Molecular Modeling of Self-Assembling Peptides.

Peptide epitopes mediate as many as 40% of protein-protein interactions and fulfill signaling, inhibition, and activation roles within the cell. Beyond protein recognition, some peptides can self- or coassemble into stable hydrogels, making them a readily available source of biomaterials. While these 3D assemblies are routinely characterized at the fiber level, there are missing atomistic details about the assembly scaffold. Such atomistic detail can be useful in the rational design of more stable scaffold structures and with improved accessibility to functional motifs. Computational approaches can in principle reduce the experimental cost of such an endeavor by predicting the assembly scaffold and identifying novel sequences that adopt said structure. Yet, inaccuracies in physical models and inefficient sampling have limited atomistic studies to short (two or three amino acid) peptides. Given recent developments in machine learning and advances in sampling strategies, we revisit the suitability of physical models for this task. We use the MELD (Modeling Employing Limited Data) approach to drive self-assembly in combination with generic data in cases where conventional MD is unsuccessful. Finally, despite recent developments in machine learning algorithms for protein structure and sequence predictions, we find the algorithms are not yet suited for studying the assembly of short peptides.

Collective Behavior of Urease pH Clocks in Nano- and Microvesicles Controlled by Fast Ammonia Transport.

The transmission of chemical signals via an extracellular solution plays a vital role in collective behavior in cellular biological systems and may be exploited in applications of lipid vesicles such as drug delivery. Here, we investigated chemical communication in synthetic micro- and nanovesicles containing urease in a solution of urea and acid. We combined experiments with simulations to demonstrate that the fast transport of ammonia to the external solution governs the pH-time profile and synchronizes the timing of the pH clock reaction in a heterogeneous population of vesicles. This study shows how the rate of production and emission of a small basic product controls pH changes in active vesicles with a distribution of sizes and enzyme amounts, which may be useful in bioreactor or healthcare applications.

Towards feedback-controlled nanomedicines for smart, adaptive delivery.

IMPACT STATEMENT: The timing and rate of release of pharmaceuticals from advanced drug delivery systems is an important property that has received considerable attention in the scientific literature. Broadly, these mostly fall into two classes: controlled release with a prolonged release rate or triggered release where the drug is rapidly released in response to an environmental stimulus. This review aims to highlight the potential for developing adaptive release systems that more subtlety modulate the drug release profile through continuous communication with its environment facilitated through feedback control. By reviewing the key elements of this approach in one place (fundamental principles of nanomedicine, enzymatic nanoreactors for medical therapies and feedback-controlled chemical systems) and providing additional motivating case studies in the context of chronobiology, we hope to inspire innovative development of novel "chrononanomedicines."

Scanning laser polarimetry quantification of retinal nerve fiber layer thinning following optic neuritis.

BACKGROUND: Several studies with optical coherence tomography (OCT) have demonstrated thinning of the retinal nerve fiber layer (RNFL) in patients with optic neuritis and multiple sclerosis. Similar studies have not been performed with scanning laser polarimetry (SLP), which relies on different physical phenomena. This study was designed to use SLP to measure axonal loss following a single episode of optic neuritis and to determine if there is a relationship between the degree of axonal loss and the degree of residual visual dysfunction. METHODS: Twenty-five patients with a single episode of optic neuritis and 15 control subjects were studied with SLP using the GDxVCC device to determine RNFL thickness in relation to visual acuity, visual fields, color vision, visual evoked potentials (VEPs), and previously published OCT data. RESULTS: SLP detected significant RNFL thinning in affected eyes compared to clinically unaffected fellow eyes in patients and in control eyes (P < 0.001). Reduced RNFL thickness was associated with significantly worse logMAR visual acuity, visual field mean deviation, and color vision. RNFL thinning correlated with reduced whole visual field and central visual field measures and VEP amplitudes. Superior and inferior quadrant RNFL thinning was related to corresponding regional visual field loss. There was a scaling factor between SLP and OCT RNFL measurements but only modest agreement. CONCLUSIONS: SLP detected functionally relevant axonal loss in eyes affected by optic neuritis. There was a scaling factor between RNFL measurements obtained with SLP and OCT but only modest agreement. Care should therefore be taken when comparing RNFL data from studies using these different devices.

