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Digital microfluidics (DMF) is a liquid handling technique that has been demonstrated to automate biological experimentation in a low-cost, rapid, and programmable manner. This review discusses the role of DMF as a "digital bioconverter"-a tool to connect the digital aspects of the design-build-learn cycle with the physical execution of experiments. Several applications are reviewed to demonstrate the utility of DMF as a digital bioconverter, namely, genetic engineering, sample preparation for sequencing and mass spectrometry, and enzyme-, immuno-, and cell-based screening assays. These applications show that DMF has great potential in the role of a centralized execution platform in a fully integrated pipeline for the production of novel organisms and biomolecules. In this paper, we discuss how the function of a DMF device within such a pipeline is highly dependent on integration with different sensing techniques and methodologies from machine learning and big data. In addition to that, we examine how the capacity of DMF can in some cases be limited by known technical and operational challenges and how consolidated efforts in overcoming these challenges will be key to the development of DMF as a major enabling technology in the computer-aided biology framework.

Biology and electronics are both expert at for accessing, analyzing, and responding to information. Biology uses ions, small molecules, and macromolecules to receive, analyze, store, and transmit information, whereas electronic devices receive input in the form of electromagnetic radiation, process the information using electrons, and then transmit output as electromagnetic waves. Generating the capabilities to connect biology-electronic modalities offers exciting opportunities to shape the future of biosensors, point-of-care medicine, and wearable/implantable devices. Redox reactions offer unique opportunities for bio-device communication that spans the molecular modalities of biology and electrical modality of devices. Here, an approach to search for redox information through an interactive electrochemical probing that is analogous to sonar is adopted. The capabilities of this approach to access global chemical information as well as information of specific redox-active chemical entities are illustrated using recent examples. An example of the use of synthetic biology to recognize external molecular information, process this information through intracellular signal transduction pathways, and generate output responses that can be detected by electrical modalities is also provided. Finally, exciting results in the use of redox reactions to actuate biology are provided to illustrate that synthetic biology offers the potential to guide biological response through electrical cues., (© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In order to deal with the complexity of biological systems and attempts to generate applicable results, current biomedical sciences are adopting concepts and methods from the engineering sciences. Philosophers of science have interpreted this as the emergence of an engineering paradigm, in particular in systems biology and synthetic biology. This article aims at the articulation of the supposed engineering paradigm by contrast with the physics paradigm that supported the rise of biochemistry and molecular biology. This articulation starts from Kuhn's notion of a disciplinary matrix, which indicates what constitutes a paradigm. It is argued that the core of the physics paradigm is its metaphysical and ontological presuppositions, whereas the core of the engineering paradigm is the epistemic aim of producing useful knowledge for solving problems external to the scientific practice. Therefore, the two paradigms involve distinct notions of knowledge. Whereas the physics paradigm entails a representational notion of knowledge, the engineering paradigm involves the notion of 'knowledge as epistemic tool'., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

In this article some of the concepts that undergird the Do It Yourself Bio or the "DIY Bio" movement will be explored; the challenges of citizen science will be considered; some of the public policy concerns linked to Do it Yourself Bio will be sketched; and some actionable recommendations made, especially for healthcare institutions.

The encounter of amateur science with synthetic biology has led to the formation of several amateur/do-it-yourself biology (DIYBio) groups worldwide. Although media outlets covered DIYBio events, most seemed only to highlight the hope, hype, and horror of what DIYBio would do in the future. Here, we analyze the European amateur biology movement to find out who they are, what they aim for and how they differ from US groups. We found that all groups are driven by a core leadership of (semi-)professional people who struggle with finding lab space and equipment. Regulations on genetic modification limit what groups can do. Differences between Europe and the US are found in the distinct regulatory environments and the European emphasis on bio-art. We conclude that DIYBio Europe has so far been a responsible and transparent citizen science movement with a solid user base that will continue to grow irrespective of media attention., (© 2014 The Authors. Bioessays published by WILEY Periodicals, Inc.)

This research focuses on BioScientist, a digital game-based, inquiry-based learning program embedded in the biology curriculum that develops inquiry skills in 8th-grade students. The aim of this paper is to demonstrate a combination of elements of digital game-based learning (DGBL) with inquiry-based learning (IBL) through BioScientist and to report on its implementation. We examined whether inquiry skills and biology learning motivation change due to BioScientist. A total of 257 eighth graders participated in the research (Nexp. = 132, Ncontrol = 125). Students in the experimental group used BioScientist at home and in the classroom. The teachers in the control group did not change their teaching practices. Students' inquiry skills were measured using the Inquiry Skills Test, and their biology learning motivation was measured using the Biology Motivation Questionnaire II. The experimental group and teachers were asked to evaluate BioScientist. The results indicated BioScientist digital game is suitable for developing inquiry skills, with the effect size being close to medium (Cohen's d = 0.46). However, biology learning motivation was not developed. Student feedback on the BioScientist game and its use for learning is favourable. Based on the teachers' responses, BioScientist can be used well in teaching biology. This research provides evidence that combining elements of digital game-based and inquiry-based learning is effective in developing inquiry skills. The game can be effectively integrated into the teaching practice, in line with the content of the biology curriculum. [ABSTRACT FROM AUTHOR]

