The slow road to the eukaryotic genome

The eukaryotic genome is a mosaic of eubacterial and archaeal genes in addition to those unique to itself. The mosaic may have arisen as the result of two prokaryotes merging their genomes, or from genes acquired from an endosymbiont of eubacterial origin. A third possibility is that the eukaryotic genome arose from successive events of lateral gene transfer over long periods of time. This theory does not exclude the endosymbiont, but questions whether it is necessary to explain the peculiar set of eukaryotic genes. We use phylogenetic studies and reconstructions of ancestral first appearances of genes on the prokaryotic phylogeny to assess evidence for the lateral gene transfer scenario. We find that phylogenies advanced to support fusion can also arise from a succession of lateral gene transfer events. Our reconstructions of ancestral first appearances of genes reveal that the various genes that make up the eukaryotic mosaic arose at different times and in diverse lineages on the prokaryotic tree, and were not available in a single lineage. Successive events of lateral gene transfer can explain the unusual mosaic structure of the eukaryotic genome, with its content linked to the immediate adaptive value of the genes its acquired. Progress in understanding eukaryotes may come from identifying ancestral features such as the eukaryotic splicesome that could explain why this lineage invaded, or created, the eukaryoticniche.

Contextualist research: Iterating between methods while following an empirically grounded approach

An alternative approach to research is described that has been developed through a succession of significant construction management research projects. The approach follows the principles of iterative grounded theory, whereby researchers iterate between alternative theoretical frameworks and emergent empirical data. Of particular importance is an orientation toward mixing methods, thereby overcoming the existing tendency to dichotomize quantitative and qualitative approaches. The approach is positioned against the existing contested literature on grounded theory, and the possibility of engaging with empirical data in a “theory free” manner is discounted. Emphasis instead is given to the way in which researchers must be theoretically sensitive as a result of being steeped in relevant literatures. Knowledge of existing literatures therefore shapes the initial research design; but emergent empirical findings cause fresh theoretical perspectives to be mobilized. The advocated approach is further aligned with notions of knowledge coproduction and the underlying principles of contextualist research. It is this unique combination of ideas which characterizes the paper's contribution to the research methodology literature within the field of construction management. Examples are provided and consideration is given to the extent to which the emergent findings are generalizable beyond the specific context from which they are derived.

A new theory of educational change - punctuated equilibrium: the case of the internationalisation of Higher Education institutions

This article argues for a new theoretical paradigm for the analysis of change in educational institutions that is able to deal with such issues as readiness for change, transformational change and the failure of change strategies. Punctuated equilibrium (Tushman and Romanelli, 1985) is a theory which has wide application. It envisages long-term change as being made up of a succession of long periods of relative stability interspersed by brief periods of rapid profound change. In the periods of stability only relatively small incremental changes are possible. The periods of transformational change may be triggered by external or internal influences. A recent study of the long-term process of internationalisation in higher education institutions shows evidence to support the theory: long periods of incremental change, events precipitating profound change and the failure of externally imposed attempts to change. Also, as the theory predicts, changes in collegial organisations are slower and more uncertain than changes in managed organisations.

Lag-1 sparing in the attentional blink: benefits and costs of integrating two events into a single episode

When people monitor a visual stream of rapidly presented stimuli for two targets (T1 and T2), they often miss T2 if it falls into a time window of about half a second after T1 onset-the attentional blink. However, if T2 immediately follows T1, performance is often reported being as good as that at long lags-the so-called Lag-1 sparing effect. Two experiments investigated the mechanisms underlying this effect. Experiment 1 showed that, at Lag 1, requiring subjects to correctly report both identity and temporal order of targets produces relatively good performance on T2 but relatively bad performance on T1. Experiment 2 confirmed that subjects often confuse target order at short lags, especially if the two targets are equally easy to discriminate. Results suggest that, if two targets appear in close succession, they compete for attentional resources. If the two competitors are of unequal strength the stronger one is more likely to win and be reported at the expense of the other. If the two are equally strong, however, they will often be integrated into the same attentional episode and thus get both access to attentional resources. But this comes with a cost, as it eliminates information about the targets' temporal order.

