Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.

The integration host factor (IHF) is a prominent example of indirect readout as it imposes one of the strongest bends on relaxed linear DNA. However, the relation between IHF and torsionally constrained DNA, as occurs physiologically, remains unclear. By using atomistic molecular dynamics simulations on DNA minicircles, we reveal, for the first time, the reciprocal influence between a DNA-bending protein and supercoiling. On one hand, the increased curvature of supercoiled DNA enhances wrapping around IHF making the final complex topologically dependent. On the other hand, IHF acts as a 'supercoiling relief' factor by compacting relaxed DNA loops and, when supercoiled, it pins the position of plectonemes in a unique and specific manner. In addition, IHF restrains under- or overtwisted DNA depending on whether the complex is formed in negatively or positively supercoiled DNA, becoming effectively a 'supercoiling buffer'. We finally provide evidence of DNA bridging by IHF and reveal that these bridges divide DNA into independent topological domains. We anticipate that the crosstalk detected here between the 'active' DNA and the multifaceted IHF could be common to other DNA-protein complexes relying on the deformation of DNA.

Lowering the Sampling Rate: Heart Rate Response during Cognitive Fatigue.

Cognitive fatigue is a mental state characterised by feelings of tiredness and impaired cognitive functioning due to sustained cognitive demands. Frequency-domain heart rate variability (HRV) features have been found to vary as a function of cognitive fatigue. However, it has yet to be determined whether HRV features derived from electrocardiogram data with a low sampling rate would remain sensitive to cognitive fatigue. Bridging this research gap is important as it has substantial implications for designing more energy-efficient and less memory-hungry wearables to monitor cognitive fatigue. This study aimed to examine (1) the level of agreement between frequency-domain HRV features derived from lower and higher sampling rates, and (2) whether frequency-domain HRV features derived from lower sampling rates could predict cognitive fatigue. Participants (N = 53) were put through a cognitively fatiguing 2-back task for 20 min whilst their electrocardiograms were recorded. Results revealed that frequency-domain HRV features derived from sampling rate as low as 125 Hz remained almost perfectly in agreement with features derived from the original sampling rate at 2000 Hz. Furthermore, frequency domain features, such as normalised low-frequency power, normalised high-frequency power, and the ratio of low- to high-frequency power varied as a function of increasing cognitive fatigue during the task across all sampling rates. In conclusion, it appears that sampling at 125 Hz is more than adequate for frequency-domain feature extraction to index cognitive fatigue. These findings have significant implications for the design of low-cost wearables for detecting cognitive fatigue.

Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family.

Specific interactions between proteins and DNA are essential to many biological processes. Yet, it remains unclear how the diversification in DNA-binding specificity was brought about, and the mutational paths that led to changes in specificity are unknown. Using a pair of evolutionarily related DNA-binding proteins, each with a different DNA preference (ParB [Partitioning Protein B] and Noc [Nucleoid Occlusion Factor], which both play roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. Combining X-ray crystallography and deep mutational scanning of the interface, we suggest that permissive mutations must be introduced before specificity-switching mutations to reprogram specificity and that mutational paths to new specificity do not necessarily involve dual-specificity intermediates. Overall, our results provide insight into the possible evolutionary history of ParB and Noc and, in a broader context, might be useful for understanding the evolution of other classes of DNA-binding proteins.

Assessing the suitability of virtual reality for psychological testing.

Virtual reality (VR) is rapidly becoming an inexpensive, mainstream technology. VR technology is superambulatory as it allows participants to be examined under standardized environments and tests anywhere. In addition, it can test participants in different virtual spaces, including environments that are unsafe, inaccessible, costly or difficult to set up, or even nonexistent. We summarize the benefits and potential problems of VR technology, but we also move beyond theoretical approaches and present a customizable, open-source VR system (PSY-VR) that allows scalable psychological testing in modifiable VR environments. This system allows users to modify the environment using a simple graphical interface, without programming expertise. Moreover, as a proof-of-concept, we compare responses in a typical Flanker task between a real laboratory and a painstakingly matched virtual laboratory. Results indicate that the VR responses are comparable to real life testing, demonstrating the utility of VR for psychological assessment studies. The predicted rapid advancement of VR immersive technologies, as well the ease of their integration with physiological metrics ensures that VR-based assessment will be the modus operandi of psychological assessment in the future. This will allow controllable, low-cost assessment on a global scale. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

880 kHz ultrasound treatment for drug delivery to the vitreous humor.

Clinical management of many chronic ophthalmological disorders requires direct delivery of drugs into the vitreous. There is an important need to investigate novel needle-less alternatives to deliver drugs to the vitreous. The purpose of this study is to assess the effects of a needle-less system using ultrasound to enhance vitreal delivery of small molecules through the sclera in an ex vivo model and to evaluate whether changes in permeability are mainly due to the heat generated by sonication. An eye cup containing 1 mL of sodium fluorescein 0.1% was placed on top of the sclera of cadaveric rabbit eyes. Treated eyes were sonicated for 10 minutes, and left in contact with the fluorescein solution for an additional 50 minutes. Control eyes received the same exposure to fluorescein solution (60 minutes) in the eye cup without ultrasound treatment. Vitreous humor was collected and analyzed using a fluorescence spectrophotometer to calculate the concentration of fluorescein that diffused into the vitreous humor. An additional set of eyes was treated using a heating probe to evaluate whether changes in permeability were mainly due to heat. Vitreous samples from ultrasound-treated eyes showed a 44.6% higher concentration of fluorescein compared to control eyes. The concentration of fluorescein in the vitreous of heat-treated eyes did not show a significant difference when compared to control eyes. Thus, phonophoresis is a promising needle-less method for vitreal drug delivery, and local heating conducted to the surface of the sclera should be mitigated because it does not enhance the efficacy of the method.

