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1.
Highly excited Rydberg atoms have many exaggerated properties. In particular, the interaction strength between such atoms can be varied over an enormous range. In a mesoscopic ensemble, such strong, long-range interactions can be used for fast preparation of desired many-particle states. We generated Rydberg excitations in an ultra-cold atomic gas and subsequently converted them into light. As the principal quantum number n was increased beyond ~70, no more than a single excitation was retrieved from the entire mesoscopic ensemble of atoms. These results hold promise for studies of dynamics and disorder in many-body systems with tunable interactions and for scalable quantum information networks. 相似文献
2.
Understanding species' interactions and the robustness of interaction networks to species loss is essential to understand the effects of species' declines and extinctions. In most studies, different types of networks (such as food webs, parasitoid webs, seed dispersal networks, and pollination networks) have been studied separately. We sampled such multiple networks simultaneously in an agroecosystem. We show that the networks varied in their robustness; networks including pollinators appeared to be particularly fragile. We show that, overall, networks did not strongly covary in their robustness, which suggests that ecological restoration (for example, through agri-environment schemes) benefitting one functional group will not inevitably benefit others. Some individual plant species were disproportionately well linked to many other species. This type of information can be used in restoration management, because it identifies the plant taxa that can potentially lead to disproportionate gains in biodiversity. 相似文献
3.
Arabidopsis Interactome Mapping Consortium 《Science (New York, N.Y.)》2011,333(6042):601-607
Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing about 6200 highly reliable interactions between about 2700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops. 相似文献
4.
Micelles protect membrane complexes from solution to vacuum 总被引：1，自引：0，他引：1
The ability to maintain interactions between soluble protein subunits in the gas phase of a mass spectrometer gives critical insight into the stoichiometry and interaction networks of protein complexes. Conversely, for membrane protein complexes in micelles, the transition into the gas phase usually leads to the disruption of interactions, particularly between cytoplasmic and membrane subunits, and a mass spectrum dominated by large aggregates of detergent molecules. We show that by applying nanoelectrospray to a micellar solution of a membrane protein complex, the heteromeric adenosine 5'-triphosphate (ATP)-binding cassette transporter BtuC2D2, we can maintain the complex intact in the gas phase of a mass spectrometer. Dissociation of either transmembrane (BtuC) or cytoplasmic (BtuD) subunits uncovers modifications to the transmembrane subunits and cooperative binding of ATP. By protecting a membrane protein complex within a n-dodecyl-beta-d-maltoside micelle, we demonstrated a powerful strategy that will enable the subunit stoichiometry and ligand-binding properties of membrane complexes to be determined directly, by precise determination of the masses of intact complexes and dissociated subunits. 相似文献
5.
Tarassov K Messier V Landry CR Radinovic S Serna Molina MM Shames I Malitskaya Y Vogel J Bussey H Michnick SW 《Science (New York, N.Y.)》2008,320(5882):1465-1470
Protein interactions regulate the systems-level behavior of cells; thus, deciphering the structure and dynamics of protein interaction networks in their cellular context is a central goal in biology. We have performed a genome-wide in vivo screen for protein-protein interactions in Saccharomyces cerevisiae by means of a protein-fragment complementation assay (PCA). We identified 2770 interactions among 1124 endogenously expressed proteins. Comparison with previous studies confirmed known interactions, but most were not known, revealing a previously unexplored subspace of the yeast protein interactome. The PCA detected structural and topological relationships between proteins, providing an 8-nanometer-resolution map of dynamically interacting complexes in vivo and extended networks that provide insights into fundamental cellular processes, including cell polarization and autophagy, pathways that are evolutionarily conserved and central to both development and human health. 相似文献
6.
Depressive disorders: toward a unified hypothesis 总被引：4，自引：0，他引：4
Our scientific understanding of psychiatric syndromes, including the phenomena of depression, has been hampered because of: (i) the use of metapsychological concepts that are difficult to test; (ii) methodological and linguistic barriers that prevent communication among psychoanalysts, behaviorists, experimental psychologists, and psychiatrists; and (iii) the reluctance of psychiatrists to accept animal models as possible approximations of certain aspects of human psychopathology. We have attempted to demonstrate that the animal models simulate some of the central features of clinical depression (for example, helplessness and object loss), thereby allowing one to rigorously investigate them from developmental, behavioral, and biochemical perspectives. The object loss model, as a concrete version of a metapsychological-psychoanalytic concept, has enabled primatologists to study the disruption of an attachment bond. The behavioral model accommodates this concept to a broader generalization: loss of reinforcement or loss of control over reinforcement. We have reviewed the evidence that these processes involve the diencephalic centers of reward or reinforcement, thereby permitting integration of the psychoanalytical and behavioral formulations with the biochemical hypotheses. Also, we have presented data strongly suggesting that the breaking of an attachment bond in the primate represents significant loss of reinforcement that induces helplessness and disrupts motivated behavior. Finally, we have argued that the depressive syndrome could be caused by interactions of genetic, chemical, developmental, and interpersonal factors, all of which impinge on the diencephalic centers of reinforcement. 相似文献
7.
