Development of novel rapid-growing and delicious Pleurotus djamor strains through hybridization

The development of fast-growing/short cropping period oyster mushroom (Pleurotus species) having good taste is one of the important needs of mushroom growers. Pleurotus djamor strain woody1, collected recently from the dead wood, has a short cropping period of 30 days but a moderately acceptable taste. One of the cultivated Pleurotus spp., P. djamor strain MDU1, has good taste but a long cropping period of 47 days. Thus, genetic improvement of P. djamor was carried out between these two strains by pairing monokaryons (anastomosis) to develop elite hybrid strains having a short cropping period and good taste. Monokaryons of parental strains showed variation in time required for germination; i.e., basidiospores of P. djamor strain woody1 germinated and developed monokaryotic colonies in 6 days, whereas that of P. djamor strain MDU1 developed monokaryotic colonies in 8 days of incubation. In addition, variation in the growth rate and morphology of the monokaryotic mycelia of both parental strains was noticed, and fast-growing monokaryons were selected for anastomosis. Out of 60 crosses made between mycelia of monokaryotic isolates of both parental strains, 20 crosses showed clamp connection, indicating that they were successful crosses. Out of 20 hybrids, two hybrid strains, viz., W2M4 and W4M4, exhibited higher yields than their parents. They exhibited the short cropping period trait, good taste attribute, and some specific volatile metabolites. This study showed that the developed two hybrid varieties, having desirable agronomic traits, could be used in mushroom farming to increase the mushroom grower's income.

Determination of 73 multi-class pesticides in okra (Abelmoschus esculentus L.) fruits using LC-MS/MS and GC-MS/MS and estimation of analytical uncertainty of measurement

This study developed a method to simultaneously determine 73 multi-class pesticides in okra fruit using LC-MS/MS and GC-MS/MS. The sample was extracted with acetonitrile and subsequent clean-up through dispersive-SPE method. The quantification level of the technique was 0.01 µg g-1 and compliance to the MRLs fixed by the regulatory bodies like EU and FSSAI. The recovery at 10, 50, and 100 µg kg-1 spiked levels; intra and inter-day precision at 50 µg kg-1 were found within 70-120% with RSD less than 15% with LC-MS/MS and GC-MS/MS. Measurement uncertainty was in the range of 1.81 to 12.91 µg kg-1 estimated at 50 µg kg-1. The matrix effects were slightly higher for LC than GC-compatible pesticides. Risk assessment for pesticides detected in the field and market samples found no hazardous to the consumers except profenofos. The proposed method is highly sensitive, reproducible for the complex matrix like okra, and meets the regulatory standards.

Determination of Synthetic Pyrethroids and Hexaconazole Residues in curry leaves and decontamination through household techniques

A multiresidue method was developed and validated for the simultaneous determination of eight synthetic pyrethroids and hexaconazole fungicide residues in curry leaves. The method involves extraction of leaf sample with ethyl acetate, purified by dispersive SPE with primary secondary amine and graphitized carbon black. The gas chromatography-electron capture detector (GC-ECD) used for residue estimation and confirmed using gas chromatography-mass spectrometry (GC-MS) with the LOQ of 0.03 μg/g. The recoveries of all pesticides were in the range of 75 to 110% with a relative standard deviation of less than 7%. The matrix effect was within the acceptable limit of less than 20% as prescribed by SANTE guidelines. The decontamination was carried out to reduce the concentration of residues in curry leaves by different household techniques and lemon juice (2%) solution was found to be more effective (35.71-56.52%) followed by 2% tamarind (23.48 to 42.94%), hot water (18.44 to 46.74%), 2% salt water (10.98 to 42.71%) and least in tap water (3.57 to 27.84%). The method was successfully applied for routine monitoring of pesticide residues in curry leaves.

