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.     

Highly selective and sensitive ‘on–off’ fluorescent chemosensor for Fe3+ ions crafted by benzofuran moiety in both experimental and theoretical methods

A benzofuran glycinamide-based chemosensor, 3-(2-([4-fluorobenzyl]amino)acetamido)benzofuran-2-carboxamide ( BGA ) was developed and synthesized for the selective and sensitive detection of Fe³⁺ ions. The photophysical properties of the probe BGA were studied using UV–visible light absorption and fluorescence spectrophotometers. The chemosensor BGA showed a marked ‘on–off’ fluorescence response towards Fe³⁺ ions in the presence of other metal ions in DMSO/H₂O solution (9/1, v/v). The very low limits of detection (LOD) were calculated to be 10 nM and 43 nM using UV–visible light absorption and fluorescence spectrophotometers, respectively. Job's plot analysis revealed the formation of a BGA -Fe³⁺ complex with a 1:1 binding stoichiometry ratio using UV–visible light spectroscopy. The sensing mechanism was also demonstrated using density functional theory calculation.     

Demethyloleuropein and beta-glucosidase activity in olive fruits

Demethyloleuropein plays a major role in the defense mechanism of olive fruits. To understand how this molecule is metabolized during different stages of maturation of olive fruits, a biomolecular approach to identify the demethyloleuropein chemistry was employed. The beta-glucosidase activity in crude extracts was assayed spectrophotometrically using the chromogenic substrate p-nitrophenyl-beta-D-glucopyranoside. Demethyloleuropein was extracted and identified by HPLC-MS from both infected and uninfected olive fruits at different physiological stages. The release of more functionally relevant dialdehydes in uninfected fruits was investigated using ESIMS/ MS. In fruits harvested in October, the activity of beta-glucosidase was significantly enhanced in uninfected fruits when compared to the infected fruits. Quantitative differences in the demethyloleuropein content from uninfected fruits showed the highest values (5.09 mg/g) in October, whereas lower levels (4.44 mg/g) were found in infected fruits. The results demonstrated that demethyloleuropein derivatives could be influenced by beta-glucosidase activity to improve the quality of the olive products with the best dialdehyde nutraceutical content.     

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.     

Freshwater fish biodiversity in the River Ganga (India): changing pattern, threats and conservation perspectives

The river Ganges is the largest river in India and the fifth longest in the world. Although, many studies on fish ecology and systematic have been conducted largely to improve fisheries but fish diversity and their distribution pattern from conservation point of view have never been adequately addressed in the Ganges. In this connection, current distribution and abundance of freshwater fishes of river Ganges was studied and assessed from April 2007 to March 2009. We documented and described 143 freshwater fish species in the all stretches of the river which is higher than what was reported earlier. Some species were observed with shift in their distribution ranges. First time, a total of 10 exotic fishes, including Pterygoplichthys anisitsi, which has never been reported from India found in the Ganges. Alterations of the hydrological pattern due to various types of hydro projects was seems to be the largest threat to fishes of Ganges. Indiscriminate and illegal fishing, pollution, water abstraction, siltation and invasion of exotic species are also threatening the fish diversity in the Ganges and as many as 29 species are listed under threatened category. The study advocates a need to identify critical fish habitats in the Ganga basin to declare them as conservation reserves to mitigate the loss of fish diversity from this mighty large river.     

Structure-function correlation of outer membrane protein porin from Paracoccus denitrificans

Porins from outer membrane of Gram-negative bacteria have a highly stable structure. Our previous studies on porin from Paracoccus denitrificans showed that the outer membrane protein porin is extremely stable toward heat, pH, and chemical denaturants. The major question we have addressed in this paper is whether the high stability of porin is a consequence of the beta-barrel structure and whether it is required for its function. To explain this we have analyzed two cases: first, we used porin wild-type and mutants and compared their structure and function; second, we compared the activity of porin preheated to different temperatures. Structural changes were monitored by infrared spectroscopy. We observed that the structural stability of porin is not equivalent to functional activity as minor alteration in the structure can result in drastic differences in the activity of porins.