Excluded Volume and Weak Interactions in Crowded Solutions Modulate Conformations and RNA Binding of an Intrinsically Disordered Tail.

The cellular milieu is a solution crowded with a significant concentration of different components (proteins, nucleic acids, metabolites, etc.). Such a crowded environment affects protein conformations, dynamics, and interactions. Intrinsically disordered proteins and regions are particularly sensitive to these effects. Here, we investigate the impact on an intrinsically disordered tail that flanks a folded domain, the N-terminal domain, and the RNA-binding domain of the SARS-CoV-2 nucleocapsid protein. We mimic the crowded environment of the cell using polyethylene glycol (PEG) and study its impact on protein conformations using single-molecule Förster resonance energy transfer. We found that high-molecular-weight PEG induces a collapse of the disordered N-terminal tail, whereas low-molecular-weight PEG induces a chain expansion. Our data can be explained by accounting for two opposing contributions: favorable interactions between the protein and crowder molecules and screening of excluded volume interactions. We further characterized the interaction between protein and RNA in the presence of crowding agents. While for all PEG molecules tested, we observed an increase in the binding affinity, the trend is not monotonic as a function of the degree of PEG polymerization. This points to the role of nonspecific protein-PEG interactions on binding in addition to the entropic effects due to crowding. To separate the enthalpic and entropic components of the effects, we investigated the temperature dependence of the association constants in the absence and presence of crowders. Finally, we compared the effects of crowding across mutations in the disordered region and found that the threefold difference in association constants for two naturally occurring variants of the SARS-CoV-2 nucleocapsid protein is reduced to almost identical affinities in the presence of crowders. Overall, our data provide new insights into understanding and modeling the contribution of crowding effects on disordered regions, including the impact of interactions between proteins and crowders and their interplay when binding a ligand.

Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms.

The ε4-allele variant of apolipoprotein E (ApoE4) is the strongest genetic risk factor for Alzheimer's disease, although it only differs from its neutral counterpart ApoE3 by a single amino acid substitution. While ApoE4 influences the formation of plaques and neurofibrillary tangles, the structural determinants of pathogenicity remain undetermined due to limited structural information. Previous studies have led to conflicting models of the C-terminal region positioning with respect to the N-terminal domain across isoforms largely because the data are potentially confounded by the presence of heterogeneous oligomers. Here, we apply a combination of single-molecule spectroscopy and molecular dynamics simulations to construct an atomically detailed model of monomeric ApoE4 and probe the effect of lipid association. Importantly, our approach overcomes previous limitations by allowing us to work at picomolar concentrations where only the monomer is present. Our data reveal that ApoE4 is far more disordered and extended than previously thought and retains significant conformational heterogeneity after binding lipids. Comparing the proximity of the N- and C-terminal domains across the three major isoforms (ApoE4, ApoE3, and ApoE2) suggests that all maintain heterogeneous conformations in their monomeric form, with ApoE2 adopting a slightly more compact ensemble. Overall, these data provide a foundation for understanding how ApoE4 differs from nonpathogenic and protective variants of the protein.

Fluorescence Correlation Spectroscopy and Phase Separation.

A quantitative understanding of the forces controlling the assembly and functioning of biomolecular condensates requires the identification of phase boundaries at which condensates form as well as the determination of tie-lines. Here, we describe in detail how Fluorescence Correlation Spectroscopy (FCS) provides a versatile approach to estimate phase boundaries of single-component and multicomponent solutions as well as insights about the transport properties of the condensate.

Ultrafast dynamics and ultrasensitive single particle spectroscopy of optically robust core/alloy shell semiconductor quantum dots.

