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Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data

Tanay, Amos; Sharan, Roded; Kupiec, Martin; Shamir, Ron
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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The dissection of complex biological systems is a challenging task, made difficult by the size of the underlying molecular network and the heterogeneous nature of the control mechanisms involved. Novel high-throughput techniques are generating massive data sets on various aspects of such systems. Here, we perform analysis of a highly diverse collection of genomewide data sets, including gene expression, protein interactions, growth phenotype data, and transcription factor binding, to reveal the modular organization of the yeast system. By integrating experimental data of heterogeneous sources and types, we are able to perform analysis on a much broader scope than previous studies. At the core of our methodology is the ability to identify modules, namely, groups of genes with statistically significant correlated behavior across diverse data sources. Numerous biological processes are revealed through these modules, which also obey global hierarchical organization. We use the identified modules to study the yeast transcriptional network and predict the function of >800 uncharacterized genes. Our analysis framework, samba (Statistical-Algorithmic Method for Bicluster Analysis), enables the processing of current and future sources of biological information and is readily extendable to experimental techniques and higher organisms.

Freezing immunoglobulins to see them move

Bongini, L.; Fanelli, D.; Piazza, F.; De Los Rios, P.; Sandin, S.; Skoglund, U.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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The issue of protein dynamics and its implications in the biological function of proteins are arousing greater and greater interest in different fields of molecular biology. In cryo-electron tomography experiments one may take several snapshots of a given biological macromolecule. In principle, a large enough collection of snapshots of the molecule may then be used to calculate its equilibrium configuration in terms of the experimentally accessible degrees of freedom and, hence, to estimate its potential energy. This information would be crucial in order to analyze the biological functions of biomolecules by directly accessing the relevant dynamical indicators. In this article, we analyze the results of cryo-electron tomography experiments performed on monoclonal murine IgG2a antibodies. We measure the equilibrium distribution of the molecule in terms of the relevant angular coordinates and build a mechanical model of the antibody dynamics. This approach enables us to derive an explicit expression of the IgG potential energy. Furthermore, we discuss the configuration space at equilibrium in relation to results from other techniques, and we set our discussion in the context of the current debate regarding conformation and flexibility of antibodies.

A coherent framework for multiresolution analysis of biological networks with “memory”: Ras pathway, cell cycle, and immune system

Barbano, Paolo Emilio; Spivak, Marina; Feng, Jiawu; Antoniotti, Marco; Mishra, Bud
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Various biological processes exhibit characteristics that vary dramatically in response to different input conditions or changes in the history of the process itself. One of the examples studied here, the Ras-PKC-mitogen-activated protein kinase (MAPK) bistable pathway, follows two distinct dynamics (modes) depending on duration and strength of EGF stimulus. Similar examples are found in the behavior of the cell cycle and the immune system. A classification methodology, based on time-frequency analysis, was developed and tested on these systems to understand global behavior of biological processes. Contrary to most traditionally used statistical and spectral methods, our approach captures complex functional relations between parts of the systems in a simple way. The resulting algorithms are capable of analyzing and classifying sets of time-series data obtained from in vivo or in vitro experiments, or in silico simulation of biological processes. The method was found to be considerably stable under stochastic noise perturbation and, therefore, suitable for the analysis of real experimental data.

Circuit topology and the evolution of robustness in two-gene circadian oscillators

Wagner, Andreas
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Many parameters driving the behavior of biochemical circuits vary extensively and are thus not fine-tuned. Therefore, the topology of such circuits (the who-interacts-with-whom) is key to understanding their central properties. I here explore several hundred different topologies of a simple biochemical model of circadian oscillations to ask two questions: Do different circuits differ dramatically in their robustness to parameter change? If so, can a process of gradual molecular evolution find highly robust topologies when starting from less robust topologies? I find that the distribution of robustness among different circuit topologies is highly skewed: Most show low robustness, whereas very few topologies are highly robust. To address the second evolutionary question, I define a topology graph, each of whose nodes corresponds to one circuit topology that shows circadian oscillations. Two nodes in this graph are connected if they differ by only one regulatory interaction within the circuit. For the circadian oscillator I study, most topologies are connected in this graph, making evolutionary transitions from low to high robustness easy. A similar approach has been used to study the evolution of robustness in biological macromolecules...

