MicroRNA-155 mediates multiple gene regulations pertinent to the role of human adipose-derived mesenchymal stem cells in skin regeneration

Introduction: The role of Adipose-derived mesenchymal stem cells (AD-MSCs) in skin wound healing remains to be fully characterized. This study aims to evaluate the regenerative potential of autologous AD-MSCs in a non-healing porcine wound model, in addition to elucidate key miRNA-mediated epigenetic regulations that underlie the regenerative potential of AD-MSCs in wounds. Methods: The regenerative potential of autologous AD-MSCs was evaluated in porcine model using histopathology and spatial frequency domain imaging. Then, the correlations between miRNAs and proteins of AD-MSCs were evaluated using an integration analysis in primary human AD-MSCs in comparison to primary human keratinocytes. Transfection study of AD-MSCs was conducted to validate the bioinformatics data. Results: Autologous porcine AD-MSCs improved wound epithelialization and skin properties in comparison to control wounds. We identified 26 proteins upregulated in human AD-MSCs, including growth and angiogenic factors, chemokines and inflammatory cytokines. Pathway enrichment analysis highlighted cell signalling-associated pathways and immunomodulatory pathways. miRNA-target modelling revealed regulations related to genes encoding for 16 upregulated proteins. miR-155-5p was predicted to regulate Fibroblast growth factor 2 and 7, C-C motif chemokine ligand 2 and Vascular cell adhesion molecule 1. Transfecting human AD-MSCs cell line with anti-miR-155 showed transient gene silencing of the four proteins at 24 h post-transfection. Discussion: This study proposes a positive miR-155-mediated gene regulation of key factors involved in wound healing. The study represents a promising approach for miRNA-based and cell-free regenerative treatment for difficult-to-heal wounds. The therapeutic potential of miR-155 and its identified targets should be further explored in-vivo.

Design, QSAR Methodology, Synthesis and Assessment of Some Structurally Different Xanthone Derivatives as Selective Cox-2 Inhibitors for their Anti-inflammatory Properties

INTRODUCTION

Inflammation can be defined as a complex biological response that is produced by body tissues to harmful agents like pathogens, irritants, and damaged cells and thereby acts as a protective response incorporating immune cells, blood vessels, and molecular mediators. Histamine, serotonin, bradykinin, leukotrienes (LTB4), prostaglandins (PGE2), prostacyclins, reactive oxygen species, proinflammatory cytokines like IL-1, IL-11, TNF- anti-inflammatory cytokines like IL-4, IL-10, IL-11, IL-6 and IL-13, etc. all have different effects on both pro and anti-inflammatory mediators. Incorporation of combinatorial chemistry and computational studies have helped the researchers to design xanthones moieties with high selectivity that can serve as a lead compound and help develop potential compounds that can act as effective COX-2 inhibitors. The study aims to design and develop different series of substituted hydroxyxanthone derivatives with anti-inflammatory potential.

METHODS

The partially purified synthetic xanthone derivatives were orally administered to the carrageenan induced paw oedemic rat models at the dose of 100 mg/kg, and their effect in controlling the degree of inflammation was measured at the time interval of 30 min, 1, 2, 3, 4 and 6 hrs. respectively. Further, these compounds were also subjected to modern analytical studies like UV, IR, NMR and mass spectrometry or their characterization.

RESULTS

The results drawn out of the in silico, in vitro, in vivo and analytical studies concluded that the hydroxyxanthone derivatives can obstruct the enzyme COX-2 and produce anti-inflammatory action potentially.

CONCLUSION

With the aim to evaluate the compounds for their anti-inflammatory activity, it was observed that the newly designed xanthonic compounds also possess a safe toxicity margin and hence can be utilized by the researchers to develop hybrid xanthonic moieties that can specifically target the enzyme COX-2.

An Automated Brain Metastasis Detection and Segmentation System from MRI with a Large Multi-Institutional Dataset

PURPOSE/OBJECTIVE(S)

Developments of automated systems for brain metastasis (BM) detection and segmentation from MRI for assisting early detection and stereotactic radiosurgery (SRS) have been reported but most based upon relatively small datasets from single institutes. This work aims to develop and evaluate a system using a large multi-institutional dataset, and to improve both identification of small/subtle BMs and segmentation accuracy of large BMs.

MATERIALS/METHODS

A 3D U-Net system was trained and evaluated to detect and segment intraparenchymal BMs with a size > 2mm using 1856 MRI volumes from 1791 patients treated with SRS from seven institutions (1539 volumes for training, 183 for validation, and 134 for testing). All patients had 3D post-Gd T1w MRI scans pre-SRS. Gross tumor volumes (GTVs) of BMs for SRS were curated by each institute first. Then, additional efforts were spent to create GTVs for the untreated and/or uncontoured BMs, including central reviews by two radiologists, to improve accuracy of ground truth. The training dataset was augmented with synthetic BMs of 3773 MRIs using a 3D generative pipeline. Our system consists of two U-Nets with one using small 3D patches dedicated for detecting small BMs and another using large 3D patches for segmenting large BMs, and a random-forest based fusion module for combining the two network outputs. The first U-Net was trained with 3D patches containing at least one BM < 0.1 cm3. For detection performance, we measured BM-level sensitivity and case-level false-positive (FP) rate. For segmentation performance, we measured BM-level Dice similarity coefficient (DSC) and 95-percentile Hausdorff distance (HD95). We also stratified performances based upon BM sizes.

