ALBERT

Description: A new study suggests that common settings used in software for analyzing brain scans may lead to false positive results. Researchers led by Anders Eklund, an electrical engineer at Linköping University in Sweden, analyzed functional magnetic resonance imaging (fMRI) data from several public databases. Certain software settings, the team found, could give rise to a false positive result up to 70% of the time. In the context of a typical fMRI experiment, that could lead researchers to wrongly conclude that activity in a certain area of the brain plays a role in a cognitive function such as perception or memory. Author: Greg Miller

Description: Author: Stella M. Hurtley

Description: The vast majority of genes in sexually reproducing eukaryotes can recombine during the production of gametes. This reshuffling generates new genotypes that may provide selective advantages. However, reshuffling does not occur among the few genes in the genomes of cytoplasmic organelles (chloroplasts and mitochondria). Instead, these organelles are almost always transmitted through maternal inheritance (1). Why is this phenomenon widespread and how is it achieved? On page 394 of this issue, Zhou et al. (2) solve part of this puzzle by identifying the enzyme that degrades sperm mitochondrial DNA after fertilization. Author: Alexander M. van der Bliek

Description: Mutualistic symbiotic relationships are those in which both species benefit; for example, the vivid colors of coral reefs come from symbiotic algae that provide their living coral hosts with nutrients and oxygen through photosynthesis in exchange for protection. A similar mutualistic relationship exists between gut-dwelling bacteria and their animal hosts (1). It remains unclear, however, to what degree symbiosis has shaped host-microbial interactions and coevolution. On page 380 of this issue, Moeller et al. show that gut bacterial strains cospeciated with hominids (apes and humans) over the past 15 million years (2). These findings set the stage for exploring the evolutionary processes that underlie the symbiotic relationship between hominids and their gut-dwelling microbes. Authors: Julia A. Segre, Nick Salafsky

Description: Author: Caroline Ash

Description: Author: Laura M. Zahn

Description: Several unprecedented videos of gelatinous sea creatures called comb jellies, or ctenophores, now threaten to upend the standard view of the evolution of the so-called through-gut. Comb jellies, jellyfish, sea sponges, and a few other creatures all were thought to lack an anus, which meant they had to eat and defecate through a single hole. These are descendants of some of the first animals to arise, so it has been thought that the through-gut and anus were an innovation that came after those lineages emerged—and perhaps something that drove the diversity of new animal forms. But on 15 March, at the Ctenopolooza meeting in St. Augustine, Florida, evolutionary biologist William Browne of the University of Miami in Florida debuted films of comb jellies pooping—and it wasn't through their mouths. Browne's videos elicited gasps from the audience, who is now rethinking when the through-gut first evolved—and whether it may have emerged more than once. Author: Amy Maxmen

Description: As you navigate a landscape, certain neurons in the brain fire at multiple locations, marking out a hexagonal grid on a mental map. The discovery of these so-called grid cells, and their role as a neuronal GPS for spatial navigation, won the 2014 Nobel Prize in Physiology or Medicine for Norwegian scientists Edvard Moser and May-Britt Moser. Now, it seems that the brain may make maps of abstract realms, too. On p. 1464, a team at the University of Oxford provides evidence that gridlike neuronal activity throughout the brain helps people organize nonnavigation knowledge—for the purposes of the new study, differences in body shape between various types of birds. Author: Emily Underwood

Description: "This missing science of heredity … is, in simple truth, ten times more important to humanity than all the chemistry and physics, all the technical and industrial science that ever has been or ever will be discovered," wrote H. G. Wells in 1903. Having dedicated more than 500 pages to the topic in his new book, The Gene, Siddhartha Mukherjee would seem to agree. The book examines human genetics, from its philosophical roots in the work of Aristotle, through Gregor Mendel's garden and Thomas Hunt Morgan's work on fruitflies, and including active work in genome editing. Author: Michael A. Goldman

Description: Author: Wei Wong

Description: For years, scientists have debated where dogs came from. Did wolves first forge their special relationship with humans in Europe, or in Asia? The answer, according to a new study, is yes. Researchers report that genetic analysis of hundreds of canines—including a nearly 5000-year-old dog unearthed on the east coast of Ireland—reveals that dogs may have been domesticated twice, once in Asia and once in Europe or the Near East, although European ancestry has mostly vanished from today's dogs. The findings could resolve a rift that has roiled the canine origins community—but experts say a lot more work needs to be done to confirm them. Author: David Grimm