Accounts of the English Crown with Italian merchant societies, 1272-1345

The credit arrangements between the three Edwards and Italian merchants were crucial for financing England’s ambitious foreign policies and ensuring the smooth running of governmental administration. The functioning of this credit system can be followed in detail through the well-kept but mostly unpublished records of the English Exchequer. This volume combines a transcription of the most important surviving accounts between the merchants and the Crown, with a parallel abstract presenting the core data in a double-entry format as credits to or debits from the king's account. This dual format was chosen to facilitate the interpretation of the source while still retaining the language and, as far as possible, the structure of the original documents. The wealth of evidence presented here has much value to add to our understanding of the financing of medieval government and the early development of banking services provided by Italian merchant societies. In particular, although the relationship between king and banker was, for the most part, mutually profitable, the English kings also acquired a reputation for defaulting on their debts and thus 'breaking' a succession of merchant societies. These documents provide an essential basis for a re-examination of the 'credit rating' of the medieval English Crown.

Longitudinal investigation of the faecal microbiota of healthy full-term infants using fluorescence in situ hybridization and denaturing gradient gel electrophoresis.

From birth onwards, the gastrointestinal (GI) tract of infants progressively acquires a complex range of micro-organisms. It is thought that by 2 years of age the GI microbial population has stabilized. Within the developmental period of the infant GI microbiota, weaning is considered to be most critical, as the infant switches from a milk-based diet (breast and/or formula) to a variety of food components. Longitudinal analysis of the biological succession of the infant GI/faecal microbiota is lacking. In this study, faecal samples were obtained regularly from 14 infants from 1 month to 18 months of age. Seven of the infants (including a set of twins) were exclusively breast-fed and seven were exclusively formula-fed prior to weaning, with 175 and 154 faecal samples, respectively, obtained from each group. Diversity and dynamics of the infant faecal microbiota were analysed by using fluorescence in situ hybridization and denaturing gradient gel electrophoresis. Overall, the data demonstrated large inter- and intra-individual differences in the faecal microbiological profiles during the study period. However, the infant faecal microbiota merged with time towards a climax community within and between feeding groups. Data from the twins showed the highest degree of similarity both quantitatively and qualitatively. Inter-individual variation was evident within the infant faecal microbiota and its development, even within exclusively formula-fed infants receiving the same diet. These data can be of help to future clinical trials (e.g. targeted weaning products) to organize protocols and obtain a more accurate outline of the changes and dynamics of the infant GI microbiota.

Improvements relating to the manufacture of coated substrates

This invention relates to the manufacture of coated substrates, and particularly, but not exclusively, to the deposition of multi-layer coatings in the manufacture of interference filters consisting of multiple thin films. An object of the invention is to allow accurate control of the deposition of a succession of layers having good uniformity, for example during the manufacture by vacuum evaporation of multilayer interference filters for use with infrared radiation of particularly long wavelength, using a method which is self calibrating and which avoids the repetitive use of individual control layers.

‘Anything can happen in the next half-hour’: Gerry Anderson’s transnational science fiction

Gerry Anderson’s 1960s puppet series have hybrid identities in relation to their medial, geographical, and production histories. This chapter ranges over his science fiction series from Supercar (1961) to Joe 90 (1968), arguing that Anderson’s television science fiction in that period crossed many kinds of boundary and border. Anderson’s television series were a compromise between his desire to make films for adults versus an available market for children’s television puppet programs, and aimed to appeal to a cross-generational family audience. They were made on film, using novel effects, for a UK television production culture that still relied largely on live and videotaped production. While commissioned by British ITV companies, the programs had notable success in the USA, achieving national networked screening as well as syndication, and they were designed to be transatlantic products. The transnational hero teams and security organisations featured in the series supported this internationalism, and simultaneously negotiated between the cultural meanings of Britishness and Americanness. By discussing their means of production, the aesthetic and narrative features of the programs, their institutional contexts, and their international distribution, this chapter argues that Anderson’s series suggest ways of rethinking the boundaries of British science fiction television in the 1960s.

