Pulse-Driven Loss of Top-Down Control: The Critical-Rate Hypothesis

In systems ranging from lakes and woodlands to coral reefs, the long-term ecosystem state may often be determined largely by rare extreme events such as wet ENSO years, droughts, or disease outbreaks. Such events can flip these systems into a contrasting state that represents either an alternative attractor or a transient that is slow enough to persist even if the frequency of events that push the system to this state is low. Here we show that escape from herbivores is a mechanism that can play a role in several state shifts of this kind. This can happen if plants become less susceptible to herbivory as they grow. Using a model we show that, surprisingly, this mechanism can lead to a situation where a brief resource pulse for plants may invoke a persistent shift to a high biomass state whereas gradual enrichment to the same resource level is insufficient to allow such a change. This counterintuitive phenomenon occurs if the numerical response of herbivores is sufficiently slow to allow the plants to use the resource pulse to escape to a safe biomass at which herbivory is reduced. Our results imply that rates of environmental change can sometimes be more important than their magnitude. This has many ramifications. On the conceptual side, our findings suggest that key mechanisms that regulate long-term ecosystem dynamics are easily missed by the traditional focus of modelers on equilibria. A more practical corollary is that increased climatic variability may have more profound effects in some ecosystems than gradual change in conditions.     

Functional architecture of higher plant photosystem II supercomplexes

Photosystem II (PSII) is a large multiprotein complex, which catalyses water splitting and plastoquinone reduction necessary to transform sunlight into chemical energy. Detailed functional and structural studies of the complex from higher plants have been hampered by the impossibility to purify it to homogeneity. In this work, homogeneous preparations ranging from a newly identified particle composed by a monomeric core and antenna proteins to the largest C₂S₂M₂ supercomplex were isolated. Characterization by biochemical methods and single particle electron microscopy allowed to relate for the first time the supramolecular organization to the protein content. A projection map of C₂S₂M₂ at 12 Å resolution was obtained, which allowed determining the location and the orientation of the antenna proteins. Comparison of the supercomplexes obtained from WT and Lhcb‐deficient plants reveals the importance of the individual subunits for the supramolecular organization. The functional implications of these findings are discussed and allow redefining previous suggestions on PSII energy transfer, assembly, photoinhibition, state transition and non‐photochemical quenching.     

Lipid body formation plays a central role in cell fate determination during developmental differentiation of Myxococcus xanthus

Cell differentiation is widespread during the development of multicellular organisms, but rarely observed in prokaryotes. One example of prokaryotic differentiation is the Gram-negative bacterium Myxococcus xanthus . In response to starvation, this gliding bacterium initiates a complex developmental programme that results in the formation of spore-filled fruiting bodies. How the cells metabolically support the necessary complex cellular differentiation from rod-shaped vegetative cells into spherical spores is unknown. Here, we present evidence that intracellular lipid bodies provide the necessary metabolic fuel for the development of spores. Formed at the onset of starvation, these lipid bodies gradually disappear until they are completely used up by the time the cells have become mature spores. Moreover, it appears that lipid body formation in M. xanthus is an important initial step indicating cell fate during differentiation. Upon starvation, two subpopulations of cells occur: cells that form lipid bodies invariably develop into spores, while cells that do not form lipid bodies end up becoming peripheral rods, which are cells that lack signs of morphological differentiation and stay in a vegetative-like state. These data indicate that lipid bodies not only fuel cellular differentiation but that their formation represents the first known morphological sign indicating cell fate during differentiation.     