Description: Author: Peter Stern

Description: Author: Leslie K. Ferrarelli

Description: One of the greatest symbols of the birth of evolutionary biology is Darwin's first sketch of an evolutionary tree, above which he wrote: “I think.” Not only are evolutionary trees central to how scientists conceptualize evolutionary processes, Darwin's words also capture a key aspect of evolutionary science: It is difficult to observe, forcing researchers to rely heavily on inference. In recent decades, studies of fast-growing microorganisms have allowed hypotheses about evolutionary processes to be tested experimentally (1). On page 1147 of this issue, Baym et al. (2) report a device for visualizing evolutionary branching as bacteria grow across a meter-scale agar slab. The results offer important insights into evolutionary dynamics in spatially extended systems. Authors: Luke McNally, Sam P. Brown

Description: The specter of neurodegenerative disease, particularly Alzheimer's disease, haunts the developed world and exacts a poorly documented toll on underdeveloped countries. With so little progress made toward finding a cure—or, better, a prevention—it is time to rethink the path to progress. This requires a change in perspective on the type of research that will make a difference. The lesson learned from cancer research is that a new commitment means rethinking the fundamental approach to the disease. Cancer research moved from taking potshots with, usually, cytotoxic drugs to a bottom-up, mechanism-based approach in which newly acquired genetic knowledge played the largest role. Today, that effort has produced a platform of knowledge from which academia and industry are drawing. For neurodegenerative disease, the genetic approach remains valid but the problem must concurrently be approached from a complementary, robust cell biological perspective, focusing on the cellular cascade of events that lead to neuronal cell death. Authors: K. S. Kosik, T. J. Sejnowski, M. E. Raichle, A. Ciechanover, D. Baltimore

Description: Temporal lobe epilepsy (TLE) is characterized by debilitating, recurring seizures and an increased risk for cognitive deficits. Mossy cells (MCs) are key neurons in the hippocampal excitatory circuit, and the partial loss of MCs is a major hallmark of TLE. We investigated how MCs contribute to spontaneous ictal activity and to spatial contextual memory in a mouse model of TLE with hippocampal sclerosis, using a combination of optogenetic, electrophysiological, and behavioral approaches. In chronically epileptic mice, real-time optogenetic modulation of MCs during spontaneous hippocampal seizures controlled the progression of activity from an electrographic to convulsive seizure. Decreased MC activity is sufficient to impede encoding of spatial context, recapitulating observed cognitive deficits in chronically epileptic mice.

Description: Mammals diversified by colonizing drastically different environments, with each transition yielding numerous molecular changes, including losses of protein function. Though not initially deleterious, these losses could subsequently carry deleterious pleiotropic consequences. We have used phylogenetic methods to identify convergent functional losses across independent marine mammal lineages. In one extreme case, Paraoxonase 1 ( PON1 ) accrued lesions in all marine lineages, while remaining intact in all terrestrial mammals. These lesions coincide with PON1 enzymatic activity loss in marine species’ blood plasma. This convergent loss is likely explained by parallel shifts in marine ancestors’ lipid metabolism and/or bloodstream oxidative environment affecting PON1’s role in fatty acid oxidation. PON1 loss also eliminates marine mammals’ main defense against neurotoxicity from specific man-made organophosphorus compounds, implying potential risks in modern environments.

Description: The turbulent surfaces of rivers and streams are natural hotspots of biogeochemical exchange with the atmosphere. At the global scale, the total river-atmosphere flux of trace gasses such as carbon dioxide depends on the proportion of Earth’s surface that is covered by the fluvial network, yet the total surface area of rivers and streams is poorly constrained. We used a global database of planform river hydromorphology and a statistical approach to show that global river and stream surface area at mean annual discharge is 773,000 ± 79,000 square kilometers (0.58 ± 0.06%) of Earth’s nonglaciated land surface, an area 44 ± 15% larger than previous spatial estimates. We found that rivers and streams likely play a greater role in controlling land-atmosphere fluxes than is currently represented in global carbon budgets.

