Life-related aspects of stellar evolution

It is generally thought that the Universe started with a big explosion (Big Bang) approximately 15 billion years ago. Hydrogen and helium were formed within the first few minutes, while all the other chemical elements are the by-products of stellar evolution that are added to the interstellar medium through the supernova explosions of the larger stars. Carbon, Oxygen, Hydrogen and Nitrogen, which constitute about 98% of the biomass of the Earth, are also among the most abundant chemical elements in the Universe. A seemingly unique combination of the fundamental laws and constants of the Universe made possible the origin and subsequent slow evolution of life.     

Fitness in the universe: Choices and necessities

We live in a universe of chance, but not of accident. Repeatedly in the course of its development choices have been made for which one can ask the reasons. One such choice is fundamental: if the proton had not so much greater mass than the electron, all matter would be fluid; and if the proton did not have exactly the same numerical charge as the electron — or some simple multiple of that charge — virtually all matter would be charged. If a universe were started with charged hydrogen, it could expand, but probably nothing more. Hydrogen, carbon, nitrogen and oxygen play as fundamental — and irreplaceable — roles in the metabolism of stars as of living organisms. Both metabolisms are coupled, through radiation from the stars providing the energy on which life must come ultimately to run on the planets. In the course of their evolution on the Earth, living organisms have found their way repeatedly and exclusively to certain types of organic molecule to perform specific functions; so, for example, the chlorophylls for photosynthesis, and carotenoids for plant phototropism and for vision. It is argued that some measure of necessity has governed these choices; and that an extended principle of natural selection has operated at all levels of material organization to produce such elements of order and compatibility in the universe.     

Dissecting the protein-RNA interface: the role of protein surface shapes and RNA secondary structures in protein-RNA recognition

Protein-RNA interactions are essential for many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. Here, we analyzed the protein surface shape (dented, intermediate or protruded) and the RNA base pairing properties (paired or unpaired nucleotides) at the interfaces of 91 protein-RNA complexes derived from the Protein Data Bank. Dented protein surfaces prefer unpaired nucleotides to paired ones at the interface, and hydrogen bonds frequently occur between the protein backbone and RNA bases. In contrast, protruded protein surfaces do not show such a preference, rather, electrostatic interactions initiate the formation of hydrogen bonds between positively charged amino acids and RNA phosphate groups. Interestingly, in many protein-RNA complexes that interact via an RNA loop, an aspartic acid is favored at the interface. Moreover, in most of these complexes, nucleotide bases in the RNA loop are flipped out and form hydrogen bonds with the protein, which suggests that aspartic acid is important for RNA loop recognition through a base-flipping process. This study provides fundamental insights into the role of the shape of the protein surface and RNA secondary structures in mediating protein-RNA interactions.     

Structure and energy of non-canonical basepairs: comparison of various computational chemistry methods with crystallographic ensembles

Different types of non-canonical basepairs, in addition to the Watson-Crick ones, are observed quite frequently in RNA. Their importance in the three dimensional structure is not fully understood, but their various roles have been proposed by different groups. We have analyzed the energetics and geometry of 32 most frequently observed basepairs in the functional RNA crystal structures using different popular empirical, semi-empirical and ab initio quantum chemical methods and compared their optimized geometry with the crystal data. These basepairs are classified into three categories: polar, non-polar and sugar-mediated, depending on the types of atoms involved in hydrogen bonding. In case of polar basepairs, most of the methods give rise to optimized structures close to their initial geometry. The interaction energies also follow similar trends, with the polar ones having more attractive interaction energies. Some of the C-H...O/N hydrogen bond mediated non-polar basepairs are also found to be significantly stable in terms of their interaction energy values. Few polar basepairs, having amino or carboxyl groups not hydrogen bonded to anything, such as G:G H:W C, show large flexibility. Most of the non-polar basepairs, except A:G s:s T and A:G w:s C, are found to be stable; indicating C-H...O/N interaction also plays a prominent role in stabilizing the basepairs. The sugar mediated basepairs show variability in their structures, due to the involvement of flexible ribose sugar. These presumably indicate that the most of the polar basepairs along with few non-polar ones act as seed for RNA folding while few may act as some conformational switch in the RNA.     