Production, stability and degradation of Trichoderma gliotoxin in growth medium, irrigation water and agricultural soil

Gliotoxin produced by Trichoderma virens is inhibitory against various phytopathogenic fungi and bacteria. However, its stability in soil-ecosystem has not yet been well-defined. This study aimed to decipher its persistence and behaviour in growth media, irrigation water and soil ecosystems. Gliotoxin production was noticed at logarithmic growth phase and converted into bis-thiomethyl gliotoxin at late stationary growth phase of T. virens in acidic growth medium. But, no gliotoxin production was observed in neutral and alkaline growth medium. Gliotoxin was stable for several days in acidic water but degraded in alkaline water. Degradation of gliotoxin was more in unsterile soil than sterile soil and also that was higher under wet soil than dry soil. Degradation of gliotoxin was hastened by alkaline pH in wet soil but not in dry soil. Under unsterile soil conditions, high soil moisture increased the degradation of gliotoxin and the degradation of gliotoxin occurred quickly in alkaline soil (in 5 days) compared to acidic soil (in 10 days). Under sterile soil conditions, high soil moisture also enhanced the degradation of gliotoxin but level of degradation was less compared to unsterile conditions. Thus, gliotoxin stability is influenced mainly by the soil wetness, soil microbial community and pH conditions.

Simultaneous determination of 79 pesticides in pigeonpea grains using GC-MS/MS and LC-MS/MS

Pigeonpea grains are important sources of vegetarian proteins. It is the paramount importance to check the pesticide residues due to their frequent use during production. The LC-MS/MS and GC-MS/MS analytical method was developed and validated for the simultaneous determination of 79 pesticide residues in pigeonpea. The LOD and LOQ of the analytical method were in the range of 0.53 to 3.97 and 1.60 to 10.05 µg kg^-1, respectively, with a correlation coefficient of more than 0.997. Average recoveries were in the range of 80 to 118.8%, with the RSD of less than 15%. Measurement uncertainty (U_x) for pesticides was in the range of 3.42 to 12.76 µg kg^-1 evaluated at 50 µg kg^-1. The method was applied to analyze the sample collected from the farmer's field. This method could be useful for routine analysis of selected pesticide residue for monitoring purposes.

Dissipation Kinetics and Environmental Risk Assessment of Thiamethoxam in the Sandy Clay Loam Soil of Tropical Sugarcane Crop Ecosystem

Thiamethoxam 75 SG has recently got registered for use against shoot borer and termites of sugarcane. It is the only neonicotinoid having label claim against both the major pests of sugarcane. The dissipation kinetics and environmental risk assessment of thiamethoxam 75 SG were studied in a typical tropical sugarcane crop ecosystem as detailed reports are lacking. Rapid and sensitive method adopted to determine the residues of thiamethoxam in the soil employing HPLC could provide more than 95.5% recoveries. The insecticide was observed to persist in the sandy clay loam soil for 60 days and reached below the detectable level of less than 0.01 mg/kg (LOQ = 0.01 mg/kg) on 75th day when applied @ 120 g a.i./ha. The half-life was worked out to be 16.50 days. At double the recommended dose (240 g a.i./ha), the insecticide persisted up to 75 days with the half-life of 16.91 days. The risk quotient values indicated medium to low level of risk to earthworms during the course of degradation of thiamethoxam in the soil.

Dissipation kinetics, dietary and ecological risk assessment of chlorantraniliprole residue in/on tomato and soil using GC-MS

An alternate single quadrupole gas chromatography coupled with electron ionization mass spectrometry (GC-EI-MS) method was developed and validated for the determination chlorantraniliprole residue in tomato and soil. The target analyte was extracted from selected matrices with acetonitrile followed by dispersive solid-phase extraction clean up with primary secondary amine and graphitized carbon black sorbent to remove co-extractives prior to analysis. Limit of quantification of the method was 0.01 μg/g and the recovery of chlorantraniliprole was in the range of 92-99% with RSD of less than 3%. The dissipation kinetics of chlorantraniliprole in tomato and soil followed first-order kinetics with the half-life of 1.26 and 1.77 days, respectively. A safe waiting period of 1 day suggested for safe consumption of tomato fruits considering the FSSAI maximum residue limit of 0.6 μg/g. The residue concentrations were reduced in the range of 13 to 64% from tomato fruit using simple household approaches. The present study suggested that the use of chlorantraniliprole in tomato does not seem to pose any dietary risk to consumers. The ecological risk quotient (RQ) values indicated that the chlorantraniliprole residues in the soil may pose a medium level of risk to earthworms and arthropods during this period.

