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.     

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.     

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.     

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.     

The yin and yang of yeast: biodiversity research and systems biology as complementary forces driving innovation in biotechnology

The aim of this article is to review how yeast has contributed to contemporary biotechnology and to seek underlying principles relevant to its future exploitation for human benefit. Recent advances in systems biology combined with new knowledge of genome diversity promise to make yeast the eukaryotic workhorse of choice for production of everything from probiotics and pharmaceuticals to fuels and chemicals. The ability to engineer new capabilities through introduction of controlled diversity based on a complete understanding of genome complexity and metabolic flux is key. Here, we briefly summarise the history that has led to these apparently simple organisms being employed in such a broad range of commercial applications. Subsequently, we discuss the likely consequences of current yeast research for the future of biotechnological innovation.     

The underwater light-field of lakes with marked physico-chemical and biotic diversity in the water column

Errors in calculation of radiant fluxes of downwelling underwaterphotosynthetically available radiation (PAR) from force-fittingstatistical values of d to vertical broad-band PAR profiles are compounded by vertical heterogeneity in suchfactors as turbidity, gilvin (= gelbstoff) and chlorophyll.Examples are given from two Tasmanian meromictic lakes wherevertical zonation of gilvin and microorganisms in the mixolimniaand across the chemoclines produces a markedly heterogeneouswater column. Localised concentrations of gilvin produce kinkedprofiles of downwelling PAR (400–700 nm) and microbialplates in the vicinity of the chemoclines act as false, reflectivebottoms, abruptly extinguishing residual PAR by absorption andscattering.     

Reassortment in vivo: driving force for diversity of human rotavirus strains isolated in the United Kingdom between 1995 and 1999

The G and P genotypes of 3,601 rotavirus strains collected in the United Kingdom between 1995 and 1999 were determined (M. Iturriza-Gómara et al., J. Clin. Microbiol. 38:4394-4401, 2000). In 95.4% of the strains the most common G and P combinations, G1P[8], G2P[4], G3P[8], and G4P[8], were found. A small but significant number (2%) of isolates from the remaining strains were reassortants of the most common cocirculating strains, e.g., G1P[4] and G2P[8]. Rotavirus G9P[6] and G9P[8] strains, which constituted 2.7% of all viruses, were genetically closely related in their G components, but the P components of the G9P[8] strains were very closely related to those of cocirculating strains of the more common G types (G1, G3, and G4). In conclusion, genetic interaction by reassortment among cocirculating rotaviruses is not a rare event and contributes significantly to their overall diversity.     

The temperature gradient as the driving force of water and solutions flow in the root

The examination of thermoosmosis in the maize primary root tissue has shown that under the rising temperature gradient (gradT) all flows are declining, which continue also under the gradT levelling between compartments. The permeability coefficients are declining similarly as flows. The reflection coefficient during the rising gradT declines, but it rises during the gradT levelling between compartments. These phenomena depend on the plant age and concentration of the bathing solution.     

The role of peroxisomes in the integration of metabolism and evolutionary diversity of photosynthetic organisms

The peroxisome is a metabolic compartment serving for the rapid oxidation of substrates, a process that is not coupled to energy conservation. In plants and algae, peroxisomes connect biosynthetic and oxidative metabolic routes and compartmentalize potentially lethal steps of metabolism such as the formation of reactive oxygen species and glyoxylate, thus preventing poisoning of the cell and futile recycling. Peroxisomes exhibit properties resembling inside-out vesicles and possess special systems for the import of specific proteins, which form multi-enzyme complexes (metabolons) linking numerous reactions to flavin-dependent oxidation, coupled to the decomposition of hydrogen peroxide by catalase. Hydrogen peroxide and superoxide originating in peroxisomes are important mediators in signal transduction pathways, particularly those involving salicylic acid. By contributing to the synthesis of oxalate, formate and other organic acids, peroxisomes regulate major fluxes of primary and secondary metabolism. The evolutionary diversity of algae has led to the presence of a wide range of enzymes in the peroxisomes that are only similar to higher plants in their direct predecessors, the Charophyceae. The appearance of seed plants was connected to the acquirement by storage tissues, of a peroxisomal fatty acid oxidation function linked to the glyoxylate cycle, which is induced during seed germination and maturation. Rearrangement of the peroxisomal photorespiratory function between different tissues of higher plants led to the appearance of different types of photosynthetic metabolism. The peroxisome may therefore have played a key role in the evolutionary formation of metabolic networks, via establishing interconnections between different metabolic compartments.     

The European ground squirrel increases diversity and structural complexity of grasslands in the Western Carpathians

Disturbances are important natural factors affecting biological diversity, community composition, and ecosystem structure. The European ground squirrel is a semi-fossorial organism, and through disturbances caused by burrowing activities, it can play an important role as an ecosystem engineer of grasslands in central and south-eastern Europe. The aim of this study was to assess the response of grassland vegetation to disturbances by the European ground squirrel. We conducted a pairwise survey within a 1-ha study site with homogenous environmental conditions. We compared the vegetation characteristics of 2?×?2-m plots placed on 30 mounds, with paired control plots situated at a distance of 10 m from each mound. The results showed that plots disturbed by the European ground squirrel achieved a higher species richness and diversity and a distinct species composition compared to the undisturbed control plots. Vertical structure of vegetation was also significantly different with a higher proportion of the high and medium vegetation layers on the mounds. Shifts in the composition of plant life forms and life strategies were reflected by the reduction of graminoids and plant competitors, and support of forbs on the mounds. These findings suggest that the European ground squirrel helps to maintain heterogeneity in grassland ecosystems and creates patches of higher diversity and higher structural complexity in the relatively homogenous grassland vegetation of the Western Carpathians.