Single non-normalized data of electron probe analyses of all glass shard samples from the Seward Peninsula and the Lipari obsidian reference standard

Permafrost degradation influences the morphology, biogeochemical cycling and hydrology of Arctic landscapes over a range of time scales. To reconstruct temporal patterns of early to late Holocene permafrost and thermokarst dynamics, site-specific palaeo-records are needed. Here we present a multi-proxy study of a 350-cm-long permafrost core from a drained lake basin on the northern Seward Peninsula, Alaska, revealing Lateglacial to Holocene thermokarst lake dynamics in a central location of Beringia. Use of radiocarbon dating, micropalaeontology (ostracods and testaceans), sedimentology (grain-size analyses, magnetic susceptibility, tephra analyses), geochemistry (total nitrogen and carbon, total organic carbon, d13Corg) and stable water isotopes (d18O, dD, d excess) of ground ice allowed the reconstruction of several distinct thermokarst lake phases. These include a pre-lacustrine environment at the base of the core characterized by the Devil Mountain Maar tephra (22 800±280 cal. a BP, Unit A), which has vertically subsided in places due to subsequent development of a deep thermokarst lake that initiated around 11 800 cal. a BP (Unit B). At about 9000 cal. a BP this lake transitioned from a stable depositional environment to a very dynamic lake system (Unit C) characterized by fluctuating lake levels, potentially intermediate wetland development, and expansion and erosion of shore deposits. Complete drainage of this lake occurred at 1060 cal. a BP, including post-drainage sediment freezing from the top down to 154 cm and gradual accumulation of terrestrial peat (Unit D), as well as uniform upward talik refreezing. This core-based reconstruction of multiple thermokarst lake generations since 11 800 cal. a BP improves our understanding of the temporal scales of thermokarst lake development from initiation to drainage, demonstrates complex landscape evolution in the ice-rich permafrost regions of Central Beringia during the Lateglacial and Holocene, and enhances our understanding of biogeochemical cycles in thermokarst-affected regions of the Arctic.

O monumento gótico como suporte da prática artística contemporânea

A presente investigação de tese de mestrado em gestão cultural tem como objetivo propor um projeto de intervenção contemporânea no Mosteiro de Santa Maria da Vitória – Batalha, onde realizei o meu estágio. O contexto arquitetónico, espacial, cultural e social como suporte da prática artística, assim como a consciência e tentativa de criação de intimidade entre um monumento gótico e um objeto artístico contemporâneo são o fio condutor deste projeto. Também tem a intenção de entender qual a importância deste género de projetos no património e na sua gestão e dinamização. Enquanto projeto, foi proposto a dois artistas plásticos contemporâneos a conceção de uma instalação artística através de uma abordagem ao lugar no seu contexto arquitetónico, histórico e também social: a perceção do espaço, assim como a desmistificação da experiência dos artistas no monumento surgem como a ilustração que inicia a proposta prática deste projeto. Desta forma, procuro o envolvimento de profissionais da gestão cultural, e das artes plásticas num processo colaborativo em que cada saber é operacionalizado dialogicamente. O Mosteiro da Batalha ganha um carater de instalação experimental relevando diferentes fazeres num todo definido coletivamente; o espetador torna-se parte integrante da obra. A experiência sensorial dos artistas no Mosteiro da Batalha é a base de todo o desenvolvimento do processo construtivo da obra, no final pretende-se criar um diálogo entre o monumento e a arte contemporânea, respeitando-se mutuamente. Com o tema O monumento gótico como suporte da prática artística contemporânea pretende-se desenvolver um estudo em especial sobre o Mosteiro de Santa Maria da Vitória e intervenções site-specific nesse contexto espacial em duas perspetivas, de um lado do artista e do outro da gestão do património. Será também uma reflexão acerca da arte contemporânea como expoente simbólico do lugar.

Sortase as a Tool in Biotechnology and Medicine

We have harnessed two reactions catalyzed by the enzyme sortase A and applied them to generate new methods for the purification and site-selective modification of recombinant protein therapeutics.

