Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles

The SARS-CoV-2 viral infection transforms host cells and produces special organelles in many ways, and we focus on the replication organelle where the replication of viral genomic RNA (vgRNA) occurs. To date, the precise cellular localization of key RNA molecules and replication intermediates has been elusive in electron microscopy studies. We use super-resolution fluorescence microscopy and specific labeling to reveal the nanoscopic organization of replication organelles that contain vgRNA clusters along with viral double-stranded RNA (dsRNA) clusters and the replication enzyme, encapsulated by membranes derived from the host endoplasmic reticulum (ER). We show that the replication organelles are organized differently at early and late stages of infection. Surprisingly, vgRNA accumulates into distinct globular clusters in the cytoplasmic perinuclear region, which grow and accommodate more vgRNA molecules as infection time increases. The localization of ER labels and nsp3 (a component of the double-membrane vesicle, DMV) at the periphery of the vgRNA clusters suggests that replication organelles are enclosed by DMVs at early infection stages which then merge into vesicle packets as infection progresses. Precise co-imaging of the nanoscale cellular organization of vgRNA, dsRNA, and viral proteins in replication organelles of SARS-CoV-2 may inform therapeutic approaches that target viral replication and associated processes.

Fat mass: a novel digital biomarker for remote monitoring that may indicate risk for malnutrition and new complications in decompensated cirrhosis

BACKGROUND

Cirrhosis is associated with sarcopaenia and fat wasting, which drive decompensation and mortality. Currently, nutritional status, through body composition assessment, is not routinely monitored in outpatients. Given the deleterious outcomes associated with poor nutrition in decompensated cirrhosis, there is a need for remotely monitoring this to optimise community care.

METHODS

A retrospective analysis was conducted on patients monitored remotely with digital sensors post hospital discharge, to assess outcomes and indicators of new cirrhosis complications. 15 patients had daily fat mass measurements as part of monitoring over a median 10 weeks, using a Withing's bioimpedance scale. The Clinical Frailty Score (CFS) was used to assess frailty and several liver disease severity scores were assessed.

RESULTS

73.3% (11/15) patients were male with a median age of 63 (52-68). There was a trend towards more severe liver disease based on CLIF-Consortium Acute Decompensation (CLIF-C AD) scores in frail patients vs. those not frail (53 vs 46, p = 0.072). When the cohort was split into patients who gained fat mass over 8 weeks vs. those that lost fat mass, the baseline CLIF-C AD scores and WBC were significantly higher in those that lost fat (58 vs 48, p = 0.048 and 11.2 × 109 vs 4.7 × 109, p = 0.031).

CONCLUSIONS

This proof-of-principle study shows feasibility for remote monitoring of fat mass and nutritional reserve in decompensated cirrhosis. Our results suggest fat mass is associated with greater severity of acute decompensation and may serve as an indicator of systemic inflammatory response. Further prospective studies are required to validate this digital biomarker.

Non-surgical organ preservation in laryngeal and hypopharyngeal cancers: an audit from the clinic

BACKGROUND

There is increasing concern regarding efficacy of organ preservation protocol in laryngeal and hypopharyngeal cancers.

METHOD

This study retrospectively assessed disease-related and functional outcomes of 191 patients with non-metastatic laryngeal or hypopharyngeal squamous cell carcinoma treated with curative intent (radiotherapy with or without chemotherapy).

RESULTS

Seventy-six patients (39.8 per cent) had a primary cancer in the larynx, and 115 patients (60.2 per cent) had a primary cancer in the hypopharynx. The median follow up was 39 months. The 3-year time to progression, overall survival, local control and laryngectomy free survival was 56.2 per cent, 76.3 per cent, 73.2 per cent and 67.2 per cent, respectively. At the time of analysis, 83 patients (43.5 per cent) were alive and disease free at their last follow up and did not require tube feeding or tracheostomy. The laryngo-oesophageal dysfunction-free survival was 61 per cent at 3 years.

CONCLUSION

Organ conservation protocols remain the standard of treatment in appropriately selected patients with laryngeal and hypopharyngeal cancers.

