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  • Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors
    Interface Focus (IF 3.514) Pub Date : 2020-10-16
    Shunzhou Wan; Andrew Potterton; Fouad S. Husseini; David W. Wright; Alexander Heifetz; Maciej Malawski; Andrea Townsend-Nicholson; Peter V. Coveney

    We apply the hit-to-lead ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and lead-optimization TIES (thermodynamic integration with enhanced sampling) methods to compute the binding free energies of a series of ligands at the A1 and A2A adenosine receptors, members of a subclass of the GPCR (G protein-coupled receptor) superfamily. Our predicted binding free

    更新日期:2020-10-16
  • On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces
    Interface Focus (IF 3.514) Pub Date : 2020-10-16
    Gerhard König; Sereina Riniker

    Force fields based on molecular mechanics (MM) are the main computational tool to study the relationship between protein structure and function at the molecular level. To validate the quality of such force fields, high-level quantum-mechanical (QM) data are employed to test their capability to reproduce the features of all major conformational substates of a series of blocked amino acids. The phase-space

    更新日期:2020-10-16
  • How quickly can we predict trimethoprim resistance using alchemical free energy methods?
    Interface Focus (IF 3.514) Pub Date : 2020-10-16
    Philip W. Fowler

    The emergence of antimicrobial resistance threatens modern medicine and necessitates more personalized treatment of bacterial infections. Sequencing the whole genome of the pathogen(s) in a clinical sample offers one way to improve clinical microbiology diagnostic services, and has already been adopted for tuberculosis in some countries. A key weakness of a genetics clinical microbiology is it cannot

    更新日期:2020-10-16
  • Large-scale binding affinity calculations on commodity compute clouds
    Interface Focus (IF 3.514) Pub Date : 2020-10-16
    S. J. Zasada; D. W. Wright; P. V. Coveney

    In recent years, it has become possible to calculate binding affinities of compounds bound to proteins via rapid, accurate, precise and reproducible free energy calculations. This is imperative in drug discovery as well as personalized medicine. This approach is based on molecular dynamics (MD) simulations and draws on sequence and structural information of the protein and compound concerned. Free

    更新日期:2020-10-16
  • Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction
    Interface Focus (IF 3.514) Pub Date : 2020-10-16
    Shunzhou Wan; Agastya P. Bhati; Stefan J. Zasada; Peter V. Coveney

    A central quantity of interest in molecular biology and medicine is the free energy of binding of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding affinity had been widely regarded as out of reach of theoretical methods owing to the lack of reproducibility of the available methods, not to mention their complexity, computational cost and time-consuming procedures

    更新日期:2020-10-16
  • The influence of base pair tautomerism on single point mutations in aqueous DNA
    Interface Focus (IF 3.514) Pub Date : 2020-10-16
    A. Gheorghiu; P. V. Coveney; A. A. Arabi

    The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton

    更新日期:2020-10-16
  • Quantum computing using continuous-time evolution
    Interface Focus (IF 3.514) Pub Date : 2020-10-16
    Viv Kendon

    Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of speed. Other types of computation using radically different architectures, including neuromorphic and quantum, promise breakthroughs in both speed and efficiency

    更新日期:2020-10-16
  • Educating and engaging new communities of practice with high performance computing through the integration of teaching and research
    Interface Focus (IF 3.514) Pub Date : 2020-10-16
    Andrea Townsend-Nicholson

    The identification of strategies by which to increase the representation of women and increase diversity in STEM fields (science, technology, engineering and mathematics), including medicine, has been a pressing matter for global agencies including the European Commission, UNESCO and numerous international scientific societies. In my role as UCL training lead for CompBioMed, a European Commission Horizon

    更新日期:2020-10-16
  • The future of carbon dioxide removal must be transdisciplinary
    Interface Focus (IF 3.514) Pub Date : 2020-08-14
    Tamara Jane Zelikova

