The diversity and complexity of the cyanobacterial thioredoxin systems

Cyanobacteria perform oxygenic photosynthesis, which makes them unique among the prokaryotes, and this feature together with their abundance and worldwide distribution renders them a central ecological role. Cyanobacteria and chloroplasts of plants and algae are believed to share a common ancestor and the modern chloroplast would thus be the remnant of an endosymbiosis between a eukaryotic cell and an ancestral oxygenic photosynthetic prokaryote. Chloroplast metabolic processes are coordinated with those of the other cellular compartments and are strictly controlled by means of regulatory systems that commonly involve redox reactions. Disulphide/dithiol exchange catalysed by thioredoxin is a fundamental example of such regulation and represents the molecular mechanism for light-dependent redox control of an ever-increasing number of chloroplast enzymatic activities. In contrast to chloroplast thioredoxins, the functions of the cyanobacterial thioredoxins have long remained elusive, despite their common origin. The sequenced genomes of several cyanobacterial species together with novel experimental approaches involving proteomics have provided new tools for re-examining the roles of the thioredoxin systems in these organisms. Thus, each cyanobacterial genome encodes between one and eight thioredoxins and all components necessary for the reduction of thioredoxins. Screening for thioredoxin target proteins in cyanobacteria indicates that assimilation and storage of nutrients, as well as some central metabolic pathways, are regulated by mechanisms involving disulphide/dithiol exchange, which could be catalysed by thioredoxins or related thiol-containing proteins.     

The complexity of living bodies and the structure of biological theories

It has been suggested that biological theories differ from physical theories because the subject matter of biology differs from the subject matter of physics especially in the fact that living bodies are more complex than nonliving bodies. It is shown that the interactional complexity of living bodies can only be expressed by invoking biological theories. The claim that living bodies are complex is, therefore, ultimately a claim about the nature of scientific theories rather than a claim about the nature of the subject matter of biology resting upon a presystematic judgement.     

The biological standard of living in 19th century Mexico and in the American West

During the mid-19th century, the United States acquired Texas and large parts of Mexican territory with the vast Mexican-born population. This paper considers the biological standard of living of the part of this population that was incarcerated in American prisons. We use their physical stature as a proxy for their biological welfare. These data confirm earlier results which showed that adult heights tended to stagnate in Mexico during the late-19th century despite considerable social and political turmoil. While there is some evidence of a decline in height among youth, the decline is slight (<1 cm). As in other 19th century samples, farmers were the tallest. Americans were taller than Mexican prisoners by about 2 cm.     

The biological standard of living and mortality in Central Italy at the beginning of the 19th century

The biological standard of living in Central Italy at the beginning of the 19th century is analyzed using newly collected data on the height of recruits in the army of the Papal States. The results reveal a decline in height for the cohorts born under French rule (1796–1815). Although this trend was common to many parts of Europe, the estimated magnitude of the decline suggests a worsening of the biological standard of living of the working classes in the Papal States even relative to that of other countries. Despite the differences in the economic systems within the Papal States, no significant geographical variation in height has been found: even the most dynamic and advanced regions experienced a dramatic height decline. Mortality also increased during the period under consideration.     

By way of introduction: modelling living systems, their diversity and their complexity: some methodological and theoretical problems

Some principles for a current methodology for biological systems' modelling are presented. It seems possible to promote a model-centred approach of these complex systems. Among present questions, the role of mechanisms producing random or quasi-random issues is underlined, because they are implied in biological diversification and in resulting complexity of living systems. Now, biodiversity is one of our societies' and scientific research's main concerns. Basically, it can be interpreted as a manner, for Life, to resist environmental hazards. Thus, one may assume that biodiversity producing mechanisms could be selected during evolution to face to corresponding risks of disappearance: necessity of chance? Therefore, analysing and modelling these ‘biological and ecological roulettes’ would be important, and not only their outputs like nowadays by using the theory of probabilities. It is then suggested that chaotic behaviours generated by deterministic dynamical systems could mimic random processes, and that ‘biological and ecological roulettes’ would be represented by such models. Practical consequences can be envisaged in terms of biodiversity management, and more generally in terms of these ‘roulettes’ control to generate selected biological and ecological events' distribution. To cite this article: A. Pavé, C. R. Biologies 329 (2006).     

