Toward Fabrication of Devices Based on Graphene/Oxide Multilayers.

Owing to its high electrical conductivity, low density, and flexibility, graphene has great potential for use as a building block in a wide range of applications from nanoelectronics to biosensing and high-frequency devices. For many device applications, it is required to deposit dielectric materials on graphene at high temperatures and in ambient oxygen. This has been proven to be highly challenging because these conditions cause significant degradation in graphene. In this work, we investigate the degradation of graphene at elevated temperatures in an oxygen atmosphere and possible protection mechanisms to enable the growth of oxide thin films on graphene at higher temperatures. We show that coating graphene with self-assembled monolayers of hexamethyldisilazane (HMDS) prior to a high-temperature deposition can significantly reduce the damage induced. Furthermore, a graphene sample treated with HMDS displayed a weaker doping effect due to weak interaction with oxygen species than bare graphene, and a much slower rate of electrical resistance degradation was exhibited during annealing. Thus, it is a promising approach that could enable the deposition of metal oxide materials on graphene at high temperatures without significant degradation in graphene quality, which is critical for a wide range of applications.

Crystalline AuNP-Decorated Strontium Niobate Thin Films: Strain-Controlled AuNP Morphologies and Optical Properties for Plasmonic Applications.

Gold nanoparticle (AuNP) decoration is a commonly used method to enhance the optical responses in many applications such as photocatalysis, biosensing, solar cells, etc. The morphology and structure of AuNPs are essential factors determining the functionality of the sample. However, tailoring the growth mechanism of AuNPs on an identical surface is not straightforward. In this study, AuNPs were deposited on the surface of a perovskite thin film, strontium niobate (SNO), using pulsed laser deposition (PLD). AuNPs exhibited a dramatic variation in their growth mechanisms, depending on whether they were deposited on SNO thin films grown on magnesium oxide (SNO/MgO) or strontium titanate (SNO/STO) substrates. On SNO/MgO, the Au aggregates form large NPs with an average size of up to 3500 nm2. These AuNPs are triangular with sharp edges and corners. The out-of-plane direction of growth is favored, and the surface coverage ratio by AuNPs is low. When deposited on SNO/STO, the average size of AuNPs is much smaller, i.e., ∼250 nm2. This reduction in the average size is accompanied by an increase in the number density of NPs. AuNPs on SNO/STO have a round shape and high coverage ratio. Such an impact from the substrate selection on the AuNP structure is significant when the sandwiched SNO film is below 80 nm thickness and is weakened for 200 nm of SNO films. X-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to characterize all samples. Strain analysis was used to explain the growth mechanism of AuNPs. The average height of AuNPs was measured by using atomic force microscopy (AFM). Ellipsometry in the visible-near-infrared (vis-NIR) region was used to characterize the optical response of all samples. AuNP-decorated SNO/MgO and SNO/STO thin films exhibit different optical properties, with only gold-decorated SNO/MgO samples showing a size-dependent epsilon-near-zero behavior of nanoparticles. These results provide an additional route to control the structure of AuNPs. They can be used for various plasmonic applications like the design and development of strain-engineered gold-nanoparticle-decorated devices for surface-enhanced Raman spectroscopy (SERS) and photocatalysis.

Optimizing Hot Electron Harvesting at Planar Metal-Semiconductor Interfaces with Titanium Oxynitride Thin Films.

Understanding metal-semiconductor interfaces is critical to the advancement of photocatalysis and sub-bandgap solar energy harvesting where electrons in the metal can be excited by sub-bandgap photons and extracted into the semiconductor. In this work, we compare the electron extraction efficiency across Au/TiO2 and titanium oxynitride (TiON)/TiO2-x interfaces, where in the latter case the spontaneously forming oxide layer (TiO2-x) creates a metal-semiconductor contact. Time-resolved pump-probe spectroscopy is used to study the electron recombination rates in both cases. Unlike the nanosecond recombination lifetimes in Au/TiO2, we find a bottleneck in the electron relaxation in the TiON system, which we explain using a trap-mediated recombination model. Using this model, we investigate the tunability of the relaxation dynamics with oxygen content in the parent film. The optimized film (TiO0.5N0.5) exhibits the highest carrier extraction efficiency (NFC ≈ 2.8 × 1019 m-3), slowest trapping, and an appreciable hot electron population reaching the surface oxide (NHE ≈ 1.6 × 1018 m-3). Our results demonstrate the productive role oxygen can play in enhancing electron harvesting and prolonging electron lifetimes, providing an optimized metal-semiconductor interface using only the native oxide of titanium oxynitride.