RESULTS

For 739 BMs in the 134 testing cases, the overall lesion-level sensitivity was 0.870 with an average case-level FP of 1.34±1.92 (95% CI: 1.02-1.67). The sensitivity was >0.969 for the BMs >0.1 cm3, but dropped to 0.755 for the BMs < 0.1 cm3 (Table 1). The average DSC and HD95 for all detected BMs were 0.786 and 1.35mm. The worse performance for BMs > 20 cm3 was caused by a case with 83 cm3 GTV and artifacts in the MRI volume.

CONCLUSION

We achieved excellent detection sensitivity and segmentation accuracy for BMs > 0.1 cm3, and promising performance for small BMs (<0.1cm3) with a controlled FP rate using a large multi-institutional dataset. Clinical utility for assisting early detection and SRS planning will be investigated. Table 1: Per-lesion detection and segmentation performance stratified by individual BM size. N is the number of BMs in each category.

Selected β-Glucans Act as Immune-Training Agents by Improving Anti-Mycobacterial Activity in Human Macrophages: A Pilot Study

Epigenetic reprogramming of innate immune cells by β-glucan in a process called trained immunity leads to an enhanced host response to a secondary infection. β-Glucans are structural components of plants, algae, fungi, and bacteria and thus recognized as non-self by human macrophages. We selected the β-glucan curdlan from Alcaligenes faecalis, WGP dispersible from Saccharomyces cerevisiae, and β-glucan-rich culture supernatant of Alternaria and investigated whether they could produce trained immunity effects leading to an increased control of virulent Mycobacterium tuberculosis. We observed a significant M. tuberculosis growth reduction in macrophages trained with curdlan and Alternaria, which also correlated with increased IL-6 and IL-1β release. WGP dispersible-trained macrophages were stratified into "non-responders" and "responders," according to their ability to control M. tuberculosis, with "responders" producing higher IL-6 levels. The addition of neutrophils to infected macrophage cultures further enhanced macrophage control of virulent M. tuberculosis, but not in a stimuli-dependent manner. Pathway enrichment analysis of DNA methylome data also highlighted hypomethylation of genes in pathways associated with signaling and cellular reorganization and motility, and "responders" to WGP training were enriched in the interferon-gamma signaling pathway. This study adds evidence that certain β-glucans show promise as immune-training agents.

methylR: a graphical interface for comprehensive DNA methylation array data analysis

MOTIVATION

DNA methylation analysis using arrays is a widely used method in research and clinical studies to study Epigenetics. Although several packages have been published to incur the results, most of them require a deep computational knowledge to perform the analysis. To resolve the limitation and to offer an easily accessible solution for researchers, we developed methylR a graphical tool that can analyze not only the raw data but also performs different downstream analyses with a few mouse clicks.

RESULTS

We used standard and established open-source published packages or pipelines in methylR. We evaluated a publicly available dataset and compared the published results with those obtained with our tool. We implemented eight downstream analysis modules that can perform multidimensional analyses to pathway enrichment. Although the main application is designed for Illumina DNA methylation array data analysis, we made the accessory modules suitable for other kinds of data analysis as well.

AVAILABILITY

Freely available at Github: https://github.com/JD2112/methylr; Webserver: https://methylr.research.liu.se.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Cardioprotective Activities of some Indian Spices: An Insight into Pharmacology and Phytochemical Investigation

Abstract

Cardiovascular disease (CVD) is the leading cause of death globally, and coronary heart disease (CHD) is the most prominent one among the spectrum of CVD. Conventional CHD drugs pose an increased risk of pharmaceutical interactions. Moreover, the possibility of tainting or substituting other medications also raises concerns. Diet and lifestyle play an important role in preventing and treating heart disease, and certain spices and supplements can help reduce the risk of heart disease and treat it. Spices have been an important part of Indian culture from the dawn of time, valued for both their culinary and medicinal virtues. Indian spices and their bioactive phytoconstituents are reported to play an ameliorating role in treating CHD. Despite the fact that the majority of these spices have an effect on organic components associated with the cardiovascular system, data on their therapeutic effects is sparse. To make the most of the enormous potential of these spices, multidisciplinary research is the need of the hour to establish them as remedies for CVDs. We endeavour to document some ethnopharmacological studies aimed to establish the cellular and molecular cardio-protective mechanisms of the spices and their bioactive phytoconstituents using recently reported in vitro and in vivo studies. Finally, we reviewed and reported the results of the recent clinical trials that have been conducted using these spices with special emphasis on their efficacy, safety, and toxicity

The spectrum of tuberculosis described as differential DNA methylation patterns in alveolar macrophages and alveolar T cells

BACKGROUND

Host innate immune cells have been identified as key players in the early eradication of Mycobacterium tuberculosis and in the maintenance of an anti-mycobacterial immune memory, which we and others have shown are induced through epigenetic reprogramming. Studies on human tuberculosis immunity are dominated by those using peripheral blood as surrogate markers for immunity. We aimed to investigate DNA methylation patterns in immune cells of the lung compartment by obtaining induced sputum from M. tuberculosis- exposed subjects including symptom-free subjects testing positively and negatively for latent tuberculosis as well as patients diagnosed with active tuberculosis. Alveolar macrophages and alveolar T cells were isolated from the collected sputum and DNA methylome analyses performed (Illumina Infinium Human Methylation 450 k).

RESULTS

Multidimensional scaling analysis revealed that DNA methylomes of cells from the tuberculosis-exposed subjects and controls appeared as separate clusters. The numerous genes that were differentially methylated between the groups were functionally connected and overlapped with previous findings of trained immunity and tuberculosis. In addition, analysis of the interferon-gamma release assay (IGRA) status of the subjects demonstrated that the IGRA status was reflected in the DNA methylome by a unique signature.

