Aging as a catabolic malfunction

Cellular degradative processes, which include lysosomal (autophagic) and proteasomal degradation, as well as catabolism of proteins by cytosolic and mitochondrial proteases, provide for a continuous turnover of cellular components, such as damaged or obsolete biomolecules and organelles. Inherent insufficiency of these degradative processes results in progressive accumulation within long-lived postmitotic cells of biological ‘garbage’ (waste material), such as various oxidized proteins, functionally effete mitochondria, and lipofuscin (age pigment), an intralysosomal, polymeric, undegradable material. There is increasing evidence that lipofuscin hampers lysosomal degradative capacity, thus promoting the aggravation of accumulated damage at old age. Being rich in redox-active iron, lipofuscin granules also may exacerbate oxidative stress levels in senescent cells. Thus, increasing the efficiency of cellular degradative pathways and preventing involvement of iron in oxidant-induced lysosomal and cellular damage may be potential strategies for anti-aging interventions.     

Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

Eukaryotic diversity in environmental samples is often assessed via PCR-based amplification of nSSU genes. However, estimates of diversity derived from pyrosequencing environmental data sets are often inflated, mainly because of the formation of chimeric sequences during PCR amplification. Chimeras are hybrid products composed of distinct parental sequences that can lead to the misinterpretation of diversity estimates. We have analyzed the effect of sample richness, evenness and phylogenetic diversity on the formation of chimeras using a nSSU data set derived from 454 Roche pyrosequencing of replicated, large control pools of closely and distantly related nematode mock communities, of known intragenomic identity and richness. To further investigate how chimeric molecules are formed, the nSSU gene secondary structure was analyzed in several individuals. For the first time in eukaryotes, chimera formation proved to be higher in both richer and more genetically diverse samples, thus providing a novel perspective of chimera formation in pyrosequenced environmental data sets. Findings contribute to a better understanding of the nature and mechanisms involved in chimera formation during PCR amplification of environmentally derived DNA. Moreover, given the similarities between biodiversity analyses using amplicon sequencing and those used to assess genomic variation, our findings have potential broad application for identifying genetic variation in homologous loci or multigene families in general.     

Cell signaling as a cognitive process

Cellular identity as defined through morphology and function emerges from intracellular signaling networks that communicate between cells. Based on recursive interactions within and among these intracellular networks, dynamical solutions in terms of biochemical behavior are generated that can differ from those in isolated cells. In this way, cellular heterogeneity in tissues can be established, implying that cell identity is not intrinsically predetermined by the genetic code but is rather dynamically maintained in a cognitive manner. We address how to experimentally measure the flow of information in intracellular biochemical networks and demonstrate that even simple causality motifs can give rise to rich, context‐dependent dynamic behavior. The concept how intercellular communication can result in novel dynamical solutions is applied to provide a contextual perspective on cell differentiation and tumorigenesis.     

Material self-assembly as a physicochemical process

Material self-assembly as exemplified in protobiogeneses is shown to be a result of molecular exchange interaction in reacting chemicals. Temporally and spatially correlated aggregates of reacting chemicals work as vertices of molecular exchange interaction. If the material accumulation rate at a locally correlated aggregate spontaneously happens to become positive at a certain time, the material accumulation due to self-assembly will increase with time afterward. A spontaneous formation of looped reaction at locally correlated aggregates of reacting chemicals can initiate a material self-assembly at succeeding times.     

Transport viewed as a catalytic process

Transport catalysis is analysed in terms of the "induced transition fit" (ITF) concept. The essentials of ITF are briefly elucidated, emphasizing the difference of substrate-protein interactions between enzymes and carriers exemplified by the paradigm ADP/ATP carrier (AAC). Two of the numerous applications of the ITF are discussed in more detail: unidirectional passive and active transport and the relation of substrate site type inhibitors to the carrier conformations. According to ITF in most cases of unidirectional transport intrinsic binding energies may be insufficient for transport catalysis and requires additional energy from ATP or electrochemical gradients. The impacts of external energy on the carrier cycle are examined for ABC transporters (mdr) and for cation-substrate co-transporters (LacY). The relations of inhibitors to the binding site of the carrier are discussed, given the paradigm examples of side specific inhibitors of the AAC. Results with the AAC suggest the induction of an abortive ground state by inhibitors, representing extreme side specific conformation of the binding center.     