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian, Aravind; Tamayo, Pablo; Mootha, Vamsi K.; Mukherjee, Sayan; Ebert, Benjamin L.; Gillette, Michael A.; Paulovich, Amanda; Pomeroy, Scott L.; Golub, Todd R.; Lander, Eric S.; Mesirov, Jill P.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.

Malaria resurgence in the East African highlands: Temperature trends revisited

Pascual, M.; Ahumada, J. A.; Chaves, L. F.; Rodó, X.; Bouma, M.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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The incidence of malaria in the East African highlands has increased since the end of the 1970s. The role of climate change in the exacerbation of the disease has been controversial, and the specific influence of rising temperature (warming) has been highly debated following a previous study reporting no evidence to support a trend in temperature. We revisit this result using the same temperature data, now updated to the present from 1950 to 2002 for four high-altitude sites in East Africa where malaria has become a serious public health problem. With both nonparametric and parametric statistical analyses, we find evidence for a significant warming trend at all sites. To assess the biological significance of this trend, we drive a dynamical model for the population dynamics of the mosquito vector with the temperature time series and the corresponding detrended versions. This approach suggests that the observed temperature changes would be significantly amplified by the mosquito population dynamics with a difference in the biological response at least 1 order of magnitude larger than that in the environmental variable. Our results emphasize the importance of considering not just the statistical significance of climate trends but also their biological implications with dynamical models.

Latent extinction risk and the future battlegrounds of mammal conservation

Cardillo, Marcel; Mace, Georgina M.; Gittleman, John L.; Purvis, Andy
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Global conservation prioritization usually emphasizes areas with highest species richness or where many species are thought to be at imminent risk of extinction. However, these strategies may overlook areas where many species have biological traits that make them particularly sensitive to future human impact but are not yet threatened because such impact is currently low. In this article, we identify such areas for the world’s mammals using latent extinction risk, the discrepancy between a species’ current extinction risk and that predicted from models on the basis of biological traits. Species with positive latent risk are currently less threatened than their biology would suggest, usually because they inhabit regions or habitats still comparatively unmodified by human activity. Using large new geographic, biological, and phylogenetic databases for nearly 4,000 mammal species, we map the global geographic distribution of latent risk to reveal areas where the mammal fauna is still relatively unthreatened but has high inherent sensitivity to disturbance. These hotspots include large areas such as the Nearctic boreal forests and tundra that are unrepresented in most current prioritization schemes, as well as high-biodiversity areas such as the island arc from Indonesia to the south Pacific. Incorporating latent extinction risk patterns into conservation planning could help guard against future biodiversity loss by anticipating and preventing species declines before they begin.

A metabolic network in the evolutionary context: Multiscale structure and modularity

Spirin, Victor; Gelfand, Mikhail S.; Mironov, Andrey A.; Mirny, Leonid A.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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The enormous complexity of biological networks has led to the suggestion that networks are built of modules that perform particular functions and are “reused” in evolution in a manner similar to reusable domains in protein structures or modules of electronic circuits. Analysis of known biological networks has revealed several modules, many of which have transparent biological functions. However, it remains to be shown that identified structural modules constitute evolutionary building blocks, independent and easily interchangeable units. An alternative possibility is that evolutionary modules do not match structural modules. To investigate the structure of evolutionary modules and their relationship to functional ones, we integrated a metabolic network with evolutionary associations between genes inferred from comparative genomics. The resulting metabolic–genomic network places metabolic pathways into evolutionary and genomic context, thereby revealing previously unknown components and modules. We analyzed the integrated metabolic–genomic network on three levels: macro-, meso-, and microscale. The macroscale level demonstrates strong associations between neighboring enzymes and between enzymes that are distant on the network but belong to the same linear pathway. At the mesoscale level...