CONCLUSIONS

This pilot study suggests that M. tuberculosis induces epigenetic reprogramming in immune cells of the lung compartment, reflected as a specific DNA methylation pattern. The DNA methylation signature emerging from the comparison of IGRA-negative and IGRA-positive subjects revealed a spectrum of signature strength with the TB patients grouping together at one end of the spectrum, both in alveolar macrophages and T cells. DNA methylation-based biosignatures could be considered for further development towards a clinically useful tool for determining tuberculosis infection status and the level of tuberculosis exposure.

The Olfactomedin-4-Defined Human Neutrophil Subsets Differ in Proteomic Profile in Healthy Individuals and Patients with Septic Shock

The specific granule glycoprotein olfactomedin-4 (Olfm4) marks a subset (1-70%) of human neutrophils and the Olfm4-high (Olfm4-H) proportion has been found to correlate with septic shock severity. The aim of this study was to decipher proteomic differences between the subsets in healthy individuals, hypothesizing that Olfm4-H neutrophils have a proteomic profile distinct from that of Olfm4 low (Olfm4-L) neutrophils. We then extended the investigation to septic shock. A novel protocol for the preparation of fixed, antibody-stained, and sorted neutrophils for LC-MS/MS was developed. In healthy individuals, 39 proteins showed increased abundance in Olfm4-H, including the small GTPases Rab3d and Rab11a. In Olfm4-L, 52 proteins including neutrophil defensin alpha 4, CXCR1, Rab3a, and S100-A7 were more abundant. The data suggest differences in important neutrophil proteins that might impact immunological processes. However, in vitro experiments revealed no apparent difference in the ability to control bacteria nor produce oxygen radicals. In subsets isolated from patients with septic shock, 24 proteins including cytochrome b-245 chaperone 1 had significantly higher abundance in Olfm4-H and 30 in Olfm4-L, including Fc receptor proteins. There was no correlation between Olfm4-H proportion and septic shock severity, but plasma Olfm4 concentration was elevated in septic shock. Thus, the Olfm4-H and Olfm4-L neutrophils have different proteomic profiles, but there was no evident functional significance of the differences in septic shock.

Coping strategies and barriers to coping in climate- vulnerable Bangladesh: a qualitative study

 

With the mental wellbeing of billions of people at risk due to climate change, more research is required to better understand mental health and psychological implications of climate vulnerability. This research contributes to understanding how people in climate vulnerable populations psychologically cope with stress with crucial implications for adaptation efforts. We conducted n = 60 qualitative in-depth interviews with men and women in Bhola, Bangladesh to elicit the lived experiences of a climate vulnerable population. We analysed data following the tenets of Grounded Theory. Through our inductive analysis, we found coping strategies where participants highlighted what they did when encountering stress, such as ‘Resignation’ or ‘Help Seeking'. Barriers to coping were, among others, limited ‘Efficacy', ‘Time’ or ‘Stigma'. We categorized coping strategies with barriers as high-barrier coping strategies and, those without reported barriers, as low- barrier coping strategies. High-barriers restricted participants - especially women - in their coping efforts and led them to using low-barrier coping strategies. Some low-barrier coping strategies can be interpreted as maladaptive if used frequently, as they are unhealthy and draw upon resources needed to adapt for the future. Maladaptive coping strategies can thus impede long-term adaptation by reducing motivation and the ability and willingness to act. To enable adaptive coping, we recommend lifting the barriers to coping through community-led interventions where community workers create platforms for sharing problems and knowledge, such as group support meetings. Sharing and discussing could strengthen efficacy and open new opportunities for functional, adaptive coping. As the negative impacts of climate change will be felt globally with more intensity and frequency, enabling adaptive coping and removing barriers to coping in frontline communities will be essential to supporting physical and mental wellbeing.

Key messages

• Barriers to adaptive coping strategies can lead people to using maladaptive low-barrier coping strategies, which draw upon resources needed for long-term adaptation.

• Enabling adaptive coping by lifting barriers to coping in climate vulnerable populations is crucial to strengthen adaptation efforts.

Methylation associated with long- or short-term survival in glioblastoma patients from the Nordic phase 3 trial

Patients with glioblastoma (GBM) have a poor outcome, but even among patients receiving the same therapies and with good prognostic factors, one can find those with exceptionally short and long survival. From the Nordic trial, which randomized GBM patients of 60 years or older between two radiotherapy arms (60 Gy or 34 Gy) or temozolomide (TMZ), we selected 59 with good prognostic factors. These selected GBM patients were equally distributed according to treatment and MGMT promoter methylation status but had long or short survival. Methylation profiling with the Illumina Infinium Methylation EPIC BeadChip arrays was performed and utilized for methylation-based CNS tumor classification, and pathway enrichment analysis of differentially methylated CpG sites (DMCs), as well as calculation of epigenetic age acceleration with three different algorithms, to compare the long and short survival groups. Samples identified by the classifier as non-GBM IDH wildtype were excluded. DMCs between long- and short-term survivors were found in patients with methylated MGMT promoter treated with TMZ (123,510), those with unmethylated MGMT treated with 60Gy radiotherapy (4,086), and with methylated MGMT promoter treated with 34Gy radiotherapy (39,649). Long-term survivors with methylated MGMT promoter treated with TMZ exhibited hypermethylation of the Wnt signaling and the platelet activation, signaling, and aggregation pathways. The joint analysis of radiotherapy arms revealed 319 DMCs between long- and short-term survivors with unmethylated MGMT and none for samples with methylated MGMT promoter. An analysis comparing epigenetic age acceleration between patients with long- and short-term survival across all treatment arms showed a decreased epigenetic age acceleration for the latter. We identified DMCs for both TMZ and RT-treated patients and epigenetic age acceleration as a potential prognostic marker, but further systematic analysis of larger patient cohorts is necessary for confirmation of their prognostic and/or predictive properties.

