Recent selection for self‐compatibility in a population of Leavenworthia alabamica

The evolution of self‐compatibility (SC) is the first step in the evolutionary transition in plants from outcrossing enforced by self‐incompatibility (SI) to self‐fertilization. In the Brassicaceae, SI is controlled by alleles of two tightly linked genes at the S‐locus. Despite permitting inbreeding, mutations at the S‐locus leading to SC may be selected if they provide reproductive assurance and/or gain a transmission advantage in a population when SC plants self‐ and outcross. Positive selection can leave a genomic signature in the regions physically linked to the focus of selection when selection has occurred recently. From an SC population of Leavenworthia alabamica with a known nonfunctional mutation at the S‐locus, we collected sequence data from a ～690 Kb region surrounding the S‐locus, as well as from regions not linked to the S‐locus. To test for recent positive selection acting at the S‐locus, we examined polymorphism and the site‐frequency spectra. Using forward simulations, we demonstrate that recent selection of the strength expected for SC at a locus formerly under balancing selection can generate patterns similar to those seen in our empirical data.     

Development of embryonic membranes in the silverfish Lepisma saccharina linnaeus (insecta: Zygentoma, Lepismatidae)

Development and fate of embryonic membranes in the silverfish Lepisma saccharina was examined throughout embryogenesis. The amnioserosal folds first arise as serosal folds that are completed by the later addition of the amnion from the embryo's margins as in archaeognaths. The close link between production of the amnion and formation of the folds should not be assigned to Dicondylia but to Pterygota as an autapomorphy. During fold formation, folding of embryonic membranes beneath the embryo is less extensive and the ventral cupping of the embryo plays a larger role comparable to that occurring in archaeognath embryos. In L. saccharina, the embryonic membrane pore (the amniopore) varies in its manner of closure, either by complete fusion of serosal folds or by formation of a serosal cuticular plug between them as in archaeognaths. Although, in many aspects of its embryogenesis, L. saccharina retains the primitiveness of archaeognaths, its amnioserosal folds persist and are well integrated into its embryogenesis as the amnioserosal fold-amniotic cavity system is established and as occurs in many pterygote embryos; this may be thus regarded as an autapomorphy of Dicondylia.     

Costs of selfing prevent the spread of a self‐compatibility mutation that causes reproductive assurance

In flowering plants, shifts from outcrossing to partial or complete self‐fertilization have occurred independently thousands of times, yet the underlying adaptive processes are difficult to discern. Selfing's ability to provide reproductive assurance when pollination is uncertain is an oft‐cited ecological explanation for its evolution, but this benefit may be outweighed by costs diminishing its selective advantage over outcrossing. We directly studied the fitness effects of a self‐compatibility mutation that was backcrossed into a self‐incompatible (SI) population of Leavenworthia alabamica, illuminating the direction and magnitude of selection on the mating‐system modifier. In array experiments conducted in two years, self‐compatible (SC) plants produced 17–26% more seed, but this advantage was counteracted by extensive seed discounting—the replacement of high‐quality outcrossed seeds by selfed seeds. Using a simple model and simulations, we demonstrate that SC mutations with these attributes rarely spread to high frequency in natural populations, unless inbreeding depression falls below a threshold value (0.57 ≤ δ_threshold ≤ 0.70) in SI populations. A combination of heavy seed discounting and inbreeding depression likely explains why outcrossing adaptations such as self‐incompatibility are maintained generally, despite persistent input of selfing mutations, and frequent limits on outcross seed production in nature.     

Pollen tube growth in the self‐compatible sweet cherry genotype, ‘Cristobalina’, is slowed down after self‐pollination

Sweet cherry is a self‐incompatible fruit tree species in the Rosaceae. As other species in the family, sweet cherry exhibits S‐RNase‐based gametophytic self‐incompatibility. This mechanism is genetically determined by the S‐locus that encodes the pollen and pistil determinants, SFB and S‐RNase, respectively. Several self‐compatible sweet cherry genotypes have been described and most of them have mutations at the S‐locus leading to self‐compatibility. However, ‘Cristobalina’ sweet cherry is self‐compatible due to a mutation in a pollen function modifier that is not linked to the S‐locus. To investigate the physiology of self‐compatibility in this cultivar, S‐locus segregation in crosses involving ‘Cristobalina’ pollen, and pollen tube growth in self‐ and cross‐pollinations, were studied. In the crosses with genotypes sharing only one S‐haplotype, the non‐self S‐haplotype was inherited more frequently than the self S‐haplotype. Pollen tube growth studies revealed that the time to travel the whole length of the style was longer for self‐pollen tubes than for cross‐pollen tubes. Together, these results suggest that ‘Cristobalina’ pollen tube growth is slower after self‐pollination than after cross‐pollination. This reproductive strategy would allow self‐fertilisation in the absence of compatible pollen but would promote cross‐fertilisation if cross‐compatible pollen is available, a possible case of cryptic self‐incompatibility. This bet‐hedging strategy might be advantageous for an ecotype that is native to the mountains of the Spanish Mediterranean coast, in the geographical limits of the distribution of this species. ‘Cristobalina’ blooming takes place very early in the season when mating possibilities are scarce and, consequently, self‐compatibility may be the only possibility for this genotype to produce offspring.     

