The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position--specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean--field approximation, which is also known as context--free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct bacterial genomes available in Genbank in April 200

New Data on the Distribution of Southern Forests for the West Siberian Plain during the Late Pleistocene: A Paleoentomological Approach

Subfossil remains of insects and branchiopod crustaceans (Cladocera and Notostraca) found in three late Pleistocene deposits in the Novosibirsk region in the vicinity of the village of Suzun have been described. The calibrated radiocarbon dates for these deposits were 24,893-25,966 cal BP (Suzun-1), 20,379-20,699 cal BP (Suzun-2), and 27,693-28,126 cal BP (Nizhny Suzun), which correspond to the onset of marine isotope stage 2 (MIS 2). The insect assemblages of these deposits are mainly represented by Coleoptera, which are noteworthy for high taxonomic and ecological diversity. At least 194 beetle species from 21 families have been found altogether. Of them, 74 species were found in the Pleistocene deposits of Western Siberia for the first time. All deposits were similar in species composition of beetles; Carabidae and Curculionidae prevailed everywhere. The ecological composition was dominated by steppe and tundra-steppe species; aquatic and riparian groups were also well represented. The Cladoceran and notostracan taxa revealed in Suzun-1 and Suzun-2 are characteristic of recent steppes rather than the forest zone of Western Siberia. The studied entomocomplexes are congruent with the periglacial Otiorhynchus-type fauna that inhabited the southern part of the West Siberian Plain at the end of the Pleistocene and had no close contemporary analogues. Cold and dry conditions, as well as the prevailing open landscapes of the tundra-steppe type, were the reconstructed conditions for this fauna. At the same time, the Suzun-1 and Suzun-2 entomocomplexes had a distinctive feature, namely a high proportion of forest species associated with both coniferous and deciduous trees. According to these data, at the beginning of MIS 2 in the Upper Ob region, spruce forests with the participation of small-leaved species (birch) were present. They were probably confined to river valleys and were not widely distributed

Insects and molluscs of the Late Pleistocene at the Gornovo site (Southern Ural foreland, Russia): New data on palaeoenvironment reconstructions

The paper presents new data on the subfossil insects and molluscs, as well a new radiocarbon date for the Gornovo site in the Southern Fore-Urals. As a result, the stratigraphic interpretation of the sediments of the lower part of the first above floodplain terrace of the Belaya River is corrected and they are assigned to the Tabulda Horizon (MIS 3) of the Upper Pleistocene in the regional scheme of the Fore-Urals Quaternary. The malacofauna of the locality is represented by 27 species of terrestrial and freshwater molluscs. The composition of molluscs in the deposits of MIS 3 indicates the succession of deposit accumulation in the river valley from the stage of reservoirs that periodically connecting with the river to the stage of the overgrown oxbow lake. Single occurrence of mollusc shells in the loams of MIS 2 is a result of sharp climate change. New insect material includes 136 species of Coleoptera from 17 families, as well as Heteroptera and Hymenoptera representatives. 29 species of beetles (Carabidae, Histeridae, Scarabaeidae, Elateridae, Tenebrionidae, Chrysomelidae, Brentidae and Curculionidae) are recorded for the Pleistocene for the first time. The insect assemblages from Gornovo site are assigned to periglacial and humid boreal faunal types. The entomofauna of the periglacial type has no analogues in the recent fauna; it corresponds to the deposits assigned to the middle of MIS 3. This entomofauna is characteristic to the MIS 2 and MIS 3 insect assemblages from the south of West Siberian Plain. Based on entomological data, the climate of the middle of MIS 3 of the Southern Fore-Urals is reconstructed as dry and cold, extracontinental, with mean July temperature not exceeding +15 °C. Steppe landscapes likely prevailed in open areas and coniferous forests were restricted to river valleys. Beetles from deposits dated to end of MIS 3 are assigned to the fauna of the boreal humid type. These insect assemblages are significantly poorer in diversity than periglacial type assemblages and are represented mainly by near water and forest Coleoptera. Based on these species, meadow and forest landscapes were reconstructed. The reconstructed mean air temperature of July ranged from +16 to +19 °C. This suggests a trend towards more mild conditions in the region connected to the climate warming at the end of MIS 3. It is likely that humidification during this period was regional, determined by the proximity of the site to the Southern Urals Mountains. © 2021 Elsevier Ltd and INQU

Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization

Principal manifolds are defined as lines or surfaces passing through ``the middle'' of data distribution. Linear principal manifolds (Principal Components Analysis) are routinely used for dimension reduction, noise filtering and data visualization. Recently, methods for constructing non-linear principal manifolds were proposed, including our elastic maps approach which is based on a physical analogy with elastic membranes. We have developed a general geometric framework for constructing ``principal objects'' of various dimensions and topologies with the simplest quadratic form of the smoothness penalty which allows very effective parallel implementations. Our approach is implemented in three programming languages (C++, Java and Delphi) with two graphical user interfaces (VidaExpert http://bioinfo.curie.fr/projects/vidaexpert and ViMiDa http://bioinfo-out.curie.fr/projects/vimida applications). In this paper we overview the method of elastic maps and present in detail one of its major applications: the visualization of microarray data in bioinformatics. We show that the method of elastic maps outperforms linear PCA in terms of data approximation, representation of between-point distance structure, preservation of local point neighborhood and representing point classes in low-dimensional spaces.Comment: 35 pages 10 figure

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

Cytokines such as TNF and FASL can trigger death or survival depending on cell lines and cellular conditions. The mechanistic details of how a cell chooses among these cell fates are still unclear. The understanding of these processes is important since they are altered in many diseases, including cancer and AIDS. Using a discrete modelling formalism, we present a mathematical model of cell fate decision recapitulating and integrating the most consistent facts extracted from the literature. This model provides a generic high-level view of the interplays between NFκB pro-survival pathway, RIP1-dependent necrosis, and the apoptosis pathway in response to death receptor-mediated signals. Wild type simulations demonstrate robust segregation of cellular responses to receptor engagement. Model simulations recapitulate documented phenotypes of protein knockdowns and enable the prediction of the effects of novel knockdowns. In silico experiments simulate the outcomes following ligand removal at different stages, and suggest experimental approaches to further validate and specialise the model for particular cell types. We also propose a reduced conceptual model implementing the logic of the decision process. This analysis gives specific predictions regarding cross-talks between the three pathways, as well as the transient role of RIP1 protein in necrosis, and confirms the phenotypes of novel perturbations. Our wild type and mutant simulations provide novel insights to restore apoptosis in defective cells. The model analysis expands our understanding of how cell fate decision is made. Moreover, our current model can be used to assess contradictory or controversial data from the literature. Ultimately, it constitutes a valuable reasoning tool to delineate novel experiments

Regulatory feedback response mechanisms to phosphate starvation in rice

Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator of PHO2 is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses

Upgrade of Biomass-Derived Levulinic Acid via Ru/C-Catalyzed Hydrogenation to γ‑Valerolactone in Aqueous−Organic−Ionic Liquids Multiphase Systems

A liquid triphase system made by an aqueous phase, an organic phase, and an ionic liquid was designed and applied to the catalytic hydrogenation/dehydration of biomass-derived levulinic acid to γ-valerolactone. This paper demonstrates that, by operating at 100−150 °C and 35 atm of H2, both in the presence of Ru/C or of a homogeneous Ru precursor, the use of the triphase system designed to match the investigated reaction allows the following: (1) to obtain up to quantitative conversions and 100% selectivity toward the desired product; (2) to recover the product by simple phase separation; and (3) to preserve the catalyst activity for in situ recycles without loss of metal. Globally the investigated reaction proves the concept that a cradle-to-grave approach to the design of a catalytic reaction system can improve the global sustainability of a chemical transformation by improving efficiency, product isolation, and catalyst recycle

Asymptotology of chemical reaction networks

doi:10.1016/j.ces.2009.09.005 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that appl