Effects of Submerged Vegetation on Water Clarity Across Climates

A positive feedback between submerged vegetation and water clarity forms the backbone of the alternative state theory in shallow lakes. The water clearing effect of aquatic vegetation may be caused by different physical, chemical, and biological mechanisms and has been studied mainly in temperate lakes. Recent work suggests differences in biotic interactions between (sub)tropical and cooler lakes might result in a less pronounced clearing effect in the (sub)tropics. To assess whether the effect of submerged vegetation changes with climate, we sampled 83 lakes over a gradient ranging from the tundra to the tropics in South America. Judged from a comparison of water clarity inside and outside vegetation beds, the vegetation appeared to have a similar positive effect on the water clarity across all climatic regions studied. However, the local clearing effect of vegetation decreased steeply with the contribution of humic substances to the underwater light attenuation. Looking at turbidity on a whole-lake scale, results were more difficult to interpret. Although lakes with abundant vegetation (>30%) were generally clear, sparsely vegetated lakes differed widely in clarity. Overall, the effect of vegetation on water clarity in our lakes appears to be smaller than that found in various Northern hemisphere studies. This might be explained by differences in fish communities and their relation to vegetation. For instance, unlike in Northern hemisphere studies, we find no clear relation between vegetation coverage and fish abundance or their diet preference. High densities of omnivorous fish and coinciding low grazing pressures on phytoplankton in the (sub)tropics may, furthermore, weaken the effect of vegetation on water clarity.     

Megacomplex organization of the oxidative phosphorylation system by structural analysis of respiratory supercomplexes from potato

The individual protein complexes of the oxidative phosphorylation system (OXPHOS complexes I to V) specifically interact and form defined supramolecular structures, the so-called “respiratory supercomplexes”. Some supercomplexes appear to associate into larger structures, or megacomplexes, such as a string of dimeric ATP synthase (complex V₂). A row-like organization of OXPHOS complexes I, III and IV into respiratory strings has also been proposed. These transient strings cannot be purified after detergent solubilization. Hence the shape and composition of the respiratory string was approached by an extensive structural characterization of all its possible building blocks, which are the supercomplexes. About 400,000 molecular projections of supercomplexes from potato mitochondria were processed by single particle electron microscopy. We obtained two-dimensional projection maps of at least five different supercomplexes, including the supercomplex I + III₂, III₂ + IV₁, V₂, I + III₂ + IV₁ and I₂ + III₂ in different types of position. From these maps the relative position of the individual complexes in the largest unit, the I₂ + III₂ + IV₂ supercomplex, could be determined in a coherent way. The maps also show that the I + III₂ + IV₁ supercomplex, or respirasome, differs from its counterpart in bovine mitochondria. The new structural features allow us to propose a consistent model of the respiratory string, composed of repeating I₂ + III₂ + IV₂ units, which is in agreement with dimensions observed in former freeze-fracture electron microscopy data.     

Antibody-specific detection of CAIX in breast and prostate cancers

Carbonic anhydrase IX (CAIX) is frequently expressed in human tumors and serves as a marker for hypoxia. Further, CAIX expression is considered a predictor of poor survival in many, but not all, cancer types. Herein, we compare the specificity of two CAIX antibodies: the M75, monoclonal antibody which recognizes an epitope in the N-terminus and a commercially available polyclonal antibody generated against a C-terminal peptide (NB100-417). Western blot analysis of multiple breast cell lines revealed that the polyclonal antibody detected both membrane-bound and soluble proteins. The M75 antibody recognized only the membrane-bound species, which is presumed to be CAIX. These data were confirmed in an aggressive prostate cell line. We further compared these antibodies in prostate tumors by immunohistochemistry. Staining with NB100 was comparable to that of the M75 antibody, but only at high dilution. Otherwise, cytoplasmic staining was also noted. Two-dimensional gel electrophoresis followed by mass spectrometric analysis revealed that the cytoplasmic protein detected by NB100 is β-tubulin. This cross-reactivity could lead to false-positives for CAIX expression in samples where cytosolic proteins are present.     

The paradox of the clumps mathematically explained

The lumpy distribution of species along a continuous one-dimensional niche axis recently found by Scheffer and van Nes (Scheffer and van Ness 2006) is explained mathematically. We show that it emerges simply from the eigenvalue and eigenvectors of the community matrix. Both the transient patterns—lumps and gaps between them—as well as the asymptotic equilibrium are explained. If the species are evenly distributed along the niche axis, the emergence of these patterns can be demonstrated analytically. The more general case, of randomly distributed species, shows only slight deviations and is illustrated by numerical simulation. This is a robust result whenever the finiteness of the niche is taken into account: it can be extended to different analytic dependence of the interaction coefficients with the distance on the niche axis (i.e., different kernel interactions), different boundary conditions, etc. We also found that there is a critical value both for the width of the species distribution σ and the number of species n below which the clusterization disappears.