    Carbon dioxide removal (CDR) represents a suite of pathways to remove carbon dioxide from the atmosphere and mitigate climate change. The importance of CDR has expanded in recent years as emission reductions are not at pace to meet climate goals. This CDR-themed issue brings together diverse perspectives in order to identify opportunities to integrate across CDR disciplines, create a more holistic

    更新日期:2020-08-14
  • Rooting carbon dioxide removal research in the social sciences.
    Interface Focus (IF 3.514) Pub Date : 2020-08-14
    Glen Dowell,Jeff Niederdeppe,Jamie Vanucchi,Timur Dogan,Kieran Donaghy,Rory Jacobson,Natalie Mahowald,Mark Milstein,T Jane Zelikova

    Reports from a variety of bodies have highlighted the role that carbon dioxide removal (CDR) technologies and practices must play in order to try to avoid the worst effects of anthropogenic climate change. Research into the feasibility of these technologies is primarily undertaken by scholars in the natural sciences, yet, as we argue in this commentary, there is great value in collaboration between

    更新日期:2020-08-14
  • Climate change mitigation potential of wetlands and the cost-effectiveness of their restoration.
    Interface Focus (IF 3.514) Pub Date : 2020-08-14
    Pierre Taillardat,Benjamin S Thompson,Michelle Garneau,Karelle Trottier,Daniel A Friess

    The cost-effective mitigation of climate change through nature-based carbon dioxide removal strategies has gained substantial policy attention. Inland and coastal wetlands (specifically boreal, temperate and tropical peatlands; tundra; floodplains; freshwater marshes; saltmarshes; and mangroves) are among the most efficient natural long-term carbon sinks. Yet, they also release methane (CH4) that can

    更新日期:2020-08-14
  • Should carbon removal be treated as waste management? Lessons from the cultural history of waste.
    Interface Focus (IF 3.514) Pub Date : 2020-08-14
    Holly Jean Buck

    Carbon dioxide is a waste product of combusting fossil fuels, and its accumulation in the atmosphere presents a planetary hazard. Carbon dioxide is also managed and used as a resource. Emerging technologies like direct air capture present the opportunity to reclaim and re-use wasted carbon, and actors in industry and policy are increasingly understanding carbon capture, utilization and storage as a

    更新日期:2020-08-14
  • Total cost of carbon capture and storage implemented at a regional scale: northeastern and midwestern United States.
    Interface Focus (IF 3.514) Pub Date : 2020-08-14
    William J Schmelz,Gal Hochman,Kenneth G Miller

    We model the costs of carbon capture and storage (CCS) in subsurface geological formations for emissions from 138 northeastern and midwestern electricity-generating power plants. The analysis suggests coal-sourced CO2 emissions can be stored in this region at a cost of $52–$60 ton−1, whereas the cost to store emission from natural-gas-fired plants ranges from approximately $80 to $90. Storing emissions

    更新日期:2020-08-14
  • Behavioural frameworks to understand public perceptions of and risk response to carbon dioxide removal.
    Interface Focus (IF 3.514) Pub Date : 2020-08-14
    Trisha R Shrum,Ezra Markowitz,Holly Buck,Robin Gregory,Sander van der Linden,Shahzeen Z Attari,Leaf Van Boven

    The adoption of carbon dioxide removal (CDR) technologies at a scale sufficient to draw down carbon emissions will require both individual and collective decisions that happen over time in different locations to enable a massive scale-up. Members of the public and other decision-makers have not yet formed strong attitudes, beliefs and preferences about most of the individual CDR technologies or taken

    更新日期:2020-08-14
  • Forest policy and management approaches for carbon dioxide removal.
    Interface Focus (IF 3.514) Pub Date : 2020-08-14
    Nicolena vonHedemann,Zachary Wurtzebach,Thomas J Timberlake,Emily Sinkular,Courtney A Schultz

    Forests increasingly will be used for carbon dioxide removal (CDR) as a natural climate solution, and the implementation of forest-based CDR presents a complex public policy challenge. In this paper, our goal is to review a range of policy tools in place to support use of forests for CDR and demonstrate how concepts from the policy design literature can inform our understanding of this domain. We explore

