The low molecular weight proteome of Halobacterium salinarum

Systematic investigation of low molecular weight proteins (LMW, below 20 kDa) in the archaeon Halobacterium salinarum resulted in a 6-fold enhancement of the identification rate, reaching 35% of the theoretical proteome in that size range. This was achieved by optimization of common protocols for protein analysis with general applicability. LMW proteins were rapidly and effectively enriched by filter membrane centrifugation followed by tricine SDS-PAGE. Without staining and with significantly shortened digestion protocols, LMW proteins were identified using an FT-ICR mass spectrometer which allows reliable protein identification by MS3 of a single peptide. In addition to a series of technical challenges, small proteins may show low gene expression levels as suggested by their low average codon adaptation index. Twenty functionally uncharacterized proteins contain a characteristic DNA/RNA binding zinc finger motif which underlines the biological relevance of the small proteome and the necessity of their analysis for systems biology.     

Constitutive expression of inter-α-inhibitor (IαI) family proteins and tumor necrosis factor-stimulated gene-6 (TSG-6) by human amniotic membrane epithelial and stromal cells supporting formation of the heavy chain-hyaluronan (HC-HA) complex

Recently, we reported HC-HA, a covalent complex formed between heavy chains (HCs) of inter-α-inhibitor (IαI) and hyaluronan (HA) by the catalytic action of tumor necrosis factor (TNF)-stimulated gene-6 (TSG-6), is responsible for human amniotic membrane (AM) anti-inflammatory, anti-scarring, and anti-angiogenic actions. At the present time, the only well characterized source of IαI is serum being produced by the liver. This study showed that AM epithelial and stromal cells and stromal matrix all stained positively for HA, HC 1, 2, and 3, bikunin, and TSG-6. TSG-6 mRNA and protein were constitutively expressed by cultured AM epithelial and stromal cells without being up-regulated by TNF. In serum-free conditions, these cells expressed IαI, leading to the formation of HC-HA complex that contained both HC1 and HC2. In contrast, only HC1 was found in the HC-HA complex purified from AM. Local production of IαI, the HC-TSG-6 intermediate complex, and HC-HA were abolished when cells were treated with siRNA to HC1, HC2, bikunin (all of which impair the biosynthesis of IαI), or TSG-6 but not to HC3. Collectively, these results indicate that AM is another tissue in addition to the liver to constitutively produce IαI and that the HC-HA complex made by this tissue is different from that found at inflammatory sites (e.g. in asthma and arthritis) and in the matrix of the cumulus oocyte complex.     

Importance of Nutrient Competition and Allelopathic Effects in Suppression of the Green Alga Scenedesmus obliquus by the Macrophytes Chara, Elodea and Myriophyllum

Possible allelopathic effects of substances released from the macrophytes Chara globularis, Elodea canadensis, Myriophyllum spicatum on the common green alga Scenedesmus obliquus were tested in the laboratory with plastic plants and untreated medium as controls. A two-phase approach was used in which first the effects of physical presence of plants was studied (phase I) followed by the effects of plant culture filtrates (phase II). In the presence of plastic plants growth was reduced only marginally, but strong growth inhibition of Scenedesmus occurred in the physical presence of all macrophytes. In contrast, filtrates from Chara had no growth inhibitory effect on Scenedesmus. Myriophyllum filtrate reduced particle-based growth rate by 7% compared to filtration controls, while Elodea culture filtrate reduced volume-based growth by 12%, chlorophyll-based growth by 28% and particle-based growth by 15%. Photosystem II-efficiency of Scenedesmus was reduced in all three macrophyte treatments in phase I, but not in filtrates from macrophyte cultures (phase II). Thus, while enzyme activity or other physiological aspects may have been affected, the current study yielded no proof for allelopathically active compounds being directed at photosynthesis. Mean particle volume (MPV) of Scenedesmus was not influenced by macrophyte exudates and cultures remained dominated by unicells. The strong growth inhibitory effects found for Scenedesmus in the physical presence of macrophytes, but not in plastic controls, and no or weaker response in nutrient-enriched filtrates, suggest nutrient competition was a more powerful driving factor than allelochemicals. However, the experimental design does not exclude disappearance of allelochemicals during the filtration process.     