All the observed universe has contributed to life.

This paper presents evidence that virtually all electrons and nuclei of the atoms that are or have been part of living matter on Earth came from almost all stars in our and nearby galaxies and even from all other galaxies in the Universe that have produced observed high-energy gamma rays. However, a standard 70 kg human is always making about 7 3He, 600 40Ca, and 3000 14N nuclei every second by radioactive decay of 3H, 40K, and 14C, respectively.     

The forest or the trees: preference for global over local image processing is reversed by prior experience in honeybees

Traditional models of insect vision have assumed that insects are only capable of low-level analysis of local cues and are incapable of global, holistic perception. However, recent studies on honeybee (Apis mellifera) vision have refuted this view by showing that this insect also processes complex visual information by using spatial configurations or relational rules. In the light of these findings, we asked whether bees prioritize global configurations or local cues by setting these two levels of image analysis in competition. We trained individual free-flying honeybees to discriminate hierarchical visual stimuli within a Y-maze and tested bees with novel stimuli in which local and/or global cues were manipulated. We demonstrate that even when local information is accessible, bees prefer global information, thus relying mainly on the object''s spatial configuration rather than on elemental, local information. This preference can be reversed if bees are pre-trained to discriminate isolated local cues. In this case, bees prefer the hierarchical stimuli with the local elements previously primed even if they build an incorrect global configuration. Pre-training with local cues induces a generic attentional bias towards any local elements as local information is prioritized in the test, even if the local cues used in the test are different from the pre-trained ones. Our results thus underline the plasticity of visual processing in insects and provide new insights for the comparative analysis of visual recognition in humans and animals.     

Euconodont hard tissue: preservation patterns of the basal body

Conodont elements, consisting of crown and basal tissue are the well-known fossilized hard parts of Conodonta (extinct marine chordates), but the taphonomic processes leading to decomposition or remineralization of the basal tissue are not well understood. Here we focus on the taphonomy of basal tissue, reviewing the published record and describing new material from Asia and Europe (248 occurrences globally). These include crown and basal tissue in conjunction, and isolated basal bodies showing different stages of preservation. Some isolated specimens resemble phosphate rings similar to those assigned to Phosphannulus universalis. High-resolution biostratigraphy indicates that the lamellar type of conodont basal tissue is found in all facies and depositional environments. Other basal tissue types, described in the literature as tubular, mesodentine, spherulitic or lamellar with canalules, are limited to the early Palaeozoic and found exclusively in siliciclastic deposits (with the exception of spherulitic tissue). Although the stratigraphic record of basal tissue spans the range of Euconodonta (Cambrian–Triassic), this study shows that most of the isolated plate and ring-like structures are derived from early Palaeozoic coniform conodonts. Basal tissue of platform-type elements has a much more fragile shape and is therefore rarely preserved as a recognizable isolated unit.     

Physiological and ecological controls on carbon sequestering in terrestrial ecosystems

Carbon cycling processes in ecosystems are generally believed to be well understood. Carbon, hydrogen, oxygen and other essential elements are chemically converted from inorganic to organic compounds primarily in the process of photosynthesis. Secondary metabolic processes cycle carbon in and among organisms and carbon is ultimately released back to the environment as CO₂ by respiratory processes. Unfortunately, our understanding of this cycle was determined under the assumption that the primary inorganic form of C (CO₂ in the atmosphere) was relatively constant. With the emerging concensus that atmospheric carbon concentration is increasing, we must now reassess our understanding of the carbon cycle. How will plants, animals and decomposers respond to a doubling of carbon supply? Will biological productivity be accelerated? If plant productivity increases will a predictable percentage of the increase be accumulated as increased standing crop? Or, is it possible that doubling the availability of CO₂ will increase metabolic activity at all trophic levels resulting in no net increase in system standing crop? The purpose of this paper is to review evidence for physiological and growth responses of plants to carbon dioxide enhancement. Essentially no research has been completed on the ecological aspects of these questions. From this review, I conclude that accurate predictions of future ecosystem responses to increasing atmospheric carbon dioxide concentration are not possible without additional understanding of physiological and ecological mechanisms.     