We utilized native peptide ligation —a well-known function of sortase A— to attach a small molecule drug specifically to the carboxy-terminus of a recombinant protein. By combining this reaction with the unique phase behavior of elastin-like polypeptides, we developed a protocol that produces homogenously-labeled protein-small molecule conjugates using only centrifugation. The same reaction can be used to produce unmodified therapeutic proteins simply by substituting a single reactant. The isolated proteins or protein-small molecule conjugates do not have any exogenous purification tags, eliminating the potential influence of these tags on bioactivity. Because both unmodified and modified proteins are produced by a general process that is the same for any protein of interest and does not require any chromatography, the time, effort, and cost associated with protein purification and modification is greatly reduced.

We also developed an innovative and unique method that attaches a tunable number of drug molecules to any recombinant protein of interest in a site-specific manner. Although the ability of sortase A to carry out native peptide ligation is widely used, we demonstrated that Sortase A is also capable of attaching small molecules to proteins through an isopeptide bond at lysine side chains within a unique amino acid sequence. This reaction —isopeptide ligation— is a new site-specific conjugation method that is orthogonal to all available protein-small conjugation technologies and is the first site-specific conjugation method that attaches the payload to lysine residues. We show that isopeptide ligation can be applied broadly to peptides, proteins, and antibodies using a variety of small molecule cargoes to efficiently generate stable conjugates. We thoroughly assessed the site-selectivity of this reaction using a variety of analytical methods and showed that in many cases the reaction is site-specific for lysines in flexible, disordered regions of the substrate proteins. Finally, we showed that isopeptide ligation can be used to create clinically-relevant antibody-drug conjugates that have potent cytotoxicity towards cancerous cells

Electrostatic Contributions to the Thermodynamics of Ribonuclease P Protein Folding

Electrostatic interactions are of fundamental importance in determining the structure and stability of macromolecules. For example, charge-charge interactions modulate the folding and binding of proteins and influence protein solubility. Electrostatic interactions are highly variable and can be both favorable and unfavorable. The ability to quantify these interactions is challenging but vital to understanding the detailed balance and major roles that they have in different proteins and biological processes. Measuring pKa values of ionizable groups provides a sensitive method for experimentally probing the electrostatic properties of a protein.

pKa values report the free energy of site-specific proton binding and provide a direct means of studying protein folding and pH-dependent stability. Using a combination of NMR, circular dichroism, and fluorescence spectroscopy along with singular value decomposition, we investigated the contributions of electrostatic interactions to the thermodynamic stability and folding of the protein subunit of Bacillus subtilis ribonuclease P, P protein. Taken together, the results suggest that unfavorable electrostatics alone do not account for the fact that P protein is intrinsically unfolded in the absence of ligand because the pKa differences observed between the folded and unfolded state are small. Presumably, multiple factors encoded in the P protein sequence account for its IUP property, which may play an important role in its function.

