Long-term forest fire ecology and dynamics in southern Switzerland

1 Pollen and charcoal analysis at two lakes in southern Switzerland revealed that fire has had a prominent role in changing the woodland composition of this area for more than 7000 years. 2 The sediment of Lago di Origlio for the period between 5100 and 3100 bc cal. was sampled continuously with a time interval of about 10 years. Peaks of charcoal particles were significantly correlated with repeated declines in pollen of Abies, Hedera, Tilia, Ulmus, Fraxinus excelsior t., Fagus and Vitis and with increases in Alnus glutinosa t., shrubs (e.g. Corylus, Salix and Sambucus nigra t.) and several herbaceous species. The final disappearance of the lowland Abies alba stands at around 3150 bc cal. may be an example of a fire-caused local extinction of a fire-intolerant species. 3 Forest fires tended to diminish pollen diversity. The charcoal peaks were preceded by pollen types indicating human activity. Charcoal minima occurred during periods of cold humid climate, when fire susceptibility would be reduced. 4 An increase of forest fires at about 2100 bc cal. severely reduced the remaining fire-sensitive plants: the mixed-oak forest was replaced by a fire-tolerant alder–oak forest. The very strong increase of charcoal influx, and the marked presence of anthropogenic indicators, point to principally anthropogenic causes. 5 We suggest that without anthropogenic disturbances Abies alba would still form lowland forests together with various deciduous broadleaved tree taxa.

Deep water provenance and dynamics of the (de)glacial Atlantic meridional overturning circulation

Reconstructing past modes of ocean circulation is an essential task in paleoclimatology and paleoceanography. To this end, we combine two sedimentary proxies, Nd isotopes (εNd) and the 231Pa/230Th ratio, both of which are not directly involved in the global carbon cycle, but allow the reconstruction of water mass provenance and provide information about the past strength of overturning circulation, respectively. In this study, combined 231Pa/230Th and εNd down-core profiles from six Atlantic Ocean sediment cores are presented. The data set is complemented by the two available combined data sets from the literature. From this we derive a comprehensive picture of spatial and temporal patterns and the dynamic changes of the Atlantic Meridional Overturning Circulation over the past ∼25 ka. Our results provide evidence for a consistent pattern of glacial/stadial advances of Southern Sourced Water along with a northward circulation mode for all cores in the deeper (>3000 m) Atlantic. Results from shallower core sites support an active overturning cell of shoaled Northern Sourced Water during the LGM and the subsequent deglaciation. Furthermore, we report evidence for a short-lived period of intensified AMOC in the early Holocene.

Morphology and dynamics of the jets of comet 67P/Churyumov-Gerasimenko: Early-phase development

Aims. The OSIRIS camera onboard the Rosetta spacecraft obtained close-up views of the dust coma of comet 67P. The jet structures can be used to trace their source regions and to examine the possible effect of gas-surface interaction. Methods. We analyzed the wide-angle images obtained in the special dust observation sequences between August and September 2014. The jet features detected in different images were compared to study their time variability. The locations of the potential source regions of some of the jets are identified by ray tracing. We used a ring-masking technique to calculate the brightness distribution of dust jets along the projected distance. Results. The jets detected between August and September 2014 mostly originated in the Hapi region. Morphological changes appeared over a timescale of several days in September. The brightness slope of the dust jets is much steeper than the background coma. This might be related to the sublimation or fragmentation of the emitted dust grains. Interaction of the expanding gas flow with the cliff walls on both sides of Hapi could lead to erosion and material down-fall to the nucleus surface.

