Pangenome-wide association study reveals the selective absence of CRISPR genes (Rv2816c-19c) in drug-resistant Mycobacterium tuberculosis.

The presence of intermittently dispersed insertion sequences and transposases in the Mycobacterium tuberculosis (Mtb) genome makes intra-genome recombination events inevitable. Understanding their effect on the gene repertoires (GR), which may contribute to the development of drug-resistant Mtb, is critical. In this study, publicly available WGS data of clinical Mtb isolates (endemic region n = 2,601; non-endemic region n = 1,130) were de novo assembled, filtered, scaffolded into assemblies, and functionally annotated. Out of 2,601 Mtb WGS data sets from endemic regions, 2,184 (drug resistant/sensitive: 1,386/798) qualified as high quality. We identified 3,784 core genes, 123 softcore genes, 224 shell genes, and 762 cloud genes in the pangenome of Mtb clinical isolates from endemic regions. Sets of 33 and 39 genes showed positive and negative associations (P < 0.01) with drug resistance status, respectively. Gene ontology clustering showed compromised immunity to phages and impaired DNA repair in drug-resistant Mtb clinical isolates compared to the sensitive ones. Multidrug efflux pump repressor genes (Rv3830c and Rv3855c) and CRISPR genes (Rv2816c-19c) were absent in the drug-resistant Mtb. A separate WGS data analysis of drug-resistant Mtb clinical isolates from the Netherlands (n = 1130) also showed the absence of CRISPR genes (Rv2816c-17c). This study highlights the role of CRISPR genes in drug resistance development in Mtb clinical isolates and helps in understanding its evolutionary trajectory and as useful targets for diagnostics development.IMPORTANCEThe results from the present Pan-GWAS study comparing gene sets in drug-resistant and drug-sensitive Mtb clinical isolates revealed intricate presence-absence patterns of genes encoding DNA-binding proteins having gene regulatory as well as DNA modification and DNA repair roles. Apart from the genes with known functions, some uncharacterized and hypothetical genes that seem to have a potential role in drug resistance development in Mtb were identified. We have been able to extrapolate many findings of the present study with the existing literature on the molecular aspects of drug-resistant Mtb, further strengthening the relevance of the results presented in this study.

High selectivity and sensitivity through nanoparticle sensors for cleanroom CO2detection.

Clean room facilities are becoming more popular in both academic and industry settings, including low-and middle-income countries. This has led to an increased demand for cost-effective gas sensors to monitor air quality. Here we have developed a gas sensor using CoNiO2nanoparticles through combustion method. The sensitivity and selectivity of the sensor towards CO2were influenced by the structure of the nanoparticles, which were affected by the reducing agent (biofuels) used during synthesis. Among all reducing agents, urea found to yield highly crystalline and uniformly distributed CoNiO2nanoparticles, which when developed into sensors showed high sensitivity and selectivity for the detection of CO2gas in the presence of common interfering volatile organic compounds observed in cleanroom facilities including ammonia, formaldehyde, acetone, toluene, ethanol, isopropanol and methanol. In addition, the urea-mediated nanoparticle-based sensors exhibited room temperature operation, high stability, prompt response and recovery rates, and excellent reproducibility. Consequently, the synthesis approach to nanoparticle-based, energy efficient and affordable sensors represent a benchmark for CO2sensing in cleanroom settings.

Localized Surface Plasmon Resonance Sensing and its Interplay with Fluidics.

In this Feature Article, we discuss the interplay between fluidics and the localized surface plasmon resonance (LSPR) sensing technique, primarily focusing on its applications in the realm of bio/chemical sensing within fluidic environments. Commencing with a foundational overview of LSPR principles from a sensing perspective, we subsequently showcase the development of a streamlined LSPR chip integrated with microfluidic structures. This integration opens the doors to advanced experiments involving fluid dynamics, greatly expanding the scope of LSPR-based research. Our discussions then turn to the practical implementation of LSPR and microfluidics in real-time biosensing, with a specific emphasis on monitoring DNA polymerase activity. Additionally, we illustrate the direct sensing of biological fluids, exemplified by the analysis of urine, while also shedding light on a unique particle assembly process that occurs on LSPR chips. We not only discuss the significance of LSPR sensing but also explore its potential to investigate a plethora of phenomena at liquid-liquid and solid-liquid interfaces. This is particularly noteworthy, as existing transduction methods and sensors fall short in fully comprehending these interfacial phenomena. Concluding our discussion, we present a futuristic perspective that provides insights into potential opportunities emerging at the intersection of fluidics and LSPR sensing.