Development of Nanopackaging for Storage and Transport of Loaded Lipid Nanoparticles.

Easily deploying new vaccines globally to combat disease outbreaks has been highlighted as a major necessity by the World Health Organization. RNA-based vaccines using lipid nanoparticles (LNPs) as a drug delivery system were employed to great effect during the recent COVID-19 pandemic. However, LNPs are still unstable at room temperature and agglomerate over time during storage, rendering them ineffective for intracellular delivery. We demonstrate the suitability of nanohole arrays (nanopackaging) as patterned surfaces to separate and store functionalized LNPs (fLNPs) in individual recesses, which can be expanded to other therapeutics. Encapsulating calcein as a model drug, we show through confocal microscopy the effective loading of fLNPs into our nanopackaging for both wet and dry systems. We prove quantifiably pH-mediated capture and subsequent unloading of over 30% of the fLNPs using QCM-D on alumina surfaces altering the pH from 5.5 to 7, displaying controllable storage at the nanoscale.

Reactivity Graph Yields Interpretable IgM Repertoire Signatures as Potential Tumor Biomarkers.

Combining adaptive and innate immunity induction modes, the repertoire of immunoglobulin M (IgM) can reflect changes in the internal environment including malignancies. Previously, it was shown that a mimotope library reflecting the public IgM repertoire of healthy donors (IgM IgOme) can be mined for efficient probes of tumor biomarker antibody reactivities. To better explore the interpretability of this approach for IgM, solid tumor-related profiles of IgM reactivities to linear epitopes of actual tumor antigens and viral epitopes were studied. The probes were designed as oriented planar microarrays of 4526 peptide sequences (as overlapping 15-mers) derived from 24 tumor-associated antigens and 209 cancer-related B cell epitopes from 30 viral antigens. The IgM reactivity in sera from 21 patients with glioblastoma multiforme, brain metastases of other tumors, and non-tumor-bearing neurosurgery patients was thus probed in a proof-of-principle study. A graph representation of the binding data was developed, which mapped the cross-reactivity of the mixture of IgM (poly)specificities, delineating different antibody footprints in the features of the graph-neighborhoods and cliques. The reactivity graph mapped the major features of the IgM repertoire such as the magnitude of the reactivity (titer) and major cross-reactivities, which correlated with blood group reactivity, non-self recognition, and even idiotypic specificities. A correlation between an aspect of this image of the IgM IgOme, namely, small cliques reflecting rare self-reactivities and the capacity of subsets of the epitopes to separate the diagnostic groups studied was found. In this way, the graph representation helped the feature selection in its filtering step and provided reduced feature sets, which, after recursive feature elimination, produced a classifier containing 51 peptide reactivities separating the three diagnostic groups with an unexpected efficiency. Thus, IgM IgOme approaches to repertoire studies is greatly augmented when self/viral antigens are used and the data are represented as a reactivity graph. This approach is most general, and if it is applicable to tumors in immunologically privileged sites, it can be applied to any solid tumors, for instance, breast or lung cancer.

Interaction of Clostridium perfringens Epsilon Toxin with the Plasma Membrane: The Role of Amino Acids Y42, Y43 and H162.

