Genome Instability Mediates the Loss of Key Traits by Acinetobacter baylyi ADP1 during Laboratory Evolution

Acinetobacter baylyi ADP1 has the potential to be a versatile bacterial host for synthetic biology because it is naturally transformable. To examine the genetic reliability of this desirable trait and to understand the potential stability of other engineered capabilities, we propagated ADP1 for 1,000 generations of growth in rich nutrient broth and analyzed the genetic changes that evolved by whole-genome sequencing. Substantially reduced transformability and increased cellular aggregation evolved during the experiment. New insertions of IS1236 transposable elements and IS1236-mediated deletions led to these phenotypes in most cases and were common overall among the selected mutations. We also observed a 49-kb deletion of a prophage region that removed an integration site, which has been used for genome engineering, from every evolved genome. The comparatively low rates of these three classes of mutations in lineages that were propagated with reduced selection for 7,500 generations indicate that they increase ADP1 fitness under common laboratory growth conditions. Our results suggest that eliminating transposable elements and other genetic failure modes that affect key organismal traits is essential for improving the reliability of metabolic engineering and genome editing in undomesticated microbial hosts, such as Acinetobacter baylyi ADP1.     

On the Attractiveness of Product Recovery: The Forces that Shape Reverse Markets

Product recovery is a major contributor for implementing sustainable business practices. Within such operations, which are either driven by legislation or economic rationales, practitioners face strategic issues concerning reverse market entry and positioning. Although the complexity of acting on reverse markets is widely acknowledged, a comprehensive framework to facilitate decision making in this area is lacking. In an attempt to fill that gap, we develop a model that supports original equipment manufacturers’ (OEMs’) assessment of the attractiveness of reverse markets. We identify, from a comprehensive literature analysis, in‐depth interviews, and engagement with a dozen companies from different countries, factors that influence key characteristics of reverse markets, and consolidate this lengthy list into a comprehensive model intuitively applicable to business practice. The model combines five forces that drive reverse markets: access to recoverable products; threat of independent recovery companies’ (IRCs’) market entry; rivalry for recoverable products; adverse effects on core business; and remarketing opportunities. We propose for each a set of attributes that influences its power and direction. To demonstrate the efficacy of the model, we apply it in two industry settings: recovery of white goods in the United Kingdom and paper recycling in Germany. The present research enables OEMs to understand the structure and forces that drive reverse markets, identify levers to influence those markets, anticipate market developments, and formulate resilient strategies for product recovery.     

基于三生空间质量的哈长城市群城市脆弱性时空演变格局及驱动力研究

高质量的三生空间是城市高品质空间布局、高效率功能体现的重要保障与载体。城市群作为城市三生空间矛盾的集中地,降低其城市脆弱性,是区域可持续发展的关键。因此,基于三生空间质量的哈长城市群城市脆弱性研究对国土空间协调与稳定发展具有重要意义。以哈长城市群11个地市为研究区域,基于生产空间质量、生活空间质量、生态空间质量构建城市脆弱性评价指标体系,运用熵权-TOPSIS评价模型、ArcGIS空间分析工具以及地理探测器对2010-2018年哈长城市群城市脆弱性的时空格局演变与驱动力进行分析。研究结果表明:①在时间变化上:整体来看,2010-2018年哈长城市群城市脆弱性呈下降的趋势,城市脆弱性空间上呈"先增强后减弱"的态势。城市脆弱性高等级地区数量呈现"先增强后减弱"的趋势,而城市脆弱性指数相似地区集中分布呈现"先减弱后增强"态势。②在空间布局上:形成了II、I级区"点状零散",V、IV级区的"边缘式"的空间分布格局。空间分布呈现"随机化",无明显集聚性。从其演化趋势类型特征上看,呈发散趋势的城市多于呈收敛趋势的城市,说明哈长城市群城市脆弱性空间差异呈逐渐增大态势。③基于三生空间质量哈长城市群城市脆弱性的空间分异主要是由城市生活空间质量脆弱性的差异引起,其次是城市生产空间质量脆弱性。其中,经济增长水平不高是城市生产空间质量脆弱性的首要因素;交通设施水平不完善、燃气资源供给力度不够、城乡差距偏大、教育水平程度偏低、信息化水平低下是城市生活空间质量脆弱性的关键因素;污水处理强度、城市绿化水平和生活垃圾无害化处理强度是影响哈长城市群城市生态空间质量脆弱性的基础要素。     

