SPART: A versatile and standardized data exchange format for species partition information

A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the “inferred species”. The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.     

Synthesis, spectroscopic and biological aspects of iron(II) complexes

Five novel coordinated complexes of iron(II) with ciprofloxacin and neutral bidentate ligands have been prepared and characterized using elemental analyses, magnetic measurements, IR spectra, UV-VIS spectral, thermogravimetric analyses, 1H-NMR and 13C-NMR. The antimicrobial activity of the individual ligands, metal salt and metal complexes with respect to Bacillus subtilis, Escherichia coli, Bacillus cereus, Staphylococcus aureus, Salmonella typhi, Serratia marcescens, Aspergillus niger, Aspergillus flavus and Lasiodiplodia theobromae were evaluated by the agar-plate technique in comparison to reference standard drugs (ofloxacin, levofloxacin and fluconozole). Binding of the complexes to DNA was studied and is discussed.     

Evaluation of fungal culture filtrate containing chitinase as a biocontrol agent against Helicoverpa armigera

AIMS: To evaluate the biocontrol efficacy of culture filtrate containing chitinase from Trichoderma harzianum against Heliothis. METHODS AND RESULTS: T. harzianum was cultured by submerged fermentation using colloidal chitin as sole carbon source. The ability of the culture filtrate to hydrolyse colloidal chitin indicated the presence of chitinase as one of its components. Biocontrol assay on Heliothis showed that the culture filtrate is a potent antifeedant as it reduced the feeding rate and body weight of the larvae. It reduced the successful pupation and increased larval and pupal mortality in a dosage-dependent manner when applied topically. The highest mortalities (70%) were recorded for groups treated with 2000 U ml(-1) chitinase activity. The percentage of adult emergence was zero for the highest chitinase concentration (2000 U ml(-1)) tried. CONCLUSIONS: The studies showed that the culture filtrate containing chitinase from T. harzianum is capable of negatively affecting the growth and metamorphosis of Heliothis larvae. SIGNIFICANCE AND IMPACT OF THE STUDY: In view of the need for safer and environmentally friendly pest management tools, the present study could help in the development of enzyme-based biopesticides against Heliothis.     

Genome Sequence of a Novel Actinophage PIS136 Isolated from a Strain of Saccharomonospora sp

A wide-host-range bacteriophage (phage) PIS136 was isolated from PA136, a strain of Saccharomonospora belonging to the group actinomycetes. Here, we present the genome sequence of the PIS136 phage, which is 94,870 bp long and contains 132 putative coding sequences and one tRNA gene. An IS element-like region with two genes for putative transposases was identified in the genome. The presence of IS element-like sequences suggests that PIS136 is still under active evolution.     

Expression,purification and characterization of the interferon-inducible,antiviral and tumour-suppressor protein,human RNase L

The interferon (IFN)-inducible, 2′,5′-oligoadenylate (2-5A)-dependent ribonuclease L (RNase L) plays key role in antiviral defense of mammalian cells. Induction by IFN and activation by double-stranded RNA lead to 2-5A cofactor synthesis, which activates RNase L by causing its dimerization. Active RNase L degrades single-stranded viral as well as cellular RNAs causing apoptosis of virus-infected cells. Earlier, we had reported that expression of recombinant human RNase L caused RNA-degradation and cell-growth inhibition in E. coli without the need for exogenous 2-5A. Expression of human RNase L in E. coli usually leads to problems of leaky expression, low yield and degradation of the recombinant protein, which demands number of chromatographic steps for its subsequent purification thereby, compromising its biochemical activity. Here, we report a convenient protocol for expression of full-length, soluble and biochemically active recombinant human RNase L as GST-RNase L fusion protein from E. coli utilizing a single-step affinity purification with an appreciable yield of the highly purified protein. Recombinant RNase L was characterized by SDS-PAGE, immunoblotting and MALDI-TOF analysis. A semi-quantitative agarose-gel-based ribonuclease assay was developed for measuring its 2-5A-dependent RNase L activity against cellular large rRNAs as substrates. The optimized expression conditions minimized degradation of the protein, making it a convenient method for purification of RNase L, which can be utilized to study effects of various agents on the RNase L activity and its protein–protein interactions.     

Cross‐Species Alleviation of Biotic and Abiotic Stresses by the Endophyte Pseudomonas aeruginosa PW09

A wheat endophytic bacterium (Pseudomonas aeruginosa PW09) was evaluated for its ability to trigger an induced systemic resistance response in cucumber against biotic and abiotic stresses. PW09 was applied to cucumber seeds, and the seedlings were subjected to Sclerotium rolfsii infection and NaCl (150 mm ). The role of PW09 was evaluated in alleviating the stresses by assessing plant mortality due to S. rolfsii infection and biomass accumulation under NaCl stress as well as at the physiological level through phenylpropanoid metabolism, antioxidant activities and proline accumulation. The endophyte reduced seedling mortality by 60% and increased biomass accumulation significantly under S. rolfsii (7%) and NaCl (18%) stresses, respectively, compared with endophyte‐untreated seedlings. Application of PW09 also induced higher accumulation of proline (1.3‐ and 1.4‐fold) and total phenolics (1.2‐ and 1.1‐fold) and activities of polyphenol oxidase (4.3‐ and 1.5‐fold), phenylalanine ammonia lyase (1.29‐ and 1.27‐fold) and superoxide dismutase (2.5‐ and 1.39‐fold) under S. rolfsii and NaCl stresses, indicating the ability of the wheat endophyte PW09 in alleviating both biotic and abiotic stresses in cucumber.