Alternative stable states, trait dispersion and ecological restoration

Didham et al. suggested that abiotically structured communities showing trait under-dispersion are more likely to exhibit alternative stable states than are competitively structured communities showing trait over-dispersion. We argue that the opposite is the logical expectation, and discuss implications for ecological restoration at local and regional scales.     

Alternative stable states in communities with intraguild predation

Intraguild predation (IGP) is a widespread ecological phenomenon in which two consumers that share a resource also engage in a predator-prey interaction. Theory on IGP predicts the occurrence of alternative stable states, but empirical evidence of such states is scarce. This raises the question of whether alternative states are a rare phenomenon that is unlikely to be observed in nature. Here we analyze a model in which the resource exhibits logistic or chemostat dynamics and consumers have saturating (Type II) functional responses. We show that alternative states can arise for a wide range of biological scenarios and that environmental constraints can make their detection difficult. Our analysis identifies three possible combinations of alternative states: (i) IG prey or IG predator, (ii) coexistence or IG predator, and (iii) coexistence or IG prey. Bifurcation diagrams reveal that alternative states are possible over large regions of the parameter space. However, they can be limited to narrow ranges along the resource productivity axis, which may make it difficult to observe the occurrence of alternative states in communities with IGP. Microcosm experiments provide a promising avenue for detecting combinations of asymptotically stable states along a productivity gradient.     

Virion swelling is not required for cotranslational disassembly of cowpea chlorotic mottle virus in vitro.

The mechanism by which virions of cowpea chlorotic mottle virus (CCMV) disassemble and allow for translation of the virion RNA is not well understood. Previous models have suggested that virion swelling is required to expose the virion RNA for translation in a process referred to as cotranslational disassembly (M. Brisco, R. Hull, and T. M. A. Wilson, Virology 148:210-217, 1986; J. W. Roenhorst, J. W. M. van Lent, and B. J. M. Verduin, Virology 164:91-98, 1988; J. W. Roenhorst, J. M. Verduin, and R. W. Goldbach, Virology 168:138-146, 1989). Previous work in our laboratory has identified point mutations in the CCMV coat protein which result in virions with altered swelling characteristics (J. Fox, F. G. Albert, J. Speir, and M. J. Young, Virology 227:229-233, 1997; J. M. Fox, X. Zhao, J. A. Speir, and M. J. Young, Virology 222:115-122, 1996). The wild-type and mutant CCMV virions were used to correlate virion swelling with the ability of virion RNA to be translated in a cell-free wheat germ extract. Mutant virions unable to swell (cpK42R) are as infectious as wild-type virions in vivo, and the levels of translated encapsidated virion RNA are similar to those of wild-type virions in vitro. Mutant virions capable of swelling but not of disassembling in vitro (cpR26C) are noninfectious and have severely reduced levels of translation of the encapsidated virion RNA in vitro. These studies suggest that virion swelling is not required for the cotranslational disassembly of CCMV. Additionally, the results indicate that there is a pH-dependent structural transition in the virion, other than swelling, that results in the RNA's being exposed for translation in vitro. An alternative model suggesting that cotranslational disassembly of CCMV involves presentation of the virion RNA through the virion fivefold axis is proposed.     

Relationship between viral DNA synthesis and virion envelopment in hepatitis B viruses.

While the intracellular pool of encapsidated hepatitis B viral DNA contains genomes in all stages of DNA replication, serum-derived virions contain predominantly mature, partially duplex, circular DNA genomes. To account for this finding, Summers and Mason proposed in 1982 that virion envelopment is somehow linked to the state of genomic maturation (J. Summers and W.S. Mason, Cell 29:403-415, 1982). Core gene mutations with phenotypes consistent with this concept have previously been identified in the duck hepatitis B virus (DHBV). Here we show that DHBV polymerase mutants with altered DNA synthesis also display defects in envelopment, and we provide quantitative estimates of the magnitude of the preference for the envelopment of mature DNA. In cells transfected with wild-type DHBV DNA, immature minus-strand DNA represents 18% of the intracellular pool but only 4% of extracellular virion DNA. A point mutation in the C-terminal domain of the polymerase strongly and selectively impairs plus-strand synthesis; in this mutant, the ratio of immature to mature DNA in the intracellular pool rises to 6:1 but is reduced to 1.5:1 in released virions. A missense mutation in the polymerase active site inactivates all viral DNA synthesis but still allows efficient RNA encapsidation; in this mutant, no detectable viral nucleic acid is enveloped and released. Thus, viral DNA synthesis is absolutely required for envelopment and export, and a strong further bias exists in favor of the export of genomes that have completed minus-strand synthesis and at least initiated plus-strand synthesis. These results imply that events within the interior of the nucleocapsid can powerfully influence its interactions with external viral envelope glycoproteins.     

