Indian Himalayan natural Arabidopsis thaliana accessions with abolished miR158 levels exhibit robust miR173-initiated trans-acting cascade silencing.

Small RNAs (sRNAs) such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) are short 20-24-nucleotide non-coding RNAs. They are key regulators of gene expression in plants and other organisms. Several 22-nucleotide miRNAs trigger biogenesis cascades of trans-acting secondary siRNAs, which are involved in various developmental and stress responses. Here we show that Himalayan Arabidopsis thaliana accessions having natural mutations in the miR158 locus exhibit robust cascade silencing of the pentatricopeptide repeat (PPR)-like locus. Furthermore, we show that these cascade sRNAs trigger tertiary silencing of a gene involved in transpiration and stomatal opening. The natural deletions or insertions in MIR158 led to improper processing of miR158 precursors, thereby blocking synthesis of mature miR158. Reduced miR158 levels led to increased levels of its target, a pseudo-PPR gene that is targeted by tasiRNAs generated by the miR173 cascade in other accessions. Using sRNA datasets derived from Indian Himalayan accessions, as well as overexpression and knockout lines of miR158, we show that absence of miR158 led to buildup of pseudo-PPR-derived tertiary sRNAs. These tertiary sRNAs mediated robust silencing of a gene involved in stomatal closure in Himalayan accessions lacking miR158 expression. We functionally validated the tertiary phasiRNA that targets NHX2, which encodes a Na+ -K+ /H+ antiporter protein, thereby regulating transpiration and stomatal conductance. Overall, we report the role of the miRNA-TAS-siRNA-pseudogene-tertiary phasiRNA-NHX2 pathway in plant adaptation.

Genome-wide DNA methylation and their transgenerational pattern differ in Arabidopsis thaliana populations originated along the elevation of West Himalaya.

Methylation at 5' cytosine of DNA molecule is an important epigenetic mark. It is known to play critical role in adaptation of organisms under different biotic and abiotic stressors via modulating gene expression and/or chromatin architecture. Plant populations evolved under variable climatic conditions may have evolved different epigenetic marks including DNA methylation. Here we, describe the genome-wide DNA methylation pattern under native field, F1 and F6 generation followed by their association with phenotypes, climate and global gene expression in the three Arabidopsis thaliana populations originated at different elevation ranges of Indian West Himalaya. We show that the global methyl cytosine (mC) content is more or less similar in the three populations but differ in their distribution across genome. There was an increase in differential methylation between the populations as elevation increased. The methylation divergence was the highest between the low and the high elevation populations. The high elevation populations were hypo-methylated than the low elevation population. The methylation in the genes was associated with population specific phenotypes and climate of the region. The genes which were differentially methylated as well as differentially expressed between the low and high elevation populations were mostly related to abiotic stresses. When grown under controlled condition, there was gain of differential methylation over native condition and the maximum percent changes was observed in CHH-sequence context. Further ~ 99.8% methylated cytosines were stably passed on from F1 to F6 generation. Overall, our data suggest that high elevation population is epigenetically more plastic under changing environmental condition.Background Arabidopsis thaliana is the model plant species and has been extensively studied to understand plants life processes. There are numerous reports on its origin, demography, evolution, epigenomes and adaptation etc. however, Indian populations of Arabidopsis thaliana evolved along wide elevation ranging from ~ 700 m amsl to ~ 3400 m amsl not explored yet. Here we, describe the genome-wide DNA methylation pattern under native field, F1 and F6 generation followed by their association with phenotypes, climate and global gene expression in the three Arabidopsis thaliana populations originated at different elevation ranges of Indian West Himalaya.Results In our study we found that total mCs percent was more or less similar in the three populations but differ in their distribution across genome. The proportion of CG-mCs was the highest, followed by CHH-mCs and CHG-mCs in all the three populations. Under native field condition the methylation divergence was more prominent between low and high elevation populations and the high elevation populations were hypo-methylated than the low elevation population. The methylation in the genes was linked to population-specific phenotypes and the regional climate. The genes that showed differential methylation and expression between low and high elevation populations were primarily associated with abiotic stress responses. When grown under controlled condition, there was gain of differential methylation compared to the native condition and the maximum percent changes was observed in CHH-sequence context. Further 99.8% methylated cytosines were stably passed on from F1 to F6 generation.Conclusions The populations of A. thaliana adapted at different climatic conditions were significantly differentially methylated both under native and controlled condition. However, the magnitude and extent of gain or loss of methylation were most significant between the low and the high elevation populations. Overall, our data suggest that high elevation population is epigenetically more plastic under changing environmental condition.