Clostridioides difficile is an emerging pathogen of One Health significance. Its highly variable genome contains mobile genetic elements (MGEs) such as transposons and prophages that influence its biology. Systematic deletion of each genetic element is required to determine their precise role in C. difficile biology and contribution to the wider mobilome. Here, Tn5397 (21 kb) and φ027 (56 kb) were deleted from C. difficile 630 and R20291, respectively, using allele replacement facilitated by CRISPR-Cas9. The 630 Tn5397 deletant transferred PaLoc at the same frequency (1x10-7) as 630 harboring Tn5397, indicating that Tn5397 alone did not mediate conjugative transfer of PaLoc. The R20291 φ027 deletant was sensitive to φ027 infection, and contained two unexpected features, a 2.7 kb remnant of the mutagenesis plasmid, and a putative catalase gene adjacent to the deleted prophage was also deleted. Growth kinetics of R20291 ^027 deletant was similar to wild type (WT) in rich medium but marginally reduced compared with WT in minimal medium. This work indicates the commonly used pMTL8000 plasmid series works well for CRISPR-Cas9-mediated gene deletion, resulting in the largest deleted locus (56.8 kb) described in C. difficile. Removal of MGEs was achieved by targeting conjugative/integrative regions to promote excision and permanent loss. The deletants created will be useful strains for investigating Tn5397 or φ027 prophage contribution to host virulence, fitness, and physiology, and a platform for other mutagenesis studies aimed at functional gene analysis without native transposon or phage interference in C. difficile 630 and R20291. [ABSTRACT FROM AUTHOR]

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Circular RNAs (circRNAs) have emerged as pivotal regulators of gene expression with diverse roles in various biological processes. In recent years, research into circRNAs' involvement in bone biology has gained significant attention, unveiling their potential as novel regulators and biomarkers in bone-related disorders and diseases. CircRNAs, characterized by their closed-loop structure, exhibit stability and resistance to degradation, underscoring their functional significance. In bone tissue, circRNAs are involved in critical processes such as osteogenic differentiation, osteoclastogenesis, and bone remodeling through intricate molecular mechanisms including microRNA regulation. Dysregulated circRNAs are associated with various bone disorders, suggesting their potential as diagnostic and prognostic biomarkers. The therapeutic targeting of these circRNAs holds promise for addressing bone-related conditions, offering new perspectives for precision medicine. Thus, circRNAs constitute integral components of bone regulatory networks, impacting both physiological bone homeostasis and pathological conditions. This review provides a comprehensive overview of circRNAs in bone biology, emphasizing their regulatory mechanisms, functional implications, and therapeutic potential. [ABSTRACT FROM AUTHOR]

Over 160 years after Darwin and 70 years after the discovery of DNA, two fundamental questions of biology remain unanswered: What differentiates the living from the nonliving? How can mechanistic and finalistic or holistic biology be unified? Niels Bohr introduced a concept of complementarity in quantum physics and based on the paradox of light as a simultaneous wave and particle, conjectured that a similar concept might exist in biology that would solve the paradox of life originating from the nonliving. Bohr proposed that two mutually exclusive-independent observations may be necessary to explain a phenomenon and provided support to Immanuel Kant's idea that the "purposive" behaviour of organisms could only be explained in teleological terms and that mechanical and teleological approaches were necessary and complementary to explain biology. We present a concept of complementarity whereby biochemical pathways or cellular channels for the flow of information are simultaneously complex and redundant and complexity and redundancy complement each other. The postulates of biological complementarity are that (1) it was an essential condition in the origin of life; (2) it provided physiological flexibility that allowed organisms to mount self-protection response and complexity to evolve in the face of deleterious mutations before the evolution of bi-parental sex; (3) it laid the foundation for the evolution of a choice of response when confronted with threat; and (4) it applies to all levels of biological organizations and, thus, can serve as a basis for the unification of mechanistic and holistic biology. It is proposed that teleology is simultaneously constitutive and heuristic: constitutive because organisms' "purposive" behaviours are adaptive and are grounded in mechanism (complexity and redundancy), and heuristic because with our finite cognition and our goal-oriented (humans alone are aware of "tomorrow") and anthropomorphic pre-disposition, teleology will remain useful as a guide to our making sense of the world, even how to ask a meaningful question. [ABSTRACT FROM AUTHOR]

