Frontiers In Biology Research Articles

Is defining life pointless? Operational definitions at the frontiers of biology

Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research practices. This paper examines the possible contributions of definitions of life in scientific domains where such definitions are used most (e.g., Synthetic Biology, Origins of Life, Alife, and Astrobiology). Rather than as classificatory tools for demarcation of natural kinds, we highlight the pragmatic utility of what we call operational definitions that serve as theoretical and epistemic tools in scientific practice. In particular, we examine contexts where definitions integrate criteria for life into theoretical models that involve or enable observable operations. We show how these definitions of life play important roles in influencing research agendas and evaluating results, and we argue that to discard the project of defining life is neither sufficiently motivated, nor possible without dismissing important theoretical and practical research.

Frontiers in biology.

Frontiers in biology.

Pattern, process, inference and prediction in extinction biology.

Extinction is a key feature of the evolutionary history of life, and assessments of extinction risk are essential for the effective protection of biodiversity. The goal in assembling this special issue of Biology Letters was to highlight problems and questions at the research frontier of extinction biology, with an emphasis on recent developments in the methodology of inferring the patterns and processes of extinction from a background of often noisy and sparse data. In selecting topics, we sought to illustrate how extinction is not simply a self-evident phenomenon, but the subject of a dynamic and quantitatively rigorous field of natural science, with practical applications to conservation.

Natural search algorithms as a bridge between organisms, evolution, and ecology

The ability to navigate is a hallmark of living systems, from single cells to higher animals. Searching for targets, such as food or mates in particular, is one of the fundamental navigational tasks many organisms must execute to survive and reproduce. Here, we argue that a recent surge of studies of the proximate mechanisms that underlie search behavior offers a new opportunity to integrate the biophysics and neuroscience of sensory systems with ecological and evolutionary processes, closing a feedback loop that promises exciting new avenues of scientific exploration at the frontier of systems biology.

The Question of the Objective Basis of Whitehead’s Theory of the Rhythm of Education: Homeostasis Research and Chronobiology

Alfred North Whitehead’s (1861–1947) theory of the rhythm of education has enjoyed much popularity and success in terms of providing a general model for conceptualizing learning, teaching, and research processes. However, in respect to the Whiteheadian notion that there is a rhythm belonging to such processes, of which educators ought to be aware, this paper asks the question of what the scientific, factual, and/or objective basis is for this claim. While I do not provide a fully worked out response to this question, in this paper, I do provide some insight as to the general direction in which it may be answered. Specifically, I point to the New Frontiers of biology, namely, areas of biological research that, to some extent, depart from its neo-Darwinian mainstream which embraces a mechanistic metaphysic. Homeostasis research and chronobiology are emerging scientific domains that can assist educational theorists in providing the necessary context within which to answer this question. Such domains of inquiry, construed holistically rather than only mechanistically, render Whitehead’s theorizing concerning the rhythm of education plausible rather than unfalsifiable.

Whither Enzymology in the Twenty First Century?

This “grand challenge” article marks the creation of a new specialty section shared between Frontiers in Chemistry and Frontiers in Molecular Biology that is dedicated to enzymology and protein chemistry. My aim in this article is to provide a personal perspective on the challenges and opportunities for field of enzymology and the directions in which it could and should move in the coming years. I hope this will challenge the reader to think more deeply about this discipline and its broader impact on science. But before gazing into the future, it is worthwhile briefly reviewing how our field has evolved until now, as it is this perspective that frames our outlook. Whither Enzymology? was the title of a symposium held in 1990 to honor the late Jeremy Knowles on the occasion of his Sixtieth birthday (Raines, 2008). Knowles was in the vanguard of a pioneering group of enzymologists who first employed the tools of physical organic chemistry to study enzyme reactions. In the 1970's his group was the first to determine the full set of elementary rate constants defining the free energy profile for an enzyme-catalyzed reaction—that of triose phosphate isomerase (Albery and Knowles, 1976). This information, put together with the crystal structure for this enzyme, allowed us to understand enzyme catalysis with the kind of precision previously only possible for simple organic molecules. Subsequently, his lab was among the first to use site-specific mutagenesis to make precisely defined changes to enzyme active sites, which combined with detailed measurements of their effect on catalysis, allowed the relationships between enzyme structure and mechanism to be elucidated. Studies such as these blew away the “fluffy clouds” obscuring the view of earlier generations of enzymologists, revealing enzymes to be exquisitely evolved, highly complex and incredibly efficient organic catalysts, but nevertheless subject to, and understood through, the basic principles of chemistry—in Knowles' words: “not different, just better” (Knowles, 1991). This view has shaped enzymology for the past 25 years, and by extension our view of cellular biology. It directly underpins the burgeoning discipline of synthetic biology, a field that involves tinkering with enzymes on a scale unimaginable in Knowles' era. The tools available to enzymologists have advanced immeasurably in the last 25 years, resulting in a paradigm shift in our approach to studying them. Not least, much of the drudgery (and perhaps also some of the fun!) of obtaining enzymes for study has been removed and the accessibility of enzymes has expanded enormously. The advent of genomic sequencing, combined with cheap, commercially available gene synthesis and protein affinity tags, allows one to select essentially any enzyme for study and produce large quantities of pure protein with minimal effort. What would once have taken many person years to accomplish can now be achieved in a few days. (Although some classes of proteins, e.g., integral membrane proteins still remain challenging to express.) Advances in structural biology mean that determining the 3-D structure of most enzymes, if not trivial, is now routine; indeed, thanks to structural proteomics initiatives, the structure is increasingly the first information to emerge for a new enzyme. Moreover, techniques for studying enzymes have become increasingly powerful: instrumentation more sensitive (for some techniques to the level of single molecules) and data analysis more sophisticated and rapid due to exponential increases in computing power. With such powerful tools and so many enzymes to explore, it seems reasonable some 25+ years on from Knowles' apotheosis, once again to pose the question: whither enzymology? In attempting to answer this question, I propose the three “grand challenges” discussed below. The first two I have chosen because they fundamentally challenge our understanding of enzyme catalysis. The first challenge is to predict enzyme catalytic activity from structure and dynamic information; the second challenge to design enzymes from scratch that approach the activity of naturally evolved enzymes. The third challenges focuses on expanding the frontiers of enzymology by discovering new enzymes that catalyze new reactions.