Discriminating tastes: self‐selection of macronutrients in two populations of grasshoppers

Abstract The capacity to self‐select an optimal balance of macronutrients (protein and carbohydrate) is studied in two populations of Melanoplus sanguinipes F. (Orthoptera: Acrididae). One population derives from the subarctic (interior of Alaska) and the other from the temperate zone (Idaho, U.S.A.). Over the duration of the fourth and fifth stadia, Alaskan grasshoppers consistently self‐select a diet centred on a 0.90 ratio of protein : carbohydrate, whereas protein and carbohydrate intake by the Idaho grasshoppers is contingent on the particular food choices presented to them. When restricted to imbalanced diets, the Alaskan grasshoppers develop more rapidly than the Idaho grasshoppers, regardless of diet composition. The Idaho grasshoppers also have a greater amount of lipid than the Alaskan grasshoppers across all diets. Performance measures (body mass, survival, developmental times) are more sensitive to dietary imbalances in the Alaskan grasshoppers than in the Idaho grasshoppers. When fed diets with low, but balanced, proportions of protein and carbohydrate, grasshoppers of both populations are able to increase consumption to compensate for the low concentration of nutrients. The results suggest that demographic responses of insects to changes in host plant quality, such as may result from climate change, may differ among populations within a species.     

Organoids and the genetically encoded self‐assembly of embryonic stem cells

Understanding the mechanisms of early embryonic patterning and the timely allocation of specific cells to embryonic regions and fates as well as their development into tissues and organs, is a fundamental problem in Developmental Biology. The classical explanation for this process had been built around the notion of positional information. Accordingly the programmed appearance of sources of Morphogens at localized positions within a field of cells directs their differentiation. Recently, the development of organs and tissues from unpatterned and initially identical stem cells (adult and embryonic) has challenged the need for positional information and even the integrity of the embryo, for pattern formation. Here we review the emerging area of organoid biology from the perspective of Developmental Biology. We argue that the events underlying the development of these systems are not purely linked to “self‐organization,” as often suggested, but rather to a process of genetically encoded self‐assembly where genetic programs encode and control the emergence of biological structures.     

Thermally induced cyclization of L‐isoleucyl‐L‐alanine in solid state: Effect of dipeptide structure on reaction temperature and self‐assembly

Thermal treatment of short‐chain oligopeptides is able to initiate the process of their self‐assembly with the formation of organic nanostructures with unique properties. On the other hand, heating can lead to a chemical reaction with the formation of new substances with specific properties and ability to form structures with different morphology. Therefore, in order to have a desired process, researcher needs to find its temperature range. In the present work, cyclization of _L‐isoleucyl‐_L‐alanine dipeptide in the solid state upon heating was studied. Kinetic parameters of this reaction were estimated within the approaches of the nonisothermal kinetics. The correlation between side chain structure of dipeptides and temperature of their cyclization in the solid state was found for the first time. This correlation may be used to predict the temperature, at which dipeptide self‐assembly changes to chemical reaction. The differences in self‐assembly of linear and cyclic dipeptides were demonstrated using atomic force microscopy. The effect of dipeptide concentration in a source solution and an organic solvent used on self‐assembly of dipeptides was shown. The new information obtained on the thermal properties and self‐assembly of linear and cyclic forms of _L‐isoleucyl‐_L‐alanine may be useful for the design of new nanomaterials based on oligopeptides, as well as for the synthesis of cyclic oligopeptides.     

