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31.
Vedrana Filić Maja Marinović Jan Faix Igor Weber 《Cellular and molecular life sciences : CMLS》2014,71(15):2775-2785
Proteins are typically categorized into protein families based on their domain organization. Yet, evolutionarily unrelated proteins can also be grouped together according to their common functional roles. Sequestering proteins constitute one such functional class, acting as macromolecular buffers and serving as an intracellular reservoir ready to release large quantities of bound proteins or other molecules upon appropriate stimulation. Another functional protein class comprises effector proteins, which constitute essential components of many intracellular signal transduction pathways. For instance, effectors of small GTP-hydrolases are activated upon binding a GTP-bound GTPase and thereupon participate in downstream interactions. Here we describe a member of the IQGAP family of scaffolding proteins, DGAP1 from Dictyostelium, which unifies the roles of an effector and a sequestrator in regard to the small GTPase Rac1. Unlike classical effectors, which bind their activators transiently leading to short-lived signaling complexes, interaction between DGAP1 and Rac1-GTP is stable and induces formation of a complex with actin-bundling proteins cortexillins at the back end of the cell. An oppositely localized Rac1 effector, the Scar/WAVE complex, promotes actin polymerization at the cell front. Competition between DGAP1 and Scar/WAVE for the common activator Rac1-GTP might provide the basis for the oscillatory re-polarization typically seen in randomly migrating Dictyostelium cells. We discuss the consequences of the dual roles exerted by DGAP1 and Rac1 in the regulation of cell motility and polarity, and propose that similar signaling mechanisms may be of general importance in regulating spatiotemporal dynamics of the actin cytoskeleton by small GTPases. 相似文献
32.
33.
Paloma Feyjoo Miguel Cabanellas-Reboredo Matías Calvo-Manazza Beatriz Morales-Nín Jorge Hernández-Urcera Manuel E. Garci 《Journal of Natural History》2016,50(9-10):543-555
The embryonic development of the squid Loligo vulgaris was observed from 183 egg masses collected from special devices deployed throughout Cabrera National Park (Baleares Islands, western Mediterranean Sea). Sequence alignment analysis of the cytochrome oxidase I gene revealed that all embryos belonged to L. vulgaris. In total, 549 egg capsules were examined. Viable egg capsules (n = 420) were classified into one of five maturation stages according to the primary external features. The length of the viable egg capsules varied between 40 and 170 mm, and increased with embryonic development. The non-viable capsules (n = 129) were categorized into four groups: I (Ginger root), non-viable II and III, and empty egg capsule (IV). The percentage of non-viable capsules (i.e. grades I, II and III) was 92.25%. Empty capsules accounted for 7.75% of the total non-viable egg capsules. Embryonic development was classified into a second scale of eight stages. Egg capsule stage and embryonic stage were significantly related (n = 420; p < 0.001), facilitating the determination of the embryo developmental phase based on the outward appearance of the egg capsules. The embryo development stage based on the external features of the egg capsules might constitute an innovative tool for in situ embryological data collection. This new method is neither time consuming nor invasive, and could be helpful in fishing cruises, for scuba diving visual census in natural habitats and for laboratory culture. Slight variability in the developmental embryonic stages within egg capsules from the same egg mass was identified. The origin of this asynchrony is discussed. Chronological appearance of organs was similar to that of the six loliginid species previously examined. However, some developmental changes in the timing or rate of events (heterochronies) were observed: Hoyle’s organ was formed earlier in L. vulgaris and the appearance of ventral chromatophores was slightly delayed (2 days) compared with the other species considered. 相似文献
34.
Dealing with Distances and Transformations for Fuzzy C-Means Clustering of Compositional Data 总被引:1,自引:0,他引:1
Javier Palarea-Albaladejo Josep Antoni Martín-Fernández Jesús A. Soto 《Journal of Classification》2012,29(2):144-169
Clustering techniques are based upon a dissimilarity or distance measure between objects and clusters. This paper focuses on the simplex space, whose elements??compositions??are subject to non-negativity and constant-sum constraints. Any data analysis involving compositions should fulfill two main principles: scale invariance and subcompositional coherence. Among fuzzy clustering methods, the FCM algorithm is broadly applied in a variety of fields, but it is not well-behaved when dealing with compositions. Here, the adequacy of different dissimilarities in the simplex, together with the behavior of the common log-ratio transformations, is discussed in the basis of compositional principles. As a result, a well-founded strategy for FCM clustering of compositions is suggested. Theoretical findings are accompanied by numerical evidence, and a detailed account of our proposal is provided. Finally, a case study is illustrated using a nutritional data set known in the clustering literature. 相似文献
35.