Frontiers in RNA biology: advances from a small fly Drosophila melanogaster

In this article, we discuss emerging frontiers in RNA biology from a historical perspective. The field is currently undergoing yet another transformative expansion. RNA-seq has revealed that splicing, and, more generally, RNA processing is far more complex than expected, and the mechanisms of regulation are correspondingly sophisticated. Our understanding of the molecular machines involved in RNA metabolism is incomplete and derives from small sample sizes. Even if we manage to complete a catalogue of molecular species, RNA isoforms and the ribonucleoprotein complexes that drive their genesis, the horizons of molecular dynamics and cell-type-specific processing mechanisms await. This is an exciting time to enter into the study of RNA biology; analytical tools, wet and dry, are advancing rapidly, and each new measurement modality brings into view another new function or activity of versatile RNA. Since the dawn of sequence-based RNA biology, we have come a long way.

Application of Imaging-Based Assays in Microplate Formats for High-Content Screening.

The use of multiparametric microscopy-based screens with automated analysis has enabled the large-scale study of biological phenomena that are currently not measurable by any other method. Collectively referred to as high-content screening (HCS), or high-content analysis (HCA), these methods rely on an expanding array of imaging hardware and software automation. Coupled with an ever-growing amount of diverse chemical matter and functional genomic tools, HCS has helped open the door to a new frontier of understanding cell biology through phenotype-driven screening. With the ability to interrogate biology on a cell-by-cell basis in highly parallel microplate-based platforms, the utility of HCS continues to grow as advancements are made in acquisition speed, model system complexity, data management, and analysis systems. This chapter uses an example of screening for genetic factors regulating mitochondrial quality control to exemplify the practical considerations in developing and executing high-content campaigns.

Epigenetics As The Driving Force In Long-Term Immunosuppression

Epigenetics is an emerging frontier of biology, with the potential for deciphering the intricate molecular and transcriptional cellular programs, therefore contributing to explain the pathological evolution of sepsis, one of the most elusive syndromes in medicine. The evolution of sepsis depends not only on the pathogen which originated the infection but also on the genetic and epigenetic background of the host. Short-term mortality of sepsis and septic shock is high, being considered a public health concern worldwide. Immunosuppression is the predominant driving force for morbidity and mortality in late deaths and long-term deaths of survivors from a sepsis episode. In this regard, apoptosis of immune cells and complex epigenetic reprogramming in immune and progenitor cells may contribute to the immunoparalysis observed in post-septic patients, who are prone to the apparition of new, opportunistic infections. Here, we review the literature and expose the most relevant results which explain the epigenetic programs contributing to the progression of sepsis. Furthermore, we revisit the role of circulating histones in the pathogenesis of sepsis and septic shock and finally we discuss about the therapeutic potential of epigenetic drugs in the treatment of sepsis.

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly, in which rhodopsin uses distinct structural elements, including TM7 and Helix 8 to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotation between the N- and C- domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signaling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.

Accentuating and Opposing Factors Leading to Development of Thoracic Aortic Aneurysms Not Due to Genetic or Inherited Conditions.