Stochastic frontier analysis of a classic self‐thinning experiment

Abstract The classic experiment that gave rise to the self‐thinning rule 40 years ago was re‐analysed using stochastic frontier functions. The estimated slope of the self‐thinning boundary line was almost identical to the original proposed value. However, contrary to the original conclusion that the self‐thinning boundary line remained invariant across the soil fertility gradient, the intercept was found to increase with soil fertility. Stochastic frontier analysis also provided a more realistic estimate of the maximum asymptotic stand density than the original work, by separating the effects of density‐dependent and density‐independent mortalities during self‐thinning in a composed error term in the model specification. The time‐course of self‐thinning across the soil fertility gradient was described by a non‐linear function, which enabled the estimation of a minimum possible stand density that could still maintain full site occupancy (i.e. the maximum asymptotic stand density at the end of self‐thinning). The maximum asymptotic stand density decreased more rapidly on more fertile soils and the difference in maximum asymptotic stand density among the five levels of soil fertility increased non‐linearly with time. Site carrying capacity was defined as stand biomass shown by the point on the self‐thinning boundary line at the end of self‐thinning. This definition led to a direct functional link between the self‐thinning boundary line and site carrying capacity for even‐aged plant populations.     

The differential contributions of herkogamy and dichogamy as mechanisms of avoiding self‐interference in four self‐incompatible Epimedium species

Self‐interference is one of the most important selective forces in shaping floral evolution. Herkogamy and dichogamy both can achieve reductions in the extent of self‐interference, but they may have different roles in minimizing self‐interference in a single species. We used four self‐incompatible Epimedium species to explore the roles of herkogamy and dichogamy in avoiding self‐interference and to test the hypothesis that herkogamy and dichogamy may be separated and become selected preferentially in the taxa. Two species (E. franchetii and E. mikinorii) expressed strong herkogamy and weak protogyny (adichogamy), whereas another two species (E. sutchuenense and E. leptorrhizum) expressed slight herkogamy and partial protandry. Field investigations indicated that there was no physical self‐interference between male function and female function regarding pollen removal and pollen deposition in all species. Self‐pollination (autonomous or facilitated) was greater in species with slight herkogamy than in those with strong herkogamy. Artificial pollination treatments revealed that self‐pollination could reduce outcrossed female fertility in all species, and we found evidence that self‐interference reduced seed set in E. sutchuenense and E. leptorrhizum in the field, but not in E. franchetii and E. mikinorii. These results indicate that well‐developed herkogamy is more effective compared with dichogamy in avoiding self‐interference in the four species. In genus Epimedium, herkogamy instead of dichogamy should be selected preferentially and evolved as an effective mechanism for avoiding self‐interference and might not need to evolve linked with dichogamy.     

Postglacial ecotype formation under outcrossing and self‐fertilization in Arabidopsis lyrata

The formation of ecotypes has been invoked as an important driver of postglacial biodiversity, because many species colonized heterogeneous habitats and experienced divergent selection. Ecotype formation has been predominantly studied in outcrossing taxa, while far less attention has been paid to the implications of mating system shifts. Here, we addressed whether substrate‐related ecotypes exist in selfing and outcrossing populations of Arabidopsis lyrata subsp. lyrata and whether the genomic footprint differs between mating systems. The North American subspecies colonized both rocky and sandy habitats during postglacial range expansion and shifted the mating system from predominantly outcrossing to predominantly selfing in a number of regions. We performed an association study on pooled whole‐genome sequence data of 20 selfing or outcrossing populations, which suggested genes involved in adaptation to substrate. Motivated by enriched gene ontology terms, we compared root growth between plants from the two substrates in a common environment and found that plants originating from sand grew roots faster and produced more side roots, independent of mating system. Furthermore, single nucleotide polymorphisms associated with substrate‐related ecotypes were more clustered among selfing populations. Our study provides evidence for substrate‐related ecotypes in A. lyrata and divergence in the genomic footprint between mating systems. The latter is the likely result of selfing populations having experienced divergent selection on larger genomic regions due to higher genome‐wide linkage disequilibrium.     

Autonomous self‐pollination in the nectarless orchid Pogonia minor

The pollination biology of the nectarless orchid Pogonia minor was investigated in central Japan. The investigation revealed that the solitary flowers failed to attract pollinators, while high rates of fruit set were observed in the natural population. Comparable levels of fruit set were obtained in bagged, artificial self‐pollinated and artificial cross‐pollinated plants, indicating that the species is not pollinator‐limited for fruit set under natural conditions. Autonomous self‐pollination in P. minor resulted from a reduced rostellum, which allowed contact between the pollinia and the stigma. Self‐pollination is thought to be an adaptive response that provides reproductive assurance under conditions of pollinator limitation. Since pollen limitation is generally known to be frequent among deceptive orchids, strong pollen limitation is probably a driving force in the autonomous self‐pollination mechanism in the nectarless orchid P. minor.     