Bioaugmentation: an approach to biological treatment of pollutants.

Industrial development and the associated generation of waste requires attention for their management, treatment, and reduction without further degrading the quality of life. Microbes and plant-based bioremediation approaches are some of the sustainable strategies for the biodegradation of harmful pollutants instead of chemical-based treatment. Bioaugmentation is one such approach where microbial strains with the ability to degrade the targeted pollutant are introduced in a polluted environment. Harnessing of microbes from various locations, especially from the site of contamination (indigenous microbes), followed by optimization of the strains, inoculum size, media, and genetic engineering of the microbes along with a combination of strategies such as bio stimulation, phytoremediation is being applied to increase the efficiency of bioaugmentation. Further, bioaugmentation is influenced by various factors such as temperature, the composition of the pollutant, and microbial inoculum which needs to be considered for maximum efficiency of the treatment process. It has numerous advantages such as low cost, sustainability, and easy handling of the contaminants however, the major limitation of bioaugmentation is to increase the survival rate of the microbes involved in remediation for a longer duration in such a highly toxic environment. The review discusses these various aspects of bioaugmentation in brief for its large-scale implementation to address the global issue of pollution and environment management.

Novel FtsZ inhibitor with potent activity against Staphylococcus aureus.

OBJECTIVES: FtsZ is an essential bacterial protein and an unexplored target for the development of antibacterial drugs. The development of a novel inhibitor targeting FtsZ offers a potential opportunity to combat drug resistance. DS01750413, a new derivative of PC190723, is a novel FtsZ inhibitor with improved in vitro and in vivo activity. The objective of this study was to investigate the efficacy of DS01750413 against Staphylococcus spp., including MRSA, in in vitro and in vivo models. METHODS: In vitro activities of DS01750413 and standard-of-care antibiotics were evaluated against clinical isolates of Gram-positive pathogens. The in vivo efficacy was evaluated in a murine systemic infection model caused by MRSA. RESULTS: DS01750413 showed potent in vitro activity against MRSA clinical isolates with MIC ranges of 0.5-1 mg/L and also demonstrated concentration-dependent bactericidal killing. In the murine bacteraemia infection model of MRSA, treatment with DS01750413 resulted in prolonged survival of animals compared with placebo-treated animals and exhibited a significant reduction in the bacterial load in liver, spleen, lungs and kidneys. CONCLUSIONS: DS01750413 showed encouraging in vitro and in vivo activity against MRSA. As a novel chemical class, DS01750413 has the potential to become clinically viable antibiotics to address the drug resistance problem by its unique novel targeting mechanism of action.

Role of extremophiles and their extremozymes in biorefinery process of lignocellulose degradation.

Technological advances in the field of life sciences have led to discovery of organisms that live in harsh environmental conditions referred to as extremophiles. These organisms have adapted themselves to thrive in extreme habitat giving these organisms an advantage over conventional mesophilic organisms in various industrial applications. Extremozymes produced by these extremophiles have high tolerance to inhospitable environmental conditions making them an ideal enzyme system for various industrial processes. A notable application of these extremophiles and extremozymes is their use in the degradation of recalcitrant lignocellulosic biomass and application in biorefineries. For maximum utilization of the trapped carbon source from this obstinate biomass, pretreatment is a necessary step that requires various physiochemical and enzymatic treatments. From search for novel extremophiles and extremozymes to development of various genetic and protein engineering techniques, investigation on extremozymes with enhanced stability and efficiency is been done. Since extremozymes are easily calibrated to work under such conditions, they have become an emerging topic in the research field of biofuel production. The review discusses the various extremozymes that play an important role in lignocellulose degradation along with recent studies on their molecular and genetic evolution for industrial application and production of biofuels and various value-added products.

Silver nanodendrites for ultralow detection of thiram based on surface-enhanced Raman spectroscopy.

Metal nanostructures with highly branched morphologies are attractive due to their fascinating plasmonic properties which are related to their unique morphological features. In this work a simple fabrication methodology is used for fabrication of surface-enhanced Raman spectroscopy (SERS) substrates composed of branched silver nanostructures with dendritic morphology. The high Raman intensity enhancement factor of the order ∼1010 was achieved which allows the detection of ∼zeptomole thiram molecules by SERS substrates. The appearance of new bands at 344 cm-1 and 1521 cm-1 provides an evidence of contribution of chemical enhancement in SERS. The observed spectral changes in SERS spectrum originate from the adsorption of the analyte on the metal surface and provide an insight into molecule-metal interaction in SERS. The extreme sensitivity of SERS substrates is discussed in terms of the distinction between electromagnetic and chemical enhancement mechanisms. Moreover, the highly sensitive SERS substrates were used for simultaneous detection of Rhodamine B and thiram molecules from their mixture with different individual concentrations demonstrating detection capabilities for the identification of pesticides with dye molecules.

