Tuning the cavity of cyclodextrins: altered sugar adaptors in protein pores

Cyclodextrins (CDs) have been widely used in host-guest molecular recognition because of their chiral and hydrophobic cavities. For example, β-cyclodextrin (βCD) lodged as a molecular adaptor in protein pores such as α-hemolysin (αHL) is used for stochastic sensing. Here, we have tuned the cavity and overall size of βCD by replacing a single oxygen atom in its ring skeleton by a disulfide unit in two different configurations to both expand our ability to detect analytes and understand the interactions of βCD with protein pores. The three-dimensional structures of the two stereoisomeric CDs have been determined by the combined application of NMR spectroscopy and molecular simulation and show distorted conformations as compared to natural βCD. The interactions of these synthetic βCD analogues with mutant αHL protein pores and guest molecules were studied by single-channel electrical recording. The dissociation rate constants for both disulfide CDs from the mutant pores show ～1000-fold increase as compared to those of unaltered βCD, but are ～10-fold lower than the dissociation rate constants for βCD from wild-type αHL. Both of the skeleton-modified CDs show altered selectivity toward guest molecules. Our approach expands the breadth in sensitivity and diversity of sensing with protein pores and suggests structural parameters useful for CD design, particularly in the creation of asymmetric cavities.     

A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis

Microfluidic technology has been utilized in the development of a modular system for DNA identification through STR (short tandem repeat) analysis, reducing the total analysis time from the ∼6 h required with conventional approaches to less than 3 h. Results demonstrate the utilization of microfluidic devices for the purification, amplification, separation and detection of 9 loci associated with a commercially-available miniSTR amplification kit commonly used in the forensic community. First, DNA from buccal swabs purified in a microdevice was proven amplifiable for the 9 miniSTR loci via infrared (IR)-mediated PCR (polymerase chain reaction) on a microdevice. Microchip electrophoresis (ME) was then demonstrated as an effective method for the separation and detection of the chip-purified and chip-amplified DNA with results equivalent to those obtained using conventional separation methods on an ABI 310 Genetic Analyzer. The 3-chip system presented here demonstrates development of a modular, microfluidic system for STR analysis, allowing for user-discretion as to how to proceed after each process during the analysis of forensic casework samples.     

Accounting for threshold uncertainty in extreme value estimation

Tail data are often modelled by fitting a generalized Pareto distribution (GPD) to the exceedances over high thresholds. In practice, a threshold is fixed and a GPD is fitted to the data exceeding . A difficulty in this approach is the selection of the threshold above which the GPD assumption is appropriate. Moreover the estimates of the parameters of the GPD may depend significantly on the choice of the threshold selected. Sensitivity with respect to the threshold choice is normally studied but typically its effects on the properties of estimators are not accounted for. In this paper, to overcome the difficulties of the fixed-threshold approach, we propose to model extreme and non-extreme data with a distribution composed of a piecewise constant density from a low threshold up to an unknown end point and a GPD with threshold for the remaining tail part. Since we estimate the threshold together with the other parameters of the GPD we take naturally into account the threshold uncertainty. We will discuss this model from a Bayesian point of view and the method will be illustrated using simulated data and a real data set.     

The viscosity-capillarity criterion for shocks and phase transitions

This paper considers admissibility criteria for non-linear conservation laws based on (i) viscosity and (ii) capillarity and viscosity. It is shown by means of specific examples that while (ii) yields results consistent with experiment for materials exhibiting phase transitions,e.g. a van der Waals fluid, (i) does not.     

Molecular predissociation dynamics revealed through multiphoton ionisation spectroscopy. I. The C1B1 states of H2O and D2O

The $\text{C}$¹B₁ states of H₂O and D₂O have been observed by means of three photon absorption (four photon ionisation) spectroscopy. Differences between the experimentally observed 3 + 1 multiphoton ionisation spectrum and that predicted by the appropriate asymmetric-top three-photon line-strength theory are attributed to $\text{C}$ state predissociation. Two separate predissociation mechanisms have been identified, one (heterogeneous) relying on a-axis parent molecular rotation to couple the bound B₁ state to an unbound state of A₁ electronic symmetry, the other (homogeneous) involving a second, dissociative excited electronic state of B₁ symmetry. Having established the detailed $\text{C}$ state predissociation dynamics, two photon absorption spectra of H₂O and D₂O ($\text{C}$ ← $\text{X}$) can be predicted accurately: studies of individual quantum-state-selected photofragmentation processes from H₂O($\text{C}$) are proposed.     

Relation between torsional frequency and ionization potential of substituent atoms in 1-fluoro-2-haloethanes and allyl halides

The potential barrier to internal rotation of 1-fluoro-2-haloethanes and allyl halides is plotted against the ionization potential of substituend atoms.     

The rotational structure of three-photon resonances of polyatomic molecules

A general formulation of the selection rules and line strengths of three-photon excitation spectra is presented for molecules of arbitrary symmetry. For symmetric-top molecules the paper extends the discussion by Nieman in the context of rovibronic transitions of NH₃. For asymmetric-top molecules it is shown that the rotational line strengths can be sensitive to quantum-mechanical interference between contributions from the various components of the three-photon vibronic transition tensor. This transition tensor is discussed within a perturbation-theory framework in terms of several models of intermediate-state participation.     

Interactions between environmental pollution and cold tolerance of soil invertebrates: a neglected field of research

The adaptations to climatic stress of invertebrates have been extensively studied and the underlying physiology is relatively well understood. It is therefore possible to predict critical lower temperature and moisture limits at which a species will suffer increased mortality. Environmental pollution can reduce the tolerance to climatic stress considerably but it is not known how significant these synergistic effects are in polluted areas. Results are presented showing examples of synergism between toxic and climatic stress. The physiological mechanisms involved in the synergistic effects are discussed.     

Pim Kinase Inhibitors Evaluated with a Single‐Molecule Engineered Nanopore Sensor

Protein kinases are critical therapeutic targets. Pim kinases are implicated in several leukaemias and cancers. Here, we exploit a protein nanopore sensor for Pim kinases that bears a pseudosubstrate peptide attached by an enhanced engineering approach. Analyte binding to the sensor peptide is measured through observation of the modulation of ionic current through a single nanopore. We observed synergistic binding of MgATP and kinase to the sensor, which was used to develop a superior method to evaluate Pim kinase inhibitors featuring label‐free determination of inhibition constants. The procedure circumvents many sources of bias or false‐positives inherent in current assays. For example, we identified a potent inhibitor missed by differential scanning fluorimetry. The approach is also amenable to implementation on high throughput chips.