Microbial insight into rhizosphere of arecanut palms of Wayanad using metagenomics

The rhizosphere bacterial diversity of a plant is considered to play an essential role in mediating plant as well as soil health. An attempt to explore the bacterial diversity in the rhizosphere of arecanut palms in Wayanad was done to obtain an understanding of dominant bacterial phylotypes and the status of nutrient concentrations in rhizosphere soil and plants. Since arecanut production in Wayanad is facing a decline, a study to understand the rhizosphere conditions of healthy palms essentially provided insight into what strategies needed to be adopted for improvement of arecanut cultivation. The nutrient imbalance involving increased iron in soil and deficiencies of calcium, magnesium, zinc, and boron in the Arecanut rhizosphere was found to be an evident reason for the decline in production. Apart from that, the biological activities in the rhizosphere by the diversity of microorganisms were studied to understand the dominant bacterial phyla and genera present in the Arecanut rhizosphere. The presence of various important bacterial phyla like Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, and Bacteroidetes revealed the presence of various beneficial soil microorganisms and emphasized the need to enhance or augment the population of native microflora for efficient nutrient cycling by increasing the organic content of the soil. Since organic carbon is an essential requirement to support bacterial diversity, proper management practice that encompasses organic carbon amendment along with proper nutritional management could enhance bacterial diversity as well as health of the arecanut palms. The study indicated that the dominant bacterial phyla contained various beneficial microorganisms that can be exploited for improving nutrient recycling in the arecanut rhizosphere

A COMPARATIVE STUDY OF STEREOCHEMICAL EFFECTS OF ANTI-PROSTATE AGENTS BY MOLECULAR DOCKING

Objective: A comparative study of anti-prostate agents to investigate the stereochemical influences on binding affinity by molecular docking.Methods: Structures of enantiomers (R and S stereoisomers) for known anti-prostate cancer (PCa) agents were drawn using ChemBioDraw 2D software. Thereafter, they were converted to 3D structures using the ChemBioDraw 3D software in which they were subjected to energy minimization using the MM2 method and then saved as PDB extension files which can be accessed using the ADT interface. AutoDock Vina (ADT) 1.5.6 software version was used for molecular docking study.Results: A total of 12 different anti-PCa agents were selected and drawn including well-known drug R-bicalutamide. All molecules showed the binding affinity with respect to the nature of stereochemistry. R-stereoisomers showed better interaction as well as binding affinity toward 1z95 (mutated androgen receptor protein involved in the progression of PCa) whereas their S-stereoisomers were found inferior in comparison.Conclusion: This study showed that CB1-R and R-bicalutamide (with R-stereochemistry) were better in binding affinity comparative to their counterpart CB1-S and S-Bicalutamide (with S-stereochemistry). All the selected anti-PCa agents were showing the effect of stereochemical center; therefore, we must choose the right kind of stereochemistry while planning to develop the newer anti-PCa agents

Dip coating of forsterite-hydroxyapatitie-poly (ɛ-caprolactone) nanocomposites on Ti6Al4Vsubstrates for its corrosion prevention

522-528Titanium and titanium alloys are extensively used in biomedical, cardiac and cardiovascular applications for their superb properties, such as good fatigue strength, low modulus, machinability, formability, corrosion resistance and biocompatibility. However, titanium and its alloys do not meet the majority of all clinical necessities. Due to these reasons, surface modification is frequently performed to enhance the mechanical, biological and chemical properties of titanium and alloys. In this work, nanocomposites coating of poly(ɛ-caprolactone)/hydroxyapatite/forsterite (PCL/HA/F) have been successfully deposited on the Ti6Al4V substratesby dip coating at room temperature. The coatings are prepared with various concentrations of forsterite/hydroxyapatite nanopowder (2, 4, 6 and 8 wt.%) with a fixed concentration of PCL (4 wt.%) and thus coated Ti6Al4V substrates are examined for corrosion resistance. PCL/Hydroxyapatite/Forsterite coatings are characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM), which clearly showed the formation of nanocomposites. Potentiodynamic polarization curves and electrochemical impedance spectroscopy (EIS) are used to investigate corrosion behavior of the coated substrates, which portrayed that the composite coating of PCL/HA/F substantially enhanced the corrosion resistance of Ti6Al4V alloy

Dip coating of forsterite-hydroxyapatitie-poly (ɛ-caprolactone) nanocomposites on Ti6Al4Vsubstrates for its corrosion prevention