A "one-pot one-step" synthesis method of Core/Alloy Shell (CAS) quantum dots (QDs) offers the scope of large scale synthesis in a less time consuming, more economical, highly reproducible and high-throughput manner in comparison to "multi-pot multi-step" synthesis for Core/Shell (CS) QDs. Rapid initial nucleation, and smooth & uniform shell growth lead to the formation of a compositionally-gradient alloyed hetero-structure with very significantly reduced interfacial trap density in CAS QDs. Thus, interfacial strain gets reduced in a much smoother manner leading to enhanced confinement for the photo-generated charge carriers in CAS QDs. Convincing proof of alloy-shelling for a CAS QD has been provided from HRTEM images at the single particle level. The band gap could be tuned as a function of composition, temperature, reactivity difference of precursors, etc. and a high PLQY and improved photochemical stability could be achieved for a small sized CAS QD. From the ultrafast exciton dynamics in CdSe and InP CAS QDs, it has been shown that (a) the hot exciton thermalization/relaxation happens in <500 fs, (b) hot electron trapping dynamics occurs within a ∼1 ps time scale, (c) band edge exciton trapping occurs within a 10-25 ps timescale and (d) for CdSe CAS QDs the hot hole gets trapped in about 35 ps. From fast PL decay dynamics, it has been shown that the amplitude of the intermediate time constant can be correlated with the PLQY. A model has been provided to understand these ultrafast to fast exciton dynamical processes. At the ultrasensitive single particle level, unlike CS QDs, CdSe CAS QDs have been shown to exhibit (a) constancy of PLmax (i.e. no bluing) and (b) constancy of PL intensity (i.e. no bleaching) of the single CAS QDs for continuous irradiation for one hour under an air atmosphere. Thus, CAS QDs hold the promise of being a superior optical probe in comparison to CS QDs both at the ensemble and at the single particle level, leading to enhanced flexibility of the CAS QDs towards designing and developing next generation application devices.

Membrane potential sensing: Material design and method development for single particle optical electrophysiology.

We review the development of "single" nanoparticle-based inorganic and organic voltage sensors, which can eventually become a viable tool for "non-genetic optogenetics." The voltage sensing is accomplished with optical imaging at the fast temporal response and high spatial resolutions in a large field of view. Inorganic voltage nanosensors utilize the Quantum Confined Stark Effect (QCSE) to sense local electric fields. Engineered nanoparticles achieve substantial single-particle voltage sensitivity (∼2% Δλ spectral Stark shift up to ∼30% ΔF/F per 160 mV) at room temperature due to enhanced charge separation. A dedicated home-built fluorescence microscope records spectrally resolved images to measure the QCSE induced spectral shift at the single-particle level. Biomaterial based surface ligands are designed and developed based on theoretical simulations. The hybrid nanobiomaterials satisfy anisotropic facet-selective coating, enabling effective compartmentalization beyond non-specific staining. Self-spiking- and patched-HEK293 cells and cortical neurons, when stained with hybrid nanobiomaterials, show clear photoluminescence intensity changes in response to membrane potential (MP) changes. Organic voltage nanosensors based on polystyrene beads and nanodisk technology utilize Fluorescence (Förster) Resonance Energy Transfer (FRET) to sense local electric fields. Voltage sensing FRET pairs achieve voltage sensitivity up to ∼35% ΔF/F per 120 mV in cultures. Non-invasive MP recording from individual targeted sites (synapses and spines) with nanodisks has been realized. However, both of these QCSE- and FRET-based voltage nanosensors yet need to reach the milestone of recording individual action potentials from individual targeted sites.

Excitation-Energy-Dependent Photoluminescence Quantum Yield is Inherent to Optically Robust Core/Alloy-Shell Quantum Dots in a Vast Energy Landscape.

The importance of alloy-shelling in optically robust Core/Alloy-Shell (CAS) QDs has been described from structural and energetic aspects. Unlike fluorescent dyes, both Core/Shell (CS) and CAS QDs exhibit excitation-energy-dependent photoluminescence quantum yield (PLQY). For both CdSe and InP CAS QDs (with metal- and nonmetal-based alloy-shelling, respectively), with increasing excitation energy, (a) the ultrafast rise-time or relaxation-time to the band-edge increases and (b) the magnitude of the normalized bleach signal decreases. Ultrasensitive single-particle spectroscopic investigation results showed that with decreasing excitation energy, (a) the fraction of ON events increases, (b) the ratio of exciton-detrapping rate/trapping rate increases, and (c) the extent of beneficial hole trapping increases. A relative decrease in PLQY with increasing excitation energy is much less pronounced in CAS QDs than in CS QDs. Unless trap states are removed completely especially in the higher-energy landscape, PLQY will remain inherently dependent on excitation energy for QDs in the vast energy landscape. When reporting the PLQY of QDs, the magnitude of the excitation energy must be mentioned.