Expression of glutathione transferase isoenzymes in the human H295R adrenal cell line and the effect of forskolin

In previous studies in our laboratory (L. Mankowitz, L. Staffas, M. Bakke, and J. Lund, Biochem J, 1995, 305, 111-118; L. Staffas, L. Mankowitz, M. S?derstr?m, A. Blanck, I. Porsch-H?llstr?m, C. Sundberg, B. Mannervik, B. Olin, J. Rydstr?m, and J.W. DePierre, Biochem J, 1992, 286, 65-72) isoenzymes of GST, primarily of the mu class, have been shown to be downregulated by adrenocorticotropic hormone (ACTH) in rat and mouse adrenal cells. In the present investigation the human adrenal H295R cell line (W.E. Rainey, I.M. Bird, and J.I. Mason, Mol Cell Endocrinol, 1994, 100, 45-50) was examined in a similar manner. Analysis by reverse-phase HPLC revealed that these cells express four isoenzymes of GST, i.e., A1, A2, P1, and M4, as well as another unidentified protein that was retained by our affinity column (elution time of 32 min) and, thus, presumably binds glutathione. Among these forms, A1 was present at the highest level. Upon addition of forskolin (an activator of adenylate cyclase which has been shown previously to mimic the effect of ACTH on adrenal cells) to the culture medium, the level of A1 decreased approximately 70% by forskolin, whereas the levels of the other isoenzymes were slightly increased, and that of the unknown form doubled. Thus, the influence of ACTH on expression of GST isoenzymes in this human adrenal cell line differs from that in rat and mouse adrenal cells.     

Kin selection in disguise?

In a recent article E.O. Wilson and B. H?lldobler (2005) describe an heuristic model for the evolution of eusociality. They present their model as an alternative to the standard model of kin selection, and describe the evolution of eusociality in terms of changes in frequency to an hypothetical eusocial allele. Here I build on sentiments of Foster et al. (2006) to suggest that the proposed model is not a clear alternative to the standard model, but appears to represent a special case of kin selection involving preferential interactions among individuals sharing the same altruistic gene. The model proposed by Wilson and H?lldobler is consistent with the ‘greenbeard’ model of kin selection, first proposed by W.D. Hamilton. Received 23 May 2006; revised 27 June 2006; accepted 5 July 2006.     

Abrupt regime shifts in space and time along rivers and connected lake systems

Regime shifts between clear and turbid water states are commonly found in shallow lakes. These shifts are attributed to a positive feedback between water clarity and submerged macrophytes (underwater plants). Altering the retention time of the water may influence these interactions and thus potentially reduce the probability of alternative stable states. Here we assessed the effect of water retention time on the occurrence of alternative states in water quality of flushed lakes, chains of lakes and rivers using a spatially explicit simple model. Our results indicate that increased flushing of lakes rapidly decreases the range of parameters with alternative stable states up to their total disappearance at a flushing rate of about 50% the algal growth rate. Similarly, in a chain of lakes or in rivers with low flowing velocity, our model predicts that alternative stable states can only occur for systems with a high retention time. Despite the lack of hysteresis at lower water retention times, we predict that abrupt changes between clear and turbid states are still possible both in time and in space. Over a wide range of parameters, the equilibrium state of the chain of lakes shows a steep gradient of vegetation cover. Further, the transient dynamics of the model often include rapid shifts in time. For example, a local regime shift that occurs upstream may propagate through the whole lake chain or river due to a domino effect. All results of the simple model could qualitatively be reproduced with a more mechanistic model. The abrupt rather than gradual response of submerged macrophytes to reduced turbidity levels still makes river systems rather resilient to management measure. The importance of the initial turbidity and the observed domino effect suggest that restoration measures should start upstream and that these measures should eventually trigger regime shifts downstream.     