Microtubule bundling and nested buckling drive stripe formation in polymerizing tubulin solutions

Liu, Yifeng; Guo, Yongxing; Valles, James M.; Tang, Jay X.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Various mechanisms govern pattern formation in chemical and biological reaction systems, giving rise to structures with distinct morphologies and physical properties. The self-organization of polymerizing microtubules (MTs) is of particular interest because of its implications for biological function. We report a study of the microscopic structure and properties of the striped patterns that spontaneously form in polymerizing tubulin solutions and propose a mechanism driving this assembly. Microscopic observations reveal that the pattern comprises wave-like MT bundles. The retardance of the solution and the fluorescence intensity of labeled MTs vary periodically in space, suggesting a coincident periodic variation in MT alignment and density. This wave-like structure forms through the development and coordinated buckling of initially aligned MT bundles. Both static magnetic fields and convective flow can induce the initial alignment. The nesting of the buckled MT bundles gives rise to density variations that are in quantitative accord with the data. We further propose that the buckling wavelength is selected by a balance between the bending energy of the bundles and the elastic energy of the MT network surrounding them. These studies reveal a unique physical chemical mechanism by which mechanical buckling couples with protein polymerization to produce macroscopic patterns. Self-organization of this type may be important to the formation of certain biological structures.

On the thermodynamic stability of a charged arginine side chain in a transmembrane helix

Dorairaj, Sudha; Allen, Toby W.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Biological membranes consist of bilayer arrangements of lipids forming a hydrophobic core that presents a physical barrier to all polar and charged molecules. This long-held notion has recently been challenged by biological translocon-based experiments that report small apparent free energies to insert charged side chains near the center of a transmembrane (TM) helix. We have carried out fully atomistic simulations to provide the free-energy profile for moving a TM helix containing a protonated Arg side chain across a lipid bilayer. Our results reveal the fundamental thermodynamics governing the stability of charged side chains in membranes and the microscopic interactions involved. Despite local membrane deformations, where large amounts of water and lipid head groups are pulled into the bilayer to interact with Arg, the free-energy barrier is 17 kcal/mol. We provide a rationale for the differences in our microscopic free energies and cell biological experiments using free-energy calculations that indicate that a protonated Arg at the central residue of a TM helix of the Leader peptidase might reside close to the interface and not at the membrane center. Our findings have implications for the gating mechanisms of voltage-gated ion channels...

Distinct requirements for Gab1 in Met and EGF receptor signaling in vivo

Schaeper, Ute; Vogel, Regina; Chmielowiec, Jolanta; Huelsken, Joerg; Rosario, Marta; Birchmeier, Walter
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Gab1 is a multiadaptor protein that has been shown to be required for multiple processes in embryonic development and oncogenic transformation. Gab1 functions by amplifying signal transduction downstream of various receptor tyrosine kinases through recruitment of multiple signaling effectors, including phosphatidylinositol 3-kinase and Shp2. Until now, the functional significance of individual interactions in vivo was not known. Here we have generated knockin mice that carry point mutations in either the P13K or Shp2 binding sites of Gab1. We show that different effector interactions with Gab1 play distinct biological roles downstream of Gab1 during the development of different organs. Recruitment of phosphatidylinositol 3-kinase by Gab1 is essential for EGF receptor-mediated embryonic eyelid closure and keratinocyte migration, and the Gab1–Shp2 interaction is crucial for Met receptor-directed placental development and muscle progenitor cell migration to the limbs. Furthermore, we investigate the dual association of Gab1 with the Met receptor. By analyzing knockin mice with mutations in the Grb2 or Met binding site of Gab1, we show that the requirements for Gab1 recruitment to Met varies in different biological contexts. Either the direct or the indirect interaction of Gab1 with Met is sufficient for Met-dependent muscle precursor cell migration...

Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses

Mock, Thomas; Samanta, Manoj Pratim; Iverson, Vaughn; Berthiaume, Chris; Robison, Matthew; Holtermann, Karie; Durkin, Colleen; BonDurant, Sandra Splinter; Richmond, Kathryn; Rodesch, Matthew; Kallas, Toivo; Huttlin, Edward L.; Cerrina, Francesco; Sussman,
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Formation of complex inorganic structures is widespread in nature. Diatoms create intricately patterned cell walls of inorganic silicon that are a biomimetic model for design and generation of three-dimensional silica nanostructures. To date, only relatively simple silica structures can be generated in vitro through manipulation of known diatom phosphoproteins (silaffins) and long-chain polyamines. Here, we report the use of genome-wide transcriptome analyses of the marine diatom Thalassiosira pseudonana to identify additional candidate gene products involved in the biological manipulation of silicon. Whole-genome oligonucleotide tiling arrays and tandem mass spectrometry identified transcripts for >8,000 genes, ≈3,000 of which were not previously described and included noncoding and antisense RNAs. Gene-specific expression profiles detected a set of 75 genes induced only under low concentrations of silicon but not under low concentrations of nitrogen or iron, alkaline pH, or low temperatures. Most of these induced gene products were predicted to contain secretory signals and/or transmembrane domains but displayed no homology to known proteins. Over half of these genes were newly discovered, identified only through the use of tiling arrays. Unexpectedly...

Strong human association with plant invasion success for Trifolium introductions to New Zealand

Gravuer, Kelly; Sullivan, Jon J.; Williams, Peter A.; Duncan, Richard P.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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It has proven difficult, when focused only on biological determinants, to explain why some plant species become naturalized in or invade new locations, whereas others fail. We analyzed the invasion of Trifolium (true clover) species into New Zealand, assessing a range of human, biogeographic, and biological influences at three key invasion stages: introduction, naturalization, and spread. We used sparse principal component analysis (SPCA) to define suites of related attributes and aggregated boosted trees to model relationships with invasion outcomes. Human and biogeographic attributes were strongly associated with success at all stages. Whereas biogeographic attributes, notably large native range, were consistently associated with success, different human factors appeared to favor success at different stages, such as presence in early trade/immigration hotspots (introduction), intentional large-scale planting (naturalization), and frequent presence as a seed contaminant (relative spread rate). Biological traits were less strongly associated with success for introduction and spread and little if at all for naturalization; we found that tall perennials with long flowering periods were more frequently selected for introduction, whereas species with extended flowering in New Zealand spread more rapidly. In addition to causal relationships...

A catalytic di-heme bis-Fe(IV) intermediate, alternative to an Fe(IV)=O porphyrin radical

Li, Xianghui; Fu, Rong; Lee, Sheeyong; Krebs, Carsten; Davidson, Victor L.; Liu, Aimin
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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High-valent iron species are powerful oxidizing agents in chemical and biological catalysis. The best characterized form of an Fe(V) equivalent described in biological systems is the combination of a b-type heme with Fe(IV)=O and a porphyrin or amino acid cation radical (termed Compound I). This work describes an alternative natural mechanism to store two oxidizing equivalents above the ferric state for biological oxidation reactions. MauG is an enzyme that utilizes two covalently bound c-type hemes to catalyze the biosynthesis of the protein-derived cofactor tryptophan tryptophylquinone. Its natural substrate is a monohydroxylated tryptophan residue present in a 119-kDa precursor protein. An EPR-silent di-heme reaction intermediate of MauG was trapped. Mössbauer spectroscopy revealed the presence of two distinct Fe(IV) species. One is consistent with an Fe(IV)=O (ferryl) species (δ = 0.06 mm/s, ΔEQ = 1.70 mm/s). The other is assigned to an Fe(IV) heme species with two axial ligands from protein (δ = 0.17 mm/s, ΔEQ = 2.54 mm/s), which has never before been described in nature. This bis-Fe(IV) intermediate is remarkably stable but readily reacts with its native substrate. These findings broaden our views of how proteins can stabilize a highly reactive oxidizing species and the scope of enzyme-catalyzed posttranslational modifications.