Covering: 2019 to 2023 Nucleoside analogues represent one of the most important classes of small molecule pharmaceuticals and their therapeutic development is successfully established within oncology and for the treatment of viral infections. However, there are currently no nucleoside analogues in clinical use for the management of bacterial infections. Despite this, a significant number of clinically recognised nucleoside analogues are known to possess some antibiotic activity, thereby establishing a potential source for new therapeutic discovery in this area. Furthermore, given the rise in antibiotic resistance, the discovery of new clinical candidates remains an urgent global priority and natural product-derived nucleoside analogues may also present a rich source of discovery space for new modalities. This Highlight, covering work published from 2019 to 2023, presents a current perspective surrounding the synthesis of natural purine nucleoside antibiotics. By amalgamating recent efforts from synthetic chemistry with advances in biosynthetic understanding and the use of recombinant enzymes, prospects towards different structural classes of purines are detailed. [ABSTRACT FROM AUTHOR]

The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on‐premises and cloud‐based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross‐platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict‐free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields. [ABSTRACT FROM AUTHOR]

Norovirus is a leading cause of acute gastroenteritis (AGE) globally. AGE resulting from norovirus causes significant morbidity and mortality in countries of all income levels, particularly among young children and older adults. Prevention of norovirus AGE represents a unique challenge as the virus is genetically diverse with multiple genogroups and genotypes cocirculating globally and causing disease in humans. Variants of the GII.4 genotype are typically the most common genotype, and other genotypes cause varying amounts of disease year-to-year, with GII.2, GII.3, and GII.6 most prevalent in recent years. Noroviruses are primarily transmitted via the fecal-oral route and only a very small number of virions are required for infection, which makes outbreaks of norovirus extremely difficult to control when they occur. Settings like long-term care facilities, daycares, and hospitals are at high risk of outbreaks and can have very high attack rates resulting in substantial costs and disease burden. Severe cases of norovirus AGE are most common in vulnerable patient populations, such as infants, the elderly, and immunocompromised individuals, with available treatments limited to rehydration therapies and supportive care. To date, there are no FDA-approved norovirus vaccines; however, several candidates are currently in development. Given the substantial human and economic burden associated with norovirus AGE, a vaccine to prevent morbidity and mortality and protect vulnerable populations could have a significant impact on global public health. [ABSTRACT FROM AUTHOR]

This review article assembles key recent advances in the synthetic chemistry and biology of specialised pro-resolving mediators (SPMs). The major medicinal chemistry developments in the design, synthesis and biological evaluation of synthetic SPM analogues of lipoxins and resolvins have been discussed. These include variations in the top and bottom chains, as well as changes to the triene core, of lipoxins, all changes intended to enhance the metabolic stability whilst retaining or improving biological activity. Similar chemical modifications of resolvins are also discussed. The biological evaluation of these synthetic SPMs is also described in some detail. Original investigations into the biological activity of endogenous SPMs led to the pairing of these ligands with the FPR2/LX receptor, and these results have been challenged in more recent work, leading to conflicting results and views, which are again discussed. [ABSTRACT FROM AUTHOR]

The binary nature of life is deeply ingrained in daily experiences, evident in the stark distinctions between life and death and the living and the inert. While this binary perspective aligns with disciplines like medicine and much of biology, uncertainties emerge in fields such as microbiology, virology, synthetic biology, and systems chemistry, where intermediate entities challenge straightforward classification as living or non-living. This contribution explores the motivations behind both binary and non-binary conceptualizations of life. Despite the perceived necessity to unequivocally define life, especially in the context of origin of life research and astrobiology, mounting evidence indicates a gray area between what is intuitively clearly alive and what is distinctly not alive. This prompts consideration of a gradualist perspective, depicting life as a spectrum with varying degrees of "lifeness". Given the current state of science, the existence or not of a definite threshold remains open. Nevertheless, shifts in epistemic granularity and epistemic perspective influence the framing of the question, and scientific advancements narrow down possible answers: if a threshold exists, it can only be at a finer level than what is intuitively taken as living or non-living. This underscores the need for a more refined distinction between the inanimate and the living. [ABSTRACT FROM AUTHOR]

The emerging field of genomic medicine offers an opportunity for biology and anatomy teachers to bring the topics of DNA, genetics, molecular processes, and evolution together into one experience. Through the genomic medicine paradigm, students see the unbroken connection between small biological topics such as mutations and their potential connection to disease phenotypes. In this paper, we present as a main example cystic fibrosis, which is an often-studied genetic disease in general biology class, for examination through the genomic medicine lens. Concepts such as genes, the plasma membrane, variation, mutations, the nucleus, and chromosomes can be used in a narrative and visual approach to genetics through the genomic medicine standpoint to engage and connect students with next-generation genomics and with the fundamental unit of life—the cell. It is through the genomic medicine lens that the cell's context and relationship to the evolving world takes place. [ABSTRACT FROM AUTHOR]