Late-glacial and Holocene vegetation history and dynamics as shown by pollen and plant macrofossil analyses in annually laminated sediments from Soppensee, central Switzerland

The palynostratigraphy of two sediment cores from Soppensee, Central Switzerland (596 m asl) was correlated with nine regional pollen assemblage zones defined for the Swiss Plateau. This biostratigraphy shows that the sedimentary record of Soppensee includes the last 15 000 years, i.e. the entire Late-glacial and Holocene environmental history. The vegetation history of the Soppensee catchment was inferred by pollen and plant-macrofossil analyses on three different cores taken in the deepest part of the lake basin (27 m). On the basis of a high-resolution varve and calibrated radiocarbonchronology it was possible to estimate pollen accumulation rates, which together with the pollen percentage data, formed the basis for the interpretation of the past vegetation dynamics. The basal sediment dates back to the last glacial. After reforestation with juniper and birch at ca. 12 700 B.P., the vegetation changed at around 12 000 B.P. to a pine-birch woodland and at the onset of the Holocene to a mixed deciduous forest. At ca. 7000 B.P., fir expanded and dominated the vegetation with beech becoming predominant at ca. 50014C-years later until sometime during the Iron Age. Large-scale deforestation, especially during the Middle Ages, altered the vegetation cover drastically. During the Late-glacial period two distinct regressive phases in vegetation development are demonstrated, namely, the Aegelsee oscillation (equivalent to the Older Dryas biozone) and the Younger Dryas biozone. No unambiguous evidence for Holocene climatic change was detected at Soppensee. Human presence is indicated by early cereal pollen and distinct pulses of forest clearance as a result of human activity can be observed from the Neolithic period onwards.

Burrowing in Marine Muds by Crack Propagation: Kinematics and Forces

The polychaete Nereis virens burrows through muddy sediments by exerting dorsoventral forces against the walls of its tongue-depressor- shaped burrow to extend an oblate hemispheroidal crack. Stress is concentrated at the crack tip, which extends when the stress intensity factor (K-I) exceeds the critical stress intensity factor (K-Ic). Relevant forces were measured in gelatin, an analog for elastic muds, by photoelastic stress analysis, and were 0.015 +/- 0.001 N (mean +/- s.d.;N= 5). Measured elastic moduli (E) for gelatin and sediment were used in finite element models to convert the forces in gelatin to those required in muds to maintain the same body shapes observed in gelatin. The force increases directly with increasing sediment stiffness, and is 0.16 N for measured sediment stiffness of E=2.7x10(4) Pa. This measurement of forces exerted by burrowers is the first that explicitly considers the mechanical behavior of the sediment. Calculated stress intensity factors fall within the range of critical values for gelatin and exceed those for sediment, showing that crack propagation is a mechanically feasible mechanism of burrowing. The pharynx extends anteriorly as it everts, extending the crack tip only as far as the anterior of the worm, consistent with wedge-driven fracture and drawing obvious parallels between soft-bodied burrowers and more rigid, wedge-shaped burrowers(i.e. clams). Our results raise questions about the reputed high energetic cost of burrowing and emphasize the need for better understanding of sediment mechanics to quantify external energy expenditure during burrowing.

The Diversity and Dynamics of Industrial Organisation: Transformation of Local Assemblers in the Vietnamese Motorcycle Industry

This paper focuses on an emerging arm's-length form of industrial organisation in the motorcycle industry, which had traditionally been characterised by tightly integrated form of organisation. By engaging in how this new form of organisation that emerged in China was transferred to Vietnam and evolved in the Vietnamese context, this paper seeks to illustrate how the rise of local firms in developing countries is driving the increased diversity and dynamics of industrial organisation in an industry that had previously been dominated by TNCs from developed countries.