Alternative Stable States Driven by Density-Dependent Toxicity

Many populations are exposed to naturally occurring or synthetic toxicants. An increasing number of studies demonstrate that the toxicity of such compounds is not only dependent on the concentration or load, but also on the biomass or density of exposed organisms. At high biomass, organisms may be able to alleviate adverse effects of the toxicant by actively lowering ambient concentrations through either a joint detoxification mechanism or growth dilution. We show in a conceptual model that this mechanism may potentially lead to alternative stable states if the toxicant is lethal at low densities of organisms, whereas a high density is able to reduce the toxicant concentrations to sub-lethal levels. We show in an example that this effect may be relevant in real ecosystems. In an earlier published experimental laboratory study, we demonstrated that ammonia toxicity in eelgrass is highly dependent on the eelgrass shoot density. Here, we used the results of these experiments to construct a model describing the complex interactions between the temperate seagrass Zostera marina and potentially lethal ammonia. Analyses of the model show that alternative stable states are indeed present over wide ranges of key-parameter settings, suggesting that the mechanism might be important especially in sheltered, eutrophicated estuaries where mixing of the water layer is poor. We argue that the same mechanism could cause alternative stable states in other biological systems as well.     

A Whole Virus Pandemic Influenza H1N1 Vaccine Is Highly Immunogenic and Protective in Active Immunization and Passive Protection Mouse Models

The recent emergence and rapid spread of a novel swine-derived H1N1 influenza virus has resulted in the first influenza pandemic of this century. Monovalent vaccines have undergone preclinical and clinical development prior to initiation of mass immunization campaigns. We have carried out a series of immunogenicity and protection studies following active immunization of mice, which indicate that a whole virus, nonadjuvanted vaccine is immunogenic at low doses and protects against live virus challenge. The immunogenicity in this model was comparable to that of a whole virus H5N1 vaccine, which had previously been demonstrated to induce high levels of seroprotection in clinical studies. The efficacy of the H1N1 pandemic vaccine in protecting against live virus challenge was also seen to be equivalent to that of the H5N1 vaccine. The protective efficacy of the H1N1 vaccine was also confirmed using a severe combined immunodeficient (SCID) mouse model. It was demonstrated that mouse and guinea pig immune sera elicited following active H1N1 vaccination resulted in 100% protection of SCID mice following passive transfer of immune sera and lethal challenge. The immune responses to a whole virus pandemic H1N1 and a split seasonal H1N1 vaccine were also compared in this study. It was demonstrated that the whole virus vaccine induced a balanced Th-1 and Th-2 response in mice, whereas the split vaccine induced mainly a Th-2 response and only minimal levels of Th-1 responses. These data supported the initiation of clinical studies with the same low doses of whole virus vaccine that had previously been demonstrated to be immunogenic in clinical studies with a whole virus H5N1 vaccine.     

Revealing the architecture of the photosynthetic apparatus in the diatom Thalassiosira pseudonana

Diatoms are a large group of marine algae that are responsible for about one-quarter of global carbon fixation. Light-harvesting complexes of diatoms are formed by the fucoxanthin chlorophyll a/c proteins and their overall organization around core complexes of photosystems (PSs) I and II is unique in the plant kingdom. Using cryo-electron tomography, we have elucidated the structural organization of PSII and PSI supercomplexes and their spatial segregation in the thylakoid membrane of the model diatom species Thalassiosira pseudonana. 3D sub-volume averaging revealed that the PSII supercomplex of T. pseudonana incorporates a trimeric form of light-harvesting antenna, which differs from the tetrameric antenna observed previously in another diatom, Chaetoceros gracilis. Surprisingly, the organization of the PSI supercomplex is conserved in both diatom species. These results strongly suggest that different diatom classes have various architectures of PSII as an adaptation strategy, whilst a convergent evolution occurred concerning PSI and the overall plastid structure.

The antenna organization of photosystem II in the diatom Thalassiosira pseudonana strongly differs from Chaetoceros gracilis, while the architecture of the photosystem I antenna remains the same.