Advances in Nanomaterials for Brain Microscopy

Supervised learning model predicts protein adsorption to carbon nanotubes

Engineered nanoparticles are advantageous for biotechnology applications including biomolecular sensing and delivery. However, testing compatibility and function of nanotechnologies in biological systems requires a heuristic approach, where unpredictable protein corona formation prevents their effective implementation. We develop a random forest classifier trained with mass spectrometry data to identify proteins that adsorb to nanoparticles based solely on the protein sequence (78% accuracy, 70% precision). We model proteins that populate the corona of a single-walled carbon nanotube (SWCNT)–based nanosensor and study the relationship between the protein’s amino acid–based properties and binding capacity. Protein features associated with increased likelihood of SWCNT binding include high content of solvent-exposed glycines and nonsecondary structure–associated amino acids. To evaluate its predictive power, we apply the classifier to identify proteins with high binding affinity to SWCNTs, with experimental validation. The developed classifier provides a step toward undertaking the otherwise intractable problem of predicting protein-nanoparticle interactions.

Supervised learning model predicts protein adsorption to carbon nanotubes

Engineered nanoparticles are advantageous for biotechnology applications including biomolecular sensing and delivery. However, testing compatibility and function of nanotechnologies in biological systems requires a heuristic approach, where unpredictable protein corona formation prevents their effective implementation. We develop a random forest classifier trained with mass spectrometry data to identify proteins that adsorb to nanoparticles based solely on the protein sequence (78% accuracy, 70% precision). We model proteins that populate the corona of a single-walled carbon nanotube (SWCNT)–based nanosensor and study the relationship between the protein’s amino acid–based properties and binding capacity. Protein features associated with increased likelihood of SWCNT binding include high content of solvent-exposed glycines and nonsecondary structure–associated amino acids. To evaluate its predictive power, we apply the classifier to identify proteins with high binding affinity to SWCNTs, with experimental validation. The developed classifier provides a step toward undertaking the otherwise intractable problem of predicting protein-nanoparticle interactions.

Near-infrared nanoscopy with carbon-based nanoparticles for the exploration of the brain extracellular space

Understanding the physiology and pathology of the brain requires detailed knowledge of its complex structures as well as dynamic internal processes at very different scales from the macro down to the molecular dimensions. A major yet poorly described brain compartment is the brain extracellular space (ECS). Signalling molecules rapidly diffuse through the brain ECS which is complex and dynamic structure at numerous lengths and time scales. In recent years, characterization of the ECS using nanomaterials has made remarkable progress, including local analysis of nanoscopic dimensions and diffusivity as well as local chemical sensing. In particular, carbon nanomaterials combined with advanced optical technologies, biochemical and biophysical analysis, offer novel promises for understanding the ECS morphology as well as neuron connectivity and neurochemistry. In this review, we present the state-of-the-art in this quest, which mainly focuses on a type of carbon nanomaterial, single walled carbon nanotubes, as fluorescent nanoprobes to unveil the ECS features in the nanometre domain.

Ground-State Depletion Nanoscopy of Nitrogen-Vacancy Centres in Nanodiamonds

The negatively charged nitrogen-vacancy ([Formula: see text]) centre in nanodiamonds (NDs) has been recently studied for applications in cellular imaging due to its better photo-stability and biocompatibility if compared to other fluorophores. Super-resolution imaging achieving 20-nm resolution of [Formula: see text] in NDs has been proved over the years using sub-diffraction limited imaging approaches such as single molecule stochastic localisation microscopy and stimulated emission depletion microscopy. Here we show the first demonstration of ground-state depletion (GSD) nanoscopy of these centres in NDs using three beams, a probe beam, a depletion beam and a reset beam. The depletion beam at 638 nm forces the [Formula: see text] centres to the metastable dark state everywhere but in the local minimum, while a Gaussian beam at 594 nm probes the [Formula: see text] centres and a 488-nm reset beam is used to repopulate the excited state. Super-resolution imaging of a single [Formula: see text] centre with a full width at half maximum of 36 nm is demonstrated, and two adjacent [Formula: see text] centres separated by 72 nm are resolved. GSD microscopy is here applied to [Formula: see text] in NDs with a much lower optical power compared to bulk diamond. This work demonstrates the need to control the NDs nitrogen concentration to tailor their application in super-resolution imaging methods and paves the way for studies of [Formula: see text] in NDs' nanoscale interactions.