Description: Developmental enhancers mediate on/off patterns of gene expression in specific cell types at particular stages during metazoan embryogenesis. They typically integrate multiple signals and regulatory determinants to achieve precise spatiotemporal expression. Such enhancers can map quite far—one megabase or more—from the genes they regulate. How remote enhancers relay regulatory information to their target promoters is one of the central mysteries of genome organization and function. A variety of contrasting mechanisms have been proposed over the years, including enhancer tracking, linking, looping, and mobilization to transcription factories. We argue that extreme versions of these mechanisms cannot account for the transcriptional dynamics and precision seen in living cells, tissues, and embryos. We describe emerging evidence for dynamic three-dimensional hubs that combine different elements of the classical models.

Description: The classical model of cytosine DNA methylation (the presence of 5-methylcytosine, 5mC) regulation depicts this covalent modification as a stable repressive regulator of promoter activity. However, whole-genome analysis of 5mC reveals widespread tissue- and cell type–specific patterns and pervasive dynamics during mammalian development. Here we review recent findings that delineate 5mC functions in developmental stages and diverse genomic compartments as well as discuss the molecular mechanisms that connect transcriptional regulation and 5mC. Beyond the newly appreciated dynamics, regulatory roles for 5mC have been suggested in new biological contexts, such as learning and memory or aging. The use of new single-cell measurement techniques and precise editing tools will enable functional analyses of 5mC in gene expression, clarifying its role in various biological processes.

Description: Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays survey only one aspect of cellular biology. Here we describe sci-CAR, a combinatorial indexing–based coassay that jointly profiles chromatin accessibility and mRNA (CAR) in each of thousands of single cells. As a proof of concept, we apply sci-CAR to 4825 cells, including a time series of dexamethasone treatment, as well as to 11,296 cells from the adult mouse kidney. With the resulting data, we compare the pseudotemporal dynamics of chromatin accessibility and gene expression, reconstruct the chromatin accessibility profiles of cell types defined by RNA profiles, and link cis-regulatory sites to their target genes on the basis of the covariance of chromatin accessibility and transcription across large numbers of single cells.

Description: Glia constitute roughly half of the cells of the central nervous system (CNS) but were long-considered to be static bystanders to its formation and function. Here we provide an overview of how the diverse and dynamic functions of glial cells orchestrate essentially all aspects of nervous system formation and function. Radial glia, astrocytes, oligodendrocyte progenitor cells, oligodendrocytes, and microglia each influence nervous system development, from neuronal birth, migration, axon specification, and growth through circuit assembly and synaptogenesis. As neural circuits mature, distinct glia fulfill key roles in synaptic communication, plasticity, homeostasis, and network-level activity through dynamic monitoring and alteration of CNS structure and function. Continued elucidation of glial cell biology, and the dynamic interactions of neurons and glia, will enrich our understanding of nervous system formation, health, and function.

Description: To understand how neurons assemble to form functional circuits, it is necessary to obtain a detailed knowledge of their diversity and to define the developmental specification programs that give rise to this diversity. Invertebrates and vertebrates appear to share common developmental principles of neuronal specification in which cascades of transcription factors temporally pattern progenitors, while spatial cues modify the outcomes of this temporal patterning. Here, we highlight these conserved mechanisms and describe how they are used in distinct neural structures. We present the questions that remain for a better understanding of neuronal specification. Single-cell RNA profiling approaches will potentially shed light on these questions, allowing not only the characterization of neuronal diversity in adult brains, but also the investigation of the developmental trajectories leading to the generation and maintenance of this diversity.

Description: Which memories are retained, where, and in what form depends on a long afterlife of the acquired information in the brain. Initial steps of consolidation may be completed within a few hours during wakefulness, but other forms of postacquisition processing take longer, extending into sleep (1, 2). The relationship between brain activity during sleep and memory consolidation remains controversial and poorly understood. On page 812 of this issue, Boyce et al. (3) demonstrate that a distinct form of hippocampal neural activity, called theta oscillation, is critical for memory formation during the rapid eye movement (REM) phase of sleep. Author: Bernat Kocsis