Cloud-resolving simulations of deep convection over a heated mountain

Cloud-resolving numerical simulations of airflow over a diurnally heated mountain ridge are conducted to explore the mechanisms and sensitivities of convective initiation under high pressure conditions. The simulations are based on a well-observed convection event from the Convective and Orographically Induced Precipitation Study (COPS) during summer 2007, where an isolated afternoon thunderstorm developed over the Black Forest mountains of central Europe, but they are idealized to facilitate understanding and reduce computational expense. In the conditionally unstable but strongly inhibited flow under consideration, sharp horizontal convergence over the mountain acts to locally weaken the inhibition and moisten the dry midtroposphere through shallow cumulus detrainment. The onset of deep convection occurs not through the deep ascent of a single updraft but rather through a rapid succession of thermals that are vented through the mountain convergence zone into the deepening cloud mass. Emerging thermals rise through the saturated wakes of their predecessors, which diminishes the suppressive effects of entrainment and allows for rapid glaciation above the freezing level as supercooled cloud drops rime onto preexisting ice particles. These effects strongly enhance the midlevel cloud buoyancy and enable rapid ascent to the tropopause. The existence and vigor of the convection is highly sensitive to small changes in background wind speed U0, which controls the strength of the mountain convergence and the ability of midlevel moisture to accumulate above the mountain. Whereas vigorous deep convection develops for U0 = 0 m s−1, deep convection is completely eliminated for U0 = 3 m s−1. Although deep convection is able to develop under intermediate winds (U0 = 1.5 m s−1), its formation is highly sensitive to small-amplitude perturbations in the initial flow.

Holocene environmental changes in the lower Thames Valley, London, UK: implications for our understanding of the history of Taxus woodland

A radiocarbon-dated multiproxy palaeoenvironmental record from the Lower Thames Valley at Hornchurch Marshes has provided a reconstruction of the timing and nature of vegetation succession against a background of Holocene climate change, relative sea level movement and human activities. The investigation recorded widespread peat formation between c. 6300 and 3900 cal. yr BP (marine ‘regression’), succeeded by evidence for marine incursion. The multiproxy analyses of these sediments, comprising pollen, Coleoptera, diatoms, and plant and wood macrofossils, have indicated significant changes in both the wetland and dryland environment, including the establishment of Alnus (Alder) carr woodland, and the decline of both Ulmus (Elm; c. 5740 cal. yr BP) and Tilia (Lime; c. 5600 cal. yr BP, and 4160–3710 cal. yr BP). The beetle faunas from the peat also suggest a thermal climate similar to that of the present day. At c. 4900 cal. yr BP, Taxus (L.; Yew) woodland colonised the peatland forming a plant community that has no known modern analogue in the UK. The precise reason, or reasons, for this event remain unclear, although changes in peatland hydrology seem most likely. The growth of Taxus on peatland not only has considerable importance for our knowledge of the vegetation history of southeast England, and NW Europe generally, but also has wider implications for the interpretation of Holocene palaeobotanical records. At c. 3900 cal. yr BP, Taxus declined on the peatland surface during a period of major hydrological change (marine incursion), an event also strongly associated with the decline of dryland woodland taxa, including Tilia and Quercus, and the appearance of anthropogenic indicators.

DMP XV palaeohydrology and palaeoenvironment: initial results and report of 2010 and 2011 fieldwork

This paper reports the results of fieldwork conducted in the 2010 and 2011 DMP field seasons and of analysis of samples collected during these and previous years. Research has involved 1) studying palaeolake sediment outcrops, 2) using ground penetrating radar (GPR) to determine their extent under the Dahān Ubārī, and 3) coring palaeolakes in order to determine their palaeoenvironmental records. Research on these samples is continuing but some initial findings are discussed in this paper. The most extensive palaeolake sediments are found within the al-Mahruqah Formation and were deposited by a giant lake system that developed in the Fazzān Basin during past humid periods. Stratigraphic analysis of Lake Megafazzān sediments suggests two different sedimentary successions, a lake margin succession distinctive for its lacustrine and palaeosol carbonates, and a clastic-dominated, intensely rootleted, basin-centre succession which has terrestrial intervals (aeolian and palaeosols) as well as in the upper parts lacustrine limestones. Both basin margin and basin centre successions are underlain by fluvial deposits. Magnetostratigraphy suggests that the formation may be as old as the mid-Pliocene. After the Lake Megafazzān phase, smaller palaeolakes developed within the basin during subsequent humid periods. One of the largest is found in the Wādī al-Hayāt in the area between Jarma and Ubārī. Similar deposits further west along the Wādī at progressively higher altitudes are interpreted as small lakes and marshes fed by springs issuing from aquifers at the base of the escarpment, last replenished during the Holocene humid phase. Dating of sediments suggests that this was between c. 11 and c. 8 ka. The Wādī ash-Shāţī palaeolake core also provides a Holocene palaeoclimate record that paints a slightly different picture, indicating lake conditions until around 7 ka, whereupon it started oscillating until around 5.5 ka when sedimentation terminates. The reasons for the differences in these records are discussed.