Fluorescent sp3 Defect-Tailored Carbon Nanotubes Enable NIR-II Single Particle Imaging in Live Brain Slices at Ultra-Low Excitation Doses

Cellular and tissue imaging in the second near-infrared window (NIR-II, ~1000–1350 nm) is advantageous for in vivo studies because of low light extinction by biological constituents at these wavelengths. However, deep tissue imaging at the single molecule sensitivity has not been achieved in the NIR-II window due to lack of suitable bio-probes. Single-walled carbon nanotubes have emerged as promising near-infrared luminescent molecular bio-probes; yet, their inefficient photoluminescence (quantum yield ~1%) drives requirements for sizeable excitation doses (~1–10 kW/cm²) that are significantly blue-shifted from the NIR-II region (<850 nm) and may thus ultimately compromise live tissue. Here, we show that single nanotube imaging can be achieved in live brain tissue using ultralow excitation doses (~0.1 kW/cm²), an order of magnitude lower than those currently used. To accomplish this, we synthesized fluorescent sp³-defect tailored (6,5) carbon nanotubes which, when excited at their first order excitonic transition (~985 nm) fluoresce brightly at ~1160 nm. The biocompatibility of these functionalized nanotubes, which are wrapped by encapsulation agent (phospholipid-polyethylene glycol), is demonstrated using standard cytotoxicity assays. Single molecule photophysical studies of these biocompatible nanotubes allowed us to identify the optimal luminescence properties in the context of biological imaging.

Histopathological study of the maternal exposure to the biologically produced silver nanoparticles on different organs of the offspring

This research for the first time presents the possibility of crossing the biologically produced SNPs through the placenta to different organs of rat offspring. SNPs were produced using Fusarium oxysporum. After adding 1 mmol final concentration of silver nitrate solution to the culture supernatant and 5 min heating, SNPs were produced, and their production was proved using visible spectrum, transmission electron microscope (TEM), and X-ray diffraction (XRD) analyses. SNPs were washed, and their concentration determined using inductively coupled plasma (ICP) instrument. SNPs were used for 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, and after determination of their half maximal inhibitory concentration (IC₅₀) dose, their toxic and nontoxic doses were determined and used for in vivo studies. A total of 24 female rats, after detection of their vaginal plugs, were divided into 3 groups each having 8 members. A control group was treated with normal saline. The other two groups were treated by toxic and nontoxic doses of SNPs, respectively. After delivery and breastfeeding, the pups were scarified, and their organs were collected and analyzed using histological examinations. Results showed that SNPs had a maximum absorbance peak around 450 nm, with polygonal and round shapes. XRD results confirmed the presence of SNPs. The concentration of the SNPs after washing was 19 ppm/mL based on the ICP results. MTT assay results showed that SNPs had a dose-dependent toxic effect. Histopathological examination results showed that SNPs could pass through the placenta; both their nontoxic and toxic doses induced somehow mild alternations in the liver, kidney, testis, and ovary and had no effects on the brains of the rat offspring. In conclusions, the use of the biologically produced SNPs should be limited during pregnancy and breastfeeding.

Smart diagnostic nano-agents for cerebral ischemia

A summary of the latest developments on imaging techniques and smart nano-diagnostics used for ischemic stroke.

Near-Infrared-II Molecular Dyes for Cancer Imaging and Surgery

Fluorescence bioimaging affords a vital tool for both researchers and surgeons to molecularly target a variety of biological tissues and processes. This review focuses on summarizing organic dyes emitting at a biological transparency window termed the near-infrared-II (NIR-II) window, where minimal light interaction with the surrounding tissues allows photons to travel nearly unperturbed throughout the body. NIR-II fluorescence imaging overcomes the penetration/contrast bottleneck of imaging in the visible region, making it a remarkable modality for early diagnosis of cancer and highly sensitive tumor surgery. Due to their convenient bioconjugation with peptides/antibodies, NIR-II molecular dyes are desirable candidates for targeted cancer imaging, significantly overcoming the autofluorescence/scattering issues for deep tissue molecular imaging. To promote the clinical translation of NIR-II bioimaging, advancements in the high-performance small molecule-derived probes are critically important. Here, molecules with clinical potential for NIR-II imaging are discussed, summarizing the synthesis and chemical structures of NIR-II dyes, chemical and optical properties of NIR-II dyes, bioconjugation and biological behavior of NIR-II dyes, whole body imaging with NIR-II dyes for cancer detection and surgery, as well as NIR-II fluorescence microscopy imaging. A key perspective on the direction of NIR-II molecular dyes for cancer imaging and surgery is also discussed.