The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities

Evolution provides a creative fount of complex and subtle adaptations that often surprise the scientists who discover them. However, the creativity of evolution is not limited to the natural world: Artificial organisms evolving in computational environments have also elicited surprise and wonder from the researchers studying them. The process of evolution is an algorithmic process that transcends the substrate in which it occurs. Indeed, many researchers in the field of digital evolution can provide examples of how their evolving algorithms and organisms have creatively subverted their expectations or intentions, exposed unrecognized bugs in their code, produced unexpectedly adaptations, or engaged in behaviors and outcomes, uncannily convergent with ones found in nature. Such stories routinely reveal surprise and creativity by evolution in these digital worlds, but they rarely fit into the standard scientific narrative. Instead they are often treated as mere obstacles to be overcome, rather than results that warrant study in their own right. Bugs are fixed, experiments are refocused, and one-off surprises are collapsed into a single data point. The stories themselves are traded among researchers through oral tradition, but that mode of information transmission is inefficient and prone to error and outright loss. Moreover, the fact that these stories tend to be shared only among practitioners means that many natural scientists do not realize how interesting and lifelike digital organisms are and how natural their evolution can be. To our knowledge, no collection of such anecdotes has been published before. This article is the crowd-sourced product of researchers in the fields of artificial life and evolutionary computation who have provided first-hand accounts of such cases. It thus serves as a written, fact-checked collection of scientifically important and even entertaining stories. In doing so we also present here substantial evidence that the existence and importance of evolutionary surprises extends beyond the natural world, and may indeed be a universal property of all complex evolving systems.

Temporal scaling of aging as an adaptive strategy of Escherichia coli

Natural selection is thought to shape the evolution of aging patterns, although how life-history trajectories orchestrate the inherently stochastic processes associated with aging is unclear. Tracking clonal growth-arrested Escherichia coli cohorts in an homogeneous environment at single-cell resolution, we demonstrate that the Gompertz law of exponential mortality characterizes bacterial lifespan distributions. By disentangling the rate of aging from age-independent components of longevity, we find that increasing cellular maintenance through the general stress pathway reduces the aging rate and rescales the lifespan distribution at the expense of growth. This trade-off between aging and growth underpins the evolutionary tuning of the general stress response pathway in adaptation to the organism's feast-or-famine lifestyle. It is thus necessary to involve both natural selection and stochastic physiology to explain aging patterns.

Two stochastic processes shape diverse senescence patterns in a single-cell organism

Despite advances in aging research, a multitude of aging models, and empirical evidence for diverse senescence patterns, understanding of the biological processes that shape senescence is lacking. We show that senescence of an isogenic Escherichia coli bacterial population results from two stochastic processes. The first process is a random deterioration process within the cell, such as generated by random accumulation of damage. This primary process leads to an exponential increase in mortality early in life followed by a late age mortality plateau. The second process relates to the stochastic asymmetric transmission at cell fission of an unknown factor that influences mortality. This secondary process explains the difference between the classical mortality plateaus detected for young mothers' offspring and the near nonsenescence of old mothers' offspring as well as the lack of a mother-offspring correlation in age at death. We observed that lifespan is predominantly determined by underlying stochastic stage dynamics. Surprisingly, our findings support models developed for metazoans that base their arguments on stage-specific actions of alleles to understand the evolution of senescence. We call for exploration of similar stochastic influences that shape aging patterns beyond simple organisms.

Second-order cooperation: Cooperative offspring as a living public good arising from second-order selection on non-cooperative individuals

Switching rate between cooperating and non-cooperating genotypes is a crucial social evolution factor, often neglected by game theory-inspired theoretical and experimental frameworks. We show that the evolution of alleles increasing the mutation or phenotypic switching rates toward cooperation is in itself a social dilemma. Although cooperative offspring are often unlikely to reproduce, due to high cost of cooperation, they can be seen both as a living public good and a part of the extended parental phenotype. The competition between individuals that generate cooperators and ones that do not is often more relevant than the competition between cooperators and non-cooperators. The dilemma of second-order cooperation we describe relates directly to eusociality, but can be also interpreted as a division of labor or a soma-germline distinction. The results of our simulations shine a new light on what Darwin had already termed a "special difficulty" of evolutionary theory and describe a novel type of cooperation dynamics.

Impact of in utero environment on the offspring of lupus patients

The number of patients affected by systemic lupus erythematosus (SLE) that decide to have children has greatly increased probably because of recent improvements in the diagnosis and management of the disease. This has stimulated our interest in defining the outcome of children, focusing both on neonatal problems and long term development. SLE patients still carry a risk of pregnancy loss. However, due to careful monitoring and treatment by a multidisciplinary team, the number of losses has dramatically decreased, but an increased number of preterm deliveries is still a problem. Neonatal lupus is linked to the presence of anti-Ro/SS-A and anti-La/SS-B antibodies in the mother, although other factors probably of fetal origin are important. Neonatal lupus is a complex condition whose most serious manifestation is the congenital heart block (CHB). Usually, children with complete CHB need permanent pacing, but apparently do not have neuropsychological problems. Studies focusing on the neuropsychological development of SLE offspring show an increased number of learning disabilities in children with normal intelligence levels. Fetal consequence of maternal treatment need to be considered choosing non teratogenic drugs, but the withdrawal of medications just because the patient is pregnant should be avoided to avoid SLE flares.

