DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications

DNA molecular combing is a technique that stretches thousands of long individual DNA molecules (up to 10 Mbp) into a parallel configuration on surface. It has previously been proposed to sequence these molecules by synthesis. However, this approach poses two critical challenges: 1-Combed DNA molecules are overstretched and therefore a nonoptimal substrate for polymerase extension. 2-The combing surface sterically impedes full enzymatic access to the DNA backbone. Here, we introduce a novel approach that attaches thousands of molecules to a removable surface, with a tunable stretching factor. Next, we dissolve portions of the surface, leaving the DNA molecules suspended as ‘bridges’. We demonstrate that the suspended molecules are enzymatically accessible, and we have used an enzyme to incorporate labeled nucleotides, as predicted by the specific molecular sequence. Our results suggest that this novel platform is a promising candidate to achieve high-throughput sequencing of Mbp-long molecules, which could have additional genomic applications, such as the study of other protein-DNA interactions.

Gravimetry and petrophysics for defining the intracratonic and rift basins of the western-central Africa zone.

The global gravity field obtained from the observations of the satellite GOCE offers new opportunities in defining density variations of Earth’s crust and mantle, allowing new insights into the structure of specific geologic features. The central African rift is a key feature in understanding of the dismemberment of Gondwana, and we contribute to defining the crustal density structure underlying the rift. The presence of a narrow and up to 12 km deep basin implies crustal stretching to allow the sediment to accumulate, but a key question is whether the stretching processes affected also the deeper layers of the crust or was limited to the upper crust. The study-area includes a sub-basin of the greater Chad sag-basin, which extends over a 1500 km by 1500 km, and occupies the center of North-Central Africa, shared between the countries of Chad, Sudan, Nigeria, Niger, Algeria, Libya and Cameroon. We find that the rifting affected the lower crust of the West African Rift and demonstrate evidence for a 1500 km long and several km thick magmatic crustal intrusion presumably associated with underplating and crustal thinning. We estimate that the stretching factor must be at least 1.5 and had affected the entire crust. To our knowledge, the identification of a continuous body of magmatic intrusions is new and has been only possible through the recent global gravity field. The magmatism has altered the thermal conditions from the time of emplacement on, and is relevant for the maturation of hydrocarbons present in the sediments. The timing of the magmatism is presumably tied to two pulses of volcanism documented in the rift, associated with the first post-rift phase from 96 to 88 Ma and the second post-rift phase from 23 Ma up to the Quaternary.

Integrated geophysical investigations of deeper stratigraphy of the Irish Rockall Basin

<p>The Rockall Trough is an elongate bathymetric depression trending NNE-SSW. It is approximately 1200 km long and up to 300 km wide, extending over the UK and Irish continental margins. The trough is underlain by the Rockall Basin, which forms part of a chain of late Paleozoic-Cenozoic sedimentary basins. The Irish Rockall Basin is vastly unexplored as compared to the UK sector, where extensive flood basalt lava flows, sill complexes and volcanic centers of Late Cretaceous-to-Early Eocene age have been described, which belong to the North Atlantic Igneous Province (NAIP) (Archer et al., 2005). An integrated study of seismic, gravity and magnetic methods elucidates the deeper stratigraphy of the Irish Rockall Basin. More than 10 km of sediments is present in the central part of the basin. We perform first arrival travel time tomography on a downward continued data set of three seismic profiles to model the velocity of the sedimentary structures down to 6 km depth. To better understand the deep structure of the basin we need to estimate the Moho depth from constrained gravity modelling. The modelling results indicate that the Moho depth varies from 12 km to 20 km depth beneath ~10 km thick sediments in the basin. This allows us to measure the crustal stretching factor β. The minimum stretching factor in the basin varies between ~7 in the north to ~6.5 in the south. These values are within the range needed for mantle serpentinisation (O'Reilly et al., 1996; Perez-Gussinye and Reston, 2001). Furthermore, we observe four volcanic ridges in the south part of the basin, which are ~20 km wide and ~ 3 km thick, possibly comprising the Barra Volcanic Ridge System (BVRS) (Scrutton and Bentley, 1988). Results indicate several failed rifting attempts times in late Mesozoic/early Cenozoic times, generating significant basic volcanism, associated with the NAIP. We resolve new volcanic ridges (of late Mesozoic/early Cenozoic age) in the southern part of the Rockall Basin, like many other volcanic ridges/centres observed in other parts of the basin, with correlatable magnetic and gravity anomalies. These may be of late Cretaceous age similar to those found on the conjugate Canadian margin.</p>