Gold-Deposited Graphene Nanosheets for Self-Cleaning Graphene Surface-Enhanced Raman Spectroscopy with Superior Charge-Transfer Contribution.

The interaction of graphene with metals initiates charge-transfer interaction-induced chemical enhancements, which critically depend on the doping effect from deposited metallic configurations. In this paper, we have explored the gold nanoparticle-decorated monolayer graphene nanosheets for the large graphene-induced Raman enhancement of adsorbed analytes, indicating the surface-enhanced Raman spectroscopy (SERS) capabilities of metal-doped graphene (G-SERS). Here, the systematically sputtered Au thickness optimization procedure revealed noticeable modifications in the graphene Raman spectra and photoluminescence (PL) background quenching, which indicated favorable charge transfer through n-type doping of chemical vapor deposition-grown graphene nanosheets. The highly consistent, individually distributed morphology of the gold nanoislands over graphene nanosheets depicted a reproducibly uniform G-SERS signal with excellent relative standard deviation values (<5%), resulting in the strongest Raman intensity enhancement factors of ∼108 (MB) (methylene blue) and 107 (DPA) (2,6-pyridinedicarboxylic acid) composed of the weakest PL background. The combined charge-transfer-induced chemical enhancement and electromagnetic enhancement from individual Au nanoislands result in a lowering of detectability down to 10-16 M (MB) and 10-11 M (DPA) concentrations with efficient time-dependent signal stability. Additionally, the GAu demonstrated its effective (∼94.4%) photocatalytic degradation capabilities by decomposing MB dye molecules from a concentration of 1 µM to 2.52 fM within 60 min. Therefore, the prominent charge-transfer contribution through controlled Au decoration over graphene nanosheets provides a potential strategy for fabricating superior SERS sensors and photocatalysts exhibiting adequate signal consistency, stability, and photodegradation efficiency through overcoming the limitations of the traditional sensing platforms.

Surface enhanced raman spectroscopy based sensitive and onsite detection of microplastics in water utilizing silver nanoparticles and nanodendrites.

Plastics, of the order of microns in size, being not visible to the naked eye, are one of the significant contributors to pollution in the environment. Thus, the detection of micron-sized plastics (microplastics (MPs)) is crucial because of its hazardous toxic effects on our surroundings. In this work, we have proposed a quick and on-site detection of MPs, such as, polyvinyl chloride (PVC), polyvinyl alcohol (PVA) and polystyrene (PS) at ultra trace level using surface-enhanced Raman spectroscopy (SERS). To detect and analyse the spectra, two different nanostructures, such as, spherical shaped Ag nanoparticles (NPs), and shape anisotropic Ag nano-dendrites (NDs) were utilised to acquire the SERS spectra. A comprehensive analysis was further performed to check and investigate the amount of enhancements due to the mentioned nanostructures. We observed the Ag NDs exhibited amplified signal intensity compared to the Ag NPs due to the shape anisotropy leading to the surface charge confinement effect to create highly dense hotspots. However, the spherical shaped polystyrene beads of micron size exhibited better enhancement in Raman signal intensity when mixed with Ag NPs due to increased surface adsorption with the NPs. Therefore, the comparative study emphasizes the ability of using solution-based nanostructure as SERS for the onsite detection of microplastics having diverge size range at low concentration.

Biogas from lignocellulosic feedstock: current status and challenges.

The organic wastes and residues generated from agricultural, industrial, and domestic activities have the potential to be converted to bioenergy. One such energy is biogas, which has already been included in rural areas as an alternative cooking energy source and agricultural activities. It is produced via anaerobic digestion of a wide range of organic nutrient sources and is an essential renewable energy source. The factors influencing biogas yield, i.e., the various substrate, their characteristics, pretreatment methods involved, different microbial types, sources, and inoculum properties, are analyzed. Furthermore, the optimization of these parameters, along with fermentation media optimization, such as optimum pH, temperature, and anaerobic digestion strategies, is discussed. Novel approaches of bioaugmentation, co-digestion, phase separation, co-supplementation, nanotechnology, and biorefinery approach have also been explored for biogas production. Finally, the current challenges and prospects of the process are discussed in the review.

