Single-cell phenotypic profiling and backtracing exposes and predicts clinically relevant subpopulations in isogenic Staphylococcus aureus communities.

Isogenic bacterial cell populations are phenotypically heterogenous and may include subpopulations of antibiotic tolerant or heteroresistant cells. The reversibility of these phenotypes and lack of biomarkers to differentiate functionally different, but morphologically identical cells is a challenge for research and clinical detection. To overcome this, we present ´Cellular Phenotypic Profiling and backTracing (CPPT)´, a fluorescence-activated cell sorting platform that uses fluorescent probes to visualize and quantify cellular traits and connects this phenotypic profile with a cell´s experimentally determined fate in single cell-derived growth and antibiotic susceptibility analysis. By applying CPPT on Staphylococcus aureus we phenotypically characterized dormant cells, exposed bimodal growth patterns in colony-derived cells and revealed different culturability of single cells on solid compared to liquid media. We demonstrate that a fluorescent vancomycin conjugate marks cellular subpopulations of vancomycin-intermediate S. aureus with increased likelihood to survive antibiotic exposure, showcasing the value of CPPT for discovery of clinically relevant biomarkers.

Silicon efficacy for the remediation of metal contaminated soil.

In the course of past two decade anthropogenic activities have reinforced, begetting soil and water defilement. A plethora of heavy metals alters and limits plant growth and yield, with opposing effect on agricultural productivity. Silicon often perceived as plant alimentary 'nonentity'. A suite of determinants associated with silicon have been lately discerned, concerning plant physiology, chemistry, gene regulation/expression and interaction with different organisms. Exogenous supplementation of silicon renders resistance against heavy-metal stress. Predominantly, plants having significant amount of silicon in root and shoot thus are barely prone to pest onset and manifest greater endurance against abiotic stresses including heavy-metal toxicity. Silicon-mediated stress management involves abatement of metal ions within soil, co-precipitation of metal ions, gene modulation associated with metal transport, chelation, activation of antioxidants (enzymatic and non-enzymatic), metal ion compartmentation and structural metamorphosis in plants. Silicon supplementation also stimulates expression of stress-resistant genes under heavy-metal toxicity to provide plant tolerance under stress conditions. Ergo, to boost metal tolerance within crops, immanent genetic potential for silicon assimilation should be enhanced. Current study, addresses the potential role and mechanistic interpretation of silicon induced mitigation of heavy-metal stress in plants.

Antimicrobial liposomes-in-nanofiber wound dressings prepared by a green and sustainable wire-electrospinning set-up.

Increasing prevalence of infected and chronic wounds demands improved therapy options. In this work an electrospun nanofiber dressing with liposomes is suggested, focusing on the dressing's ability to support tissue regeneration and infection control. Chloramphenicol (CAM) was the chosen antibiotic, added to the nanofibers after first embedded in liposomes to maintain a sustained drug release. Nanofibers spun from five different polymer blends were tested, where pectin and polyethylene oxide (PEO) was identified as the most promising polymer blend, showing superior fiber formation and tensile strength. The wire-electrospinning setup (WES) was selected for its pilot-scale features, and water was applied as the only solvent for green electrospinning and to allow direct liposome incorporation. CAM-liposomes were added to Pectin-PEO nanofibers in the next step. Confocal imaging of rhodamine-labelled liposomes indicated intact liposomes in the fibers after electrospinning. This was supported by the observed in vitroCAM-release, showing that Pectin-PEO-nanofibers with CAM-liposomes had a delayed drug release compared to controls. Biological testing confirmed the antimicrobial efficacy of CAM and good biocompatibility of all CAM-nanofibers. The successful fiber formation and green production process with WES gives a promising outlook for industrial upscaling.

Raloxifene, a SERM targets PD-L1: an in-silico study.

