that Boolean networks and reaction systems exhibit isomorphic behaviours under the synchronous, general/fully asynchronous and most permissive semantics. [ABSTRACT FROM AUTHOR]

ChatGPT, a recently developed product by openAI, is successfully leaving its mark as a multi-purpose natural language based chatbot. In this paper, we are more interested in analyzing its potential in the field of computational biology. A major share of work done by computational biologists these days involve coding up bioinformatics algorithms, analyzing data, creating pipelining scripts and even machine learning modeling and feature extraction. This paper focuses on the potential influence (both positive and negative) of ChatGPT in the mentioned aspects with illustrative examples from different perspectives. Compared to other fields of computer science, computational biology has (1) less coding resources, (2) more sensitivity and bias issues (deals with medical data), and (3) more necessity of coding assistance (people from diverse background come to this field). Keeping such issues in mind, we cover use cases such as code writing, reviewing, debugging, converting, refactoring, and pipelining using ChatGPT from the perspective of computational biologists in this paper. [ABSTRACT FROM AUTHOR]

Students in environmental sciences, ecology, or wildlife management are often reluctant to acquire training in basic laboratory techniques. To advocate the importance of this training, we reviewed literature in the fields of biological and environmental science for one frequently used technique--centrifugation--and evaluated whether centrifugation parameters are properly expressed. Centrifugation is used to extract and purify different types of biomolecules for further characterization or quantification. The repeatability of the procedure depends on the proper identification of parameters defining the gravitational force applied to a solution, for example the duration, distance from central axis, and angular velocity. Correctly expressing rotation velocity--the "speed"--is therefore crucial to ensuring repeatability and the possibility of using the same protocols in different laboratories. When scrutinizing the materials and methods sections of publications in ecology, zoology, botany, or general biology journals, we noticed that velocity is expressed in different ways and essential information is often missing. We sampled 2000 articles in different fields of biological sciences that recorded centrifugation as a technique in the materials and methods section. We found centrifugation velocity to be properly expressed in gravitational force "g" in only 47.8% of the papers. The score dropped to 40.4% in journals specialized in ecology. We use this analysis to advocate for a minimum of training in the techniques of biochemistry that are of common use in environmental sciences. Better training would allow higher reproducibility of results in scientific publications. [ABSTRACT FROM AUTHOR]

Well‐conducted systematic reviews are invaluable for synthesising research findings. The conclusions of a review depend on how the research question was formulated, how relevant studies were found and how studies were selected for synthesis.Here, we present a practical guide for ecologists and evolutionary biologists on formulating a question for a systematic review, and finding a representative sample of research findings.We explain the steps involved using a worked example and practical training exercises. Throughout this guide we share tricks of the trade, included rules of thumb and software that we have found useful.We hope our paper helps demystify the systematic search process and encourages more researchers to adopt a systematic and reproducible approach when searching the literature. [ABSTRACT FROM AUTHOR]

This paper describes and explores how translational research models, embedded in institutions and standards, interact with the epistemic and material practices of cell biologists of ageing, a field re-energized by emergent technoscientific promises that hinge on the possibility of eliminating or manipulating senescent cells to tackle age-related diseases. Drawing on a 3-year long lab ethnography, the paper suggests that knowledge making in cell biology of ageing relies on two different epistemic and material cultures, to then argue that these cultures combine in four different types of experimental systems, only one of which can properly be seen as pertaining to translation as usually conceived. The paper further analyses how cell biologists articulate the linear temporality of translational research with the unfolding experimental chains where, by shifting between types of experimental system, cell biologists are able to generatively reconfigure their epistemic objects, and the consequences of this fragile arrangements for the field. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "Alternative use of miRNA-biogenesis co-factors in plants at low temperatures." The authors discovered errors in the published figures and have provided corrected versions. The errors include the inclusion of two photographs of the same pistil with different gain parameters in Figure 1B and the duplication of a blot in Figure 2B. The authors have reviewed the original images and created corrected figures. The errors do not impact the results and conclusions of the paper. [Extracted from the article]

This document is a correction notice for an article titled "Alternative use of miRNA-biogenesis co-factors in plants at low temperatures." The authors discovered errors in the published figures and have provided corrected versions. The errors include the inclusion of two photographs of the same pistil with different gain parameters in Figure 1B and the duplication of a blot in Figure 2B. The authors have reviewed the original images and created corrected figures. The errors do not impact the results and conclusions of the paper. [Extracted from the article]

Natural selection is a general process that operates in different populations. To characterise natural selection as a mechanism within the framework of the new mechanistic philosophy, it is required to identify a pertinent phenomenon for which natural selection is responsible. Firstly, every case identified by evolutionary biologists as instances of natural selection must align with this mechanistic characterisation. Secondly, natural selection should genuinely be responsible for the attributed phenomenon. While philosophers often posit producing adaptation as the quintessential phenomenon, Pérez-González and Luque challenge this perspective, contending that not all instances of natural selection are cases where natural selection produces adaptation. This paper further supports Pérez-González and Luque's objection and demonstrates that natural selection is also not responsible for the increased frequency of traits with a greater expected number of offspring. Furthermore, the paper argues that even if there is a phenomenon that allows for the mechanistic characterisation of natural selection to encompass all instances, it is improbable that natural selection assumes responsibility for it. Consequently, characterising natural selection as a mechanism emerges as an implausible stance. [ABSTRACT FROM AUTHOR]