Left-right differences in the proximal femur's strength of post-menopausal women: a multicentric finite element study

The strength of both femurs was estimated in 198 post-menopausal women through subject-specific finite element models. Important random differences between contralateral femurs were found in a significant number of subjects, pointing to the usefulness of further studies to understand if strength-based classification of patients at risk of fracture can be affected by laterality issues.

INTRODUCTION

Significant, although small, differences exist in mineral density and anatomy of contralateral proximal femurs. These differences, and their combined effect, may result in a side difference in femurs' strength. However, this has never been tested on a large sample of a homogenous population.

METHODS

The strength of both femurs was estimated in 198 post-menopausal women through CT-derived finite element models, built using a validated procedure, in sideways fall conditions. The impact of the resulting asymmetry on the classification of subjects at risk of fracture was analysed.

RESULTS

The small difference observed between sides (the right femur on average 4 % stronger than the left) was statistically significant but mechanically negligible. In contrast, higher random differences (absolute difference between sides with respect to mean value) were found: on average close to 15 % (compared to 9.2 % for areal bone mineral density (aBMD) alone), with high scatter among the subjects. When using a threshold-based classification, the right and left femurs were discordant up to over 20 % of cases (K always lower than 0.60) but the left femur was concordant (mean K = 0.84) with the minimum strength between right and left.

CONCLUSION

Considering both femurs may be important when trying to classify subjects at risk of failure with strength estimates. Future studies including fracture assessment would be necessary to quantify the real impact.

Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations

Natural cooperative systems take many forms, ranging from one-dimensional cyanobacteria arrays to fractal-like biofilms. We use in silico experimental systems to study a previously overlooked factor in the evolution of cooperation, physical shape of the population. We compare the emergence and maintenance of cooperation in populations of digital organisms that inhabit bulky (100 × 100 cells) or slender (4 × 2500) toroidal grids. Although more isolated subpopulations of secretors in a slender population could be expected to favor cooperation, we find the opposite: secretion evolves to higher levels in bulky populations. We identify the mechanistic explanation for the shape effect by analyzing the lifecycle and dynamics of cooperator patches, from their emergence and growth, to invasion by noncooperators and extinction. Because they are constrained by the population shape, the cooperator patches expand less in slender than in bulky populations, leading to fewer cooperators, less public good secretion, and generally lower cooperation. The patch dynamics and mechanisms of shape effect are robust across several digital cooperation systems and independent of the underlying basis for cooperation (public good secretion or a cooperation game). Our results urge for a greater consideration of population shape in the study of the evolution of cooperation across experimental and modeling systems.

Mobile genetic elements are involved in bacterial sociality

Mobile genetic elements in bacteria are enriched in genes participating in social behaviors, suggesting an evolutionary link between gene mobility and social evolution. Cooperative behaviors, like the production of secreted public good molecules, are susceptible to the invasion of non-cooperative individuals, and their evolutionary maintenance requires mechanisms ensuring that benefits are directed preferentially to cooperators. In order to investigate the reasons for the mobility of public good genes, we designed a synthetic bacterial system where we control and quantify the transfer of public good production genes. In our recent study, we have experimentally shown that horizontal transfer helps maintain public good production in the face of both non-producer organisms and non-producer plasmids. Transfer spreads genes to neighboring cells, thus increasing relatedness and directing a higher proportion of public good benefits to producers. The effect is the strongest when public good genes undergo epidemics dynamics, making horizontal transfer especially relevant for pathogenic bacteria that repeatedly infect new hosts and base their virulence on costly public goods. The promotion of cooperation may be a general consequence of horizontal gene transfer in prokaryotes. Our work has an intriguing parallel, cultural transmission, where horizontal transfer, such as teaching, may preferentially promote cooperative behaviors.

Nanoscale probing the kinetics of oriented bacterial cell growth using atomic force microscopy

Probing oriented bacterial cell growth on the nanoscale: A novel open-top micro-channel is developed to facilitate the AFM imaging of physically trapped but freely growing bacteria. The growth curves of individual Escherichia coli cells with nanometer resolution and their kinetic nano-mechanical properties are quantitatively measured.

Locally measured microstructural parameters are better associated with vertebral strength than whole bone density

Whole vertebrae areal and volumetric bone mineral density (BMD) measurements are not ideal predictors of vertebral fractures. We introduce a technique which enables quantification of bone microstructural parameters at precisely defined anatomical locations. Results show that local assessment of bone volume fraction at the optimal location can substantially improve the prediction of vertebral strength.

INTRODUCTION

Whole vertebrae areal and volumetric BMD measurements are not ideal predictors of vertebral osteoporotic fractures. Recent studies have shown that sampling bone microstructural parameters in smaller regions may permit better predictions. In such studies, however, the sampling location is described only in general anatomical terms. Here, we introduce a technique that enables the quantification of bone volume fraction and microstructural parameters at precisely defined anatomical locations. Specific goals of this study were to investigate at what anatomical location within the vertebrae local bone volume fraction best predicts vertebral-body strength, whether this prediction can be improved by adding microstructural parameters and to explore if this approach could better predict vertebral-body strength than whole bone volume fraction and finite element (FE) analyses.