Prospective randomized comparison of bone transport versus Masquelet technique in infected gap nonunion of tibia

AIM

The present prospective randomized study compared the bone transport technique (BT) and Masquelet technique (MT) in the treatment of infected gap non-union of the tibia.

PATIENTS AND METHODS

Total 25 patients with infected gap non-union of the tibia with bone gap upto 6 cm were randomised into BT group (group I, 13 patients) and MT (group II, 12 patients). The mean age was 31.77 years in group I and 39.67 years in group II. The mean intra-operative bone gap was 3.92 cm in group I and 3.79 cm in group II. Monolateral fixator was applied in nine patients each in both groups, while four and three fractures were stabilized with ring fixators in group I and II, respectively. Mean follow-up was 31.62 months and 30.42 months in group I and II, respectively. Bone and functional results were compared using the association for the study and application of the method of Ilizarov (ASAMI) criteria.

RESULTS

The average fixator period was 9.42 and 16.33 months in group I and II, respectively (p < 0.001). Union was achieved in 12 (92%) patients and 6 (50%) patients in group I and II, respectively. The functional results were excellent (eight and two), good (four and six), fair (zero and three) and poor (one and one) in group I and II respectively, (p 0.23). The Bone results were excellent, good and poor in nine, three and one patients in group I, and three, three and six patients in group II respectively, (p 0.109).

CONCLUSIONS

The functional and bone results were comparable but more reliable in bone transport than the Masquelet technique. The fixator duration and incidence of non-union were higher in MT group. Ilizarov bone transport technique should be preferred in infected non-union of the tibia with bone loss upto 6 cm.

Epigenetic rewiring of pathways related to odour perception in immune cells exposed to SARS-CoV-2 in vivo and in vitro

A majority of SARS-CoV-2 recoverees develop only mild-to-moderate symptoms, while some remain completely asymptomatic. Although viruses, including SARS-CoV-2, may evade host immune responses by epigenetic mechanisms including DNA methylation, little is known about whether these modifications are important in defence against and healthy recovery from COVID-19 in the host. To this end, epigenome-wide DNA methylation patterns from COVID-19 convalescents were compared to uninfected controls from before and after the pandemic. Peripheral blood mononuclear cell (PBMC) DNA was extracted from uninfected controls, COVID-19 convalescents, and symptom-free individuals with SARS-CoV-2-specific T cell-responses, as well as from PBMCs stimulated in vitro with SARS-CoV-2. Subsequently, the Illumina MethylationEPIC 850K array was performed, and statistical/bioinformatic analyses comprised differential DNA methylation, pathway over-representation, and module identification analyses. Differential DNA methylation patterns distinguished COVID-19 convalescents from uninfected controls, with similar results in an experimental SARS-CoV-2 infection model. A SARS-CoV-2-induced module was identified in vivo, comprising 66 genes of which six (TP53, INS, HSPA4, SP1, ESR1, and FAS) were present in corresponding in vitro analyses. Over-representation analyses revealed involvement in Wnt, muscarinic acetylcholine receptor signalling, and gonadotropin-releasing hormone receptor pathways. Furthermore, numerous differentially methylated and network genes from both settings interacted with the SARS-CoV-2 interactome. Altered DNA methylation patterns of COVID-19 convalescents suggest recovery from mild-to-moderate SARS-CoV-2 infection leaves longstanding epigenetic traces. Both in vitro and in vivo exposure caused epigenetic modulation of pathways thataffect odour perception. Future studies should determine whether this reflects host-induced protective antiviral defense or targeted viral hijacking to evade host defence.

CD4+CCR6+ T cells dominate the BCG-induced transcriptional signature

BACKGROUND

The century-old Mycobacterium bovis Bacillus Calmette-Guerin (BCG) remains the only licensed vaccine against tuberculosis (TB). Despite this, there is still a lot to learn about the immune response induced by BCG, both in terms of phenotype and specificity.

METHODS

We investigated immune responses in adult individuals pre and 8 months post BCG vaccination. We specifically determined changes in gene expression, cell subset composition, DNA methylome, and the TCR repertoire induced in PBMCs and CD4 memory T cells associated with antigen stimulation by either BCG or a Mycobacterium tuberculosis (Mtb)-derived peptide pool.

FINDINGS

Following BCG vaccination, we observed increased frequencies of CCR6+ CD4 T cells, which includes both Th1* (CXCR3+CCR6+) and Th17 subsets, and mucosal associated invariant T cells (MAITs). A large number of immune response genes and pathways were upregulated post BCG vaccination with similar patterns observed in both PBMCs and memory CD4 T cells, thus suggesting a substantial role for CD4 T cells in the cellular response to BCG. These upregulated genes and associated pathways were also reflected in the DNA methylome. We described both qualitative and quantitative changes in the BCG-specific TCR repertoire post vaccination, and importantly found evidence for similar TCR repertoires across different subjects.

INTERPRETATION

The immune signatures defined herein can be used to track and further characterize immune responses induced by BCG, and can serve as reference for benchmarking novel vaccination strategies.

DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types

Flow cytometry is a classical approach used to define cell types in peripheral blood. While DNA methylation signatures have been extensively employed in recent years as an alternative to flow cytometry to define cell populations in peripheral blood, this approach has not been tested in lung-derived samples. Here, we compared bronchoalveolar lavage with a more cost-effective and less invasive technique based on sputum induction and developed a DNA methylome-based algorithm that can be used to deconvolute the cell types in such samples. We analysed the DNA methylome profiles of alveolar macrophages and lymphocytes cells isolated from the pulmonary compartment. The cells were isolated using two different methods, sputum induction and bronchoalveolar lavage. A strong positive correlation between the DNA methylome profiles of cells obtained with the two isolation methods was found. We observed the best correlation of the DNA methylomes when both isolation methods captured cells from the lower parts of the lungs. We also identified unique patterns of CpG methylation in DNA obtained from the two cell populations, which can be used as a signature to discriminate between the alveolar macrophages and lymphocytes by means of open-source algorithms. We validated our findings with external data and obtained results consistent with the previous findings. Our analysis opens up a new possibility to identify different cell populations from lung samples and promotes sputum induction as a tool to study immune cell populations from the lung.

Integrated multiplex network based approach for hub gene identification in oral cancer

Background: The incidence of Oral Cancer (OC) is high in Asian countries, which goes undetected at its early stage. The study of genetics, especially genetic networks holds great promise in this endeavor. Hub genes in a genetic network are prominent in regulating the whole network structure of genes. Thus identification of such genes related to specific cancer types can help in reducing the gap in OC prognosis. Methods: Traditional study of network biology is unable to decipher the inter-dependencies within and across diverse biological networks. Multiplex network provides a powerful representation of such systems and encodes much richer information than isolated networks. In this work, we focused on the entire multiplex structure of the genetic network integrating the gene expression profile and DNA methylation profile for OC. Further, hub genes were identified by considering their connectivity in the multiplex structure and the respective protein-protein interaction (PPI) network as well. Results: 46 hub genes were inferred in our approach with a high prediction accuracy (96%), outstanding Matthews coefficient correlation value (93%) and significant biological implications. Among them, genes PIK3CG, PIK3R5, MYH7, CDC20 and CCL4 were differentially expressed and predominantly enriched in molecular cascades specific to OC. Conclusions: The identified hub genes in this work carry ontological signatures specific to cancer, which may further facilitate improved understanding of the tumorigenesis process and the underlying molecular events. Result indicates the effectiveness of our integrated multiplex network approach for hub gene identification. This work puts an innovative research route for multi-omics biological data analysis.

A high-throughput screening assay based on automated microscopy for monitoring antibiotic susceptibility of Mycobacterium tuberculosis phenotypes

Background

Efficient high-throughput drug screening assays are necessary to enable the discovery of new anti-mycobacterial drugs. The purpose of our work was to develop and validate an assay based on live-cell imaging which can monitor the growth of two distinct phenotypes of Mycobacterium tuberculosis and to test their susceptibility to commonly used TB drugs.

Results

Both planktonic and cording phenotypes were successfully monitored as fluorescent objects using the live-cell imaging system IncuCyte S3, allowing collection of data describing distinct characteristics of aggregate size and growth. The quantification of changes in total area of aggregates was used to define IC₅₀ and MIC values of selected TB drugs which revealed that the cording phenotype grew more rapidly and displayed a higher susceptibility to rifampicin. In checkerboard approach, testing pair-wise combinations of sub-inhibitory concentrations of drugs, rifampicin, linezolid and pretomanid demonstrated superior growth inhibition of cording phenotype.

Conclusions

Our results emphasize the efficiency of using automated live-cell imaging and its potential in high-throughput whole-cell screening to evaluate existing and search for novel antimycobacterial drugs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02212-3.

Innate Immune Invisible Ultrasmall Gold Nanoparticles-Framework for Synthesis and Evaluation

Nanomedicine is seen as a potential central player in the delivery of personalized medicine. Biocompatibility issues of nanoparticles have largely been resolved over the past decade. Despite their tremendous progress, less than 1% of applied nanosystems can hit their intended target location, such as a solid tumor, and this remains an obstacle to their full ability and potential with a high translational value. Therefore, achieving immune-tolerable, blood-compatible, and biofriendly nanoparticles remains an unmet need. The translational success of nanoformulations from bench to bedside involves a thorough assessment of their design, compatibility beyond cytotoxicity such as immune toxicity, blood compatibility, and immune-mediated destruction/rejection/clearance profile. Here, we report a one-pot process-engineered synthesis of ultrasmall gold nanoparticles (uGNPs) suitable for better body and renal clearance delivery of their payloads. We have obtained uGNP sizes of as low as 3 nm and have engineered the synthesis to allow them to be accurately sized (almost nanometer by nanometer). The synthesized uGNPs are biocompatible and can easily be functionalized to carry drugs, peptides, antibodies, and other therapeutic molecules. We have performed in vitro cell viability assays, immunotoxicity assays, inflammatory cytokine analysis, a complement activation study, and blood coagulation studies with the uGNPs to confirm their safety. These can help to set up a long-term safety-benefit framework of experimentation to reveal whether any designed nanoparticles are immune-tolerable and can be used as payload carriers for next-generation vaccines, chemotherapeutic drugs, and theranostic agents with better body clearance ability and deep tissue penetration.

Assessment of cosmesis and quality of life and their correlation using novel, validated methods in breast cancer patients who had undergone breast conservation therapy

PURPOSE

To assess cosmesis [Breast Cancer Conservation Treatment. Cosmetic Results (BCCT.CORE) software] & QOL [EORTC QLQ (Quality of Life Questionnaire)-C30, BR23 questionnaires] using objective methods &to correlate effect of cosmesis on QOL (Quality of life) in breast cancer patients post BCT (Breast conservation therapy) using a cross-sectional observational study from a tertiary hospital.