Super-Resolution Imaging of Highly Curved Membrane Structures in Giant Vesicles Encapsulating Molecular Condensates.

Molecular crowding is an inherent feature of cell interiors. Synthetic cells as provided by giant unilamellar vesicles (GUVs) encapsulating macromolecules (poly(ethylene glycol) and dextran) represent an excellent mimetic system to study membrane transformations associated with molecular crowding and protein condensation. Similarly to cells, such GUVs exhibit highly curved structures like nanotubes. Upon liquid-liquid phase separation their membrane deforms into apparent kinks at the contact line of the interface between the two aqueous phases. These structures, nanotubes, and kinks, have dimensions below optical resolution. Here, these are studied with super-resolution stimulated emission depletion (STED) microscopy facilitated by immobilization in a microfluidic device. The cylindrical nature of the nanotubes based on the superior resolution of STED and automated data analysis is demonstrated. The deduced membrane spontaneous curvature is in excellent agreement with theoretical predictions. Furthermore, the membrane kink-like structure is resolved as a smoothly curved membrane demonstrating the existence of the intrinsic contact angle, which describes the wettability contrast of the encapsulated phases to the membrane. Resolving these highly curved membrane structures with STED imaging provides important insights in the membrane properties and interactions underlying cellular activities.

Near-Ergodic CsPbBr3 Perovskite Nanocrystal with Minimal Statistical Aging.

Optical robustness, uniformity, ergodicity, statistical aging, etc. dictate the applicability of nanocrystals. Based on a series of multimodal statistical analyses such as the Kolmogorov-Smirnov test, Lévy statistics, etc., we demonstrate that for CsPbBr3 perovskite nanocrystals (PNCs): (a) the extent of heterogeneity in the quality and associated physical processes is minimal; (b) the optical robustness is very high, and (c) indeed, a single PNC can depict optical behavior of its ensemble. In addition, toward prospective applications, an optically robust CsPbBr3 PNC exhibits (i) near-ergodicity and (ii) minimal statistical aging, which are extremely vital and complementary to its high defect tolerance.

Near-Unity Photoluminescence Quantum Yield and Highly Suppressed Blinking in a Toxic-Metal-Free Quantum Dot.

There is no literature report of simultaneously achieving near-unity PLQY (ensemble level) and highly suppressed blinking (ultrasensitive single-particle spectroscopy (SPS) level) in a toxic-metal-free QD. In this Letter we report accomplishing near-unity PLQY (96%) and highly suppressed blinking (>80% ON fraction) in a toxic-metal-free CuInS2/ZnSeS Core/Alloy-Shell (CAS) QD. In addition, (i) gigantic enhancement of PLQY (from 15% (Core) to 96% (CAS QD)), (ii) ultrahigh stability over 1 year without significant reduction of PLQY at the ensemble level, (iii) high magnitude (nearly 3 times) of electron detrapping/trapping rate, and (iv) very long ON duration (∼2 min) without blinking at the SPS level enable this ultrasmall (∼3.3 nm) CAS QD to be quite suitable for single-particle tracking/bioimaging. A model explaining all these excellent optical properties has been provided. This ultrabright CAS QD has been successfully utilized toward fabrication of low-cost microcontroller-based stable and bright yellow and white QD-LEDs.

Unravelling halide-dependent charge carrier dynamics in CsPb(Br/Cl)3 perovskite nanocrystals.

With an increasing bromide content in CsPb(Br/Cl)3 perovskite nanocrystals (PNCs), the steady state photoluminescence quantum yield value increases from 28% to 50% to 76%. Ultrafast transient absorption analyses reveal that the normalized band edge population increases more than two-fold on excitation at the band edge with increasing bromide content, and the hot exciton trapping time increases from 450 fs to 520 fs to 700 fs with increasing bromide content. Ultrasensitive single particle spectroscopic analyses reveal that the peak of the ON fraction distribution increases from 0.65 to 0.75 to 0.85 with increasing bromide content. More specifically, the percentage of PNCs with the ON fraction >75% increases four fold from 24% to 50% to 98% with increasing bromide content. Moreover, the ratio of the detrapping rate and trapping rate increases more than 25 fold with an increase in bromide content, signifying the excitons remaining in the trap state for a smaller time with increasing bromide content. In order to standardize the measurement and analyses, all these three PNCs have the same size and shape, and all the excitations have been made at the same energy above the band edge for all three PNCs and for both ultrafast transient absorption and ultrasensitive single particle measurements.