Assemblages of sea stars (Echinodermata: Asteroidea) and brittle stars (Echinodermata: Ophiuroidea) in the Weddell Sea (Antarctica) and off Northeast Greenland (Arctic): a comparison of diversity and abundance

Composition and distribution of asteroid and ophiuroid assemblages were investigated by means of Agassiz trawl catches at 34 stations in 220- to 1,200-m depth in the Weddell Sea and at 17 stations in 90- and 830-m depth off Northeast Greenland. A total of 86 species (48 sea stars, 38 brittle stars) were identified in the Weddell Sea whereas off Northeast Greenland a total of 26 species (16 sea stars, 10 brittle stars) were recorded. In both study areas, brittle stars were numerically more important than sea stars, and abundances generally decreased with water depths. Multivariate analyses revealed a conspicuous depth zonation of sea and brittle stars off Greenland. Very high abundances of Ophiocten sericeum and Ophiura robusta characterized the assemblages on shallow shelf banks whereas in greater depths Ophiopleura borealis, Ophioscolex glacialis and Ophiacantha bidentata became dominant, albeit at significantly lower densities. Mass occurrences of brittle stars, such as those recorded on Greenlandic shelf banks, have not been discovered in the Weddell Sea, where distinct assemblages were discriminated in deep shelf trenches as well as on the eastern and southern shelf. Ophioplocus incipiens, Ophiurolepis martensi and Ophiurolepis brevirima were the most prominent species on the eastern shelf. Ophiacantha antarctica, Ophiurolepis gelida and Ophionotus victoriae on the southern shelf, and Ophiosparte gigas as well as the asteriod Hymenaster sp., in the shelf trenches. Overall, the Weddell Sea housed conspicuously more asterozoan species than the waters off Greenland. Higher species diversity was also evident at both a regional and local scale, especially for the eastern Weddell Sea shelf. However, because many species from the Weddell Sea are closely related, the Weddell Sea assemblages were not significantly different from the Greenland ones in terms of taxonomic diversity and distinctness. Received: 29 April 1996/Accepted: 10 June 1996     

Coordinating mitosis with cell polarity: Molecular motors at the cell cortex

In many cell divisions, the position of the spindle apparatus is coordinated with polarity signals at the cell cortex so that copies of the genome are delivered to regions of the cell that are designated for differential inheritance by the two progeny. To coordinate spindle position with cell polarity, the spindle interfaces with elements on the cortex, where molecular motors often produce the forces that power displacement. Here we describe the molecular pathways by which cortical motors translocate the spindle in budding yeast, where the mechanisms are understood relatively well, and we compare these pathways to spindle positioning processes in metazoan systems, where the molecular details are less well understood.     

Photomodulation of conformational states. III. Water-soluble bis-cysteinyl-peptides with (4-aminomethyl) phenylazobenzoic acid as backbone constituent

In previous studies we have shown that light-induced cis/trans isomerization of the azobenzene moiety in cyclo-[Ala-Cys-Ala-Thr-Cys-Asp-Gly-Phe-AMPB] [AMPB: (4-aminomethyl)phenylazobenzoic acid] leads both in the monocyclic and in the oxidized bicyclic form to markedly differentiated conformational states in DMSO, a fact that lends itself for photomodulation of the redox potential of such bis-cysteinyl-peptides. For this purpose water-soluble systems are required, and this was achieved by replacing three residues outside the Cys-Ala-Thr-Cys active-site motif of thioredoxin reductase with lysines. The resulting cyclo-[Lys-Cys-Ala-Thr-Cys-Asp-Lys-Lys-AMPB] fully retains its photoresponsive properties in water as well assessed by uv and CD measurements. Paralleling results of the previously investigated azobenzene-containing cyclic peptides, the trans --> cis isomerization of the water-soluble monocyclic and oxidized bicyclic peptide is accompanied by a marked transition from a well-defined conformation to an ensemble of possible conformations. However, the conformational preferences are very dissimilar from those of the DMSO-soluble peptides. In fact, hydrogen bonds as well as secondary structure elements were found that change in the mono- and bicyclic peptide upon irradiation. The photo switch between different turn types and hydrogen bonding networks offers the structural rational for the significantly differentiated redox potentials, but also the possibility of monitoring by femtosecond uv-vis and ir spectroscopy fast and ultra fast backbone rearrangement processes following the electronic trans --> cis isomerization.     