Unconventional Breathing Currents Far beyond the Quantum Tunneling Distances in Large-Gapped Nanoplasmonic Systems.

Localized surface plasmon resonance (LSPR) in plasmonic nanoparticles propels the field of plasmo-electronics, holding promise for transformative optoelectronic devices through efficient light-to-current conversion. Plasmonic excitations strongly influence the charge distribution within nanoparticles, giving rise to electromagnetic fields that can significantly impact the macroscopic charge flows within the nanoparticle housing material. In this study, we present evidence of ultralow, unconventional breathing currents resulting from dynamic irradiance interactions between widely separated nanoparticles, extending far beyond conventional electron (quantum) tunneling distances. We develop an electric analogue model and derive an empirical expression to elucidate the generation of these unconventional breathing currents in cascaded nanoplasmonic systems under irradiance modulation. This technique and theoretical model have significant potential for applications requiring a deeper understanding of current dynamics, particularly on large nanostructured surfaces relevant to photocatalysis, energy harvesting, sensing, imaging, and the development of future photonic devices.

Recognizing the Less Explored "Active Solid"-"Moving Liquid" Interfaces in Bio/Chemical Sensors.

Bio/chemical sensors possess a plethora of advantageous features that have proven to be invaluable tools in detecting and monitoring biomolecules, facilitating advancements in healthcare, environmental monitoring, food safety, and more. However, when it comes to their routine use in continuous fluid flow conditions, an intricate web of solid-liquid interfacial phenomena emerges, which requires a deep understanding of the sensor surface and fluid interations. These interfacial phenomena encompass a broad spectrum of physical, chemical, and biological processes, other than the actual detection, that influence the sensor's response. In this context, perhaps exploring a new theme "active solid"-"moving liquid" interface will unleash the full potential of bio/chemical sensors in any flow-based application.

Gold Nanoparticle Enabled Localized Surface Plasmon Resonance on Unique Gold Nanomushroom Structures for On-Chip CRISPR-Cas13a Sensing.

A novel localized surface plasmon resonance (LSPR) system based on the coupling of gold nanomushrooms (AuNMs) and gold nanoparticles (AuNPs) is developed to enable a significant plasmonic resonant shift. The AuNP size, surface chemistry, and concentration are characterized to maximize the LSPR effect. A 31 nm redshift is achieved when the AuNMs are saturated by the AuNPs. This giant redshift also increases the full width of the spectrum and is explained by the 3D finite-difference time-domain (FDTD) calculation. In addition, this LSPR substrate is packaged in a microfluidic cell and integrated with a CRISPR-Cas13a RNA detection assay for the detection of the SARS-CoV-2 RNA targets. Once activated by the target, the AuNPs are cleaved from linker probes and randomly deposited on the AuNM substrate, demonstrating a large redshift. The novel LSPR chip using AuNP as an indicator is simple, specific, isothermal, and label-free; and thus, provides a new opportunity to achieve the next generation multiplexing and sensitive molecular diagnostic system.

Point-of-care diagnostics for sepsis using clinical biomarkers and microfluidic technology.

Sepsis is a life-threatening immune response which is caused by a wide variety of sources and is a leading cause of mortality globally. Rapid diagnosis and appropriate antibiotic treatment are critical for successful patient outcomes; however, current molecular diagnostic techniques are time-consuming, costly and require trained personnel. Additionally, there is a lack of rapid point-of-care (POC) devices available for sepsis detection despite the urgent requirements in emergency departments and low-resource areas. Recent advances have been made toward developing a POC test for early sepsis detection that will be more rapid and accurate compared to conventional techniques. Within this context, this review discusses the use of current and novel biomarkers for early sepsis diagnosis using microfluidics devices for POC testing.

