Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages.

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation. © 2013 Elsevier Ltd.

A three-dimensional tunnel model for calculation of train-induced ground vibration

The frequency range of interest for ground vibration from underground urban railways is approximately 20 to 100 Hz. For typical soils, the wavelengths of ground vibration in this frequency range are of the order of the spacing of train axles, the tunnel diameter and the distance from the tunnel to nearby building foundations. For accurate modelling, the interactions between these entities therefore have to be taken into account. This paper describes an analytical three-dimensional model for the dynamics of a deep underground railway tunnel of circular cross-section. The tunnel is conceptualised as an infinitely long, thin cylindrical shell surrounded by soil of infinite radial extent. The soil is modelled by means of the wave equations for an elastic continuum. The coupled problem is solved in the frequency domain by Fourier decomposition into ring modes circumferentially and a Fourier transform into the wavenumber domain longitudinally. Numerical results for the tunnel and soil responses due to a normal point load applied to the tunnel invert are presented. The tunnel model is suitable for use in combination with track models to calculate the ground vibration due to excitation by running trains and to evaluate different track configurations. © 2006 Elsevier Ltd. All rights reserved.

Monitoring tunnel deformation induced by close-proximity bored tunneling using distributed optical fiber strain measurements

The paper describes the use of optical fiber Brillouin Optical Time Domain Reflectometry (BOTDR) to monitor the strain distribution in an existing tunnel while a twin tunnel was bored at close-proximity. The twin circular bored tunnels between Serangoon and Bartley stations on the new Circle Line Stage 3 subway in Singapore were constructed at close-proximity to avoid underpinning the foundations of adjacent buildings. The minimum clear separation of the two tunnels is 2.3m (0.4 times the tunnel diameter). The Outer Tunnel was constructed first, followed by the Inner Tunnel, with the earth-pressure balance tunnel boring machines maintained at a minimum of 100m apart. In this trial application of BOTDR, the strain distribution along the Outer Tunnel was measured, in order to monitor its deformation due to the boring of the Inner Tunnel at close-proximity. The aim of the trial application was to determine the practicality of this monitoring method for future use in 'live' tunnels. This paper compares the measurements obtained from optical fiber BOTDR with conventional methods of tunnel monitoring and describes preliminary installation and workmanship guidelines derived from lessons learnt during this trial. © 2007 ASCE.

A comparison of two models for the vibration response of piled foundations to inertial and underground-railway-induced loadings

The vibration response of piled foundations due to ground-borne vibration produced by an underground railway is a largely-neglected area in the field of structural dynamics. However, this continues to be an important aspect of research as it is expected that the presence of piled foundations can have a significant influence on the propagation and transmission of the wavefield produced by the underground railway. This paper presents a comparison of two methods that can be employed in calculating the vibration response of a piled foundation: an efficient semi-analytical model, and a Boundary Element model. The semi-analytical model uses a column or an Euler beam to model the pile, and the soil is modelled as a linear, elastic continuum that has the geometry of a thick-walled cylinder with an infinite outer radius and an inner radius equal to the radius of the pile. The boundary element model uses a constant-element BEM formulation for the halfspace, and a rectangular discretisation of the circular pile-soil interface. The piles are modelled as Timoshenko beams. Pile-soil-pile interactions are inherently accounted for in the BEM equations, whereas in the semi-analytical model these are quantified using the superposition of interaction factors. Both models use the method of joining subsystems to incorporate the incident wavefield generated by the underground railway into the pile model. Results are computed for a single pile subject to an inertial loading, pile-soil-pile interactions, and a pile group subjected to excitation from an underground railway. The two models are compared in terms of accuracy, computation time, versatility and applicability, and guidelines for future vibration prediction models involving piled foundations are proposed.

The effect of floor heat source area on the induced airflow in a room

We examine the role of heat source geometry in determining rates of airflow and thermal stratification in natural displacement ventilation flows. We modify existing models to account for heat sources of finite (non-zero) area, such as formed by a sun patch warming the floor of a room. Our model allows for predictions of the steady stratification and ventilation flow rates that develop in a room due to a circular heat source at floor level. We compare our theoretical predictions with predictions for the limiting cases of a point source of heat (yielding a stratified interior), and a uniformly heated floor (yielding a mixed interior). Our theory shows a smooth transition between these two limits, which themselves result in extremes of ventilation, as the ratio of the heat source radius to the room height increases. Our model for the transition from displacement to mixing ventilation is compared to previous work and demonstrates that the transition can occur for smaller sources than previously thought, particularly for rooms with large floor area compared to ceiling height. © 2009 Elsevier Ltd.