uCARE Chem Suite and uCAREChemSuiteCLI: Tools for bacterial resistome prediction.

In the era of antibiotic resistance, in silico prediction of bacterial resistome profiles, likely to be associated with inactivation of new potential antibiotics is of utmost importance. Despite this, to the best of our knowledge, no tool exists for such prediction. Therefore, under the rationale that drugs with similar structures have similar resistome profiles, we developed two models, a deterministic model and a stochastic model, to predict the bacterial resistome likely to neutralize uncharacterized but potential chemical structures. The current version of the tool involves the prediction of a resistome for Escherichia coli and Pseudomonas aeruginosa. The deterministic model on omitting two diverse but relatively less characterized drug classes, polyketides and polypeptides showed an accuracy of 87%, a sensitivity of 85%, and a precision of 89%, whereas the stochastic model predicted antibiotic classes of the test set compounds with an accuracy of 72%, a sensitivity of 75%, and a precision of 83%. The models have been implemented in both a standalone package and an online server, uCAREChemSuiteCLI and uCARE Chem Suite, respectively. In addition to resistome prediction, the online version of the suite enables the user to visualize the chemical structure, classify compounds in 19 predefined drug classes, perform pairwise alignment, and cluster with database compounds using a graphical user interface. AVAILABILITY: uCARE Chem Suite can be browsed at: https://sauravsaha.shinyapps.io/ucarechemsuite2/, and uCAREChemSuiteCLI can be installed from:1. CRAN (https://cran.r-project.org/package=uCAREChemSuiteCLI) and2. GitHub (https://github.com/sauravbsaha/uCAREChemSuiteCLI).

Correction to: Transcriptome-wide identification of genes involved in Ascorbate-Glutathione cycle (Halliwell-Asada pathway) and related pathway for elucidating its role in antioxidative potential in finger millet (Eleusine coracana (L.)).

[This corrects the article DOI: 10.1007/s13205-018-1511-9.].

Transcriptome-wide identification of genes involved in Ascorbate-Glutathione cycle (Halliwell-Asada pathway) and related pathway for elucidating its role in antioxidative potential in finger millet (Eleusine coracana (L.)).

Finger millet is being recognized as a potential future crop due to their nutrient contents and antioxidative properties, which are much higher compared to the other minor millets for providing health benefits. The synthesis of these nutritional components is governed by the expression of several gene(s). Therefore, it is necessary to characterize these genes for understanding the molecular mechanisms behind de novo synthesis of nutrient components. Apart from this, these important compounds could also serve as candidate genes for imparting stress tolerance in other crop plants also. In the present study, effort has been made to identify genes involved in Ascorbate-Glutathione cycle (Halliwell-Asada Pathway) and related pathway genes for elucidating its role in antioxidative potential mechanism through transcriptome data analysis. APX, DHAR, MDHAR, GR, and SOD have been identified as the key genes of the pathway in two genotypes GP-1 (low Ca2+) and GP-45 (high Ca2+) of finger millet with reference to rice as a model system, besides, 30 putatively expressed genes/proteins were also investigated. Furthermore, the sequences of identified genes were analyzed systematically; gene ontology (GO) annotation and enrichment analysis of assembled unitranscripts were also performed using Blast2GO. As a result, 49 GO terms, 5 Enzyme Commission (EC) numbers, and 2 KEGG pathway maps were generated. GO results revealed that these genes are mainly involved in two biological processes (BP), viz., oxidation-reduction process (GO:0055114) and cellular oxidant detoxification (GO:0098869), and showed oxidoreductase activity (GO:0016491). KEGG analysis showed that APX, DHAR, MDHAR, and GR are directly connected to biosynthetic pathways of secondary metabolites, mainly polyphenolic compounds (flavonoid, tannin, and lignin) involved in glutathione metabolism (KEGG:00480) and ascorbate and aldarate metabolism (KEGG:00053). While SOD, is indirectly connected and also has significant medicinal attributes and antioxidant properties. Moreover, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were also calculated for expression analysis and found that the FPKM values of genes present in GP-1 are higher than that of GP-45. Thus, GP-1 genotype was found to have higher stress regulated gene expression in comparison to GP-45. Taken together, the present transcriptome-based investigation unlocks new avenues for systematic functional analysis of novel ROS scavenging candidate genes that could be effectively applied for improvising human health and nutrition.

Salinity induced physiological and biochemical changes in the freshly separated cyanobionts of Azolla microphylla and Azolla caroliniana.

Freshly separated cyanobionts of Azolla microphylla and Azolla caroliniana plants exposed to salinity showed decline in the cellular constituents such as chlorophyll (23.1 and 38.9%) and protein (12.9 and 19.3%). However, an increase in the carotenoid and sugar content was observed. Exposure to salinity stress reduced the heterocyst frequency (35.4 and 57.2%) and nitrogenase activity (37.7 and 46.3%) of the cyanobionts. Increase in the activity of antioxidant enzymes such as super oxide dismutase (50.6 and 11.5%), ascorbate peroxidase (63.7 and 57.9%), catalase (94.2 and 22.5%) as well as non-enzymatic antioxidant proline (18.8 and 13.3%) was also observed in response to salinity. The cyanobionts exhibited significant increase in the intracellular Na(+) level and reduced intracellular K(+)/Na(+) and Ca(2+)/Na(+) ratio in response to salinity. The results demonstrate the adverse impact of salinity on the freshly separated cyanobionts as similar to free living cyanobacteria. These results may be helpful in the critical evaluation of salinity tolerance mechanism of the cyanobiont and its interaction with the host.