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Impact of the human circadian system, exercise, and their interaction on cardiovascular function

Scheer, Frank A. J. L.; Hu, Kun; Evoniuk, Heather; Kelly, Erin E.; Malhotra, Atul; Hilton, Michael F.; Shea, Steven A.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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The risk of adverse cardiovascular events peaks in the morning (≈9:00 AM) with a secondary peak in the evening (≈8:00 PM) and a trough at night. This pattern is generally believed to be caused by the day/night distribution of behavioral triggers, but it is unknown whether the endogenous circadian system contributes to these daily fluctuations. Thus, we tested the hypotheses that the circadian system modulates autonomic, hemodynamic, and hemostatic risk markers at rest, and that behavioral stressors have different effects when they occur at different internal circadian phases. Twelve healthy adults were each studied in a 240-h forced desynchrony protocol in dim light while standardized rest and exercise periods were uniformly distributed across the circadian cycle. At rest, there were large circadian variations in plasma cortisol (peak-to-trough ≈85% of mean, peaking at a circadian phase corresponding to ≈9:00 AM) and in circulating catecholamines (epinephrine, ≈70%; norepinephrine, ≈35%, peaking during the biological day). At ≈8:00 PM, there was a circadian peak in blood pressure and a trough in cardiac vagal modulation. Sympathetic variables were consistently lowest and vagal markers highest during the biological night. We detected no simple circadian effect on hemostasis...

Structure of the bacteriophage T4 long tail fiber receptor-binding tip

Bartual, Sergio G.; Otero, José M.; Garcia-Doval, Carmela; Llamas-Saiz, Antonio L.; Kahn, Richard; Fox, Gavin C.; van Raaij, Mark J.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Bacteriophages are the most numerous organisms in the biosphere. In spite of their biological significance and the spectrum of potential applications, little high-resolution structural detail is available on their receptor-binding fibers. Here we present the crystal structure of the receptor-binding tip of the bacteriophage T4 long tail fiber, which is highly homologous to the tip of the bacteriophage lambda side tail fibers. This structure reveals an unusual elongated six-stranded antiparallel beta-strand needle domain containing seven iron ions coordinated by histidine residues arranged colinearly along the core of the biological unit. At the end of the tip, the three chains intertwine forming a broader head domain, which contains the putative receptor interaction site. The structure reveals a previously unknown beta-structured fibrous fold, provides insights into the remarkable stability of the fiber, and suggests a framework for mutations to expand or modulate receptor-binding specificity.

Neural signatures of autism

Kaiser, Martha D.; Hudac, Caitlin M.; Shultz, Sarah; Lee, Su Mei; Cheung, Celeste; Berken, Allison M.; Deen, Ben; Pitskel, Naomi B.; Sugrue, Daniel R.; Voos, Avery C.; Saulnier, Celine A.; Ventola, Pamela; Wolf, Julie M.; Klin, Ami; Vander Wyk, Brent C.;
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Functional magnetic resonance imaging of brain responses to biological motion in children with autism spectrum disorder (ASD), unaffected siblings (US) of children with ASD, and typically developing (TD) children has revealed three types of neural signatures: (i) state activity, related to the state of having ASD that characterizes the nature of disruption in brain circuitry; (ii) trait activity, reflecting shared areas of dysfunction in US and children with ASD, thereby providing a promising neuroendophenotype to facilitate efforts to bridge genomic complexity and disorder heterogeneity; and (iii) compensatory activity, unique to US, suggesting a neural system–level mechanism by which US might compensate for an increased genetic risk for developing ASD. The distinct brain responses to biological motion exhibited by TD children and US are striking given the identical behavioral profile of these two groups. These findings offer far-reaching implications for our understanding of the neural systems underlying autism.