Numerical Modelling to Evaluate Sedimentation Effects on Heat Flow and Subsidence during Continental Rifting

Sedimentation impacts thermal and subsidence evolution in continental rifting. Estimating the blanketing effect of sediments is crucial to reconstructing the heat flow during rifting. The sedimentary load affects the basin subsidence rate. Numerical investigation of these effects requires active and complex simulations of the thermal structure, lithospheric stretching, and sedimentation. In this paper, we introduce a numerical model to quantify these effects, which was developed using the COMSOL Multiphysics® simulation software. Our numerical setting for the analytical and numerical solutions of thermal structure and subsidence is based on previous continental rifting studies. In our model, we accumulate a column of 5 m thick sediment layers with varied stretching factors and sedimentation rates, spanning the syn-rift to early post-rift phases over a period of 12 myr. Our results provide intuitive models to understand these sedimentation effects. The models show that an increase in sedimentation thickness significantly decreases surface heat flow, leading to lower geothermal temperature, and amplifies the subsidence magnitude. The findings also demonstrate that increases in the stretching factor and sedimentation rate enhance the blanketing effect and subsidence rate. Based on these results, we discuss key outcomes for geological applications and the possible limitations of our approach.

Inkjet printed self-healable strain sensor based on graphene and magnetic iron oxide nano-composite on engineered polyurethane substrate

In recent years, self-healing property has getting tremendous attention in the future wearable electronic. This paper proposes a novel cut-able and highly stretchable strain sensor utilizing a self-healing function from magnetic force of magnetic iron oxide and graphene nano-composite on an engineered self-healable polyurethane substrate through commercialized inkjet printer DMP-3000. Inducing the magnetic property, magnetic iron oxide is applied to connect between graphene flacks in the nano-composite. To find the best nano-composite, the optimum graphene and magnetic iron oxide blending ratio is 1:1. The proposed sensor shows a high mechanical fracture recovery, sensitivity towards strain, and excellent self-healing property. The proposed devices maintain their performance over 10,000 times bending/relaxing cycles, and 94% of their function are recovered even after cutting them. The device also demonstrates stretchability up to 54.5% and a stretching factor is decreased down to 32.5% after cutting them. The gauge factor of the device is 271.4 at 35%, which means its sensitivity is good. Hence, these results may open a new opportunity towards the design and fabrication of future self-healing wearable strain sensors and their applied electronic devices.

Constraining Basin Parameters Using a Known Subsidence History

Temperature history is one of the most important factors driving subsidence and the overall tectono-stratigraphic evolution of a sedimentary basin. The McKenzie model has been widely applied for subsidence modelling and stretching factor estimation for sedimentary basins formed in an extensional tectonic environment. Subsidence modelling requires values of physical parameters (e.g., crustal thickness, lithospheric thickness, stretching factor) that may not always be available. With a given subsidence history of a basin estimated using a stratigraphic backstripping method, these parameters can be estimated by quantitatively comparing the known subsidence curve with modelled subsidence curves. In this contribution, a method to compare known and modelled subsidence curves is presented, aiming to constrain valid combinations of the stretching factor, crustal thickness, and lithospheric thickness of a basin. Furthermore, a numerical model is presented that takes into account the effect of sedimentary cover on thermal history and subsidence modelling of a basin. The parameter fitting method presented here is first applied to synthetically generated subsidence curves. Next, a case study using a known subsidence curve from the Campos Basin, offshore Brazil, is considered. The range of stretching factors estimated for the Campos basin from this study is in accordance with previous work, with an additional estimate of corresponding lithospheric thickness. This study provides insight into the dependence of thermal history and subsidence modelling methods on assumptions regarding model input parameters. This methodology also allows for the estimation of valid combinations of physical lithospheric parameters, where the subsidence history is known.

Backstripping the Briançonnais (Western Alps) to test Alpine rifting models

<p>During the Mesozoic, the relative movement of African and Eurasian plates caused the opening of the Tethys Ocean. The rifting phase is well charted by the stratigraphic sequence of Western Alps, which provide an exceptional record of continental margin evolution. The Briançonnais domain occupies a pivotal place for testing various rifting models. This domain contains a remarkably uniform succession of very shallow-water carbonates of Triassic age, capped by Middle-Jurassic shallow-water carbonates or by non-deposition before passing abruptly up into deep-water facies. Here we show that the back-stripped Mesozoic tectonic evolution of the Briançonnais block can be applied to investigate models of lithospheric stretching. Applying the Airy correction, we found that the Triassic is characterised by a constant tectonic subsidence rate of 17 m/Ma. If this is the result of “post-rift” thermal re-equilibration of upper mantle after late Palaeozoic rifting, this rift phase occurred with a stretching factor of c 1.4. That this thermal subsidence was modulated by differential uplift and erosion of the Briançonnais in the early Jurassic implies significant mantle thinning, reducing net density of the Briançonnais lithosphere. The subsidence of more than 3000m during Bathonian-Callovian stages are too rapid to be explained by thermal re-equilibration: it suggests substantial crustal thinning. Our results demonstrate that a uniform stretching model is not able to explain the Jurassic isostatic movement of the Briançonnais domain. It is consistent with two-stage, depth-variable stretching of the Briançonnais lithosphere during the Jurassic. Our study represents a starting point for more sophisticated and developed numerical models, to explain rapid vertical movements in hyper-extended continental margins.</p>