High sequence selectivity in DNA-protein interactions was analyzed by measuring discrimination by Eco RI endonuclease between the recognition site GAATTC and systematically altered DNA sites. Base analogue substitutions that preserve the sequence-dependent conformational motif of the GAATTC site permit deletion of single sites of protein-base contact at a cost of +1 to +2 kcal/mol. However, the introduction of any one incorrect natural base pair costs +6 to +13 kcal/mol in transition state interaction energy, the resultant of the following interdependent factors: deletion of one or two hydrogen bonds between the protein and a purine base; unfavourable steric apposition between a group on the protein and an incorrectly placed functional group on a base; disruption of a pyrimidine contact with the protein; loss of some crucial interactions between protein and DNA phosphates; and an increased energetic cost of attaining the required DNA conformation in the transition state complex. Eco RI endonuclease thus achieves stringent discrimination by both "direct readout" (protein-base contracts) and "indirect readout" (protein-phosphate contacts and DNA conformation) of the DNA sequence. 相似文献
8.
Uetz P Dong YA Zeretzke C Atzler C Baiker A Berger B Rajagopala SV Roupelieva M Rose D Fossum E Haas J 《Science (New York, N.Y.)》2006,311(5758):239-242
The comprehensive yeast two-hybrid analysis of intraviral protein interactions in two members of the herpesvirus family, Kaposi sarcoma-associated herpesvirus (KSHV) and varicella-zoster virus (VZV), revealed 123 and 173 interactions, respectively. Viral protein interaction networks resemble single, highly coupled modules, whereas cellular networks are organized in separate functional submodules. Predicted and experimentally verified interactions between KSHV and human proteins were used to connect the viral interactome into a prototypical human interactome and to simulate infection. The analysis of the combined system showed that the viral network adopts cellular network features and that protein networks of herpesviruses and possibly other intracellular pathogens have distinguishing topologies. 相似文献
9.
Jansen R Yu H Greenbaum D Kluger Y Krogan NJ Chung S Emili A Snyder M Greenblatt JF Gerstein M 《Science (New York, N.Y.)》2003,302(5644):449-453
We have developed an approach using Bayesian networks to predict protein-protein interactions genome-wide in yeast. Our method naturally weights and combines into reliable predictions genomic features only weakly associated with interaction (e.g., messenger RNAcoexpression, coessentiality, and colocalization). In addition to de novo predictions, it can integrate often noisy, experimental interaction data sets. We observe that at given levels of sensitivity, our predictions are more accurate than the existing high-throughput experimental data sets. We validate our predictions with TAP (tandem affinity purification) tagging experiments. Our analysis, which gives a comprehensive view of yeast interactions, is available at genecensus.org/intint. 相似文献
10.
Most studies of protein networks operate on a high level of abstraction, neglecting structural and chemical aspects of each interaction. Here, we characterize interactions by using atomic-resolution information from three-dimensional protein structures. We find that some previously recognized relationships between network topology and genomic features (e.g., hubs tending to be essential proteins) are actually more reflective of a structural quantity, the number of distinct binding interfaces. Subdividing hubs with respect to this quantity provides insight into their evolutionary rate and indicates that additional mechanisms of network growth are active in evolution (beyond effective preferential attachment through gene duplication). 相似文献
11.
Specificity and stability in topology of protein networks 总被引：4，自引：0，他引：4
Molecular networks guide the biochemistry of a living cell on multiple levels: Its metabolic and signaling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory network. To address topological properties of these two networks, we quantified correlations between connectivities of interacting nodes and compared them to a null model of a network, in which all links were randomly rewired. We found that for both interaction and regulatory networks, links between highly connected proteins are systematically suppressed, whereas those between a highly connected and low-connected pairs of proteins are favored. This effect decreases the likelihood of cross talk between different functional modules of the cell and increases the overall robustness of a network by localizing effects of deleterious perturbations. 相似文献
12.
Yu H Braun P Yildirim MA Lemmens I Venkatesan K Sahalie J Hirozane-Kishikawa T Gebreab F Li N Simonis N Hao T Rual JF Dricot A Vazquez A Murray RR Simon C Tardivo L Tam S Svrzikapa N Fan C de Smet AS Motyl A Hudson ME Park J Xin X Cusick ME Moore T Boone C Snyder M Roth FP Barabási AL Tavernier J Hill DE Vidal M 《Science (New York, N.Y.)》2008,322(5898):104-110
Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering approximately 20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy. 相似文献
13.
A synthetic peptide from fibronectin inhibits experimental metastasis of murine melanoma cells 总被引：55，自引：0，他引：55
Adhesive interactions between cells and the extracellular matrix occur at several stages of metastasis. Such interactions might be inhibited by synthetic peptide probes derived from the cell-binding regions of matrix molecules. Gly-Arg-Gly-Asp-Ser (GRGDS) is a pentapeptide sequence that appears to be critical for cell interaction with fibronectin. Coinjection of GRGDS with B16-F10 murine melanoma cells dramatically inhibited the formation of lung colonies in C57BL/6 mice. Two closely related control peptides, in which specific amino acids within the GRGDS sequence were transposed or substituted, displayed little or no activity. Inhibition by GRGDS was dose-dependent, noncytotoxic, and did not result from an impairment of cellular tumorigenicity. GRGDS may function by inhibiting tumor cell retention in the lung since radiolabeled B16-F10 tumor cells injected with the peptide were lost at a substantially greater rate than control cells. 相似文献
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15.
