Analysis of the formation of flower shapes in wild species and cultivars of tree peony using the MADS-box subfamily gene

Tree peony (Paeonia suffricotisa) cultivars have a unique character compared with wild species; the stamen petalody results in increased whorls of petals and generates different flower forms, which are one of the most important traits for cultivar classification. In order to investigate how petaloid stamens are formed, we obtained the coding sequence (666 bp) and genomic DNA sequence of the PsTM6 genes (belongs to B subfamily of MADS-box gene family) from 23 tree peony samples, Five introns and six exons consisted of the genomic DNA sequence. The analysis of cis-acting regulatory elements in the third and fourth intron indicated that they were highly conserved in all samples. Partial putative amino acids were analyzed and the results suggested that functional differentiation of PsTM6 paralogs apparently affected stamen petalody and flower shape formation due to due to amino acid substitution caused by differences in polarity and electronic charge. Sliding window analysis indicated that the different regions of PsTM6 were subjected to different selection forces, especially in the K domain. This is the first attempt to investigate genetic control of the stamen petalody based on the PsTM6 sequence. This will provide a basis for understanding the evolution of PsTM6 and its the function of in determining stamen morphology of tree peony.     

Optimal flower lifetimes

Summary ESS floral lifetimes satisfy the product theorem from sex allocation theory. The dimensionless time investment per flower is a symmetric function of two dimensionless gain : cost ratios, one for each gender function.     

Abstract shapes of RNA

The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity of generating suboptimal solutions. While this can be accomplished by a number of programs, the user is often confronted with large outputs of similar structures, although he or she is interested in structures with more fundamental differences, or, in other words, with different abstract shapes. Here, we formalize the concept of abstract shapes and introduce their efficient computation. Each shape of an RNA molecule comprises a class of similar structures and has a representative structure of minimal free energy within the class. Shape analysis is implemented in the program RNAshapes. We applied RNAshapes to the prediction of optimal and suboptimal abstract shapes of several RNAs. For a given energy range, the number of shapes is considerably smaller than the number of structures, and in all cases, the native structures were among the top shape representatives. This demonstrates that the researcher can quickly focus on the structures of interest, without processing up to thousands of near-optimal solutions. We complement this study with a large-scale analysis of the growth behaviour of structure and shape spaces. RNAshapes is available for download and as an online version on the Bielefeld Bioinformatics Server.     

Regulating shapes and sizes

Mutations at many loci lead to altered shapes and sizes, suggesting complex regulation of the overall morphology of an organism. Two recent studies present data on how orientation of growth axes and perception of maturation signals might regulate growth processes.     

Simulating realistic membrane shapes

Biological membranes exhibit diversity in their shapes and complexity in chemical compositions that are linked to many cellular functions. These two central features of biomembranes have been the subject of numerous simulation studies, using a diverse range of computational techniques. Currently, the field is able to capture this complexity at increasing levels of realism and connect the microscopic view on protein–lipid interactions to cellular morphologies at the level of entire organelles. Here we highlight recent advances in this topic, identify current bottlenecks, and sketch possible ways ahead.     

Memory shapes microbial populations

Correct decision making is fundamental for all living organisms to thrive under environmental changes. The patterns of environmental variation and the quality of available information define the most favourable strategy among multiple options, from randomly adopting a phenotypic state to sensing and reacting to environmental cues. Cellular memory—the ability to track and condition the time to switch to a different phenotypic state—can help withstand environmental fluctuations. How does memory manifest itself in unicellular organisms? We describe the population-wide consequences of phenotypic memory in microbes through a combination of deterministic modelling and stochastic simulations. Moving beyond binary switching models, our work highlights the need to consider a broader range of switching behaviours when describing microbial adaptive strategies. We show that memory in individual cells generates patterns at the population level coherent with overshoots and non-exponential lag times distributions experimentally observed in phenotypically heterogeneous populations. We emphasise the implications of our work in understanding antibiotic tolerance and, in general, bacterial survival under fluctuating environments.     

花的演化律

被子植物花瓣数的演化是有一定规律的，它是以不大于自然数5为演化基数。花的其它部分的数目，是花基数的整数倍。     

Ethylene and flower senescence

The end of the relatively short life of carnations held in air is associated with climacteric rises in ethylene production and respiration, and coordinate rises in activity of the enzymes of the ethylene biosynthetic pathway. Carnation sensescence is associated with derepression of specific genes, increased polyribosome activity, and major changes in patterns of protein synthesis. Isotopic competition assays indicate the presence in carnation petals of ethylene binding activity with the expected characteristics of the physiological ethylene receptor. Inhibition of ethylene production and/or ethylene binding (whether in selected varieties, or by treatment with chemicals) results in longer-lived carnations. Examination of other flowers shows that the carnation is not a universal paradigm for flower senescence. The response to ethylene varies widely, and in many species petal wilting occurs without any apparent involvement of ethylene.     