Occurrence and Function of Hoogsteen Base Pairs in Nucleic Acids

Nucleic acids (DNA and RNA) play essential roles in the central dogma of biology for the storage and transfer of genetic information. The unique chemical and conformational structures of nucleic acids – the double helix composed of complementary Watson-Crick base pairs, provide the structural basis to carry out their biological functions. DNA double helix can dynamically accommodate Watson-Crick and Hoogsteen base-pairing, in which the purine base is flipped by ~180° degrees to adopt syn rather than anti conformation as in Watson-Crick base pairs. There is growing evidence that Hoogsteen base pairs play important roles in DNA replication, recognition, damage or mispair accommodation and repair. Here, we constructed a database for existing Hoogsteen base pairs in DNA duplexes by a structure-based survey from the Protein Data Bank, and structural analyses based on the resulted Hoogsteen structures revealed that Hoogsteen base pairs occur in a wide variety of biological contexts and can induce DNA kinking towards the major groove. As there were documented difficulties in modeling Hoogsteen or Watson-Crick by crystallography, we collaborated with the Richardsons’ lab and identified potential Hoogsteen base pairs that were mis-modeled as Watson-Crick base pairs which suggested that Hoogsteen can be more prevalent than it was thought to be. We developed solution NMR method combined with the site-specific isotope labeling to characterize the formation of, or conformational exchange with Hoogsteen base pairs in large DNA-protein complexes under solution conditions, in the absence of the crystal packing force. We showed that there are enhanced chemical exchange, potentially between Watson-Crick and Hoogsteen, at a sharp kink site in the complex formed by DNA and the Integration Host Factor protein. In stark contrast to B-form DNA, we found that Hoogsteen base pairs are strongly disfavored in A-form RNA duplex. Chemical modifications N1-methyl adenosine and N1-methyl guanosine that block Watson-Crick base-pairing, can be absorbed as Hoogsteen base pairs in DNA, but rather potently destabilized A-form RNA and caused helix melting. The intrinsic instability of Hoogsteen base pairs in A-form RNA endows the N1-methylation as a functioning post-transcriptional modification that was known to facilitate RNA folding, translation and potentially play roles in the epitranscriptome. On the other hand, the dynamic property of DNA that can accommodate Hoogsteen base pairs could be critical to maintaining the genome stability.

Detrital layer thickness in 12 varved sediment cores in Lake Mondsee and related flood events AD1976-2005

A succession of 23 sub-millimetre to maximum 12-mm-thick, mostly flood-triggered detrital layers, deposited between 1976 and 2005, was analysed in 12 varved surface sediment cores from meso-scale peri-alpine Lake Mondsee applying microfacies and high-resolution micro X-ray fluorescence analyses. Detailed intrabasin comparison of these layers enabled identification of (i) different source areas of detrital sediments, (ii) flood-triggered sediment flux and local erosion events, and (iii) seasonal differences of suspended flood sediment distribution within the lake basin. Additional calibration of the detrital layer record with river discharge and precipitation data reveals different empirical thresholds for flood layer deposition for different parts of the basin. At proximal locations detrital layer deposition requires floods exceeding a daily discharge of 40 m**3/s, whereas at a location 2 km more distal an hourly discharge of 80 m**3/s and at least 2 days of discharge above 40 m**3/s are necessary. Furthermore, we observe a better correlation between layer thickness and flood amplitude in the depocentre than in distal and proximal areas of the basin. Although our results are partly site-specific, the applied dual calibration approach is suitable to precisely decipher flood layer formation processes and, thereby, improve the interpretation of long flood time series from lake sediments.

R-script modified VS-Lite model

Drought is a key factor affecting forest ecosystem processes at different spatio-temporal scales. For accurately modeling tree functioning ? and thus for producing reliable simulations of forest dynamics ? the consideration of the variability in the timing and extent of drought effects on tree growth is essential, particularly in strongly seasonal climates such as in the Mediterranean area. Yet, most dynamic vegetation models (DVMs) do not include this intra-annual variability of drought effects on tree growth. We present a novel approach for linking tree-ring data to drought simulations in DVMs. A modified forward model of tree-ring width (VS-Lite) was used to estimate seasonal- and site-specific growth responses to drought of Scots pine (Pinus sylvestris L.), which were subsequently implemented in the DVM ForClim. Ring-width data from sixteen sites along a moisture gradient from Central Spain to the Swiss Alps, including the dry inner Alpine valleys, were used to calibrate the forward ring-width model, and inventory data from managed Scots pine stands were used to evaluate ForClim performance. The modified VS-Lite accurately estimated the year-to-year variability in ring-width indices and produced realistic intra-annual growth responses to soil drought, showing a stronger relationship between growth and drought in spring than in the other seasons and thus capturing the strategy of Scots pine to cope with drought. The ForClim version including seasonal variability in growth responses to drought showed improved predictions of stand basal area and stem number, indicating the need to consider intra-annual differences in climate-growth relationships in DVMs when simulating forest dynamics. Forward modeling of ring-width growth may be a powerful tool to calibrate growth functions in DVMs that aim to simulate forest properties in across multiple environments at large spatial scales.

