Non-random coextinctions in phylogenetically structured mutualistic networks

The interactions between plants and their animal pollinators and seed dispersers have moulded much of Earth's biodiversity. Recently, it has been shown that these mutually beneficial interactions form complex networks with a well-defined architecture that may contribute to biodiversity persistence. Little is known, however, about which ecological and evolutionary processes generate these network patterns. Here we use phylogenetic methods to show that the phylogenetic relationships of species predict the number of interactions they exhibit in more than one-third of the networks, and the identity of the species with which they interact in about half of the networks. As a consequence of the phylogenetic effects on interaction patterns, simulated extinction events tend to trigger coextinction cascades of related species. This results in a non-random pruning of the evolutionary tree and a more pronounced loss of taxonomic diversity than expected in the absence of a phylogenetic signal. Our results emphasize how the simultaneous consideration of phylogenetic information and network architecture can contribute to our understanding of the structure and fate of species-rich communities.     

Re-evaluation of protein kinase CK2 pleiotropy: new insights provided by a phosphoproteomics analysis of CK2 knockout cells

CK2 denotes a ubiquitous and pleiotropic protein kinase whose holoenzyme is composed of two catalytic (α and/or α′) and two regulatory β subunits. The CK2 consensus sequence, S/T-x-x-D/E/pS/pT is present in numerous phosphosites, but it is not clear how many of these are really generated by CK2. To gain information about this issue, advantage has been taken of C2C12 cells entirely deprived of both CK2 catalytic subunits by the CRISPR/Cas9 methodology. A comparative SILAC phosphoproteomics analysis reveals that, although about 30% of the quantified phosphosites do conform to the CK2 consensus, only one-third of these are substantially reduced in the CK2α/α′^(?/?) cells, consistent with their generation by CK2. A parallel study with C2C12 cells deprived of the regulatory β subunit discloses a role of this subunit in determining CK2 targeting. We also find that phosphosites notoriously generated by CK2 are not fully abrogated in CK2α/α′^(?/?) cells, while some phosphosites unrelated to CK2 are significantly altered. Collectively taken our data allow to conclude that the phosphoproteome generated by CK2 is not as ample and rigidly pre-determined as it was believed before. They also show that the lack of CK2 promotes phosphoproteomics perturbations attributable to kinases other than CK2.     

Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band

We report a new mechanism in carcinogenesis involving coordinate long-range epigenetic gene silencing. Epigenetic silencing in cancer has always been envisaged as a local event silencing discrete genes. However, in this study of silencing in colorectal cancer, we found common repression of the entire 4-Mb band of chromosome 2q.14.2, associated with global methylation of histone H3 Lys9. DNA hypermethylation within the repressed genomic neighborhood was localized to three separate enriched CpG island 'suburbs', with the largest hypermethylated suburb spanning 1 Mb. These data change our understanding of epigenetic gene silencing in cancer cells: namely, epigenetic silencing can span large regions of the chromosome, and both DNA-methylated and neighboring unmethylated genes can be coordinately suppressed by global changes in histone modification. We propose that loss of gene expression can occur through long-range epigenetic silencing, with similar implications as loss of heterozygosity in cancer.     

Maxwell's color statistics: From reduction of visible errors to reduction to invisible molecules

This paper presents a cross-disciplinary and multi-disciplinary account of Maxwell's introduction of statistical models of molecules for the composition of gases. The account focuses on Maxwell's deployment of statistical models of data in his contemporaneous color researches as established in Cambridge mathematical physics, especially by Maxwell's seniors and mentors. The paper also argues that the cross-disciplinary, or cross-domain, transfer of resources from the natural and social sciences took place in both directions and relied on the complex intra-disciplinary, or intra-domain, dynamics of Maxwell's researches in natural sciences, in color theory, physical astronomy, electromagnetism and dynamical theory of gases, as well as involving a variety of types of communicating and mediating media, from material objects to concepts, techniques and institutions.     

The accuracy of IMF and OECD forecasts for G7 countries

This paper analyses the size and nature of the errors in GDP forecasts in the G7 countries from 1971 to 1995. These GDP short‐term forecasts are produced by the Organization for Economic Cooperation and Development and by the International Monetary Fund, and published twice a year in the Economic Outlook and in the World Economic Outlook, respectively. The evaluation of the accuracy of the forecasts is based on the properties of the difference between the realization and the forecast. A forecast is considered to be accurate if it is unbiased and efficient. A forecast is unbiased if its average deviation from the outcome is zero, and it is efficient if it reflects all the information that is available at the time the forecast is made. Finally, we also examine tests of directional accuracy and offer a non‐parametric method of assessment. Copyright © 2000 John Wiley & Sons, Ltd.     

An excitable gene regulatory circuit induces transient cellular differentiation

Certain types of cellular differentiation are probabilistic and transient. In such systems individual cells can switch to an alternative state and, after some time, switch back again. In Bacillus subtilis, competence is an example of such a transiently differentiated state associated with the capability for DNA uptake from the environment. Individual genes and proteins underlying differentiation into the competent state have been identified, but it has been unclear how these genes interact dynamically in individual cells to control both spontaneous entry into competence and return to vegetative growth. Here we show that this behaviour can be understood in terms of excitability in the underlying genetic circuit. Using quantitative fluorescence time-lapse microscopy, we directly observed the activities of multiple circuit components simultaneously in individual cells, and analysed the resulting data in terms of a mathematical model. We find that an excitable core module containing positive and negative feedback loops can explain both entry into, and exit from, the competent state. We further tested this model by analysing initiation in sister cells, and by re-engineering the gene circuit to specifically block exit. Excitable dynamics driven by noise naturally generate stochastic and transient responses, thereby providing an ideal mechanism for competence regulation.     

Supramolecular self-assembled molecules as organic directing agent for synthesis of zeolites

Solid materials with uniform micropores, such as zeolites, can act as selective catalysts and adsorbents for molecular mixtures by separating those molecules small enough to enter their pores while leaving the larger molecules behind. Zeolite A is a microporous material with a high void volume. Despite its widespread industrial use in, for example, molecular separations and in detergency, its capability as a petroleum-refining material is limited owing to its poor acid-catalytic activity and hydrothermal stability, and its low hydrophobicity. These characteristics are ultimately a consequence of the low framework Si/Al ratio (normally around one) and the resulting high cationic fraction within the pores and cavities. Researchers have modified the properties of type-A zeolites by increasing the Si/Al compositions up to a ratio of three. Here we describe the synthesis of zeolite A structures exhibiting high Si/Al ratios up to infinity (pure silica). We synthesize these materials, named ITQ-29, using a supramolecular organic structure-directing agent obtained by the self-assembly, through pi-pi type interactions, of two identical organic cationic moieties. The highly hydrophobic pure-silica zeolite A can be used for hydrocarbon separations that avoid oligomerization reactions, whereas materials with high Si/Al ratios give excellent shape-selective cracking additives for increasing propylene yield in fluid catalytic cracking operations. We have also extended the use of our supramolecular structure-directing agents to the synthesis of a range of other zeolites.