Otávio Bueno Steven French James Ladyman 《Studies in History and Philosophy of Science Part B: Studies in History and Philosophy of Modern Physics》2012,43(2):95-104
We offer a framework to represent the roles of empirical and theoretical factors in theory construction, and examine a case study to illustrate how the framework can be used to illuminate central features of scientific reasoning. The case study provides an extension of French and Ladyman's (1997) analysis of Fritz and Heinz London's model of superconductivity to accommodate the role of the analogy between superconductivity and diamagnetic phenomena in the development of the model between 1935 and 1937. We focus on this case since it allows us to separate the roles of empirical and theoretical factors, and so provides an example of the utility of the approach that we have adopted. We conclude the paper by drawing on the particular framework here developed to address a range of concerns. 相似文献
36.
Periodic mesoporous materials formed through the cooperative self-assembly of surfactants and framework building blocks can assume a variety of structures, and their widely tuneable properties make them attractive hosts for numerous applications. Because the molecular movement in the pore system is the most important and defining characteristic of porous materials, it is of interest to learn about this behaviour as a function of local structure. Generally, individual fluorescent dye molecules can be used as molecular beacons with which to explore the structure of--and the dynamics within--these porous hosts, and single-molecule fluorescence techniques provide detailed insights into the dynamics of various processes, ranging from biology to heterogeneous catalysis. However, optical microscopy methods cannot directly image the mesoporous structure of the host system accommodating the diffusing molecules, whereas transmission electron microscopy provides detailed images of the porous structure, but no dynamic information. It has therefore not been possible to 'see' how molecules diffuse in a real nanoscale pore structure. Here we present a combination of electron microscopic mapping and optical single-molecule tracking experiments to reveal how a single luminescent dye molecule travels through linear or strongly curved sections of a mesoporous channel system. In our approach we directly correlate porous structures detected by transmission electron microscopy with the diffusion dynamics of single molecules detected by optical microscopy. This opens up new ways of understanding the interactions of host and guest. 相似文献
37.
Cdk1 is sufficient to drive the mammalian cell cycle 总被引:1,自引:0,他引:1
Santamaría D Barrière C Cerqueira A Hunt S Tardy C Newton K Cáceres JF Dubus P Malumbres M Barbacid M 《Nature》2007,448(7155):811-815
38.
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite 总被引:6,自引:0,他引:6
Warnecke F Luginbühl P Ivanova N Ghassemian M Richardson TH Stege JT Cayouette M McHardy AC Djordjevic G Aboushadi N Sorek R Tringe SG Podar M Martin HG Kunin V Dalevi D Madejska J Kirton E Platt D Szeto E Salamov A Barry K Mikhailova N Kyrpides NC Matson EG Ottesen EA Zhang X Hernández M Murillo C Acosta LG Rigoutsos I Tamayo G Green BD Chang C Rubin EM Mathur EJ Robertson DE Hugenholtz P Leadbetter JR 《Nature》2007,450(7169):560-565
From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding 'higher' Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H2 metabolism, CO2-reductive acetogenesis and N2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-microl environment can be. 相似文献
39.
Engel GS Calhoun TR Read EL Ahn TK Mancal T Cheng YC Blankenship RE Fleming GR 《Nature》2007,446(7137):782-786
Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke 'hopping' of excited-state populations along discrete energy levels. Two-dimensional Fourier transform electronic spectroscopy has mapped these energy levels and their coupling in the Fenna-Matthews-Olson (FMO) bacteriochlorophyll complex, which is found in green sulphur bacteria and acts as an energy 'wire' connecting a large peripheral light-harvesting antenna, the chlorosome, to the reaction centre. The spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex. But the intricate dynamics of quantum coherence, which has no classical analogue, was largely neglected in the analyses-even though electronic energy transfer involving oscillatory populations of donors and acceptors was first discussed more than 70 years ago, and electronic quantum beats arising from quantum coherence in photosynthetic complexes have been predicted and indirectly observed. Here we extend previous two-dimensional electronic spectroscopy investigations of the FMO bacteriochlorophyll complex, and obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path. 相似文献
40.
The significance of nitrification for oceanic new production 总被引:1,自引:0,他引:1
The flux of organic material sinking to depth is a major control on the inventory of carbon in the ocean. To first order, the oceanic system is at equilibrium such that what goes down must come up. Because the export flux is difficult to measure directly, it is routinely estimated indirectly by quantifying the amount of phytoplankton growth, or primary production, fuelled by the upward flux of nitrate. To do so it is necessary to take into account other sources of biologically available nitrogen. However, the generation of nitrate by nitrification in surface waters has only recently received attention. Here we perform the first synthesis of open-ocean measurements of the specific rate of surface nitrification and use these to configure a global biogeochemical model to quantify the global role of nitrification. We show that for much of the world ocean a substantial fraction of the nitrate taken up is generated through recent nitrification near the surface. At the global scale, nitrification accounts for about half of the nitrate consumed by growing phytoplankton. A consequence is that many previous attempts to quantify marine carbon export, particularly those based on inappropriate use of the f-ratio (a measure of the efficiency of the 'biological pump'), are significant overestimates. 相似文献