Titanium and titanium alloys are extensively used in biomedical, cardiac and cardiovascular applications for their superb properties, such as good fatigue strength, low modulus, machinability, formability, corrosion resistance and biocompatibility. However, titanium and its alloys do not meet the majority of all clinical necessities. Due to these reasons, surface modification is frequently performed to enhance the mechanical, biological and chemical properties of titanium and alloys. In this work, nanocomposites coating of poly(ɛ-caprolactone)/hydroxyapatite/forsterite (PCL/HA/F) have been successfully deposited on the Ti6Al4V substratesby dip coating at room temperature. The coatings are prepared with various concentrations of forsterite/hydroxyapatite nanopowder (2, 4, 6 and 8 wt.%) with a fixed concentration of PCL (4 wt.%) and thus coated Ti6Al4V substrates are examined for corrosion resistance. PCL/Hydroxyapatite/Forsterite coatings are characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM), which clearly showed the formation of nanocomposites. Potentiodynamic polarization curves and electrochemical impedance spectroscopy (EIS) are used to investigate corrosion behavior of the coated substrates, which portrayed that the composite coating of PCL/HA/F substantially enhanced the corrosion resistance of Ti6Al4V alloy

Dry matter dynamics and carbon flux along riverine forests of Gori valley, Western Himalaya

IntroductionRiverine forests in the Himalaya represent a biodiverse, dynamic, and complex ecosystem that offers numerous ecosystem services to local and downstream communities and also contributes to the regional carbon cycle. However, these forests have not been assessed for their contribution to dry matter dynamics and carbon flux. We studied these parameters along three classes of riverine forests in eastern Uttarakhand, dominated by Macaranga, Alnus, and Quercus-Machilus forest.MethodsUsing volume equations, we assessed tree biomass, carbon storage, and sequestration in the study area.ResultsThe total standing tree biomass in Macaranga, Alnus, and Quercus-Machilus forest ranged from 256.6 to 558.1  Mg  ha−1, 460.7 to 485.8 Mg ha−1, and 508.6 to 692.1 Mg ha−1, respectively. A total of 77.6–79.6% of vegetation biomass was stored in the aboveground biomass and 20.4–22.4% in belowground plant parts across the riverine forests. The carbon stock in Macaranga forest ranged from 115.5 to 251.1 Mg ha−1, in Alnus forest from 207.3 to 218.6 Mg ha−1, and in Quercus-Machilus forest from 228.9 to 311.4 Mg ha−1. The mean annual litterfall was accounted maximum for Quercus-Machilus forest (5.94  ±  0.54 Mg ha−1 yr.−1), followed by Alnus (5.57  ±  0.31 Mg ha−1 yr.−1) and Macaranga forest (4.67  ±  0.39 Mg ha−1 yr.−1). The highest value of litterfall was recorded during summer (3.40  ±  0.01 Mg ha−1 yr.−1) and the lowest in winter (0.74  ±  0.01 Mg ha−1 yr.−1). The mean value of net primary productivity and carbon sequestration was estimated to be highest in Quercus-Machilus forest (15.8  ±  0.9 Mg ha−1 yr.−1 and 7.1  ±  0.9 Mg C ha−1 yr.−1, respectively) and lowest in Alnus forest (13.9  ±  0.3 Mg ha−1 yr.−1 and 6.1  ±  0.3 Mg C ha−1 yr.−1, respectively).DiscussionThe results highlight that riverine forests play a critical role in providing a large sink for atmospheric CO2. To improve sustainable ecosystem services and climate change mitigation, riverine forests must be effectively managed and conserved in the region

Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures

Long RNA molecules are at the core of gene regulation across all kingdoms of life, whilst also serving as genomes in RNA viruses. Few studies have addressed the basic physical properties of long single-stranded RNAs. Long RNAs with non-repeating sequences usually adopt highly ramified secondary structures and are better described as branched polymers. In order to test whether a branched polymer model can estimate the overall sizes of large RNAs we employed fluorescence correlation spectroscopy to examine the hydrodynamic radii of a broad spectrum of biologically important RNAs, ranging from viral genomes to long non-coding regulatory RNAs. The relative sizes of long RNAs measured at low ionic strength correspond well to those predicted by two theoretical approaches that treat the effective branching associated with secondary structure formation – one employing the Kramers theorem for calculating radii of gyration, and the other featuring the metric of “maximum ladder distance”. Upon addition of multivalent cations, most RNAs are found to be compacted as compared with their original, low-ionic-strength sizes. These results suggest that sizes of long RNAmolecules are determined by the branching pattern of their secondary structures. They also experimentally validate the proposed computational approaches for estimating hydrodynamic radii of single-stranded RNAs, which use generic RNA structure prediction tools and thus can be universally applied to a wide range of long RNAs

A comprehensive platform for highly multiplexed mammalian functional genetic screens

<p>Abstract</p> <p>Background</p> <p>Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP) is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens.</p> <p>Results</p> <p>Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens.</p> <p>Conclusion</p> <p>Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray) based deconvolution methods.</p