In vivo and in vitro sustained release of ranibizumab from a nanoporous thin-film device.

Current administration of ranibizumab and other therapeutic macromolecules to the vitreous and retina carries ocular risks, a high patient treatment burden, and compliance barriers that can lead to suboptimal treatment. Here we introduce a device that produces sustained release of ranibizumab in the vitreous cavity over the course of several months. Composed of twin nanoporous polymer thin films surrounding a ranibizumab reservoir, these devices provide release of ranibizumab over 16 weeks in vitro and 12 weeks in vivo, without exhausting the initial drug payload. Following implantation in vivo, devices were well-tolerated and showed no sign of immune response. This platform presents a potential solution to the challenge of delivering protein therapeutics to the vitreous and retina for sustained periods of time.

Riboflavin and ultraviolet A as adjuvant treatment against Acanthamoeba cysts.

BACKGROUND: Experimental studies have shown that the standard dose of riboflavin (R) or R + ultraviolet-A (UVA) as solo treatment are not able to exterminate Acanthamoeba cysts or even trophozoites. The purpose of this study is to determine whether the application of R + UVA can enhance the cysticidal effects of cationic antiseptic agents in vitro. METHODS: The log of either polyhexamethylene biguanide or chlorhexidine minimal cysticidal concentration in solutions containing riboflavin (concentrations 0.1, 0.05 and 0.025%) plus either Acanthamoeba castellanii cysts or Acanthamoeba polyphaga cysts was determined and compared in groups treated with UVA 30 mW/cm(2) for 30 min and in control groups (with no exposure to UVA). A permutation test was used to determine the P value associated with treatment. RESULTS: Regardless of the riboflavin concentration and UVA treatment condition, no trophozoites were seen in plates where the cysts were previously exposed to cationic antiseptic agent concentrations ≥200 µg/mL for Acanthamoeba castellanii samples and ≥100 µg/mL for A. polyphaga samples. There was no statistical evidence that R + UVA treatment was associated with minimal cysticidal concentration (P = 0.82). CONCLUSION: R + UVA in doses up to 10 times higher than recommended for corneal crosslinking does not enhance the cysticidal effect of either polyhexamethylene biguanide or chlorhexidine in vitro.

Ultrasound-enhanced penetration of topical riboflavin into the corneal stroma.

PURPOSE: To determine whether ultrasound treatment can promote the permeation of topical riboflavin into the corneal stroma. METHODS: Fresh cadaveric rabbit eyes with intact epithelium were left for 45 minutes in riboflavin 0.1% solution and divided in the following groups: A--untreated, epithelium-on; B--ultrasound-treated (1 W/cm(2) at 880 kHz for 6 minutes) with epithelium-on; and C--epithelium-off (no ultrasound). Eyes were removed from the riboflavin solution, corneas were excised, and group B was divided into B1 (with epithelium maintained) and B2 (epithelium removed for the fluorescence analysis). Confocal microscopy was performed to quantify the fluorescence intensity in the cornea according to the distance from the surface (with epithelium in groups A and B1; without epithelium in groups B2 and C). RESULTS: The average fluorescence intensity of riboflavin at a depth of 100, 150, 200, and 250 µm was 69.97, 58.83, 49.23, and 41.72 arbitrary units (A.U.) in group A, respectively; 255.26, 206.01, 159.81, 124.20 A.U. in group B1; 218.90, 177.90, 141.43, 110.45 A.U. in group B2; and 677.64, 420.10, 250.72 and 145.07 A.U. in group C. The difference in fluorescence was statistically significant between groups A and B1 (P = 0.001) and groups B2 and C (P < 0.0001). CONCLUSIONS: Ultrasound treatment increased the entry of topical riboflavin into the corneal stroma despite the presence of a previously intact epithelial barrier. This approach may offer a means of achieving clinically useful concentrations of riboflavin within the cornea with minimum epithelial damage, thereby improving the risk profile of corneal cross-linking procedures.

Modularity and scaling in fast movements: power amplification in mantis shrimp.

Extremely fast animal actions are accomplished with mechanisms that reduce the duration of movement. This process is known as power amplification. Although many studies have examined the morphology and performance of power-amplified systems, little is known about their development and evolution. Here, we examine scaling and modularity in the powerful predatory appendages of a mantis shrimp, Gonodactylaceus falcatus (Crustacea, Stomatopoda). We propose that power-amplified systems can be divided into three units: an engine (e.g., muscle), an amplifier (e.g., spring), and a tool (e.g., hammer). We tested whether these units are developmentally independent using geometric morphometric techniques that quantitatively compare shapes. Additionally, we tested whether shape and several mechanical features are correlated with size and sex. We found that the morphological regions that represent the engine, amplifier, and tool belong to independent developmental modules. In both sexes, body size was positively correlated with the size of each region. Shape, however, changed allometrically with appendage size only in the amplifier (both sexes) and tool (males). These morphological changes were correlated with strike force and spring force (amplifier), but not spring stiffness (amplifier). Overall, the results indicate that each functional unit belongs to different developmental modules in a power-amplified system, potentially allowing independent evolution of the engine, amplifier, and tool.