    更新日期:2020-08-14
  • Climate change mitigation as a co-benefit of regenerative ranching: insights from Australia and the United States.
    Interface Focus (IF 3.514) Pub Date : 2020-08-14
    Hannah Gosnell,Susan Charnley,Paige Stanley

    ‘Managed grazing’ is gaining attention for its potential to contribute to climate change mitigation by reducing bare ground and promoting perennialization, thereby enhancing soil carbon sequestration (SCS). Understanding why ranchers adopt managed grazing is key to developing the right incentives. In this paper, we explore principles and practices associated with the larger enterprise of ‘regenerative

    更新日期:2020-08-14
  • The origin and rise of complex life: progress requires interdisciplinary integration and hypothesis testing
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Rachel Wood; Philip C. J. Donoghue; Timothy M. Lenton; Alexander G. Liu; Simon W. Poulton

    Understanding of the triggers and timing of the rise of complex life ca 2100 to 720 million years ago has expanded dramatically in recent years. This theme issue brings together diverse and novel geochemical and palaeontological data presented as part of the Royal Society ‘The origin and rise of complex life: integrating models, geochemical and palaeontological data’ discussion meeting held in September

    更新日期:2020-07-20
  • Reconciling proxy records and models of Earth's oxygenation during the Neoproterozoic and Palaeozoic.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Rosalie Tostevin,Benjamin J W Mills

    A hypothesized rise in oxygen levels in the Neoproterozoic, dubbed the Neoproterozoic Oxygenation Event, has been repeatedly linked to the origin and rise of animal life. However, a new body of work has emerged over the past decade that questions this narrative. We explore available proxy records of atmospheric and marine oxygenation and, considering the unique systematics of each geochemical system

    更新日期:2020-07-20
  • On the use of models in understanding the rise of complex life.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Timothy M Lenton

    Recently, several seemingly irreconcilably different models have been proposed for relationships between Earth system processes and the rise of complex life. These models provide very different scenarios of Proterozoic atmospheric oxygen and ocean nutrient levels, whether they constrained complex life, and of how the rise of complex life affected biogeochemical conditions. For non-modellers, it can

    更新日期:2020-07-20
  • Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Graham E Budd,Richard P Mann

    Important evolutionary events such as the Cambrian Explosion have inspired many attempts at explanation: why do they happen when they do? What shapes them, and why do they eventually come to an end? However, much less attention has been paid to the idea of a ‘null hypothesis’—that certain features of such diversifications arise simply through their statistical structure. Such statistical features also

    更新日期:2020-07-20
  • Insights into eukaryogenesis from the fossil record.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Susannah M Porter

    Eukaryogenesis—the process by which the eukaryotic cell emerged—has long puzzled scientists. It has been assumed that the fossil record has little to say about this process, in part because important characters such as the nucleus and mitochondria are rarely preserved, and in part because the prevailing model of early eukaryotes implies that eukaryogenesis occurred before the appearance of the first

    更新日期:2020-07-20
  • The origin of phagocytosis in Earth history.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Daniel B Mills

    Phagocytosis, or ‘cell eating’, is a eukaryote-specific process where particulate matter is engulfed via invaginations of the plasma membrane. The origin of phagocytosis has been central to discussions on eukaryogenesis for decades­, where it is argued as being either a prerequisite for, or consequence of, the acquisition of the ancestral mitochondrion. Recently, genomic and cytological evidence has

    更新日期:2020-07-20
  • Nucleus preservation in early Ediacaran Weng'an embryo-like fossils, experimental taphonomy of nuclei and implications for reading the eukaryote fossil record.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Weichen Sun,Zongjun Yin,John A Cunningham,Pengju Liu,Maoyan Zhu,Philip C J Donoghue