MATERIALS & METHODS

Cosmesis & QOL had been assessed in all biopsy-proven adult patients of unilateral breast cancer, who had undergone BCT with minimum three months post-BCT & three months post last adjuvant chemotherapy cycle, whichever is delivered last (with just hormonal therapy or followup remaining based on hormone receptor status). Pearson chi-square & Kendall correlation Tau-b tests had been used for testing association between Cosmesis & QOL. Variation of QOL scores between Cosmetic groups had been assessed using Mann-Whitney U-test.

RESULTS

Cosmesis was Excellent/Good in 60.4 % of patients. 58.4 % of patients had Excellent/Good Quality of Life. Cosmesis & QOL had a positive correlation (intermediate strength) [Kendall correlation factor-0.484]. QOL-Global scale had better median scores in Excellent/ Good cosmetic group when compared to Fair/Poor group, while for functional & symptomatic scales, contrary had been true. Difference of median-scores between the two groups hadn't been statistically significant in five aspects - being upset over hair loss (p-0.09), sexual-enjoyment (p-0.33), nausea-vomiting (p-0.29), constipation (p0.32) & diarrhea (p-0.72).

CONCLUSION

About 2/3rds of patients post-BCT had Excellent/Good Cosmesis & Excellent/Good QOL. Every measure taken before, during & post-BCT to improve Cosmesis might result in better QOL. Future studies must use more accurate three-dimensional methods to assess Cosmesis & its effect on QOL.

Genome-wide identification and expression analysis of the plant specific LIM genes in Gossypium arboreum under phytohormone, salt and pathogen stress

Asiatic cotton (Gossypium arboreum) cultivated as ‘desi cotton’ in India, is renowned for its climate resilience and robustness against biotic and abiotic stresses. The genome of G. arboreum is therefore, considered as a valued reserve of information for discovering novel genes or gene functions for trait improvements in the present context of cotton cultivation world-wide. In the present study, we carried out genome-wide analysis of LIM gene family in desi cotton and identified twenty LIM domain proteins (GaLIMs) which include sixteen animals CRP-like GaLIMs and four plant specific GaLIMs with presence (GaDA1) or absence (GaDAR) of UIM (Ubiquitin Interacting Motifs). Among the sixteen CRP-like GaLIMs, eleven had two conventional LIM domains while, five had single LIM domain which was not reported in LIM gene family of the plant species studied, except in Brassica rapa. Phylogenetic analysis of these twenty GaLIM proteins in comparison with LIMs of Arabidopsis, chickpea and poplar categorized them into distinct αLIM1, βLIM1, γLIM2, δLIM2 groups in CRP-like LIMs, and GaDA1 and GaDAR in plant specific LIMs group. Domain analysis had revealed consensus [(C-X₂-C-X₁₇-H-X₂-C)-X₂-(C-X₂-C-X₁₇-C-X₂-H)] and [(C-X₂-C-X₁₇-H-X₂-C)-X₂-(C-X₄-C-X₁₅-C-X₂-H)] being conserved as first and/or second LIM domains of animal CRP-like GaLIMs, respectively. Interestingly, single LIM domain containing GaLIM15 was found to contain unique consensus with longer inter-zinc-motif spacer but shorter second zinc finger motif. All twenty GaLIMs showed variable spatio-temporal expression patterns and accordingly further categorized into distinct groups of αLIM1, βLIM1, γLIM2 δLIM2 and plant specific LIM (DA1/DAR). For the first time, response of GaDA1/DAR under the influence of biotic and abiotic stresses were studied in cotton, involving treatments with phytohormones (Jasmonic acid and Abscisic acid), salt (NaCl) and wilt causing pathogen (Fusarium oxysporum). Expressions patterns of GaDA1/DAR showed variable response and identified GaDA2 as a probable candidate gene for stress tolerance in G. arboreum.

Autologous haematopoietic stem cell transplantation as a first-line disease-modifying therapy in patients with 'aggressive' multiple sclerosis

BACKGROUND

Autologous haematopoietic stem cell transplantation (AHSCT) is an effective treatment for patients with multiple sclerosis (MS) who have highly active disease, despite the use of standard disease-modifying therapies (DMTs). However, the optimal time for offering AHSCT to patients with 'aggressive' MS is yet to be established.

OBJECTIVES

The objective was to explore the safety and efficacy of AHSCT as a first-line DMT in patients with 'aggressive' MS.

METHODS

All patients with 'aggressive' MS who received AHSCT as a first-line DMT in five European and North American centres were retrospectively evaluated.

RESULTS

Twenty patients were identified. The median interval between diagnosis and AHSCT was 5 (1-20) months. All had multiple poor prognostic markers with a median pre-transplant Expanded Disability Status Scale (EDSS) score of 5.0 (1.5-9.5). After a median follow-up of 30 (12-118) months, the median EDSS score improved to 2.0 (0-6.5, p < 0.0001). No patient had further relapses. Three had residual magnetic resonance imaging (MRI) disease activities in the first 6 months post-transplant, but no further new or enhancing lesions were observed in subsequent scans.

CONCLUSION

AHSCT is safe and effective as a first-line DMT in inducing rapid and sustained remission in patients with 'aggressive' MS.

Energy saving and Fuzzy-PID position control of electro-hydraulic system by leakage compensation through proportional flow control valve

In this article, the focus is on the energy efficiency along with the position control of the linear actuator used in heavy earth moving equipment. It is quite evident that linear actuators are one of the critical machinery components used in the construction and mining activities like in booms of excavation equipment. The proposed work employed two different hydraulic circuits and a contrast has been carried out in terms of the energy efficiency. In one hydraulic circuit, the conventional proportional directional control valve (PDCV) is used for the position control. In another one, an innovative solution of using proportional flow control valve (PFCV) by creating artificial leakage between the two ends of the actuator is evaluated according to its energy efficiency. The extra flow coming from the pump during position control is by-passed by PFCV rather than the pressure relief valve in PDCV. This reduces the energy loss in the form of heat and increases the efficiency of the hydraulic circuit. The simulation of the hydraulic circuit is performed using MATLAB/Simulink and results are compared with the experiments and it is found that hydraulic circuit using PFCV is 8.5% more energy efficient than the conventional circuit using PDCV. The position control of the actuator is done using PID controller tuned by the fuzzy controller.