In vitro pathogenicity assay for the ergot fungus Claviceps purpurea

The pathogenic development of the biotrophic ergot fungus Claviceps purpurea is strictly limited to the ovary of grasses. Early colonization stages occur within a defined spatio-temporal course of events, including the directed growth to the vascular tissue for nutrient supply. To characterize mutant strains with putative defects in pathogenicity, the close observation of the infection pathway is therefore indispensable. Here, we describe the establishment of a new pathogenicity assay, based on the in vitro cultivation of isolated rye ovaries. The pathogenic development of a wild-type strain of C. purpurea was compared with the infection of mature rye flowers on whole plants. Up to the sixth day post inoculation, the route of infection within the isolated ovaries was maintained and temporally equal to that seen in mature flowers. Therefore, the in vitro pathogenicity assay is an effective alternative to the whole-plant infection tests, and suitable for detailed infection studies and screening high numbers of mutants for defects in early pathogenesis.     

Spatial correlation as leading indicator of catastrophic shifts

Generic early-warning signals such as increased autocorrelation and variance have been demonstrated in time-series of systems with alternative stable states approaching a critical transition. However, lag times for the detection of such leading indicators are typically long. Here, we show that increased spatial correlation may serve as a more powerful early-warning signal in systems consisting of many coupled units. We first show why from the universal phenomenon of critical slowing down, spatial correlation should be expected to increase in the vicinity of bifurcations. Subsequently, we explore the applicability of this idea in spatially explicit ecosystem models that can have alternative attractors. The analysis reveals that as a control parameter slowly pushes the system towards the threshold, spatial correlation between neighboring cells tends to increase well before the transition. We show that such increase in spatial correlation represents a better early-warning signal than indicators derived from time-series provided that there is sufficient spatial heterogeneity and connectivity in the system.     

Large species shifts triggered by small forces

Changes in species composition of communities seem to proceed gradually at first sight, but remarkably rapid shifts are known to occur. Although disrupting disturbances seem an obvious explanation for such shifts, evidence for large disturbances is not always apparent. Here we show that complex communities tend to move through occasional catastrophic shifts in response to gradual environmental change or evolution. This tendency is caused by multiple attractors that may exist in such systems. We show that alternative attractors arise robustly in randomly generated multispecies models, especially if competition is symmetrical and if interspecific competition is allowed to exceed intraspecific competition. Inclusion of predators as a second trophic level did not alter the results greatly, although it reduced the probability of alternative attractors somewhat. These results suggest that alternative attractors may commonly arise from interactions between large numbers of species. Consequently, the response of complex communities to environmental change is expected to be characterized by hysteresis and sudden shifts. Some unexplained regime shifts observed in ecosystems could be related to alternative attractors arising from complex species interactions. Additionally, our results support the idea that ancient mass extinctions may partly be due to an intrinsic loss of stability of species configurations.     

Chemical polymorphism of the essential oils from populations of Thymus caespititius grown on the islands Pico,Faial and Graciosa (Azores)

The compositions of the essential oils isolated from the aerial parts of 11 populations of Thymus caespititius collected during the flowering phase on Pico, Faial and Graciosa (Azores) were studied by GC and GC-MS. The monoterpene fraction was dominant in all the oils analysed (55-90%) and consisted mainly of oxygen-containing compounds (44-79%). Sesquiterpenes represented an important fraction of the oils from the populations grown on Graciosa (13-28%). In contrast, this fraction was rather small in the oils from the populations grown on Pico and Faial (6-11%). Despite this, oxygen-containing compounds (4-18%) were always dominant. Cluster analysis of all identified oil components grouped the oils into three main clusters that corresponded with their main components. The oils from the 11 populations studied showed a clear chemical polymorphism that, in some cases, was more evident among populations growing on the same island than among those from different islands.     

