Adaptive coevolutionary networks: a review

Adaptive networks appear in many biological applications. They combine topological evolution of the network with dynamics in the network nodes. Recently, the dynamics of adaptive networks has been investigated in a number of parallel studies from different fields, ranging from genomics to game theory. Here we review these recent developments and show that they can be viewed from a unique angle. We demonstrate that all these studies are characterized by common themes, most prominently: complex dynamics and robust topological self-organization based on simple local rules.

Epidemic dynamics on an adaptive network

Many real-world networks are characterized by adaptive changes in their topology depending on the state of their nodes. Here we study epidemic dynamics on an adaptive network, where the susceptibles are able to avoid contact with the infected by rewiring their network connections. This gives rise to assortative degree correlation, oscillations, hysteresis, and first order transitions. We propose a low-dimensional model to describe the system and present a full local bifurcation analysis. Our results indicate that the interplay between dynamics and topology can have important consequences for the spreading of infectious diseases and related applications.

Internal olefins to linear amines

The selective synthesis of linear amines from internal olefins or olefin mixtures was achieved through a catalytic one-pot reaction consisting of an initial olefin isomerization followed by hydroformylation and reductive amination. Key to the success is the use of specially designed phosphine ligands in the presence of rhodium catalysts. This reaction constitutes an economically attractive and environmentally favorable synthesis of linear aliphatic amines.

Adaptive coevolutionary networks: a review

Adaptive networks appear in many biological applications. They combine topological evolution of the network with dynamics in the network nodes. Recently, the dynamics of adaptive networks has been investigated in a number of parallel studies from different fields, ranging from genomics to game theory. Here we review these recent developments and show that they can be viewed from a unique angle. We demonstrate that all these studies are characterized by common themes, most prominently: complex dynamics and robust topological self-organization based on simple local rules.

Immunoglobulin epitope spreading and autoimmune disease after peptide immunization: Sm B/B'-derived PPPGMRPP and PPPGIRGP induce spliceosome autoimmunity

Autoantibodies from many patients with systemic lupus erythematosus bind the Sm autoantigen B/B' polypeptide. The binding of serial serum specimens to the 233 overlapping octapeptides of Sm B/B' have shown that of the B/B'-derived octapeptides, PPPGMRPP and PPPGIRGP are early targets of the autoimmune response in some lupus patients. Rabbits immunized with PPPGMRPP and PPPGIRGP develop antibodies which not only bind these octapeptides, but also subsequently bind many other octapeptides of Sm B/B'. Eventually, the rabbits immunized with one octapeptide develop autoantibodies that bind other spliceosomal proteins including D, 70K, A, and C. Any mechanisms that operate to maintain tolerance or anergy for the spliceosome are thus overcome. Features considered typical of human systemic lupus erythematosus are also found in these peptide-immunized animals, such as antinuclear antibodies, anti-Sm precipitins, anti-double-stranded DNA, thrombocytopenia, seizures, and proteinuria. This disease model provides access to a mechanism for the development of humoral autoimmunity and may provide a basis to explain the immunopathogenesis of lupus in humans.

Self-organized criticality as a fundamental property of neural systems

The neural criticality hypothesis states that the brain may be poised in a critical state at a boundary between different types of dynamics. Theoretical and experimental studies show that critical systems often exhibit optimal computational properties, suggesting the possibility that criticality has been evolutionarily selected as a useful trait for our nervous system. Evidence for criticality has been found in cell cultures, brain slices, and anesthetized animals. Yet, inconsistent results were reported for recordings in awake animals and humans, and current results point to open questions about the exact nature and mechanism of criticality, as well as its functional role. Therefore, the criticality hypothesis has remained a controversial proposition. Here, we provide an account of the mathematical and physical foundations of criticality. In the light of this conceptual framework, we then review and discuss recent experimental studies with the aim of identifying important next steps to be taken and connections to other fields that should be explored.

Uninformed individuals promote democratic consensus in animal groups

Conflicting interests among group members are common when making collective decisions, yet failure to achieve consensus can be costly. Under these circumstances individuals may be susceptible to manipulation by a strongly opinionated, or extremist, minority. It has previously been argued, for humans and animals, that social groups containing individuals who are uninformed, or exhibit weak preferences, are particularly vulnerable to such manipulative agents. Here, we use theory and experiment to demonstrate that, for a wide range of conditions, a strongly opinionated minority can dictate group choice, but the presence of uninformed individuals spontaneously inhibits this process, returning control to the numerical majority. Our results emphasize the role of uninformed individuals in achieving democratic consensus amid internal group conflict and informational constraints.