Description: Last week, at the Sixth Annual Traumatic Brain Injury Conference in Arlington, Virginia, neurologist Samuel Gandy presented a former National Football League player's positron emission tomography (PET) scan as the "most dramatic" evidence yet of chronic traumatic encephalopathy (CTE) in a living person. "I've never seen anything like it," he said of the scan, which used a PET tracer called T807 to reveal deposits of a sticky, helical protein called tau in the player's brain. The announcement could represent a milestone for tau imaging, a promising but controversial strategy for diagnosing neurodegenerative diseases such as Alzheimer's in living patients. If the science pans out, it could also transform the medical and legal status of CTE, which at present can only be officially diagnosed after death, when a pathologist looks for tau in brain tissue. Author: Emily Underwood

Description: Earlier this month, György Buzsáki of New York University in New York City showed a slide that sent a murmur through an audience in the Grand Ballroom of New York's Midtown Hilton during the annual meeting of the Cognitive Neuroscience Society. It wasn't just the grisly image of a human cadaver with more than 200 electrodes inserted into its brain that set people whispering; it was what those electrodes detected—or rather, what they failed to detect. When Buzsáki and his colleague, Antal Berényi of the University of Szeged in Hungary, mimicked an increasingly popular form of brain stimulation by applying alternating electrical current to the outside of the cadaver's skull, the electrodes inside registered little. Hardly any current entered the brain. On closer study, the pair discovered that up to 90% of the current had been redirected by the skin covering the skull, which acted as a "shunt," Buzsáki said. For many meeting attendees, the unusual study heightened serious doubts about the mechanism and effectiveness of transcranial direct current stimulation, an experimental, noninvasive treatment that uses electrodes to deliver weak current to a person's scalp or forehead. Author: Emily Underwood

Description: Author: Leslie K. Ferrarelli

Description: The field of molecular evolution is concerned with evolutionary changes in genes and genomes and the underlying driving forces behind those changes. Current studies in molecular evolution are almost entirely retrospective, with a focus on the mutations that were fixed during evolution, and the conclusions are often explanatory, offering no predictive insights. Because only a tiny fraction of all mutations that have ever occurred during evolution have been fixed, the “successes” that we see today provide an incomplete or even biased understanding of the evolutionary process. One way to circumvent this problem is to obtain the whole fitness landscape of a gene to understand, prospectively, chance and necessity in evolution (see the figure). Two studies in this issue, by Li et al. on page 837 (1) and Puchta et al. on page 840 (2), each take on this challenge by characterizing the in vivo fitness landscape of two RNA genes. Authors: Xionglei He, Li Liu

Description: The worldwide human obesity epidemic has provoked a great deal of experimentation to understand the biological controls of energy expenditure and food intake, two processes that together determine energy balance. Because food intake relies on feeding behavior that is determined by the brain, studies have focused on how the central nervous system receives and behaviorally responds to signals of metabolic status. On page 1293 of this issue, Lagerlöf et al. (1) report that a glycosylation enzyme serves as a neuronal nutrient sensor that is critical in the control of food intake and body weight. Author: Gary J. Schwartz

Description: Author: Sacha Vignieri

Description: Changes in gene regulatory networks (GRNs) underlie many phenotypic differences between species. However, the mechanisms of GRN evolution are still being debated (1–5). Explaining how GRNs originate, diversify, and maintain their identities despite regulatory element turnover is essential for developing mechanistic explanations for the origin, diversification, and conservation of homologous characters between species. Among the major outstanding questions in GRN evolution is whether individual cis-regulatory elements arise de novo through the gradual accumulation of mutations that increase the regulatory potential of existing DNA or whether cis-regulatory elements originate more rapidly through concerted processes. On page 1083 of this issue, Chuong et al. provide evidence that concerted processes, involving endogenous retroviruses (ERVs), which are remarkably abundant in mammalian genomes, have contributed to the evolution of the regulatory systems that control the mammalian immune system (6). Author: Vincent J. Lynch

Description: Contrary to classical economic supposition (1), understanding people's preferences and decisions is not as simple as observing their actions. Indeed, there are many reasons for behaving altruistically, such as being moved by someone's suffering (empathy) or feeling obliged to return a favor (reciprocity) (2, 3). One of the major challenges for social psychologists and neuroscientists is to characterize the different motives underlying our interactions with other people. On page 1074 in this issue, Hein et al. (4) show that knowing how distinct areas in the human brain communicate with each other can tell us why someone behaves altruistically. Authors: Sebastian Gluth, Laura Fontanesi