    The challenge of identifying fossilized organelles has long hampered attempts to interpret the fossil record of early eukaryote evolution. We explore this challenge through experimental taphonomy of nuclei in a living eukaryote and microscale physical and chemical characterization of putative nuclei in embryo-like fossils from the early Ediacaran Weng'an Biota. The fossil nuclei exhibit diverse preservational

    更新日期:2020-07-20
  • Aluminosilicate haloes preserve complex life approximately 800 million years ago.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Ross P Anderson,Nicholas J Tosca,Gianfelice Cinque,Mark D Frogley,Ioannis Lekkas,Austin Akey,Gareth M Hughes,Kristin D Bergmann,Andrew H Knoll,Derek E G Briggs

    Mudstone-hosted microfossils are a major component of the Proterozoic fossil record, particularly dominating the record of early eukaryotic life. Early organisms possessed no biomineralized parts to resist decay and controls on their fossilization in mudstones are poorly understood. Consequently, the Proterozoic fossil record is compromised—we do not know whether changing temporal/spatial patterns

    更新日期:2020-07-20
  • Preservation of erniettomorph fossils in clay-rich siliciclastic deposits from the Ediacaran Wood Canyon Formation, Nevada.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    J G Hall,E F Smith,N Tamura,S C Fakra,T Bosak

    Three-dimensionally preserved Ediacaran fossils occur globally within sandstone beds. Sandy siliciclastic deposits of the Ediacaran Wood Canyon Formation (WCF) in the Montgomery Mountains, Nevada, contain two fossil morphologies with similar shapes and sizes: one exhibits mm-scale ridges and a distinct lower boundary and the other is devoid of these diagnostic features. We interpret these as taphomorphs

    更新日期:2020-07-20
  • The rise and early evolution of animals: where do we stand from a trace-fossil perspective?
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    M Gabriela Mángano,Luis A Buatois

    The trace-fossil record provides a wealth of information to track the rise and early evolution of animals. It comprises the activity of both hard- and soft-bodied organisms, is continuous through the Ediacaran (635–539 Ma)– Cambrian (539–485 Ma) transition, yields insights into animal behaviour and their role as ecosystem engineers, and allows for a more refined characterization of palaeoenvironmental

    更新日期:2020-07-20
  • Biostratinomy of the Ediacara Member (Rawnsley Quartzite, South Australia): implications for depositional environments, ecology and biology of Ediacara organisms.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Mary L Droser,Lidya G Tarhan,Scott D Evans,Rachel L Surprenant,James G Gehling

    The Precambrian Ediacara Biota—Earth's earliest fossil record of communities of macroscopic, multicellular organisms—provides critical insights into the emergence of complex life on our planet. Excavation and reconstruction of nearly 300 m2 of fossiliferous bedding planes in the Ediacara Member of the Rawnsley Quartzite, at the National Heritage Ediacara fossil site Nilpena in South Australia, have

    更新日期:2020-07-20
  • The influence of environmental setting on the community ecology of Ediacaran organisms.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Emily G Mitchell,Nikolai Bobkov,Natalia Bykova,Alavya Dhungana,Anton V Kolesnikov,Ian R P Hogarth,Alexander G Liu,Tom M R Mustill,Nikita Sozonov,Vladimir I Rogov,Shuhai Xiao,Dmitriy V Grazhdankin

    The broad-scale environment plays a substantial role in shaping modern marine ecosystems, but the degree to which palaeocommunities were influenced by their environment is unclear. To investigate how broad-scale environment influenced the community ecology of early animal ecosystems, we employed spatial point process analyses (SPPA) to examine the community structure of seven late Ediacaran (558–550

    更新日期:2020-07-20
  • Harnessing hypoxia as an evolutionary driver of complex multicellularity.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Emma U Hammarlund

    Animal tissue requires low-oxygen conditions for its maintenance. The need for low-oxygen conditions contrasts with the idea of an evolutionary leap in animal diversity as a result of expanding oxic conditions. To accommodate tissue renewal at oxic conditions, however, vertebrate animals and vascular plants demonstrate abilities to access hypoxia. Here, I argue that multicellular organisms sustain