Active scaffolds for on-demand drug and cell delivery

Zhao, Xuanhe; Kim, Jaeyun; Cezar, Christine A.; Huebsch, Nathaniel; Lee, Kangwon; Bouhadir, Kamal; Mooney, David J.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Porous biomaterials have been widely used as scaffolds in tissue engineering and cell-based therapies. The release of biological agents from conventional porous scaffolds is typically governed by molecular diffusion, material degradation, and cell migration, which do not allow for dynamic external regulation. We present a new active porous scaffold that can be remotely controlled by a magnetic field to deliver various biological agents on demand. The active porous scaffold, in the form of a macroporous ferrogel, gives a large deformation and volume change of over 70% under a moderate magnetic field. The deformation and volume variation allows a new mechanism to trigger and enhance the release of various drugs including mitoxantrone, plasmid DNA, and a chemokine from the scaffold. The porous scaffold can also act as a depot of various cells, whose release can be controlled by external magnetic fields.

Socioeconomic legacy yields an invasion debt

Essl, Franz; Dullinger, Stefan; Rabitsch, Wolfgang; Hulme, Philip E.; Hülber, Karl; Jarošík, Vojtěch; Kleinbauer, Ingrid; Krausmann, Fridolin; Kühn, Ingolf; Nentwig, Wolfgang; Vilà, Montserrat; Genovesi, Piero; Gherardi, Francesca; Desprez-Loustau,
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Globalization and economic growth are widely recognized as important drivers of biological invasions. Consequently, there is an increasing need for governments to address the role of international trade in their strategies to prevent species introductions. However, many of the most problematic alien species are not recent arrivals but were introduced several decades ago. Hence, current patterns of alien-species richness may better reflect historical rather than contemporary human activities, a phenomenon which might be called “invasion debt.” Here, we show that across 10 taxonomic groups (vascular plants, bryophytes, fungi, birds, mammals, reptiles, amphibians, fish, terrestrial insects, and aquatic invertebrates) in 28 European countries, current numbers of alien species established in the wild are indeed more closely related to indicators of socioeconomic activity from the year 1900 than to those from 2000, although the majority of species introductions occurred during the second half of the 20th century. The strength of the historical signal varies among taxonomic groups, with those possessing good capabilities for dispersal (birds, insects) more strongly associated with recent socioeconomic drivers. Nevertheless, our results suggest a considerable historical legacy for the majority of the taxa analyzed. The consequences of the current high levels of socioeconomic activity on the extent of biological invasions will thus probably not be completely realized until several decades into the future.

Statistical method for revealing form-function relations in biological networks

Mugler, Andrew; Grinshpun, Boris; Franks, Riley; Wiggins, Chris H.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions—lists of the most important players and the pairwise interactions between them. Both for large networks (in which statistical analysis is often framed in terms of the abundance of repeated small subgraphs) and for small networks which can be analyzed in greater detail (or even synthesized in vivo and subjected to experiment), revealing the relationship between the topology of small subgraphs and their biological function has been a central goal. We here seek to pose this revelation as a statistical task, illustrated using a particular setup which has been constructed experimentally and for which parameterized models of transcriptional regulation have been studied extensively. The question “how does function follow form” is here mathematized by identifying which topological attributes correlate with the diverse possible information-processing tasks which a transcriptional regulatory network can realize. The resulting method reveals one form-function relationship which had earlier been predicted based on analytic results, and reveals a second for which we can provide an analytic interpretation. Resulting source code is distributed via http://formfunction.sourceforge.net.

Mercury reduction and complexation by natural organic matter in anoxic environments

Gu, Baohua; Bian, Yongrong; Miller, Carrie L.; Dong, Wenming; Jiang, Xin; Liang, Liyuan
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Mercuric Hg(II) species form complexes with natural dissolved organic matter (DOM) such as humic acid (HA), and this binding is known to affect the chemical and biological transformation and cycling of mercury in aquatic environments. Dissolved elemental mercury, Hg(0), is also widely observed in sediments and water. However, reactions between Hg(0) and DOM have rarely been studied in anoxic environments. Here, under anoxic dark conditions we show strong interactions between reduced HA and Hg(0) through thiolate ligand-induced oxidative complexation with an estimated binding capacity of ~3.5 μmol Hg/g HA and a partitioning coefficient >106 mL/g. We further demonstrate that Hg(II) can be effectively reduced to Hg(0) in the presence of as little as 0.2 mg/L reduced HA, whereas production of Hg(0) is inhibited by complexation as HA concentration increases. This dual role played by DOM in the reduction and complexation of mercury is likely widespread in anoxic sediments and water and can be expected to significantly influence the mercury species transformations and biological uptake that leads to the formation of toxic methylmercury.