Effect of Selenium Nanoparticle Size on IL-6 Detection Sensitivity in a Lateral Flow Device.

Sepsis is the body's response to an infection. Existing diagnostic testing equipment is not available in primary care settings and requires long waiting times. Lateral flow devices (LFDs) could be employed in point-of-care (POC) settings for sepsis detection; however, they currently lack the required sensitivity. Herein, LFDs are constructed using 150-310 nm sized selenium nanoparticles (SeNPs) and are compared to commercial 40 nm gold nanoparticles (AuNPs) for the detection of the sepsis biomarker interleukin-6 (IL-6). Both 310 and 150 nm SeNPs reported a lower limit of detection (LOD) than 40 nm AuNPs (0.1 ng/mL compared to 1 ng/mL), although at the cost of test line visual intensity. This is to our knowledge the first use of larger SeNPs (>100 nm) in LFDs and the first comparison of the effect of the size of SeNPs on assay sensitivity in this context. The results herein demonstrate that large SeNPs are viable alternatives to existing commercial labels, with the potential for higher sensitivity than standard 40 nm AuNPs.

Addressing the Silent Spread of Monkeypox Disease with Advanced Analytical Tools.

Monkeypox disease is caused by a virus which belongs to the orthopoxvirus genus of the poxviridae family. This disease has recently spread out to several non-endemic countries. While some cases have been linked to travel from endemic regions, more recent infections are thought to have spread in the community without any travel links, raising the risks of a wider outbreak. This state of public health represents a highly unusual event which requires urgent surveillance. In this context, the opportunities and technological challenges of current bio/chemical sensors, nanomaterials, nanomaterial characterization instruments, and artificially intelligent biosystems collectively called "advanced analytical tools" are reviewed here, which will allow early detection, characterization, and inhibition of the monkeypox virus (MPXV) in the community and limit its expansion from endemic to pandemic. A summary of background information is also provided from biological and epidemiological perspective of monkeypox to support the scientific case for its holistic management using advanced analytical tools.

Measuring the Radius of Gyration and Intrinsic Flexibility of Viral Proteins in Buffer Solution Using Small-Angle X-ray Scattering.

Measuring structural features of proteins dispersed in buffer solution, in contrast to crystal form, is indispensable in understanding morphological characteristics of the biomolecule in a native environment. We report on the structure and apparent viscosity of unfolded α and ß variants of SARS-CoV-2 spike proteins dispersed in buffer solutions. The radius of gyration of the ß variant is found to be larger than that of the α variant, while the ab initio computation of one of the possible particle-like bodies is consistent with the small-angle X-ray scattering (SAXS) profiles resembling a conformation similar to the three-dimensional structure of the folded state of the corresponding α and ß spike variant. However, a smaller radius of gyration with respect to the predicted folded state of 2.4 and 2.7 is observed for both α and ß variants, respectively. Our work complements the structural characterization of spike proteins using cryo-electron microscopy techniques. The measurement/analysis discussed here might be useful for quick and cost-effective evaluation of several protein structures, let alone mutated viral proteins, which is useful for drug discovery/development applications.

Unraveling the liquid gliding on vibrating solid liquid interfaces with dynamic nanoslip enactment.

Slip length describes the classical no-slip boundary condition violation of Newtonian fluid mechanics, where fluids glide on the solid surfaces. Here, we propose a new analytical model validated by experiments for characterization of the liquid slip using vibrating solid surfaces. Essentially, we use a microfluidic system integrated with quartz crystal microbalance (QCM) to investigate the relationship between the slip and the mechanical response of a vibrating solid for a moving fluid. We discover a liquid slip that emerges especially at high flow rates, which is independent of the surface wetting condition, having significant contributions to the changes in resonant frequency of the vibrating solid and energy dissipation on its surface. Overall, our work will lead to consideration of 'missing slip' in the vibrating solid-liquid systems such as the QCM-based biosensing where traditionally frequency changes are interpreted exclusively with mass change on the sensor surface, irrespective of the flow conditions.