Structural kinetic modeling of metabolic networks

To develop and investigate detailed mathematical models of metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, kinetic modeling is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a quantitative account of the dynamical capabilities of a metabolic system, without requiring any explicit information about the functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a statistical exploration of the comprehensive parameter space. The method is exemplified on two paradigmatic metabolic systems: the glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.

Transmission of viruses via contact in ahousehold setting: experiments using bacteriophage straight phiX174 as a model virus

Contamination of the environment with pathogens is the prerequisite for contact infections. The aim of this study was to elucidate how viruses can be transmitted from a primary contact person to further individuals. Bacteriophage straight phiX174 was chosen as a model virus. In its stability straight phiX174 is comparable with the most resistant human pathogenic viruses, e.g. polio- or parvoviruses. About 10(7)pfu were applied to exposed contact points such as door handles or the hands of volunteers. After touching of these handles and common social contacts like hand shaking, re-isolation rates were determined from the hands of our test persons. Contaminated door handles and skin surfaces were found to be efficient sources for potential infection. At least 14 persons could be contaminated by horizontal spread, one after the other by touching the same door handle. Successive transmission from one person to another could be followed up to the sixth contact person. These results were confirmed under everyday life conditions in a flat shared by four students. The transmission could not be prevented by the usual standards of hand hygiene, practised in this household. straight phiX174 could be reisolated after 24h from the hands of all persons tested even after normal use and cleaning of their hands. This might be improved by the use of liquid soap dispensers.

Failure of adaptive self-organized criticality during epileptic seizure attacks

Critical dynamics are assumed to be an attractive mode for normal brain functioning as information processing and computational capabilities are found to be optimal in the critical state. Recent experimental observations of neuronal activity patterns following power-law distributions, a hallmark of systems at a critical state, have led to the hypothesis that human brain dynamics could be poised at a phase transition between ordered and disordered activity. A so far unresolved question concerns the medical significance of critical brain activity and how it relates to pathological conditions. Using data from invasive electroencephalogram recordings from humans we show that during epileptic seizure attacks neuronal activity patterns deviate from the normally observed power-law distribution characterizing critical dynamics. The comparison of these observations to results from a computational model exhibiting self-organized criticality (SOC) based on adaptive networks allows further insights into the underlying dynamics. Together these results suggest that brain dynamics deviates from criticality during seizures caused by the failure of adaptive SOC.

Dextromethorphan protects against cerebral injury following transient focal ischemia in rabbits

We investigated dextromethorphan, both a dextrorotatory opioid derivative and a clinically tested N-methyl-D-aspartate (NMDA) receptor antagonist, in a rabbit model of transient focal cerebral ischemia. Fourteen rabbits were randomly assigned to treatment with a 20 mg/kg i.v. loading dose followed by a 10 mg/kg/hr infusion of 0.4% dextromethorphan in normal saline or with an equivalent volume of normal saline alone. One hour after treatment, the rabbits underwent a 1-hour occlusion of the left internal carotid and anterior cerebral arteries followed by 4 hours of reperfusion. The seven dextromethorphan-treated rabbits showed a significant decrease in the area of neocortical severe ischemic neuronal damage (10.5%) compared with the seven normal saline-treated controls (49.6%, p less than 0.001). The dextromethorphan-treated rabbits also demonstrated significantly smaller areas of cortical edema (10.2%) on magnetic resonance imaging than the controls (38.6%, p less than 0.01). Analysis of somatosensory evoked potentials revealed recovery of the ipsilateral amplitude to contralateral values within 5 minutes of reperfusion in the dextromethorphan-treated rabbits but not in the controls (p less than 0.01). In our rabbit model of transient focal cerebral ischemia, dextromethorphan appears to protect the brain against ischemic neuronal damage and edema, as well as to promote neurophysiologic recovery. This clinically available drug should be further investigated as having potential therapeutic value in the treatment of stroke.