Mormyroidea is a superfamily of weakly electric African fishes with great potential as a model in a variety of biomedical research areas including systems neuroscience, muscle cell and craniofacial development, ion channel biophysics, and flagellar/ciliary biology. However, they are currently difficult to breed in the laboratory setting, which is essential for any tractable model organism. As such, there is a need to better understand the reproductive biology of mormyroids to breed them more reliably in the laboratory to effectively use them as a biomedical research model. This review seeks to (1) briefly highlight the biomedically relevant phenotypes of mormyroids and (2) compile information about mormyroid reproduction including sex differences, breeding season, sexual maturity, gonads, gametes, and courtship/spawning behaviors. We also highlight areas of mormyroid reproductive biology that are currently unexplored and/or have the potential for further investigation that may provide insights into more successful mormyroid laboratory breeding methods. Research Highlights: Mormyroids have great potential as a model in biomedical research, but are difficult to breed in the lab.Reviewing literature on mormyroid reproductive biology reveals common themes throughout the group and highlights areas where further research may inform lab breeding efforts. [ABSTRACT FROM AUTHOR]

This quasi-experimental research was conducted to find out the effects of game-based and project-based approaches on Grade 10 learners' performance in biology of Ramon Avanceña National High School, Iloilo City. Purposive sampling design was used and researcher-made instrument for pre-test and post-test on learners' performance was also utilized in gathering data. It was found out that the grade 10 learners' performance in biology before they were exposed to game and project-based approaches was fairly satisfactory. There was no significant difference in the pretest scores of the group of learners in the game-based and project-based approaches. The Grade 10 learners' performance in biology after they were exposed to game-based and project-based approaches was very satisfactory. There was significant difference in the pre-test and post-test scores of learners in the game-based and project-based approaches. There was no significant difference in the post-test scores of learners in the game-based and project-based approaches. [ABSTRACT FROM AUTHOR]

Selection of content for a school syllabus is important in achieving progress towards inclusive generalisations which characterise powerful knowledge. Biology as a discipline progresses from knowledge of individual facts to inclusive generalisations such as homeostasis, energy transformations, heredity, and evolution. The present study evaluated the selection of content in the official biology syllabus for the seventh and eighth years of schooling in four diverse jurisdictions: Kenya, South Africa, British Columbia (Canada) and Singapore. The purpose was to determine whether and how content selection enabled progression to inclusive generalisations in biology and to compare selection, sequencing and progression among the four jurisdictions. General Topic Trace Mapping was used to compare each syllabus to a generic reference syllabus structured according to inclusive generalisations. Although there was some agreement in the scope of topics selected, jurisdictions varied in the way it was organised. Kenya included more everyday knowledge than other jurisdictions. British Columbia and Singapore selected content according to unifying themes, whereas South Africa and Kenya did not. South Africa selected content that enabled progression towards inclusive generalisations, but did not explicitly identify the generalisations. This study supports the contention that powerful knowledge in biology may be construed differently in diverse jurisdictions. [ABSTRACT FROM AUTHOR]

Protein therapeutics are an important and growing class of medicine with discovery and development cycles that are long, expensive, and frequently unsuccessful. The current wave of drug development is dominated by multispecific drugs, which can achieve impressive therapeutic efficacy by interacting with more than one target to accomplish complex biological function. Generative biology, the integration of modern artificial intelligence (AI)/machine learning (ML) methods with advanced life science technologies, will accelerate the discovery and development of complex protein therapeutics. Effectively translating the potential of these innovations into practically impactful advances in protein drug development will require seamless integration of both wet- and dry-laboratory technologies. Generative biology combines artificial intelligence (AI), advanced life sciences technologies, and automation to revolutionize the process of designing novel biomolecules with prescribed properties, giving drug discoverers the ability to escape the limitations of biology during the design of next-generation protein therapeutics. Significant hurdles remain, namely: (i) the inherently complex nature of drug discovery, (ii) the bewildering number of promising computational and experimental techniques that have emerged in the past several years, and (iii) the limited availability of relevant protein sequence-function data for drug-like molecules. There is a need to focus on computational methods that will be most practically effective for protein drug discovery and on building experimental platforms to generate the data most appropriate for these methods. Here, we discuss recent advances in computational and experimental life sciences that are most crucial for impacting the pace and success of protein drug discovery. [ABSTRACT FROM AUTHOR]

In November 2023, structural biologists from different countries and different disciplines gathered at the Cell Symposium: Structural biology from the nanoscale to cellular mesoscale to discuss recent breakthroughs, including structures of proteins and macromolecular complexes in a cellular context as well as virus structures obtained by using different techniques. At the symposium, Cell editor Jia Cheng and Karin Kühnel, editor-in-chief of Structure , spoke with Drs. Beili Wu, Mingjie Zhang, and Zihe Rao about their experiences doing structural biology research in China and about their perspectives for the future. An edited transcript of the conversation is presented below, and the full conversation is available with the article online. [ABSTRACT FROM AUTHOR]