METHODS

Eighteen T12 vertebrae were scanned in a micro-computed tomography (CT) system and FE meshes were made using a mesh-morphing tool. For each element, bone microstructural parameters were measured and correlated with vertebral compressive strength as measured experimentally. Whole bone volume fraction and FE-predicted vertebral strength were also compared to the experimental measurements.

RESULTS

A significant association between local bone volume fraction measured at a specific central region and vertebral-body strength was found that could explain up to 90% of the variation. When including all microstructural parameters in the regression, the predictive value of local measurements could be increased to 98%. Whole bone volume fraction could explain only 64% and FE analyses 76% of the variation in bone strength.

CONCLUSIONS

A local assessment of volume fraction at the optimal location can substantially improve the prediction of bone strength. Local assessment of other microstructural parameters may further improve this prediction but is not clinically feasible using current technology.

Genetic architecture promotes the evolution and maintenance of cooperation

When cooperation has a direct cost and an indirect benefit, a selfish behavior is more likely to be selected for than an altruistic one. Kin and group selection do provide evolutionary explanations for the stability of cooperation in nature, but we still lack the full understanding of the genomic mechanisms that can prevent cheater invasion. In our study we used Aevol, an agent-based, in silico genomic platform to evolve populations of digital organisms that compete, reproduce, and cooperate by secreting a public good for tens of thousands of generations. We found that cooperating individuals may share a phenotype, defined as the amount of public good produced, but have very different abilities to resist cheater invasion. To understand the underlying genetic differences between cooperator types, we performed bio-inspired genomics analyses of our digital organisms by recording and comparing the locations of metabolic and secretion genes, as well as the relevant promoters and terminators. Association between metabolic and secretion genes (promoter sharing, overlap via frame shift or sense-antisense encoding) was characteristic for populations with robust cooperation and was more likely to evolve when secretion was costly. In mutational analysis experiments, we demonstrated the potential evolutionary consequences of the genetic association by performing a large number of mutations and measuring their phenotypic and fitness effects. The non-cooperating mutants arising from the individuals with genetic association were more likely to have metabolic deleterious mutations that eventually lead to selection eliminating such mutants from the population due to the accompanying fitness decrease. Effectively, cooperation evolved to be protected and robust to mutations through entangled genetic architecture. Our results confirm the importance of second-order selection on evolutionary outcomes, uncover an important genetic mechanism for the evolution and maintenance of cooperation, and suggest promising methods for preventing gene loss in synthetically engineered organisms.

Expression of a novel P22 ORFan gene reveals the phage carrier state in Salmonella typhimurium

We discovered a novel interaction between phage P22 and its host Salmonella Typhimurium LT2 that is characterized by a phage mediated and targeted derepression of the host dgo operon. Upon further investigation, this interaction was found to be instigated by an ORFan gene (designated pid for phage P22 encoded instigator of dgo expression) located on a previously unannotated moron locus in the late region of the P22 genome, and encoding an 86 amino acid protein of 9.3 kDa. Surprisingly, the Pid/dgo interaction was not observed during strict lytic or lysogenic proliferation of P22, and expression of pid was instead found to arise in cells that upon infection stably maintained an unintegrated phage chromosome that segregated asymmetrically upon subsequent cell divisions. Interestingly, among the emerging siblings, the feature of pid expression remained tightly linked to the cell inheriting this phage carrier state and became quenched in the other. As such, this study is the first to reveal molecular and genetic markers authenticating pseudolysogenic development, thereby exposing a novel mechanism, timing, and populational distribution in the realm of phage-host interactions.

Trade-off between bile resistance and nutritional competence drives Escherichia coli diversification in the mouse gut

Bacterial diversification is often observed, but underlying mechanisms are difficult to disentangle and remain generally unknown. Moreover, controlled diversification experiments in ecologically relevant environments are lacking. We studied bacterial diversification in the mammalian gut, one of the most complex bacterial environments, where usually hundreds of species and thousands of bacterial strains stably coexist. Herein we show rapid genetic diversification of an Escherichia coli strain upon colonisation of previously germ-free mice. In addition to the previously described mutations in the EnvZ/OmpR operon, we describe the rapid and systematic selection of mutations in the flagellar flhDC operon and in malT, the transcriptional activator of the maltose regulon. Moreover, within each mouse, the three mutant types coexisted at different levels after one month of colonisation. By combining in vivo studies and determination of the fitness advantages of the selected mutations in controlled in vitro experiments, we provide evidence that the selective forces that drive E. coli diversification in the mouse gut are the presence of bile salts and competition for nutrients. Altogether our results indicate that a trade-off between stress resistance and nutritional competence generates sympatric diversification of the gut microbiota. These results illustrate how experimental evolution in natural environments enables identification of both the selective pressures that organisms face in their natural environment and the diversification mechanisms.