Optic nerve atrophy and retinal nerve fibre layer thinning following optic neuritis: evidence that axonal loss is a substrate of MRI-detected atrophy.

Magnetic resonance imaging (MRI) measures of brain atrophy are often considered to be a marker of axonal loss in multiple sclerosis (MS) but evidence is limited. Optic neuritis is a common manifestation of MS and results in optic nerve atrophy. Retinal nerve fibre layer (RNFL) imaging is a non-invasive way of detecting axonal loss following optic neuritis. We hypothesise that if the optic nerve atrophy that develops following optic neuritis is contributed to by axonal loss, it will correlate with thinning of the RNFL. Twenty-five patients were studied at least 1 year after a single unilateral attack of optic neuritis without recurrence, with a selection bias towards incomplete recovery. They had MR quantification of optic nerve cross-sectional area and optic nerve lesion length, as well as optical coherence tomography (OCT) measurement of mean RNFL thickness and macular volume, quantitative visual testing, and visual evoked potentials (VEPs). Fifteen controls were also studied. Significant optic nerve atrophy (mean decrease 30% versus controls), RNFL thinning (mean decrease 33% versus controls), and macular volume loss occurred in patients' affected eyes when compared with patients' unaffected eyes and healthy controls. The optic nerve atrophy was correlated with the RNFL thinning, macular volume loss, visual acuity, visual field mean deviation, and whole field VEP amplitude but not latency. These findings suggest that axonal loss contributes to optic nerve atrophy following a single attack of optic neuritis. By inference, axonal loss due to other post-inflammatory brain lesions is likely to contribute to the global MRI measure of brain atrophy in multiple sclerosis.

Optic nerve diffusion tensor imaging in optic neuritis.

Diffusion tensor magnetic resonance imaging (DT-MRI) provides in vivo information about the pathology of multiple sclerosis lesions. Increases in mean diffusivity (MD) and reductions in fractional anisotropy (FA) have been found and may represent axonal disruption. The optic nerve is an ideal structure for study by DT-MRI but previous clinical studies did not obtain the full diffusion tensor necessary to calculate MD and FA. In this study, a technique that was specifically developed to achieve full diffusion tensor measurements from the optic nerve (zonal oblique multislice (ZOOM) echoplanar imaging) was applied to 25 patients with a single unilateral episode of optic neuritis at least one year previously, and 15 controls. The intraorbital nerves were segmented on non-diffusion-weighted images and the regions of interest transferred to MD, FA, and eigenvalue maps to obtain quantitative data. Quantitative visual testing and electrophysiology were also performed. In affected nerves, mean MD and mean orthogonal eigenvalue lambda( perpendicular) were elevated, and mean FA reduced compared with clinically unaffected contralateral nerves (P < 0.001) and control nerves (P < 0.001). The mean principal eigenvalue lambda\\ was significantly increased in affected nerves compared to contralateral unaffected nerves (P = 0.04) but not compared to control nerves (P = 0.13). There was no association of clinical measures of visual function in affected eyes with the DT-MRI parameters but there was a significant correlation of the whole field visual evoked potential (VEP) amplitude with MD (r = -0.57, P = 0.006) and lambda( perpendicular) (r = -0.56, P = 0.007). These findings suggest that optic nerve DT-MRI measures provide an indication of the structural integrity of axons.

Retinal nerve fiber layer axonal loss and visual dysfunction in optic neuritis.

