Peptide transport in Bacillus subtilis - structure and specificity in the extracellular solute binding proteins OppA and DppE.

Peptide transporters play important nutritional and cell signalling roles in Bacillus subtilis, which are pronounced during stationary phase adaptations and development. Three high-affinity ATP-binding cassette (ABC) family transporters are involved in peptide uptake - the oligopeptide permease (Opp), another peptide permease (App) and a less well-characterized dipeptide permease (Dpp). Here we report crystal structures of the extracellular substrate binding proteins, OppA and DppE, which serve the Opp and Dpp systems, respectively. The structure of OppA was determined in complex with endogenous peptides, modelled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with K d values of 0.4 and 2 µM, respectively, as measured by isothermal titration calorimetry. Differential scanning fluorescence experiments with a wider panel of ligands showed that OppA has highest affinity for tetra- and penta-peptides. The structure of DppE revealed the unexpected presence of a murein tripeptide (MTP) ligand, l-Ala-d-Glu-meso-DAP, in the peptide binding groove. The mode of MTP binding in DppE is different to that observed in the murein peptide binding protein, MppA, from Escherichia coli, suggesting independent evolution of these proteins from an OppA-like precursor. The presence of MTP in DppE points to a role for Dpp in the uptake and recycling of cell wall peptides, a conclusion that is supported by analysis of the genomic context of dpp, which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in Firmicutes.

BOSC: a better oscillation detection method, extracts both sustained and transient rhythms from rat hippocampal recordings.

Neuronal population oscillations at a variety of frequencies can be readily seen in electroencephalographic (EEG) as well as local field potential recordings in many different species. Although these brain rhythms have been studied for many years, the methods for identifying discrete oscillatory epochs are still widely variable across studies. The "better oscillation detection" (BOSC) method applies standardized criteria to detect runs of "true" oscillatory activity and rejects transient events that do not reflect actual rhythms. It does so by estimating the background spectrum of the actual signal to derive detection criteria that include both power and duration thresholds. This method has not yet been applied to nonhuman data. Here, we test the BOSC method on two important rat hippocampal oscillatory signals, the theta rhythm and slow oscillation (SO), two large amplitude and mutually exclusive states. The BOSC method detected both the relatively sustained theta rhythm and the relatively transient SO apparent under urethane anesthesia and was relatively resilient to spectral features that changed across states, complementing previous findings for human EEG. Detection of oscillatory activity using the BOSC method (but not more traditional Fourier transform-based power analysis) corresponded well with human expert ratings. Moreover, for near-continuous theta, BOSC proved useful for detecting discrete disruptions that were associated with sudden and large amplitude phase shifts of the ongoing rhythm. Thus, the BOSC method accurately extracts oscillatory and nonoscillatory episodes from field potential recordings and produces systematic, objective, and consistent results-not only across frequencies, brain regions, tasks, and waking states, as shown previously, but also across species and for both sustained and transient rhythms. Thus, the BOSC method will facilitate more direct comparisons of oscillatory brain activity across all types of experimental paradigms.

A better oscillation detection method robustly extracts EEG rhythms across brain state changes: the human alpha rhythm as a test case.

Oscillatory activity is a principal mode of operation in the brain. Despite an intense resurgence of interest in the mechanisms and functions of brain rhythms, methods for the detection and analysis of oscillatory activity in neurophysiological recordings are still highly variable across studies. We recently proposed a method for detecting oscillatory activity from time series data, which we call the BOSC (Better OSCillation detection) method. This method produces systematic, objective, and consistent results across frequencies, brain regions and tasks. It does so by modeling the functional form of the background spectrum by fitting the empirically observed spectrum at the recording site. This minimizes bias in oscillation detection across frequency, region and task. Here we show that the method is also robust to dramatic changes in state that are known to influence the shape of the power spectrum, namely, the presence versus absence of the alpha rhythm, and can be applied to independent components, which are thought to reflect underlying sources, in addition to individual raw signals. This suggests that the BOSC method is an effective tool for measuring changes in rhythmic activity in the more common research scenario wherein state is unknown.

FG7142, yohimbine, and ßCCE produce anxiogenic-like effects in the elevated plus-maze but do not affect brainstem activated hippocampal theta.

The neurobiological underpinnings of anxiety are of paramount importance to selective and efficacious pharmaceutical intervention. Hippocampal theta frequency in urethane anaesthetized rats is suppressed by all known (and some previously unknown) anti-anxiety (anxiolytic) drugs. Although these findings support the predictive validity of this assay, its construct validity (i.e., whether theta frequency actually indexes anxiety per se) has not been a subject of systematic investigation. We reasoned that if anxiolytic drugs suppress hippocampal theta frequency, then drugs that increase anxiety (i.e., anxiogenic agents) should increase theta frequency, thus providing evidence of construct validity. We used three proven anxiogenic drugs--two benzodiazepine receptor inverse agonists, N-methyl-ß-carboline-3-carboxamide (FG7142) and ß-carboline-3-carboxylate ethyl ester (ßCCE), and one α2 noradrenergic receptor antagonist, 17α-hydroxy-yohimban-16α-carboxylic acid methyl ester (yohimbine) as pharmacological probes to assess the construct validity of the theta model. Although all three anxiogenic drugs significantly increased behavioural measures of anxiety in the elevated plus-maze, none of the three increased the frequency of hippocampal theta oscillations in the neurophysiological model. As a positive control, we demonstrated that diazepam, a proven anxiolytic drug, decreased the frequency of hippocampal theta, as in all other studies using this model. Given this discrepancy between the significant effects of anxiogenic drugs in the behavioural model and the null effects of these drugs in the neurophysiological model, we conclude that the construct validity of the hippocampal theta model of anxiety is questionable.