Total electrification of large-scale nanophotonic arrays by frictional charges.

Localized surface plasmon resonance (LSPR) of metallic nanostructures is a unique phenomenon that controls the light in sub-wavelength volumes and enhances the light-matter interactions. Traditionally, the excitation and measurement of LSPR require bulky external light sources, and efforts to scale down to nano-plasmonic devices have predominantly relied on the system's miniaturization and associated accessories. Addressing this, here we show the generation and detection of LSPR wavelength (λLSPR) shifts in large-area nanostructured Au surfaces using frictional charges generated by triboelectric surfaces. We observe a complex interplay of the localized surface plasmons with frictional charges via concurrent spectroscopic and triboelectric measurements undertaken for the detection of bioconjugation in the streptavidin-biotin complex. When subjected to multivariate principal component analysis, a strong correlation between the triboelectric peak-to-peak voltage output response and the λLSPR shift is observed. Furthermore, we reveal a landscape of the interfacial events involved in the electrical generation/detection of the LSPR by using theoretical models and surface characterization. The demonstrated concept of electrification of plasmon resonance thus provides the underlying basis for the subsequent development of self-powered nano-plasmonic sensors and opens new horizons for advanced nanophotonic applications.

Effect of Functional Electrical Stimulation on Capillary Blood Flow to Muscle.

Functional electrical stimulation (FES) modifies red blood cells (RBCs) flux in blood capillaries of muscle. In this work, we aim to investigate changes in the RBC flux in small and large capillaries due to FES using zinc oxide nanowires (ZnO NWs) based electrode at different stimulation parameters. The RBC flux was significantly increased immediately after stimulation, which was evident from decreasing light intensity measured in the region of interest. Clinical Relevance- FES has numerous forms and functions. The benefit of FES is the increased blood flow to a muscle which is contracted abnormally. This work explores the use of FES to increase the blood flow and RBC flux in blood capillaries of stimulated muscle as FES generate muscle contraction and absorption.

Elucidating Sensitivity and Stability Relationship of Gold-Carbon Hybrid LSPR Sensors Using Principal Component Analysis.

Sensitive localized surface plasmon resonance (LSPR) sensing is achieved using nanostructured geometries of noble metals which typically have dimensions less than 100 nm. Among the plethora of geometries and materials, the spherical geometries of gold (Au) are widely used to develop sensitive bio/chemical sensors due to ease of manufacturing and biofunctionlization. One major limitation of spherical-shaped geometries of Au, used for LSPR sensing, is their low refractive index (RI) sensitivity which is commonly addressed by adding another material to the Au nanostructures. However, the process of addition of new material on Au nanostructures, while retaining the LSPR of Au, often comes with a trade-off which is associated with the instability of the developed composite, especially in harsh chemical environments. Addressing this challenge, we develop a Au-graphene-layered hybrid (Au-G) with high stability (studied up to 2 weeks here) and enhanced RI sensitivity (a maximum of 180.1 nm/RIU) for generic LSPR sensing applications using spherical Au nanostructures in harsh chemical environments, involving organic solvents. Additionally, by virtue of principal component analysis, we correlate stability and sensitivity of the developed system. The relationship suggests that the shelf life of the material is proportional to its sensitivity, while the stability of the sensor during the measurement in liquid environment decreases when the sensitivity of the material is increased. Though we uncover this relationship for the LSPR sensor, it remains evasive to explore similar relationships within other optical and electrochemical transduction techniques. Therefore, our work serves as a benchmark report in understanding/establishing new correlations between sensing parameters.

Biosensors for rapid detection of bacterial pathogens in water, food and environment.

