Corruption of phage display libraries by target-unrelated clones: Diagnosis and countermeasures

Phage display is used to discover peptides or proteins with a desired target property—most often, affinity for a target selector molecule. Libraries of phage clones displaying diverse surface peptides are subject to a selection process designed to enrich for the target behavior and subsequently propagated to restore phage numbers. A recurrent problem is enrichment of clones, called target-unrelated phages or peptides (TUPs), that lack the target behavior. Many TUPs are propagation related; they have mutations conferring a growth advantage and are enriched during the propagations accompanying selection. Unlike other filamentous phage libraries, fd-tet-based libraries are relatively resistant to propagation-related TUP corruption. Their minus-strand origin is disrupted by a large cassette that simultaneously confers resistance to tetracycline and imposes a rate-limiting growth defect that cannot be bypassed with simple mutations. Nonetheless, a new type of propagation-related TUP emerged in the output of in vivo selections from an fd-tet library. The founding clone had a complex rearrangement that restored the minus-strand origin while retaining tetracycline resistance. The rearrangement involved two recombination events, one with a contaminant having a wild-type minus-strand origin. The founder’s infectivity advantage spread by simple recombination to clones displaying different peptides. We propose measures for minimizing TUP corruption.     

Ultrasound and matter--physical interactions

The basic physical characteristics of ultrasound waves are reviewed in terms of the typical displacements, velocities, accelerations and pressures generated in various fluid media as a function of frequency. The effects on wave propagation of interfaces are considered, and the way in which waves are reflected, transmitted and mode converted at interfaces introduced. Then the nonlinear propagation of high amplitude ultrasound is explained, and its consequences, including the generation of harmonic frequencies and enhanced attenuation, considered. The absorption of ultrasonic waves and the resulting heat deposition in absorbing media are described together with factors determining the resulting temperature rises obtained. In the case of tissue these include conduction and perfusion. The characteristics of cavitation in fluid media are also briefly covered. Finally, secondary nonlinear physical effects are described. These include radiation forces on interfaces and streaming in fluids.     

Plant population growth and competition in a light gradient: a mathematical model of canopy partitioning

Can a difference in the heights at which plants place their leaves, a pattern we call canopy partitioning, make it possible for two competing plant species to coexist? To find out, we examine a model of clonal plants living in a nonseasonal environment that relates the dynamical behavior and competitive abilities of plant populations to the structural and functional features of the plants that form them. This examination emphasizes whole plant performance in the vertical light gradient caused by self-shading. This first of three related papers formulates a prototype single species Canopy Structure Model from biological first principles and shows how all plant properties work together to determine population persistence and equilibrium abundance. Population persistence is favored, and equilibrium abundance is increased, by high irradiance, high maximum photosynthesis rate, rapid saturation of the photosynthetic response to increased irradiance, low tissue respiration rate, small amounts of stem and root tissue necessary to support the needs of leaves, and low density of leaf, stem, and root tissues. In particular, equilibrium abundance decreases as mean leaf height increases because of the increased cost of manufacturing and maintaining stem tissue. All conclusions arise from this formulation by straightforward analysis. The argument concludes by stating this formulation's straightforward extension, called a Canopy Partitioning Model, to two competing species.     

An evolutionary hybrid cellular automaton model of solid tumour growth

We propose a cellular automaton model of solid tumour growth, in which each cell is equipped with a micro-environment response network. This network is modelled using a feed-forward artificial neural network, that takes environmental variables as an input and from these determines the cellular behaviour as the output. The response of the network is determined by connection weights and thresholds in the network, which are subject to mutations when the cells divide. As both available space and nutrients are limited resources for the tumour, this gives rise to clonal evolution where only the fittest cells survive. Using this approach we have investigated the impact of the tissue oxygen concentration on the growth and evolutionary dynamics of the tumour. The results show that the oxygen concentration affects the selection pressure, cell population diversity and morphology of the tumour. A low oxygen concentration in the tissue gives rise to a tumour with a fingered morphology that contains aggressive phenotypes with a small apoptotic potential, while a high oxygen concentration in the tissue gives rise to a tumour with a round morphology containing less evolved phenotypes. The tissue oxygen concentration thus affects the tumour at both the morphological level and on the phenotype level.     

Impact of mate availability, population size, and spatial aggregation of morphs on sexual reproduction in a distylous, aquatic plant

In distylous, self-incompatible plants, clonal propagation, unbalanced floral morph frequencies, and reduced population size can interfere with the functioning of distyly by compromising legitimate intermorph pollinations, resulting in reduced reproductive output. Here, we examined the mating system and the impact of mate availability, population size, and spatial aggregation of morphs on reproductive output in the distylous, clonal, aquatic plant Hottonia palustris. Controlled pollinations under greenhouse conditions detected no spontaneous selfing without the action of a pollen vector (autonomous autogamy) and demonstrated very low fruit and seed development after self-pollination. Intermorph (legitimate) crossings resulted in high reproductive output in both floral morphs (long- and short-styled individuals), whereas intramorph (illegitimate) crossings decreased fruit and seed development by more than 50%, indicating that the species has partial intramorph-incompatibility. In natural populations, small population size and increasing deviation of floral morph frequencies negatively affected reproductive outcome. Individuals of the majority morph type developed significantly fewer fruit and seeds than individuals of the minority morph type. This rapid decline in fecundity was symmetrical, indicating that regardless of which morph was in the majority, the same patterns of negative frequency-dependent mating occurred. Increasing spatial isolation between compatible morphs significantly reduced fruit and seed set in both morphs similarly. This study provides clear indications of frequency- and context-dependent mating in natural populations of a distylous plant species.     