Evidence for an evolutionary antagonism between Mrr and Type III modification systems

The Mrr protein of Escherichia coli is a laterally acquired Type IV restriction endonuclease with specificity for methylated DNA. While Mrr nuclease activity can be elicited by high-pressure stress in E. coli MG1655, its (over)expression per se does not confer any obvious toxicity. In this study, however, we discovered that Mrr of E. coli MG1655 causes distinct genotoxicity when expressed in Salmonella typhimurium LT2. Genetic screening enabled us to contribute this toxicity entirely to the presence of the endogenous Type III restriction modification system (StyLTI) of S. typhimurium LT2. The StyLTI system consists of the Mod DNA methyltransferase and the Res restriction endonuclease, and we revealed that expression of the LT2 mod gene was sufficient to trigger Mrr activity in E. coli MG1655. Moreover, we could demonstrate that horizontal acquisition of the MG1655 mrr locus can drive the loss of endogenous Mod functionality present in S. typhimurium LT2 and E. coli ED1a, and observed a strong anti-correlation between close homologues of MG1655 mrr and LT2 mod in the genome database. This apparent evolutionary antagonism is further discussed in the light of a possible role for Mrr as defense mechanism against the establishment of epigenetic regulation by foreign DNA methyltransferases.

Extensive Risk Analysis of Mechanical Failure for an Epiphyseal Hip Prothesis: A Combined Numerical—Experimental Approach

There has been recent renewed interest in proximal femur epiphyseal replacement as an alternative to conventional total hip replacement. In many branches of engineering, risk analysis has proved to be an efficient tool for avoiding premature failures of innovative devices. An extensive risk analysis procedure has been developed for epiphyseal hip prostheses and the predictions of this method have been compared to the known clinical outcomes of a well-established contemporary design, namely hip resurfacing devices.

Clinical scenarios leading to revision (i.e. loosening, neck fracture and failure of the prosthetic component) were associated with potential failure modes (i.e. overload, fatigue, wear, fibrotic tissue differentiation and bone remodelling). Driving parameters of the corresponding failure mode were identified together with their safe thresholds. For each failure mode, a failure criterion was identified and studied under the most relevant physiological loading conditions. All failure modes were investigated with the most suitable investigation tool, either numerical or experimental.

Results showed a low risk for each failure scenario either in the immediate postoperative period or in the long term. These findings are in agreement with those reported by the majority of clinical studies for correctly implanted devices. Although further work is needed to confirm the predictions of this method, it was concluded that the proposed risk analysis procedure has the potential to increase the efficacy of preclinical validation protocols for new epiphyseal replacement devices.

Emergence of variability in isogenic Escherichia coli populations infected by a filamentous virus

The spread of epidemics not only depends on the average number of parasites produced per host, but also on the existence of highly infectious individuals. It is widely accepted that infectiousness depends on genetic and environmental determinants. However, even in clonal populations of host and viruses growing in homogeneous conditions, high variability can exist. Here we show that Escherichia coli cells commonly display high differentials in viral burst size, and address the kinetics of emergence of such variability with the non-lytic filamentous virus M13. By single-cell imaging of a virally-encoded fluorescent reporter, we monitor the viral charge distribution in infected bacterial populations at different time following infection. A mathematical model assuming autocatalytic virus replication and inheritance of bacterial growth rates quantitatively reproduces the experimental distributions, demonstrating that deterministic amplification of small host inhomogeneities is a mechanism sufficient to explain large and highly skewed distributions. This mechanism of amplification is general and may occur whenever a parasite has an initial phase of exponential growth within its host. Moreover, it naturally reproduces the shift towards higher virulence when the host is experimenting poor conditions, as observed commonly in host-parasite systems.

Coherent detection of electron dephasing

We show that an Aharonov-Bohm ring with asymmetric electron injection can act as a coherent detector of electron dephasing. The presence of a dephasing source in one of the two arms of a moderately-to-highly asymmetric ring changes the response of the system from total reflection to complete transmission while preserving the coherence of the electrons propagating from the ring, even for strong dephasing. We interpret this phenomenon as an implementation of an interaction-free measurement.

Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence

Background

Microbes engage in a remarkable array of cooperative behaviors, secreting shared proteins that are essential for foraging, shelter, microbial warfare, and virulence. These proteins are costly, rendering populations of cooperators vulnerable to exploitation by nonproducing cheaters arising by gene loss or migration. In such conditions, how can cooperation persist?

Results

Our model predicts that differential gene mobility drives intragenomic variation in investment in cooperative traits. More mobile loci generate stronger among-individual genetic correlations at these loci (higher relatedness) and thereby allow the maintenance of more cooperative traits via kin selection. By analyzing 21 Escherichia genomes, we confirm that genes coding for secreted proteins—the secretome—are very frequently lost and gained and are associated with mobile elements. We show that homologs of the secretome are overrepresented among human gut metagenomics samples, consistent with increased relatedness at secretome loci across multiple species. The biosynthetic cost of secreted proteins is shown to be under intense selective pressure, even more than for highly expressed proteins, consistent with a cost of cooperation driving social dilemmas. Finally, we demonstrate that mobile elements are in conflict with their chromosomal hosts over the chimeric ensemble's social strategy, with mobile elements enforcing cooperation on their otherwise selfish hosts via the cotransfer of secretome genes with “mafia strategy” addictive systems (toxin-antitoxin and restriction-modification).

Conclusion

Our analysis matches the predictions of our model suggesting that horizontal transfer promotes cooperation, as transmission increases local genetic relatedness at mobile loci and enforces cooperation on the resident genes. As a consequence, horizontal transfer promoted by agents such as plasmids, phages, or integrons drives microbial cooperation.