Description: For many evolutionary biologists, nothing gets their dander up faster than suggesting evolution is anything other than the process of natural selection, acting on random mutations. So some are uneasy that the John Templeton Foundation has awarded $8.7 million to U.K., Swedish, and U.S. researchers for experimental and theoretical work intended to put a revisionist view of evolution, the so-called extended evolutionary synthesis, on a sounder footing. Using a variety of plants, animals, and microbes, the researchers will study the possibility that organisms can influence their own evolution and that inheritance can take place through routes other than the genetic material. Critics are against evolutionary biologists accepting this money and argue that evolutionary theory already embraces the best of these ideas. But others are pleased as the money should help clarify the importance of different aspects of the extended synthesis. Author: Elizabeth Pennisi

Description: Brain electrical activity differs markedly between wakefulness and sleep. Concomitant shifts in the ion composition of brain extracellular fluids were thought to be a consequence rather than a cause of the sleep-wake–dependent changes in neuronal activity. On page 550 of this issue, Ding et al. (1) report the surprising observation that ionic changes in the extracellular fluid are a potent control of sleep-wake–dependent neuronal activity. Authors: Hans-Peter Landolt, Sebastian C. Holst

Description: Neuroscience is becoming big science, with the 2013 launches of the European Union's Human Brain Project and the United States's Brain Research through Advancing Innovative Neurotechnology (BRAIN) initiative leading the way. Last week, leaders of these massive, multi-institution projects and others around the world met at Johns Hopkins University in Baltimore, Maryland, to discuss an even loftier goal: a global neuroscience collaboration that would link their efforts and rival big science investments in astronomy and physics. More than 60 neuroscientists from 12 countries pitched diverse visions for such a project at the meeting, sponsored by the Kavli Foundation and the National Science Foundation. Author: Emily Underwood

Description: Clinical observations indicate that the paramedian region of the thalamus is a critical node for controlling wakefulness. However, the specific nucleus and neural circuitry for this function remain unknown. Using in vivo fiber photometry or multichannel electrophysiological recordings in mice, we found that glutamatergic neurons of the paraventricular thalamus (PVT) exhibited high activities during wakefulness. Suppression of PVT neuronal activity caused a reduction in wakefulness, whereas activation of PVT neurons induced a transition from sleep to wakefulness and an acceleration of emergence from general anesthesia. Moreover, our findings indicate that the PVT–nucleus accumbens projections and hypocretin neurons in the lateral hypothalamus to PVT glutamatergic neurons’ projections are the effector pathways for wakefulness control. These results demonstrate that the PVT is a key wakefulness-controlling nucleus in the thalamus.

Description: The salience of behaviorally relevant stimuli is dynamic and influenced by internal state and external environment. Monitoring such changes is critical for effective learning and flexible behavior, but the neuronal substrate for tracking the dynamics of stimulus salience is obscure. We found that neurons in the paraventricular thalamus (PVT) are robustly activated by a variety of behaviorally relevant events, including novel ("unfamiliar") stimuli, reinforcing stimuli and their predicting cues, as well as omission of the expected reward. PVT responses are scaled with stimulus intensity and modulated by changes in homeostatic state or behavioral context. Inhibition of the PVT responses suppresses appetitive or aversive associative learning and reward extinction. Our findings demonstrate that the PVT gates associative learning by providing a dynamic representation of stimulus salience.

Description: The color patterns of African cichlid fishes provide notable examples of phenotypic convergence. Across the more than 1200 East African rift lake species, melanic horizontal stripes have evolved numerous times. We discovered that regulatory changes of the gene agouti-related peptide 2 ( agrp2 ) act as molecular switches controlling this evolutionarily labile phenotype. Reduced agrp2 expression is convergently associated with the presence of stripe patterns across species flocks. However, cis-regulatory mutations are not predictive of stripes across radiations, suggesting independent regulatory mechanisms. Genetic mapping confirms the link between the agrp2 locus and stripe patterns. The crucial role of agrp2 is further supported by a CRISPR-Cas9 knockout that reconstitutes stripes in a nonstriped cichlid. Thus, we unveil how a single gene affects the convergent evolution of a complex color pattern.