Origins of flower morphology

Flowers evolved in many steps, probably starting long before flowering plants (angiophytes) originated. Certain parts of flowers are conservative and have not changed much during evolution; others are evolutionarily highly plastic. Here conservative features are discussed and an attempt is made to trace them back through their evolutionary history. Microsporangia and ovules (which develop into seeds) are preangiophyte floral elements. Angiospermy, combined with postgenital fusion, was the most prominent key innovation in angiophytes. Angiospermy and thecal organization of stamens originated earlier than all clades of extant angiosperms (the crown group of angiophytes). Differentiation of a perianth into calyx and corolla and syncarpy appeared after the first branching of the basalmost clades of extant angiosperms. Sympetaly and floral tubes as well as tenuinucellar, unitegmic ovules originated as major innovations in the clade that led to asterids. An obvious trend in flower evolution is increased synorganisation of parts, which led to new structures. Fixation of floral organ number and position was a precondition for synorganization. Concomitantly, plasticity changed from number and position of organs to shape of the new structures. Character distribution mapped onto cladograms indicates that key innovations do not appear suddenly, but start with trials and only later become deeply rooted genetically in the organization. This is implied from the common occurrence of reversals in the early history of an innovation. J. Exp. Zool. (Mol. Dev. Evol.) 291:105-115, 2001.     

Somatic polyploidy and its consequences for flower coloration and flower morphology in azalea

Flower colour variegation is not only a phenomenon of importance to horticulture, the phenotype involved is also often used as a scientific model system for the study of complex gene regulation processes. In the course of such studies on azalea, we observed a correlation between flower colour patterns, flower morphology and somatic polyploidy. Using high-resolution flow cytometry of nuclear DNA, the ploidy level was determined in flowers of different azalea sport families. Sports exhibiting variegated flowers with broad (>7 mm), differently coloured, petal edges (picotee type) proved to be tetraploid in the petal edge but diploid in the rest of the flower tissue. Neither flower colour pattern nor ploidy differences are periclinal chimeric in origin, but seem to be correlated with the topographic location of the cells within the flower tissue, i.e. the margin of the petals. The possible role of gene dosage effects and cell size involved in the remarkable correlation between somatic polyploidy, (flavonoid) gene expression and flower morphology is discussed.     

How cell death shapes cancer

Apoptosis has been established as a mechanism of anti-cancer defense. Members of the BCL-2 family are critical mediators of apoptotic cell death in health and disease, often found to be deregulated in cancer and believed to lead to the survival of malignant clones. However, over the years, a number of studies pointed out that a model in which cell death resistance unambiguously acts as a barrier against malignant disease might be too simple. This is based on paradoxical observations made in tumor patients as well as mouse models indicating that apoptosis can indeed drive tumor formation, at least under certain circumstances. One possible explanation for this phenomenon is that apoptosis can promote proliferation critically needed to compensate for cell loss, for example, upon therapy, and to restore tissue homeostasis. However, this, at the same time, can promote tumor development by allowing expansion of selected clones. Usually, tissue resident stem/progenitor cells are a major source for repopulation, some of them potentially carrying (age-, injury- or therapy-induced) genetic aberrations deleterious for the host. Thereby, apoptosis might drive genomic instability by facilitating the emergence of pathologic clones during phases of proliferation and subsequent replication stress-associated DNA damage. Tumorigenesis initiated by repeated cell attrition and repopulation, as confirmed in different genetic models, has parallels in human cancers, exemplified in therapy-induced secondary malignancies and myelodysplastic syndromes in patients with congenital bone marrow failure syndromes. Here, we aim to review evidence in support of the oncogenic role of stress-induced apoptosis.     

Asymptotics of RNA shapes.

RNA shapes, introduced by Giegerich et al. (2004), provide a useful classification of the branching complexity for RNA secondary structures. In this paper, we derive an exact value for the asymptotic number of RNA shapes, by relying on an elegant relation between non-ambiguous, context-free grammars, and generating functions. Our results provide a theoretical upper bound on the length of RNA sequences amenable to probabilistic shape analysis (Steffen et al., 2006; Voss et al., 2006), under the assumption that any base can basepair with any other base. Since the relation between context-free grammars and asymptotic enumeration is simple, yet not well-known in bioinformatics, we give a self-contained presentation with illustrative examples. Additionally, we prove a surprising 1-to-1 correspondence between pi-shapes and Motzkin numbers.