Current topics in genome evolution: Molecular mechanisms of new gene formation

Comparative genome analyses reveal that most functional domains of human genes have homologs in widely divergent species. These shared functional domains, however, are differentially shuffled among evolutionary lineages to produce an increasing number of domain architectures. Combined with duplication and adaptive evolution, domain shuffling is responsible for the great phenotypic complexity of higher eukaryotes. Although the domain-shuffling hypothesis is generally accepted, determining the molecular mechanisms that lead to domain shuffling and novel gene creation has been challenging, as sequence features accompanying the formation of known genes have been obscured by accumulated mutations. The growing availability of genome sequences and EST databases allows us to study the characteristics of newly emerged genes. Here we review recent genome-wide DNA and EST analyses, and discuss the three major molecular mechanisms of gene formation: (1) atypical spicing, both within and between genes, followed by adaptation, (2) tandem and interspersed segmental duplications, and (3) retrotransposition events. Received 18 October 2006; received after revision 18 November 2006; accepted 28 November 2006     

[FeFe] hydrogenases and their evolution: a genomic perspective

Most hydrogenases (H2ases), the enzymes that produce or oxidize dihydrogen, possess dimetallic active sites and belong to either one of two phylogenetically distinct classes, the [NiFe] and the [FeFe] H2ases. These families of H2ases share a number of similarities regarding active site structure and reaction mechanism, as a result of convergent evolution. They are otherwise alien to each other, in particular with respect to protein sequence and structure, maturation mechanisms, and distribution among the realms of life. One of the interesting features of [FeFe] H2ases is their occurrence in anaerobic bacteria, anaerobic protists, and mitochondriate eukaryotes. They thus have the potential to report on important evolutionary events, including transitions from the prokaryote to the eukaryote lifestyle. Genome sequences yield a variety of [FeFe] H2ase sequences that have been implemented to shed light on the evolution of these proteins and their host organisms.     

Environmental impacts of household appliances in Europe and scenarios for their impact reduction

Assessing the environmental impact due to consumption of goods and services is a pivotal step towards achieving the sustainable development goal related to responsible production and consumption (i.e. SDG 12). Household appliances plays a crucial role and should be assessed in a systemic manner, namely considering all life cycle stages, technological efficiency, and affluence aspects. The present study assess the impact of such household appliances used in Europe, and tests scenarios of potential impact reduction at various scales. Life cycle assessment is applied to 14 different household appliances (ranging from dishwashers to television devices) selected to build a set of representative products, based on their economic value and diffusion in households in Europe. Related impacts are calculated with the Environmental Footprint method for calculating a Consumer Footprint “appliances” for the baseline year 2010. A number of scenarios encompassing eco-solutions on a technical level, changes in consumption pattern, behavioral changes, as well as the combination of all these aspects are run to estimate the Consumer Footprint related to household appliances for the year 2030, compared against this baseline scenario. The baseline Consumer Footprint is confirming the importance of the use phase in leading the impacts in almost all impact categories. Testing different scenarios concludes that there is a reduction of the impact for most of the categories (with up to 67% for the ozone depletion potential, and still around 35% for the global warming potential), while two of the here examined impact categories (i.e. land-use and mineral resource depletion) show an overall potential that is even negative – i.e. the results of all scenarios are higher than the ones of the 2010 baseline scenario. The increase in purchase and use of such appliances may offset energy efficiency benefits in some of the examined categories. Hence, the assessment of sustainability of appliances consumption should always include several scales, from the efficiency of the products (micro scale), to the improvement of the energy mix (meso scale), up to accounting for socio-economic drivers and patterns of consumption affecting the overall appliances stock (macro scale).     