Differentiation of the bone-tissue remodeling response to axial and torsional loading in the turkey ulna

The ability of bone tissue to differentiate between axial and torsional loading was determined with use of a functionally isolated turkey-ulna model of bone adaptation. Surface modeling and intracortical remodeling were quantified after four weeks of 5000 cycles per day of axial loading sufficient to cause 1000 microstrain normal to the long axis of the bone (five ulnae), 5000 cycles per day of torsional loading sufficient to cause 1000 microstrain of shear strain (five ulnae), or disuse (six ulnae). Of these three distinct regimens, only disuse caused a significant change in gross areal properties (12 per cent loss of bone; p < 0.05) as compared with those in the contralateral, intact control ulnae (sixteen ulnae). This finding suggested that both axial and torsional loading conditions were suitable substitutes for functional signals normally responsible for bone homeostasis. However, the intracortical response was strongly dependent on the manner in which the bone was loaded. Axial loading increased the number of intracortical pores by a factor of seven as compared with that in the controls (246 +/- 40.5 compared with 36 +/- 8.5 pores); it also increased the area lost because of porosis as compared with that in the controls (1.39 +/- 0.252 compared with 0.202 +/- 0.062 square millimeter); however, the mean size of the individual pores was similar to that in the controls (0.00565 +/- 0.0019 compared with 0.00561 +/- 0.0029 square millimeter). Conversely, torsional loading failed to increase substantially the number of pores (67 +/- 22.6 pores), the area of bone lost because of porosis (0.352 +/- 0.114 square millimeter), or the size of the pores (0.00525 +/- 0.0035 square millimeter) as compared with those in the controls. Although disuse failed to increase substantially the number of intracortical pores (59 +/- 22.4 pores), significant area (1.05 +/- 0.35 square millimeters; p < 0.05) was lost within the cortex because of a threefold increase in the mean size of each pore (0.0178 +/- 0.0126 square millimeter). It appears that bone tissue can readily differentiate between distinct components of the strain environment, with strain per se necessary to retain coupled formation and resorption, shear strain achieving this goal by maintaining the status quo, and axial strain increasing intracortical turnover but retaining coupling. While it is clear that load influences bone mass and morphology, it is also clear that specific parameters within the strain environment have distinct strategic roles in defining this architecture.

HLA-B27 binding of peptide from its own sequence and similar peptides from bacteria: implications for spondyloarthropathies

The spondyloarthropathies are associated by an unknown mechanism with HLA-B27 and certain bacteria. HLA-B27 shares sequence with proteins from enteric bacteria. The B*2705 sequence contains a nonapeptide, LRRYLENGK, predicted to bind in the binding cleft of B27. Some nonapeptides from enteric organisms that share sequence with this nonapeptide of B27 also bind B27. These observations suggest an unappreciated mechanism for autoimmunity that may operate in the B27-associated spondyloarthropathies involving peptides bound to and derived from histocompatibility alleles.

In vitro fertilization and embryo development in vitro and in vivo in the tiger (Panthera tigris)

A study was conducted to evaluate the adaptability to the tiger of an in vitro fertilization/embryo culture system previously developed in the domestic cat. In Trial I (July 1989), 10 female tigers were treated with either 2,500 (n = 5) or 5,000 (n = 5) IU eCG i.m. and with 2,000 IU hCG i.m. 84 h later. In Trial II (January 1990), 6 females (5 of which were treated in Trial I) were given 2,500 IU eCG i.m. and 2,000 IU hCG i.m. 84 h later. Twenty-four to twenty-six hours after hCG treatment, all tigers were subjected to laparoscopy, and oocytes were aspirated transabdominally. On the basis of follicular development (follicles greater than or equal to 2 mm in diameter), all females responded to exogenous gonadotropins (range, 6-52 follicles/female). Follicle number and oocyte recovery rate were unaffected (p greater than 0.05) by eCG dose or time of year. A total of 456 oocytes were collected from 468 follicles (97.4% recovery; mean, 28.5 +/- 3.4 oocytes/female). Of these, 378 (82.9%) qualified as mature, 48 (10.5%) as immature, and 30 (6.6%) as degenerate. During Trial I, 8 electroejaculates were collected from 7 male tigers, and in Trial II, 3 semen samples were collected from 3 males. Motile sperm were recovered on each occasion; the overall mean (+/- SEM) ejaculate volume was 7.5 +/- 0.7 ml, the number of motile sperm/ejaculate was 105.9 +/- 20.6 x 10(6), and the percentage of structurally normal sperm/ejaculate was 81.4 +/- 2.0%. After swim-up processing, 0.05 x 10(6) motile sperm were co-cultured with 10 or fewer tiger oocytes in a humidified atmosphere (38 degrees C) of 5% CO2 in air. Of the 358 mature oocytes inseminated, 227 (63.4%) were fertilized. Oocytes from 2 females became contaminated in culture and, therefore, were excluded from embryo cleavage calculations. Of the remaining 195 fertilized oocytes, 187 (95.9%) cleaved to the two-cell stage. No parthenogenetic cleavage was observed in noninseminated control oocytes (n = 20). Eighty-six good-to-excellent-quality two- to four-cell embryos were transferred surgically into the oviducts of 4 of the original oocyte donors in Trial I and 2 females in Trial II. A pregnancy occurred in 1 female in Trial II, and 3 live-born cubs were delivered by Caesarean section 107 days after embryo transfer. Of the 56 cleaved embryos cultured in vitro in Ham's F10 for 72 h, 14 (25.0%) were at the sixteen-cell stage, and 15 (26.8%) were morulae.(ABSTRACT TRUNCATED AT 400 WORDS)

