Construction and reconfiguration of dynamic DNA origami assemblies with coiled-coil patches and patterns

DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well-defined micron-scale structures through hierarchical self-assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structure and properties. Here we report the integration of DNA origami hinge nanodevices and coiled-coil peptides into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, we make multiple higher order assemblies by organizing clusters of peptides (i.e. patches) or arranging single peptides (i.e. patterns) on the surfaces of DNA origami to control the relative orientation of devices. We use coiled-coil interactions to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA-based actuation. Actuation of linear assemblies leads to micron scale motions and ~2.5-10-fold increase in bending stiffness. Our results provide a foundation for stimulus responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.

Using deep learning for pruning region detection and plant organ segmentation in dormant spur-pruned grapevines

Even though mechanization has dramatically decreased labor requirements, vineyard management costs are still affected by selective operations such as winter pruning. Robotic solutions are becoming more common in agriculture, however, few studies have focused on grapevines. This work aims at fine-tuning and testing two different deep neural networks for: (i) detecting pruning regions (PRs), and (ii) performing organ segmentation of spur-pruned dormant grapevines. The Faster R-CNN network was fine-tuned using 1215 RGB images collected in different vineyards and annotated through bounding boxes. The network was tested on 232 RGB images, PRs were categorized by wood type (W), orientation (Or) and visibility (V), and performance metrics were calculated. PR detection was dramatically affected by visibility. Highest detection was associated with visible intermediate complex spurs in Merlot (0.97), while most represented coplanar simple spurs allowed a 74% detection rate. The Mask R-CNN network was trained for grapevine organs (GOs) segmentation by using 119 RGB images annotated by distinguishing 5 classes (cordon, arm, spur, cane and node). The network was tested on 60 RGB images of light pruned (LP), shoot-thinned (ST) and unthinned control (C) grapevines. Nodes were the best segmented GOs (0.88) and general recall was higher for ST (0.85) compared to C (0.80) confirming the role of canopy management in improving performances of hi-tech solutions based on artificial intelligence. The two fine-tuned and tested networks are part of a larger control framework that is under development for autonomous winter pruning of grapevines.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11119-023-10006-y.

Physician and patient satisfaction with the switch to remote outpatient encounters in epilepsy clinics during the Covid-19 pandemic

PURPOSE

Analyzing parents' and physicians' opinions regarding phone-based encounters in emergency shifts of a French pediatric epilepsy center compared to traditional face-to-face encounters during the first lockdown of the COVID-19 pandemic METHODS: Prospective monocentric study on remote encounters at Necker rare epilepsy reference center from March 20th, 2020 to April 23rd, 2020 due to lockdown measures. This study was conducted with a survey based on 5-point Likert scales (LS_-2/2) designed for both parents and physicians. We compared first versus follow-up encounters as well as physicians' and parents' opinions.

RESULTS

We had a total of 224 responses, among which 204 were completed by physicians (91%) and 173 (84,4%) by parents. Twenty five were first encounters (14,2%). Physicians pointed out the need for clinical examination (42.6%), mainly for first encounters (p=0.0004). Physicians rated the quality of communication lower (p=0.003) as their capacity to answer parents' questions (p=0.004). They were significantly less satisfied with remote encounters compared to parents (p<10^-4). We identified six urgent (2.9%) and 50 semi-urgent (24%) situations requiring programming face-to-face encounter during or shortly after the lockdown.

CONCLUSION

Remote encounters could be a helpful practice for pediatric patients with epilepsy in emergency situations such as pandemics. It allowed the identification and prioritization of emergency situations. Physicians were less positive than parents. We raised the possible use of remote encounters in association to face-to-face encounters for routine follow-up of pediatric patients with epilepsy.

