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Satellite-detected fluorescence reveals global physiology of ocean phytoplankton  [PDF]
M. J. Behrenfeld,T. K. Westberry,E. S. Boss,R. T. O'Malley
Biogeosciences Discussions , 2008,
Abstract: Phytoplankton photosynthesis links global ocean biology and climate-driven fluctuations in the physical environment. These interactions are largely expressed through changes in phytoplankton physiology, but physiological status has proven extremely challenging to characterize globally. Phytoplankton fluorescence does provide a rich source of physiological information long exploited in laboratory and field studies, and is now observed from space. Here we use satellite-based fluorescence measurements to evaluate light-absorption and energy-dissipation processes influencing phytoplankton light use efficiency and demonstrate its utility as a global physiological indicator of iron-limited growth conditions. This new tool provides a path for monitoring climate-phytoplankton physiology interactions, improving descriptions of light use efficiency in ocean productivity models, evaluating nutrient-stress predictions in ocean ecosystem models, and appraising phytoplankton responses to natural iron enrichments or purposeful iron fertilizations activities.
Network Physiology reveals relations between network topology and physiological function  [PDF]
Amir Bashan,Ronny P. Bartsch,Jan W. Kantelhardt,Shlomo Havlin,Plamen Ch. Ivanov
Quantitative Biology , 2012, DOI: 10.1038/ncomms1705
Abstract: The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and quantifying dynamical networks of diverse systems with different types of interactions is a challenge. Here, we develop a framework to probe interactions among diverse systems, and we identify a physiologic network. We find that each physiologic state is characterized by a specific network structure, demonstrating a robust interplay between network topology and function. Across physiologic states the network undergoes topological transitions associated with fast reorganization of physiologic interactions on time scales of a few minutes, indicating high network flexibility in response to perturbations. The proposed system-wide integrative approach may facilitate the development of a new field, Network Physiology.
Satellite-detected fluorescence reveals global physiology of ocean phytoplankton
M. J. Behrenfeld, T. K. Westberry, E. S. Boss, R. T. O'Malley, D. A. Siegel, J. D. Wiggert, B. A. Franz, C. R. McClain, G. C. Feldman, S. C. Doney, J. K. Moore, G. Dall'Olmo, A. J. Milligan, I. Lima,N. Mahowald
Biogeosciences (BG) & Discussions (BGD) , 2009,
Abstract: Phytoplankton photosynthesis links global ocean biology and climate-driven fluctuations in the physical environment. These interactions are largely expressed through changes in phytoplankton physiology, but physiological status has proven extremely challenging to characterize globally. Phytoplankton fluorescence does provide a rich source of physiological information long exploited in laboratory and field studies, and is now observed from space. Here we evaluate the physiological underpinnings of global variations in satellite-based phytoplankton chlorophyll fluorescence. The three dominant factors influencing fluorescence distributions are chlorophyll concentration, pigment packaging effects on light absorption, and light-dependent energy-quenching processes. After accounting for these three factors, resultant global distributions of quenching-corrected fluorescence quantum yields reveal a striking consistency with anticipated patterns of iron availability. High fluorescence quantum yields are typically found in low iron waters, while low quantum yields dominate regions where other environmental factors are most limiting to phytoplankton growth. Specific properties of photosynthetic membranes are discussed that provide a mechanistic view linking iron stress to satellite-detected fluorescence. Our results present satellite-based fluorescence as a valuable tool for evaluating nutrient stress predictions in ocean ecosystem models and give the first synoptic observational evidence that iron plays an important role in seasonal phytoplankton dynamics of the Indian Ocean. Satellite fluorescence may also provide a path for monitoring climate-phytoplankton physiology interactions and improving descriptions of phytoplankton light use efficiencies in ocean productivity models.