In the first of many thematic issues marking the 30th anniversary of Cell Chemical Biology , we highlight the contribution of chemical biology to RNA biology in a special issue on RNA modulation. We asked several leaders in the field to share their opinions on the current challenges and opportunities in RNA biology. [Display omitted] In the first of many thematic issues marking the 30th anniversary of Cell Chemical Biology , we highlight the contribution of chemical biology to RNA biology in a Special Issue on RNA Modulation. We asked several leaders in the field to share their opinion on the current challenges and opportunities in RNA biology. [ABSTRACT FROM AUTHOR]

Problem-Based Learning (PBL) is acknowledged as an effective pedagogical approach that facilitates a deeper understanding of concepts, surpassing a 90% comprehension rate. Renowned as a dynamic and student-centered activity, PBL fosters out-of-the-box thinking, thereby supporting the enhancement of students' skills and creativity. This paper specifically delves into the application of problem-based learning in the context of the third-year undergraduate Biology for Engineers course. PBL activities tailored for the Biology for Engineers curriculum are meticulously crafted to provide students with a progressive and comprehensive grasp of biological concepts, coupled with their practical applications in the realm of engineering. By adopting a creative, applied, and design thinking approach, PBL enables students to traverse the intricacies of the biology course effectively. In the Biology for Engineers course, PBL activities are strategically designed to facilitate a step-by-step acquisition of in-depth knowledge and a nuanced understanding of the real-life applications of biology in engineering contexts. [ABSTRACT FROM AUTHOR]

This editorial published in the journal Frontiers in Microbiology explores recent advancements in the study of free-living amoebae, which are single-celled microorganisms found in water and soil. While most of these amoebae are harmless, some species can cause opportunistic infections. The editorial highlights new research on topics such as extracellular vesicles, zoonotic bacteria, drug development, and epidemiology. It also discusses the potential impact of artificial intelligence on amoebae research. One study mentioned in the article used machine learning algorithms to identify potential compounds for treating acanthamoeba infections, and researchers discovered a marine microbial metabolite that showed promise in this regard. The article provides detailed information on the study's methodology and findings. [Extracted from the article]

Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field. [ABSTRACT FROM AUTHOR]

The aim of this study is to define epigenetic literacy and describe how it can be included in school biology. Epigenetics is a new field of research in biology with abundant societal consequences and conceptual implications on how genetics is understood. Epigenetics explains how genes are regulated, thereby clarifying cell differentiation, and providing an understanding of how the environment interacts with genes. Students are bound to encounter epigenetic knowledge and applications related to issues such as health, food, and exercise in the media and their everyday lives. Consequently, there is a need to develop epigenetic literacy. Nevertheless, epigenetics is missing in biology curricula and is almost unknown among teachers and students. Research on epigenetics in science education is scarce, and we do not know what and how to teach. Therefore, we conducted a policy Delphi study with a panel of experts to define an epigenetic literacy framework for teaching in secondary education in relation to Robert's Vision I and Vision II perspectives on epigenetic literacy. Participants were 41 recognized international experts representing 11 countries and five areas of expertise. The experts suggested that epigenetics should be introduced in the lower secondary genetics course (students aged 13–15 years), but also addressed in other relevant areas of biology. The study generated six content themes: epigenetics as a metaphor; epigenetics connecting nature with nurture; epigenetics as a dynamic process; epigenetic mechanisms; epigenetics and inheritance; and epigenetics and nature of science, and five sociocultural themes for contextualization: epigenetics and lifestyle; epigenetics and diseases; epigenetics and ethics; epigenetics and policies; and epigenetics and forensics. Taken together, these themes constitute the epigenetic literacy framework. Further, we uncover divergent meanings in the expert panel—as is typical of policy Delphi studies—and connect the framework to genetic literacy and learning progressions in genetics education. [ABSTRACT FROM AUTHOR]

