Increased competence as a process of surviving in shared information spaces

Connections between people and groups are growing more frequent and more intense. Cultural events, changes in laws, activities of organizations, and new ideas elsewhere affect one's own decisions and activities more and more. This development has strong implications for the way people can increase their competence and how they can affect what happens to their own community or geographical area. In this paper consequences are considered for a special type of tool, the so-called problem language, that appears to be intimately entwined with many other tools in operations research, cybernetics, and systems research. The language appears most adequate in situations where boundaries can be found such that external events have minimal impact on what happens inside those boundaries. The change in connectivity makes finding such boundaries less and less probable. This suggests looking for another language, to structure the processes necessary when one intends to overcome difficulties that cannot be represented and solved as problems. A language of access is proposed, derived partly from studies in areas where it has never been possible to find boundaries as indicated. Within the framework of this language one can derive methods of externalization that imply speeding up flows of information in a shared workspace or shared information space. Their implementation is greatly facilitated—or even made possible at all—by recent developments in information technology.     

Temporal dissection of p53 function in vitro and in vivo

To investigate the functions of the p53 tumor suppressor, we created a new knock-in gene replacement mouse model in which the endogenous Trp53 gene is substituted by one encoding p53ER(TAM), a p53 fusion protein whose function is completely dependent on ectopic provision of 4-hydroxytamoxifen. We show here that both tissues in vivo and cells in vitro derived from such mice can be rapidly toggled between wild-type and p53 knockout states. Using this rapid perturbation model, we define the kinetics, dependence, persistence and reversibility of p53-mediated responses to DNA damage in tissues in vivo and to activation of the Ras oncoprotein and stress in vitro. This is the first example to our knowledge of a new class of genetic model that allows the specific, rapid and reversible perturbation of the function of a single endogenous gene in vivo.     

An astrolabe attributed to Gerard Mercator,c. 1570

The Istituto e Museo di Storia della Scienza, Florence, Italy, possesses an astrolabe with five latitude plates that is now attributed to the Duisburg workshop of Gerard Mercator. Although it is known that Mercator made instruments, this is the first surviving example to be identified. Another latitude plate is shown to come from the workshop of the Florentine, Giovan Battista Giusti. A seventh plate, possibly engraved by Rumold Mercator, provides the only known Mercatorian polar stereographic projection. The role of Egnazio Danti, cosmographer to the Grand Duke of Tuscany, in the acquisition of the astrolabe in about 1570 is considered.     

Structural basis of latency in plasminogen activator inhibitor-1.

Human plasminogen activator inhibitor-1 (PAI-1) is the fast-acting inhibitor of tissue plasminogen activator and urokinase and is a member of the serpin family of protease inhibitors. Serpins normally form complexes with their target proteases that dissociate very slowly as cleaved species and then fold into a highly stable inactive state in which the residues that flank the scissile bond (P1 and P1';) are separated by about 70 A. PAI-1 also spontaneously folds into a stable inactive state without cleavage; this state is termed 'latent' because inhibitory activity can be restored through denaturation and renaturation. Here we report the structure of intact latent PAI-1 determined by single-crystal X-ray diffraction to 2.6 A resolution. The three-dimensional structure reveals that residues on the N-terminal side of the primary recognition site are inserted as a central strand of the largest beta sheet, in positions similar to the corresponding residues in the cleaved form of the serpin alpha 1-proteinase inhibitor (alpha 1-PI). Residues C-terminal to the recognition site occupy positions on the surface of the molecule distinct from those of the corresponding residues in cleaved serpins or in the intact inactive serpin homologue, ovalbumin, and its cleavage product, plakalbumin. The structure of latent PAI-1 is similar to one formed after cleavage in other serpins, and the stability of both latent PAI-1 and cleaved serpins may be derived from the same structural features.     

Selective activation of p53-mediated tumour suppression in high-grade tumours

Non-small cell lung carcinoma (NSCLC) is the leading cause of cancer-related death worldwide, with an overall 5-year survival rate of only 10-15%. Deregulation of the Ras pathway is a frequent hallmark of NSCLC, often through mutations that directly activate Kras. p53 is also frequently inactivated in NSCLC and, because oncogenic Ras can be a potent trigger of p53 (ref. 3), it seems likely that oncogenic Ras signalling has a major and persistent role in driving the selection against p53. Hence, pharmacological restoration of p53 is an appealing therapeutic strategy for treating this disease. Here we model the probable therapeutic impact of p53 restoration in a spontaneously evolving mouse model of NSCLC initiated by sporadic oncogenic activation of endogenous Kras. Surprisingly, p53 restoration failed to induce significant regression of established tumours, although it did result in a significant decrease in the relative proportion of high-grade tumours. This is due to selective activation of p53 only in the more aggressive tumour cells within each tumour. Such selective activation of p53 correlates with marked upregulation in Ras signal intensity and induction of the oncogenic signalling sensor p19(ARF)( )(ref. 6). Our data indicate that p53-mediated tumour suppression is triggered only when oncogenic Ras signal flux exceeds a critical threshold. Importantly, the failure of low-level oncogenic Kras to engage p53 reveals inherent limits in the capacity of p53 to restrain early tumour evolution and in the efficacy of therapeutic p53 restoration to eradicate cancers.     

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.     

Systems practice from the start: Some experiences in a biotechnology company

Many specialist biotechnology companies have been founded to exploit new and fundamental discoveries in biotechnology—recombinant DNA and monoclonal antibodies. Celltech Limited, founded by the author and generally accepted as the UK's leading company in this field, was based from the start on a number of key systems ideas. Four of these are described and discussed in this paper: the use of succinct statements checked by the CATWOE mnemonic from soft systems methodology; the establishment of coherent systems for managing strategic matters, operational matters, and the development of people; a project management system using a matrix approach; and an approach to external relations influenced by Ashby's Law of Requisite Variety. The paper is concluded with two ideas arising out of practice: the relation of compartmentation and systems boundaries and a methodological suggestion derived from Jürgen Habermas' characterization of the basis for excellent communications.