Silk Film Stiffness Modulates Corneal Epithelial Cell Mechanosignaling

Silk fibroin films are excellent candidate biomaterials for corneal tissue engineering due to their optical transparency, biocompatibility, and mechanical strength. Their tunable chemical and mechanical properties open the possibility of engineering cellular microenvironments that can both mimic native corneal tissue and provide stimuli to actively promote wound regeneration. While silk film mechanical properties, such as surface topography, have demonstrated the ability to control corneal epithelial cell wound regenerating behavior, few studies have explored the stiffness tunability of these films and its cellular effects. Cells are known actively sense the stiffness of their surroundings and processes such as cell adhesion, migration, proliferation, and expression of stem markers can be strongly influenced by matrix stiffness. This study develops technical solutions that allow for both the fabrication of films with stiffnesses similar to corneal tissue and also for their characterization in an aqueous, native-like environment at a scale relevant to cellular forces. Physiological evidence demonstrates that corneal epithelial cells are mechanosensitive to films of different stiffnesses and show that cell spreading, cytoskeletal tension, and molecular mechanotransducer localization are associated with film stiffness. These results indicate that silk film stiffness can be used to regulate cell behavior for the purposes of ocular surface repair.

The role of protein restriction and interaction with antibiotics in the regulation of compensatory growth in pigs: growth performance, serum hormone concentrations, and messenger RNA levels in component tissues of the endocrine growth axis

The present study investigated the effects of protein restriction and antibiotics on the hypothalamus-pituitary-liver growth axis during the compensatory growth of growing and finishing pigs. Growth performance, serum hormones, and messenger RNA (mRNA) levels of hormones and their receptors in growth axis tissues were recorded for analyses. A total of 64 piglets (large white × Landrace × Duroc cross) with an initial weight of 10.07 ± 0.14 kg were randomly divided into 4 treatment groups of 16 piglets per group. The dietary treatments consisted of 2 protein levels (14% and 20%) and 2 antibiotic levels (no antibiotics and 20 mg/kg colistin sulfate with 50 mg/kg kitasamycin) in a 2 × 2 factorial arrangement. The study was performed over 30 d for the first stage (S1, restriction phase) and 74 d for the second stage (S2, realimentation phase). The 4 treatment diets were maintained throughout the duration in the restriction phase. The 4 groups were fed the same diet in the realimentation phase. The trial period totaled 104 d. Protein restriction decreased BW, average daily food intake, and ADG in weaning pigs (P < 0.01) and induced compensatory growth after feeding a normal diet during the growth of finishing pigs. Average daily gain increased during the last phase of compensatory growth (P < 0.01). Protein restriction increased serum GH and leptin (LEP) and the mRNA levels of liver IGF-1 receptor (IGF-1-R; P < 0.01) but decreased serum IGF-1 (P < 0.01) and the mRNA levels of liver GH receptor (GH-R; P < 0.01) and IGF-1 (P < 0.05) in weaning piglets. Serum GH was increased, but serum IGF-1 was decreased during the realimentation phase (P < 0.05). Antibiotics increased the mRNA levels of GHRH (P < 0.05) and decreased somatostatin (P < 0.01) in the hypothalamus of weaning pigs. Protein restriction and antibiotics had no interactions across the entire trial. In conclusion, the slowing of growth caused by early protein restriction may be compensated for in the later stages of pig raising, and the mechanism of compensation is related to the regulation of GH, IGF-1, GH-R, and IGF-1-R.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

Scientific Approaches to AIDS Prevention and Control in China

The HIV epidemic in China started among intravenous drug users in the late 1980s. The second wave of the epidemic was caused by an outbreak in the paid plasma donors in central China in the mid-1990s. Sexually transmitted HIV cases have steadily increased and comprised more than half the reported HIV/AIDS infections since 2007. In the last 5 years, there has been a sharp increase of HIV infection in men who have sex with men. The HIV epidemic in China has expanded from high-risk groups to the general population and from rural regions to urban areas. This brief article discusses the history of HIV epidemics in China and the challenges facing the current AIDS control efforts in the country. It explains that only scientific approaches can sustain the national AIDS control programs and introduce the type of research needed to address those challenges. The selected research areas include molecular epidemiology, drug resistance surveillance, and the Chinese HIV vaccine research.