Foraminiferal assemblage and statistical analysis of surface sediment samples from the Golfe d'Arguin, Mauritania

With the growing pressure of eutrophication in tropical regions, the Mauritian shelf provides a natural situation to understand the variability in mesotrophic assemblages. Site-specific dynamics occur throughout the 1200 m depth gradient. The shallow assemblages divide into three types of warm-water mesotrophic foraminiferal assemblages, which is not only a consequence of high primary productivity restricting light to the benthos but due to low pore water oxygenation, shelf geomorphology, and sediment partitioning. In the intermediate depth (approx. 500 m), the increase in foraminiferal diversity is due to the cold-water coral habitat providing a greater range of micro niches. Planktonic species characterise the lower bathyal zone, which emphasizes the reduced benthic carbonate production at depth. Although, due to the strong hydrodynamics within the Golf, planktonic species occur in notable abundances through out the whole depth gradient. Overall, this study can easily be compared to other tropical marine settings investigating the long-term effects of tropical eutrophication and the biogeographic distribution of carbonate producing organisms.

Mg/Ca and Sr/Ca in calcites and estimated distribution coefficients in marine sediments (Table 2)

Recrystallization processes in marine sediments can alter the extent to which biogenic calcite composition serves as a proxy of oceanic chemical and isotopic history. Models of calcite recrystallization developed to date have resulted in significant insights into these processes, but are not completely adequate to describe the conditions of recrystallization. Marine sediments frequently have concentration gradients in interstitial dissolved calcium, magnesium, and strontium which have probably evolved during sediment accumulation. Realistic, albeit simplified, models of the temporal evolution of interstitial water profiles of Ca, Mg, and Sr were used with several patterns of recrystallization rate variation to predict the composition of recrystallized inorganic calcite. Comparison of predictions with measured Mg/Ca and Sr/Ca ratios in severely altered calcite samples from several Deep Sea Drilling Project sites demonstrates that models incorporating temporal variation in interstitial water composition more successfully predict observed calcite compositions than do models which rely solely on present-day interstitial water chemistry. Temporal changes in interstitial composition are particularly important in interpreting Mg/Ca ratios in conjunction with Sr/Ca ratios. Estimates of Mg distribution coefficients from previous observations in marine sediments, much lower than those in laboratory studies of inorganic calcite, are confirmed by these results. Evaluation of the effects of diagenetic alteration of biogenic calcium carbonate sediment must be a site-specific process, taking into account accumulation history, present interstitial chemistry and its variation in the past, and sample depths and ages.

Statistically robust representation and comparison of mortality profiles in archaeozoology

Archaeozoological mortality profiles have been used to infer site-specific subsistence strategies. There is however no common agreement on the best way to present these profiles and confidence intervals around age class proportions. In order to deal with these issues, we propose the use of the Dirichlet distribution and present a new approach to perform age-at-death multivariate graphical comparisons. We demonstrate the efficiency of this approach using domestic sheep/goat dental remains from 10 Cardial sites (Early Neolithic) located in South France and the Iberian Peninsula. We show that the Dirichlet distribution in age-at-death analysis can be used: (i) to generate Bayesian credible intervals around each age class of a mortality profile, even when not all age classes are observed; and (ii) to create 95% kernel density contours around each age-at-death frequency distribution when multiple sites are compared using correspondence analysis. The statistical procedure we present is applicable to the analysis of any categorical count data and particularly well-suited to archaeological data (e.g. potsherds, arrow heads) where sample sizes are typically small.

Sound Art and Public Engagement in the Built Environment: Reflections from an Architecture Center

This article explores the deployment of sound in architectural-curatorial and community engagement contexts through the work of PLACE, a multidisciplinary not-for-profit architecture center in Belfast, Northern Ireland. The author, who worked with PLACE and contributed to the projects discussed here, contextualizes architecture centers and their relationship with sound before examining the specific case of sound and sound art in Northern Ireland and case studies of projects delivered by PLACE. Specifically, the article evaluates two sound installation artworks and three community engagement projects for young audiences. As a means of curating urbanism and architecture, sound-art-as-public-art affords useful strategies to examine, describe or critique the environment as alternatives to traditional architecture exhibition formats. Sound’s temporality and materiality allow sound art works to exist as temporary sculptural interventions in the urban sphere, with attendant implications for public art procurement and urban acoustics. Rich territories of engagement are opened when using sound in a community participatory context.