Environmental impacts of household appliances in Europe and scenarios for their impact reduction

Assessing the environmental impact due to consumption of goods and services is a pivotal step towards achieving the sustainable development goal related to responsible production and consumption (i.e. SDG 12). Household appliances plays a crucial role and should be assessed in a systemic manner, namely considering all life cycle stages, technological efficiency, and affluence aspects. The present study assess the impact of such household appliances used in Europe, and tests scenarios of potential impact reduction at various scales. Life cycle assessment is applied to 14 different household appliances (ranging from dishwashers to television devices) selected to build a set of representative products, based on their economic value and diffusion in households in Europe. Related impacts are calculated with the Environmental Footprint method for calculating a Consumer Footprint “appliances” for the baseline year 2010. A number of scenarios encompassing eco-solutions on a technical level, changes in consumption pattern, behavioral changes, as well as the combination of all these aspects are run to estimate the Consumer Footprint related to household appliances for the year 2030, compared against this baseline scenario. The baseline Consumer Footprint is confirming the importance of the use phase in leading the impacts in almost all impact categories. Testing different scenarios concludes that there is a reduction of the impact for most of the categories (with up to 67% for the ozone depletion potential, and still around 35% for the global warming potential), while two of the here examined impact categories (i.e. land-use and mineral resource depletion) show an overall potential that is even negative – i.e. the results of all scenarios are higher than the ones of the 2010 baseline scenario. The increase in purchase and use of such appliances may offset energy efficiency benefits in some of the examined categories. Hence, the assessment of sustainability of appliances consumption should always include several scales, from the efficiency of the products (micro scale), to the improvement of the energy mix (meso scale), up to accounting for socio-economic drivers and patterns of consumption affecting the overall appliances stock (macro scale).     

Environmental impacts of household appliances in Europe and scenarios for their impact reduction

Assessing the environmental impact due to consumption of goods and services is a pivotal step towards achieving the sustainable development goal related to responsible production and consumption (i.e. SDG 12). Household appliances plays a crucial role and should be assessed in a systemic manner, namely considering all life cycle stages, technological efficiency, and affluence aspects. The present study assess the impact of such household appliances used in Europe, and tests scenarios of potential impact reduction at various scales. Life cycle assessment is applied to 14 different household appliances (ranging from dishwashers to television devices) selected to build a set of representative products, based on their economic value and diffusion in households in Europe. Related impacts are calculated with the Environmental Footprint method for calculating a Consumer Footprint “appliances” for the baseline year 2010. A number of scenarios encompassing eco-solutions on a technical level, changes in consumption pattern, behavioral changes, as well as the combination of all these aspects are run to estimate the Consumer Footprint related to household appliances for the year 2030, compared against this baseline scenario. The baseline Consumer Footprint is confirming the importance of the use phase in leading the impacts in almost all impact categories. Testing different scenarios concludes that there is a reduction of the impact for most of the categories (with up to 67% for the ozone depletion potential, and still around 35% for the global warming potential), while two of the here examined impact categories (i.e. land-use and mineral resource depletion) show an overall potential that is even negative – i.e. the results of all scenarios are higher than the ones of the 2010 baseline scenario. The increase in purchase and use of such appliances may offset energy efficiency benefits in some of the examined categories. Hence, the assessment of sustainability of appliances consumption should always include several scales, from the efficiency of the products (micro scale), to the improvement of the energy mix (meso scale), up to accounting for socio-economic drivers and patterns of consumption affecting the overall appliances stock (macro scale).     

The functioning and interrelationships of blood capillaries and lymphatics

Summary the structure and function of blood capillaries, as related to permeability, depends on tight, close and (in injured vessels) open junctional regions, small vesicles, vacuoles (in injured vessels) and fenestrae. The basement membrane presents a hindrance to the larger macromolecules, at high flow rates, but not to small molecules. The connective tissue channels are probably the paths by which macromolecules, and most of the small ones, pass from the arterial-limbs to the venous ones, and to the lymphatics. In some regions these channels are grouped in special systems: the prelymphatics. The initial lymphatics take up material via open junctions, which close during tissue-compression. The collecting lymphatics retain the lymph because they do not have open junctions.In the close junctional regions the motive force for water flow is the result of Starling's forces; diffusion is very important for other small molecules. The small vesicles transport macromolecules slowly by Brownian motion, as may the vacuoles, but possibly these latter are moved actively.There is much evidence that colloids can develop high effective osmotic pressures even across pores much larger than their molecules, and that proteins can be dragged up a concentration gradient by the resultant fluid flow. On the basis of this, hypotheses have been developed about the functioning of venous-limb fenestrae and the initial lymphatics, for which there is much theoretical, in vitro, and in vivo evidence. Thus, in fenestrae and regions there is held to be a large local circulation through the tissues, of which a quantitatively small, but qualitatively vital, part goes to the lymphatics. Material is considered usually to enter these latter because of the relative concentration of the lymph.It is becoming increasingly evident that in the study of the microvasculature, as with other systems, there is much to be gained by quantifying fine structural observations and by combining and contrasting this data, via physical laws, with that obtained by other methods where the characteristics of whole organs and regions are studied. Thus one can obtain interrelated information, which is not possible by either method alone, and which gives us a vital, comprehensive, perspective of the ways in which whole systems function, and how different systems interact. In this paper I shall show how this approach has yielded much that is new about the functioning of different kinds of blood capillaries, of the tissue channels, of the whole lymphatic system, and of the ways they affect each other.Most of the author's work reported here was financed by the Australian Research Grants Committee.     