Effect of mutator P. aeruginosa on antibiotic resistance acquisition and respiratory function in cystic fibrosis

BACKGROUND

Cystic fibrosis patients suffer from recurrent bacterial infections that result in progressive deterioration of their respiratory function. Despite intensive antibiotic treatment, Pseudomonas aeruginosa is the main cause of such infections, with clones progressively developing multiple antibiotic resistance. We determined the relationship between the presence of P. aeruginosa mutator strains and cystic fibrosis clinical characteristics.

METHODS

We analyzed 136 strains of P. aeruginosa isolated from the expectorations of 36 CF patients. On all strains, mutation frequencies were determined by the mutation rate to rifampicin, and antibiotic susceptibility was determined by the disk diffusion method. The epidemiological relatedness of these 136 P. aeruginosa strains was studied by pulsed-field gel electrophoresis. The appearance of new antibiotic resistance by sequential analysis of genotypically identical strains was determined. Lung function test results, that is, forced expiratory volume in 1 sec and vital capacity, were also recorded from these patients.

RESULTS

We showed that bacteria with an enhanced mutation rate increase the rate of acquisition of new antibiotic resistance threefold and are associated with the deterioration of lung function.

CONCLUSIONS

This study demonstrates the effect of mutator bacteria on the efficiency of patient treatment and on their respiratory function. Given the consequence of antibiotic treatment failure and lung deterioration on the prognosis of CF patients, antibiotic treatment strategies may need to be optimized to prevent the emergence of mutator clones.

Stress shielding and stress concentration of contemporary epiphyseal hip prostheses

After the first early failures, proximal femoral epiphyseal replacement is becoming popular again. Prosthesis-to-bone load transfer is critical for two reasons: stress shielding is suspected of being responsible for a number of failures of early epiphyseal prostheses; stress concentration is probably responsible of the relevant number of early femoral neck fractures in resurfaced patients. The scope of this work was to experimentally investigate the load transfer of a commercial epiphyseal prosthesis (Birmingham Hip Replacement (BHR)) and an innovative prototype proximal epiphyseal replacement. To investigate bone surface strain, ten cadaveric femurs were instrumented with 15 triaxial strain gauges. In addition the cement layer of the prototype was instrumented with embedded gauges to estimate the strain in the adjacent trabecular bone. Six different loading configurations were investigated, with and without muscles. For the BHR prosthesis, significant stress shielding was observed on the posterior side of the head-neck region (the strain was halved); a pronounced stress concentration was observed on the anterior surface (up to five times in some specimens); BHR was quite sensitive to the different loading configurations. For the prototype, the largest stress shielding was observed in the neck region (lower than the BHR; alteration less than 20 per cent); some stress concentration was observed at the head region, close to the rim of the prosthesis (alteration less than 20 per cent); the different loading configurations had similar effects. Such large alterations with respect to the pre-operative conditions were found only in regions where the strain level was low. Conversely, alterations were moderate where the strain was higher. Thus, prosthesis-to-bone load transfer of both devices has been elucidated; the prototype preserved a stress distribution closer to the physiological condition.

Evolutionary ecology of microbial wars: within-host competition and (incidental) virulence

Invading an occupied niche is a formidable ecological challenge, and one of particular human importance in the context of food-borne microbial pathogens. We discuss distinct categories of invader-triggered environmental change that facilitate invasion by emptying their niche of competitors. Evidence is reviewed that gut bacteria use such strategies to manipulate their environment (via bacteriocins, temperate phage viruses or immuno-manipulation) at the expense of their competitors are reviewed. The possible virulence implications of microbial warfare among multiple co-infecting strains are diverse. Killing competitors can reduce virulence by reducing overall microbial densities, or increase virulence if for example the allelopathic mechanism involves immuno-manipulation. Finally, we place microbial anti-competitor strategies in a social evolution framework, highlighting how costly anti-competitor strategies can be understood as examples of microbial spite. We conclude by discussing other invasive species that have also developed such proactive strategies of invasion.

Strain distribution in the proximal human femoral metaphysis

There is significant interest in the stress—strain state in the proximal femoral metaphysis, because of its relevance for hip fractures and prosthetic replacements. The scope of this work was to provide a better understanding of the strain distribution, and of its correlation with the different directions of loading, and with bone quality. A total of 12 pairs of human femurs were instrumented with strain gauges. Six loading configurations were designed to cover the range of directions spanned by the hip joint force. Inter-specimen variability was reduced if paired specimens were considered. The principal strain magnitude varied greatly between loading configurations. This suggests that different loading configurations need to be simulated in vitro. The strain magnitude varied between locations but, on average, was compatible with the strain values measured in vivo. The strain magnitudes and the direction of principal tensile strain in the head and neck were compatible with the spontaneous fractures of the proximal femur reported in some subjects. The principal tensile strain was significantly larger where the cortical bone was thinner; the compressive strain was larger where the cortical bone was thicker. The direction of the principal strain varied significantly between measurement locations but varied little between loading configurations. This suggests that the anatomy and the distribution of anisotropic material properties enable the proximal femur to respond adequately to the changing direction of daily loading.