Heparan sulfate regulates ephrin-A3/EphA receptor signaling

Irie, Fumitoshi; Okuno, Misako; Matsumoto, Kazu; Pasquale, Elena B.; Yamaguchi, Yu
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Increasing evidence indicates that many signaling pathways involve not only ligands and receptors but also various types of coreceptors and matrix components as additional layers of regulation. Signaling by Eph receptors and their ephrin ligands plays a key role in a variety of biological processes, such as axon guidance and topographic map formation, synaptic plasticity, angiogenesis, and cancer. Little is known about whether the ephrin-Eph receptor signaling system is subject to such additional layers of regulation. Here, we show that ephrin-A3 binds to heparan sulfate, and that the presence of cell surface heparan sulfate is required for the full biological activity of ephrin-A3. Among the ephrins tested, including ephrin-A1, -A2, -A5, -B1, and -B2, only ephrin-A3 binds heparin or heparan sulfate. Ephrin-A3-dependent EphA receptor activation is reduced in mutant cells that are defective in heparan sulfate synthesis, in wild-type cells from which cell surface heparan sulfate has been removed, and in the hippocampus of conditional knockout mice defective in heparan sulfate synthesis. Ephrin-A3-dependent cell rounding is impaired in CHO cells lacking heparan sulfate, and cortical neurons lacking heparan sulfate exhibit impaired growth cone collapse. In contrast...

Increasing corn for biofuel production reduces biocontrol services in agricultural landscapes

Landis, Douglas A.; Gardiner, Mary M.; van der Werf, Wopke; Swinton, Scott M.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Increased demand for corn grain as an ethanol feedstock is altering U.S. agricultural landscapes and the ecosystem services they provide. From 2006 to 2007, corn acreage increased 19% nationally, resulting in reduced crop diversity in many areas. Biological control of insects is an ecosystem service that is strongly influenced by local landscape structure. Here, we estimate the value of natural biological control of the soybean aphid, a major pest in agricultural landscapes, and the economic impacts of reduced biocontrol caused by increased corn production in 4 U.S. states (Iowa, Michigan, Minnesota, and Wisconsin). For producers who use an integrated pest management strategy including insecticides as needed, natural suppression of soybean aphid in soybean is worth an average of $33 ha−1. At 2007–2008 prices these services are worth at least $239 million y−1 in these 4 states. Recent biofuel-driven growth in corn planting results in lower landscape diversity, altering the supply of aphid natural enemies to soybean fields and reducing biocontrol services by 24%. This loss of biocontrol services cost soybean producers in these states an estimated $58 million y−1 in reduced yield and increased pesticide use. For producers who rely solely on biological control...

Multilayer three-dimensional super resolution imaging of thick biological samples

Vaziri, Alipasha; Tang, Jianyong; Shroff, Hari; Shank, Charles V.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Recent advances in optical microscopy have enabled biological imaging beyond the diffraction limit at nanometer resolution. A general feature of most of the techniques based on photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM) has been the use of thin biological samples in combination with total internal reflection, thus limiting the imaging depth to a fraction of an optical wavelength. However, to study whole cells or organelles that are typically up to 15 μm deep into the cell, the extension of these methods to a three-dimensional (3D) super resolution technique is required. Here, we report an advance in optical microscopy that enables imaging of protein distributions in cells with a lateral localization precision better than 50 nm at multiple imaging planes deep in biological samples. The approach is based on combining the lateral super resolution provided by PALM with two-photon temporal focusing that provides optical sectioning. We have generated super-resolution images over an axial range of ≈10 μm in both mitochondrially labeled fixed cells, and in the membranes of living S2 Drosophila cells.