Structure Variation And Dynamics of the Nuclear Ribosomal Intergenic Spacer Region in Key Gibberella Fujikuroi Complex Species

The intergenic spacer (IGS) region of the ribosomal DNA was cloned and sequenced in eight species within the Gibberella fujikuroi species complex with anamorphs in the genus Fusarium , a group that includes the most relevant toxigenic species. DNA sequence analyses revealed two categories of repeated elements: long repeats and short repeats of 125 and 8 bp, respectively. Long repeats were present in two copies and were conserved in all the species analyzed, whereas different numbers of short repeat elements were observed, leading to species-specific IGS sequences with different length. In Fusarium subglutinans and Fusarium nygamai , these differences seemed to be the result of duplication and deletion events. Here, we propose a model based on unequal crossing over that can explain these processes. The partial IGS sequence of 22 Fusarium proliferatum isolates was also obtained to study variation at the intraspecific level. The results revealed no differences in terms of number or pattern of repeated elements and detected frequent gene conversion events. These results suggest that the homogenization observed at the intraspecific level might not be achieved primarily by unequal crossing-over events but rather by processes associated with recombination such as gene conversion events.

Identification and dynamics of polyglycine II nanocrystals in Argiope trifasciata flagelliform silk

Spider silks combine a significant number of desirable characteristics in one material, including large tensile strength and strain at breaking, biocompatibility, and the possibility of tailoring their properties. Major ampullate gland silk (MAS) is the most studied silk and their properties are explained by a double lattice of hydrogen bonds and elastomeric protein chains linked to polyalanine β-nanocrystals. However, many basic details regarding the relationship between composition, microstructure and properties in silks are still lacking. Here we show that this relationship can be traced in flagelliform silk (Flag) spun by Argiope trifasciata spiders after identifying a phase consisting of polyglycine II nanocrystals. The presence of this phase is consistent with the dominant presence of the –GGX– and –GPG– motifs in its sequence. In contrast to the passive role assigned to polyalanine nanocrystals in MAS, polyglycine II nanocrystals can undergo growing/collapse processes that contribute to increase toughness and justify the ability of Flag to supercontract.