Description: Animals constantly update their body posture to meet behavioral demands, but little is known about the neural signals on which this depends. We therefore tracked freely foraging rats in three dimensions while recording from the posterior parietal cortex (PPC) and the frontal motor cortex (M2), areas critical for movement planning and navigation. Both regions showed strong tuning to posture of the head, neck, and back, but signals for movement were much less dominant. Head and back representations were organized topographically across the PPC and M2, and more neurons represented postures that occurred less often. Simultaneous recordings across areas were sufficiently robust to decode ongoing behavior and showed that spiking in the PPC tended to precede that in M2. Both the PPC and M2 strongly represent posture by using a spatially organized, energetically efficient population code.

Description: Memory resides in engram cells distributed across the brain. However, the site-specific substrate within these engram cells remains theoretical, even though it is generally accepted that synaptic plasticity encodes memories. We developed the dual-eGRASP (green fluorescent protein reconstitution across synaptic partners) technique to examine synapses between engram cells to identify the specific neuronal site for memory storage. We found an increased number and size of spines on CA1 engram cells receiving input from CA3 engram cells. In contextual fear conditioning, this enhanced connectivity between engram cells encoded memory strength. CA3 engram to CA1 engram projections strongly occluded long-term potentiation. These results indicate that enhanced structural and functional connectivity between engram cells across two directly connected brain regions forms the synaptic correlate for memory formation.

Description: Consumer genomics databases have reached the scale of millions of individuals. Recently, law enforcement authorities have exploited some of these databases to identify suspects via distant familial relatives. Using genomic data of 1.28 million individuals tested with consumer genomics, we investigated the power of this technique. We project that about 60% of the searches for individuals of European descent will result in a third-cousin or closer match, which theoretically allows their identification using demographic identifiers. Moreover, the technique could implicate nearly any U.S. individual of European descent in the near future. We demonstrate that the technique can also identify research participants of a public sequencing project. On the basis of these results, we propose a potential mitigation strategy and policy implications for human subject research.

Description: Consolidation of spatial and episodic memories is thought to rely on replay of neuronal activity sequences during sleep. However, the network dynamics underlying the initial storage of memories during wakefulness have never been tested. Although slow, behavioral time scale sequences have been claimed to sustain sequential memory formation, fast ("theta") time scale sequences, nested within slow sequences, could be instrumental. We found that in rats traveling passively on a model train, place cells formed behavioral time scale sequences but theta sequences were degraded, resulting in impaired subsequent sleep replay. In contrast, when the rats actively ran on a treadmill while being transported on the train, place cells generated clear theta sequences and accurate trajectory replay during sleep. Our results support the view that nested sequences underlie the initial formation of memory traces subsequently consolidated during sleep.

Description: Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.

Description: Whether fear attenuation is mediated by inhibition of the original memory trace of fear with a new memory trace of safety or by updating of the original fear trace toward safety has been a long-standing question in neuroscience and psychology alike. In particular, which of the two scenarios underlies the attenuation of remote (month-old) fear memories is completely unknown, despite the impetus to better understand this process against the backdrop of enduring traumata. We found—chemogenetically and in an engram-specific manner—that effective remote fear attenuation is accompanied by the reactivation of memory recall–induced neurons in the dentate gyrus and that the continued activity of these neurons is critical for fear reduction. This suggests that the original memory trace of fear actively contributes to remote fear attenuation.

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bernstein, Rachel -- New York, N.Y. -- Science. 2015 Jun 26;348(6242):1506. doi: 10.1126/science.348.6242.1506.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rachel Bernstein is a staff writer for Science Careers. For more on life and careers, visit ScienceCareers.org. Send your story to SciCareerEditor@aaas.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26113726" target="_blank"〉PubMed〈/a〉