The behavior and the morphology of sea lilies with shortened stalks: implications on the evolution of feather stars

Extant crinoids can be divided into two groups, stalked sea lilies and stalkless feather stars. Feather stars are considered to have evolved from stalked ancestors by losing most of the stalk, but other differences are present between the two groups. The unsegmented centrodorsal, long and curved cirri near the crown, small calyx, and the ability to swim are all feather star features not found in the sea lilies. To figure out which of the above features evolved directly correlating with loss of the stalk in feather stars, we cut off the stalk from the sea lily Metacrinus rotundus and kept them alive in an aquarium. The specimens with shortened stalks were able to stand and crawl with their arms without the support of their stalks, but swimming was not observed for any of the animals. Morphologically, neither fusion of the remaining segments nor the reduction of the size of the calyx were observed, but the cirri became long and curved near the crown. Therefore, the extant sea lilies possess a potential to adapt to incidents of stalk loss. Specimens autotomizing most of their stalks were observed, suggesting that the potential is actually employed in nature. This mechanism linking the reduction of the stalk and the changes in the morphology of cirri may have played an important role in the evolution of the feather stars, if the stalked ancestors of feather stars also possessed this potential. Experimental zoological approaches as this study may provide new insights to the questions of evolution.     

What do we know about growth of vessel elements of secondary xylem in woody plants?

Despite extensive knowledge about vessel element growth and the determination of the axial course of vessels, these processes are still not fully understood. They are usually explained as resulting primarily from hormonal regulation in stems. This review focuses on an increasingly discussed aspect – mechanical conditions in the vascular cambium. Mechanical conditions in cambial tissue are important for the growth of vessel elements, as well as other cambial derivatives. In relation to the type of stress acting on cambial cells (compressive versus tensile stress) we: (i) discuss the shape of the enlarging vessel elements observed in anatomical sections; (ii) present hypotheses regarding the location of intrusive growth of vessel elements and cambial initials; (iii) explain the relationship between the growth of vessel elements and fibres; and (iv) consider the effect of mechanical stress in determining the course of a vessel. We also highlight the relationship between mechanical stress and transport of the most extensively studied plant hormone – auxin. We conclude that the integration of a biomechanical factor with the commonly acknowledged hormonal regulation could significantly enhance the analysis of the formation of vessel elements as well as entire vessels, which transport water and minerals in numerous plant species.     

Tuning of Thioredoxin Redox Properties by Intramolecular Hydrogen Bonds

Thioredoxin-like proteins contain a characteristic C-x-x-C active site motif and are involved in a large number of biological processes ranging from electron transfer, cellular redox level maintenance, and regulation of cellular processes. The mechanism for deprotonation of the buried C-terminal active site cysteine in thioredoxin, necessary for dissociation of the mixed-disulfide intermediate that occurs under thiol/disulfide mediated electron transfer, is not well understood for all thioredoxin superfamily members. Here we have characterized a 8.7 kD thioredoxin (BC3987) from Bacillus cereus that unlike the typical thioredoxin appears to use the conserved Thr8 side chain near the unusual C-P-P-C active site to increase enzymatic activity by forming a hydrogen bond to the buried cysteine. Our hypothesis is based on biochemical assays and thiolate pK_a titrations where the wild type and T8A mutant are compared, phylogenetic analysis of related thioredoxins, and QM/MM calculations with the BC3987 crystal structure as a precursor for modeling of reduced active sites. We suggest that our model applies to other thioredoxin subclasses with similar active site arrangements.     