Clostridium perfringens epsilon toxin (Etx) is a pore forming toxin that causes enterotoxaemia in ruminants and may be a cause of multiple sclerosis in humans. To date, most in vitro studies of Etx have used the Madin-Darby canine kidney (MDCK) cell line. However, studies using Chinese hamster ovary (CHO) cells engineered to express the putative Etx receptor, myelin and lymphocyte protein (MAL), suggest that amino acids important for Etx activity differ between species. In this study, we investigated the role of amino acids Y42, Y43 and H162, previously identified as important in Etx activity towards MDCK cells, in Etx activity towards CHO-human MAL (CHO-hMAL) cells, human red blood cells (hRBCs) and synthetic bilayers using site-directed mutants of Etx. We show that in CHO-hMAL cells Y42 is critical for Etx binding and not Y43 as in MDCK cells, indicating that surface exposed tyrosine residues in the receptor binding domain of Etx impact efficiency of cell binding to MAL-expressing cells in a species-specific manner. We also show that Etx mutant H162A was unable to lyse CHO-hMAL cells, lysed hRBCs, whilst it was able to form pores in synthetic bilayers, providing evidence of the complexity of Etx pore formation in different lipid environments.

The Effects of Cholesterol Oxidation on Erythrocyte Plasma Membranes: A Monolayer Study.

Cholesterol plays a key role in the molecular and mesoscopic organisation of lipid membranes and it is expected that changes in its molecular structure (e.g., through environmental factors such as oxidative stress) may affect adversely membrane properties and function. In this study, we present evidence that oxidation of cholesterol has significant effects on the mechanical properties, molecular and mesoscopic organisation and lipid-sterol interactions in condensed monolayers composed of the main species found in the inner leaflet of the erythrocyte membrane. Using a combination of experimental methods (static area compressibility, surface dilatational rheology, fluorescence microscopy, and surface sensitive X-ray techniques) and atomistic molecular dynamics simulations, we show that oxidation of cholesterol to 7-ketocholesterol leads to stiffening of the monolayer (under both static and dynamic conditions), significant changes in the monolayer microdomain organisation, disruption in the van der Waals, electrostatic and hydrophobic interactions between the sterol and the other lipid species, and the lipid membrane hydration. Surface sensitive X-ray techniques reveal that, whilst the molecular packing mode is not significantly affected by cholesterol oxidation in these condensed phases, there are subtle changes in membrane thickness and a significant decrease in the coherence length in monolayers containing 7-ketocholesterol.

On-chip integrated graphene aptasensor with portable readout for fast and label-free COVID-19 detection in virus transport medium.

Graphene field-effect transistor (GFET) biosensors exhibit high sensitivity due to a large surface-to-volume ratio and the high sensitivity of the Fermi level to the presence of charged biomolecules near the surface. For most reported GFET biosensors, bulky external reference electrodes are used which prevent their full-scale chip integration and contribute to higher costs per test. In this study, GFET arrays with on-chip integrated liquid electrodes were employed for COVID-19 detection and functionalized with either antibody or aptamer to selectively bind the spike proteins of SARS-CoV-2. In the case of the aptamer-functionalized GFET (aptasensor, Apt-GFET), the limit-of-detection (LOD) achieved was about 103 particles per mL for virus-like particles (VLPs) in clinical transport medium, outperforming the Ab-GFET biosensor counterpart. In addition, the aptasensor achieved a LOD of 160 aM for COVID-19 neutralizing antibodies in serum. The sensors were found to be highly selective, fast (sample-to-result within minutes), and stable (low device-to-device signal variation; relative standard deviations below 0.5%). A home-built portable readout electronic unit was employed for simultaneous real-time measurements of 12 GFETs per chip. Our successful demonstration of a portable GFET biosensing platform has high potential for infectious disease detection and other health-care applications.

Restriction of the Global IgM Repertoire in Antiphospholipid Syndrome.