Information and evolution

Résumé Les auteurs discutent la formulation quantitative de l'évolution comme un procès qui augmente le contenu de l'entité thermodynamique d'information dans la biosphère.     

Organization and expression of the poxvirus genome

Summary Poxviruses comprise a large group of very complex animal DNA viruses which replicate in the cytoplasm of infected cells. Vaccinia virus, the most studied poxvirus, has a linear, double stranded DNA genome with an approximate molecular weight of 120×10⁶ (180 kilobase pairs). The two strands of the DNA molecule are naturally cross-linked at both termini. In addition, the vaccinia virus genome contains very long inverted terminal repetitions of approximately 10 kilobase pairs which are further characterized by the presence of direct tandem repeats of a 70-base-pair sequence arranged in two blocks of 13 and 17 copies, respectively. A central region of the genome is highly conserved between different orthopoxviruses. In contrast, the ends are hypervariable and may contain extensive deletions and complex, symmetrical sequences rearrangements. Vaccinia virus gene expression is divided into two stages. Early in infection, RNA complementary to one half of one strand-equivalent of the genome is transcribed within subviral particles by the virion-associated RNA polymerase. Later in infection, after DNA replication, RNA complementary to one entire strand-equivalent is transcribed. RNA made late in infection is very heterogeneous in length and a large fraction of it contains self-complementary sequences. Late genes are clustered near the central region of the genome. Vaccinia virus mRNAs do not appear to be synthesized by a splicing mechanism.     

Hormones and vertebrate evolution

Résumé On sait que chez les vertébrés la structure moléculaire de certaines hormones, telles que les hormones thyroïdiennes, est restée sans changement pendant l'histoire évolutionnaire du groupe. L'auteur discute la fixation par les protochordés des iodures marqués, et la signification pour l'origine des hormones thyroïdiennes de la localisation des combinaisons organiques d'¹³¹I dans la tunique des urochordés et dans l'endostyle de ceux-ci et de l'amphioxus.Si on considère le groupe d'hormones avec molécules protéiques ou polypeptidiques, on trouve parmi elles des différences qui indiquent l'existence de quelques caractéristiques individuelles. Quant aux plus grandes molécules, elles diffèrent les unes des autres par les propriétés antigeniques et les poids moléculaires, peutêtre par rapport au développement de specificité protéique. Les plus petites molécules polypeptidiques, telles que les polypeptides hypothalamiques, montrent des différences en ce qui concerne les acides aminés. Ces variations sont accompagnées par des différences qui constituent en théorie une base pour l'évolution adaptive, mais il n'est pas facile de faire une corrélation entre elles et les caractères physiologiques des divers groupes.On doit donc admettre que le cours d'évolution ne dépend pas seulement des variations moléculaires des hormones, mais que des hormones déjà existantes sont utilisées pour établir de nouvelles fonctions. Pour comprendre alors la pleine signification des variations moléculaires des hormones, il faut chercher d'autres fonctions; on doit aussi étudier beaucoup d'autres espèces, surtout parmi les vertébrés inférieurs.     

Reticulate evolution and cladism: Tests for the direction of evolution

Summary Reticulate evolution between ancestral-descendant lineages can be critically tested for by investigating the relationship between out-group and mid-point roots on numerically derived cladograms. The western grass-snake provides a worked example for the theoretical test.