Homophily and the Speed of Social Mobilization: The Effect of Acquired and Ascribed Traits

Large-scale mobilization of individuals across social networks is becoming increasingly prevalent in society. However, little is known about what affects the speed of social mobilization. Here we use a framed field experiment to identify and measure properties of individuals and their relationships that predict mobilization speed. We ran a global social mobilization contest and recorded personal traits of the participants and those they recruited. We studied the effects of ascribed traits (gender, age) and acquired traits (geography, and information source) on the speed of mobilization. We found that homophily, a preference for interacting with other individuals with similar traits, had a mixed role in social mobilization. Homophily was present for acquired traits, in which mobilization speed was faster when the recuiter and recruit had the same trait compared to different traits. In contrast, we did not find support for homophily for the ascribed traits. Instead, those traits had other, non-homophily effects: Females mobilized other females faster than males mobilized other males. Younger recruiters mobilized others faster, and older recruits mobilized slower. Recruits also mobilized faster when they first heard about the contest directly from the contest organization, and decreased in speed when hearing from less personal source types (e.g. family vs. media). These findings show that social mobilization includes dynamics that are unlike other, more passive forms of social activity propagation. These findings suggest relevant factors for engineering social mobilization tasks for increased speed.     

Wall Relaxation and the Driving Forces for Cell Expansive Growth

When water uptake by growing cells is prevented, the turgor pressure and the tensile stress in the cell wall are reduced by continued wall loosening. This process, termed in vivo stress relaxation, provides a new way to study the dynamics of wall loosening and to measure the wall yield threshold and the physiological wall extensibility. Stress relaxation experiments indicate that wall stress supplies the mechanical driving force for wall yielding. Cell expansion also requires water absorption. The driving force for water uptake during growth is created by wall relaxation, which lowers the water potential of the expanding cells. New techniques for measuring this driving force show that it is smaller than believed previously; in elongating stems it is only 0.3 to 0.5 bar. This means that the hydraulic resistance of the water transport pathway is small and that rate of cell expansion is controlled primarily by wall loosening and yielding.     

Analyzing the Long Term Cohesive Effect of Sector Specific Driving Forces

Financial markets are partially composed of sectors dominated by external driving forces, such as commodity prices, infrastructure and other indices. We characterize the statistical properties of such sectors and present a novel model for the coupling of the stock prices and their dominating driving forces, inspired by mean reverting stochastic processes. Using the model we were able to explain the market sectors’ long term behavior and estimate the coupling strength between stocks in financial markets and the sector specific driving forces. Notably, the analysis was successfully applied to the shipping market, in which the Baltic dry index (BDI), an assessment of the price of transporting the major raw materials by sea, influences the shipping financial market. We also present the analysis of other sectors—the gold mining market and the food production market, for which the model was also successfully applied. The model can serve as a general tool for characterizing the coupling between external forces and affected financial variables and therefore for estimating the risk in sectors and their vulnerability to external stress.     

The Evolution of Theoretically Useful Traits

The purely theoretical notion of fitness or optimality that is employed for instance in optimization theory has come under attack from those who think that only a more historically based notion of fitness could have a central role in evolutionary explanation. They argue that the key notion is proven usefulness rather than theoretical usefulness. This paper articulates a notion of theoretical usefulness and defends its role in functional evolutionary explanations.     