    更新日期:2020-07-20
  • Weathering, alteration and reconstructing Earth's oxygenation.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Noah J Planavsky,Leslie J Robbins,Balz S Kamber,Ronny Schoenberg

    Deciphering the role—if any—that free oxygen levels played in controlling the timing and tempo of the radiation of complex life is one of the most fundamental questions in Earth and life sciences. Accurately reconstructing Earth's redox history is an essential part of tackling this question. Over the past few decades, there has been a proliferation of research employing geochemical redox proxies in

    更新日期:2020-07-20
  • The evolution of complex life and the stabilization of the Earth system.
    Interface Focus (IF 3.514) Pub Date : 2020-06-12
    Jonathan L Payne,Aviv Bachan,Noel A Heim,Pincelli M Hull,Matthew L Knope

    The half-billion-year history of animal evolution is characterized by decreasing rates of background extinction. Earth's increasing habitability for animals could result from several processes: (i) a decrease in the intensity of interactions among species that lead to extinctions; (ii) a decrease in the prevalence or intensity of geological triggers such as flood basalt eruptions and bolide impacts;

    更新日期:2020-07-20
  • Sleep, circadian rhythms and health.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Russell G Foster

    At the core of human thought, for the majority of individuals in the developed nations at least, there is the tacit assumption that as a species we are unfettered by the demands imposed by our biology and that we can do what we want, at whatever time we choose, whereas in reality every aspect of our physiology and behaviour is constrained by a 24 h beat arising from deep within our evolution. Our daily

    更新日期:2020-04-17
  • Sleep, disruption and the 'nightmare of total illumination' in late nineteenth and early twentieth-century dystopian fiction.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Laura E Ludtke

    This article addresses the charge that the introduction of the electric light in the late nineteenth century increased disruptions to the human body's biological processes and interfered with the oscillating sleeping-waking cycle. By considering the nineteenth century research into the factors that motivate and disrupt sleep in concert with contemporary discussions of the physiology of street lighting

    更新日期:2020-04-17
  • Why sleep matters for young people who may get depressed.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Guy M Goodwin

    Depression and anxiety are negative emotional states familiar to us all through personal experience. Less familiar are severe states of depression, in particular, which can actually shorten the lives of sufferers by over a decade. The relationship of these very severe states of illness to the milder cases more common earlier in development is important. Most patients who have suffered from depression

    更新日期:2020-04-17
  • Sleep deprivation and stress: a reciprocal relationship.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Mathieu Nollet,William Wisden,Nicholas P Franks

    Sleep is highly conserved across evolution, suggesting vital biological functions that are yet to be fully understood. Animals and humans experiencing partial sleep restriction usually exhibit detrimental physiological responses, while total and prolonged sleep loss could lead to death. The perturbation of sleep homeostasis is usually accompanied by an increase in hypothalamic-pituitary-adrenal (HPA)

    更新日期:2020-04-17
  • Historicising stress: anguish and insomnia in the middle ages.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    William MacLehose

    While the concept of 'stress' in the modern sense is a twentieth-century innovation, many of the symptoms we associate with the modern condition appear in historical materials going back many centuries. But how did premodern people understand and experience these symptoms and their relation to sleep? This study focuses on the rich materials from the central middle ages in Western Europe, a period during

    更新日期:2020-04-17
  • Sleep and stress management in Enlightenment literature and poetry.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Clark Lawlor,Ashleigh Blackwood

    'Sleep and stress management in Enlightenment literature and poetry' argues that the relationship between sleep and stress, as we now call it, was well known in long eighteenth-century Britain. This period was one of changing theories about the nature of the body and mind due to the shift from received wisdom and religious dogma to modern experimental science, although there were some continuities

    更新日期:2020-04-17
  • Fagged out: overwork and sleeplessness in Victorian professional life.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Sally Shuttleworth