Genome size as a mutation-selection-drift process

A novel method for estimating neutral rates and patterns of DNA evolution in Drosophila takes advantage of the propensity of non-LTR retrotransposable elements to create nonfunctional, transpositionally inactive copies as a product of transposition. For many LINE elements, most copies present in a genome at any one time are nonfunctional "dead-on-arrival" (DOA) copies. Because these are off-shoots of active, transpositionally competent "master" lineages, in a gene tree of a LINE element from multiple samples from related species, the DOA lineages are expected to map to the terminal branches and the active lineages to the internal branches, the primary exceptions being when the sample includes DOA copies that are allelic or orthologous. Analysis of nucleotide substitutions and other changes along the terminal branches therefore allows estimation of the fixation process in the DOA copies, which are unconstrained with respect to protein coding; and under selective neutrality, the fixation process estimates the underlying mutational pattern. We have studied the retroelement Helena in Drosophila. An unexpectedly high rate of DNA loss was observed, yielding a half-life of unconstrained DNA sequences approximately 60-fold faster in Drosophila than in mammals. The high rate of DNA loss suggests a straightforward explanation of the seeming paradox that Drosophila has many fewer pseudogenes than found in mammalian species. Differential rates of deletion in different taxa might also contribute to the celebrated C-value paradox of why some closely related organisms can have very different DNA contents. New data presented here rule out the possibility that the transposition process itself is highly mutagenic, hence the observed linear relation between number of deletions and number of nucleotide substitutions is most easily explained by the hypothesis that both types of changes accumulate in unconstrained sequences over time.     

Recombination hotspots as a point process

The variation of the recombination rate along chromosomal DNA is one of the important determinants of the patterns of linkage disequilibrium. A number of inferential methods have been developed which estimate the recombination rate and its variation from population genetic data. The majority of these methods are based on modelling the genealogical process underlying a sample of DNA sequences and thus explicitly include a model of the demographic process. Here we propose a different inferential procedure based on a previously introduced framework where recombination is modelled as a point process along a DNA sequence. The approach infers regions containing putative hotspots based on the inferred minimum number of recombination events; it thus depends only indirectly on the underlying population demography. A Poisson point process model with local rates is then used to infer patterns of recombination rate estimation in a fully Bayesian framework. We illustrate this new approach by applying it to several population genetic datasets, including a region with an experimentally confirmed recombination hotspot.     

Reductive dehalogenation as a respiratory process

Anaerobic bacteria can reductively dehalogenate aliphatic and aromatic halogenated compounds in a respiratory process. Only a few of these bacteria have been isolated in pure cultures. However, long acclimation periods, substrate specificity, high dehalogenation rates, and the possibility to enrich for the dehalogenation activity by subcultivation in media containing an electron donor indicate that many of the reductive dehalogenations in the environment are catalyzed by specific bacteria. Molecular hydrogen or formate appear to be good electron donors for the enrichment of such organisms. Furthermore, systems have to be employed which supply the cultures with the halogenated compounds beyond their toxicity level. All bacteria that are presently available in pure culture and grow with a halogenated compound as electron acceptor are members of new genera. Based on experimental results with the membrane-impermeable electron mediator methyl viologen, a model of the respiration system ofDehalobacter restrictus, a tetrachloroethene-dechlorinating bacterium, is presented. Further studies of the biochemistry and energetics of respiratory-dehalogenating strains will help to understand the mechanisms involved and perhaps reveal the evolutionary origin of the dehalogenating enzyme systems.Abbreviations PCE tetrachloroethene - TCE trichloroethene - cis-1,2-DCE cis-1,2-dichloroethene - PCER tetrachloroethene reductase     

Morphogenesis as a macroscopic self-organizing process

We start from reviewing different epistemological constructions used for explaining morphogenesis. Among them, we explore the explanatory power of a law-centered approach which includes top-down causation and the basic concepts of a self-organization theory. Within such a framework, we discuss the morphomechanical models based upon the presumption of feedbacks between mechanical stresses imposed onto a given embryo part from outside and those generated within the latter as a kind of active response. A number of elementary morphogenetic events demonstrating that these feedbacks are directed towards hyper-restoration (restoration with an overshoot) of the initial state of mechanical stresses are described. Moreover, we show that these reactions are bound together into the larger scale feedbacks. That permits to suggest a reconstruction of morphogenetic successions in early Metazoan development concentrated around two main archetypes distinguished by the blastopores geometry. The perspectives of applying the same approach to cell differentiation are outlined. By discussing the problem of positional information we suggest that the developmental pathway of a given embryo part depends upon its preceded deformations and the corresponding mechanical stresses rather than upon its static position at any moment of development.     

A metagenetic approach for revealing community structure of marine planktonic copepods

Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species‐level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species‐level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field‐collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass‐dominant species in each field‐collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.     