OBJECTIVES: Immunotherapeutic interventions in cancer have been considerably successful and widely accepted for cancer treatment, but are costly and cannot be afforded by all patients. Because of the high cost, the pharmaceutical research groups across the world are sufficiently motivated to discover or design small molecule inhibitors to treat cancer through inhibition of the immune checkpoint proteins previously targeted with monoclonal antibodies. The presented study was designed with an aim to establish raloxifene, a selective estrogen receptor modulator (SERM) as a potential ligand of the immune checkpoint protein Programmed death ligand-1 (PD-L1). METHODS: In the presented study, the in-silico approach was used for identifying a lead molecule against PD-L1. The hits were screened using the similarity-search method, and drug-likeliness analysis, and the leads were identified through ligand-docking using Autodock. In-vitro cytotoxicity analysis was carried out using the standard sulphorhodamine B (SRB) assay and the wound healing analysis to show the inhibition of cellular migration was performed using the standard scratch assay. RESULTS: The in-silico study revealed that raloxifene showed a high drug likelihood and higher binding affinity with PD-L1 as compared to the positive control (BMS-1166; BMS is Bristol Myers Squibb). The binding of raloxifene was shown to occur in the same region as the FDA-approved monoclonal antibodies atezolizumab and durvalumab, indicating the potential of raloxifene for PD1/PD-L1 blockade. In the in-vitro studies, raloxifene showed a time-dependent reduction in IC50 values for the cell line HCT116 (colon cancer). The scratch assay also revealed that raloxifene significantly reduced the migratory potential of HCT-116 cells in-vitro. CONCLUSIONS: PD-L1 is a potential target of the SERM raloxifene in-silico. Overall, this study is one step further towards immune checkpoint blockade using small-molecule inhibitors.

Bio-mimetic selectivity in Hg2+ sensing developed via electro-copolymerized PEDOT and benzothiazole-Au nanoparticles composite.

To eliminate the potential health risks of mercury, development of stable and selective mercury sensor with high sensitivity is the need of the hour. To address this, a novel PEDOT-AA-BTZ-Au-based Hg2+ selective, hybrid electrochemical sensor has been designed by following a simple protocol for electrode fabrication. The electrode was designed by carefully optimizing the onset oxidation potential of supramolecule 2-(anthracen-9-yl)benzo[d]thiazole (AA-BTZ) and conducting polymer poly-(3,4-ethylenedioxythiophene) (PEDOT), using copolymerization approach followed by dropcasting of gold nanoparticles (AuNPs). The designed electrode offered synergistic effects thus augmenting the electrical conductivity and adsorption capacity as depicted by its porous surface morphology. The highly sensitive analytical signal was generated by sulphur pockets present in AA-BTZ and PEDOT conducting framework. This is further complemented by the selectivity offered by the soft interactions between AuNPs and Hg2+ resulting in a low detection limit of 0.60 nM. The prepared system was further utilized for sensing Hg2+ ion in real systems including lake water and cosmetic samples. Low interference from other ions and better reproducibility further established the suitability of the designed transducer system for future on-site sensing.

The pesticide thiamethoxam induced toxicity in Brassica juncea and its detoxification by Pseudomonas putida through biochemical and molecular modifications.

Insecticides are extensively exploited by humans to destroy the pests one such compound thiamethoxam is widely used over crops to offer control over wide-array of sucking insect pests. The present study unravels the detoxification potential of Pseudomonas putida in thiamethoxam exposed B. juncea seedlings. The thiamethoxam application curtailed the fresh weight, dry weight and seedling length by 106.22%, 80.29% and 116.78% while P. putida revived these growth parameters in thiamethoxam exposed B. juncea seedlings by 59.65%, 72.99% and 164.56% respectively. The exogenous supplementation of P. putida resuscitated the photosynthetic efficiency of B. juncea seedlings exposed to thiamethoxam as total chlorophyll, chlorophyll a, chlorophyll b, carotenoid, flavonoid and anthocyanin contents were enhanced by 169.42%, 62.90%, 72.89%, 78.53%, 47.36% and 515.15% respectively in contrast to TMX exposed seedlings. Further, P. putida pre-treatment reinvigorated the osmoprotectant content in B. juncea seedlings grown in thiamethoxam as trehalose, glycine betaine and proline contents were thrusted by 21.20%, 58.98% and 34.26% respectively. The thiamethoxam exposure exorbitated the superoxide anion, hydrogen peroxide and MDA levels by 223.03%, 130.18% and 74.63% while P. putida supplementation slackened these oxidative burst levels by 41.75%, 3.79% and 29.09% respectively in thiamethoxam treated seedlings. Notably, P. putida inoculation in thiamethoxam exposed seedlings upregulated the enzymatic antioxidant and non-enzymatic antioxidant activities as SOD, CAT and glutathione were enhanced by 163.76%, 99.29% and 114.91% respectively in contrast to thiamethoxam treated seedlings. The gene expression analysis exhibited the negative impact of thiamethoxam on B. juncea seedlings as conferred by upregulation of chlorophyllase by 443.86 folds whereas P. putida application in thiamethoxam exposed seedlings downregulated the chlorophyllase expression by 248.73 folds and upregulated CXE, GST, NADH and POD genes by 0.44, 4.07, 1.43 and 0.98 folds respectively suggesting the molecular-level thiamethoxam detoxification efficiency of P. putida.