Modelling the effectiveness of grass buffer strips in managing muddy floods under a changing climate

Muddy floods occur when rainfall generates runoff on agricultural land, detaching and transporting sediment into the surrounding natural and built environment. In the Belgian Loess Belt, muddy floods occur regularly and lead to considerable economic costs associated with damage to property and infrastructure. Mitigation measures designed to manage the problem have been tested in a pilot area within Flanders and were found to be cost-effective within three years. This study assesses whether these mitigation measures will remain effective under a changing climate. To test this, the Water Erosion Prediction Project (WEPP) model was used to examine muddy flooding diagnostics (precipitation, runoff, soil loss and sediment yield) for a case study hillslope in Flanders where grass buffer strips are currently used as a mitigation measure. The model was run for present day conditions and then under 33 future site-specific climate scenarios. These future scenarios were generated from three earth system models driven by four representative concentration pathways and downscaled using quantile mapping and the weather generator CLIGEN. Results reveal that under the majority of future scenarios, muddy flooding diagnostics are projected to increase, mostly as a consequence of large scale precipitation events rather than mean changes. The magnitude of muddy flood events for a given return period is also generally projected to increase. These findings indicate that present day mitigation measures may have a reduced capacity to manage muddy flooding given the changes imposed by a warming climate with an enhanced hydrological cycle. Revisions to the design of existing mitigation measures within existing policy frameworks are considered the most effective way to account for the impacts of climate change in future mitigation planning. 

Ecological effects of flow and temperature regimes on fish communities in temperate rivers

Les organismes aquatiques sont adaptés à une grande variabilité hydrique et thermique des rivières. Malgré ceci, la régulation des eaux suscite des changements aux débits qui peuvent provoquer des impacts négatifs sur la biodiversité et les processus écologiques en rivière. Celle-ci peut aussi causer des modifications au niveau des régimes thermiques et des caractéristiques de l’habitat du poisson. Des données environnementales et biologiques décrivant l’habitat du poisson existent, mais elles sont incomplètes pour plusieurs rivières au Canada et de faible qualité, limitant les relations quantitatives débit-température-poissons à un petit nombre de rivières ou à une région étudiée. La recherche menée dans le cadre de mon doctorat concerne les impacts de la génération d'hydroélectricité sur les rivières; soit les changements aux régimes hydriques et thermiques reliés à la régulation des eaux sur la variation des communautés ichtyologiques qui habitent les rivières régulées et naturelles au Canada. Suite à une comparaison d’échantillonnage de pêche, une méthode constante pour obtenir des bons estimés de poisson (richesse, densité et biomasse des espèces) a été établie pour évaluer la structure de la communauté de poissons pour l’ensemble des rivières ciblées par l’étude. Afin de mieux comprendre ces changements environnementaux, les principales composantes décrivant ces régimes ont été identifiées et l’altération des régimes hydriques pour certaines rivières régulées a été quantifiée. Ces résultats ont servi à établir la relation significative entre le degré de changement biotique et le degré de changement hydrique pour illustrer les différences entre les régimes de régulation. Pour faire un complément aux indices biotiques déjà calculés pour l’ensemble des communautés de poissons (diversité, densité et biomasse des espèces par rivière), les différences au niveau des guildes de poissons ont été quantifiées pour expliquer les divers effets écologiques dus aux changements de régimes hydriques et thermiques provenant de la gestion des barrages. Ces derniers résultats servent à prédire pour quels traits écologiques ou groupes d’espèces de poissons les composantes hydriques et thermiques sont importantes. De plus, ces derniers résultats ont servi à mettre en valeur les variables décrivant les régimes thermiques qui ne sont pas toujours inclues dans les études hydro-écologiques. L’ensemble des résultats de cette thèse ont des retombées importantes sur la gestion des rivières en évaluant, de façon cohérente, l’impact de la régulation des rivières sur les communautés de poissons et en développant des outils de prévision pour la restauration des écosystèmes riverains.