Experimental evidence that human impacts drive fire ant invasions and ecological change

King, Joshua R.; Tschinkel, Walter R.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Biological invasions are often closely associated with human impacts and it is difficult to determine whether either or both are responsible for the negative impacts on native communities. Here, we show that human activity, not biological invasion, is the primary driver of negative effects on native communities and of the process of invasion itself. In a large-scale experiment, we combined additions of the exotic fire ant, Solenopsis invicta, with 2 disturbance treatments, mowing and plowing, in a fully crossed factorial design. Results indicate that plowing, in the absence of fire ants, greatly diminished total native ant abundance and diversity, whereas fire ants, even in the absence of disturbance, diminished some, but not all, native ant abundance and diversity. Transplanted fire ant colonies were favored by disturbance. In the absence of disturbance and on their own, fire ants do not invade the forest habitats of native ants. Our results demonstrate that fire ants are “passengers” rather than “drivers” of ecological change. We propose that fire ants may be representative of other invasive species that would be better described as disturbance specialists. Current pest management and conservation strategies should be reassessed to better account for the central role of human impacts in the process of biological invasion.

Activation of EGFR on monocytes is required for human cytomegalovirus entry and mediates cellular motility

Chan, Gary; Nogalski, Maciej T.; Yurochko, Andrew D.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Human cytomegalovirus (HCMV) rapidly induces a mobile and functionally unique proinflammatory monocyte following infection that is proposed to mediate viral spread. The cellular pathways used by HCMV to initiate these biological changes remain unknown. Here, we document the expression of the epidermal growth factor receptor (EGFR) on the surface of human peripheral blood monocytes but not on other blood leukocyte populations. Inhibition of EGFR signaling abrogated viral entry into monocytes, indicating that EGFR can serve as a cellular tropism receptor. Moreover, HCMV-activated EGFR was required for the induction of monocyte motility and transendothelial migration, two biological events required for monocyte extravasation into peripheral tissue, and thus viral spread. Transcriptome analysis revealed that HCMV-mediated EGFR signaling up-regulated neural Wiskott–Aldrich syndrome protein (N-WASP), an actin nucleator whose expression and function are normally limited in leukocytes. Knockdown of N-WASP expression blocked HCMV-induced but not phorbol 12-myristate 13-acetate (PMA)-induced monocyte motility, suggesting that a switch to and/or the distinct use of a new actin nucleator controlling motility occurs during HCMV infection of monocytes. Together...

Biological imaging with 4D ultrafast electron microscopy

Flannigan, David J.; Barwick, Brett; Zewail, Ahmed H.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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Advances in the imaging of biological structures with transmission electron microscopy continue to reveal information at the nanometer length scale and below. The images obtained are static, i.e., time-averaged over seconds, and the weak contrast is usually enhanced through sophisticated specimen preparation techniques and/or improvements in electron optics and methodologies. Here we report the application of the technique of photon-induced near-field electron microscopy (PINEM) to imaging of biological specimens with femtosecond (fs) temporal resolution. In PINEM, the biological structure is exposed to single-electron packets and simultaneously irradiated with fs laser pulses that are coincident with the electron pulses in space and time. By electron energy-filtering those electrons that gained photon energies, the contrast is enhanced only at the surface of the structures involved. This method is demonstrated here in imaging of protein vesicles and whole cells of Escherichia coli, both are not absorbing the photon energy, and both are of low-Z contrast. It is also shown that the spatial location of contrast enhancement can be controlled via laser polarization, time resolution, and tomographic tilting. The high-magnification PINEM imaging provides the nanometer scale and the fs temporal resolution. The potential of applications is discussed and includes the study of antibodies and immunolabeling within the cell.