Application of melatonin and PGPR alleviates thiamethoxam induced toxicity by regulating the TCA cycle in Brassica juncea L.

Thiamethoxam, a broad spectrum, neonicotinoid insecticide, is used on various crops including Brassica juncea L. to protect from intruding insects such as leaf-hoppers, aphids, thrips and white-flies. Exposure to thiamethoxam causes acute malady such as tumour development, cell apoptosis, liver damage and neurotoxicity. Melatonin is entailed in umpteen developmental processes of plants, including stress responses. The pleiotropic effects of melatonin in modulating plant growth validate it's imperative contribution as multi-regulatory substance. Exiguous information is known about the role of Pseudomonas putida in improving plant growth under thiamethoxam stress. Taking these aspects into consideration the contemporary study investigates the role of melatonin and Pseudomonas putida strain MTCC 3315 in alleviating the thiamethoxam induced toxicity in B. juncea plant. Fourier Transform Infrared Spectroscopy (FTIR) analysis uncloaked that thiamethoxam induced stress primarily affects the protein content of plant as compared to lipids, carbohydrates and cell wall components. Organic acid profiling of the treated samples carried-out by High-Performance Liquid Chromatography (HPLC), reported an upregulation in the level of organic acids, malic acid (110%), citric acid (170%), succinic acid (81%), fumaric acid (40%) and ascorbic acid (55%) in thiamethoxam treated plants compared to the investigational untreated plants. The melatonin treated seedlings grown under thiamethoxam stress, exhibit increased level of malic acid, citric acid, succinic acid, fumaric acid and ascorbic acid by 81%, 0.94%, 11%, 21% and 6% respectively. Further, thiamethoxam stressed plants inoculated with Pseudomonas putida showed stupendous up-regulation by 161% (malic acid), by 14% (citric acid), by 33% (succinic acid), by 30% (fumaric acid), by 100% (oxalic acid) respectively. Lastly, the combinatorial application of melatonin and Pseudomonas putida resulted in prodigious upsurge of malic acid by 165%, succinic acid by 69%, fumaric acid by 42% respectively in contrast to distinct melatonin and Pseudomonas putida treatments. The accumulation of organic acids ascertains the defence against thiamethoxam stress and corresponds to meet the energy generation requirement to skirmish thiamethoxam mediated abiotic stress in Brassica juncea plant.

Structural insights into the amino acid usage variations in the profilin gene family.

Profilin protein is present ubiquitously in all forms of life and is allied with allergic responses among atopic individuals. In addition to this, profilins from various food sources are also associated with IgE cross-reactivity and are thus classified as pan-allergens. The present study unravels the physicochemical basis of differential amino acid usage patterns observed in the profilin gene family. Correspondence analysis based on amino acid usage of allergen and non-allergen profilins revealed discrete clusters among them, signifying differential patterns of amino acid usage. The amino acids, namely methionine, proline, histidine, glutamine, glutamic acid, tryptophan and glycine were found to be more frequently utilised by the allergen profilins compared to the non-allergens. Correlation analysis revealed that physicochemical features like protein disorder, trypsin digestion and solubility differed significantly among the allergen and non-allergen profilins, thus supporting the observations from correspondence analysis. In addition, comprehensive sequence analysis revealed that the allergen profilins possess conserved motifs which may correlate with their distinct physicochemical features. An in-depth structural analysis revealed that the over-represented amino acids in allergen profilins have a propensity of being exposed on the surface, which may be attributed to their distinct allergenic characteristics. The distinguished physicochemical features observed among allergens and non-allergens can be employed as descriptors to develop machine learning-based allergenicity prediction models.