A novel approach for the energy recovery and position control of a hybrid hydraulic excavator

The heavy earth moving machineries (HEMM) like hydraulic excavator play a major role in construction and mining industries. In this context, the energy saving strategies in hydraulic excavator needs to be addressed considering its vital importance. Since the hydraulic excavators are subjected to heavy loads, hence the opportunity to harness the potential gravitational energy (GPE) remains a key area which can be effectively explored in order to minimize the energy consumption in consideration with hydraulic excavator. In the projected system, the potential energy is stored as pressure energy in hydro-pneumatic accumulator. The upward movement of the boom is executed with the help of prime mover during the starting of the first duty cycle. In the latter duty cycles, the stored pressurized energy is utilized together with the prime mover energy capable to execute the upward movement of the boom. The position of the boom cylinder is controlled by using the conventional PID controller using proportional flow control valve (PFCV) and accumulator. The error between the actual position and demand position of the linear actuator is minimized along with attainment of superior controlled performance while utilizing Model Predictive Controller (MPC). The pressurized accumulator with PFCV has been utilized to cater the different position demands. This has been also justified both experimentally and analytically with the error in the permissible range of 2%. It has been observed that the proposed system is 10% more efficient in contrast to the conventional system.

Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects

The protection against tuberculosis induced by the Bacille Calmette Guérin (BCG) vaccine is unpredictable. In our previous study, altered DNA methylation pattern in peripheral blood mononuclear cells (PBMCs) in response to BCG was observed in a subgroup of individuals, whose macrophages killed mycobacteria effectively (‘responders’). These macrophages also showed production of Interleukin-1β (IL-1β) in response to mycobacterial stimuli before vaccination. Here, we hypothesized that the propensity to respond to the BCG vaccine is reflected in the DNA methylome. We mapped the differentially methylated genes (DMGs) in PBMCs isolated from responders/non-responders at the time point before vaccination aiming to identify possible predictors of BCG responsiveness. We identified 43 DMGs and subsequent bioinformatic analyses showed that these were enriched for actin-modulating pathways, predicting differences in phagocytosis. This could be validated by experiments showing that phagocytosis of mycobacteria, which is an event preceding mycobacteria-induced IL-1β production, was strongly correlated with the DMG pattern.

A randomized study to compare palonosetron with ondansetron for prevention of postoperative nausea and vomiting following middle ear surgeries

Background and Aims:

Postoperative nausea and vomiting (PONV) has multifactorial etiology. It is a commonly encountered morbidity after anesthesia specially following middle ear surgery. Various antiemetic medications have been tried with mixed responses. Palonosetron is a newer 5-hydroxytryptamine (5-HT₃) receptor antagonist marketed for PONV prophylaxis. This study was designed to compare the efficacy of palonosetron and ondansetron in preventing PONV after middle ear surgeries.

Material and Methods:

One hundred patients of ASA class 1 or 2, aged 18 years and above, weighing between 40 and 90 kg scheduled for elective middle ear surgeries were randomly assigned into palonosetron group (n = 50) and ondansetron group (n = 50). Palonosetron was administered in dose of 1 mcg/kg maximum up to 75 mcg and ondansetron in dose of 0.1 mg/kg maximum up to 8 mg. Intraoperative monitoring of QTc interval was also done to see any significant change after the antiemetic administration. The incidence of nausea, vomiting, and side effects were recorded over 2, 12, and 24 hours postoperatively. All parameters were compared between the two groups as mean ± standard deviation and as count (%). Two sided P values of <0.05 were considered significant.

Results:

The incidence of PONV (P = 0.002), nausea (P = 0.0002) and vomiting (P = 0.006) was significantly lower in palonosetron group than in ondansetron group in 2- to 12-hour period. QTc interval prolongation, a known side effect of ondansetron was not found in palonosetron group intraoperatively.

Conclusion:

Palonosetron was found to be superior to ondansetron up to 12 hours after the surgery with no significant effect on QTc interval.

Studies on the interaction of a synthetic nitro-flavone derivative with DNA: A multi-spectroscopic and molecular docking approach

Interaction of a ligand with DNA is often the basis of drug action of many molecules. Flavones are important in this regard as their structural features confer them the ability to bind to DNA. 2-(4-Nitrophenyl)-4H-chromen-4-one (4NCO) is an important biologically active synthetic flavone derivative. We are therefore interested in studying its interaction with DNA. Absorption spectroscopy studies included standard and reverse titration, effect of ionic strength on titration, determination of stoichiometry of binding and thermal denaturation. Spectrofluorimetry techniques included fluorimetric titration, quenching studies and fluorescence displacement assay. Assessment of relative viscosity and estimation of thermodynamic parameters from CD spectral studies were also undertaken. Furthermore, molecular docking analyses were also done with different short DNA sequences. The fluorescent flavone 4NCO reversibly interacted with DNA through partial intercalation as well as minor-groove binding. The binding constant and the number of binding sites were of the order 10⁴ M^-1 and 1 respectively. The binding stoichiometry with DNA was found to be 1:1. The nature of the interaction of 4NCO with DNA was hydrophobic in nature and the process of binding was spontaneous, endothermic and entropy-driven. The flavone also showed a preference for binding to GC rich sequences. The study presents a profile for structural and thermodynamic parameters, for the binding of 4NCO with DNA. DNA is an important target for ligands that are effective against cell proliferative disorders. In this regard, the molecule 4NCO is important since it can exert its biological activity through its DNA binding ability and can be a potential drug candidate.