Analysis and optimization for a hexapod walking robot for planetary missions

La tecnología de las máquinas móviles autónomas ha sido objeto de una gran investigación y desarrollo en las últimas décadas. En muchas actividades y entornos, los robots pueden realizar operaciones que son duras, peligrosas o simplemente imposibles para los humanos. La exploración planetaria es un buen ejemplo de un entorno donde los robots son necesarios para realizar las tareas requeridas por los científicos. La reciente exploración de Marte con robots autónomos nos ha mostrado la capacidad de las nuevas tecnologías. Desde la invención de la rueda, que esta acertadamente considerado como el mayor invento en la historia del transporte humano, casi todos los vehículos para exploración planetaria han empleado las ruedas para su desplazamiento. Las nuevas misiones planetarias demandan maquinas cada vez mas complejas. En esta Tesis se propone un nuevo diseño de un robot con patas o maquina andante que ofrecerá claras ventajas en entornos extremos. Se demostrara que puede desplazarse en los terrenos donde los robots con ruedas son ineficientes, convirtiéndolo en una elección perfecta para misiones planetarias. Se presenta una reseña histórica de los principales misiones espaciales, en particular aquellos dirigidos a la exploración planetaria. A través de este estudio será posible analizar las desventajas de los robots con ruedas utilizados en misiones anteriores. El diseño propuesto de robot con patas será presentado como una alternativa para aquellas misiones donde los robots con ruedas puedan no ser la mejor opción. En esta tesis se presenta el diseño mecánico de un robot de seis patas capaz de soportar las grandes fuerzas y momentos derivadas del movimiento de avance. Una vez concluido el diseño mecánico es necesario realizar un análisis que permita entender el movimiento y comportamiento de una maquina de esta complejidad. Las ecuaciones de movimiento del robot serán validadas por dos métodos: cinemático y dinámico. Dos códigos Matlab® han sido desarrollados para resolver dichos sistemas de ecuaciones y han sido verificados por un tercer método, un modelo de elementos finitos, que también verifica el diseño mecánico. El robot con patas presentado, ha sido diseñado para la exploración planetaria en Marte. El comportamiento del robot durante sus desplazamientos será probado mediante un código de Matlab®, desarrollado para esta tesis, que permite modificar las trayectorias, el tipo de terreno, y el número y altura de los obstáculos. Estos terrenos y requisitos iniciales no han sido elegidos de forma aleatoria, si no que están basados en mi experiencia como miembro del equipo de MSL-NASA que opera un instrumento a bordo del rover Curiosity en Marte. El robot con patas desarrollado y fabricado por el Centro de Astrobiología (INTA-CSIC), esta basado en el diseño mecánico y análisis presentados en esta tesis. ABSTRACT The autonomous machines technology has undergone a major research and development during the last decades. In many activities and environments, robots can perform operations that are tought, dangerous or simply imposible to humans. Planetary exploration is a good example of such environment where robots are needed to perform the tasks required by the scientits. Recent Mars exploration based on autonomous vehicles has shown us the capacity of the new technologies. From the invention of the wheel, which is rightly regarded as the greatest invention in the history of human transportation, nearly all-planetary vehicles are based in wheeled locomotion, but new missions demand new types of machines due to the complex tasks needed to be performed. It will be proposed in this thesis a new design of a legged robot or walking machine, which may offer clear advantages in tough environments. This Thesis will show that the proposed walking machine can travel, were terrain difficulties make wheeled vehicles ineffective, making it a perfect choice for planetary mission. A historical background of the main space missions, in particular those aimed at planetary exploration will be presented. From this study the disadvantages found in the existing wheel rovers will be analysed. The legged robot designed will be introduced as an alternative were wheeled rovers could be no longer the best option for planetary exploration. This thesis introduces the mechanical design of a six-leg robot capable of withstanding high forces and moments due to the walking motion. Once the mechanical design is concluded, and in order to analyse a machine of this complexity an understanding of its movement and behaviour is mandatory. This movement equation will be validated by two methods: kinematics and dynamics. Two Matlab® codes have been developed to solve the systems of equations and validated by a third method, a finite element model, which also verifies the mechanical design. The legged robot presented has been designed for a Mars planetary exploration. The movement behaviour of the robot will be tested in a Matlab® code developed that allows to modify the trajectories, the type of terrain, number and height of obstacles. These terrains and initial requirements have not been chosen randomly, those are based on my experience as a member of the MSL NASA team, which operates an instrument on-board of the Curiosity rover in Mars. The walking robot developed and manufactured by the Center of Astrobiology (CAB) is based in the mechanical design and analysis that will be presented in this thesis.

The use of site-directed fluorophore labeling and donor–donor energy migration to investigate solution structure and dynamics in proteins

The use of molecular genetics for introducing fluorescent molecules enables the use of donor–donor energy migration to determine intramolecular distances in a variety of proteins. This approach can be applied to examine the overall molecular dimensions of proteins and to investigate structural changes upon interactions with specific target molecules. In this report, the donor–donor energy migration method is demonstrated by experiments with the latent form of plasminogen activator inhibitor type 1. Based on the known x-ray structure of plasminogen activator inhibitor type 1, three positions forming the corners of a triangle were chosen. Double Cys substitution mutants (V106C-H185C, H185C-M266C, and M266C-V106C) and corresponding single substitution mutants (V106C, H185C, and M266C) were created and labeled with a sulfhydryl specific derivative of BODIPY (=the D molecule). The side lengths of this triangle were obtained from analyses of the experimental data. The analyses account for the local anisotropic order and rotational motions of the D molecules, as well as for the influence of a partial DD-labeling. The distances, as determined from x-ray diffraction, between the Cα-atoms of the positions V106C–H185C, H185C–M266C, and M266C–V106C were 60.9, 30.8, and 55.1 Å, respectively. These are in good agreement with the distances of 54 ± 4, 38 ± 3, and 55 ± 3 Å, as determined between the BODIPY groups attached via linkers to the same residues. Although the positions of the D-molecules and the Cα-atoms physically cannot coincide, there is a reasonable agreement between the methods.