The potential for basic research to uncover the inner workings of regenerative processes and produce meaningful medical therapies has inspired scientists, clinicians, and patients for hundreds of years. Decades of studies using a handful of highly regenerative model organisms have significantly advanced our knowledge of key cell types and molecular pathways involved in regeneration. However, many questions remain about how regenerative processes unfold in regeneration-competent species, how they are curtailed in non-regenerative organisms, and how they might be induced (or restored) in humans. Recent technological advances in genomics, molecular biology, computer science, bioengineering, and stem cell research hold promise to collectively provide new experimental evidence for how different organisms accomplish the process of regeneration. In theory, this new evidence should inform the design of new clinical approaches for regenerative medicine. A deeper understanding of how tissues and organs regenerate will also undoubtedly impact many adjacent scientific fields. To best apply and adapt these new technologies in ways that break long-standing barriers and answer critical questions about regeneration, we must combine the deep knowledge of developmental and evolutionary biologists with the hard-earned expertise of scientists in mechanistic and technical fields. To this end, this perspective is based on conversations from a workshop we organized at the Banbury Center, during which a diverse cross-section of the regeneration research community and experts in various technologies discussed enduring questions in regenerative biology. Here, we share the questions this group identified as significant and unanswered, i.e., known unknowns. We also describe the obstacles limiting our progress in answering these questions and how expanding the number and diversity of organisms used in regeneration research is essential for deepening our understanding of regenerative capacity. Finally, we propose that investigating these problems collaboratively across a diverse network of researchers has the potential to advance our field and produce unexpected insights into important questions in related areas of biology and medicine. This Perspective highlights the fundamental questions in the regeneration process from start to finish and how they might be addressed to facilitate cross-species studies. [ABSTRACT FROM AUTHOR]

Poeciliids are widely recognized as successful invaders, possessing traits associated with invasion success. Native to Central America and south‐eastern Mexico, the twospot livebearer (Pseudoxiphophorus bimaculatus) is a species recently recognized as invasive in both Central and northern Mexico. Despite its invasive status, limited research exists on its invasion process and the potential threats it poses to native species. In this study, we conducted a comprehensive review of the current knowledge on the twospot livebearer and mapped its current and potential distribution worldwide. The twospot livebearer shares similar traits with other successful invaders within the same family. Notably, it exhibits high fecundity throughout the year and demonstrates resilience to highly polluted and oxygen‐deprived water conditions. This fish serves as a host for several parasites, including generalists, and has been extensively translocated for commercial purposes. Recently, it has also been used for biocontrol within its native range. Apart from existing outside its native range, the twospot livebearer, under current climate conditions and if transported there, could readily colonize biodiversity hotspots in tropical zones worldwide, including the Caribbean Islands, the Horn of Africa, North of Madagascar Island, south‐eastern Brazil, and others located in southern and eastern Asia. Given that this fish is highly plastic and our Species Distribution Model, we consider that all areas with a habitat suitability >0.2 should prevent its arrival and establishment. Our findings underscore the urgent need to recognize this species as a threat to freshwater native topminnows and prevent its introduction and spread. [ABSTRACT FROM AUTHOR]

The number of students opting for science subjects, particularly biology, beyond compulsory school level has been decreasing substantially in recent decades in Mauritius. This decline is of major concern when scientific literacy and the need for science-based employment are considered fundamental to face both local and global challenges. Although several studies have identified a range of factors to explain students' choice of subjects and the low number of students opting for biology at post-compulsory level, there is little known about how policies respond to the issue. In this article, we explore how policies are responding, drawing on 25 biology education policy documents and focus groups with twelve students, ten educational officials and six parents. The findings of this study suggest that the actions undertaken in attempts to address the issue of poor uptake of biology could have been undertaken in a more coherent way, with an appropriate overarching policy frame to inform the actions. We argue that current policy actions are too state-centred, with policy-makers adopting a top-down approach where policies are simply meant to be implemented by schools. We also argue that more needs to be done to acknowledge and incorporate inputs from other stakeholders, including students. [ABSTRACT FROM AUTHOR]

Although there are more than 10,000 reptile species, and reptiles have historically contributed to our understanding of biology, genetics research into class Reptilia has lagged compared with other animals. Here, we summarize recent progress in genetics of coloration in reptiles, with a focus on the leopard gecko, Eublepharis macularius. We highlight genetic approaches that have been used to examine variation in color and pattern formation in this species as well as to provide insights into mechanisms underlying skin cancer. We propose that their long breeding history in captivity makes leopard geckos one of the most promising emerging reptilian models for genetic studies. More broadly, technological advances in genetics, genomics, and gene editing may herald a golden era for studies of reptile biology. [ABSTRACT FROM AUTHOR]