Conventional techniques (e.g., culture-based method) for bacterial detection typically require a central laboratory and well-trained technicians, which may take several hours or days. However, recent developments within various disciplines of science and engineering have led to a major paradigm shift in how microorganisms can be detected. The analytical sensors which are widely used for medical applications in the literature are being extended for rapid and on-site monitoring of the bacterial pathogens in food, water and the environment. Especially, within the low-resource settings such as low and middle-income countries, due to the advantages of low cost, rapidness and potential for field-testing, their use is indispensable for sustainable development of the regions. Within this context, this paper discusses analytical methods and biosensors which can be used to ensure food safety, water quality and environmental monitoring. In brief, most of our discussion is focused on various rapid sensors including biosensors and microfluidic chips. The analytical performances such as the sensitivity, specificity and usability of these sensors, as well as a brief comparison with the conventional techniques for bacteria detection, form the core part of the discussion. Furthermore, we provide a holistic viewpoint on how future research should focus on exploring the synergy of different sensing technologies by developing an integrated multiplexed, sensitive and accurate sensors that will enable rapid detection for food safety, water and environmental monitoring.

Nanoplasmonic biosensor for rapid detection of multiple viral variants in human serum.

As viruses constantly change due to mutation, variants are expected to emerge demanding development of sensors capable of detecting multiple variants using one single sensor platform. Herein, we report the integration of a synthetic binder against SARS-CoV-2 with a nanoplasmonic-based sensing technology, which enables the successful detection of spike proteins of Alpha, Beta and Gamma variants of SARS CoV-2. The recognition event is achieved by specific nanostructured molecularly imprinted polymers (nanoMIPs), developed against a region of the receptor binding domain (RBD) of the SARS CoV-2 spike protein. The transduction is based on the principle of localized surface plasmon resonance (LSPR) associated with silver nanostructures. The nanoMIPs-functionalised LSPR sensor allows for the detection of all 3 protein variants with a limit of detection of 9.71 fM, 7.32 fM and 8.81 pM using wavelength shifts respectively for Alpha, Beta and Gamma spike protein variants. This can be achieved within 30 min from the sample collection, both from blood and using nasal swab, thus making this sensor suitable for rapid detection of COVID-19. Additionally, the turnaround time for sensor development and validation can be completed in less than 8 weeks, making it suitable for addressing future pandemic needs without the requirement for biological binding agents, which is one of the bottlenecks to the supply chain in diagnostic devices.

Endorsing a Hidden Plasmonic Mode for Enhancement of LSPR Sensing Performance in Evolved Metal-insulator Geometry Using an Unsupervised Machine Learning Algorithm.

Large-area nanoplasmonic structures with pillared metal-insulator geometry, also called nanomushrooms (NM), consist of an active spherical-shaped plasmonic material such as gold as its cap and silicon dioxide as its stem. NM is a geometry which evolves from its precursor, nanoislands (NI) consisting of aforementioned spherical structures on flat silicon dioxide substrates, via selective physical or chemical etching of the silicon dioxide. The NM geometry is well-known to provide enhanced localized surface plasmon resonance (LSPR) sensitivity in biosensing applications as compared to NI. However, precise optical phenomenon behind this enhancement is unknown and often associated with the existence of electric fields in the large fraction of the spatial region between the pillars of NM, usually accessible by the biomolecules. Here, we uncover the association of LSPR enhancement in such geometries with a hidden plasmonic mode by conducting magneto-optics measurements and by deconvoluting the absorbance spectra obtained during the local refractive index change of the NM and NI geometries. By the virtue of principal component analysis, an unsupervised machine learning technique, we observe an explicit relationship between the deconvoluted modes of LSPR, the differential absorption of left and right circular polarized light, and the refractive index sensitivity of the LSPR sensor. Our findings may lead to the development of new approaches to extract unknown properties of plasmonic materials or establish new fundamental relationships between less understood photonic properties of nanomaterials.

HigB1 Toxin in Mycobacterium tuberculosis Is Upregulated During Stress and Required to Establish Infection in Guinea Pigs.

