Catálogo de publicaciones - revistas

<jats:sec> <jats:title>BACKGROUND</jats:title> <jats:p>As global climate change accelerates, one of the most urgent tasks for the coming decades is to develop accurate predictions about biological responses to guide the effective protection of biodiversity. Predictive models in biology provide a means for scientists to project changes to species and ecosystems in response to disturbances such as climate change. Most current predictive models, however, exclude important biological mechanisms such as demography, dispersal, evolution, and species interactions. These biological mechanisms have been shown to be important in mediating past and present responses to climate change. Thus, current modeling efforts do not provide sufficiently accurate predictions. Despite the many complexities involved, biologists are rapidly developing tools that include the key biological processes needed to improve predictive accuracy. The biggest obstacle to applying these more realistic models is that the data needed to inform them are almost always missing. We suggest ways to fill this growing gap between model sophistication and information to predict and prevent the most damaging aspects of climate change for life on Earth.</jats:p> </jats:sec> <jats:sec> <jats:title>ADVANCES</jats:title> <jats:p>On the basis of empirical and theoretical evidence, we identify six biological mechanisms that commonly shape responses to climate change yet are too often missing from current predictive models: physiology; demography, life history, and phenology; species interactions; evolutionary potential and population differentiation; dispersal, colonization, and range dynamics; and responses to environmental variation. We prioritize the types of information needed to inform each of these mechanisms and suggest proxies for data that are missing or difficult to collect. We show that even for well-studied species, we often lack critical information that would be necessary to apply more realistic, mechanistic models. Consequently, data limitations likely override the potential gains in accuracy of more realistic models. Given the enormous challenge of collecting this detailed information on millions of species around the world, we highlight practical methods that promote the greatest gains in predictive accuracy. Trait-based approaches leverage sparse data to make more general inferences about unstudied species. Targeting species with high climate sensitivity and disproportionate ecological impact can yield important insights about future ecosystem change. Adaptive modeling schemes provide a means to target the most important data while simultaneously improving predictive accuracy.</jats:p> </jats:sec> <jats:sec> <jats:title>OUTLOOK</jats:title> <jats:p>Strategic collections of essential biological information will allow us to build generalizable insights that inform our broader ability to anticipate species’ responses to climate change and other human-caused disturbances. By increasing accuracy and making uncertainties explicit, scientists can deliver improved projections for biodiversity under climate change together with characterizations of uncertainty to support more informed decisions by policymakers and land managers. Toward this end, a globally coordinated effort to fill data gaps in advance of the growing climate-fueled biodiversity crisis offers substantial advantages in efficiency, coverage, and accuracy. Biologists can take advantage of the lessons learned from the Intergovernmental Panel on Climate Change’s development, coordination, and integration of climate change projections. Climate and weather projections were greatly improved by incorporating important mechanisms and testing predictions against global weather station data. Biology can do the same. We need to adopt this meteorological approach to predicting biological responses to climate change to enhance our ability to mitigate future changes to global biodiversity and the services it provides to humans.</jats:p> <jats:fig fig-type="figure" orientation="portrait" position="float"> <jats:caption> <jats:title>Emerging models are beginning to incorporate six key biological mechanisms that can improve predictions of biological responses to climate change.</jats:title> <jats:p>Models that include biological mechanisms have been used to project (clockwise from top) the evolution of disease-harboring mosquitoes, future environments and land use, physiological responses of invasive species such as cane toads, demographic responses of penguins to future climates, climate-dependent dispersal behavior in butterflies, and mismatched interactions between butterflies and their host plants. Despite these modeling advances, we seldom have the detailed data needed to build these models, necessitating new efforts to collect the relevant data to parameterize more biologically realistic predictive models.</jats:p> </jats:caption> <jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" orientation="portrait" position="float" xlink:href="353_aad8466_fa.jpeg" /> </jats:fig> </jats:sec>