    The paper sets current concerns with insomnia in our 24/7 society in the context of nineteenth-century anxieties about the pressures of overwork and sleeplessness in professional culture. Following a case study of a sleepless prime minister, William Gladstone, it explores the early history of sleep research, including the first recordings of a brain pulse during sleep by Angelo Mosso. In parallel with

    更新日期:2020-04-17
  • The challenges of adolescent sleep.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Gaby Illingworth

    Sleep is vital for our physical, emotional and cognitive health. However, adolescents face many challenges where their sleep is concerned. This is reflected in their sleep patterns including the timing of their sleep and how much sleep they achieve on a regular basis: their sleep is characteristically delayed and short. Notably, insufficient sleep is associated with impairments in adolescent functioning

    更新日期:2020-04-17
  • Accounting for sleep loss in early modern England.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Sasha Handley

    How did people in the sixteenth and seventeenth centuries account for sleep loss? This article answers this question through an in-depth analysis of the life-writings of six early modern women and men that suffered from periodic or persistent episodes of sleep loss. It focuses on the ways in which these health crises were understood to impede the ordinary functions of body and mind, while also revealing

    更新日期:2020-04-17
  • Dickens's nightmare: dreams, memory and trauma.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Melissa Dickson

    This article considers the role of stress in nineteenth-century literature and culture as both a catalyst for, and a symptom of, troubled sleep. Taking the figure of Charles Dickens as my principal case study, I investigate Dickens's fictional and non-fictional explorations of sleep as a space and time where traumatic memories might be relived and repeated, where grief and longing might be articulated

    更新日期:2020-04-17
  • Insomnia and the late nineteenth-century insomniac: the case of Albert Kimball.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Matthew Beaumont

    This article explores the emergence, in late nineteenth-century Britain and the USA, of the 'insomniac' as a distinct pathological and social archetype. Sleeplessness has of course been a human problem for millennia, but only since the late-Victorian period has there been a specific diagnostic name for the individual who suffers chronically from insufficient sleep. The introductory section of the article

    更新日期:2020-04-17
  • 'Slepen al the nyght with open ye': Personal reflections after 35 years of being on-call.
    Interface Focus (IF 3.514) Pub Date : 2020-04-17
    Chris Fitzpatrick

    The European Working Time Directive (2003) has had a significant impact in reducing the total number of hours worked per week, as well as shift-lengths. There is, however, no agreement on optimal shift-lengths and day/night work balance in different medical specialities. Given the time it takes for clinical events to unfold, particularly in relation to labour, there may be advantages in retaining the

    更新日期:2020-04-17
  • Multiscale modelling of drug transport and metabolism in liver spheroids.
    Interface Focus (IF 3.514) Pub Date : 2020-02-14
    Joseph A Leedale,Jonathan A Kyffin,Amy L Harding,Helen E Colley,Craig Murdoch,Parveen Sharma,Dominic P Williams,Steven D Webb,Rachel N Bearon

    In early preclinical drug development, potential candidates are tested in the laboratory using isolated cells. These in vitro experiments traditionally involve cells cultured in a two-dimensional monolayer environment. However, cells cultured in three-dimensional spheroid systems have been shown to more closely resemble the functionality and morphology of cells in vivo. While the increasing usage of

    更新日期:2020-02-14
  • In vitro and computational modelling of drug delivery across the outer blood-retinal barrier.
    Interface Focus (IF 3.514) Pub Date : 2020-02-14
    Alys E Davies,Rachel L Williams,Gaia Lugano,Serban R Pop,Victoria R Kearns

    The ability to produce rapid, cost-effective and human-relevant data has the potential to accelerate the development of new drug delivery systems. Intraocular drug delivery is an area undergoing rapid expansion, due to the increase in sight-threatening diseases linked to increasing age and lifestyle factors. The outer blood-retinal barrier (OBRB) is important in this area of drug delivery, as it separates

    更新日期:2020-02-14
  • Applications of novel bioreactor technology to enhance the viability and function of cultured cells and tissues.
    Interface Focus (IF 3.514) Pub Date : 2020-02-14
    H W Hoyle,L A Smith,R J Williams,S A Przyborski