Chronic hepatitis B virus (HBV) infections affect over 250 million people worldwide, and over 800,000 are expected to die yearly from complications including cirrhosis and primary hepatocellular carcinoma. While clinically available nucleoside analog-based antiviral therapies inhibit virus production, they cannot cure infections due to the persistence of covalently closed circular (cccDNA) in the nuclei of infected hepatocytes. Hence, the goals of future curative antiviral therapies for chronic hepatitis B are to either eliminate or permanently silence transcription from cccDNA. Novel antiviral approaches building on a better understanding of the mechanisms underlying transcriptional regulation and the stability of HBV cccDNA will be necessary to accomplish such goals. To advance our understanding of cccDNA biology, we have employed a CRISPR/Cas9-based system to produce extrachromosomal circular (ec) DNA from plasmid DNA integrated into the host genome originally developed by Moller et al. [Nucleic Acid Research 46:(22) e131, 2018]. We modified the enhanced green fluorescent protein (EGFP) reporter system to include portions of the HBV genome encoding wild-type and inactive hepatitis B virus X (HBx) proteins on ecDNA to mimic cccDNA. We demonstrated that expression of EGFP is inhibited by the SMC5/6 complex, as is cccDNA, and that HBx expression can reverse transcriptional silencing of ecDNA. Moreover, we demonstrated that ecDNA is lost during cell division. The system described in this report permits investigations on ecDNA and enables large-scale screening of compound libraries for small molecules targeting host factors involved in ecDNA and, by inference, cccDNA transcription, maintenance, and loss during cell division. IMPORTANCE Hepatitis B virus cccDNA is the key target for the necessary development of antiviral therapies aimed at curing chronic hepatitis B. The CRISPR-based system to produce covalently closed circular (cccDNA)-like extrachromosomal DNAs described in this report enables large-scale screens of chemical libraries to identify drug candidates with the potential to permanently inactivate cccDNA. Moreover, this approach permits investigations on unresolved problems as described in this report concerning cccDNA biology including mechanisms of SMC5/6-dependent transcriptional silencing and the contributions of the SMC5/6 complex to cccDNA stability in resting and dividing hepatocytes. [ABSTRACT FROM AUTHOR]

Integrating the nature of science (NOS) into textbooks is one of the challenges in science curricula. This case study assessed the issue based on a sample of high school biology textbooks in Mainland China. We quantitatively compared changes in the extent, quality, and distribution of NOS representations between 2004 and 2019 editions. Three main findings emerged: (i) NOS representations have improved in the 2019 editions compared to the 2004 editions, with a 42% increase in frequency and a score growth rate of 70%. (ii) There was an imbalanced distribution of NOS aspects, focusing on 'empirical' and 'tentative' aspects and omitting 'theory-laden', 'myth of 'the scientific method', 'scientific theories', 'scientific laws', and 'social and cultural embeddedness in science aspects. All NOS aspects were heavily weighted towards the genetics theme. (iii) NOS in the 2019 editions is still addressed as it was in the 2004 editions, with unsolved aspects omitted yet again or addressed inadequately. These results constitute direct evidence for future textbook revisions. [ABSTRACT FROM AUTHOR]

Development of synthetic biology toolkits for engineering plants As the response to environmental variables is critical to plants, plant synthetic biology relies on the design of synthetic gene circuits (SGCs) capable of recognizing external inputs and processing them to generate a desired output. Keywords: Bioengineering; genetic parts; microfluidics; plant synthetic biology EN Bioengineering genetic parts microfluidics plant synthetic biology 3787 3790 4 07/20/23 20230718 NES 230718 B Plant synthetic biology allows for the reprogramming of biological systems to promote sustainable agriculture. [16] highlight the potential of combining protoplast assays with synthetic biology techniques to create high-throughput discovery platforms for studying gene function, plant metabolic diversity, and the development of novel breeding and synthetic biology tools. [Extracted from the article]

This special issue reflects the diversity of approaches to new and old problems in plant biology, showcasing the wide range of applications of bioinformatics in plant biology, and we hope that it will support the continuing development of bioinformatics tools and methods for a new generation of technological advance. Bioinformatics has revolutionized plant biology, enabling researchers to harness analytical advancements and reveal the enormous complexity of plant genomes, relationships, and biology. Despite advances in genome assembly methods, genome annotation remains one of the most challenging bottlenecks facing plant genome science, with intron length variation, divergent TE dynamics, and low sequence conservation hampering the annotation efforts of non-model genome projects. [Extracted from the article]

The emergence of precision biology has been driven by the development of advanced technologies and techniques in high-resolution biological research systems. Enhancer-mediated transcriptional regulation, a complex network of gene expression and regulation in eukaryotes, has attracted significant attention as a promising avenue for investigating the underlying mechanisms of biological processes and diseases. To address biological problems with precision, large amounts of data, functional information, and research on the mechanisms of action of biological molecules is required to address biological problems with precision. Enhancers, including typical enhancers and super enhancers, play a crucial role in gene expression and regulation within this network. The identification and targeting of disease-associated enhancers hold the potential to advance precision medicine. In this review, we present the concepts, progress, importance, and challenges in precision biology, transcription regulation, and enhancers. Furthermore, we propose a model of transcriptional regulation for multi-enhancers and provide examples of their mechanisms in mammalian cells, thereby enhancing our understanding of how enhancers achieve precise regulation of gene expression in life processes. Precision biology holds promise in providing new tools and platforms for discovering insights into gene expression and disease occurrence, ultimately benefiting individuals and society as a whole. [ABSTRACT FROM AUTHOR]

