Short-time AOIs-based representative scanpath identification and scanpath aggregation.

A new algorithm to identify a representative scanpath in a sample is presented and evaluated with eye-tracking data. According to Gestalt theory, each fixation of the scanpath should be on an area of interest (AOI) of the stimuli. As with existing methods, we first identify the AOIs and then extract the fixations of the representative scanpath from the AOIs. In contrast to existing methods, we propose a new concept of short-time AOI and extract the fixations of representative scanpath from the short-time AOIs. Our method outperforms the existing methods on two publicly available datasets. Our method can be applied to arbitrary visual stimuli, including static stimuli without natural segmentation, as well as dynamic stimuli. Our method also provides a solution for issues caused by the selection of scanpath similarity.

Statistical modeling of dynamic eye-tracking experiments: Relative importance of visual stimulus elements for gaze behavior in the multi-group case.

This paper presents a model that allows group comparisons of gaze behavior while watching dynamic video stimuli. The model is based on the approach of Coutrot and Guyader (2017) and allows linear combinations of feature maps to form a master saliency map. The feature maps in the model are, for example, the dynamically salient contents of a video stimulus or predetermined areas of interest. The model takes into account temporal aspects of the stimuli, which is a crucial difference to other common models. The multi-group extension of the model introduced here allows to obtain relative importance plots, which visualize the effect of a specific feature of a stimulus on the attention and visual behavior for two or more experimental groups. These plots are interpretable summaries of data with high spatial and temporal resolution. This approach differs from many common methods for comparing gaze behavior between natural groups, which usually only include single-dimensional features such as the duration of fixation on a particular part of the stimulus. The method is illustrated by contrasting a sample of a group of persons with particularly high cognitive abilities (high achievement on IQ tests) with a control group on a psycholinguistic task on the conceptualization of motion events. In the example, we find no substantive differences in relative importance, but more exploratory gaze behavior in the highly gifted group. The code, videos, and eye-tracking data we used for this study are available online.

Structure-based engineering of a minimal porin reveals loop-independent channel closure.

Porins, like outer membrane protein G (OmpG) of Escherichia coli, are ideal templates among ion channels for protein and chemical engineering because of their robustness and simple architecture. OmpG shows fast transitions between open and closed states, which were attributed to loop 6 (L6). As flickering limits single-channel-based applications, we pruned L6 by either 8 or 12 amino acids. While the open probabilities of both L6 variants resemble that of native OmpG, their gating frequencies were reduced by 63 and 81%, respectively. Using the 3.2 Å structure of the shorter L6 variant in the open state, we engineered a minimal porin (220 amino acids), where all remaining extramembranous loops were truncated. Unexpectedly, this minimized porin still exhibited gating, but it was 5-fold less frequent than in OmpG. The residual gating of the minimal pore is hence independent of L6 rearrangements and involves narrowing of the ion conductance pathway most probably driven by global stretching-flexing deformations of the membrane-embedded ß-barrel.

Voltage-dependent anion channels: the wizard of the mitochondrial outer membrane.

Voltage dependent anion channels (VDACs) are the most abundant proteins in the outer mitochondrial membrane. Although they are essential in metabolite exchange, cell defense and apoptosis, the molecular mechanism of these VDAC-mediated processes remains elusive. Here we review recent progress in terms of VDACs' structure and regulation, with a special focus on the molecular aspects of gating and the interaction with effector proteins.

Discovery of Novel UDP-N-Acetylglucosamine Acyltransferase (LpxA) Inhibitors with Activity against Pseudomonas aeruginosa.

This study describes a novel series of UDP-N-acetylglucosamine acyltransferase (LpxA) inhibitors that was identified through affinity-mediated selection from a DNA-encoded compound library. The original hit was a selective inhibitor of Pseudomonas aeruginosa LpxA with no activity against Escherichia coli LpxA. The biochemical potency of the series was optimized through an X-ray crystallography-supported medicinal chemistry program, resulting in compounds with nanomolar activity against P. aeruginosa LpxA (best half-maximal inhibitory concentration (IC50) <5 nM) and cellular activity against P. aeruginosa (best minimal inhibitory concentration (MIC) of 4 µg/mL). Lack of activity against E. coli was maintained (IC50 > 20 µM and MIC > 128 µg/mL). The mode of action of analogues was confirmed through genetic analyses. As expected, compounds were active against multidrug-resistant isolates. Further optimization of pharmacokinetics is needed before efficacy studies in mouse infection models can be attempted. To our knowledge, this is the first reported LpxA inhibitor series with selective activity against P. aeruginosa.

Ribo-attenuators: novel elements for reliable and modular riboswitch engineering.

Riboswitches are structural genetic regulatory elements that directly couple the sensing of small molecules to gene expression. They have considerable potential for applications throughout synthetic biology and bio-manufacturing as they are able to sense a wide range of small molecules and regulate gene expression in response. Despite over a decade of research they have yet to reach this considerable potential as they cannot yet be treated as modular components. This is due to several limitations including sensitivity to changes in genetic context, low tunability, and variability in performance. To overcome the associated difficulties with riboswitches, we have designed and introduced a novel genetic element called a ribo-attenuator in Bacteria. This genetic element allows for predictable tuning, insulation from contextual changes, and a reduction in expression variation. Ribo-attenuators allow riboswitches to be treated as truly modular and tunable components, thus increasing their reliability for a wide range of applications.

Flexibility of the N-terminal mVDAC1 segment controls the channel's gating behavior.

Since the solution of the molecular structures of members of the voltage dependent anion channels (VDACs), the N-terminal α-helix has been the main focus of attention, since its strategic location, in combination with its putative conformational flexibility, could define or control the channel's gating characteristics. Through engineering of two double-cysteine mVDAC1 variants we achieved fixing of the N-terminal segment at the bottom and midpoint of the pore. Whilst cross-linking at the midpoint resulted in the channel remaining constitutively open, cross-linking at the base resulted in an "asymmetric" gating behavior, with closure only at one electric field's orientation depending on the channel's orientation in the lipid bilayer. Additionally, and while the native channel adopts several well-defined closed states (S1 and S2), the cross-linked variants showed upon closure a clear preference for the S2 state. With native-channel characteristics restored following reduction of the cysteines, it is evident that the conformational flexibility of the N-terminal segment plays indeed a major part in the control of the channel's gating behavior.