The extraordinary expansion of Toxin Antitoxin (TA) modules in the genome of Mycobacterium tuberculosis has received significant attention over the last few decades. The cumulative evidence suggests that TA systems are activated in response to stress conditions and are essential for M. tuberculosis pathogenesis. In M. tuberculosis, Rv1955-Rv1956-Rv1957 constitutes the only tripartite TAC (Toxin Antitoxin Chaperone) module. In this locus, Rv1955 (HigB1) encodes for the toxin and Rv1956 (HigA1) encodes for antitoxin. Rv1957 encodes for a SecB-like chaperone that regulates HigBA1 toxin antitoxin system by preventing HigA1 degradation. Here, we have investigated the physiological role of HigB1 toxin in stress adaptation and pathogenesis of Mycobacterium tuberculosis. qPCR studies revealed that higBA1 is upregulated in nutrient limiting conditions and upon exposure to levofloxacin. We also show that the promoter activity of higBA1 locus in M. tuberculosis is (p)ppGpp dependent. We observed that HigB1 locus is non-essential for M. tuberculosis growth under different stress conditions in vitro. However, guinea pigs infected with higB1 deletion strain exhibited significantly reduced bacterial loads and pathological damage in comparison to the animals infected with the parental strain. Transcriptome analysis suggested that deletion of higB1 reduced the expression of genes involved in virulence, detoxification and adaptation. The present study describes the role of higB1 toxin in M. tuberculosis physiology and highlights the importance of higBA1 locus during infection in host tissues.

Doping Independent Work Function and Stable Band Gap of Spinel Ferrites with Tunable Plasmonic and Magnetic Properties.

Tuning optical or magnetic properties of nanoparticles, by addition of impurities, for specific applications is usually achieved at the cost of band gap and work function reduction. Additionally, conventional strategies to develop nanoparticles with a large band gap also encounter problems of phase separation and poor crystallinity at high alloying degree. Addressing the aforementioned trade-offs, here we report Ni-Zn nanoferrites with energy band gap (Eg) of ≈3.20 eV and a work function of ≈5.88 eV. While changes in the magnetoplasmonic properties of the Ni-Zn ferrite were successfully achieved with the incorporation of bismuth ions at different concentrations, there was no alteration of the band gap and work function in the developed Ni-Zn ferrite. This suggests that with the addition of minute impurities to ferrites, independent of their changes in the band gap and work function, one can tune their magnetic and optical properties, which is desired in a wide range of applications such as nanobiosensing, nanoparticle based catalysis, and renewable energy generation using nanotechnology.

Deterministic particle assembly on nanophotonic chips.

HYPOTHESIS: Controlled particle assembly from a dilute suspension droplet is challenging yet important for many lab-on-a-chip and biosensing applications. The formation of hot spots on the localized surface plasmonic resonance (LSPR) substrates induced by laser excitation can generate microbubbles. These microbubbles, upon the laser removal, shrink and collapse due to electron energy dissipation, leading to guided particle assembly on the LSPR substrate. EXPERIMENTS: After depositing dilute silica particles dispersions on both nanoisland (AuNI) and planar gold (Au) plasmonic substrates (referred to as LSPR and SPR substrates respectively), microbubbles were formed when a laser beam was applied. Particle dispersion concentration, laser power, and the radius of circular laser sequence were varied to produce different sizes of particle clusters on the LSPR substrate after bubble shrinkage upon the laser removal. To stabilize the assembled structures over time, sodium chloride (NaCl) was ad ded to the dispersions. FINDINGS: Even though thermo-plasmonic flow and microbubbles can be produced with SPR substrates, particle assembly is only possible on LSPR substrates because of electron energy dissipation via nanoscale air gaps trapped in the LSPR substrate. By tuning the laser power, the radius of the circular laser sequence, and the particle dispersion concentration, the number of particles in the assembled structure can be controlled. The addition of NaCl to the dispersion can screen the electrostatic charges among the particles and between the particles and substrate, favoring hydrogen bonding and stabilizing the assembled structures for hours. These findings establish a new framework for utilizing nanophotonic chips where particle assembly can be achieved by a single source of light.