The typical anti-phospholipid antibodies (APLA) in the anti-phospholipid syndrome (APS) are reactive with the phospholipid-binding protein ß2GPI as well as a growing list of other protein targets. The relation of APLA to natural antibodies and the fuzzy set of autoantigens involved provoked us to study the changes in the IgM repertoire in APS. To this end, peptides selected by serum IgM from a 7-residue linear peptide phage display library (PDL) were deep sequenced. The analysis was aided by a novel formal representation of the Igome (the mimotope set reflecting the IgM specificities) in the form of a sequence graph. The study involved women with APLA and habitual abortions (n=24) compared to age-matched clinically healthy pregnant women (n=20). Their pooled Igomes (297 028 mimotope sequences) were compared also to the global public repertoire Igome of pooled donor plasma IgM (n=2 796 484) and a set of 7-mer sequences found in the J regions of human immunoglobulins (n=4 433 252). The pooled Igome was represented as a graph connecting the sequences as similar as the mimotopes of the same monoclonal antibody. The criterion was based on previously published data. In the resulting graph, identifiable clusters of vertices were considered related to the footprints of overlapping antibody cross-reactivities. A subgraph based on the clusters with a significant differential expression of APS patients' mimotopes contained predominantly specificities underrepresented in APS. The differentially expressed IgM footprints showed also an increased cross-reactivity with immunoglobulin J regions. The specificities underexpressed in APS had a higher correlation with public specificities than those overexpressed. The APS associated specificities were strongly related also to the human peptidome with 1 072 mimotope sequences found in 7 519 human proteins. These regions were characterized by low complexity. Thus, the IgM repertoire of the APS patients was found to be characterized by a significant reduction of certain public specificities found in the healthy controls with targets representing low complexity linear self-epitopes homologous to human antibody J regions.

Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells.

The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.

Detection of Glial Fibrillary Acidic Protein in Patient Plasma Using On-Chip Graphene Field-Effect Biosensors, in Comparison with ELISA and Single-Molecule Array.

Glial fibrillary acidic protein (GFAP) is a discriminative blood biomarker for many neurological diseases, such as traumatic brain injury. Detection of GFAP in buffer solutions using biosensors has been demonstrated, but accurate quantification of GFAP in patient samples has not been reported, yet in urgent need. Herein, we demonstrate a robust on-chip graphene field-effect transistor (GFET) biosensing method for sensitive and ultrafast detection of GFAP in patient plasma. Patients with moderate-severe traumatic brain injuries, defined by the Mayo classification, are recruited to provide plasma samples. The binding of target GFAP with the specific antibodies that are conjugated on a monolayer GFET device triggers the shift of its Dirac point, and this signal change is correlated with the GFAP concentration in the patient plasma. The limit of detection (LOD) values of 20 fg/mL (400 aM) in buffer solution and 231 fg/mL (4 fM) in patient plasma have been achieved using this approach. In parallel, for the first time, we compare our results to the state-of-the-art single-molecule array (Simoa) technology and the classic enzyme-linked immunosorbent assay (ELISA) for reference. The GFET biosensor shows competitive LOD to Simoa (1.18 pg/mL) and faster sample-to-result time (<15 min), and also it is cheaper and more user-friendly. In comparison to ELISA, GFET offers advantages of total detection time, detection sensitivity, and simplicity. This GFET biosensing platform holds high promise for the point-of-care diagnosis and monitoring of traumatic brain injury in GP surgeries and patient homes.

Phytoplankton bloom detection during the COVID-19 lockdown with remote sensing data: Using Copernicus Sentinel-3 for north-western Arabian/Persian Gulf case study.

To examine whether a country-wide COVID-19 lockdown affected phytoplankton development, variability of chlorophyll-a concentrations in the north-western Arabian/Persian Gulf (Kuwait Bay) was investigated using remote sensing instruments Sentinel OLCI between 2018 and 2020 and compared to available in situ collected data. Satellite-retrieved chlorophyll concentrations considerably increased in inshore waters of Kuwait Bay, 1-2 months following the initiation of the 24/7 curfew. The extremely high concentrations of dissolved inorganic nutrients, especially ammonia, and coincided phytoplankton bloom were revealed in June-July 2020 by opportunity field sampling, supporting the satellite-derived bloom detection. Remote sensing operational monitoring with high spatial resolution sensors provides an exceptional opportunity for emergency analysis and decision making in conditions of natural or anthropogenic crises, which forces the development of regional remote sensing algorithms for the shallow marine environment of the Gulf.

Enhancing Structural Properties and Performance of Graphene-Based Devices Using Self-Assembled HMDS Monolayers.