Mechanical-Bending-Induced Fluorescence Enhancement in Plastically Flexible Crystals of a GFP Chromophore Analogue.

Single crystals of optoelectronic materials that respond to external stimuli, such as mechanical, light, or heat, are immensely attractive for next generation smart materials. Here we report single crystals of a green fluorescent protein (GFP) chromophore analogue with irreversible mechanical bending and associated unusual enhancement of the fluorescence, which is attributed to the strained molecular packing in the perturbed region. Soft crystalline materials with such fluorescence intensity modulations occurring in response to mechanical stimuli under ambient pressure conditions will have potential implications for the design of technologically relevant tunable fluorescent materials.

Mechanical Tension of Biomembranes Can Be Measured by Super Resolution (STED) Microscopy of Force-Induced Nanotubes.

Membrane tension modulates the morphology of plasma-membrane tubular protrusions in cells but is difficult to measure. Here, we propose to use microscopy imaging to assess the membrane tension. We report direct measurement of membrane nanotube diameters with unprecedented resolution using stimulated emission depletion (STED) microscopy. For this purpose, we integrated an optical tweezers setup in a commercial microscope equipped for STED imaging and established micropipette aspiration of giant vesicles. Membrane nanotubes were pulled from the vesicles at specific membrane tension imposed by the aspiration pipet. Tube diameters calculated from the applied tension using the membrane curvature elasticity model are in excellent agreement with data measured directly with STED. Our approach can be extended to cellular membranes and will then allow us to estimate the mechanical membrane tension within the force-induced nanotubes.

Extent of Shallow/Deep Trap States beyond the Conduction Band Minimum in Defect-Tolerant CsPbBr3 Perovskite Quantum Dot: Control over the Degree of Charge Carrier Recombination.

Perovskite quantum dots (PQDs) are known to be defect-tolerant, possessing a clean band gap with optically inactive benign defect states. However, we show that there exist significant deep trap states beyond the conduction band minimum, although the extent of shallow trap states is observed to be minimal. The extent of deep trap states beyond the conduction band minimum seems to be significant in PQDs; however, the extent is less than that of even optically robust CdSe- and InP-based core/alloy-shell QDs. In-depth analyses based on ultrafast transient absorption and ultrasensitive single-particle spectroscopic investigations decode the underlying degree of charge carrier recombination in CsPbBr3 PQDs, which is quite important for energy applications.

A Study on the Pattern of Self-reported Tobacco Addiction in Hypertensive Patients in Gujarat, India.

BACKGROUND: Both hypertension (HTN) and tobacco addiction pose a threat to the health, environment, and socioeconomic status (SES) of the people. When tobacco use disorder exists in people with HTN, it hastens the disease progress and causes early complications. The present study aimed to study the knowledge and practice of tobacco addiction in patients with HTN and find out the correlates of knowledge and practice of tobacco addiction. METHODS: A cross-sectional study was conducted for a period of one year in the Jamnagar District of Western Gujarat, India. Out of total 400 samples, 50% were collected from the five selected Community Health Centers (CHCs) by random sampling and the rest from non-communicable disease (NCD) clinics at the tertiary care hospital of the district. FINDINGS: Most of the patients were in their fifties or above (67.0%), women (57.0%), and married (86.5%). Only 12.0% had awareness about the hazards of tobacco addiction and the prevalence of tobacco addiction was 11%. It was found that use of smokeless tobacco (SLT) among samples was the highest (72.7%) followed by dual consumption, i.e., SLT and smoking (20.5%). The frequency of consumption was ≥ 5 times/day in 54.5%, 70.4% were addicted for > 10 years, and only 15.9% had ever tried to quit tobacco while only 11.4% had successfully quit it. It was seen that those who were aged < 50 years, men, literates, employed, and those belonging to higher SES and urban residence had better knowledge of the health hazards. This was found to have significant statistical association. CONCLUSION: The results provide valuable insight into the tobacco addiction in patients with HTN on which non-pharmacological treatment of HTN can be based.