Description: Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated before biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from more than 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cusanovich, Darren A -- Daza, Riza -- Adey, Andrew -- Pliner, Hannah A -- Christiansen, Lena -- Gunderson, Kevin L -- Steemers, Frank J -- Trapnell, Cole -- Shendure, Jay -- 1DP1HG007811/DP/NCCDPHP CDC HHS/ -- New York, N.Y. -- Science. 2015 May 22;348(6237):910-4. doi: 10.1126/science.aab1601. Epub 2015 May 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Genome Sciences, Seattle, WA, USA. ; Oregon Health and Science University, Department of Molecular and Medical Genetics, Portland, OR, USA. ; Illumina, Inc., Advanced Research Group, San Diego, CA, USA. ; University of Washington, Department of Genome Sciences, Seattle, WA, USA. shendure@uw.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25953818" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kloor, Keith -- New York, N.Y. -- Science. 2015 Feb 13;347(6223):699. doi: 10.1126/science.347.6223.699.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25678635" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reczek, Colleen R -- Chandel, Navdeep S -- New York, N.Y. -- Science. 2015 Dec 11;350(6266):1317-8. doi: 10.1126/science.aad8671.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine and Robert H. Lurie Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. ; Department of Medicine and Robert H. Lurie Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. nav@northwestern.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26659042" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kloosterman, Wigard P -- New York, N.Y. -- Science. 2015 Jun 12;348(6240):1205-6. doi: 10.1126/science.aac5277.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584CG Utrecht, Netherlands. w.kloosterman@umcutrecht.nl.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26068832" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bernstein, Rachel -- New York, N.Y. -- Science. 2015 Apr 17;348(6232):269. doi: 10.1126/science.348.6232.269.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25883332" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, Justin -- New York, N.Y. -- Science. 2015 Jan 2;347(6217):34-5. doi: 10.1126/science.1261627.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉HarvardX, Harvard University, Cambridge, MA 02476, USA. justin_reich@harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25554779" target="_blank"〉PubMed〈/a〉

Description: Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with 〉40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing 〉35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that 〉73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sunagawa, Shinichi -- Coelho, Luis Pedro -- Chaffron, Samuel -- Kultima, Jens Roat -- Labadie, Karine -- Salazar, Guillem -- Djahanschiri, Bardya -- Zeller, Georg -- Mende, Daniel R -- Alberti, Adriana -- Cornejo-Castillo, Francisco M -- Costea, Paul I -- Cruaud, Corinne -- d'Ovidio, Francesco -- Engelen, Stefan -- Ferrera, Isabel -- Gasol, Josep M -- Guidi, Lionel -- Hildebrand, Falk -- Kokoszka, Florian -- Lepoivre, Cyrille -- Lima-Mendez, Gipsi -- Poulain, Julie -- Poulos, Bonnie T -- Royo-Llonch, Marta -- Sarmento, Hugo -- Vieira-Silva, Sara -- Dimier, Celine -- Picheral, Marc -- Searson, Sarah -- Kandels-Lewis, Stefanie -- Tara Oceans coordinators -- Bowler, Chris -- de Vargas, Colomban -- Gorsky, Gabriel -- Grimsley, Nigel -- Hingamp, Pascal -- Iudicone, Daniele -- Jaillon, Olivier -- Not, Fabrice -- Ogata, Hiroyuki -- Pesant, Stephane -- Speich, Sabrina -- Stemmann, Lars -- Sullivan, Matthew B -- Weissenbach, Jean -- Wincker, Patrick -- Karsenti, Eric -- Raes, Jeroen -- Acinas, Silvia G -- Bork, Peer -- New York, N.Y. -- Science. 2015 May 22;348(6237):1261359. doi: 10.1126/science.1261359.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. ; CEA-Institut de Genomique, GENOSCOPE, 2 rue Gaston Cremieux, 91057 Evry, France. ; Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Maritim de la Barceloneta, 37-49, Barcelona E08003, Spain. ; Sorbonne Universites, UPMC, Universite Paris 06, CNRS-IRD-MNHN, LOCEAN Laboratory, 4 Place Jussieu, 75005 Paris France. ; CNRS, UMR 7093, Laboratoire d'Oceanographie de Villefranche-sur-Mer, Observatoire Oceanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universites, UPMC Universite Paris 06, UMR 7093, LOV, Observatoire Oceanologique, F-06230 Villefranche-sur-mer, France. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Laboratoire de Physique des Oceans UBO-IUEM, Place Copernic 29820 Plouzane, France. ; Aix Marseille Universite CNRS IGS UMR 7256, 13288 Marseille, France. ; Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA. ; Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Maritim de la Barceloneta, 37-49, Barcelona E08003, Spain. Department of Hydrobiology, Federal University of Sao Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 Sao Carlos, Sao Paulo, Brazil. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, UPMC Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. ; CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, UPMC Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; CNRS UMR 7232, BIOM, Avenue du Fontaule, 66650 Banyuls-sur-Mer, France. Sorbonne Universites Paris 06, OOB UPMC, Avenue du Fontaule, 66650 Banyuls-sur-Mer, France. ; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy. ; CEA-Institut de Genomique, GENOSCOPE, 2 rue Gaston Cremieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. ; Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-001, Japan. ; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany. ; Department of Geosciences, Laboratoire de Meteorologie Dynamique (LMD), Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Oceans UBO-IUEM, Place Copernic, 29820 Plouzane, France. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de. ; Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de. ; Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Maritim de la Barceloneta, 37-49, Barcelona E08003, Spain. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbruck-Centre for Molecular Medicine, 13092 Berlin, Germany. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25999513" target="_blank"〉PubMed〈/a〉