The performance of graphene devices is often limited by defects and impurities induced during device fabrication. Polymer residue left on the surface of graphene after photoresist processing can increase electron scattering and hinder electron transport. Furthermore, exposing graphene to plasma-based processing such as sputtering of metallization layers can increase the defect density in graphene and alter the device performance. Therefore, the preservation of the high-quality surface of graphene during thin-film deposition and device manufacturing is essential for many electronic applications. Here, we show that the use of self-assembled monolayers (SAMs) of hexamethyldisilazane (HMDS) as a buffer layer during the device fabrication of graphene can significantly reduce damage, improve the quality of graphene, and enhance device performance. The role of HMDS has been systematically investigated using surface analysis techniques and electrical measurements. The benefits of HMDS treatment include a significant reduction in defect density compared with as-treated graphene and more than a 2-fold reduction of contact resistance. This surface treatment is simple and offers a practical route for improving graphene device interfaces, which is important for the integration of graphene into functional devices such as electronics and sensor devices.

Carbon-Dot-Enhanced Graphene Field-Effect Transistors for Ultrasensitive Detection of Exosomes.

Graphene field-effect transistors (GFETs) are suitable building blocks for high-performance electrical biosensors, because graphene inherently exhibits a strong response to charged biomolecules on its surface. However, achieving ultralow limit-of-detection (LoD) is limited by sensor response time and screening effect. Herein, we demonstrate that the detection limit of GFET biosensors can be improved significantly by decorating the uncovered graphene sensor area with carbon dots (CDs). The developed CDs-GFET biosensors used for exosome detection exhibited higher sensitivity, faster response, and three orders of magnitude improvements in the LoD compared with nondecorated GFET biosensors. A LoD down to 100 particles/µL was achieved with CDs-GFET sensor for exosome detection with the capability for further improvements. The results were further supported by atomic force microscopy (AFM) and fluorescent microscopy measurements. The high-performance CDs-GFET biosensors will aid the development of an ultrahigh sensitivity biosensing platform based on graphene for rapid and early diagnosis of diseases.

Complementary Metal-Oxide-Semiconductor Compatible Deposition of Nanoscale Transition-Metal Nitride Thin Films for Plasmonic Applications.

Transition-metal nitrides have received significant interest for use within plasmonic and optoelectronic devices because of their tunability and environmental stability. However, the deposition temperature remains a significant barrier to widespread adoption through the integration of transition-metal nitrides as plasmonic materials within complementary metal-oxide-semiconductor (CMOS) fabrication processes. Binary, ternary, and layered plasmonic transition-metal nitride thin films based on titanium and niobium nitride are deposited using high-power impulse magnetron sputtering (HIPIMS) technology. The increased plasma densities achieved in the HIPIMS process allow thin films with high plasmonic quality to be deposited at CMOS-compatible temperatures of less than 300 °C. Thin films are deposited on a range of industrially relevant substrates and display-tunable plasma frequencies in the ultraviolet to visible spectral ranges. Strain-mediated tunability is discovered in layered films compared to that in ternary films. The thin film quality, combined with the scalability of the deposition process, indicates that HIPIMS deposition of nitride films is an industrially viable technique and can pave the way toward the fabrication of next-generation plasmonic and optoelectronic devices.

Effect of DMSO on the Mechanical and Structural Properties of Model and Biological Membranes.

Dimethyl sulfoxide (DMSO) is widely used in a number of biological and biotechnological applications, mainly because of its effects on the cell plasma membrane, but the molecular origins of this action are yet to be fully clarified. In this work, we used two- and three-component synthetic membranes (liposomes) and the plasma membrane of human erythrocytes to investigate the effect of DMSO when added to the membrane-solvating environment. Fourier transform infrared spectroscopy and thermal fluctuation spectroscopy revealed significant differences in the response of the two types of liposome systems to DMSO in terms of the bilayer thermotropic behavior, available free volume of the bilayer, its excess surface area, and bending elasticity. DMSO also alters the mechanical properties of the erythrocyte membrane in a concentration-dependent manner and is capable of increasing membrane permeability to ATP at even relatively low concentrations (3% v/v and above). Taken in its entirety, these results show that DMSO is likely to have a differential effect on heterogeneous biological membranes, depending on their local composition and structure, and could affect membrane-hosted biological functions.