<jats:sec> <jats:title>INTRODUCTION</jats:title> <jats:p>In DNA double helices, hydrogen bonds connect the base pairs across the two strands, and stacking bonds act along the helical axis between neighboring base pairs. Our understanding of DNA and the way it is processed in biology would profit from improved knowledge about the elementary bonds in DNA. Detailed knowledge of the time scales for breaking and forming individual base pairs and base-pair stacks would also help to make more informed decisions in the design of dynamic DNA-based nanoscale devices.</jats:p> </jats:sec> <jats:sec> <jats:title>RATIONALE</jats:title> <jats:p>The goal of this work is to measure the dynamics of DNA base-pair stacking at the level of individual base-pair steps. Because stacking interactions act perpendicularly to the hydrogen bonds, it should be possible to use mechanical forces to break stacking while leaving hydrogen bonds intact. To realize such measurements, we combine the positioning capabilities of DNA origami with single-molecule manipulation, as enabled by dual-beam optical traps. To make the weak single–base-pair stacking interactions experimentally accessible, we prepared parallel arrays of blunt-end DNA double helices to take advantage of avidity effects when these arrays form stacking interactions (see the figure). Our design allowed controlling the number and the sequences of the base-pair stacks. Noise-suppressing by stiff DNA origami beams connected by a flexible polymer tether enabled the repeated detection of unbinding and rebinding of stacking contacts at low forces (down to 2 piconewtons) with high time resolution (up to 1 kHz).</jats:p> </jats:sec> <jats:sec> <jats:title>RESULTS</jats:title> <jats:p> We sampled all 16 sequence combinations of installing a particular interfacial base pair on the array on the left beam and another base pair in the array on the right beam, and we created arrays with two, four, and six blunt ends. We could measure the force-dependent lifetimes for all base-pair step sequence combinations in the presence of 20 mM MgCl <jats:sup>2</jats:sup> , which is a condition typically used in DNA nanotechnology. For a subset of base-pair step combinations, we also obtained data in the presence of 500 mM NaCl, which mimics the conditions in the cell nucleus. The base-pair stack arrays spontaneously dissociated at average rates ranging from 0.02 to 500 per second, where the dissociation time scale strongly depended on the sequence combination and the stack array size. For a given sequence combination, larger array sizes always had larger lifetimes, as expected from avidity. Another key feature revealed in the lifetime data was the low sensitivity of the stacking interactions on the extent of pulling force. This phenomenon reflects short-ranged interaction potentials. Concerning rebinding of the stack arrays, we found that the rebinding kinetics depended much more strongly on the applied force, which may be understood by considering that rebinding of the stacks requires a thermally activated contraction of the flexible tether—which was the same for all variants—against an opposing force tether contraction. However, the rebinding kinetics was independent, within experimental error, of the base-pair step sequence combination and the size of the array under study. We used a model to estimate the free-energy increments per single base-pair stack from the kinetic rates that we measured with stack arrays. The free-energy increments per stack ranged from –0.8 to –3.4 kilocalories per mole. Our data reveals a trend in the stacking-strength hierarchy that may be associated with the extent of geometrical atomic overlap between the bases within a base-pair step. </jats:p> </jats:sec> <jats:sec> <jats:title>CONCLUSION</jats:title> <jats:p>Our data provides a quantitative basis for the rational design of dynamic DNA-based nanoscale machines and assemblies. Nanoengineers can directly read off the expected lifetimes of stack arrays for all sequence combinations and for various array sizes and at salt conditions that are commonly used in the field. With this data, design solutions for transition kinetics may be generated that cover several orders of magnitudes in lifetime, from milliseconds to several seconds. The sequence-resolved information obtained in our experiments may inform kinetic models of DNA hybridization and may help in adjusting force fields to perform more realistic molecular dynamics simulations. More generally, our experimental methods advance the capabilities of single-molecule mechanical experiments. Using the tethered-beam system, target molecules may be placed and exposed in controlled orientations and stoichiometry so as to study the weak forces occurring between them in solution. A variety of interactions between various kinds of molecules may be studied in the future due to the modularity and the addressability of the DNA origami–based tethered-beam system.</jats:p> <jats:fig fig-type="figure" orientation="portrait" position="float"> <jats:caption> <jats:title>How strong is DNA base-pair stacking?</jats:title> <jats:p>Schematic illustration of the experimental system that we developed to measure the strength of base-pair stacking on the level of single particles. The system consists of two tethered DNA origami beams that feature parallel arrays of blunt-end DNA double helices. The beams may be attached to two micrometer-sized beads for manipulation in a dual-beam optical trap. With this system, we could measure lifetimes at which DNA base-pair stacks spontaneously dissociate as a function of force applied in the helical direction.</jats:p> </jats:caption> <jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" orientation="portrait" position="float" xlink:href="353_aaf5508_Fa.jpeg" /> </jats:fig> </jats:sec>