Covishield India: demystifying myths through an early multicenter study.

OBJECTIVES: Nationwide COVID-19 vaccination was initiated in India on January 16, 2021, in a phased manner with vaccines including Covishield. This vaccine was indigenously prepared by Serum Institute of India in line with the Oxford-AstraZeneca ChAdOx1 vaccine developed at the University of Oxford. This is the first multicenter study to assess the safety of the indigenously prepared Covishield vaccine in India. STUDY DESIGN: Multicenter observational descriptive study. METHODS: This was a multicenter study carried out in northern and eastern India. Individuals who received the first dose of the Covishield vaccine were followed up for 7 days to check for any adverse effects or systemic effects post vaccination. The data were collected by the authors with a participant-administered questionnaire. The primary end point was the incidence of adverse or systemic effects within 7 days post vaccination. RESULTS: No serious adverse or systemic effects were noted in 7 days of follow-up. Nonserious systemic effects were seen in 42.0% of individuals post vaccination. Myalgia and/or fatigue was the most common effect of vaccination in 25.7%, followed by fever in 22.0% of individuals. In most individuals, the systemic effects started 6 to 12 hours post vaccination. There were no reports of fresh onset of systemic effects of any kind beyond 48 hours of vaccination. Women and older adults tolerated the vaccination better. CONCLUSIONS: The absence of serious adverse effects in our study will help allay fears around vaccine acceptance and give a boost to the vaccination campaign worldwide.

DISTRIBUTION OF RADON AND URANIUM LEVELS IN GROUNDWATER OF DISTRICT PALWAL, SOUTHERN HARYANA, INDIA.

Scintillation-detector-based SMART RnDuo (AQTEK System, India) and LED fluorimeter (Quantalase Instrument, India) were used for measurements of radon and uranium concentration in 54 groundwater samples collected from different locations in the Palwal district of Haryana (India). Radon in 26% and uranium in 54% of samples were found to be at higher levels than the maximum contamination limit (11 Bq l-1) for drinking water recommended by US Environmental Protection Agency and provisional guideline level (30 µg l-1) stated by World Health Organization.

Comparison of in-vitro and in-vivo parameters of whole blood derived random donor platelets (RDP) after over-night hold with RDP prepared after 2-h hold: Single centre report from India.

BACKGROUND: Random Donor Platelet (RDP) derived from whole blood is the major source of platelets in India. At our centre, we prepare RDPs by buffy coat method after a holding period of 2-hours (THRDP) as per current regulatory guidelines. Overnight hold of buffy coats before RDP preparation (OHRDP) would logistically optimise the manpower usage at our centre. The aim of this study was to compare both in-vitro as well as in-vivo parameters of OHRDPs with THRDPs. METHODOLOGY: Hematological (Platelet, leucocyte counts), physical (pH and Swirling) and biochemical parameters (pO2, pCO2, lactate, bicarbonate and glucose) as well as platelet activation markers were tested in THRDPs and OHRDPs each at Day-1 and Day-5 as in-vitro studies. Separately, in-vivo study was done where Corrected count increment (CCI) and percentage platelet recovery (PPR) were considered. All parameters were expressed as Mean ± Standard deviation and were analysed using paired t-test with level of significance, p < 0.05. RESULTS: OHRDPs had higher platelet counts and lower leucocytes and CD62 P expression than THRDPs. All other markers were well within the quality control range in both groups. No significant differences were seen in the two groups when comparing CCI and PPR. CONCLUSION: OHRDPs were found to be as good or better as compared to the THRDPs in the in-vitro part of our study. Additionally, there were no significant differences between the two groups when they were compared in vivo. This makes us conclude that overnight hold of buffy coats may be implemented at our center.

Multifunctional Nanofibrous Dressing with Antimicrobial and Anti-Inflammatory Properties Prepared by Needle-Free Electrospinning.

