The use of photogrammetry in the conservation of painted outdoor sculpture:Adressing Jean Dubutffet’s <i>Jardin d'Email</i>

This research evaluates the use of innovative imaging technolo- gies to aid the conservation of large-scale contemporary painted outdoor sculpture. It explores photogrammetry and image- based 3D modelling as tools during the conservation of Jardin d’émail (1974) by Jean Dubuffet (1901-1985), owned by the Kröller-Müller Museum.In partnership with the 4D Research Lab at the University of Amsterdam, 3D digital models of the sculpture and two scale-models were created.This research assesses the effectiveness of using 3D digital models to inform the repainting of the sculpture’s black lines on white background as part of the treatment process. The use of photogrammetry to document the patterns and forms of the sculpture and scale-models is also evaluated. The creation of 3D digital models from the photogrammetric data allows for devi- ation analysis to be carried out, highlighting where areas of the scale-model and sculpture deviate significantly. The 3D models were uploaded on an app for use on tablets to enable responsive access during treatment. This research showed that photogram- metry is not only useful for large scale sculpture documentation, but can also aid the treatment of outdoor sculpture by producing geometrically accurate representations of the scale-model to be used as a reference during repainting

The use of photogrammetry in the conservation of painted outdoor sculpture:Adressing Jean Dubutffet’s <i>Jardin d'Email</i>

This research evaluates the use of innovative imaging technolo- gies to aid the conservation of large-scale contemporary painted outdoor sculpture. It explores photogrammetry and image- based 3D modelling as tools during the conservation of Jardin d’émail (1974) by Jean Dubuffet (1901-1985), owned by the Kröller-Müller Museum.In partnership with the 4D Research Lab at the University of Amsterdam, 3D digital models of the sculpture and two scale-models were created.This research assesses the effectiveness of using 3D digital models to inform the repainting of the sculpture’s black lines on white background as part of the treatment process. The use of photogrammetry to document the patterns and forms of the sculpture and scale-models is also evaluated. The creation of 3D digital models from the photogrammetric data allows for devi- ation analysis to be carried out, highlighting where areas of the scale-model and sculpture deviate significantly. The 3D models were uploaded on an app for use on tablets to enable responsive access during treatment. This research showed that photogram- metry is not only useful for large scale sculpture documentation, but can also aid the treatment of outdoor sculpture by producing geometrically accurate representations of the scale-model to be used as a reference during repainting

Asymmetric relationships between proteins shape genome evolution

An investigation of metabolic networks in E. coli and S. cerevisiae reveals that asymmetric protein interactions affect gene expression, the relative effect of gene-knockouts and genome evolution

Кризис экономики роста как системы: причины и следствия

Актуальность данной работы продиктована кризисным состоянием современной модели экономики. В основе этой модели лежат постулаты о необходимости постоянного роста экономики, который обеспечивается за счет конечного потребления. В обеспечение же реализации такой модели положены монетарные подходы и методы стимулирования потребительского спроса как основного драйвера экономического роста. Венцом данной модели стала долговая экономика потребления обществ индивидуалистов, не имеющих системы традиционных ценностей, а ориентирующихся на иллюзорные временные цели краткосрочного периода. Так, эгоцентрическая модель экономики заняла главенствующее положение по отношению к экологической модели экономики, обнажив массу системообразующих противоречий. Будущее оказалось под угрозой… Целью данной работы является анализ исходных причин этих противоречий, факторов возникновения кризисных явлений и угроз, с которыми столкнулось человечество на современном этапе развития, а также возможных альтернатив устранения этих противоречий и угроз. The relevance of this work is dictated by a critical state of the modern model of the economy. The basis of this model is construed by postulates about the need for sustained economic growth, which is provided by end-use. Monetary approaches and methods of consumer demand stimulation as a main incentive of economic growth guarantee the model implementation. On the top of this model there is a debt consumer economy of a society of individualists who do not have a system of traditional values, but instead have illusory short-term goals. Thus, an egocentric model of the economy has taken a dominant position in relation to an ecological economic model, revealing a lot of systemic contradictions. The future was under threat... The aim of this work is the analysis of the causes of these conflicts, the factors of crisis phenomena, the threats, which mankind faced at this stage of development, and the possible ways of elimination of the contradictions and threats as well. Methods: comparative analysis and synthesis of theoretical fundamental economic sources and assumptions, practical research and personal experience of various Russian and foreign scientists and business practitioners, the results, observations and conclusions arising from the personal experience of the author and his own theoretical research and inventions, and analysis of statistical data

Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners

<p>Abstract</p> <p>Background</p> <p>Enzymes in the radical SAM (rSAM) domain family serve in a wide variety of biological processes, including RNA modification, enzyme activation, bacteriocin core peptide maturation, and cofactor biosynthesis. Evolutionary pressures and relationships to other cellular constituents impose recognizable grammars on each class of rSAM-containing system, shaping patterns in results obtained through various comparative genomics analyses.</p> <p>Results</p> <p>An uncharacterized gene cluster found in many Actinobacteria and sporadically in Firmicutes, Chloroflexi, Deltaproteobacteria, and one Archaeal plasmid contains a PqqE-like rSAM protein family that includes Rv0693 from <it>Mycobacterium tuberculosis</it>. Members occur clustered with a strikingly well-conserved small polypeptide we designate "mycofactocin," similar in size to bacteriocins and PqqA, precursor of pyrroloquinoline quinone (PQQ). Partial Phylogenetic Profiling (PPP) based on the distribution of these markers identifies the mycofactocin cluster, but also a second tier of high-scoring proteins. This tier, strikingly, is filled with up to thirty-one members per genome from three variant subfamilies that occur, one each, in three unrelated classes of nicotinoproteins. The pattern suggests these variant enzymes require not only NAD(P), but also the novel gene cluster. Further study was conducted using SIMBAL, a PPP-like tool, to search these nicotinoproteins for subsequences best correlated across multiple genomes to the presence of mycofactocin. For both the short chain dehydrogenase/reductase (SDR) and iron-containing dehydrogenase families, aligning SIMBAL's top-scoring sequences to homologous solved crystal structures shows signals centered over NAD(P)-binding sites rather than over substrate-binding or active site residues. Previous studies on some of these proteins have revealed a non-exchangeable NAD cofactor, such that enzymatic activity <it>in vitro </it>requires an artificial electron acceptor such as N,N-dimethyl-4-nitrosoaniline (NDMA) for the enzyme to cycle.</p> <p>Conclusions</p> <p>Taken together, these findings suggest that the mycofactocin precursor is modified by the Rv0693 family rSAM protein and other enzymes in its cluster. It becomes an electron carrier molecule that serves <it>in vivo </it>as NDMA and other artificial electron acceptors do <it>in vitro</it>. Subclasses from three different nicotinoprotein families show "only-if" relationships to mycofactocin because they require its presence. This framework suggests a segregated redox pool in which mycofactocin mediates communication among enzymes with non-exchangeable cofactors.</p

Detection of Biochemical Pathways by Probabilistic Matching of Phyletic Vectors

A phyletic vector, also known as a phyletic (or phylogenetic) pattern, is a binary representation of the presences and absences of orthologous genes in different genomes. Joint occurrence of two or more genes in many genomes results in closely similar binary vectors representing these genes, and this similarity between gene vectors may be used as a measure of functional association between genes. Better understanding of quantitative properties of gene co-occurrences is needed for systematic studies of gene function and evolution. We used the probabilistic iterative algorithm Psi-square to find groups of similar phyletic vectors. An extended Psi-square algorithm, in which pseudocounts are implemented, shows better sensitivity in identifying proteins with known functional links than our earlier hierarchical clustering approach. At the same time, the specificity of inferring functional associations between genes in prokaryotic genomes is strongly dependent on the pathway: phyletic vectors of the genes involved in energy metabolism and in de novo biosynthesis of the essential precursors tend to be lumped together, whereas cellular modules involved in secretion, motility, assembly of cell surfaces, biosynthesis of some coenzymes, and utilization of secondary carbon sources tend to be identified with much greater specificity. It appears that the network of gene coinheritance in prokaryotes contains a giant connected component that encompasses most biosynthetic subsystems, along with a series of more independent modules involved in cell interaction with the environment

The evolutionary signal in metagenome phyletic profiles predicts many gene functions

Background. The function of many genes is still not known even in model organisms. An increasing availability of microbiome DNA sequencing data provides an opportunity to infer gene function in a systematic manner. Results. We evaluated if the evolutionary signal contained in metagenome phyletic profiles (MPP) is predictive of a broad array of gene functions. The MPPs are an encoding of environmental DNA sequencing data that consists of relative abundances of gene families across metagenomes. We find that such MPPs can accurately predict 826 Gene Ontology functional categories, while drawing on human gut microbiomes, ocean metagenomes, and DNA sequences from various other engineered and natural environments. Overall, in this task, the MPPs are highly accurate, and moreover they provide coverage for a set of Gene Ontology terms largely complementary to standard phylogenetic profiles, derived from fully sequenced genomes. We also find that metagenomes approximated from taxon relative abundance obtained via 16S rRNA gene sequencing may provide surprisingly useful predictive models. Crucially, the MPPs derived from different types of environments can infer distinct, non-overlapping sets of gene functions and therefore complement each other. Consistently, simulations on &gt; 5000 metagenomes indicate that the amount of data is not in itself critical for maximizing predictive accuracy, while the diversity of sampled environments appears to be the critical factor for obtaining robust models. Conclusions. In past work, metagenomics has provided invaluable insight into ecology of various habitats, into diversity of microbial life and also into human health and disease mechanisms. We propose that environmental DNA sequencing additionally constitutes a useful tool to predict biological roles of genes, yielding inferences out of reach for existing comparative genomics approaches

Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

The packaging and organization of genomic DNA into chromatin represents an additional regulatory layer of gene expression, with specific nucleosome positions that restrict the accessibility of regulatory DNA elements. The mechanisms that position nucleosomes in vivo are thought to depend on the biophysical properties of the histones, sequence patterns, like phased di-nucleotide repeats and the architecture of the histone octamer that folds DNA in 1.65 tight turns. Comparative studies of human and P. falciparum histones reveal that the latter have a strongly reduced ability to recognize internal sequence dependent nucleosome positioning signals. In contrast, the nucleosomes are positioned by AT-repeat sequences flanking nucleosomes in vivo and in vitro. Further, the strong sequence variations in the plasmodium histones, compared to other mammalian histones, do not present adaptations to its AT-rich genome. Human and parasite histones bind with higher affinity to GC-rich DNA and with lower affinity to AT-rich DNA. However, the plasmodium nucleosomes are overall less stable, with increased temperature induced mobility, decreased salt stability of the histones H2A and H2B and considerable reduced binding affinity to GC-rich DNA, as compared with the human nucleosomes. In addition, we show that plasmodium histone octamers form the shortest known nucleosome repeat length (155bp) in vitro and in vivo. Our data suggest that the biochemical properties of the parasite histones are distinct from the typical characteristics of other eukaryotic histones and these properties reflect the increased accessibility of the P. falciparum genome