Protonation and stability of the globular domain of influenza virus hemagglutinin.

A partial dissociation of the HA1 subunits of influenza virus hemagglutinin (HA) is considered to be the initial step of conformational changes of the HA ectodomain leading to a membrane fusion active conformation (L. Godley, J. Pfeifer, D. Steinhauer, B. Ely, G. Shaw, R. Kaufman, E. Suchanek, C. Pabo, J.J. Skehel, D.C. Wiley, and S. Wharton, 1992, Cell 68:635-645; G.W. Kemble, D.L.Bodian, J. Rose, I.A. Wilson, and J.M. White, 1992, J. Virol. 66:4940-4950). Here, we explore a mechanism that provides an understanding of the physical and chemical basis for such dissociation and relies on two essential observations. First, based on the x-ray structure of HA from X31 (I.A. Wilson, J.J. Skehel, and D.C. Wiley, 1981, Nature 289:366-373), and by employing techniques of molecular modeling, we show that the protonation of the HA1 subunits is enhanced at the conditions known to trigger conformational changes of the HA ectodomain. Second, we found that the dependence of the calculated relative degree of protonation of the HA1 domain on temperature and pH is similar to that observed experimentally for the conformational change of HA assessed by proteinase K sensitivity. We suggest that at the pH-temperature conditions typical for the conformational change of HA and membrane fusion, dissociation of the HA1 subunits is caused by the enhanced protonation of the HA1 subunits leading to an increase in the positive net charge of these subunits and, in turn, to a weakened attraction between them.     

Book Review

Book reviewed in this articles:
Battarbee, R.W., Mason, Sir John, Renberg, I. & Tailing, J.F. (1990) Palaeolimnology and Lake Acidification .     

Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme.

High resolution crystal structures have been determined for six chicken-type lysozymes that were constructed to investigate putative intermediates in the evolution of the lysozymes of modern game birds (Malcolm, B. A., Wilson, K. P., Matthews, B. W., Kirsch, J. F., and Wilson, A. C. (1990) Nature 345, 86-89). The amino acid replacements include Thr-40----Ser, Ile-55----Val, and Ser-91----Thr, as well as combinations of these substitutions. Residues 40, 55, and 91 are buried within the core of chicken lysozyme. The replacements therefore involve the insertion and/or removal of methyl groups from the protein interior. The mutant proteins have normal activities, and their thermal stabilities span a range of 7 degrees C, with some variants more stable and some less stable than the naturally occurring forms. Comparison of the crystal structures shows the overall structures to be very similar, but there are differences in the packing of side chains in the region of the replacements. The x-ray coordinates were used to evaluate the repacking of side chains in the protein interior and to attempt to evaluate the contributions of the different energetic interactions toward the overall stability of each variant. The results illustrate how proteins can compensate for potentially destabilizing substitutions in different ways and underscore the importance of high resolution structural data if changes in protein thermostability due to changes in protein sequence are to be understood. The findings also suggest that protein stability can be increased by mutations that lower strain in the protein interior while maintaining total buried hydrophobic surface area.     

The amino terminus of the herpes simplex virus 1 protein Vhs mediates membrane association and tegument incorporation

Assembly of herpes simplex viruses (HSV) is a poorly understood process involving multiple redundant interactions between large number of tegument and envelope proteins. We have previously shown (G. E. Lee, G. A. Church, and D. W. Wilson, J. Virol. 77:2038-2045, 2003) that the virion host shutoff (Vhs) tegument protein is largely insoluble in HSV-infected cells and is also stably associated with membranes. Here we demonstrate that both insolubility and stable membrane binding are stimulated during the course of an HSV infection. Furthermore, we have found that the amino-terminal 42 residues of Vhs are sufficient to mediate membrane association and tegument incorporation when fused to a green fluorescent protein (GFP) reporter. Particle incorporation correlates with sorting to cytoplasmic punctate structures that may correspond to sites of HSV assembly. We conclude that the amino terminus of Vhs mediates targeting to sites of HSV assembly and to the viral tegument.     