2D luminescence imaging of pH in vivo

Schreml, Stephan; Meier, Robert J.; Wolfbeis, Otto S.; Landthaler, Michael; Szeimies, Rolf-Markus; Babilas, Philipp
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Luminescence imaging of biological parameters is an emerging field in biomedical sciences. Tools to study 2D pH distribution are needed to gain new insights into complex disease processes, such as wound healing and tumor metabolism. In recent years, luminescence-based methods for pH measurement have been developed. However, for in vivo applications, especially for studies on humans, biocompatibility and reliability under varying conditions have to be ensured. Here, we present a referenced luminescent sensor for 2D high-resolution imaging of pH in vivo. The ratiometric sensing scheme is based on time-domain luminescence imaging of FITC and ruthenium(II)tris-(4,7-diphenyl-1,10-phenanthroline). To create a biocompatible 2D sensor, these dyes were bound to or incorporated into microparticles (aminocellulose and polyacrylonitrile), and particles were immobilized in polyurethane hydrogel on transparent foils. We show sensor precision and validity by conducting in vitro and in vivo experiments, and we show the versatility in imaging pH during physiological and chronic cutaneous wound healing in humans. Implementation of this technique may open vistas in wound healing, tumor biology, and other biomedical fields.

Intramembrane cavitation as a unifying mechanism for ultrasound-induced bioeffects

Krasovitski, Boris; Frenkel, Victor; Shoham, Shy; Kimmel, Eitan
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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The purpose of this study was to develop a unified model capable of explaining the mechanisms of interaction of ultrasound and biological tissue at both the diagnostic nonthermal, noncavitational (<100 mW·cm−2) and therapeutic, potentially cavitational (>100 mW·cm−2) spatial peak temporal average intensity levels. The cellular-level model (termed “bilayer sonophore”) combines the physics of bubble dynamics with cell biomechanics to determine the dynamic behavior of the two lipid bilayer membrane leaflets. The existence of such a unified model could potentially pave the way to a number of controlled ultrasound-assisted applications, including CNS modulation and blood–brain barrier permeabilization. The model predicts that the cellular membrane is intrinsically capable of absorbing mechanical energy from the ultrasound field and transforming it into expansions and contractions of the intramembrane space. It further predicts that the maximum area strain is proportional to the acoustic pressure amplitude and inversely proportional to the square root of the frequency () and is intensified by proximity to free surfaces, the presence of nearby microbubbles in free medium, and the flexibility of the surrounding tissue. Model predictions were experimentally supported using transmission electron microscopy (TEM) of multilayered live-cell goldfish epidermis exposed in vivo to continuous wave (CW) ultrasound at cavitational (1 MHz) and noncavitational (3 MHz) conditions. Our results support the hypothesis that ultrasonically induced bilayer membrane motion...

Antarctic and Arctic populations of the ciliate Euplotes nobilii show common pheromone-mediated cell-cell signaling and cross-mating

Di Giuseppe, Graziano; Erra, Fabrizio; Dini, Fernando; Alimenti, Claudio; Vallesi, Adriana; Pedrini, Bill; Wüthrich, Kurt; Luporini, Pierangelo
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Wild-type strains of the protozoan ciliate Euplotes collected from different locations on the coasts of Antarctica, Tierra del Fuego and the Arctic were taxonomically identified as the morpho-species Euplotes nobilii, based on morphometric and phylogenetic analyses. Subsequent studies of their sexual interactions revealed that mating combinations of Antarctic and Arctic strains form stable pairs of conjugant cells. These conjugant pairs were isolated and shown to complete mutual gene exchange and cross-fertilization. The biological significance of this finding was further substantiated by demonstrating that close homology exists among the three-dimensional structures determined by NMR of the water-borne signaling pheromones that are constitutively secreted into the extracellular space by these interbreeding strains, in which these molecules trigger the switch between the growth stage and the sexual stage of the life cycle. The fact that Antarctic and Arctic E. nobilii populations share the same gene pool and belong to the same biological species provides new support to the biogeographic model of global distribution of eukaryotic microorganisms, which had so far been based exclusively on studies of morphological and phylogenetic taxonomy.