The SNARE protein family of Leishmania major
Sébastien Besteiro, Graham H Coombs, Jeremy C Mottram
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-250
Abstract: Bioinformatic searches of the L. major genome revealed a total of 27 SNARE domain-containing proteins that could be classified in structural groups by phylogenetic analysis. 25 of these possessed the expected features of functional SNAREs, whereas the other two could represent kinetoplastid-specific proteins that might act as regulators of the SNARE complexes. Other differences of Leishmania SNAREs were the absence of double SNARE domain-containing and of the brevin classes of these proteins. Members of the Qa group of Leishmania SNAREs showed differential expressions profiles in the two main parasite forms whereas their GFP-tagging and in vivo expression revealed localisations in the Golgi, late endosome/lysosome and near the flagellar pocket.The early-branching eukaryote L. major apparently possess a SNARE repertoire that equals in number the one of metazoans such as Drosophila, showing that the machinery for vesicle fusion is well conserved throughout the eukaryotes. However, the analysis revealed the absence of certain types of SNAREs found in metazoans and yeast, while suggesting the presence of original SNAREs as well as others with unusual localisation. This study also presented the intracellular localisation of the L. major SNAREs from the Qa group and reveals that these proteins could be useful as organelle markers in this parasitic protozoon.Eukaryotic cells contain many internal organelles surrounded by membrane boundaries, where specialised and essential functions are performed. The traffic between these different organelles is mainly mediated by vesicular transport [1]. The mechanism required for this type of transport involves a complex and specifically regulated machinery that allows budding of vesicles from a donor compartment, followed by their translocation to their target, to which they have to dock and then fuse. Among the lipid and protein factors that are thought to be involved in these processes, a large family of proteins called soluble N-eth
SNARE Zippering and Synaptic Strength  [PDF]
Rene C. Prashad, Milton P. Charlton
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0095130
Abstract: Synapses vary widely in the probability of neurotransmitter release. We tested the hypothesis that the zippered state of the trans-SNARE (Soluble N-ethylmaleimide-sensitive factor Attachment protein REceptor) complex determines initial release probability. We tested this hypothesis at phasic and tonic synapses which differ by 100-1000-fold in neurotransmitter release probability. We injected, presynaptically, three Clostridial neurotoxins which bind and cleave at different sites on VAMP to determine whether these sites were occluded by the zippering of the SNARE complex or open to proteolytic attack. Under low stimulation conditions, the catalytic light-chain fragment of botulinum B (BoNT/B-LC) inhibited evoked release at both phasic and tonic synapses and cleaved VAMP; however, neither BoNT/D-LC nor tetanus neurotoxin (TeNT-LC) were effective in these conditions. The susceptibility of VAMP to only BoNT/B-LC indicated that SNARE complexes at both phasic and tonic synapses were partially zippered only at the N-terminal end to approximately the zero-layer with the C-terminal end exposed under resting state. Therefore, the existence of the same partially zippered state of the trans-SNARE complex at both phasic and tonic synapses indicates that release probability is not determined solely by the zippered state of the trans-SNARE complex at least to the zero-layer.
SNARE Protein Mimicry by an Intracellular Bacterium  [PDF]
Cédric Delevoye,Michael Nilges,Pierre Dehoux,Fabienne Paumet,Stéphanie Perrinet,Alice Dautry-Varsat,Agathe Subtil
PLOS Pathogens , 2008, DOI: 10.1371/journal.ppat.1000022
Abstract: Many intracellular pathogens rely on host cell membrane compartments for their survival. The strategies they have developed to subvert intracellular trafficking are often unknown, and SNARE proteins, which are essential for membrane fusion, are possible targets. The obligate intracellular bacteria Chlamydia replicate within an intracellular vacuole, termed an inclusion. A large family of bacterial proteins is inserted in the inclusion membrane, and the role of these inclusion proteins is mostly unknown. Here we identify SNARE-like motifs in the inclusion protein IncA, which are conserved among most Chlamydia species. We show that IncA can bind directly to several host SNARE proteins. A subset of SNAREs is specifically recruited to the immediate vicinity of the inclusion membrane, and their accumulation is reduced around inclusions that lack IncA, demonstrating that IncA plays a predominant role in SNARE recruitment. However, interaction with the SNARE machinery is probably not restricted to IncA as at least another inclusion protein shows similarities with SNARE motifs and can interact with SNAREs. We modelled IncA's association with host SNAREs. The analysis of intermolecular contacts showed that the IncA SNARE-like motif can make specific interactions with host SNARE motifs similar to those found in a bona fide SNARE complex. Moreover, point mutations in the central layer of IncA SNARE-like motifs resulted in the loss of binding to host SNAREs. Altogether, our data demonstrate for the first time mimicry of the SNARE motif by a bacterium.
Human Scalp Electroencephalography Reveals that Repetition Suppression Varies with Expectation  [PDF]
Christopher Summerfield,Valentin Wyart,Vanessa Mareike Johnen,Vincent de Gardelle
Frontiers in Human Neuroscience , 2011, DOI: 10.3389/fnhum.2011.00067
Abstract: Repetitions of a sensory event elicit lower levels of brain activity than its initial presentation (“repetition suppression,” RS). According to one view, RS depends on the biophysics of neuronal discharge, and is thus an automatic consequence of stimulus processing (“fatigue” model). Another account suggests that RS depends on the statistical structure of the environment, and occurs when repeated stimuli are less surprising than novel stimuli (“surprise reduction” model). In support of the latter view, functional magnetic resonance imaging studies have shown that RS is modulated by the local probability of repetition. However, single-cell recordings from macaque inferotemporal area (IT) have failed to replicate this finding. Here, we recorded scalp electroencephalography from human participants viewing pairs of faces that repeated (face1–face1) or alternated (face1–face2), in contexts in which repetitions were expected or unexpected. As previously described, event-related potentials in the range of 100–400 ms recorded at posterior electrode sites and at the vertex differed between repetitions and alternations. Critically, at central electrodes, we observed that the difference between repeated and alternating stimuli was attenuated when repetitions were unexpected, as predicted by the surprise reduction model. These findings demonstrate that the modulation of RS by repetition probability is observable using direct neural recording methods in human participants, and that it occurs relatively late (>300 ms) post-stimulus. Finally, we found that theta-band (4–8 Hz) spectral power over central electrodes varied with the three-way interaction between of repetition, expectation, and the rate of change of the environment, consistent with recent reports that frontal theta may be a hallmark of learning processes originating in the anterior cingulate and medial prefrontal cortex.