Cathepsin L inactivates alpha 1-proteinase inhibitor by cleavage in the reactive site region

The lysosomal cysteine proteinases cathepsin L and cathepsin B were examined for their effect on the neutrophil elastase inhibitory activity of human alpha 1-proteinase inhibitor (alpha 1PI). Human cathepsin L catalytically inactivated human alpha 1PI by cleavage of the bonds Glu354-Ala355 and Met358-Ser359 (the serine proteinase inhibitory site). Cathepsin B did not inactivate alpha 1PI, even when equimolar amounts of enzyme were employed. Cathepsin L is the first human proteinase shown to catalytically inactivate alpha 1PI. These findings, in conjunction with other reports, suggest that alpha 1PI contains a proteolytically sensitive region encompassing residues 350-358. Taken together with the discovery of the elastinolytic activity of cathepsin L (Mason, R. W., Johnson, D. A., Barrett, A. J., and Chapman, H. A. (1986) Biochem. J. 233, 925-927), the present findings emphasize the possible importance of cathepsin L in the pathological proteolysis of elastin and diminish the role that can be attributed to cathepsin B in such processes.     

The effect of turbidity state and microhabitat on macroinvertebrate assemblages: a pilot study of six shallow lakes

Shallow lakes can occur in two alternative stable states, a clear-water state and a turbid state. This is associated with separate assemblages of fish, zooplankton and plants. Little is known about whether macroinvertebrate assemblages differ across both stable states. This study investigated this in a connected set of three turbid and three clear-water shallow lakes. To overcome confounding effects of differences in spatial structure of macrophytes in turbid and clear-water lakes, we sampled three microhabitats that occurred in both alternative stable states: open water, sago pondweed (Potamogeton pectinatus) and reed (Phragmites australis). Univariate analyses indicated no differences in the number of organisms, taxon richness or diversity between turbid and clear-water lakes. Multivariate analysis, however, showed significant differences in the macroinvertebrate community structure of both stable states. Nine taxa explained a significant amount of the variation between both lake types, of which seven preferred the clear-water lakes. The number of organisms and the taxon richness were higher in reed than in the other microhabitats, but diversity and evenness did not differ among the microhabitats. Multivariate analyses could separate all three microhabitats. Eight taxa, mainly detritus feeders and collector–gatherers, explained most of the variation in the data and preferred the reed microhabitat. The effects of stable state (6.8% explained variance) and microhabitat (13.1% explained variance) on the macroinvertebrate assemblages were largely independent from each other (1.5% shared variance). Although macroinvertebrates are not implemented in the initial theory of stable states, our results show clearly different assemblages across both stable states.     

Book reviews

Book Reviewed in this article Ecology of Desert Organisms G. N. Louw and M. K. Seely Introduction to Ecological Biochemistry J. B. Harborne Saline Lakes—Proceedings of the Second International Symposium on Athalassic (Inland) Saline Lakes, held in Saskatchewan, Canada, June 1982, Developments in Hydrobiology 16 Edited by U. T. Hammer, Dr W. Junk BV Saltmarsh Ecology. Tertiary Level Bioloqy Series S. P. Long and C. F. Mason Variable Plants and Herbivores in Natural and Managed Systems Edited by R. F. Denno and M. S. McClure     

When are alternative stable states more likely to occur?

T. Fukami and W. G. Lee argue that the logical expectation from ecological theory is that competitively-structured assemblages will be more likely to exhibit alternative stable states than abiotically-structured assemblages. We suggest that there are several important misinterpretations in their arguments, and that the substance of their hypothesis has both a weak basis in ecological theory and is not supported by empirical evidence which shows that alternative stable states occur more frequently in natural systems subject to moderate- to harsh abiotic extremes. While this debate is founded in ecological theory, it has important applied implications for restoration management. Sound theoretical predictions about when to expect alternative stable states can only aid more effective restoration if theoretical expectations can be shown to translate into predictable empirical outcomes. If strongly abiotically- or disturbance-structured systems are more likely to exhibit catastrophic phase shifts in community structure that can be resilient to management efforts, then restoration ecologists will need to treat these systems differently in terms of the types of management inputs that are required.     