<jats:sec> <jats:title>BACKGROUND</jats:title> <jats:p>For centuries, thinkers have considered whether and how climatic conditions influence the nature of societies and the performance of economies. A multidisciplinary renaissance of quantitative empirical research has begun to illuminate key linkages in the coupling of these complex natural and human systems, uncovering notable effects of climate on health, agriculture, economics, conflict, migration, and demographics.</jats:p> </jats:sec> <jats:sec> <jats:title>ADVANCES</jats:title> <jats:p>Past scholars of climate-society interactions were limited to theorizing on the basis of anecdotal evidence; advances in computing, data availability, and study design now allow researchers to draw generalizable causal inferences tying climatic events to social outcomes. This endeavor has demonstrated that a range of climate factors have substantial influence on societies and economies, both past and present, with important implications for the future.</jats:p> <jats:p> Temperature, in particular, exerts remarkable influence over human systems at many social scales; heat induces mortality, has lasting impact on fetuses and infants, and incites aggression and violence while lowering human productivity. High temperatures also damage crops, inflate electricity demand, and may trigger population movements within and across national borders. Tropical cyclones cause mortality, damage assets, and reduce economic output for long periods. Precipitation extremes harm economies and populations predominately in agriculturally dependent settings. These effects are often quantitatively substantial; for example, we compute that temperature depresses current U.S. maize yields roughly 48%, warming trends since 1980 elevated conflict risk in Africa by 11%, and future warming may slow global economic growth rates by 0.28 percentage points year <jats:sup>−1</jats:sup> . </jats:p> <jats:p> Much research aims to forecast impacts of future climate change, but we point out that society may also benefit from attending to ongoing impacts of climate in the present, because current climatic conditions impose economic and social burdens on populations today that rival in magnitude the projected end-of-century impacts of climate change. For instance, we calculate that current temperature climatologies slow global economic growth roughly 0.25 percentage points year <jats:sup>−1</jats:sup> , comparable to the additional slowing of 0.28 percentage points year <jats:sup>−1</jats:sup> projected from future warming. </jats:p> <jats:p>Both current and future losses can theoretically be avoided if populations adapt to fully insulate themselves from the climate—why this has not already occurred everywhere remains a critical open question. For example, clear patterns of adaptation in health impacts and in response to tropical cyclones contrast strongly with limited adaptation in agricultural and macroeconomic responses to temperature. Although some theories suggest these various levels of adaptation ought to be economically optimal, in the sense that costs of additional adaptive actions should exactly balance the benefits of avoided climate-related losses, there is no evidence that allows us to determine how closely observed “adaptation gaps” reflect optimal investments or constrained suboptimal adaptation that should be addressed through policy.</jats:p> </jats:sec> <jats:sec> <jats:title>OUTLOOK</jats:title> <jats:p>Recent findings provide insight into the historical evolution of the global economy; they should inform how we respond to modern climatic conditions, and they can guide how we understand the consequences of future climate changes. Although climate is clearly not the only factor that affects social and economic outcomes, new quantitative measurements reveal that it is a major factor, often with first-order consequences. Research over the coming decade will seek to understand the numerous mechanisms that drive these effects, with the hope that policy may interfere with the most damaging pathways of influence.</jats:p> <jats:p>Both current and future generations will benefit from near-term investigations. “Cracking the code” on when, where, and why adaptation is or is not successful will generate major social benefits today and in the future. In addition, calculations used to design global climate change policies require as input “damage functions” that describe how social and economic losses accrue under different climatic conditions, essential elements that now can (and should) be calibrated to real-world relationships. Designing effective, efficient, and fair policies to manage anthropogenic climate change requires that we possess a quantitative grasp of how different investments today may affect economic and social possibilities in the future.</jats:p> <jats:fig fig-type="figure" orientation="portrait" position="float"> <jats:caption> <jats:title>Two globes depict two possible futures for how the climate might change and how those changes are likely to affect humanity, based on recent empirical findings.</jats:title> <jats:p>Base colors are temperature change under “Business as usual” (left, RCP 8.5) and “stringent emissions mitigation” (right, RCP 2.6). Overlaid are composite satellite images of nighttime lights with rescaled intensity reflecting changes in economic productivity in each climate scenario.</jats:p> </jats:caption> <jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" orientation="portrait" position="float" xlink:href="353_aad9837_Fa.jpeg" /> </jats:fig> </jats:sec>