Regime Shifts in the Sahara and Sahel: Interactions between Ecological and Climatic Systems in Northern Africa

The Sahara and Sahel regions of northern Africa have complex environmental histories punctuated by sudden and dramatic regime shifts in climate and ecological conditions. Here we review the current understanding of the causes and consequences of two environmental regime shifts in the Sahara and Sahel. The first regime shift is the sudden transition from vegetated to desert conditions in the Sahara about 5500 years ago. Geologic data show that wet environmental conditions in this region—giving rise to extensive vegetation, lakes, and wetlands—came to an abrupt end about 5500 years ago. Explanations for climatic changes in northern Africa during the Holocene have suggested that millennial-scale changes in the Earths orbit could have caused the wet conditions that prevailed in the early Holocene and the dry conditions prevalent today. However, the orbital hypothesis, by itself, does not explain the sudden regime shift 5500 years ago. Several modeling studies have proposed that strong, nonlinear feedbacks between vegetation and the atmosphere could amplify the effects of orbital variations and create two alternative stable states (or regimes) in the climate and ecosystems of the Sahara: a green Sahara and a desert Sahara. A recent coupled atmosphere-ocean-land model confirmed that there was a sudden shift from the green Sahara to the desert Sahara regime approximately 5500 years ago. The second regime shift is the onset of a major 30-year drought over the Sahel around 1969. Several lines of evidence have suggested that the interactions between atmosphere and vegetation act to reinforce either a wet Sahel or a dry Sahel climatic regime, which may persist for decades at a time. Recent modeling studies have indicated that the shift from a wet Sahel to a dry Sahel regime was caused by strong feedbacks between the climate and vegetation cover and may have been triggered by slow changes in either land degradation or sea-surface temperatures. Taken together, we conclude that the existence of alternative stable states (or regimes) in the climate and ecosystems of the Sahara and Sahel may be the result of strong, nonlinear interactions between vegetation and the atmosphere. Although the shifts between these regimes occur rapidly, they are made possible by slow, subtle changes in underlying environmental conditions, including slow changes in incoming solar radiation, sea-surface temperatures, or the degree of land degradation.     

High level expression and secretion of truncated forms of herpes simplex virus type 1 and type 2 glycoprotein D by the methylotrophic yeast Pichia pastoris

Herpes simplex virus type 1 and 2 (HSV-1 and -2) glycoproteins D (gD-1 and gD-2) play a role in the entry of the virus into the host cell. Availability of substantial amounts of these proteins, or large fragments thereof, will be needed to allow studies at the molecular level. We studied the potency of the Pichia pastoris yeast expression system to produce soluble forms of gD. The DNA sequences encoding the extracellular domains of gD [amino acids 1-314 (gD-1(1-314)) and amino acids 1-254 (gD-1(1-254)) of gD-1 and amino acids 1-314 of gD-2 (gD-2(1-314))] were cloned into the P. pastoris yeast expression vector pPIC9. Two truncated forms of gD-1 were fitted with a His tail (designated as gD-1(1-314His) and gD-1(1-254His)) to facilitate their purification. Large amounts of gD-1(1-314) and gD-1(1-314His) (280-300mg/L induction medium) were produced. The yields of recombinant gD-1(1-254) and gD-1(1-254His) were lower: 20-36mg/L, and the yield of the gD-2(1-314) fragment was much lower: 6mg/L. SDS-PAGE analysis revealed multiple glycosylated species of the larger gD fragments, ranging in apparent molecular weight from 31 to 78kDa. The smaller gD-1(1-254) fragment appeared as two bands with molecular weights of 33 and 31kDa. All recombinant proteins produced by P. pastoris were recognized, as expected, by a panel of MAbs (A16, DL6, A18, DL11, HD1, ABDI, and AP7). In addition, we showed that gD-1(1-314), gD-2(1-314), and gD-1(1-254His) were able to interfere with binding of HSV to susceptible cells. These results indicate that the conformations of the recombinant proteins closely resemble those of native gD.