Macroinvertebrate Diversity in Urban and Rural Ponds: Implications for Freshwater Biodiversity Conservation

Ponds are among the most biodiverse freshwater ecosystems, yet face significant threats from removal, habitat degradation and a lack of legislative protection globally. Information regarding the habitat quality and biodiversity of ponds across a range of land uses is vital for the long term conservation and management of ecological resources. In this study we examine the biodiversity and conservation value of macroinvertebrates from 91 lowland ponds across 3 land use types (35 floodplain meadow, 15 arable and 41 urban ponds). A total of 224 macroinvertebrate taxa were recorded across all ponds, with urban ponds and floodplain ponds supporting a greater richness than arable ponds at the landscape scale. However, at the alpha scale, urban ponds supported lower faunal diversity (mean: 22 taxa) than floodplain (mean: 32 taxa) or arable ponds (mean: 30 taxa). Floodplain ponds were found to support taxonomically distinct communities compared to arable and urban ponds. A total of 13 macroinvertebrate taxa with a national conservation designation were recorded across the study area and 12 ponds (11 floodplain and 1 arable pond) supported assemblages of high or very high conservation value. Pond conservation currently relies on the designation of individual ponds based on very high biodiversity or the presence of taxa with specific conservation designations. However, this site specific approach fails to acknowledge the contribution of ponds to freshwater biodiversity at the landscape scale. Ponds are highly appropriate sites outside of protected areas (urban/arable), with which the general public are already familiar, for local and landscape scale conservation of freshwater habitats.

'Scratch' locative audio drama - report to BBC executives on trial at BBC FreeThinking 2008

‘Scratch’ investigates the use of physical space as a representation of narrative and dramatic structure. An audio-drama, it is a world-first in being location-sensitive without being tied to any particular place (preceding attempts by others have emphasised location-specific aspects of the genre). Developed in collaboration with and part-funded by BBC Radio Drama, it builds on research undertaken for ‘Dragons’ (output 4). It uses pre-recorded audio on GPS-enabled mobile devices allowing sounds to be virtually attached to locations in an outdoor space. As participants move, they encounter scenes forming a coherent drama which behave differently if the same place is visited more than once. This translocational approach opens novel artistic possibilities exploited through team expertise in narrative, sound design and advanced interaction. It is also significant in the economics of broadcast media as a more viable proposition than the many experimental locative experiences which have been site-specific: this was of great interest to the BBC. The public performance selected for BBC FreeThinking, 1-2 September 2008 in Liverpool as part of European Capital of Culture was reported in a co-authored 2009 conference presentation at ISEA, Belfast, 26-29 August 2009 and in a co-authored short chapter in Spierling and Szilas (eds.) Interactive Storytelling, Springer 2008. Boyd Davis directed the project and devised and undertook the evaluation with 40 trial listeners, reporting to BBC executives (http://researchonline.rca.ac.uk/1000/) for whom a second trial was also run in London in 2009. The evaluation used interview, video observation and a questionnaire combining an open question at the beginning with more specific questions later, avoiding channelling respondents' reactions immediately after the experience into issues which might not be uppermost in their minds, while also yielding data capable of rigorous analysis. The evaluation was to provide feedback to the makers of the drama and to guide policy at the BBC. [287] Participants were recruited principally through the publicity for FreeThinking 2008 – mainly via the festival website. The average age of participants was 40. The gender of participants was 20 males, 17 females and 3 null returns. The evaluation strategy was to combine an open question at the beginning with more specific questions later. In this way we avoided channeling respondents' initial opinions immediately after the experience into issues which might not be uppermost in their minds, while also yielding data capable of rigorous analysis. The purpose of the evaluation was to provide guidance for ourselves as the makers of the drama and to guide policy at the BBC on locative and other interactive media. The responses are analysed in the report.