Stability and dynamics in a hyperthermophilic protein with melting temperature close to 200°C

The rubredoxin protein from the hyperthermophilic archaebacterium Pyrococcus furiosus was examined by a hydrogen exchange method. Even though the protein does not exhibit reversible thermal unfolding, one can determine its stability parameters—free energy, enthalpy, entropy, and melting temperature—and also the distribution of stability throughout the protein, by using hydrogen exchange to measure the reversible cycling of the protein between native and unfolded states that occurs even under native conditions.

Solution structure and dynamics of GCN4 cognate DNA: NMR investigations

A 12 bp long GCN4-binding, self-complementary duplex DNA d(CATGACGTCATG)2 has been investigated by NMR spectroscopy to study the structure and dynamics of the molecule in aqueous solution. The NMR structure of the DNA obtained using simulated annealing and iterative relaxation matrix calculations compares quite closely with the X-ray structure of ATF/CREB DNA in complex with GCN4 protein (DNA-binding domain). The DNA is also seen to be curved in the free state and this has a significant bearing on recognition by the protein. The dynamic characteristics of the molecule have been studied by 13C relaxation measurements at natural abundance. A correlation has been observed between sequence-dependent dynamics and recognition by GCN4 protein.

Symmetry, stability, and dynamics of multidomain and multicomponent protein systems

Symmetry is commonly observed in many biological systems. Here we discuss representative examples of the role of symmetry in structural molecular biology. Point group symmetries are observed in many protein oligomers whose three-dimensional atomic structures have been elucidated by x-ray crystallography. Approximate symmetry also occurs in multidomain proteins. Symmetry often confers stability on the molecular system and results in economical usage of basic components to build the macromolecular structure. Symmetry is also associated with cooperativity. Mild perturbation from perfect symmetry may be essential in some systems for dynamic functions.

Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA

Both the bacterial RecA protein and the eukaryotic Rad51 protein form helical nucleoprotein filaments on DNA that catalyze strand transfer between two homologous DNA molecules. However, only the ATP-binding cores of these proteins have been conserved, and this same core is also found within helicases and the F1-ATPase. The C-terminal domain of the RecA protein forms lobes within the helical RecA filament. However, the Rad51 proteins do not have the C-terminal domain found in RecA, but have an N-terminal extension that is absent in the RecA protein. Both the RecA C-terminal domain and the Rad51 N-terminal domain bind DNA. We have used electron microscopy to show that the lobes of the yeast and human Rad51 filaments appear to be formed by N-terminal domains. These lobes are conformationally flexible in both RecA and Rad51. Within RecA filaments, the change between the “active” and “inactive” states appears to mainly involve a large movement of the C-terminal lobe. The N-terminal domain of Rad51 and the C-terminal domain of RecA may have arisen from convergent evolution to play similar roles in the filaments.

Optical initialization, readout, and dynamics of a Mn spin in a quantum dot

We have investigated the spin preparation efficiency by optical pumping of individual Mn atoms embedded in CdTe/ZnTe quantum dots. Monitoring the time dependence of the intensity of the fluorescence during the resonant optical pumping process in individual quantum dots allows to directly probe the dynamics of the initialization of the Mn spin. This technique presents the convenience of including preparation and readout of the Mn spin in the same step. Our measurements demonstrate that Mn spin initialization, at zero magnetic field, can reach an efficiency of 75% and occurs in the tens of nanoseconds range when a laser resonantly drives at saturation one of the quantum-dot transition. We observe that the efficiency of optical pumping changes from dot-to-dot and is affected by a magnetic field of a few tens of millitesla applied in Voigt or Faraday configuration. This is attributed to the local strain distribution at the Mn location which predominantly determines the dynamics of the Mn spin under weak magnetic field. The spectral distribution of the spin-flip-scattered photons from quantum dots presenting a weak optical pumping efficiency reveals a significant spin relaxation for the exciton split in the exchange field of the Mn spin.