Description: Jan et al. (Research Articles, 7 November 2014, p. 716) propose that ribosomes translating secretome messenger RNAs (mRNAs) traffic from the cytosol to the endoplasmic reticulum (ER) upon emergence of the signal peptide and return to the cytosol after termination. An accounting of controls demonstrates that mRNAs initiate translation on ER-bound ribosomes and that ribosomes are retained on the ER through many cycles of translation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reid, David W -- Nicchitta, Christopher V -- GM101533/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Jun 12;348(6240):1217. doi: 10.1126/science.aaa7257. Epub 2015 Jun 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Cardiovascular and Metabolic Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore. ; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA. christopher.nicchitta@duke.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26068841" target="_blank"〉PubMed〈/a〉

Description: According to the disease module hypothesis, the cellular components associated with a disease segregate in the same neighborhood of the human interactome, the map of biologically relevant molecular interactions. Yet, given the incompleteness of the interactome and the limited knowledge of disease-associated genes, it is not obvious if the available data have sufficient coverage to map out modules associated with each disease. Here we derive mathematical conditions for the identifiability of disease modules and show that the network-based location of each disease module determines its pathobiological relationship to other diseases. For example, diseases with overlapping network modules show significant coexpression patterns, symptom similarity, and comorbidity, whereas diseases residing in separated network neighborhoods are phenotypically distinct. These tools represent an interactome-based platform to predict molecular commonalities between phenotypically related diseases, even if they do not share primary disease genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435741/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435741/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Menche, Jorg -- Sharma, Amitabh -- Kitsak, Maksim -- Ghiassian, Susan Dina -- Vidal, Marc -- Loscalzo, Joseph -- Barabasi, Albert-Laszlo -- P01-HL083069/HL/NHLBI NIH HHS/ -- P50 HG004233/HG/NHGRI NIH HHS/ -- P50-HG004233/HG/NHGRI NIH HHS/ -- R37 HL061795/HL/NHLBI NIH HHS/ -- R37-HL061795/HL/NHLBI NIH HHS/ -- RC2-HL101543/HL/NHLBI NIH HHS/ -- U01 HG001715/HG/NHGRI NIH HHS/ -- U01 HG007690/HG/NHGRI NIH HHS/ -- U01 HL108630/HL/NHLBI NIH HHS/ -- U01-HG001715/HG/NHGRI NIH HHS/ -- U01-HG007690/HG/NHGRI NIH HHS/ -- U01-HL108630/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2015 Feb 20;347(6224):1257601. doi: 10.1126/science.1257601.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Complex Networks Research and Department of Physics, Northeastern University, 110 Forsyth Street, 111 Dana Research Center, Boston, MA 02115, USA. Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. Center for Network Science, Central European University, Nador u. 9, 1051 Budapest, Hungary. ; Center for Complex Networks Research and Department of Physics, Northeastern University, 110 Forsyth Street, 111 Dana Research Center, Boston, MA 02115, USA. Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. ; Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. ; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA. ; Center for Complex Networks Research and Department of Physics, Northeastern University, 110 Forsyth Street, 111 Dana Research Center, Boston, MA 02115, USA. Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. Center for Network Science, Central European University, Nador u. 9, 1051 Budapest, Hungary. Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA. alb@neu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25700523" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sundquist, Wesley I -- Ullman, Katharine S -- P50 GM082545/GM/NIGMS NIH HHS/ -- R01 AI051174/AI/NIAID NIH HHS/ -- R01 GM112080/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Jun 19;348(6241):1314-5. doi: 10.1126/science.aac7083.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA. wes@biochem.utah.edu katharine.ullman@hci.utah.edu. ; Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5650, USA. wes@biochem.utah.edu katharine.ullman@hci.utah.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26089496" target="_blank"〉PubMed〈/a〉