Axonal loss is thought to be a likely cause of persistent disability after a multiple sclerosis relapse; therefore, noninvasive in vivo markers specific for axonal loss are needed. We used optic neuritis as a model of multiple sclerosis relapse to quantify axonal loss of the retinal nerve fiber layer (RNFL) and secondary retinal ganglion cell loss in the macula with optical coherence tomography. We studied 25 patients who had a previous single episode of optic neuritis with a recruitment bias to those with incomplete recovery and 15 control subjects. Optical coherence tomography measurement of RNFL thickness and macular volume, quantitative visual testing, and electrophysiological examination were performed. There were highly significant reductions (p < 0.001) of RNFL thickness and macular volume in affected patient eyes compared with control eyes and clinically unaffected fellow eyes. There were significant relationships among RNFL thickness and visual acuity, visual field, color vision, and visual-evoked potential amplitude. This study has demonstrated functionally relevant changes indicative of axonal loss and retinal ganglion cell loss in the RNFL and macula, respectively, after optic neuritis. This noninvasive RNFL imaging technique could be used in trials of experimental treatments that aim to protect optic nerves from axonal loss.

Optic nerve diffusion measurement from diffusion-weighted imaging in optic neuritis.

BACKGROUND AND PURPOSE: Increases in apparent diffusion coefficient (ADC) from diffusion-weighted (DW) imaging are thought to be due to axonal disruption, and changes have been well documented in multiple sclerosis lesions. DW imaging of the optic nerves, however, presents many challenges. The goal of this study was to measure ADC in patients with optic neuritis by using zonal oblique multisection echoplanar imaging. METHODS: The optic nerves of eighteen patients who had experienced an attack of optic neuritis 1 year previously and 11 control subjects were imaged with the diffusion sequence (usable data were available from 16 patients and 10 control subjects). The orbital optic nerves were segmented by a blinded observer by using a computer-assisted threshold-based contouring technique, and the mean ADC was determined. RESULTS: The mean ADC from diseased optic nerves was 1324 x 10(-6) mm2/s, compared with 990 x 10(-6) mm2/s from healthy contralateral optic nerves (P = .005 versus diseased optic nerves) and 928 x 10(-6) mm2/s from control optic nerves (P = .006 versus diseased optic nerves and P = .40 versus healthy contralateral optic nerves). The diseased optic nerve ADC correlated with both visual (e.g., r(S) = 0.73; P = .001 for logMAR visual acuity) and electrophysiological parameters (e.g., r(S) = -0.57, P = .021 for visual evoked potential central field amplitude [VEP]). CONCLUSION: It has been possible to apply DW imaging in a patient population, and, in the chronic phase following optic neuritis, the correlation of mean ADC with the clinical and electrophysiological parameters suggests that the ADC is giving a surrogate measure of axonal disruption in the chronic, postinflammatory optic nerve lesion.

Adaptive cortical plasticity in higher visual areas after acute optic neuritis.

The ability to distinguish adaptive cortical reorganization may help to target future therapeutic strategies after neurological insult. We investigated cortical plasticity by prospectively applying visual functional magnetic resonance imaging (fMRI) and optic nerve MRI to 20 patients with acute optic neuritis at baseline, 1, 3, 6, and 12 months. We performed three types of correlation analyses to investigate the relationships between fMRI activity, clinical function, and optic nerve structure. The first analysis directly correlated the fMRI response to clinical function or optic nerve structure and found dynamic relations especially within the first 3 months. The second analysis used a novel technique that modeled the fMRI response and optic nerve structure together with clinical function, to determine the contribution fMRI made to clinical function after accounting for structural factors. Significant effects were found at baseline only, within the right peristriate cortex, and bilaterally in the lateral occipital complexes, which are normally involved in higher order visual processing. The third analysis investigated the relation between the modeled visual recovery rate and fMRI response but found no significant effects. The key findings of this study are from the second analysis and suggest a genuine adaptive role for cortical reorganization within extrastriate visual areas early after optic neuritis.