生物入侵已成为世界性的生态、经济问题,是人类当前面临的巨大挑战.作为入侵生物中一个重要组分的外来入侵植物,其入侵不仅改变了入侵地地上植物群落的多样性,而且对入侵地的地下生态系统也产生了深刻影响.国内外的生态学家对于外来植物的入侵虽已提出多个机制假说,但真正机理还未明确.近年来兴起的外来入侵植物与入侵地土壤生态过程相互影响的研究为外来植物入侵机理的揭示提供了新思路.从两个方面综述了近年来对外来入侵植物与入侵地地下生态系统相互作用的研究结果:(1)入侵植物与入侵地土壤微生物的相互影响:外来入侵植物可通过破坏土著植物与土壤微生物问的共生关系、分泌化感物质影响入侵地微生物群落结构和功能、逃避原产地土传天敌、改变入侵地的微生物群落结构进而间接改变土壤养分循环等途径实现入侵;(2)入侵植物与入侵地土壤养分的相互影响:主要是入侵植物与入侵地土壤氮、磷、钾等几种大量元素及其他元素之间的相互作用.在综述国内外研究的基础上,探讨了外来入侵植物入侵机理研究中存在的问题及未来的研究方向,以期为外来植物入侵的预防、控制与生境恢复提供依据. 相似文献
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17.
Zhong WEI Ville-Petri FRIMAN Thomas POMMIER Stefan GEISEN Alexandre JOUSSET Qirong SHEN 《农业科学与工程前沿(英文版)》2020,7(3):317-328
Managing plant health is a great challenge for modern food production and is further complicated by the lack of common ground between the many disciplines involved in disease control. Here we present the concept of rhizosphere immunity, in which plant health is considered as an ecosystem level property emerging from networks of interactions between plants, microbiota and the surrounding soil matrix. These interactions can potentially extend the innate plant immune system to a point where the rhizosphere immunity can fulfil all four core functions of a full immune system: pathogen prevention, recognition, response and homeostasis. We suggest that considering plant health from a meta-organism perspective will help in developing multidisciplinary pathogen management strategies that focus on steering the whole plant-microbe-soil networks instead of individual components. This might be achieved by bringing together the latest discoveries in phytopathology, microbiome research, soil science and agronomy to pave the way toward more sustainable and productive agriculture. 相似文献
18.
Acar M Pando BF Arnold FH Elowitz MB van Oudenaarden A 《Science (New York, N.Y.)》2010,329(5999):1656-1660
Coping with variations in network dosage is crucial for maintaining optimal function in gene networks. We explored how network structure facilitates network-level dosage compensation. By using the yeast galactose network as a model, we combinatorially deleted one of the two copies of its four regulatory genes and found that network activity was robust to the change in network dosage. A mathematical analysis revealed that a two-component genetic circuit with elements of opposite regulatory activity (activator and inhibitor) constitutes a minimal requirement for network-dosage invariance. Specific interaction topologies and a one-to-one interaction stoichiometry between the activating and inhibiting agents were additional essential elements facilitating dosage invariance. This mechanism of network-dosage invariance could represent a general design for gene network structure in cells. 相似文献
19.
Trotzky S Cheinet P Fölling S Feld M Schnorrberger U Rey AM Polkovnikov A Demler EA Lukin MD Bloch I 《Science (New York, N.Y.)》2008,319(5861):295-299
Quantum mechanical superexchange interactions form the basis of quantum magnetism in strongly correlated electronic media. We report on the direct measurement of superexchange interactions with ultracold atoms in optical lattices. After preparing a spin-mixture of ultracold atoms in an antiferromagnetically ordered state, we measured coherent superexchange-mediated spin dynamics with coupling energies from 5 hertz up to 1 kilohertz. By dynamically modifying the potential bias between neighboring lattice sites, the magnitude and sign of the superexchange interaction can be controlled, thus allowing the system to be switched between antiferromagnetic and ferromagnetic spin interactions. We compare our findings to predictions of a two-site Bose-Hubbard model and find very good agreement, but are also able to identify corrections that can be explained by the inclusion of direct nearest-neighbor interactions. 相似文献
20.
Centola D 《Science (New York, N.Y.)》2011,334(6060):1269-1272
How does the composition of a population affect the adoption of health behaviors and innovations? Homophily--similarity of social contacts--can increase dyadic-level influence, but it can also force less healthy individuals to interact primarily with one another, thereby excluding them from interactions with healthier, more influential, early adopters. As a result, an important network-level effect of homophily is that the people who are most in need of a health innovation may be among the least likely to adopt it. Despite the importance of this thesis, confounding factors in observational data have made it difficult to test empirically. We report results from a controlled experimental study on the spread of a health innovation through fixed social networks in which the level of homophily was independently varied. We found that homophily significantly increased overall adoption of a new health behavior, especially among those most in need of it. 相似文献