Suppression subtractive hybridization analysis reveals expression of conserved and novel genes in male accessory glands of the ant Leptothorax gredleri
Angelika Oppelt, Fernanda C Humann, Marion Fuessl, Sergio V Azevedo, David S Marco Antonio, Jürgen Heinze, Klaus Hartfelder
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-273
Abstract: By a suppression subtractive hybridization protocol we obtained 20 unique sequences (USs). Twelve had mutual best matches with genes predicted for Apis mellifera and Nasonia vitripennis. Functional information (Gene Ontology) was available only for seven of these, including intracellular signaling, energy-dependent transport and metabolic enzyme activities. The remaining eight USs did not match sequences from other species. Six genes were further analyzed by quantitative RT-PCR in three life cycle stages of male ants. A gene with carboxy-lyase activity and one of unpredicted function were significantly overexpressed in accessory glands of sexually mature males.Our study is the first one to investigate differential gene expression in ants in a context related to mating. Our findings indicate that male accessory glands of L. gredleri express a series of genes that are unique to this species, possibly representing novel genes, in addition to conserved ones for which functions can be predicted. Identifying differentially expressed genes might help to better understand molecular mechanisms involved in reproductive processes in eusocial Hymenoptera. While the novel genes could account for rapidly evolving ones driven by intra-sexual conflict between males, conserved genes imply that rather beneficial traits might get fixed by a process described as inter-sexual cooperation between males and females.Substances produced by the male accessory glands (MAGs) of insects and transferred into the female genital tract during mating are known to reduce pathogen transmission, to form mating plugs or spermatophores, and to be important in sperm competition. In addition, they trigger fundamental changes in female physiology, behavior, and reproduction [1-4]. The major biologically active components of MAG secretions are carbohydrates, lipids, and in particular accessory gland proteins (Acps) [1].In Drosophila melanogaster, more than 100 Acps have been identified [5]. They play roles i
Phylogeny of the SNARE vesicle fusion machinery yields insights into the conservation of the secretory pathway in fungi
Nickias Kienle, Tobias H Kloepper, Dirk Fasshauer
BMC Evolutionary Biology , 2009, DOI: 10.1186/1471-2148-9-19
Abstract: Here, we make use of the increasing amount of genomic data to investigate the history of the SNARE family during fungi evolution. Moreover, since different SNARE family members are thought to demarcate different organelles and vesicles, this approach allowed us to compare the organization of the endomembrane systems of yeast and animal cells. Our data corroborate the notion that fungi generally encompass a relatively simple set of SNARE proteins, mostly comprising the SNAREs of the proto-eukaryotic cell. However, all fungi contain a novel soluble SNARE protein, Vam7, which carries an N-terminal PX-domain that acts as a phosphoinositide binding module. In addition, the points in fungal evolution, at which lineage-specific duplications and diversifications occurred, could be determined. For instance, the endosomal syntaxins Pep12 and Vam3 arose from a gene duplication that occurred within the Saccharomycotina clade.Although the SNARE repertoire of baker's yeast is highly conserved, our analysis reveals that it is more deviated than the ones of basal fungi. This highlights that the trafficking pathways of baker's yeast are not only different to those in animal cells but also are somewhat different to those of many other fungi.Over the last decades, the organization of the secretory and endocytic pathways has been studied in a variety of different eukaryotic organisms. These studies have revealed that the principal organization of the endomembrane system and the molecular machineries involved in vesicular trafficking are conserved among all eukaryotes. In general, the transport between different intracellular organelles is mediated by cargo-laden vesicles that bud from a donor and then specifically fuse with an acceptor compartment. Key players during the final fusion step are the so-called SNARE proteins. These proteins are a large family of small cytoplasmically orientated membrane proteins that are typically tail-anchored. Their key characteristic is the so-called SN
植物SNARE蛋白的结构与功能  [PDF]
植物学报 , 2005,
Abstract: ?在真核生物细胞囊泡运输过程中的膜融合主要是由SNARE蛋白介导的,SNARE蛋白的结构高度保守。研究发现,植物中的SNARE蛋白促进植物细胞板形成,能与离子通道蛋白相互作用,有利于植物的正常生长发育,能提高植物的抗病性及参与植物的向重力性作用。应用基因组学和蛋白质组学技术结合细胞学水平上的分析方法有助于深入揭示植物SNARE蛋白家族成员的功能,明确SNARE蛋白在信号转导途径中的作用,阐明动植物免疫系统的区别和联系。
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