Reversal of compensatory flow in severe intrauterine growth restriction: middle cerebral artery and intracardiac volume flow modifications

AIM

The aim of the study was to investigate cerebral and cardiac volume flow modifications in a group of preterm severely growth restricted (GR) fetuses with absent end diastolic flow (AEDF) in the umbilical artery.

METHODS

Doppler indices of GR fetuses born at less than 32 weeks of gestation with AEDF in umbilical artery were longitudinally analyzed. Ductus venosus S/A, umbilical artery PI, middle cerebral artery (MCA) pulsatility index (PI), MCA volume flow and intracardiac flows were checked daily. The value of volume flow was determined by multiplying the vessel area obtained by means of a power angiography by the integral of the velocimetric curve. In Group 1 the time of delivery was decided when abnormal Doppler index in ductus venosus (S/A>3) was detected. In Group 2, decisions about delivery were based on maternal indications or on various cardiotocographic (CTG) abnormalities. The division in the two groups was made with a retrospective method.

RESULTS

Fifteen GR fetuses were studied: seven cases entered Group 1 and eight cases Group 2. In Group 2 velocimetric (PI) and quantitative (volume flow) values remained stable until delivery. In all cases in Group 1 ductus venosus anomalies (S/A>3) were preceded by 24 hours by cerebral volume flow indices indicating the loss of MCA vasodilatation and by changes in intracardiac volume flow indices, while the PI increase in MCA was present only 24 hours after the changes detected by the volume flow study and were simultaneous to ductus venosus modifications.

CONCLUSION

The decrease in volume flow through the middle cerebral artery occurs at least 24 hours before the increase of middle cerebral artery PI and before the ductus venosus anomalies. Flow through the four cardiac valves show modification in agreement to the changes of the middle cerebral artery flow.

Viruses' life history: towards a mechanistic basis of a trade-off between survival and reproduction among phages

Life history theory accounts for variations in many traits involved in the reproduction and survival of living organisms, by determining the constraints leading to trade-offs among these different traits. The main life history traits of phages—viruses that infect bacteria—are the multiplication rate in the host, the survivorship of virions in the external environment, and their mode of transmission. By comparing life history traits of 16 phages infecting the bacteria Escherichia coli, we show that their mortality rate is constant with time and negatively correlated to their multiplication rate in the bacterial host. Even though these viruses do not age, this result is in line with the trade-off between survival and reproduction previously observed in numerous aging organisms. Furthermore, a multiple regression shows that the combined effects of two physical parameters, namely, the capsid thickness and the density of the packaged genome, account for 82% of the variation in the mortality rate. The correlations between life history traits and physical characteristics of virions may provide a mechanistic explanation of this trade-off. The fact that this trade-off is present in this very simple biological situation suggests that it might be a fundamental property of evolving entities produced under constraints. Moreover, such a positive correlation between mortality and multiplication reveals an underexplored trade-off in host–parasite interactions.

A comparison of life-history traits of 16 phages infecting E. coli reveals that although these viruses don't age, there is a trade-off between mortality and growth rate, which parallels that observed in many other species.

Dissecting the genetic components of adaptation of Escherichia coli to the mouse gut

While pleiotropic adaptive mutations are thought to be central for evolution, little is known on the downstream molecular effects allowing adaptation to complex ecologically relevant environments. Here we show that Escherichia coli MG1655 adapts rapidly to the intestine of germ-free mice by single point mutations in EnvZ/OmpR two-component signal transduction system, which controls more than 100 genes. The selective advantage conferred by the mutations that modulate EnvZ/OmpR activities was the result of their independent and additive effects on flagellin expression and permeability. These results obtained in vivo thus suggest that global regulators may have evolved to coordinate activities that need to be fine-tuned simultaneously during adaptation to complex environments and that mutations in such regulators permit adjustment of the boundaries of physiological adaptation when switching between two very distinct environments.

The mammalian intestine is a privileged physiological site to study how coevolution between hosts and the trillions of bacteria present in the microbiota has shaped the genome of each partner and promoted the development of mutualistic interactions. Herein we have used germ-free mice, a simplified albeit ecologically relevant system, to analyse intestinal adaptation of a model bacterial strain, Escherichia coli MG1655. Our results show that single point mutations in the ompB master regulator confer a striking selective adaptive advantage. OmpB comprises EnvZ, a transmembrane sensor with a dual kinase/phosphatase activity, and OmpR, a transcription factor controlling more than 100 target genes. In response to environmental changes, EnvZ modulates the phosphorylation and thereby the transcriptional activity of OmpR. We further show that the selective advantage conferred by OmpB mutations is related to their additive and independent effects on genes regulating permeability and flagellin expression, two major set of genes controlled by OmpR. These results suggest that global regulators may have evolved to coordinate physiological activities necessary for adaptation to complex environments and that mutations offer a complementary genetic mechanism to adjust the scale of the physiological regulation controlled by these regulators in distinct environments.