Adaptive genetic differentiation in life-history traits between populations of <Emphasis Type="Italic">Mimulus guttatus</Emphasis> with annual and perennial life-cycles

The optimal allocation to sexual and vegetative reproduction as well as the optimal values of other life-history characteristics such as phenology, growth and mating system are likely to depend on the life-cycle of the organism. I tested whether plants of Mimulus guttatus originating from temporarily wet populations where the species has an enforced annual life-cycle have higher allocation to sexual reproduction, lower allocation to vegetative reproduction, more rapid phenology, faster growth, and floral traits associated with a self-fertilizing mating system than plants from permanently wet populations where the species has a perennial life-cycle. I grew a total of 1377 plants originating from three populations with an annual life-cycle and 11 populations with a perennial life-cycle in a greenhouse under permanently and temporarily wet conditions. Plants of M. guttatus in permanently wet conditions had significantly more vegetative reproduction and tended to have a faster growth than plants in the temporarily wet conditions, indicating plasticity in these life-history traits. Plants from populations with an annual life-cycle invested significantly more in sexual reproduction and significantly less in vegetative reproduction than the ones from populations with a perennial life-cycle. Moreover, this study showed that plants originating from populations with an annual life-cycle have a significantly faster development and floral traits associated with autonomous self-fertilization. In conclusion, this study suggests that there has been adaptive evolution of life history traits of M. guttatus in response to natural watering conditions that determine the life span of the species.     

Differential effects of water depth and sediment type on clonal growth of the submersed macrophyte <Emphasis Type="Italic">Vallisneria natans</Emphasis>

The response of clonal growth and ramet morphology to water depth (from 60 to 260 cm) and sediment type (sand versus organic clay) was investigated for the stoloniferous submersed macrophyte Vallisneria natans in an outdoor pond experiment. Results showed that water depth significantly affected clonal growth of V. natans in terms of clone weight, number of ramets, number of generations, clonal radius and stolon length. V. natans showed an optimal clonal growth at water depths of 110–160 cm, but at greater depths clonal growth was severely retarded. A high allometric effect was exhibited in ramet morphology. Along the sequentially produced ramet generations, ramet weight and plant height decreased while stolon length and the root:leaf weight ratio increased. When using ramet generations as covariate, sediment type rather than water depth more strongly affected the ramet characteristics. For plants grown in clay, ramet weight, ramet height and stolon length were greater, and plants exhibited lower root:leaf weight ratio. These data suggest that water depth and sediment type have differential effects on clonal growth of V. natans: Water depth appears primarily to affect numerical increase in ramets and spatial spread, whereas sediment type mainly affects biomass accumulation and biomass allocation. Handling editor: S. M. Thomaz     

留兰香组织培养及快速繁殖条件的优化

以留兰香(Menthaspicata L.)茎尖为实验材料,对外植体消毒、不定芽增殖和试管苗移栽生根的最佳条件进行研究。结果表明,最佳外植体消毒方法为:用体积分数75%乙醇浸泡30s,再用1.0g·L-1HgCl2浸泡10min,培养7d后外植体生长状况良好。正交实验结果表明,在附加0.2mg·L-16-BA和0.02mg·L-1NAA的MS培养基中,留兰香不定芽的增殖倍数最高,试管苗生长状况最好。在含25mg·L-16-BA和50mg·L-1NAA的混合溶液中浸泡1h,移栽试管苗的生根率可达100%,且根较长。     

Local above‐ground persistence of vascular plants: Life‐history trade‐offs and environmental constraints

Questions: 1. Which plant traits and habitat characteristics best explain local above‐ground persistence of vascular plant species and 2. Is there a trade‐off between local above‐ground persistence and the ability for seed dispersal and below‐ground persistence in the soil seed bank? Locations: 845 long‐term permanent plots in terrestrial habitats across the Netherlands. Methods: We analysed the local above‐ground persistence of vascular plants in permanent plots (monitored once a year for ca. 16 year) with respect to functional traits and habitat preferences using survival statistics (Kaplan‐Meier analysis and Cox’ regression). These methods account for censored data and are rarely used in vegetation ecology. Results: Local above‐ground persistence is determined by both functional traits (especially the ability to form long‐lived clonal connections) and habitat preferences (especially nutrient requirements). Above‐ground persistence is negatively related to the ability for dispersal by wind and to the ability to accumulate a long‐term persistent soil seed bank (‘dispersal through time’) and is positively related to the ability for dispersal by water. Conclusions: Most species have a half‐life expectation over 15 years, which may contribute to time lags after changes in habitat quality or ‐configuration (‘extinction debt’). There is evidence for a trade‐off relationship between local above‐ground persistence and below‐ground seed persistence, while the relationship with dispersal in space is vector specific. The rate of species turnover increases with productivity.