Evaluation of the feasibility and acceptability of ReWin-A digital therapeutic rehabilitation innovation for people with stroke-related disabilities in India

Background

Developing culturally appropriate, scalable interventions to meet the growing needs for stroke rehabilitation is a significant problem of public health concern. Therefore, systematic development and evaluation of a scalable, inclusive, technology-driven solution for community-based stroke care are of immense public health importance in India. ReWin is a digital therapeutics platform that was developed systematically. This study aimed to evaluate its feasibility and acceptability in an Indian context.

Objectives

Phase-1: To pilot the intervention for identifying operational issues and finalize the intervention. Phase-2: To assess the feasibility and acceptability of ReWin intervention in an Indian context.

Methods

Design: Mixed-methods research design. Setting: Participant's home and rehabilitation centers. Participants were selected from rehabilitation centers in South India. Participants: Ten stroke survivors and their caregivers, as well as four rehabilitation service providers were recruited for phase 1. Thirty stroke survivors who were treated and discharged from the hospital, and their caregivers as well as 10 rehabilitation service providers were recruited for Phase 2. Intervention: ReWin a digital therapeutic platform with the provider and patient app for the rehabilitation of physical disabilities following stroke was piloted. Process: Evaluation of the intervention was completed in two phases. In the first phase, the preliminary intervention was field-tested with 10 stroke survivors and four rehabilitation service providers for 2 weeks. In the second phase, the finalized intervention was provided to a further 30 stroke survivors to be used in their homes with support from their carers as well as to 10 rehabilitation service providers for 4 weeks. Outcome measures: Primary outcomes: (1) operational difficulties in using the ReWin intervention; (2) feasibility and acceptability of the ReWin intervention in an Indian setting.

Results

Field-testing identified operational difficulties related to 1. Therapeutic content; 2. Format; 3. Navigation; 4. Connectivity, 5. Video-streaming, 6. Language; and 7. Comprehensibility of the animated content. The intervention was reviewed, revised and finalized before pilot testing. Findings from the pilot testing showed that the ReWin intervention was feasible and acceptable. About 76% of the participants had used ReWin for more than half of the intervention period of 4 weeks. Ninety percentage of the stroke care providers and about 60% of the stroke survivors and caregivers felt that the content of ReWin was very relevant to the needs of the stroke survivors. Forty percentage of the stroke survivors and caregivers rated ReWin intervention as excellent. Another 45% of the stroke survivors and caregivers as well as 90% of the stroke care providers rated ReWin intervention as very good based on its overall credibility, usability, and user-friendliness.

Conclusions

ReWin has all the essential components to connect care providers and consumers not just for stroke rehabilitation but for several other health conditions with the use of several other technological features that support rehabilitation of persons with disabilities and strengthen rehabilitation in health systems worldwide. It is critical to amalgamate ReWin and other evidence-based interventions for rehabilitation to innovate scalable solutions and promote universal health coverage for stroke care worldwide.

PINE: Post-Quantum Based Incentive Technique for Non-Cooperating Nodes in Internet of Everything

The Internet of Everything (IoE) is a smart system that interconnects smart entities by incorporating low-cost or low-energy gadgets that are useful for communication with people, processes, data, and devices/things. In such an instantaneously connected environment, network-enabled heterogeneous devices may exhibit non-cooperative behaviour which may lead to the degradation of the network. To address this performance degradation, the proposed Post-quantum based Incentive technique for Non-cooperating nodes in internet of Everything (PINE) protocol provides an end-to-end reliable solution by incorporating location-aware post-quantum encryption in these networks while addressing the non-cooperative behaviour of the nodes by employing an effective strategy in a bi-directional multi-hop relay environment. This proposed protocol further aims to evaluate the consequences of non-cooperative nodes by considering various metrics, namely, number of nodes, message size, execution time, memory consumption, average residual energy, percentage of selfish nodes, and blackhole nodes detection, aiming to achieve significant accuracy in an IoE environment.