The structure and major cell types of the multi-layer human cornea have been extensively studied. However, various cell states in specific cell types and key genes that define the cell states are not fully understood, hindering our comprehension of corneal homeostasis, related diseases, and therapeutic discovery. Single-cell RNA sequencing is a revolutionary and powerful tool for identifying cell states within tissues such as the cornea. This review provides an overview of current single-cell RNA sequencing studies on the human cornea, highlighting similarities and differences between them, and summarizing the key genes that define corneal cell states reported in these studies. In addition, this review discusses the opportunities and challenges of using single-cell RNA sequencing to study corneal biology in health and disease. [ABSTRACT FROM AUTHOR]

The proposal for this special issue was inspired by the main themes around which we organize a series of satellite workshops at Artificial Life conferences (including some of the latest European Conferences on Artificial Life), the title of which is "SB-AI: What can Synthetic Biology (SB) offer to Artificial Intelligence (AI)?" Through these articles, the special issue Biology in AI promotes original directions on AI within and through the scenario of the synthetic modeling of life and cognition. [Extracted from the article]

Lichens are a diverse group of organisms. They are both commonly observed but also mysterious. It has long been known that lichens are composite symbiotic associations of at least one fungus and an algal or cyanobacterial partner, but recent evidence suggests that they may be much more complex. We now know that there can be many constituent microorganisms in a lichen, organized into reproducible patterns that suggest a sophisticated communication and interplay between symbionts. We feel the time is right for a more concerted effort to understand lichen biology. Rapid advances in comparative genomics and metatranscriptomic approaches, coupled with recent breakthroughs in gene functional studies, suggest that lichens may now be more tractable to detailed analysis. Here we set out some of the big questions in lichen biology, and we speculate about the types of gene functions that may be critical to their development, as well as the molecular events that may lead to initial lichen formation. We define both the challenges and opportunities in lichen biology and offer a call to arms to study this remarkable group of organisms. Ubiquitous, yet still mysterious, lichens have seen increasing attention in recent years. In this Essay, Scharnagl et al. discuss recent advances in lichen biology, and the potential for a golden age of lichens. [ABSTRACT FROM AUTHOR]

Research on microbiota dynamics in humans (Gilbert et al., 2018), model organisms (Douglas, 2019), and free‐ranging, wild animals (Grond et al., 2018) has taken off in the past decades, and even in nonmodel organisms, research has already shifted from initial characterization studies to those examining associations with behaviour and fitness (Bodawatta et al., 2022; Corl et al., 2020; Risely et al., 2018; Turjeman et al., 2020). The microbiota is known to change through pregnancy and parturition (Koren et al., 2012), and there is also evidence in humans that infertility may be associated with microbiota composition (Silva & Giacobini, 2019), but how the microbiota is related to reproductive fitness in free‐ranging species is largely understudied or primarily focused on pathogen transmission (sexually transmitted infection) (Lombardo, 1998; Sheldon, 1993). In a From the Cover article in this issue of Molecular Ecology, Leclaire et al. (2022) begin to tease apart the relationship between the microbiota and reproductive fitness using the black‐legged kittiwake (Rissa tridactyla) as their study species. Following characterization of the microbiota in multiple body sites of breeders and nonbreeders, they discovered that breeding and nonbreeding females had distinct microbiota, that higher performing female breeders had lower abundances of potentially pathogenic taxa, and that feathers of these birds were characterized by reduced microbiota diversity compared to low‐performance breeders. Leclaire and her colleagues provide some of the first evidence of body‐wide differences in microbiota composition in relation to breeding status. Their research further supports the relationship between the microbiota and host fitness, and additional studies focusing on this topic can continue to unravel intricacies in host‐microbiota‐reproductive strategy evolution (Comizzoli et al., 2021; Rowe et al., 2020). Here, I review the results of Leclaire et al. (2022) and provide a wider context for their research by reviewing other studies in the field, focusing on avian species. [ABSTRACT FROM AUTHOR]

The analysis of super-enhancers (SEs) has recently attracted attention in elucidating the molecular mechanisms of cancer and other diseases. SEs are genomic structures that strongly induce gene expression and have been reported to contribute to the overexpression of oncogenes. Because the analysis of SEs and integrated analysis with other data are performed using large amounts of genome-wide data, artificial intelligence technology, with machine learning at its core, has recently begun to be utilized. In promoting precision medicine, it is important to consider information from SEs in addition to genomic data; therefore, machine learning technology is expected to be introduced appropriately in terms of building a robust analysis platform with a high generalization performance. In this review, we explain the history and principles of SE, and the results of SE analysis using state-of-the-art machine learning and integrated analysis with other data are presented to provide a comprehensive understanding of the current status of SE analysis in the field of medical biology. Additionally, we compared the accuracy between existing machine learning methods on the benchmark dataset and attempted to explore the kind of data preprocessing and integration work needed to make the existing algorithms work on the benchmark dataset. Furthermore, we discuss the issues and future directions of current SE analysis. [ABSTRACT FROM AUTHOR]