A serial MRI study following optic nerve mean area in acute optic neuritis.

This study assessed optic nerve mean area on serial MRI in a cohort of patients with a first episode of acute unilateral optic neuritis to assess the effects of a single acute inflammatory demyelinating lesion. Twenty-nine patients with a median delay from onset of visual symptoms of 13 days (range 7-24 days) were recruited. After a clinical examination and visual evoked potential (VEP) measurement, each patient had their optic nerves imaged with a coronal fat-saturated short echo fast fluid-attenuated inversion recovery sequence. Twenty-one patients had serial examinations after 2, 4, 8, 12, 26 and 52 weeks. In addition, 32 control subjects had their optic nerves imaged up to three times. The mean cross-sectional area of the intra-orbital portion of each optic nerve was calculated by a blinded observer using a computer-assisted contouring technique. At baseline, the mean area of diseased optic nerves was 16.1 mm2 compared with 13.4 mm2 for healthy contralateral optic nerves (20.1% higher, P < 0.0001) and 13.6 mm2 for controls (18.4% higher, P = 0.0003). The diseased optic nerve mean area declined over time, from initial swelling to later atrophy. The mean decline at 52 weeks was -0.0018 mm2/day (95% confidence interval -0.0038 to -0.00051). At 52 weeks, the mean area of diseased optic nerves was 11.3 mm2 compared with 12.8 mm2 for healthy contralateral optic nerves (11.7% lower, P = 0.032) and 13.1 mm2 for controls (13.7% lower, P = 0.008). The 52 week diseased optic nerve mean area was not significantly affected by the baseline mean area. There was an association between baseline optic nerve mean area and logMAR visual acuity (rS = 0.46, P = 0.012) and visual field mean deviation (rS = -0.55, P = 0.002), but there was no evidence of an association between 1 year mean area and visual outcome. There was no evidence of association between baseline, rates of decline or 1 year diseased optic nerve mean areas and any of the baseline, 1 year or time-averaged VEP variables. The present study shows a consistent pattern of changes associated with individual inflammatory demyelinating lesions in the optic nerve. Acutely, there was swelling, consistent with the presence of acute inflammation, which was related to visual impairment. Over the longer term, there was loss of tissue. The lack of association between 1 year optic nerve mean area and visual outcome may reflect a mild loss of tissue, redundancy or remodelling of function.

Visual recovery following acute optic neuritis--a clinical, electrophysiological and magnetic resonance imaging study.

This study reports the prospective follow-up of a cohort of patients with acute optic neuritis examined with serial visual tests, visual evoked potentials (VEPs), conventional and triple-dose gadolinium (Gd)-enhanced magnetic resonance imaging (MRI) to examine which factors are important in visual recovery. Thirty-three patients were recruited with acute unilateral optic neuritis. A clinical and VEP assessment was performed on each. Optic nerve MRI was performed using fast spin echo (FSE) (on all) and triple-dose Gd-enhanced T1-weighted sequences (n = 28). Optic nerve lesion lengths were measured. Serial assessments were performed on 22 of the patients up to one-year. Serial Gd-enhanced optic nerve imaging was performed on 15 of the patients until enhancement ceased. The final 30-2 Humphrey visual field mean deviation (MD) was 2.55 dB higher in patients in the lowest quartile of initial Gd-enhanced lesion length compared with the other quartiles (p < 0.01) but recovery was not related to the duration of enhancement. The initial recovery of Humphrey MD was 4.60 dB units per day in patients with good eventual recoveries (MD > -6.0 dB) and 0.99 dB per day in poor-recovery patients (p = 0.02).Good-recovery patients had mean central field VEP amplitudes 2.29 microV higher during recovery than poor-recovery patients (p = 0.047). The results suggest that factors which are associated with a better prognosis are: having a short acute lesion on triple-dose gadolinium enhanced imaging, higher VEP amplitudes during recovery and a steep gradient of the initial improvement in vision.