Respiratory Morbidity among Indian Tea Industry Workers

Background:

Indian tea industry workers are exposed to various exposures at their workplace.

Objective:

To investigate the respiratory health of Indian tea industry workers.

Methods:

We administered a respiratory questionnaire to and measured lung function in workers of 34 tea gardens and 46 tea factories. We used correlation matrices to test the association between their respiratory symptoms and lung functions.

Results:

The garden workers complained of shortness of breath 3 times higher than the factory workers. However, nasal allergy was more predominant among the factory workers compared to garden workers (69.6% vs 41.2%, p=0.02). The factory workers had higher total (median 107.3% vs 92.9%, p=0.05, as measured by R at 5 Hz) and peripheral airway resistance (143.8% vs 61.1%, p=0.005, as measured by R at 5–20 Hz) than the garden workers. Respiratory symptoms were inversely associated with airway obstruction as measured by the ratio between forced expiratory volume in 1 second (FEV₁) and forced vital capacity (FVC) and positively correlated with increased overall airway reactance among the workers.

Conclusion:

Respiratory symptoms and increased allergen susceptibility of Indian tea industry workers due to occupational exposures warrant routine systematic surveillance of their workplace air quality and health monitoring.

Innate and humoral recognition of the products of cell death: differential antigenicity and immunogenicity in lupus

While apoptotic debris is believed to constitute the original antigenic insult in lupus (which is characterized by a time-dependent diversification of autoreactivity), whether such debris and autoantibodies specifically recognizing its constituents mediate differential effects on innate and humoral responses in lupus-prone mice is currently unknown. Apoptotic blebs (as opposed to cellular lysate) enhanced preferentially the maturation of dendritic cells (DCs) from bone marrow precursors drawn from lupus-prone mice. Murine, somatically mutated, apoptotic cell-reactive immunoglobulin (Ig)G monoclonal antibodies demonstrated enhanced recognition of DCs and also displayed a prominent lupus strain-specific bias in mediating DC maturation. Further, immunization of such antibodies specifically in lupus-prone mice resulted in widespread humoral autoreactivity; hypergammaglobulinaemia (a hallmark of systemic autoimmunity) was observed, accompanied by enhanced antibody titres to cellular moieties. Induced antibodies recognized antigens distinct from those recognized by the antibodies employed for immunization; in particular, nephritis-associated anti-double stranded (ds) DNA antibodies and neonatal lupus-associated anti-Ro60 antibodies were elicited by a non-dsDNA, non-Ro60 reactive antibody, and Sm was a favoured target. Further, only in lupus-prone mice did such immunization enhance the kinetics of humoral anti-self responses, resulting in the advanced onset of glomerulosclerosis. These studies reveal that preferential innate and humoral recognition of the products of cell death in a lupus milieu influence the indices associated with autoimmune pathology.

Quality of tuberculosis care in India: a systematic review

BACKGROUND

While Indian studies have assessed care providers' knowledge and practices, there is no systematic review on the quality of tuberculosis (TB) care.

METHODS

We searched multiple sources to identify studies (2000-2014) on providers' knowledge and practices. We used the International Standards for TB Care to benchmark quality of care.

RESULTS

Of the 47 studies included, 35 were questionnaire surveys and 12 used chart abstraction. None assessed actual practice using standardised patients. Heterogeneity in the findings precluded meta-analysis. Of 22 studies evaluating provider knowledge about using sputum smears for diagnosis, 10 found that less than half of providers had correct knowledge; 3 of 4 studies assessing self-reported practices by providers found that less than a quarter reported ordering smears for patients with chest symptoms. In 11 of 14 studies that assessed treatment, less than one third of providers knew the standard regimen for drug-susceptible TB. Adherence to standards in practice was generally lower than correct knowledge of those standards. Eleven studies with both public and private providers found higher levels of appropriate knowledge/practice in the public sector.

CONCLUSIONS

Available evidence suggests suboptimal quality of TB care, particularly in the private sector. Improvement of quality of care should be a priority for India.

Redox signalling to nuclear regulatory proteins by reactive oxygen species contributes to oestrogen-induced growth of breast cancer cells

Background:

17β-Oestradiol (E2)-induced reactive oxygen species (ROS) have been implicated in regulating the growth of breast cancer cells. However, the underlying mechanism of this is not clear. Here we show how ROS through a novel redox signalling pathway involving nuclear respiratory factor-1 (NRF-1) and p27 contribute to E2-induced growth of MCF-7 breast cancer cells.

Methods:

Chromatin immunoprecipitation, qPCR, mass spectrometry, redox western blot, colony formation, cell proliferation, ROS assay, and immunofluorescence microscopy were used to study the role of NRF-1.

Results:

The major novel finding of this study is the demonstration of oxidative modification of phosphatases PTEN and CDC25A by E2-generated ROS along with the subsequent activation of AKT and ERK pathways that culminated in the activation of NRF-1 leading to the upregulation of cell cycle genes. 17β-Oestradiol-induced ROS by influencing nuclear proteins p27 and Jab1 also contributed to the growth of MCF-7 cells.

Conclusions:

Taken together, our results present evidence in the support of E2-induced ROS-mediated AKT signalling leading to the activation of NRF-1-regulated cell cycle genes as well as the impairment of p27 activity, which is presumably necessary for the growth of MCF-7 cells. These observations are important because they provide a new paradigm by which oestrogen may contribute to the growth of breast cancer.