The Influence of lithosphere and basement properties on the stretching factor and the development of extensional faults across the Otway Basin and eastern Bight Basin

<p>The Influence of lithosphere and basement properties on the stretching factor and the development of extensional faults across the Otway Basin and eastern Bight Basin</p><ol><li><strong> KHARAZIZADEH*, W.P. SCHELLART, J.C. DUARTE </strong></li> </ol><p>School of Earth, Atmosphere and Environment, Monash University, Clayton, VIC 3800, Australia</p><p>Department of Earth Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands</p><p>Instituto Dom Luiz (ILD) and Geology Department, Faculty of Sciences of the University of Lisbon, Campo Grande, Lisbon, Portugal  </p><p> </p><p>*[email protected]</p><p>*[email protected]</p><p> </p><p><strong>Abstract</strong></p><p>The large southern continental margin of Australia, with a wide variety of sedimentary basins, formed during Mesozoic rifting. The evolution of sedimentary basins is mainly controlled by plate tectonic activity and the mechanism of continental extension. This work presents a comparative study between two main depocentres of the Bight Basin (Ceduna, Duntroon sub-basins) and the Otway Basin. Here, the total amount of extension (∆L) and stretching factor (β) have been measured across the Otway Basin and eastern Bight Basin. The results show significant variation in extensional stretching along the basins, with the smallest stretching factors in the Ceduna and Duntroon sub-basins (1.2<β<1.4), and the largest amount of extension (~ 177 km) and the largest stretching factor (β=1.85) in the eastern part of the passive margin. The regions with the lowest β factor are underlain mostly by thicker lithosphere, while the regions with the largest β factor and amount of extension are related to younger and thinner lithosphere. The main basement structures have been mapped throughout South Australia and Victoria to examine the possible relationships between the new pattern of extensional faults and old basement fabrics. The distribution pattern of normal faults varies considerably along onshore and offshore components of basins. It is proposed that in some regions fault strike varies due to changes in orientation of pre-existing structures in the basement. For example, the north-south Coorong Shear Zone seems to affect the geometry of normal faults by changing their strike from E-W to NW-SE and also, in the easternmost part of the basin, the Bambra Fault changes the strike of normal faults to the NE-SW. Also, the NE-SW basement structures in the western part of the Gawler Craton have some control on normal faults in the western Ceduna sub-basin. Normal faults in the easternmost and westernmost parts of the Otway Basin have a similar orientation to the basement faults. However, in most regions basement faults are perpendicular to the normal faults and there is a minor influence on the new pattern of faulting. Our results imply that the properties of the continental lithosphere (age, thickness and strength of lithosphere) exert a major influence on the β factor and amount of crustal extension but only a minor influence on the geometry of extensional faults.</p><p><strong>Keywords:</strong> Otway Basin, Ceduna and Duntroon sub-basins, rifting, total amount of extension, β factor, normal faults, lithosphere properties</p><p> </p>

Temporal Change of Spectra and Lyapunov Exponent Volcanic Tremor at Raung Volcano, Indonesia

Spectral Analyses and estimation maximal lyapunov exponent (MLE) of volcanic tremor recorded at Raung Volcano were carried out to investigate dynamical systems regarding to their generating system. Their results of both analyses can explain the temporal change in frequency and deterministic processes of the dynamical system. Spectral analysis of volcanic tremor was estimated by the average periodogram method which includes division, Fast Fourier Transformation and averaging. MLE was estimated by graphing the relationship between Stretching Factor (S) and the number of points in the tractor (N) diagram. Content frequency of volcanic tremor Raung Volcano is range from 2.68 to 3.7 Hz. Temporally, there is no significant change, which means that there is no change in the geometry of the Raung volcanic tremor source. This is also shown by the maximal lyapunov exponent which is temporarily constant and positive. That shows that the source process of Raung volcano is chaotic