The effect of end‐group substitution on surface self‐assembly of peptides

Biofouling, the undesirable accumulation of organisms onto surfaces, affects many areas including health, water, and energy. We previously designed a tripeptide that self‐assembles into a coating that prevents biofouling. The peptide comprises three amino acids: DOPA, which allows its adhesion to the surface, and two fluorinated phenylalanine residues that direct its self‐assembly into a coating and acquire it with antifouling properties. This short peptide has an ester group at its C‐terminus. To examine the importance of this end group for the self‐assembly and antifouling properties of the peptide, we synthesized and characterized tripeptides with different end groups (ester, amide, or carboxylic group). Our results indicate that different groups at the C‐terminus of the peptide can lead to a change in the peptide assembly on the surface and its adsorption process. However, this change only affects the antifouling properties of the coating toward Gram‐positive bacteria (Staphylococcus epidermidis), whereas Gram‐negative bacteria (Escherichia coli) are not affected.     

Coevolutionary constraints in the sequence‐space of macromolecular complexes reflect their self‐assembly pathways

Is the order in which biomolecular subunits self‐assemble into functional macromolecular complexes imprinted in their sequence‐space? Here, we demonstrate that the temporal order of macromolecular complex self‐assembly can be efficiently captured using the landscape of residue‐level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high‐affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183–1189. © 2017 Wiley Periodicals, Inc.     

Impact of external odor on self‐grooming of lesser flat‐headed bats,Tylonycteris pachypus

Grooming is a common behavior of some mammals. Previous studies have shown that grooming is a means by which animals clean themselves, remove ectoparasites, and lower their body temperature. It is also involved in olfactory communication. Bats belong to the order Chiroptera and, like most mammals, are the natural host of many ectoparasites. Bat grooming, including licking and scratching, is one of the ways to reduce the adverse effects caused by ectoparasites. Bat grooming may also be induced by exogenous odor. In this study, we used lesser flat‐headed bats (Tylonycteris pachypus) to test the hypothesis that exogenous odor affects the self‐grooming behavior of bats. Results showed that external odor from distantly related species caused lesser flat‐headed bats to spend more time in self‐grooming. Lesser flat‐headed bats that received odor from humans spent the longest time in self‐grooming, followed by those that received odor from a different species of bats (T. robustula). Lesser flat‐headed bats that received odor form the same species of bats, either from the same or a different colony, spent the least amount of time in self‐grooming. These results suggest that bats can recognize conspecific and heterospecific through body scent.     

The predominant roles of the sequence periodicity in the self‐assembly of collagen‐mimetic mini‐fibrils

Collagen fibrils represent a unique case of protein folding and self‐association. We have recently successfully developed triple‐helical peptides that can further self‐assemble into collagen‐mimetic mini‐fibrils. The 35 nm axially repeating structure of the mini‐fibrils, which is designated the d‐period, is highly reminiscent of the well‐known 67 nm D‐period of native collagens when examined using TEM and atomic force spectroscopy. We postulate that it is the pseudo‐identical repeating sequence units in the primary structure of the designed peptides that give rise to the d‐period of the quaternary structure of the mini‐fibrils. In this work, we characterize the self‐assembly of two additional designed peptides: peptide Col877 and peptide Col108rr. The triple‐helix domain of Col877 consists of three pseudo‐identical amino acid sequence units arranged in tandem, whereas that of Col108rr consists of three sequence units identical in amino acid composition but different in sequence. Both peptides form stable collagen triple helices, but only triple helices Col877 self‐associate laterally under fibril forming conditions to form mini‐fibrils having the predicted d‐period. The Co108rr triple helices, however, only form nonspecific aggregates having no identifiable structural features. These results further accentuate the critical involvement of the repeating sequence units in the self‐assembly of collagen mini‐fibrils; the actual amino acid sequence of each unit has only secondary effects. Collagen is essential for tissue development and function. This novel approach to creating collagen‐mimetic fibrils can potentially impact fundamental research and have a wide range of biomedical and industrial applications.     