Suppressed Blinking under Normal Air Atmosphere in Toxic-Metal-Free, Small Sized, InP-Based Core/Alloy-Shell/Shell Quantum Dots.

Suppressed blinking has been reported in large (diameter ∼14.1 nm) core/shell InP quantum dots (QDs) under reduced air environment. We report here suppressed blinking with approximately four times smaller (diameter ∼3.6 nm) core/alloy-shell/shell InP QDs under ambient air atmosphere. The ⟨ON fraction⟩ has been obtained to be 0.65. Approximately 26% of the single QDs exhibit ON fraction >80%. The smaller ON exponent (1.19) magnitude in comparison to the OFF exponent (1.45) indicates longer ON events are interrupted by smaller OFF events. ON event truncation time is ∼1.5 times that of the OFF event, signifying the detrapping rate is much higher than the trapping rate. Interestingly, the detrapping rate/trapping rate (single-particle level property) could be directly correlated to the photoluminescence quantum yield (ensemble level property). An additional exponential term required to fit the probability density distribution of the ON event duration could be correlated with hole trapping, leading to extended ON times (>60 s).

Reply to the 'Comment on ""Where does the fluorescing moiety reside in a carbon dot?"- Investigations based on fluorescence anisotropy decay and resonance energy transfer dynamics"' by H. C. Joshi, Phys. Chem. Chem. Phys., 2019, 21, DOI: 10.1039/c9cp00136k.

The claim that the analysis regarding resonance energy transfer should have been made using different equations than those that we have used is negated based on the following points: (1) we are well aware of the equations the author has provided in his comment. The equation (eqn (3) mentioned below) that the author has written is undoubtedly too simple to describe the complex system delineated in our original paper. This particular equation is perhaps OK for simple dye (donor and acceptor) systems; however, such a simple equation is never enough for nanoparticle/quantum dot systems. (2) Another equation suggested by the author in his comment (eqn (2)) contains a parameter called donor concentration in excited state. We have categorically described in page 6-7 of our original paper why it is difficult to measure the donor concentration accurately even in the ground state. When the donor concentration can't be known accurately it can't be used in the suggested equation. (3) Donor-acceptor distance calculated by eqn (3)/Table 1 provided by the author deviates more than 100% from the distance that is physically feasible. Such kinds of problems are well documented in the literature. (4) One of the papers cited by the author in his comment and many other published papers clearly mention that in the case when all donor molecules/particles do not take part in the resonance energy transfer process or the stoichiometry of a donor-acceptor complex is not known or deviates strongly from 1 : 1, especially in quantum dots or any other nanomaterial system, it is not possible to extract accurate dynamical information related to RET from donor decay. Instead risetime of acceptor yields much more accurate information. Such situations do arise in our system as well.

A population-based study on tobacco consumption in urban slums: Its prevalence, pattern, and determinants.

BACKGROUND: India suffers from a huge burden of substance abuse and associated morbidity and mortality. Among all substance use, tobacco consumption is the most common and yet the most widely accepted one. This study aimed to estimate the prevalence of tobacco consumption, to find out the type of tobacco products used and to assess the factors influencing tobacco consumption in the slums of Shillong city. MATERIALS AND METHODS: A cross-sectional, community-based study was carried out in 330 respondents aged 15 and above. Chi-square test was used to compare proportions, and Student's t-test was used to compare groups for continuous variables. RESULTS: The prevalence of current tobacco consumption was found to be 73.9%, and the rate of quitting was found to be 4.3%. The prevalence of tobacco consumption was observed to be higher in males (52.4%) compared to 21.5% in females. Highly significant statistical association was observed between tobacco consumption and age, gender, and occupation. The statistical association between tobacco consumption and religion and education was found to be statistically significant. Ever use of tobacco in any form as well as smokeless form peaked in 24-34 years, while smoking was more prevalent among 15-24 year olds. The prevalence of smokeless tobacco was higher (47.5%) as compared to the prevalence of smoking (28.2%), closely followed by dual use (24.3%). The most popular smoked and smokeless forms were found to be cigarettes and khaini, respectively. CONCLUSIONS: Tobacco consumption was found to be highly prevalent and was much higher than the national average hinting toward its association with higher incidence of various malignancies in the region and calling for immediate action toward propelling its prevention and control by all stakeholders.