The biological standard of living in Indonesia during the 20th century: Evidence from the age at menarche

This article analyses long-term changes in the mean age at menarche (MAM) as a biological indicator of changes in the standard of living in Indonesia. It finds that MAM was about 15.5 for birth cohorts in the late-19th century, decreasing to 14.5 by the 1930s, at which level it stagnated until the gradual decrease resumed since the early 1960s to around 12.5 in the mid-2000s. The article considers that long-term improvements in nutrition, educational attainment and health care explain these trends. An international comparison of long-term changes finds that MAM in Indonesia was much lower than in Korea and China until respectively 1970 and 1990, but comparable to Japan until 1950 and to Malaysia until 1930. The article presents reasons why these differences are unlikely to be related to dissimilarities in climate and ethnicity, and concludes that they are indicative of relative standards of living.     

Pseudocyclic transformation in the evolution of modular organisms and the problem of the integrity of biological systems

Pseudocyclic (P) integration was very important in the evolution of modular organisms. Its wide distribution was possible because of their morphogenesis, ontogeny, and systemic specifics. P-transformations are often related to changes around the boundaries of subsystems and structures, with a relatively low integrity of modular biosystems.     

The relationships between taxonomy and conservation biology in the century of extinctions

The 21st century will be that of the crisis of biodiversity and of extinctions: a majority of the planet's species might disappear before having even been studied by man. The discipline in charge of this study, taxonomy, is currently facing severe problems, concerning its status inside biology and its relationships with conservation biology. Yet taxonomy and conservation biology would have much to gain to becoming allies rather than largely foreign disciplines. This would require some important changes in mentality and behaviour.     

RNA damage in biological conflicts and the diversity of responding RNA repair systems

RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.     

Synergistic changes in river-lake runoff systems in the Yangtze River basin and their driving force differences

Climate change and human activities simultaneously alter river–lake relationships. Determining the dynamics of river–lake runoff systems on multiple time scales and their differences in response to driving forces can provide insights into hydrological processes and water resource management. This study investigates the synergistic evolution of river–lake runoff systems in the middle and lower reaches of the Yangtze River basin (MLYR) using the cross-wavelet transform method. The effects of different driving force changes on river–lake runoff regimes are quantified based on the Budyko hypothesis, and an InVEST model is developed to assess the spatial and temporal patterns of habitat quality. The results indicate that during the variation period, the runoff distributions of the Yangtze River–Dongting Lake and Yangtze River–-Poyang Lake runoff systems are both skewed towards lower values in the flood seasons compared with those in the base period. The storage of lakes mitigates the extent of human disturbance to the mainstream hydrological regime, particularly under extremely low conditions. From 1960 to 2021, five significant resonance periods are indicated in the river–lake runoff system, and the phase–angle relationships indicate a positive phase coupling between the lake and mainstream hydrological regimes, with the lake lagging behind the mainstream; however, this interaction tends to weaken. In the mainstream and Dongting Lake basins, subsurface conditions are the dominant factor contributing to runoff variability, with contributions ranging from 50.9% to 72.6%; in the Poyang Lake basin, precipitation is the dominant factor, with a contribution of 50.6%; and in the Han River basin, changes in the potential evapotranspiration contribute to 50.6% of runoff variability. The proportion of high habitat quality in the MLYR is approximately 52%, the Dongting and Poyang Lake basins indicate a high habitat quality rating. However, frequent human activity is the main reason of conversion from higher habitats to lower ones, which may result in wetland habitat degradation.