Modeling the competition between aggregation and self‐assembly during virus‐like particle processing

Understanding and controlling aggregation is an essential aspect in the development of pharmaceutical proteins to improve product yield, potency and quality consistency. Even a minute quantity of aggregates may be reactogenic and can render the final product unusable. Self‐assembly processing of virus‐like particles (VLPs) is an efficient method to quicken the delivery of safe and efficacious vaccines to the market at low cost. VLP production, as with the manufacture of many biotherapeutics, is susceptible to aggregation, which may be minimized through the use of accurate and practical mathematical models. However, existing models for virus assembly are idealized, and do not predict the non‐native aggregation behavior of self‐assembling viral subunits in a tractable nor useful way. Here we present a mechanistic mathematical model describing VLP self‐assembly that accounts for partitioning of reactive subunits between the correct and aggregation pathways. Our results show that unproductive aggregation causes up to 38% product loss by competing favorably with the productive nucleation of self‐assembling subunits, therefore limiting the availability of nuclei for subsequent capsid growth. The protein subunit aggregation reaction exhibits an apparent second‐order concentration dependence, suggesting a dimerization‐controlled agglomeration pathway. Despite the plethora of possible assembly intermediates and aggregation pathways, protein aggregation behavior may be predicted by a relatively simple yet realistic model. More importantly, we have shown that our bioengineering model is amenable to different reactor formats, thus opening the way to rational scale‐up strategies for products that comprise biomolecular assemblies. Biotechnol. Bioeng. 2010;107: 550–560. © 2010 Wiley Periodicals, Inc.     

Directed self‐immobilization of alkaline phosphatase on micro‐patterned substrates via genetically fused metal‐binding peptide

Current biotechnological applications such as biosensors, protein arrays, and microchips require oriented immobilization of enzymes. The characteristics of recognition, self‐assembly and ease of genetic manipulation make inorganic binding peptides an ideal molecular tool for site‐specific enzyme immobilization. Herein, we demonstrate the utilization of gold binding peptide (GBP1) as a molecular linker genetically fused to alkaline phosphatase (AP) and immobilized on gold substrate. Multiple tandem repeats (n = 5, 6, 7, 9) of gold binding peptide were fused to N‐terminus of AP (nGBP1‐AP) and the enzymes were expressed in E. coli cells. The binding and enzymatic activities of the bi‐functional fusion constructs were analyzed using quartz crystal microbalance spectroscopy and biochemical assays. Among the multiple‐repeat constructs, 5GBP1‐AP displayed the best bi‐functional activity and, therefore, was chosen for self‐immobilization studies. Adsorption and assembly properties of the fusion enzyme, 5GBP1‐AP, were studied via surface plasmon resonance spectroscopy and atomic force microscopy. We demonstrated self‐immobilization of the bi‐functional enzyme on micro‐patterned substrates where genetically linked 5GBP1‐AP displayed higher enzymatic activity per area compared to that of AP. Our results demonstrate the promising use of inorganic binding peptides as site‐specific molecular linkers for oriented enzyme immobilization with retained activity. Directed assembly of proteins on solids using genetically fused specific inorganic‐binding peptides has a potential utility in a wide range of biosensing and bioconversion processes. Biotechnol. Bioeng. 2009;103: 696–705. © 2009 Wiley Periodicals, Inc.     

Breeding systems in Cyrtanthus (Amaryllidaceae): variation in self‐sterility and potential for ovule discounting

• Breeding systems of plants determine their reliance on pollinators and ability to produce seeds following self‐pollination. Self‐sterility, where ovules that are penetrated by self‐pollen tubes that do not develop into seeds, is usually considered to represent either a system of late‐acting self‐incompatibility or strong early inbreeding depression. Importantly, it can lead to impaired female function through ovule or seed discounting when stigmas receive mixtures of self and cross pollen, unless cross pollen is able to reach the ovary ahead of self pollen (‘prepotency’). Self‐sterility associated with ovule penetration by self‐pollen tubes appears to be widespread among the Amaryllidaceae.
• We tested for self‐sterility in three Cyrtanthus species – C. contractus, C. ventricosus and C. mackenii – by means of controlled hand‐pollination experiments. To determine the growth rates and frequency of ovule penetration by self‐ versus cross‐pollen tubes, we used fluorescence microscopy to examine flowers of C. contractus harvested 24, 48 and 72 h after pollination, in conjunction with a novel method of processing these images digitally. To test the potential for ovule discounting (loss of cross‐fertilisation opportunities when ovules are disabled by self‐pollination), we pollinated flowers of C. contractus and C. mackenii with mixtures of self‐ and cross pollen.
• We recorded full self‐sterility for C. contractus and C. ventricosus, and partial self‐sterility for C. mackenii. In C. contractus, we found no differences in the growth rates of self‐ and cross‐pollen tubes, nor in the proportions of ovules penetrated by self‐ and cross‐pollen tubes. In this species, seed set was depressed (relative to cross‐pollinated controls) when flowers received a mixture of self and cross pollen, but this was not the case for C. mackenii.
• These results reveal variation in breeding systems among Cyrtanthus species and highlight the potential for gender conflict in self‐sterile species in which ovules are penetrated and disabled by pollen tubes from self pollen.