Fission yeast does not age under favorable conditions, but does so after stress

BACKGROUND

Many unicellular organisms age: as time passes, they divide more slowly and ultimately die. In budding yeast, asymmetric segregation of cellular damage results in aging mother cells and rejuvenated daughters. We hypothesize that the organisms in which this asymmetry is lacking, or can be modulated, may not undergo aging.

RESULTS

We performed a complete pedigree analysis of microcolonies of the fission yeast Schizosaccharomyces pombe growing from a single cell. When cells were grown under favorable conditions, none of the lineages exhibited aging, which is defined as a consecutive increase in division time and increased death probability. Under favorable conditions, few cells died, and their death was random and sudden rather than following a gradual increase in division time. Cell death correlated with the inheritance of Hsp104-associated protein aggregates. After stress, the cells that inherited large aggregates aged, showing a consecutive increase in division time and an increased death probability. Their sisters, who inherited little or no aggregates, did not age.

CONCLUSIONS

We conclude that S. pombe does not age under favorable growth conditions, but does so under stress. This transition appears to be passive rather than active and results from the formation of a single large aggregate, which segregates asymmetrically at the subsequent cell division. We argue that this damage-induced asymmetric segregation has evolved to sacrifice some cells so that others may survive unscathed after severe environmental stresses.

Management of blunt injuries to the spleen

Background

Non-operative management (NOM) of blunt splenic injuries is nowadays considered the standard treatment. The present study identified selection criteria for primary operative management (OM) and planned NOM.

Methods

All adult patients with blunt splenic injuries treated at Berne University Hospital, Switzerland, between 2000 and 2008 were reviewed.

Results

There were 206 patients (146 men) with a mean(s.d.) age of 38·2(19·1) years and an Injury Severity Score of 30·9(11·6). The American Association for the Surgery of Trauma classification of the splenic injury was grade 1 in 43 patients (20·9 per cent), grade 2 in 52 (25·2 per cent), grade 3 in 60 (29·1 per cent), grade 4 in 42 (20·4 per cent) and grade 5 in nine (4·4 per cent). Forty-seven patients (22·8 per cent) required immediate surgery. Transfusion of at least 5 units of red cells (odds ratio (OR) 13·72, 95 per cent confidence interval 5·08 to 37·01), Glasgow Coma Scale score below 11 (OR 9·88, 1·77 to 55·16) and age 55 years or more (OR 3·29, 1·07 to 10·08) were associated with primary OM. The rate of primary OM decreased from 33·3 to 11·9 per cent after the introduction of transcatheter arterial embolization in 2005. Overall, 159 patients (77·2 per cent) qualified for NOM, which was successful in 143 (89·9 per cent). The splenic salvage rate was 69·4 per cent. In multivariable analysis age at least 40 years was the only factor independently related to failure of NOM (OR 13·58, 2·76 to 66·71).

Conclusion

NOM of blunt splenic injuries has a low failure rate. Advanced age is independently associated with an increased failure rate.