Progress towards automated diabetic ocular screening: a review of image analysis and intelligent systems for diabetic retinopathy

Patients with diabetes require annual screening for effective timing of sight-saving treatment. However, the lack of screening and the shortage of ophthalmologists limit the ocular health care available. This is stimulating research into automated analysis of the reflectance images of the ocular fundus. Publications applicable to the automated screening of diabetic retinopathy are summarised. The review has been structured to mimic some of the processes that an ophthalmologist performs when examining the retina. Thus image processing tasks, such as vessel and lesion location, are reviewed before any intelligent or automated systems. Most research has been undertaken in identification of the retinal vasculature and analysis of early pathological changes. Progress has been made in the identification of the retinal vasculature and the more common pathological features, such as small aneurysms and exudates. Ancillary research into image preprocessing has also been identified. In summary, the advent of digital data sets has made image analysis more accessible, although questions regarding the assessment of individual algorithms and whole systems are only just being addressed.

Energy transduction on the nanosecond time scale: early structural events in a xanthopsin photocycle

Photoactive yellow protein (PYP) is a member of the xanthopsin family of eubacterial blue-light photoreceptors. On absorption of light, PYP enters a photocycle that ultimately transduces the energy contained in a light signal into an altered biological response. Nanosecond time-resolved x-ray crystallography was used to determine the structure of the short-lived, red-shifted, intermediate state denoted [pR], which develops within 1 nanosecond after photoelectronic excitation of the chromophore of PYP by absorption of light. The resulting structural model demonstrates that the [pR] state possesses the cis conformation of the 4-hydroxyl cinnamic thioester chromophore, and that the process of trans to cis isomerization is accompanied by the specific formation of new hydrogen bonds that replace those broken upon excitation of the chromophore. Regions of flexibility that compose the chromophore-binding pocket serve to lower the activation energy barrier between the dark state, denoted pG, and [pR], and help initiate entrance into the photocycle. Direct structural evidence is provided for the initial processes of transduction of light energy, which ultimately translate into a physiological signal.

Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography

The biological activity of macromolecules is accompanied by rapid structural changes. The photosensitivity of the carbon monoxide complex of myoglobin was used at the European Synchrotron Radiation Facility to obtain pulsed, Laue x-ray diffraction data with nanosecond time resolution during the process of heme and protein relaxation after carbon monoxide photodissociation and during rebinding. These time-resolved experiments reveal the structures of myoglobin photoproducts, provide a structural foundation to spectroscopic results and molecular dynamics calculations, and demonstrate that time-resolved macromolecular crystallography can elucidate the structural bases of biochemical mechanisms on the nanosecond time scale.

Sedimentation behavior of native and reduced apolipoprotein A-II from human high density lipoproteins

The solution properties of human serum apolipoprotein A-II, both in the native and in the reduced forms, were investigated by the technique of sedimentation equilibrium in the analytical ultracentrifuge. For both proteins, the apparent weight average molecular weights determined in neutral buffer systems were found to be dependent on protein concentration and invariant with the rotor speeds used (16,000 to 44,000 rpm) indicating a reversible self-association. These results were also found to be independent of temperature between 5 and 30 degrees C. The pattern of self-association of native apolipoprotein A-II could best be described by a monomer-dimer-trimer equilibrium, in agreement with previously reported data (Vitello, L B., and Scanu, A. M. (1975), Biochemistry 15, 1161). The self-association pattern of apolipoprotein A-II reduced in the presence of 50 mM dithiothreitol conformed with a monomer-dimer-tetramer equilibrium similar to that reported for the native single chain apolipoprotein A-II of the rhesus monkey (Barbeau, D. L., et al. (1977), J. Biol. Chem. 252, 6745), but differing significantly from that reported for the reduced and carboxymethylated human product (Osborne, J. C. , et al. (1975), Biochemistry 14, 3741).