Aging process modulates nonlinear dynamics in liver cell metabolism

Regulatory dynamics of energy metabolism in living cells entails a coordinated response of multiple enzyme networks that operate under non-equilibrium conditions. Here we show that mitochondrial dysfunctions associated with the aging process significantly modify nonlinear dynamical signatures in free radical generation/removal, thereby altering energy metabolism in liver cells. We support our data with a plausible biochemical mechanism for modified bioenergetics that involves uncoupling protein-2 that is up-regulated in aged cells as an adaptive response to mitigate increased oxidative stress. Combining high spatial and temporal resolution imaging and bio-energetic measurements, our work provides experimental support to the hypothesis that mitochondria manifest nonlinear dynamical behavior for efficiently regulating energy metabolism in intact cells, and any partial or complete reduction in this behavior would contribute to organ dysfunctions including the aging process and other disease processes.     

Regional Mapping of Neostriatal Neurotransmitter Systems as a Function of Aging

The purpose of the present investigation was to map chemically the distribution of certain neurotransmitter systems in the neostriatum of rats aged 6, 16, and 26 months. This mapping was carried out by microdissection of discrete striatal regions coupled with radiometric assays for choline acetyltransferase (ChAT), glutamate decarboxylase (GAD), dopamine (DA), and norepinephrine (NA). In all age groups, ChAT, DA, and NA were highest in the rostral relative to the caudal neostriatum. Additionally, ChAT was higher in the lateral than in the medial region, whereas GAD was more homogeneously distributed within the striatum. ChAT activity was decreased significantly primarily in the caudal regions in rats aged 16 and 26 months. DA levels were decreased in the caudal striatum in rats aged 26 months. NA levels were found to be significantly decreased primarily in the rostral neostriatal regions of the oldest rats. GAD activity remained unchanged in all age groups. These regional changes in selected neurotransmitter systems may underlie specific motor and cognitive deficits that often occur during aging.     

Toxic HAB species from the Sea of Okhotsk detected by a metagenetic approach,seasonality and environmental drivers

During recent decades, the distribution of harmful algal bloom (HAB) species has expanded worldwide together with the increase of blooms and toxicity events. In this study, the presence of toxic HAB species in the Sea of Okhotsk was investigated based on metagenetic data collected during 6 years of weekly monitoring. Operational taxonomic units (OTUs) associated with the toxic HAB species were detected based on amplifying 18S V7-V9 and 28S D1 rRNA gene regions. In total, 43 unique OTUs associated with toxic HAB species were revealed, with 26 of those previously not reported from the Sea of Okhotsk. More OTUs belonging to dinoflagellates were detected by 18S, whereas a similar number of OTUs associated with dinoflagellates and diatoms were detected by targeting the 28S region. Species belonging to genera Alexandrium, Karenia and Karlodinium were mainly associated with OTUs under Dinophyceae, whereas Bacillariophyceae was represented by the species belonging to genus Pseudo-nitzschia. From the detected OTUs, 22 showed a clear seasonal pattern with the majority of those appearing during summer-autumn. For Alexandrium pacificum, Aureococcus anophagefferens, and Pseudo-nitzschia pungens, the seasonal pattern was detected based on both rRNA regions. Additionally, 14 OTUs were detected during all seasons and two OTUs appeared sporadically. OTUs associated with the toxic species had low relative read abundances, which together with other factors such as similar and variable morphology as well as usage of fixatives, may explain why those species have previously not been detected by light microscopy. Environmental parameters, especially water temperature, significantly (<0.05) influenced the variability in OTU relative abundances and displayed significant (<0.05) correlations with the unique OTUs. The results of this study demonstrate the usefulness of the metagenetic approach for phytoplankton monitoring, which is especially relevant for detecting toxic HAB species.     

Communication in man as a random process

Zusammenfassung Diese Arbeit untersucht die Analogien zwischen den statistischen Gesetzen der Sprache und denjenigen im Bereich der Physik. Es wird gezeigt, daß die Entwicklung eines Textes durch einen Zufallsvorgang beschrieben werden kann, dessen Stetigkeitszustand nahezu übereinstimmt mit dem Verhältnis, das zwischen den entsprechenden linguistischen Parametern besteht.     

Hydraulic development as a process of response

The relationship between political organization and hydraulic development is discussed, using illustrations from the Valley of Oaxaca, Mexico. It is suggested that change in political organization toward greater or lesser centralization of control over local water resource use may be part of a social response to environmental degradation (in this case, a receding water table) resulting from the effects of change in resource use (in this case, intensified water extraction). Economic stress due to environmental degradation varies in duration and intensity; such variations must be taken into account in understanding shifts in response patterns. Small-scale hydraulic development which places pressure on the availability of water for irrigation may elicit an initial response of centralization of control over its use to correct for the disturbance, water shortage. However, this response itself tends to exacerbate the disturbance through reducing previously existing homeostatic controls on the extraction of water and hence leads to greater economic stress, up to the point at which new responses must take place. Other kinds of environmental disturbance resulting from initial development attempts appear to have similar feedback effects which contribute to potential systemic instability.