Julie Savidge was among the first small but significant tranche of women field biologists. Her PhD research on the Pacific Island of Guam, published in 1987, stands as a textbook example of ecological problem solving and the first example of the devastating impact of an introduced reptile on an island fauna, the consequences of which continue today. Yet, her findings initially were strongly and publicly challenged. This paper is a brief biography of Julie, as one of the more successful of those pioneer women conservation biologists to work in the Pacific region. It tracks her early life, her influences and career path, and her struggles to balance work and family, particularly in the stressful world of academia. Julie Savidge was among the first small, but significant tranche of women field biologists. Her PhD research on the Pacific Island of Guam, stands as a textbook example of ecological problem solving and the first example of the devastating impact of an introduced reptile on an island fauna, the consequences of which continue today. This paper is a brief biography of Julie's life. [ABSTRACT FROM AUTHOR]

Successful bioinspired design depends on practitioners' access to biological data in a relevant form. Although multiple open-access biodiversity databases exist, their presentation is often adapted to life scientists, rather than bioinspired designers. In this paper, we present a new tool, "Bioinspire-Explore", for navigating biodiversity data in order to uncover biological systems of interest for a range of sectors. Bioinspire-Explore allows users to search for inspiring biological models via taxa (species, genera, etc.) as an entry point. It provides information on a taxon's position in the "tree of life", its distribution and climatic niche, as well as its appearance. Bioinspire-Explore also shows users connections in the bioinspiration literature between their taxon of interest and associated biological processes, habitats, and physical measurements by way of their semantic proximity. We believe Bioinspire-Explore has the potential to become an indispensable resource for both biologists and bioinspired designers in different fields. [ABSTRACT FROM AUTHOR]

Introduction: After more than 100 years of generating monoculture batch culture growth curves, microbial ecologists and evolutionary biologists still lack a reference method for inferring growth rates. Our work highlights the challenges of estimating the growth rate from growth curve data. It shows that inaccurate estimates of growth rates significantly impact the estimated relative fitness, a principal quantity in evolution and ecology. Methods and results: First, we conducted a literature review and found which methods are currently used to estimate growth rates. These methods differ in the meaning of the estimated growth rate parameter. Mechanistic models estimate the intrinsic growth rate μ, whereas phenomenological methods -- both modelbased and model-free -- estimate the maximum per capita growth rate μ Using math and simulations, we show the conditions in which μmax is not a good estimator of μ. Then, we demonstrate that inaccurate absolute estimates of μ are not overcome by calculating relative values. Importantly, we find that poor approximations for μ sometimes lead to wrongly classifying a beneficial mutant as deleterious. Finally, we re-analyzed four published data sets, using most of the methods found in our literature review. We detected no single best-fitting model across all experiments within a data set and found that the Gompertz models, which were among the most commonly used, were often among the worst-fitting. Discussion: Our study suggests how experimenters can improve their growth rate and associated relative fitness estimates and highlights a neglected but fundamental problem for nearly everyone who studies microbial populations in the lab. [ABSTRACT FROM AUTHOR]

This article is an interview with Mohima Mukherjee, the first author of a paper titled "Endoplasmic reticulum stress impedes regulated secretion by governing key exocytotic and granulogenic molecular switches." The study focuses on the impact of endoplasmic reticulum (ER) stress on the production and delivery of dense core vesicles and synaptic vesicles in neurons and neuroendocrine cells. The researchers found that ER stress delays the delivery of these vesicles, and reducing ER stress alleviates this delay. They also discovered that ER stress reduces the levels of SNAP25, a protein responsible for package delivery, through the activation of ATF4. This study provides insights into the disruption of vital messages caused by ER stress and its potential contribution to health problems. The author chose to publish in the Journal of Cell Science due to its reputation, history of landmark discoveries in cell biology, and rigorous peer review process. Mohima Mukherjee expresses gratitude to mentors and colleagues who have supported her research journey. She is currently focusing on other projects and completing her PhD, with the goal of pursuing a career in academic research. Outside of science, she is trained in Hindustani classical music and is passionate about protecting stray animals and serving underprivileged communities. [Extracted from the article]

Advancing spatially resolved transcriptomics (ST) technologies help biologists comprehensively understand organ function and tissue microenvironment. Accurate spatial domain identification is the foundation for delineating genome heterogeneity and cellular interaction. Motivated by this perspective, a graph deep learning (GDL) based spatial clustering approach is constructed in this paper. First, the deep graph infomax module embedded with residual gated graph convolutional neural network is leveraged to address the gene expression profiles and spatial positions in ST. Then, the Bayesian Gaussian mixture model is applied to handle the latent embeddings to generate spatial domains. Designed experiments certify that the presented method is superior to other state-of-the-art GDL-enabled techniques on multiple ST datasets. The codes and dataset used in this manuscript are summarized at https://github.com/narutoten520/SCGDL. [ABSTRACT FROM AUTHOR]

The brain is an electric organ. As such, for well over a hundred years, physicists, engineers, biologists, and physicians have used electromagnetic theory to try to understand how the brain works and to diagnose and treat disease. The field of electro-neuroscience is immense with thousands of papers being published each year. In this paper, we provide physics students with an introduction to the field using a conventional model of the head that employs four concentric spheres having different conductivities to represent the scalp, skull, cerebrospinal fluid (CSF), and the brain itself. To ground the discussion, we use the specific case of non-invasive DC electrical stimulation of the brain through electrodes applied to the surface of the scalp, a procedure known as transcranial DC stimulation or tDCS. Currently, tDCS is under clinical investigation for such diseases as depression, anxiety, and chronic pain as well as to enhance the performance of athletes and the training of fighter pilots. We solve the corresponding physics problem from a charge perspective and explain why the charge distributions look the way they do using what we call the "sensing pixel" technique. This paper can introduce students to the ways in which electromagnetic theory is being applied to problems in neuroscience; in this case, the problem of how to non-invasively stimulate the brain to treat disease or improve performance. [ABSTRACT FROM AUTHOR]