An active wound dressing should address the main goals in wound treatment, which are improved wound healing and reduced infection rates. We developed novel multifunctional nanofibrous wound dressings with three active ingredients: chloramphenicol (CAM), beta-glucan (ßG) and chitosan (CHI), of which ßG and CHI are active nanofiber-forming biopolymers isolated from the cell walls of Saccharomyces cerevisiae and from shrimp shells, respectively. To evaluate the effect of each active ingredient on the nanofibers' morphological features and bioactivity, nanofibers with both ßG and CHI, only ßG, only CHI and only copolymers, polyethylene oxide (PEO) and hydroxypropylmethylcellulose (HPMC) were fabricated. All four nanofiber formulations were also prepared with 1% CAM. The needle-free NanospiderTM technique allowed for the successful production of defect-free nanofibers containing all three active ingredients. The CAM-containing nanofibers had a burst CAM-release and a high absorption capacity. Nanofibers with all active ingredients (ßG, CHI and CAM) showed a concentration-dependent anti-inflammatory activity, while maintaining the antimicrobial activity of CAM. The promising anti-inflammatory properties, together with the high absorption capacity and antimicrobial effect, make these multifunctional nanofibers promising as dressings in local treatment of infected and exuding wounds, such as burn wounds.

Base Composition and Host Adaptation of the SARS-CoV-2: Insight From the Codon Usage Perspective.

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading rapidly all over the world and has raised grave concern globally. The present research aims to conduct a robust base compositional analysis of SARS-CoV-2 to reveal adaptive intricacies to the human host. Multivariate statistical analysis revealed a complex interplay of various factors including compositional constraint, natural selection, length of viral coding sequences, hydropathicity, and aromaticity of the viral gene products that are operational to codon usage patterns, with compositional bias being the most crucial determinant. UpG and CpA dinucleotides were found to be highly preferred whereas, CpG dinucleotide was mostly avoided in SARS-CoV-2, a pattern consistent with the human host. Strict avoidance of the CpG dinucleotide might be attributed to a strategy for evading a human immune response. A lower degree of adaptation of SARS-CoV-2 to the human host, compared to Middle East respiratory syndrome (MERS) coronavirus and SARS-CoV, might be indicative of its milder clinical severity and progression contrasted to SARS and MERS. Similar patterns of enhanced adaptation between viral isolates from intermediate and human hosts, contrasted with those isolated from the natural bat reservoir, signifies an indispensable role of the intermediate host in transmission dynamics and spillover events of the virus to human populations. The information regarding avoided codon pairs in SARS-CoV-2, as conferred by the present analysis, promises to be useful for the design of vaccines employing codon pair deoptimization based synthetic attenuated virus engineering.

Environmental survival of SARS-CoV-2 - A solid waste perspective.

The advent of COVID-19 has kept the whole world on their toes. Countries are maximizing their efforts to combat the virus and to minimize the infection. Since infectious microorganisms may be transmitted by variety of routes, respiratory and facial protection is required for those that are usually transmitted via droplets/aerosols. Therefore this pandemic has caused a sudden increase in the demand for personal protective equipment (PPE) such as gloves, masks, and many other important items since, the evidence of individual-to-individual transmission (through respiratory droplets/coughing) and secondary infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). But the disposal of these personal protective measures remains a huge question mark towards the environmental impact. Huge waste generation demands proper segregation according to waste types, collection, and recycling to minimize the risk of infection spread through aerosols and attempts to implement measures to monitor infections. Hence, this review focuses on the impact of environment due to improper disposal of these personal protective measures and to investigate the safe disposal methods for these protective measures by using the safe, secure and innovative biological methods such as the use of Artificial Intelligence (AI) and Ultraviolet (UV) lights for killing such deadly viruses.

Natural compounds from Clerodendrum spp. as possible therapeutic candidates against SARS-CoV-2: An in silico investigation.