Potential SARS-CoV-2 Preimmune IgM Epitopes.

While studying the human public IgM igome as represented by a library of 224,087 linear mimotopes, three exact matches to peptides in the proteins of SARS-CoV-2 were found: two in the open reading frame 1ab and one in the spike protein. Joining the efforts to fast track SARS-CoV-2 vaccine development, here we describe briefly these potential epitopes in comparison to mimotopes representing peptides of SARS-CoV, HCoV 229E and OC43.

Sand and dust storm trajectories from Iraq Mesopotamian flood plain to Kuwait.

Although Kuwait is greatly impacted by sand and dust storms (SDS) from Southern Iraq, to date little is known about the nature of these storms. Kuwait is vulnerable to SDS trajectories from the middle Euphrates region, specifically, from two "hot spot" areas (Al-Batha and Mamlahat Al-Samawah) of 4550 km2 located 250 km from its northern border. This study explores the transboundary SDS jets originating from Southern Iraq using Moderate Resolution Imaging Spectroradiometer (MODIS) images obtained from Aqua and Terra satellites over a twelve-year period (2007-2018). Furthermore, an analysis of a 5-day diurnal variation (two days prior, the day of the SDS occurrence, and two days after) explored the hourly patterns of visibility and wind speed, as well as grain size distribution of soil samples to better understand grain size compositions and sediment transport mechanisms. Satellite images confirmed that dust storm jets originated from the "hot spot" in southern Iraq and spread over Kuwait and extended to neighboring Arab Gulf countries as far as Bahrain (900 km) and Qatar (1200 km). In general, the highest wind speed and lowest visibility values were recorded in Northern of Kuwait, with suspended dust sustained for two days following the dust storm. The largest silt and clay fractions (grains ≤63 µm) were identified at the center and west Sabkha region of the "hot spot" area. Very fine sand particles (63-250 µm) were identified within the crescent sand dunes (Barchans) and artificial sand dunes (Al-Fajr). It is recommended that sustainable rehabilitation and land restoration of the "hot spot" area will result in the elimination of the long-range transport of SDS jet streams affecting the downwind Gulf countries.

Tunable Three-Dimensional Plasmonic Arrays for Large Near-Infrared Fluorescence Enhancement.

Metal-enhanced fluorescence (MEF), resulting from the near-field interaction of fluorophores with metallic nanostructures, has emerged as a powerful tool for dramatically improving the performance of fluorescence-based biomedical applications. Allowing for lower autofluorescence and minimal photoinduced damage, the development of multifunctional and multiplexed MEF platforms in the near-infrared (NIR) windows is particularly desirable. Here, a low-cost fabrication method based on nanosphere lithography is applied to produce tunable three-dimensional (3D) gold (Au) nanohole-disc arrays (Au-NHDAs). The arrays consist of nanoscale glass pillars atop nanoholes in a Au thin film: the top surfaces of the pillars are Au-covered (effectively nanodiscs), and small Au nanoparticles (nanodots) are located on the sidewalls of the pillars. This 3D hole-disc (and possibly nanodot) construct is critical to the properties of the device. The versatility of our approach is illustrated through the production of uniform and highly reproducible Au-NHDAs with controlled structural properties and tunable optical features in the NIR windows. Au-NHDAs allow for a very large NIR fluorescence enhancement (more than 400 times), which is attributed to the 3D plasmonic structure of the arrays that allows strong surface plasmon polariton and localized surface plasmon resonance coupling through glass nanogaps. By considering arrays with the same resonance peak and the same nanodisc separation distance, we show that the enhancement factor varies with nanodisc diameter. Using computational electromagnetic modeling, the electric field enhancement at 790 nm was calculated to provide insights into excitation enhancement, which occurs due to an increase in the intensity of the electric field. Fluorescence lifetime measurements indicate that the total fluorescence enhancement may depend on controlling excitation enhancement and therefore the array morphology. Our findings provide important insights into the mechanism of MEF from 3D plasmonic arrays and establish a low-cost versatile approach that could pave the way for novel NIR-MEF bioapplications.