A lay epidemiological study on coexistent stress in hypertension: Its prevalence, risk factors, and implications in patients' lives.

INTRODUCTION: Hypertension poses a global challenge in terms of morbidity and mortality. Worldwide prevalence of hypertension is over 40%. Management of hypertension targets blood pressure control to prevent disease complications. Though stress and hypertension are closely related, stress management is often overlooked in the treatment of hypertension. AIMS: (1) To estimate the prevalence of stress in hypertensive patients and (2) to study the associated risk factors of stress and its implications in disease management. MATERIALS AND METHODS: It was a hospital-based, cross-sectional study done in Western India for 1 year. Data were collected from 400 hypertensive patients attending the selected health institutions using a pretested questionnaire. Chi-square tests were done using Medcalc 10.4.8.0. RESULTS: The prevalence of stress in hypertensive patients was found to be 84.3%. Only 2.4% of these patients sought help from any health professional for stress. The most common stressors found in the patients were financial dependence on others, living in rented house, having a daughter of marriageable age because of associated dowry, death of a loved one, sleep-related problem, and owing a debt among others. Significant statistical association (P < 0.05) of stress was observed with the type of family and socioeconomic status. A highly significant association (P < 0.001) of stress with religion and residential area (whether urban non-slum, slum, or rural) was observed. Stress in individuals leads to poorer compliance with treatment and blood pressure control. CONCLUSION: Coexistent stress should be diagnosed and managed in patients of hypertension for proper disease management and control.

Instantaneous, room-temperature, open-air atmosphere, solution-phase synthesis of perovskite quantum dots through halide exchange employing non-metal based inexpensive HCl/HI: ensemble and single particle spectroscopy.

Herein, the instantaneous synthesis of highly crystalline, uniform-sized (ca. 11.3 ± 0.1 nm), blue-to-green to yellow to red-emitting all-inorganic perovskite quantum dots (CsPbBr3 and mixed halide PQDs) was achieved at room temperature under an open-air atmosphere (no glove box) through halide exchange in the solution phase employing easily available, inexpensive non-metal-based halide sources such as HCl and HI. No complicated pre-treatment of the halide source was required. Moreover, these PQDs were stable for a few weeks under an open-air atmosphere. The PL emission spectra are quite narrow, and the PLQYs are quite high (80% for even Br/I mixed PQDs). At the single particle level, the 〈ON fraction〉 has been noted to vary from 75% to 85% for different PQDs, the m ON values are close to 1.0, and the m OFF values are >1.5. The latter indicates that long ON durations are more probable. The increase in the ON event truncation time (from 2.7 to 4.0 s) and the concomitant decrease in the OFF event truncation time (from 6.6 to 4.3 s) could be correlated with the increase in the PLQY (from 0.55 to 0.75). In addition, an interesting memory effect could be observed in both the ON and the OFF event durations.

Asymmetric Ionic Conditions Generate Large Membrane Curvatures.

Biological membranes possess intrinsic asymmetry. This asymmetry is associated not only with leaflet composition in terms of membrane species but also with differences in the cytosolic and periplasmic solutions containing macromolecules and ions. There has been a long quest for understanding the effect of ions on the physical and morphological properties of membranes. Here, we elucidate the changes in the mechanical properties of membranes exposed to asymmetric buffer conditions and the associated curvature generation. As a model system, we used giant unilamellar vesicles (GUVs) with asymmetric salt and sugar solutions on the two sides of the membrane. We aspirated the GUVs into micropipettes and attached small beads to their membranes. An optical tweezer was used to exert a local force on a bead, thereby pulling out a membrane tube from the vesicle. The assay allowed us to measure the spontaneous curvature and the bending rigidity of the bilayer in the presence of different ions and sugar. At low sugar/salt (inside/out) concentrations, the membrane spontaneous curvature generated by NaCl and KCl is close to zero, but negative in the presence of LiCl. In the latter case, the membrane bulges away from the salt solution. At high sugar/salt conditions, the membranes were observed to become more flexible and the spontaneous curvature was enhanced to even more negative values, comparable to those generated by some proteins. Our findings reveal the reshaping role of alkali chlorides on biomembranes.