Relating protein conformational changes to packing efficiency and disorder

Changes in protein conformation play key roles in facilitating various biochemical processes, ranging from signaling and phosphorylation to transport and catalysis. While various factors that drive these motions such as environmental changes and binding of small molecules are well understood, specific causative effects on the structural features of the protein due to these conformational changes have not been studied on a large scale. Here, we study protein conformational changes in relation to two key structural metrics: packing efficiency and disorder. Packing has been shown to be crucial for protein stability and function by many protein design and engineering studies. We study changes in packing efficiency during conformational changes, thus extending the analysis from a static context to a dynamic perspective and report some interesting observations. First, we study various proteins that adopt alternate conformations and find that tendencies to show motion and change in packing efficiency are correlated: residues that change their packing efficiency show larger motions. Second, our results suggest that residues that show higher changes in packing during motion are located on the changing interfaces which are formed during these conformational changes. These changing interfaces are slightly different from shear or static interfaces that have been analyzed in previous studies. Third, analysis of packing efficiency changes in the context of secondary structure shows that, as expected, residues buried in helices show the least change in packing efficiency, whereas those embedded in bends are most likely to change packing. Finally, by relating protein disorder to motions, we show that marginally disordered residues which are ordered enough to be crystallized but have sequence patterns indicative of disorder show higher dislocation and a higher change in packing than ordered ones and are located mostly on the changing interfaces. Overall, our results demonstrate that between the two conformations, the cores of the proteins remain mostly intact, whereas the interfaces display the most elasticity, both in terms of disorder and change in packing efficiency. By doing a variety of tests, we also show that our observations are robust to the solvation state of the proteins.     

The Rediscovery of a Long Described Species Reveals Additional Complexity in Speciation Patterns of Poeciliid Fishes in Sulfide Springs

The process of ecological speciation drives the evolution of locally adapted and reproductively isolated populations in response to divergent natural selection. In Southern Mexico, several lineages of the freshwater fish species of the genus Poecilia have independently colonized toxic, hydrogen sulfide-rich springs. Even though ecological speciation processes are increasingly well understood in this system, aligning the taxonomy of these fish with evolutionary processes has lagged behind. While some sulfide spring populations are classified as ecotypes of Poecilia mexicana, others, like P. sulphuraria, have been described as highly endemic species. Our study particularly focused on elucidating the taxonomy of the long described sulfide spring endemic, Poecilia thermalis Steindachner 1863, and investigates if similar evolutionary patterns of phenotypic trait divergence and reproductive isolation are present as observed in other sulfidic species of Poecilia. We applied a geometric morphometric approach to assess body shape similarity to other sulfidic and non-sulfidic fish of the genus Poecilia. We also conducted phylogenetic and population genetic analyses to establish the phylogenetic relationships of P. thermalis and used a population genetic approach to determine levels of gene flow among Poecilia from sulfidic and non-sulfidic sites. Our results indicate that P. thermalis'' body shape has evolved in convergence with other sulfide spring populations in the genus. Phylogenetic analyses placed P. thermalis as most closely related to one population of P. sulphuraria, and population genetic analyses demonstrated that P. thermalis is genetically isolated from both P. mexicana ecotypes and P. sulphuraria. Based on these findings, we make taxonomic recommendations for P. thermalis. Overall, our study verifies the role of hydrogen sulfide as a main factor shaping convergent, phenotypic evolution and the emergence of reproductive isolation between Poecilia populations residing in adjacent sulfidic and non-sulfidic environments.     

Cis-acting RNA elements in human and animal plus-strand RNA viruses

The RNA genomes of plus-strand RNA viruses have the ability to form secondary and higher-order structures that contribute to their stability and to their participation in inter- and intramolecular interactions. Those structures that are functionally important are called cis-acting RNA elements because their functions cannot be complemented in trans. They can be involved not only in RNA/RNA interactions but also in binding of viral and cellular proteins during the complex processes of translation, RNA replication and encapsidation. Most viral cis-acting RNA elements are located in the highly structured 5′- and 3′-nontranslated regions of the genomes but sometimes they also extend into the adjacent coding sequences. In addition, some cis-acting RNA elements are embedded within the coding sequences far away from the genomic ends. Although the functional importance of many of these structures has been confirmed by genetic and biochemical analyses, their precise roles are not yet fully understood. In this review we have summarized what is known about cis-acting RNA elements in nine families of human and animal plus-strand RNA viruses with an emphasis on the most thoroughly characterized virus families, the Picornaviridae and Flaviviridae.