Mutations in two global regulators lower individual mortality in Escherichia coli

There has been considerable investigation into the survival of bacterial cells under stress conditions, but little is known about the causes of mortality in the absence of exogenous stress. That there is a basal frequency of cell death in such populations may reflect that it is either impossible to avoid all lethal events, or alternatively, that it is too costly. Here, through a genetic screen in the model organism Escherichia coli, we identify two mutants with lower frequencies of mortality: rssB and fliA. Intriguingly, these two genes both affect the levels of different sigma factors within the cell. The rssB mutant displays enhanced resistance to multiple external stresses, possibly indicating that the cell gains its increased vitality through elevated resistance to spontaneous, endogenous stresses. The loss of fliA does not result in elevated stress resistance; rather, its survival is apparently due to a decreased physical stress linked to the insertion of the flagellum through the membrane and energy saved through the loss of the motor proteins. The identification of these two mutants implies that reducing mortality is not impossible; rather, due to its cost, it is subject to trade-offs with other traits that contribute to the competitive success of the organism.

Evolution of virulence: triggering host inflammation allows invading pathogens to exclude competitors

Virulence is generally considered to benefit parasites by enhancing resource-transfer from host to pathogen. Here, we offer an alternative framework where virulent immune-provoking behaviours and enhanced immune resistance are joint tactics of invading pathogens to eliminate resident competitors (transferring resources from resident to invading pathogen). The pathogen wins by creating a novel immunological challenge to which it is already adapted. We analyse a general ecological model of 'proactive invasion' where invaders not adapted to a local environment can succeed by changing it to one where they are better adapted than residents. However, the two-trait nature of the 'proactive' strategy (provocation of, and adaptation to environmental change) presents an evolutionary conundrum, as neither trait alone is favoured in a homogenous host population. We show that this conundrum can be resolved by allowing for host heterogeneity. We relate our model to emerging empirical findings on immunological mediation of parasite competition.

The durability of public goods changes the dynamics and nature of social dilemmas

An implicit assumption underpins basic models of the evolution of cooperation, mutualism and altruism: The benefits (or pay-offs) of cooperation and defection are defined by the current frequency or distribution of cooperators. In social dilemmas involving durable public goods (group resources that can persist in the environment–ubiquitous from microbes to humans) this assumption is violated. Here, we examine the consequences of relaxing this assumption, allowing pay-offs to depend on both current and past numbers of cooperators. We explicitly trace the dynamic of a public good created by cooperators, and define pay-offs in terms of the current public good. By raising the importance of cooperative history in determining the current fate of cooperators, durable public goods cause novel dynamics (e.g., transient increases in cooperation in Prisoner's Dilemmas, oscillations in Snowdrift Games, or shifts in invasion thresholds in Stag-hunt Games), while changes in durability can transform one game into another, by moving invasion thresholds for cooperation or conditions for coexistence with defectors. This enlarged view challenges our understanding of social cheats. For instance, groups of cooperators can do worse than groups of defectors, if they inherit fewer public goods, while a rise in defectors no longer entails a loss of social benefits, at least not in the present moment (as highlighted by concerns over environmental lags). Wherever durable public goods have yet to reach a steady state (for instance due to external perturbations), the history of cooperation will define the ongoing dynamics of cooperators.

Microcontact printing of living bacteria arrays with cellular resolution

Arrays of living bacteria were printed on agarose substrate with cellular resolution using elastomeric stamps with a high aspect ratio generated by reverse in situ lithography (RISL). The printed bacteria reproduced the original stamp patterns with high fidelity and continued growing as in bulk culture. This methodology provides a simple route to any desired bacterial spatial 2D distribution and may be applied to screening as well as to studies of bacteria phenotypic variability, population dynamics, and ecosystem evolution.

Changes in femur stress after hip resurfacing arthroplasty: response to physiological loads

BACKGROUND

Hip resurfacing arthroplasty is being increasingly considered as an alternative to total hip arthroplasty in young, active patients. Hip resurfacing arthroplasty is reported to preserve the normal joint mechanics. However, there is concern, in the short term, due to frequent occurrence of femoral neck fractures.

METHODS

We evaluated changes in femoral mechanics after hip resurfacing arthroplasty. We used an experimentally validated, distributed material finite element model of a cadaveric femur before and after hip resurfacing arthroplasty. Bone stiffness and strength values representing normal, elderly and osteoporotic bone were used. For a physiological load case, bone strains were compared with literature values for total hip arthroplasty and a risk of fracture scalar calculated.

FINDINGS

The changes in peak stresses after hip resurfacing arthroplasty were low in relation to the failure strength of bone and the fracture risk was low. The intact and implanted finite element models showed bone strains after hip resurfacing arthroplasty were closer to the intact condition than after total hip arthroplasty.

INTERPRETATION

The bone stresses predicted after resurfacing in both the normal and aged femoral neck were not sufficient to be a potential cause of fracture.

Experimental validation of a finite element model of a composite tibia

Composite bones are synthetic models made to simulate the mechanical behaviour of human bones. Finite element (FE) models of composite bone can be used to evaluate new and modified designs of joint prostheses and fixation devices. The aim of the current study was to create an FE model of a composite tibia and to validate it against results obtained from a comprehensive set of experiments. For this, 17 strain rosettes were attached to a composite tibia (model 3101, Pacific Research Laboratories, Vashon, Washington, USA). Surface strains and displacements were measured under 13 loading conditions. Two FE models were created on the basis of computed tomography scans. The models differed from each other in the mesh and material properties assigned. The experiments were simulated on them and the results compared with experimental results. The more accurate model was selected on the basis of regression analysis. In general, experimental strain measurements were highly repeatable and compared well with published results. The more accurate model, in which the inner elements representing the foam were assigned isotropic material properties and the elements representing the epoxy layer were assigned transversely isotropic material properties, was able to simulate the mechanical behaviour of the tibia with acceptable accuracy. The regression line for all axial loads combined had a slope of 0.999, an intercept of -6.24 microstrain, and an R2 value of 0.962. The root mean square error as a percentage was 5 per cent.