‘The Pages are Bugged': the politics of listening in the poetry of W.S. Graham

This paper probes the public dimensions of the work of the twentieth-century Scottish poet W. S. Graham. It draws upon the public contacts and contexts that Graham's lyrics structure and reconfigure, in texts that have appeared to critics to demonstrate the poet's textual aloneness, his intellectual and geographical banishment. Repeatedly addressing his St Ives community of artists and writers, lovers and companions, Graham's work sets up strategic routes through a succession of publicly-minded verbal engagements. Refusing to allow one passively to listen in to the poet's isolation, the lyrics invite, rebuff, tease, avoid, dally with, and proposition audiences and interlocutors. Graham's poetry speaks from within and without tradition, location and heritage, subtly attuning readers to the politics of its handling of national allegiance, identity, class and patronage.

Early–Middle Holocene vegetation history, climate change and human activities at Lago Riane (Ligurian Apennines, NW Italy)

The radiocarbon-dated palaeoecological study of Lago Riane (Ligurian Apennines, NW Italy) presented here forms part of a wider investigation into the relationships between Holocene vegetation succession, climate change and human activities in the northern Apennines. The record of vegetation history from Lago Riane indicates that, since the end of the last glaciation, climate change and prehistoric human activities, combined with several local factors, have strongly influenced the pattern and timing of natural vegetation succession. The pollen record indicates an important change in vegetation cover at Lago Riane at ~8500–8200 cal. years b.p., coincident with a well-known period of rapid climate change. At ~6100 cal. years b.p., Fagus woodland colonised Lago Riane during a period of climate change and expansion of Late Neolithic human activities in the upland zone of Liguria. A marked decline in Abies woodland, and the expansion of Fagus woodland, at ~4700 cal. years b.p., coincided with further archaeological evidence for pastoralism in the mountains of Liguria during the Copper Age. At ~3900–3600 cal. years b.p. (Early to Middle Bronze Age transition), a temporary expansion of woodland at Lago Riane has been provisionally attributed to a decline in human pressure on the environment during a period of short-term climate change

Testing the sustainability and sensitivity to climatic change of terrace agricultural systems in the Peruvian Andes: a pilot study

The results of an integrated geoarchaeological and palaeoecological pilot study of a prehistoric agricultural terrace and nearby mire basin are presented. They reveal two stages of terrace construction for the cultivation of Zea mays during the Middle Horizon (615–695 AD) and late, Late Intermediate Period (1200–1400 AD). These stages were strongly associated with evidence for vegetation succession, destabilisation and erosion of the surrounding landscape, and changes in mire surface wetness. The reasons for agricultural terrace abandonment and/or reconstruction are uncertain, with only circumstantial evidence for climatically induced agricultural change.

Winckelmann and the invention of antiquity: history and aesthetics in the age of Altertumswissenschaft

This volume provides a new perspective on the emergence of the modern study of antiquity, Altertumswissenschaft, in eighteenth-century Germany through an exploration of debates that arose over the work of the art historian Johann Joachim Winckelmann between his death in 1768 and the end of the century. This period has long been recognised as particularly formative for the development of modern classical studies, and over the past few decades has received increased attention from historians of scholarship and of ideas. Winckelmann's eloquent articulation of the cultural and aesthetic value of studying the ancient Greeks, his adumbration of a new method for studying ancient artworks, and his provision of a model of cultural-historical development in terms of a succession of period styles, influenced both the public and intra-disciplinary self-image of classics long into the twentieth century. Yet this area of Winckelmann's Nachleben has received relatively little attention compared with the proliferation of studies concerning his importance for late eighteenth-century German art and literature, for historians of sexuality, and his traditional status as a 'founder figure' within the academic disciplines of classical archaeology and the history of art. Harloe restores the figure of Winckelmann to classicists' understanding of the history of their own discipline and uses debates between important figures, such as Christian Gottlob Heyne, Friedrich August Wolf, and Johann Gottfried Herder, to cast fresh light upon the emergence of the modern paradigm of classics as Altertumswissenschaft: the multi-disciplinary, comprehensive, and historicizing study of the ancient world.