The Evolution of Dimorphic Traits: Predicting the Genetic Correlation between Environments

Many traits vary in a dichotomous manner, although the underlying genetic determination is polygenic. The genetic basis of such dimorphic traits can be analyzed using the threshold model, in which it is assumed that there is a continuously distributed underlying character and the phenotype is determined by whether the character is above or below a threshold. Threshold traits frequently vary with environmental variables such as photoperiod, temperature and density. This effect can be accounted for using a threshold model in which (1) there is a critical value of the environmental variable at which a genotype switches to the alternate morph, and (2) switch (threshold) points are normally distributed in the population. I term this the environmental threshold (ET) model. I show that the ET model predicts that across environments differing in only one factor the genetic correlation will be 1. This prediction is supported by data from three wing dimorphic insects. Evidence is presented that the genetic correlation between environments differing in two components (temperature and photoperiod) is less than 1.     

Combating the Assumption of Evolutionary Progress: Lessons from the Decay and Loss of Traits

Contrary to popular belief, evolution is not necessarily progressive. Indeed, traits are often lost or substantially reduced in the process of evolution. In this article, we present several case studies that can be used in the classroom to illustrate both the ubiquity and diversity of cases of trait loss. Our recently acquired knowledge of genetic and developmental processes can provide insight into how traits are gained and lost through evolution. Several practical applications also emerge from studies of trait loss and degeneration, and we focus on those with medical relevance. Examining trait loss also provides perspective on the crucial differences between Darwinian evolution and social Darwinism. We encourage educators to devote greater attention to trait loss in secondary biology and undergraduate evolution courses, and discuss how such information may be best incorporated into evolution curricula.     

Statistical Mechanics and the Evolution of Polygenic Quantitative Traits

The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ > 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection.     

Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics

Kinetochores are multi-protein complexes that mediate the physical coupling of sister chromatids to spindle microtubule bundles (called kinetochore (K)-fibres) from respective poles. These kinetochore-attached K-fibres generate pushing and pulling forces, which combine with polar ejection forces (PEF) and elastic inter-sister chromatin to govern chromosome movements. Classic experiments in meiotic cells using calibrated micro-needles measured an approximate stall force for a chromosome, but methods that allow the systematic determination of forces acting on a kinetochore in living cells are lacking. Here we report the development of mathematical models that can be fitted (reverse engineered) to high-resolution kinetochore tracking data, thereby estimating the model parameters and allowing us to indirectly compute the (relative) force components (K-fibre, spring force and PEF) acting on individual sister kinetochores in vivo. We applied our methodology to thousands of human kinetochore pair trajectories and report distinct signatures in temporal force profiles during directional switches. We found the K-fibre force to be the dominant force throughout oscillations, and the centromeric spring the smallest although it has the strongest directional switching signature. There is also structure throughout the metaphase plate, with a steeper PEF potential well towards the periphery and a concomitant reduction in plate thickness and oscillation amplitude. This data driven reverse engineering approach is sufficiently flexible to allow fitting of more complex mechanistic models; mathematical models of kinetochore dynamics can therefore be thoroughly tested on experimental data for the first time. Future work will now be able to map out how individual proteins contribute to kinetochore-based force generation and sensing.     

Rapid Evolution of Novel Traits in Microorganisms

The use of natural microorganisms in biotransformations is frequently constrained by their limited tolerance to the high concentrations of metabolites and solvents required for effective industrial production. In many cases, more robust strains have to be generated by random mutagenesis and selection. This process of directed evolution can be accelerated in mutator strains, which carry defects in one or more of their DNA repair genes. However, in order to use mutator strains, it is essential to restore the normal low mutation rate of the selected organisms immediately after selection to prevent the accumulation of undesirable spontaneous mutations. To enable this process, we constructed temperature-sensitive plasmids that temporarily increase the mutation frequency of their hosts by 20- to 4,000-fold. Under appropriate selection pressure, microorganisms transformed with mutator plasmids can be quickly evolved to exhibit new, complex traits. By using this approach, we were able to increase the tolerance of three bacterial strains to dimethylformamide by 10 to 20 g/liter during only two subsequent transfers. Subsequently, the evolved strains were returned to their normal low mutation rate by curing the cells of the mutator plasmids. Our results demonstrate a new and efficient method for rapid strain improvement based on in vivo mutagenesis.