Ecology of microbial invasions: amplification allows virus carriers to invade more rapidly when rare

Locally adapted residents present a formidable barrier to invasion . One solution for invaders is to kill residents . Here, we explore the comparative ecological dynamics of two distinct microbial mechanisms of killing competitors, via the release of chemicals (e.g., bacteriocins ) and via the release of parasites (e.g., temperate phage ). We compared the short-term population dynamics of susceptible E. coli K12 and isogenic carriers of phage varphi80 in experimental cultures to that anticipated by mathematical models using independently derived experimental parameters. Whereas phages are a direct burden to their carriers because of probabilistic host lysis, by killing competitor bacteria they can indirectly benefit bacterial kin made immune by carrying isogenic phage. This is similar to previously described bacteriocin-mediated effects. However, unlike chemical killing, viable phage trigger an epidemic among susceptible competitors, which become factories producing more phage. Amplification makes phage carriers able to invade well-mixed susceptibles even faster when rare, whereas chemical killers can only win in a well-mixed environment when sufficiently abundant. We demonstrate that for plausible parameters, the release of chemical toxins is superior as a resident strategy to repel invasions, whereas the release of temperate phage is superior as a strategy of invasion.

Caenorhabditis elegans as a simple model to study phenotypic and genetic virulence determinants of extraintestinal pathogenic Escherichia coli

Extraintestinal pathogenic Escherichia coli (ExPEC) strains cause disease by invading normally sterile niches within the host body, e.g., urinary tract, blood and cerebrospinal fluid. Infections due to ExPEC strains, in particular urinary tract infections, cause considerable morbidity and significant health-care costs. The goal of our study is to evaluate whether Caenorhabditis elegans can be used as a model to study phenotypic and genetic virulence determinants of ExPEC strains. For this purpose, we used a collection of 31 E. coli strains isolated during acute extra-intestinal infections or from the feces of healthy individuals. For all strains, the phylogeny, the presence of ExPEC virulence factors, the resistance to biologically relevant stressors (bile, human serum and lysozyme), the motility, the growth rate, the virulence in C. elegans and in a murine septicaemia model has been established. The results show that there is a strong link between virulence in C. elegans and certain phenotypic and genetic virulence predictors of ExPEC strains determinable in vitro. Furthermore, there is a significant correlation between virulence of different ExPEC strains in C. elegans and in the murine model. Therefore, our results suggest that C. elegans can be used as a model to study virulence determinants of ExPEC strains.

[The intestinal flora: the scales without the sword]

The intestine is colonised by a vast population of resident bacteria which have established mutualistic relationships with their host throughout evolution, progressing from commensalism to symbiotic interactions. Intestinal bacteria benefit from resources available in their host, but reciprocally provide advantages to their host, by supplying enzymatic activities not encoded in the host genome, by promoting maturation of the intestine and of the gut associated immune system as well as by modifying the host metabolism. The commensal bacteria, although deprived of pathogenic attributes, might however become a danger for the host in case of translocation, acquisition of pathogenic features or via the inappropriate activation of intestinal inflammation. Remarkably, the commensal flora promotes the onset of innate and adaptive immune defences which, in turn, allow to set up a subtle balance between the host and the flora that promotes the symbiosis.

A new software tool for 3D motion analyses of the musculo-skeletal system

BACKGROUND

Many clinical and biomechanical research studies, particularly in orthopaedics, nowadays involve forms of movement analysis. Gait analysis, video-fluoroscopy of joint replacement, pre-operative planning, surgical navigation, and standard radiostereometry would require tools for easy access to three-dimensional graphical representations of rigid segment motion. Relevant data from this variety of sources need to be organised in structured forms. Registration, integration, and synchronisation of segment position data are additional necessities. With this aim, the present work exploits the features of a software tool recently developed within a EU-funded project ('Multimod') in a series of different research studies.

METHODS

Standard and advanced gait analysis on a normal subject, in vivo fluoroscopy-based three-dimensional motion of a replaced knee joint, patellar and ligament tracking on a knee specimen by a surgical navigation system, stem-to-femur migration pattern on a patient operated on total hip replacement, were analysed with standard techniques and all represented by this innovative software tool. Segment pose data were eventually obtained from these different techniques, and were successfully imported and organised in a hierarchical tree within the tool.

FINDINGS

Skeletal bony segments, prosthesis component models and ligament links were registered successfully to corresponding marker position data for effective three-dimensional animations. These were shown in various combinations, in different views, from different perspectives, according to possible specific research interests.

INTERPRETATION

Bioengineering and medical professionals would be much facilitated in the interpretation of the motion analysis measurements necessary in their research fields, and would benefit therefore from this software tool.