ECOLOGICAL THEORY. A general consumer-resource population model

Food-web dynamics arise from predator-prey, parasite-host, and herbivore-plant interactions. Models for such interactions include up to three consumer activity states (questing, attacking, consuming) and up to four resource response states (susceptible, exposed, ingested, resistant). Articulating these states into a general model allows for dissecting, comparing, and deriving consumer-resource models. We specify this general model for 11 generic consumer strategies that group mathematically into predators, parasites, and micropredators and then derive conditions for consumer success, including a universal saturating functional response. We further show how to use this framework to create simple models with a common mathematical lineage and transparent assumptions. Underlying assumptions, missing elements, and composite parameters are revealed when classic consumer-resource models are derived from the general model.

Enrichment and foodchain stability: the impact of different forms of predator-prey interaction

We propose a simple model of an ecological foodchain of arbitrary length. The model is very general in nature and describes a whole class of foodchains. Using the methods of qualitative analysis the model's stability can be analysed without restricting the predator-prey interaction to any specific functional form. The model can therefore be used to study the effect of different functional forms on the stability of the foodchain. We demonstrate that the stability of steady states may strongly depend on the exact functional form of the interaction function used. It is shown that a class of interaction functions exists, which are similar to the widely used Holling functions but bestow radically different stability properties upon the model. An example is shown in which enrichment has a stabilizing effect on the foodchain. By contrast enrichment destabilizes steady states if Holling functions are used.

The rpg4-mediated resistance to wheat stem rust (Puccinia graminis) in barley (Hordeum vulgare) requires Rpg5, a second NBS-LRR gene, and an actin depolymerization factor

The rpg4 gene confers recessive resistance to several races of wheat stem rust (Puccinia graminis f. sp. tritici) and Rpg5 provides dominant resistance against isolates of the rye stem rust (P. graminis f. sp. secalis) in barley. The rpg4 and Rpg5 genes are tightly linked on chromosome 5H, and positional cloning using high-resolution populations clearly separated the genes, unambiguously identifying Rpg5; however, the identity of rpg4 remained unclear. High-resolution genotyping of critical recombinants at the rpg4/Rpg5 locus, designated here as rpg4-mediated resistance locus (RMRL) delimited two distinct yet tightly linked loci required for resistance, designated as RMRL1 and RMRL2. Utilizing virus-induced gene silencing, each gene at RMRL1, i.e., HvRga1 (a nucleotide-binding site leucine-rich repeat [NBS-LRR] domain gene), Rpg5 (an NBS-LRR-protein kinase domain gene), and HvAdf3 (an actin depolymerizing factor-like gene), was individually silenced followed by inoculation with P. graminis f. sp. tritici race QCCJ. Silencing each gene changed the reaction type from incompatible to compatible, indicating that all three genes are required for rpg4-mediated resistance. This stem rust resistance mechanism in barley follows the emerging theme of unrelated pairs of genetically linked NBS-LRR genes required for specific pathogen recognition and resistance. It also appears that actin cytoskeleton dynamics may play an important role in determining resistance against several races of stem rust in barley.

Generalized models as a universal approach to the analysis of nonlinear dynamical systems

We present a universal approach to the investigation of the dynamics in generalized models. In these models the processes that are taken into account are not restricted to specific functional forms. Therefore a single generalized models can describe a class of systems which share a similar structure. Despite this generality, the proposed approach allows us to study the dynamical properties of generalized models efficiently in the framework of local bifurcation theory. The approach is based on a normalization procedure that is used to identify natural parameters of the system. The Jacobian in a steady state is then derived as a function of these parameters. The analytical computation of local bifurcations using computer algebra reveals conditions for the local asymptotic stability of steady states and provides certain insights on the global dynamics of the system. The proposed approach yields a close connection between modelling and nonlinear dynamics. We illustrate the investigation of generalized models by considering examples from three different disciplines of science: a socioeconomic model of dynastic cycles in china, a model for a coupled laser system and a general ecological food web.

Early warning signals for critical transitions: a generalized modeling approach

Critical transitions are sudden, often irreversible, changes that can occur in a large variety of complex systems; signals that warn of critical transitions are therefore highly desirable. We propose a new method for early warning signals that integrates multiple sources of information and data about the system through the framework of a generalized model. We demonstrate our proposed approach through several examples, including a previously published fisheries model. We regard our method as complementary to existing early warning signals, taking an approach of intermediate complexity between model-free approaches and fully parameterized simulations. One potential advantage of our approach is that, under appropriate conditions, it may reduce the amount of time series data required for a robust early warning signal.