<jats:sec> <jats:title>INTRODUCTION</jats:title> <jats:p> Technologies that enable the longitudinal tracking and recording of molecular events into genomic DNA would be useful for the detailed monitoring of cellular state in artificial and native contexts. Although previous systems have been used to memorize digital information such as the presence or absence of biological signals, tools for recording analog information such as the duration or magnitude of biological activity in human cells are needed. Here, we present Mammalian Synthetic Cellular Recorders Integrating Biological Events (mSCRIBE), a memory system for storing analog biological information in the form of accumulating DNA mutations in human cells. mSCRIBE leverages self-targeting guide RNAs (stgRNAs) that are engineered to direct <jats:italic>Streptococcus pyogenes</jats:italic> Cas9 cleavage against DNA loci that encode the stgRNAs, thus accumulating mutations at stgRNA loci as a record of stgRNA or Cas9 expression. </jats:p> </jats:sec> <jats:sec> <jats:title>RATIONALE</jats:title> <jats:p>The RNA-guided DNA endonuclease Cas9 introduces a double-stranded break in target DNA containing a 5′-NGG-3′ protospacer-adjacent motif (PAM) and homology to the specificity-determining sequence (SDS) of a small guide RNA (sgRNA). Once a double-strand break is introduced, the targeted DNA can be repaired via error-prone DNA repair mechanisms in human cells. We hypothesized that if a PAM sequence were introduced in the DNA locus encoding the sgRNA, the transcribed sgRNA would direct Cas9 to cleave its own encoding DNA, thus acting as a stgRNA. After error-prone repair, the mutagenized stgRNA locus should continue to be transcribed and enact additional rounds of continuous, self-targeted mutagenesis. Thus, the stgRNA locus should acquire mutations corresponding to the level of activity of the Cas9-stgRNA complex. We hypothesized that by linking the expression of stgRNA or Cas9 to biological events of interest, one could then record the duration and/or intensity of such events in the form of accumulated mutations at the stgRNA locus. The recorded information could be read by sequencing the stgRNA locus or by other related strategies.</jats:p> </jats:sec> <jats:sec> <jats:title>RESULTS</jats:title> <jats:p> We first built a stgRNA by engineering a sgRNA-encoding DNA locus to contain a 5′-NGG-3′ PAM immediately downstream of the SDS-encoding region. We then validated that the stgRNA could undergo multiple rounds of self-targeted mutagenesis by building a mutation-based toggling reporter system in which the progressive accumulation of mutations at the stgRNA locus is reported by individual cells toggling between green and red fluorescent protein expression. Next, we analyzed the sequence-evolution properties of stgRNAs in order to devise a sequence-based recording metric that conveys information on the duration and/or magnitude of stgRNA activity. We showed that computationally designed stgRNAs that contain longer SDSs of length 30, 40, and 70 nucleotides are able to accumulate mutations over longer durations of time. We demonstrated the analog nature of mSCRIBE by building a tumor necrosis factor–α (TNFα)–inducible Cas9 expression system and observing graded increases in the recording metric as a function of increasing TNFα concentration and/or duration of exposure in vitro <jats:italic>.</jats:italic> By designing doxycycline and isopropyl-β- <jats:sc>d</jats:sc> thiogalactoside-inducible stgRNA expression systems, we also showed inducible, multiplexed recording at two independent DNA loci. Last, we confirmed that human cells containing TNFα-responsive mSCRIBE units can record lipopolysaccharide (LPS)–induced acute inflammation events over time in mice. </jats:p> </jats:sec> <jats:sec> <jats:title>CONCLUSION</jats:title> <jats:p>We demonstrate that sgRNAs can be engineered to function as stgRNAs. By linking stgRNA or Cas9 expression to specific biological events of interest—such as the presence of small molecules, exposure to TNFα, or LPS-induced inflammation—we validated mSCRIBE as an analog memory device that records information about the duration and/or magnitude of biological events. Moreover, we demonstrated that multiple biological events can be simultaneously monitored by using independent stgRNA loci. We envision that this platform for genomically encoded memory in human cells should be broadly useful for studying biological systems and longitudinal and dynamic events in vitro and in situ, such as signaling pathways, gene regulatory networks, and tissue heterogeneity involved in development, healthy cell function, and disease pathogenesis.</jats:p> <jats:fig fig-type="figure" orientation="portrait" position="float"> <jats:caption> <jats:title>Continuously evolving stgRNAs.</jats:title> <jats:p>The Cas9-stgRNA complex cleaves the DNA locus from which the stgRNA is transcribed, leading to error-prone DNA repair. Multiple rounds of transcription and DNA cleavage can occur, resulting in progressive mutagenesis of the DNA encoding the stgRNA. The accumulation of mutations in the stgRNA locus provides a molecular record of cellular events that regulate stgRNA or Cas9 expression.</jats:p> </jats:caption> <jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" orientation="portrait" position="float" xlink:href="353_aag0511_fa.jpeg" /> </jats:fig> </jats:sec>