Understanding and unraveling the pathophysiology of thoracic aortic aneurysm (TAA), a vascular disease with a potentially high-mortality rate, is one of the next frontiers in vascular biology. The processes leading to the formation of TAA, of unknown cause, so-called degenerative TAA, are complex. This review advances the concept of promoters and inhibitors of the development of degenerative TAA. Promoters of TAA development include age, blood pressure elevation, increased pulse pressure, neurohumeral factors increasing blood pressure, inflammation specifically IFN-γ, IL-1 β, IL-6, TNF-α, and S100 A12; the coagulation system specifically plasmin, platelets, and thrombin as well as matrix metalloproteinases (MMPs). SMAD-2 signaling and specific microRNAs modulate TAA development. The major inhibitors or factors opposing TAA development are the constituents of the aortic wall (elastic lamellae, collagen, fibulins, fibronectin, proteoglycans, and vascular smooth muscle cells), which maintain normal aortic dimensions in the face of aortic wall stress, specific tissue MMP inhibitors, plasminogen activator inhibitor-1, protease nexin-1, and Syndecans. Increases in promoters and reductions in inhibitors expand the thoracic aorta leading to TAA formation.

Insights into the importance for designing curcumin-inspired anticancer agents by a prooxidant strategy: The case of diarylpentanoids

Developing anticancer agents by a prooxidant strategy has attracted increasing attention in recent years, although it is not conventional in medicinal chemistry and is completely opposite to antioxidant therapy. In this work, a panel of diarylpentanoids as the curcumin mono-carbonyl analogs were designed and synthesized, and their cytotoxic and proapoptotic mechanisms against human lung cancer A549 cells were investigated at the frontiers of chemistry and biology. It was found that compared with curcumin, the compounds (A1, B1, and C1) bearing two ortho substituents on the aromatic rings, especially A1, exhibit significantly increased cytotoxic and proapoptotic activities through a Michael acceptor unit-dependent prooxidant-mediated mechanism. The prooxidative ability is governed not only by their electrophilicity but also by their geometry, cellular uptake and metabolic stability, and TrxR-inhibitory activity. Mechanistic investigation reveals that the compound A1 could effectively and irreversibly modify the TrxR by virtue of the above optimal biochemical parameters, and convert this antioxidant enzyme into a reactive oxygen species (ROS) promoter, resulting in a burst of the intracellular ROS including H2O2 and O2–•. The ROS generation is associated with falling apart in the redox buffering system, and subsequently induces increases in Ca2+ influx and oxidative stress, collapse of mitochondrial membrane potential, and activation of caspase-9 and caspase-3, ultimately leading to cell apoptosis. This work highlights the feasibility in designing curcumin-inspired anticancer agents by a prooxidant strategy, and gives us useful information on how to design them.

Thinking big with small molecules.

Synthetic chemistry has enabled scientists to explore the frontiers of cell biology, limited only by the laws of chemical bonding and reactivity. As we investigate biological questions of increasing complexity, new chemical technologies can provide systems-level views of cellular function. Here we discuss some of the molecular probes that illustrate this shift from a “one compound, one gene” paradigm to a more integrated approach to cell biology.

Complexity and the Emergence of Meaning in the Natural Sciences and Philosophy

The article examines the notion of self-organization and explores the reality of biological processes from an epistemological point of view. First, I briefly analyze what is currently regarded as one of the most important discoveries not only in physics, but also in biology—namely, complex systems and deterministic chaos; secondly, I offer some reflections on the new frontiers of contemporary biology— namely, functional genomics and systems biology. The central part of the article focuses on the epistemological transition from genetic determinism to the new conception of “meaning” as emergence.

Back to the future of RNA structure.

Back to the future of RNA structure.

Chromatin regulation at the frontier of synthetic biology.

As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including 'epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication.

Mammalian conservation: scientific frontiers and socio-political pitfalls

Introduction: The frontiers of conservation biology are rapidly advancing. This is partly because of scientific achievements, but also it is because the human predicament continues to deteriorate in spite of heroic but inadequate efforts to make the human enterprise sustainable. Of greatest importance is the need to escape from the confrontational mode that pervades our social and political discussions. We must trade this conflict for a realization that there is only one objective for all of humanity, and that is the sustainability of human civilization. Mammalian conservation can play a major role in this struggle, but to do this we must take the initiative to promote meaningful dialogue with politicians, policy makers, economists, sociologists, and the public at large. At the same time, we must continue to be at the frontiers of our science while not neglecting the pursuit of much needed basic research on taxonomy, life history, and distribution of the world’s mammals. Some social, political, and strategic considerations: Themes suggested to enhance such communication are: non-confrontational cooperation, life support services, optimism, systems thinking, and adapting to various political regimes. Frontiers of conservation science: Eight leading edge topics are suggested for the science component of conservation: 1) community tipping points, 2) trophic cascades, 3) landscape or ecoscape perspective, 4) role of common species in community dynamics, 5) climate change complications, 6) role of genetics, 6) social dynamics, 7) microorganism synergisms, and 8) translocations. Mammalian conservationists are poised to play a significant role in humanity’s efforts to confront the myriad of intertwined problems that we face. Given that humans belong to the same taxonomic class that is the subject of our expertise, we have special responsibility to provide that leadership. Key words: captive breeding, climate change, community tipping points, conservation genetics, cooperation, landscape perspective, life support services, microbiota synergisms, new conservation, optimism, social behavior, sustainable civilization, systems perspective, translocations, trophic cascades.