    As the field of tissue engineering continues to advance rapidly, so too does the complexity of cell culture techniques used to generate in vitro tissue constructs, with the overall aim of mimicking the in vivo microenvironment. This complexity typically comes at a cost with regards to the size of the equipment required and associated expenses. We have developed a small, low-cost bioreactor system which

    更新日期:2020-02-14
  • A novel workflow for three-dimensional analysis of tumour cell migration.
    Interface Focus (IF 3.514) Pub Date : 2020-02-14
    Sophie Ketchen,Arndt Rohwedder,Sabine Knipp,Filomena Esteves,Nina Struve,Michelle Peckham,John E Ladbury,Alistair Curd,Susan C Short,Anke Brüning-Richardson

    The limitations of two-dimensional analysis in three-dimensional (3D) cellular imaging impair the accuracy of research findings in biological studies. Here, we report a novel 3D approach to acquisition, analysis and interpretation of tumour spheroid images. Our research interest in mesenchymal-amoeboid transition led to the development of a workflow incorporating the generation and analysis of 3D data

    更新日期:2020-02-14
  • Mathematical modelling of fluid flow and solute transport to define operating parameters for in vitro perfusion cell culture systems.
    Interface Focus (IF 3.514) Pub Date : 2020-02-14
    Lauren Hyndman,Sean McKee,Nigel J Mottram,Bhumika Singh,Steven D Webb,Sean McGinty

    In recent years, there has been a move away from the use of static in vitro two-dimensional cell culture models for testing the chemical safety and efficacy of drugs. Such models are increasingly being replaced by more physiologically relevant cell culture systems featuring dynamic flow and/or three-dimensional structures of cells. While it is acknowledged that such systems provide a more realistic

    更新日期:2020-02-14
  • Possible mechanisms of CO2 reduction by H2 via prebiotic vectorial electrochemistry.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    Rafaela Vasiliadou,Nikolay Dimov,Nicolas Szita,Sean F Jordan,Nick Lane

    Methanogens are putatively ancestral autotrophs that reduce CO2 with H2 to form biomass using a membrane-bound, proton-motive Fe(Ni)S protein called the energy-converting hydrogenase (Ech). At the origin of life, geologically sustained H+ gradients across inorganic barriers containing Fe(Ni)S minerals could theoretically have driven CO2 reduction by H2 through vectorial chemistry in a similar way to

    更新日期:2019-11-01
  • Radionuclide-induced defect sites in iron-bearing minerals may have accelerated the emergence of life.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    Adrian Ponce

    The emergence of life on Earth (and elsewhere) must have occurred in a milieu that is far from equilibrium, such as at alkaline hydrothermal vents that would have harboured built-in gradients in temperature, redox potential and pH along with precipitated iron-bearing minerals capable of separating these gradients, concentrating reactants and catalysing requisite protobiotic reactions. Iron-bearing

    更新日期:2019-11-01
  • Catalysts, autocatalysis and the origin of metabolism.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    Martina Preiner,Joana C Xavier,Andrey do Nascimento Vieira,Karl Kleinermanns,John F Allen,William F Martin

    If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO2, N2 and H2. Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and biotic processes in biological systems, it becomes evident that chemical activation

    更新日期:2019-11-01
  • Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    Robert K Szilagyi,Rebecca Hanscam,Eric M Shepard,Shawn E McGlynn

    Cysteine is the only coded amino acid in biology that contains a thiol functional group. Deprotonated thiolate is essential for anchoring iron-sulfur ([Fe-S]) clusters, as prosthetic groups to the protein matrix. [Fe-S] metalloproteins and metalloenzymes are involved in biological electron transfer, radical chemistry, small molecule activation and signalling. These are key metabolic and regulatory

    更新日期:2019-11-01
  • Isoprenoids enhance the stability of fatty acid membranes at the emergence of life potentially leading to an early lipid divide.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    Sean F Jordan,Eloise Nee,Nick Lane