Angle distortion model for predicting enediyne activation towards Bergman cyclization: an alternate to the distance theory

The kinetics of Bergman cyclization (BC) of enediynes into 1,4-benzene diradicals (also known as p-benzynes) have attracted interest ever since the discovery of natural enediynes which pointed out a surprising reactivity profile difference across enediynes with varying structural architectures. From the analysis of experimental kinetic data, several models were proposed to have a structure-kinetics correlation, out of which, the cd-distance model and the transition state model are the most accepted ones. Recently, Houk et al. introduced a distortion model to explain the regioselectivity of nucleophilic addition to unsymmetrical o-benzynes based on the geometry of the transition state. In the case of BC, since the reaction is endothermic, the transition state geometrically resembles the product structure which implies that in the reaction pathway, the sp-carbons of enediynes are transformed into the trigonal sp² carbons of the benzenoid product. Thus, greater bending of the interior angles at the proximal alkyne carbons in the enediynes will lead to a lower activation barrier for the BC and hence faster cyclization. This hypothesis has been tested on a series of enediynes including natural product surrogates and the extent of deviation correlates well with the kinetic results. A cut-off value for the average internal proximal angles has been proposed to categorize enediynes as per their reactivity under ambient conditions. We believe that this distortion theory offers an alternative model in designing new unnatural enediynes with desired kinetic stabilities.

Structurally similar enediynes showed decrease in interior proximal bond angles (P_a and P_b) with increase in reactivity. Enediynes with average interior proximal angles [(P_a + P_b)/2] less than 166° undergo cyclization under ambient conditions.

Protamine loops DNA in multiple steps

Protamine proteins dramatically condense DNA in sperm to almost crystalline packing levels. Here, we measure the first step in the in vitro pathway, the folding of DNA into a single loop. Current models for DNA loop formation are one-step, all-or-nothing models with a looped state and an unlooped state. However, when we use a Tethered Particle Motion (TPM) assay to measure the dynamic, real-time looping of DNA by protamine, we observe the presence of multiple folded states that are long-lived (∼100 s) and reversible. In addition, we measure folding on DNA molecules that are too short to form loops. This suggests that protamine is using a multi-step process to loop the DNA rather than a one-step process. To visualize the DNA structures, we used an Atomic Force Microscopy (AFM) assay. We see that some folded DNA molecules are loops with a ∼10-nm radius and some of the folded molecules are partial loops—c-shapes or s-shapes—that have a radius of curvature of ∼10 nm. Further analysis of these structures suggest that protamine is bending the DNA to achieve this curvature rather than increasing the flexibility of the DNA. We therefore conclude that protamine loops DNA in multiple steps, bending it into a loop.

Improved Electrostatic Embedding for Fragment-Based Chemical Shift Calculations in Molecular Crystals

Fragment-based methods predict nuclear magnetic resonance (NMR) chemical shielding tensors in molecular crystals with high accuracy and computational efficiency. Such methods typically employ electrostatic embedding to mimic the crystalline environment, and the quality of the results can be sensitive to the embedding treatment. To improve the quality of this embedding environment for fragment-based molecular crystal property calculations, we borrow ideas from the embedded ion method to incorporate self-consistently polarized Madelung field effects. The self-consistent reproduction of the Madelung potential (SCRMP) model developed here constructs an array of point charges that incorporates self-consistent lattice polarization and which reproduces the Madelung potential at all atomic sites involved in the quantum mechanical region of the system. The performance of fragment- and cluster-based ¹H, ¹³C, ¹⁴N, and ¹⁷O chemical shift predictions using SCRMP and density functionals like PBE and PBE0 are assessed. The improved embedding model results in substantial improvements in the predicted ¹⁷O chemical shifts and modest improvements in the ¹⁵N ones. Finally, the performance of the model is demonstrated by examining the assignment of the two oxygen chemical shifts in the challenging γ-polymorph of glycine. Overall, the SCRMP-embedded NMR chemical shift predictions are on par with or more accurate than those obtained with the widely used gauge-including projector augmented wave (GIPAW) model.