Improvements in the Optical Recording of Neuron Activity Using Voltage-Dependent Dyes

Studies of the electrical activity and plasticity of neural networks, individual nerve cells, and their subcellular compartments are now impractical without using optical methods to visualize functional signals which allow electrical events to be recorded both in many neurons simultaneously and in individual dendrites and axons and provide for linking these data to precise morphological images. Use of voltage-sensitive dyes (VSD) is the only of the small number of currently available methods which combines high spatial resolution with the ability to record ultrafast signals (<0.1 msec) in real time with a high signal:noise ratio. Significant progress in applying VSD has been made in the last decade, particularly in analysis of the occurrence and encoding of electrical signals in dendrites and axons, and has resulted from improvements in the method associated with using the best dyes in combination with sequential improvements in apparatus and optical instruments. This has allowed the method to demonstrate its value and effectiveness and advance from purely technical areas to the arsenal of major equipment in the world’s leading laboratories working at the frontiers of cell biology and neurophysiology.

Cancer gene therapy: Prospects of using human sodium iodide symporter gene in non-thyroidal cancer

Gene therapy is one of the promising therapeutic strategies evolved rapidly in the frontier of translational biology in cancer. To overcome the off target effect of conventional cancer therapies it is the most flourishing approach in present epoch. Various researches in this context are ongoing to eradicate devastating cancer cells with minimal or no side effects. Of the various gene therapy protocols developed, a set of genes called suicide genes, are being actively pursued as potential strategy. Briefly, this strategy involves tumor targeted delivery of a therapy/reporter gene to convert a systematically administered pro-drug into a cytotoxic drug which in turn induces tumor cell death. Additionally, advancement in small animal imaging modalities facilitates real-time monitoring of the delivered transgene by using appropriate imaging probe developed against the transgene. Non-invasive monitoring helps to realize precise transgene delivery and also aid to understand therapy response. In this background, we have reviewed potential suicide genes frequently explored for cancer treatment, which supports both diagnostic and therapeutic applications with special emphasis on sodium iodide symporter (NIS). Apart from its natural expression in thyroid, NIS protein expression has raised the possibility of using radioiodide therapy and diagnosis in few non-thyroidal cancers as well. In this review, we also covered various challenges to get NIS gene therapeutics from bench to bedside in various non-thyroidal cancers.

Murine Embryonic Stem Cells Synthesize Retinoic Acid to Promote their Own Differentiation

Objective:Embryonic stem cells (ESC) pluripotency is maintained through a complex interplay of different signaling pathways and a network of transcription factors. Although much is known about this pluripotency selfrenewal circuitry, the molecular events that lead ESC to exit from pluripotency and begin differentiation are currently less known. All-trans retinoic acid (atRA), plays important and pleiotropic roles in embryonic development and ESC differentiation. The objective of the present study is to check the autocrine synthesis of atRA by ESC, test its role in spontaneous differentiation of ESC as embryoid bodies (EBs), and analyze the expression of the enzymes and proteins involved in atRA synthesis pathway. Methods: ESC, undifferentiated or differentiating as EBs, were grown in absence or presence of atRA, retinol, or the RAR antagonist CD2665, and Brachyury expression was analyzed as marker of ESC differentiation state. ESC or EBs-conditioned medium was produced in absence or presence of retinol and tested on RARE-luciferase reporter cells. RT-qPCR analysis of atRA biosynthetic pathway components was performed on undifferentiated or differentiating ESC. Finally, microarray gene expression profile was used to identify direct atRA target genes in ESC. Results: Here, we demonstrate that atRA promotes early steps of ESC differentiation, and that ESC increase their capacity to synthesize atRA during spontaneous differentiation as EBs, up-regulating RDH1, RDH10, ADH3, RALDH2, and CRABP2. Among 35 transcription factors (TFs) regulated by atRA in ESC, 3 TFs up-regulated (Snai1, Gata6, Cdx1) are known to be involved in ESC pluripotency exit and 3 TFs down-regulated (Otx2, Id2 and Arid1a) are involved in ESC pluripotency maintaining. Conclusion: Cultivation and controlled differentiation of ESC has opened new frontiers both in regenerative medicine and biology of development. Here, we demonstrated that RA is synthesized by ESC during spontaneous differentiation as EBs and takes an active role to promote their own differentiation process.