Sortase-catalyzed transformations that improve the properties of cytokines

Popp, Maximilian W.; Dougan, Stephanie K.; Chuang, Tzu-Ying; Spooner, Eric; Ploegh, Hidde L.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Recombinant protein therapeutics often suffer from short circulating half-life and poor stability, necessitating multiple injections and resulting in limited shelf-life. Conjugation to polyethylene glycol chains (PEG) extends the circulatory half-life of many proteins, but the methods for attachment often lack specificity, resulting in loss of biological activity. Using four-helix bundle cytokines as an example, we present a general platform that uses sortase-mediated transpeptidation to facilitate site-specific attachment of PEG to extend cytokine half-life with full retention of biological activity. Covalently joining the N and C termini of proteins to obtain circular polypeptides, again executed using sortase, increases thermal stability. We combined both PEGylation and circularization by exploiting two distinct sortase enzymes and the use of a molecular suture that allows both site-specific PEGylation and covalent closure. The method developed is general, uses a set of easily accessible reagents, and should be applicable to a wide variety of proteins, provided that their termini are not involved in receptor binding or function.

Radiation damage in protein crystals is reduced with a micron-sized X-ray beam

Sanishvili, Ruslan; Yoder, Derek W.; Pothineni, Sudhir Babu; Rosenbaum, Gerd; Xu, Shenglan; Vogt, Stefan; Stepanov, Sergey; Makarov, Oleg A.; Corcoran, Stephen; Benn, Richard; Nagarajan, Venugopalan; Smith, Janet L.; Fischetti, Robert F.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Radiation damage is a major limitation in crystallography of biological macromolecules, even for cryocooled samples, and is particularly acute in microdiffraction. For the X-ray energies most commonly used for protein crystallography at synchrotron sources, photoelectrons are the predominant source of radiation damage. If the beam size is small relative to the photoelectron path length, then the photoelectron may escape the beam footprint, resulting in less damage in the illuminated volume. Thus, it may be possible to exploit this phenomenon to reduce radiation-induced damage during data measurement for techniques such as diffraction, spectroscopy, and imaging that use X-rays to probe both crystalline and noncrystalline biological samples. In a systematic and direct experimental demonstration of reduced radiation damage in protein crystals with small beams, damage was measured as a function of micron-sized X-ray beams of decreasing dimensions. The damage rate normalized for dose was reduced by a factor of three from the largest (15.6 μm) to the smallest (0.84 μm) X-ray beam used. Radiation-induced damage to protein crystals was also mapped parallel and perpendicular to the polarization direction of an incident 1-μm X-ray beam. Damage was greatest at the beam center and decreased monotonically to zero at a distance of about 4 μm...

Targeting kidney mesangium by nanoparticles of defined size

Choi, Chung Hang J.; Zuckerman, Jonathan E.; Webster, Paul; Davis, Mark E.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Nanoparticles are being investigated for numerous medical applications and are showing potential as an emerging class of carriers for drug delivery. Investigations on how the physicochemical properties (e.g., size, surface charge, shape, and density of targeting ligands) of nanoparticles enable their ability to overcome biological barriers and reach designated cellular destinations in sufficient amounts to elicit biological efficacy are of interest. Despite proven success in nanoparticle accumulation at cellular locations and occurrence of downstream therapeutic effects (e.g., target gene inhibition) in a selected few organs such as tumor and liver, reports on effective delivery of engineered nanoparticles to other organs still remain scarce. Here, we show that nanoparticles of ~75 ± 25-nm diameters target the mesangium of the kidney. These data show the effects of particle diameter on targeting the mesangium of the kidney. Because many diseases originate from this area of the kidney, our findings establish design criteria for constructing nanoparticle-based therapeutics for targeting diseases that involve the mesangium of the kidney.