Spectroscopic investigation on the production of clay bricks with SCBA waste

In this paper, the effect of sugarcane bagasse ash (SCBA) addition to the brick making clay has been analyzed using spectroscopic techniques. For that, mixtures of brick making clay (BMC) with sugarcane bagasse ash (SCBA) in proportions of 0-20 wt.% were hydraulic uniaxially pressed and sintered at temperatures of 800-1100 °C. The partial replacement of the brick making clay with SCBA was studied with chemical and mineralogical analyzes (XRF and X-ray diffraction). The quantitative estimation of minerals was made by FTIR analysis. The results of FT-IR reveal that kaolinite, quartz, and lignin are predominant, whereas, cellulose and calcite are in moderate levels. In addition, magnetite and hematite are found in trace level. The overall results reveal that the brick making clay substituted with 15 wt.% of SCBA can open up a new path for the fabrication of quality bricks at low cost.

An insight on electrospun-nanofibers-inspired modern drug delivery system in the treatment of deadly cancers

This review gives an insight into the process of electrospinning, its essential parameters, the types of drug incorporation and the works reported on common dreadful cancers.

Review: physico-chemical modification as a versatile strategy for the biocompatibility enhancement of biomaterials

Physico-chemical modification induced improvement in biocompatibility of materials.

Gallic acid: prospects and molecular mechanisms of its anticancer activity

Gallic acid (GA) is a phenolic acid found in many dietary substances. It is a natural compound found in gallnuts, sumac, witch-hazel, clove, tealeaves, oak bark, sundew and other plants. Edibles like blackberry, hot chocolate, common walnut and Indian gooseberry contain GA.

Prospects of common biomolecules as coating substances for polymeric biomaterials

The concept of using common biomolecules like proteins, carbohydrates,etc., for improving the biocompatibility seems rational and effective because of the bio-friendly surface that they present, remains closer in mimicking the innate environment.

Synthesis of Some New Isoxazoline Derivatives of Chalconised Indoline 2-one as a Potential Analgesic, Antibacterial and Anthelmimtic Agents

A series of novel 1[5”-(2”’-substituted phenyl)-4”,5”’-dihydro isoxazole-3”-yl]-3-[(4 substituted phenyl)imino]1-3-dihydro-2H-indole-2-one were synthesized from different substituted chalconised indole-2,3-dione was prepared from the different chalconised Isatin. The structures of the compounds were elucidated by elemental and spectral (IR, ¹H NMR, and MS) analysis. The synthesized compounds were screened for their analgesic activity by the acetic acid induced Writhing method and in vitro antimicrobial activity against the Gram-positive bacteria—Staphylococcus aureus and the Gram-negative bacteria—Pseudomonas auroginosa, Pseudomonas mirabilis, and E. coli by the cup plate agar diffusion method. Compounds 6a₁, 6a₃, 6b₃, and 6b₂ were found to be active against bacteria. The compounds 6a₁, 6b₃, and 6a₃ show a significant analgesic activity. Synthesized compounds also screened for anthelmintic activity against Pheretima posthuma. Compounds 6a₁, 6b₁, and 6b₃ show significant anthelmintic activity.

Quality of care among type 2 diabetes mellitus patients residing in an urban slum of Chennai Corporation -- a community-based cross-sectional study

Despite the high prevalence, serious long term complications and established evidence based guidelines for management of diabetes mellitus the quality of care is still deficient in developed and developing countries. So a study of these factors and their influence on the quality of care is necessary to tackle diabetes in the community. The objectives of the study were to assess the quality of care in type 2 diabetes patients of 35 years and above age group and to identify the factors associated with it. It is a community-based cross-sectional study done among urban slum people of Chennai, in which 323 adults with type 2 diabetes were interviewed in the above said age group. Variables like age, sex, income, duration of diabetes, healthcare delivery of choice, treatment prescribed, compliance to treatment, family history of diabetes, presence of comorbid illnesses and quality of care indicators were studied and appropriate statistical analysis was carried out. Only 26 adults (8%) received good quality of care in this study. The adults who received good quality of care were among male sex (p < 0.005), high income group (p < 0.001), patients with good compliance to treatment (p < 0.001) and those who preferred private health facility for treatment (p < 0.001). The present current study indicates very low quality of care among this community. The management of diabetes in our setting was suboptimal and even the minimum achievable goals were not reached.