<jats:sec> <jats:title>INTRODUCTION</jats:title> <jats:p>Embryonic development and tissue homeostasis depend on cooperation between specialized cell types. Resident macrophages are professional phagocytes that survey their surroundings; eliminate unfit cells, microorganisms, and metabolic waste; and produce a large range of bioactive molecules and growth factors. Resident macrophages also serve tissue-specific purposes: For example, microglia in the central nervous system support neuronal circuit development, Kupffer cells scavenge blood particles and dying red blood cells in the liver, and alveolar macrophages uptake surfactant and remove airborne pollutants and microbes from the airways. Resident macrophage diversity in adult mice is reflected in tissue-specific gene expression profiles, which may be due to responses to specific cues from their microenvironment, different developmental processes, and the contribution of distinct progenitors cell types. Altogether, the mechanisms responsible for the generation of tissue-resident macrophage diversity remain unclear.</jats:p> </jats:sec> <jats:sec> <jats:title>RATIONALE</jats:title> <jats:p> Tissue-resident macrophages originate, at least in part, from mesodermal erythro-myeloid progenitors (EMPs) from the yolk sac, which invade the embryo proper at the onset of organogenesis. These tissue-resident macrophages are also self-maintained in postnatal tissues, independently of definitive hematopoietic stem cells (HSCs) in a steady state. We therefore hypothesized that resident macrophages represent a founding cell type within most organ <jats:italic /> anlagen. In this model, the generation of macrophage diversity, as observed in the tissues of postnatal mice, may be integral to organogenesis. </jats:p> </jats:sec> <jats:sec> <jats:title>RESULTS</jats:title> <jats:p> To test this hypothesis and explore the molecular basis of macrophage diversity in mammals, we performed a spatiotemporal analysis of macrophage development in mice, from embryonic day 9 (E9) to 3 weeks after birth. Unbiased single-cell RNA sequencing (RNA-seq) analysis of CD45 <jats:sup>+</jats:sup> cells, combined with RNA-seq analyses of sorted cell populations, genetic fate mapping, and in situ analyses, revealed that EMPs give rise to a population of premacrophages (pMacs) that colonize the whole embryo from E9.5, as they acquire a core macrophage differentiation program that includes pattern recognition, scavengers, and cytokine receptors. The chemokine receptor <jats:italic>Cx3cr1</jats:italic> is up-regulated in pMacs and is important for embryo colonization, which is delayed in <jats:italic>Cx3cr1</jats:italic> -deficient embryos. Fate mapping of pMacs using a <jats:italic>Tnfrsf11a</jats:italic> –Cre reporter labels homogeneously fetal and adult tissue-resident macrophages but not HSCs and their progeny. Transcriptional regulators that identify postnatal tissue-resident macrophages in the brain, liver, kidney, skin, and lung were specifically up-regulated immediately after colonization. These dynamic changes mark the onset of diversification into adult macrophages. We identified <jats:italic>Id3</jats:italic> as a Kupffer cell–specific transcriptional regulator. Deletion of <jats:italic>Id3</jats:italic> in pMacs resulted in Kupffer cell deficiency but did not affect development of microglia and kidney macrophages. </jats:p> </jats:sec> <jats:sec> <jats:title>CONCLUSION</jats:title> <jats:p>Our study shows that EMP-derived precursors colonize embryonic tissues and simultaneously acquire a full core macrophage program. This is followed by their diversification into tissue-specific macrophages during organogenesis, likely via the expression of distinct sets of transcriptional regulators. These results indicate that differentiation of tissue-resident macrophages is an integral part of organogenesis and identify a spatiotemporal molecular road map for the generation of macrophage diversity in vivo. Our findings provide a conceptual framework to analyze and understand the consequence(s) of genetic variation for macrophage contribution to development, homeostasis, and disease pathogenesis in different tissues and will support efforts to differentiate specialized macrophages in vitro.</jats:p> </jats:sec>

<jats:p>The emergence of Zika in the Americas is a stark reminder of how quickly public health challenges of infectious diseases can change. The need for a safe and effective vaccine is immediate. Yet, like the Ebola epidemic 2 years ago, we find ourselves without a vaccine to combat this latest threat. When surveillance points to a possible emergence of a new infectious disease of potential public health importance, we need procedural and funding mechanisms that can quickly identify candidate vaccines and drive research and development toward licensure and production. Even if such a vaccine is not yet licensed, having it ready for immediate large trials when a regional crisis occurs will be a major advantage over our current reactive system.</jats:p>

<jats:p>A roundup of weekly science policy and related news.</jats:p>