Evolutionary dynamics of coding and non-coding transcriptomes.

Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive assessments of transcript sequences and expression levels. Here, we review the initial wave of the new generation of comparative transcriptomic studies in mammals and vertebrate outgroup species in the context of earlier work. Together with various large-scale genomic and epigenomic data, these studies have unveiled commonalities and differences in the dynamics of gene expression evolution for various types of coding and non-coding genes across mammalian lineages, organs, developmental stages, chromosomes and sexes. They have also provided intriguing new clues to the regulatory basis and phenotypic implications of evolutionary gene expression changes.

A recent change in size distribution of blue mussels (Mytilus edulis) in the western part of the Gulf of Finland

Markus Öst & Mikael Kilpi

Developmental change in isoproterenol-mediated relaxation of pulmonary veins of fetal and newborn lambs.

beta-Adrenergic agonists are important regulators of perinatal pulmonary circulation. They cause vasodilation primarily via the adenyl cyclase-adenosine 3',5'-cyclic monophosphate (cAMP) pathway. We examined the responses of isolated fourth-generation pulmonary veins of term fetal (145 +/- 2 days gestation) and newborn (10 +/- 1 days) lambs to isoproterenol, a beta-adrenergic agonist. In vessels preconstricted with U-46619 (a thromboxane A2 analog), isoproterenol induced greater relaxation in pulmonary veins of newborn lambs than in those of fetal lambs. The relaxation was eliminated by propranolol, a beta-adrenergic antagonist. Forskolin, an activator of adenyl cyclase, also caused greater relaxation of veins of newborn than those of fetal lambs. 8-Bromoadenosine 3',5'-cyclic monophosphate, a cell membrane-permeable analog of cAMP, induced a similar relaxation of all vessels. Biochemical studies show that isoproterenol and forskolin induced a greater increase in cAMP content and in adenyl cyclase activity of pulmonary veins in the newborn than in the fetal lamb. These results demonstrate that beta-adrenergic-agonist-mediated relaxation of pulmonary veins increases with maturation. An increase in the activity of adenyl cyclase may contribute to the change.

A phylogenetic study of the phosphoenolpyruvate carboxylase multigene family in Poaceae: understanding the molecular changes linked to C4 photosynthesis evolution

Phylogenetic reconstructions have supported several independent appearances of C₄ photosynthesis within grasses (Poaceae). These recurrent appearances appear to contradict the large number of biochemical and morphological changes required to change from C₃ to C₄, a paradox that leads to questions about the genetic changes underlying C₄ evolution. In this study, we analysed sequences encoding phosphoenolpyruvate carboxylases (PEPCs) in grasses in order to gain insights into the origin of the ppc-C₄ gene, which encodes a key enzyme in the C₄ pathway. We screened databanks for PEPC genes or cDNAs in grasses. A coding sequence of 1130 base pairs was used to build phylogenetic trees that supported the existence of four distinct PEPC gene lineages. Ppc-C₄ present in all C₄ grasses was also found in two C₃ species. The ppc-C₄ clade was congruent with the species tree, suggesting orthologous evolution. This result would imply that ppc-C₄ appeared without any duplication event. Nevertheless, caution is needed since the sampling of our study is still far from comprehensive. Further investigation with an increased sampling is recommended to elucidate the evolutionary changes underlying ppc-C₄ gene evolution in grasses.

Small scale underwater change detection

In this paper, we present a method to deal with the constraints of the underwater medium for finding changes between sequences of underwater images. One of the main problems of underwater medium for automatically detecting changes is the low altitude of the camera when taking pictures. This emphasise the parallax effect between the images as they are not taken exactly at the same position. In order to solve this problem, we are geometrically registering the images together taking into account the relief of the scene

Patterns of split sex ratio in ants have multiple evolutionary causes based on different within-colony conflicts.

Split sex ratio-a pattern where colonies within a population specialize in either male or queen production-is a widespread phenomenon in ants and other social Hymenoptera. It has often been attributed to variation in colony kin structure, which affects the degree of queen-worker conflict over optimal sex allocation. However, recent findings suggest that split sex ratio is a more diverse phenomenon, which can evolve for multiple reasons. Here, we provide an overview of the main conditions favouring split sex ratio. We show that each split sex-ratio type arises due to a different combination of factors determining colony kin structure, queen or worker control over sex ratio and the type of conflict between colony members.

GIS analysis of change in an agricultural landscape in Central Finland

Selostus: Keskisuomalaisen maatalousmaiseman muutosten GIS-analyysi

Change in defense mechanisms and coping patterns during the course of 2-year-long psychotherapy and psychoanalysis for recurrent depression: a pilot study of a randomized controlled trial.

Very little research has been conducted so far to study the potential mechanisms of change in long-term active psychological treatments of recurrent depression. The present pilot randomized controlled trial aimed to determine the feasibility of studying the change process occurring in patients during the course of 2-year-long dynamic psychotherapy, psychoanalysis, and cognitive therapy, as compared with clinical management. In total, eight outpatients presenting with recurrent depression, two patients per treatment arm, were included. All patients were randomly assigned to one of the four treatment conditions. Defense mechanisms and coping patterns were assessed using validated observer-rated methodology based on transcribed, semistructured follow-along independent dynamic interviews. The results indicated that, whereas some patients in the active treatments changed on the symptomatic levels, some others remained unchanged during the course of their 2-year-long treatment. However, with regard to potential mechanisms of change in these patients, changes in defense mechanisms and coping patterns were revealed to be important processes over time in successful therapies and, to a lesser extent, in less successful treatments. No change was found either on outcome or on the process measure for the control condition, that is, clinical management. These results are discussed along with previous data comparing change in defense mechanisms and coping during the course of treatments.

Tree of Sex: A database of sexual systems

The vast majority of eukaryotic organisms reproduce sexually, yet the nature of the sexual system and the mechanism of sex determination often vary remarkably, even among closely related species. Some species of animals and plants change sex across their lifespan, some contain hermaphrodites as well as males and females, some determine sex with highly differentiated chromosomes, while others determine sex according to their environment. Testing evolutionary hypotheses regarding the causes and consequences of this diversity requires interspecific data placed in a phylogenetic context. Such comparative studies have been hampered by the lack of accessible data listing sexual systems and sex determination mechanisms across the eukaryotic tree of life. Here, we describe a database developed to facilitate access to sexual system and sex chromosome information, with data on sexual systems from 11,038 plant, 705 fish, 173 amphibian, 593 non-avian reptilian, 195 avian, 479 mammalian, and 11,556 invertebrate species.