Direct visualization reveals dynamics of a transient intermediate during protein assembly

Zhang, Xin; Lam, Vinh Q.; Mou, Yun; Kimura, Tetsunari; Chung, Jaeyoon; Chandrasekar, Sowmya; Winkler, Jay R.; Mayo, Stephen L.; Shan, Shu-ou
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Interactions between proteins underlie numerous biological functions. Theoretical work suggests that protein interactions initiate with formation of transient intermediates that subsequently relax to specific, stable complexes. However, the nature and roles of these transient intermediates have remained elusive. Here, we characterized the global structure, dynamics, and stability of a transient, on-pathway intermediate during complex assembly between the Signal Recognition Particle (SRP) and its receptor. We show that this intermediate has overlapping but distinct interaction interfaces from that of the final complex, and it is stabilized by long-range electrostatic interactions. A wide distribution of conformations is explored by the intermediate; this distribution becomes more restricted in the final complex and is further regulated by the cargo of SRP. These results suggest a funnel-shaped energy landscape for protein interactions, and they provide a framework for understanding the role of transient intermediates in protein assembly and biological regulation.

Variability in krill biomass links harvesting and climate warming to penguin population changes in Antarctica

Trivelpiece, Wayne Z.; Hinke, Jefferson T.; Miller, Aileen K.; Reiss, Christian S.; Trivelpiece, Susan G.; Watters, George M.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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The West Antarctic Peninsula (WAP) and adjacent Scotia Sea support abundant wildlife populations, many of which were nearly extirpated by humans. This region is also among the fastest-warming areas on the planet, with 5–6 °C increases in mean winter air temperatures and associated decreases in winter sea-ice cover. These biological and physical perturbations have affected the ecosystem profoundly. One hypothesis guiding ecological interpretations of changes in top predator populations in this region, the “sea-ice hypothesis,” proposes that reductions in winter sea ice have led directly to declines in “ice-loving” species by decreasing their winter habitat, while populations of “ice-avoiding” species have increased. However, 30 y of field studies and recent surveys of penguins throughout the WAP and Scotia Sea demonstrate this mechanism is not controlling penguin populations; populations of both ice-loving Adélie and ice-avoiding chinstrap penguins have declined significantly. We argue in favor of an alternative, more robust hypothesis that attributes both increases and decreases in penguin populations to changes in the abundance of their main prey, Antarctic krill. Unlike many other predators in this region, Adélie and chinstrap penguins were never directly harvested by man; thus...

Forming giant vesicles with controlled membrane composition, asymmetry, and contents

Richmond, David L.; Schmid, Eva M.; Martens, Sascha; Stachowiak, Jeanne C.; Liska, Nicole; Fletcher, Daniel A.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Growing knowledge of the key molecular components involved in biological processes such as endocytosis, exocytosis, and motility has enabled direct testing of proposed mechanistic models by reconstitution. However, current techniques for building increasingly complex cellular structures and functions from purified components are limited in their ability to create conditions that emulate the physical and biochemical constraints of real cells. Here we present an integrated method for forming giant unilamellar vesicles with simultaneous control over (i) lipid composition and asymmetry, (ii) oriented membrane protein incorporation, and (iii) internal contents. As an application of this method, we constructed a synthetic system in which membrane proteins were delivered to the outside of giant vesicles, mimicking aspects of exocytosis. Using confocal fluorescence microscopy, we visualized small encapsulated vesicles docking and mixing membrane components with the giant vesicle membrane, resulting in exposure of previously encapsulated membrane proteins to the external environment. This method for creating giant vesicles can be used to test models of biological processes that depend on confined volume and complex membrane composition, and it may be useful in constructing functional systems for therapeutic and biomaterials applications.

Structural plasticity of a transmembrane peptide allows self-assembly into biologically active nanoparticles

Tarasov, Sergey G.; Gaponenko, Vadim; Howard, O. M. Zack; Chen, Yuhong; Oppenheim, Joost J.; Dyba, Marzena A.; Subramaniam, Sriram; Lee, Youngshim; Michejda, Christopher; Tarasova, Nadya I.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Significant efforts have been devoted to the development of nanoparticular delivering systems targeting tumors. However, clinical application of nanoparticles is hampered by insufficient size homogeneity, difficulties in reproducible synthesis and manufacturing, frequent high uptake in the liver, systemic toxicity of the carriers (particularly for inorganic nanoparticles), and insufficient selectivity for tumor cells. We have found that properly modified synthetic analogs of transmembrane domains of membrane proteins can self-assemble into remarkably uniform spherical nanoparticles with innate biological activity. Self-assembly is driven by a structural transition of the peptide that adopts predominantly a beta-hairpin conformation in aqueous solutions, but folds into an alpha-helix upon spontaneous fusion of the nanoparticles with cell membrane. A 24-amino acid peptide corresponding to the second transmembrane helix of the CXCR4 forms self-assembled particles that inhibit CXCR4 function in vitro and hamper CXCR4-dependent tumor metastasis in vivo. Furthermore, such nanoparticles can encapsulate hydrophobic drugs, thus providing a delivery system with the potential for dual biological activity.

Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

Lucks, Julius B.; Mortimer, Stefanie A.; Trapnell, Cole; Luo, Shujun; Aviran, Sharon; Schroth, Gary P.; Pachter, Lior; Doudna, Jennifer A.; Arkin, Adam P.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential to their function. Thus there is a growing need to develop technologies that enable rapid characterization of structural features within complex RNA populations. We have developed a high-throughput technique, SHAPE-Seq, that can simultaneously measure quantitative, single nucleotide-resolution secondary and tertiary structural information for hundreds of RNA molecules of arbitrary sequence. SHAPE-Seq combines selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry with multiplexed paired-end deep sequencing of primer extension products. This generates millions of sequencing reads, which are then analyzed using a fully automated data analysis pipeline, based on a rigorous maximum likelihood model of the SHAPE-Seq experiment. We demonstrate the ability of SHAPE-Seq to accurately infer secondary and tertiary structural information, detect subtle conformational changes due to single nucleotide point mutations, and simultaneously measure the structures of a complex pool of different RNA molecules. SHAPE-Seq thus represents a powerful step toward making the study of RNA secondary and tertiary structures high throughput and accessible to a wide array of scientific pursuits...

Raft domains of variable properties and compositions in plasma membrane vesicles

Levental, Ilya; Grzybek, Michal; Simons, Kai
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Biological membranes are compartmentalized for functional diversity by a variety of specific protein–protein, protein–lipid, and lipid–lipid interactions. A subset of these are the preferential interactions between sterols, sphingolipids, and saturated aliphatic lipid tails responsible for liquid–liquid domain coexistence in eukaryotic membranes, which give rise to dynamic, nanoscopic assemblies whose coalescence is regulated by specific biochemical cues. Microscopic phase separation recently observed in isolated plasma membranes (giant plasma membrane vesicles and plasma membrane spheres) (i) confirms the capacity of compositionally complex membranes to phase separate, (ii) reflects the nanoscopic organization of live cell membranes, and (iii) provides a versatile platform for the investigation of the compositions and properties of the phases. Here, we show that the properties of coexisting phases in giant plasma membrane vesicles are dependent on isolation conditions—namely, the chemicals used to induce membrane blebbing. We observe strong correlations between the relative compositions and orders of the coexisting phases, and their resulting miscibility. Chemically unperturbed plasma membranes reflect these properties and validate the observations in chemically induced vesicles. Most importantly...

Network-based prediction for sources of transcriptional dysregulation using latent pathway identification analysis

Pham, Lisa; Christadore, Lisa; Schaus, Scott; Kolaczyk, Eric D.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Understanding the systemic biological pathways and the key cellular mechanisms that dictate disease states, drug response, and altered cellular function poses a significant challenge. Although high-throughput measurement techniques, such as transcriptional profiling, give some insight into the altered state of a cell, they fall far short of providing by themselves a complete picture. Some improvement can be made by using enrichment-based methods to, for example, organize biological data of this sort into collections of dysregulated pathways. However, such methods arguably are still limited to primarily a transcriptional view of the cell. Augmenting these methods still further with networks and additional -omics data has been found to yield pathways that play more fundamental roles. We propose a previously undescribed method for identification of such pathways that takes a more direct approach to the problem than any published to date. Our method, called latent pathway identification analysis (LPIA), looks for statistically significant evidence of dysregulation in a network of pathways constructed in a manner that implicitly links pathways through their common function in the cell. We describe the LPIA methodology and illustrate its effectiveness through analysis of data on (i) metastatic cancer progression...