Development and Validation of a New Tool to Measure Performance Knowledge and Communication Skill of Multidisciplinary Health Science Learners on Radiation Emergency Preparedness and Response Management.

OBJECTIVE: The purpose of the study was to design, develop, and validate a newer tool on radiation emergency preparedness responses (RadEM-PREM IPE tool) to measure communication, knowledge, performance skills in multidisciplinary health science learners. METHODS: The study design is a prospective, single centric, pilot study. Five subject experts designed, analyzed, and selected items of the instrument for relevant content and domain. Psychometrics that the tool assessed were content validity, internal consistency, test-retest reliability, and intraclass correlation coefficient. Twenty-eight participants completed test-retest reliability for validation of 21 sorted out items calculated percentage of agreement >70% I-CVI/UA (item content validity index with universal acceptability) and S-CVI/UA (scale content validity index with universal agreement method). RESULTS: Items with percentage agreement >70% and I-CVI over 0.80 were kept, ranged from 0.70 to 0.78 were revised, and below 0.70 were rejected. Items with kappa values ranging from 0.04 to 0.59 were revised and ≥0.74 were retained. Internal consistency assessed using Cronbach's alpha was 0.449. Positive correlation between attitude and communication (r = 0.448), between performance and communication (r = 0.443) were statistically significant at 0.01 level. Overall, intraclass correlation coefficient for all the measures is 0.646, which is statistically significant at 0.05 level (P < 0.05). CONCLUSIONS: Study concludes that the RadEM-PREM IPE tool would be a new measuring tool to assess knowledge, performance, and communication skills of interprofessional radiation emergency response team learner's evaluation.

Innovations in CAZyme gene diversity and its modification for biorefinery applications.

For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.

Modulation of miRNA expression in natural populations of A. thaliana along a wide altitudinal gradient of Indian Himalayas.

Plant populations growing along an altitudinal gradient are exposed to different environmental conditions. They are excellent resources to study regulatory mechanisms adopted by plants to respond to different environmental stresses. Regulation by miRNA is one of such strategies. Here, we report how different miRNAs are preferentially expressed in the three natural populations of A. thaliana originating from a wide altitudinal range. The expression level of miRNAs was mostly governed by temperature and radiation. Majority of the identified miRNAs expressed commonly in the three populations. However, 30 miRNAs expressed significantly at different level between the low and the high altitude populations. Most of these miRNAs regulate the genes associated with different developmental processes, abiotic stresses including UV, cold, secondary metabolites, etc. Further, the expression of miR397 and miR858 involved in lignin biosynthesis and regulation of secondary metabolites respectively, may be regulated by light intensity. A few miRNAs expressed at increasing level with the increase in the altitude of the site indicating environment driven tight regulation of these miRNAs. Further, several novel miRNAs and isomiR diversity specific to the Himalayas are reported which might have an adaptive advantage. To the best of our knowledge, this is the first report on miRNA expression from natural plant populations.

Pharmacological profile of AW-814141, a novel, potent, selective and orally active inhibitor of p38 MAP kinase.

The p38 mitogen activated protein kinase (MAPK) is a key signaling molecule that plays a crucial role in the progression of various inflammatory diseases such as rheumatoid arthritis (RA), asthma and chronic obstructive pulmonary disease. The objective of the present study was to evaluate the anti-inflammatory activity of a p38 MAPK inhibitor, AW-814141. AW-814141 inhibited enzymatic activity of recombinant p38-alpha and beta isoforms with IC(50) value of 100nM and 158nM, respectively. AW-814141 also inhibited the release of tumor necrosis factor (TNF)-alpha by lipopolysaccharide (LPS) treated human peripheral blood mononuclear cells with an IC(50) value of 212nM and demonstrated selectivity against a panel of few kinases. Oral administration of AW-814141 (10mpk) in LPS-injected mice resulted in a significant reduction in TNF-alpha production in the circulation. In a carrageenan-induced rat paw edema model and collagen-induced arthritis model (CIA), AW-814141 dose dependently inhibited paw swelling. In different in vivo efficacy models, efficacy of AW-814141 was found to be better as compared to the reference compounds (Vx-745 and BIRB-796). This study demonstrated that AW-814141 is a novel p38 MAPK inhibitor and it displays promising in vitro and in vivo anti-inflammatory activities and can be used for the treatment of rheumatoid arthritis.