    Two key problems concern cell membranes during the emergence and early evolution of life: what was their initial composition, and why did the membranes of archaea and bacteria diverge? The composition of the first cell membranes could shed light on the most likely environment for the emergence of life. The opposing stereochemistry of modern lipid glycerol-phosphate headgroups in bacteria and archaea

    更新日期:2019-11-01
  • Intrinsic concentration cycles and high ion fluxes in self-assembled precipitate membranes.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    Yang Ding,Julyan H E Cartwright,Silvana S S Cardoso

    Concentration cycles are important for bonding of basic molecular building components at the emergence of life. We demonstrate that oscillations occur intrinsically in precipitation reactions when coupled with fluid mechanics in self-assembled precipitate membranes, such as at submarine hydrothermal vents. We show that, moreover, the flow of ions across one pore in such a prebiotic membrane is larger

    更新日期:2019-11-01
  • Fougerite: the not so simple progenitor of the first cells.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    Simon Duval,Frauke Baymann,Barbara Schoepp-Cothenet,Fabienne Trolard,Guilhem Bourrié,Olivier Grauby,Elbert Branscomb,Michael J Russell,Wolfgang Nitschke

    We here review the extraordinary mineralogical properties of green rusts and their naturally occurring form, fougerite, and discuss the pertinence of these properties within the alkaline hydrothermal vent (AHV) hypothesis for life's emergence. We put forward an extended version of the AHV scenario which enhances the conformity between extant life and its earliest progenitor by extensively making use

    更新日期:2019-11-01
  • Protein three-dimensional structures at the origin of life.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    E James Milner-White

    Proteins are relatively easy to synthesize, compared to nucleic acids and it is likely that there existed a stage prior to the RNA world which can be called the protein world. Some of the three-dimensional (3D) peptide structures in these proteins have, we argue, been conserved since then and may constitute the oldest biological relics in existence. We focus on 3D peptide motifs consisting of up to

    更新日期:2019-11-01
  • Prospecting for life.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    Michael J Russell

    Books with titles like 'The Call of the Wild' seemed to set a path for a life. Thus, I would be an explorer-a plan that did not work out so well, at least at first. On leaving school I got a job as a 'Works Chemist Improver', testing Ni catalysts for the hydrogenation of phenol to cyclohexanol. Taking night classes I passed enough exams to study geology at Queen Mary College, London. Armed thus I travelled

    更新日期:2019-11-01
  • On the origin of degeneracy in the genetic code.
    Interface Focus (IF 3.514) Pub Date : 2019-10-24
    D L Gonzalez,S Giannerini,R Rosa

    The degeneracy of amino acid coding is one of the most crucial and enigmatic aspects of the genetic code. Different theories about the origin of the genetic code have been developed. However, to date, there is no comprehensive hypothesis on the mechanism that might have generated the degeneracy as we observe it. Here, we provide a new theory that explains the origin of the degeneracy based only on

    更新日期:2019-11-01
  • On the beneficent thickness of water.
    Interface Focus (IF 3.514) Pub Date : 2019-10-18
    E Branscomb,M J Russell

    In the 1930s, Lars Onsager published his famous 'reciprocal relations' describing free energy conversion processes. Importantly, these relations were derived on the assumption that the fluxes of the processes involved in the conversion were proportional to the forces (free energy gradients) driving them. For chemical reactions, however, this condition holds only for systems operating close to equilibrium-indeed

    更新日期:2019-11-01
  • Probing complexity: thermodynamics and computational mechanics approaches to origins studies.
    Interface Focus (IF 3.514) Pub Date : 2019-10-18
    Stuart J Bartlett,Patrick Beckett

    This paper proposes new avenues for origins research that apply modern concepts from stochastic thermodynamics, information thermodynamics and complexity science. Most approaches to the emergence of life prioritize certain compounds, reaction pathways, environments or phenomena. What they all have in common is the objective of reaching a state that is recognizably alive, usually positing the need for

    更新日期:2019-11-01
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