Properties of the stable aerobic and anaerobic half-reduced states of NADPH-cytochrome c reductase.

The microsomal flavoprotein, NADPH-cytochrome c reductase, has been reexamined to determine: (1) the nature of the flavine bound to the enzyme and (2) the oxidation-reduction state of the "half-reduced" form of the flavoprotein. Iyanagi and Mason (Iyanagi, T., and Mason, H.S. (1973), Biochemistry 12, 2297) have recently proposed that NADPH-cytochrome c reductase contains both FAD and FMN as prosthetic groups in lieu of FAD as the sole constituent, as suggested by all previous studies of this enzyme. The data presented herein, utilizing the recently published fluorometric procedure of Faeder and Siegel (Faeder, E. J., and Siegle, L. M. (1973), Anal. Biochem. 53, 332) for the determination of FAD and FMN in mixtures, confirm the conclusions of Iyanagi and Mason for both rat and pig liver reductase preparations. Data for other flavoproteins are also presented. Iyanagi and Mason have also concluded that the air-stable "semiquinone" is a form of NADPH-cytochrome c reductase reduced by one electron per two falvines (F-FH). The present studies, however, do not agree with this conclusion, but instead support our previous results which indicate that both the aerobic and anaerobic half-reduced states of this flavoprotein exist in the two-electron reduced form (FH-FH). Removal of NADP+ does not affect the spectrum of the air-stable half-reduced form of the flavoprotein, nor does it affect the back titration of this intermediate by potassium ferricyanide. The possible implications of these observations on the catalytic cycle of the flavines of NADPH-cytochrome c reductase are discussed.     

Wetland macrophyte diversity, trophic status and phytoplankton： a case study of the cascading effects of an invasive herbivore

Shallow water bodies can exist in alternative stable states, a clear water state with high coverage of macrophytes or a turbid state with high phytoplankton biomass. The alternative equilibria hypothesis has been proposed to explain the occurrence of the alternative stable states (Scheffer et al., 1993)[1], which assumes that: 1),     

Physical characterization of serpin conformations

The native serpin fold is characterized by being metastable. This thermodynamic characteristic is manifested in the conversion of the native state to other more stable conformations. Whilst this structural transition is required for proteinase inhibition and regulation of a range of biological phenomena, inappropriate structural changes can result in a number of disease states. Identification of these alternative conformations has been essential in our understanding of serpin structure and function. However, identifying these alternative forms is also important if we are not to misinterpret data due to the formation of these states during in vitro studies. The different physical properties of these alternative serpin conformational states make it possible to use a range of standard laboratory techniques to identify these structures. In this chapter, we will outline these general approaches that can be used routinely to identify the alternative serpin conformational states.     

Apparent dipeptidyl peptidase activities of acylamino acid-releasing enzymes

An acylamino acid-releasing enzyme purified from porcine liver showed peptidase activity above pH 8. Of the non-acylated peptides tested, this peptidase activity was only exerted on peptides with Gly or Ala at their N-termini. These results are consistent with the previous observations for similar enzymes from sheep red blood cells (Witheiler, J. & Wilson, D.B. (1972) J. Biol. Chem. 247, 2217-2221) and beef liver (Gade, W. & Brown, J.L. (1978) J. Biol. Chem. 253, 5012-5018). The pH dependence of the peptidase activity showed that only peptides with uncharged N-terminal amino acids such as glycyl- or alanyl-peptides act as substrates for the enzyme. These results suggest that the peptidase activity seen for the acylamino acid-releasing enzyme is an intrinsic activity of the enzyme that is triggered by misrecognition of uncharged smaller N-terminal amino acids in non-acylated peptides as acyl groups at higher pHs.