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has rattled global public health, with researchers struggling to find specific therapeutic solutions. In this context, the present study employed an in silico approach to assess the inhibitory potential of the phytochemicals obtained from GC-MS analysis of twelve Clerodendrum species against the imperative spike protein, main protease enzyme Mpro and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. An extensive molecular docking investigation of the phytocompounds at the active binding pockets of the viral proteins revealed promising inhibitory potential of the phytochemicals taraxerol, friedelin and stigmasterol. Decent physicochemical attributes of the compounds in accordance with Lipinski's rule of five and Veber's rule further established them as potential therapeutic candidates against SARS-CoV-2. Molecular mechanics-generalized Born surface area (MM-GBSA) binding free energy estimation revealed that taraxerol was the most promising candidate displaying the highest binding efficacy with all the concerned SARS-CoV-2 proteins included in the present analysis. Our observations were supported by robust molecular dynamics simulations of the complexes of the viral proteins with taraxerol for a timescale of 40 nanoseconds. It was striking to note that taraxerol exhibited better binding energy scores with the concerned viral proteins than the drugs that are specifically targeted against them. The present results promise to provide new avenues to further evaluate the potential of the phytocompound taraxerol in vitro and in vivo towards its successful deployment as a SARS-CoV-2 inhibitor and combat the catastrophic COVID-19.Communicated by Ramaswamy H. Sarma.

Immuno-Informatics Quest against COVID-19/SARS-COV-2: Determining Putative T-Cell Epitopes for Vaccine Prediction.

BACKGROUND: Since December 2019, a novel coronavirus, SARS-CoV-2, has caused global public health issues after being reported for the first time in Wuhan province of China. So far, there have been approximately 14.8 million confirmed cases and 0.614 million deaths due to the SARS-CoV-2 infection globally, and still, numbers are increasing. Although the virus has caused a global public health concern, no effective treatment has been developed. OBJECTIVE: One of the strategies to combat the COVID-19 disease caused by SARS-CoV-2 is the development of vaccines that can make humans immune to these infections. Considering this approach, in this study, an attempt has been made to design epitope-based vaccine for combatting COVID-19 disease by analyzing the complete proteome of the virus by using immuno-informatics tools. METHODS: The protein sequence of the SARS-CoV-2 was retrieved and the individual proteins were checked for their allergic potential. Then, from non-allergen proteins, antigenic epitopes were identified that could bind with MHCII molecules. The epitopes were modeled and docked to predict the interaction with MHCII molecules. The stability of the epitope-MHCII complex was further analyzed by performing a molecular dynamics simulation study. The selected vaccine candidates were also analyzed for their global population coverage and conservancy among SARS-related coronavirus species. RESULTS: The study has predicted 5 peptide molecules that can act as potential candidates for epitope- based vaccine development. Among the 5 selected epitopes, the peptide LRARSVSPK can be the most potent epitope because of its high geometric shape complementarity score, low ACE and very high response towards it by the world population (81.81% global population coverage). Further, molecular dynamic simulation analysis indicated the formation of a stable epitope-MHCII complex. The epitope LRARSVSPK was also found to be highly conserved among the SARS-CoV- -2 isolated from different countries. CONCLUSION: The study has predicted T-cell epitopes that can elicit a robust immune response in the global human population and act as potential vaccine candidates. However, the ability of these epitopes to act as vaccine candidate needs to be validated in wet lab studies.

Evaluation of Normal Morphology of Mandibular Condyle: A Radiographic Survey.

OBJECTIVES: The temporomandibular joint (TMJ) is a complex, highly specialized joint. Along with the teeth, these joints are considered to be a "tri-joint complex." Mandibular condyle morphology is characterized by a rounded bone projection with an upper biconvex and oval surface in axial plane. Anatomical knowledge of the TMJ is one of the basic foundations of clinical practice, allowing the understanding of TMJ pathologies and fabrication of condylar prostheses. The cross-sectional descriptive study was undertaken to evaluate normal variation in the condylar morphology on radiographs in persons without TMJ symptomatology and its relation to age, gender, dentition status, chewing habits, parafunctional habits, history of orthodontic treatment, and denture wearing was assessed. MATERIAL AND METHODS: A total of 350 subjects without TMJ symptomatology included in the study were further grouped by age, gender, dentition status, chewing habits, parafunctional habits, history of orthodontic treatment, and denture wearing history. Panoramic radiograph was taken for the assessment of condylar morphology. RESULTS: A significant association between dentition status and bilaterally similar condylar morphology was noticed. Bilaterally similar condyles were seen in 81.4% of subjects. Round-shaped condyles were seen in 176 (62%) persons. Loss of bilateral occlusion tends to alter the condylar morphology. Association between normal chewing habits and bilaterally similar condyle shapes was significant. CONCLUSION: The study describes the normal morphology of mandibular condyles in a population attending the tertiary dental care center, Kozhikode. The dentition status and chewing habits of individuals had a significant role in determining condylar morphology.

Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones.

Antibiotic resistance is rising and we urgently need to gain a better quantitative understanding of how antibiotics act, which in turn would also speed up the development of new antibiotics. Here, we describe a computational model (COMBAT-COmputational Model of Bacterial Antibiotic Target-binding) that can quantitatively predict antibiotic dose-response relationships. Our goal is dual: We address a fundamental biological question and investigate how drug-target binding shapes antibiotic action. We also create a tool that can predict antibiotic efficacy a priori. COMBAT requires measurable biochemical parameters of drug-target interaction and can be directly fitted to time-kill curves. As a proof-of-concept, we first investigate the utility of COMBAT with antibiotics belonging to the widely used quinolone class. COMBAT can predict antibiotic efficacy in clinical isolates for quinolones from drug affinity (R2>0.9). To further challenge our approach, we also do the reverse: estimate the magnitude of changes in drug-target binding based on antibiotic dose-response curves. We overexpress target molecules to infer changes in antibiotic-target binding from changes in antimicrobial efficacy of ciprofloxacin with 92-94% accuracy. To test the generality of our approach, we use the beta-lactam ampicillin to predict target molecule occupancy at MIC from antimicrobial action with 90% accuracy. Finally, we apply COMBAT to predict antibiotic concentrations that can select for resistance due to novel resistance mutations. Using ciprofloxacin and ampicillin as well defined test cases, our work demonstrates that drug-target binding is a major predictor of bacterial responses to antibiotics. This is surprising because antibiotic action involves many additional effects downstream of drug-target binding. In addition, COMBAT provides a framework to inform optimal antibiotic dose levels that maximize efficacy and minimize the rise of resistant mutants.

Cellular signalling pathways mediating the pathogenesis of chronic inflammatory respiratory diseases: an update.

Respiratory disorders, especially non-communicable, chronic inflammatory diseases, are amongst the leading causes of mortality and morbidity worldwide. Respiratory diseases involve multiple pulmonary components, including airways and lungs that lead to their abnormal physiological functioning. Several signaling pathways have been reported to play an important role in the pathophysiology of respiratory diseases. These pathways, in addition, become the compounding factors contributing to the clinical outcomes in respiratory diseases. A range of signaling components such as Notch, Hedgehog, Wingless/Wnt, bone morphogenetic proteins, epidermal growth factor and fibroblast growth factor is primarily employed by these pathways in the eventual cascade of events. The different aberrations in such cell-signaling processes trigger the onset of respiratory diseases making the conventional therapeutic modalities ineffective. These challenges have prompted us to explore novel and effective approaches for the prevention and/or treatment of respiratory diseases. In this review, we have attempted to deliberate on the current literature describing the role of major cell signaling pathways in the pathogenesis of pulmonary diseases and discuss promising advances in the field of therapeutics that could lead to novel clinical therapies capable of preventing or reversing pulmonary vascular pathology in such patients.

Transcriptome Profiling of Staphylococcus aureus Associated Extracellular Vesicles Reveals Presence of Small RNA-Cargo.

Bacterial extracellular vesicles (EVs) have a vital role in bacterial pathogenesis. However, to date, the small RNA-cargo of EVs released by the opportunistic pathogen Staphylococcus aureus has not been characterized. Here, we shed light on the association of small RNAs with EVs secreted by S. aureus MSSA476 cultured in iron-depleted bacteriologic media supplemented with a subinhibitory dosage of vancomycin to mimic infection condition. Confocal microscopy analysis on intact RNase-treated EVs indicated that RNA is associated with EV particles. Transcriptomic followed by bioinformatics analysis of EV-associated RNA revealed the presence of potential gene regulatory small RNAs and high levels of tRNAs. Among the EV-associated enriched small RNAs were SsrA, RsaC and RNAIII. Our finding invites new insights into the potential role of EV-associated RNA as a modulator of host-pathogen interaction.