Persistence, dietary and ecological risk assessment of indoxacarb residue in/on tomato and soil using GC-MS

An efficient single quadrupole gas chromatography with mass spectrometry method was developed and validated for the determination of indoxacarb residues in tomato and soil. Residues were extracted from the samples using acetonitrile as extracting solvent and the extracts were purified through primary secondary amine and graphitized carbon black. Recoveries were obtained in the range of 92.12-110.51% with the relative standard deviation of 1.32-4.32%. Indoxacarb dissipated with half-life of 3.12-3.21 and 1.24-1.35d for tomato and soil, respectively following doses of indoxacarb 14.5% SC at 60, 90 and 120 g.a.i./ha. Safe waiting periods were found to be 1-3d. The residues were removed from tomato fruit was in the range of 16.73 to 54.32% using simple decontamination approaches. The present study suggest that the use of indoxacarb in tomato at recommended dose, does not seem to pose any dietary risk to the consumers. The soil RQ values indicated low level of risk to earthworms and arthropods.

Dissipation kinetics of beta-cyfluthrin and imidacloprid in tea and their transfer from processed tea to infusion

Dissipation kinetics of mixed formulation consisting beta-cyfluthrin and imidacloprid in tea crop under an open field ecosystem was investigated. The mixed formulation was applied on tea plant at recommended (27 + 63) and double the recommended (54 + 126g a.i./ha) dose and residues were determined using gas chromatography-electron capture detector and high performance liquid chromatography-photodiode array detector for beta-cyfluthrin and imidacloprid, respectively. The limit of quantification of analytical method was 0.05µg/g and the average recoveries were ranged from 88.36% to 103.49% with relative standard deviations of less than 6% at three spiked levels. The experimental results showed that in the green tea leaves imidacloprid dissipated faster than beta-cyfluthrin with the half-life ranging between 1.20-1.39 and 2.89-3.15days, respectively. The beta-cyfluthrin residues present in the processed tea not transferred into the tea infusion during the infusion process and imidacloprid transferred in the range 43.12-49.7%. On the basis of the transfer of residues from processed tea to infusion, a waiting period of 17 days for tea plucking after pesticide application at recommended dose may be suggested.

Development, validation and application of a sensitive analytical method for residue determination and dissipation of imidacloprid in sugarcane under tropical field condition

A simple and sensitive analytical method has been developed and validated for the determination of trace amounts of imidacloprid in/on sugarcane sett, stalk and leaf. The method optimized in the present study requires less volume of organic solvent and time. Hence, this method is suitable for high-throughput analyses involving large number of samples. The limit of detection (LOD) and limit of quantification (LOQ) of the method were 0.003 and 0.01 mg/kg, respectively. The recovery and relative standard deviation were more than 93 % and less than 4 %, respectively. Thus, it is obvious that the analytical method standardized in this study is more precise and accurate enough to determine the residues of imidacloprid in sugarcane sett, stalk and leaf. The dissipation and translocation of imidacloprid residues from treated cane setts to leaf and stalk were studied by adopting this method. In sugarcane setts, the residues of imidacloprid persisted up to 120 days with half-life of 15.4 days at its recommended dose (70 g a.i./ha). The residues of imidacloprid were found to be translocated from setts to stalk and leaf. The imidacloprid residues were detected up to 105 days in both leaf and stalk. Dipping of sugarcane setts in imidacloprid at its recommended dose may result in better protection of cane setts and established crop because of higher initial deposit (>100 mg/kg) and longer persistence (>120 days).

Persistence and dissipation kinetics of chlorantraniliprole 0.4G in the soil of tropical sugarcane ecosystem

Chlorantraniliprole 0.4 % GR has been in use for managing early shoot borer and top borer of sugarcane. Persistence and dissipation kinetics of granular formulation of chlorantraniliprole were studied in the soil of tropical sugarcane ecosystem by employing simple and sensitive analytical method. Limit of quantification of the method was 0.01 mg/kg and the recovery of chlorantraniliprole was in the range of 92.3-99.7 % with RSD of 1.14-3.0 %. The initial deposit of chlorantraniliprole in the soil was 0.513 and 1.031 mg/kg for the recommended (75 g a.i./ha) and double the recommended (150 g a.i./ha) doses, respectively. The residues were quantified up to 30 days after treatment irrespective of the doses applied. Half-life (t 1/2) was 6.60 and 6.73 days, respectively, for recommended and double the recommended doses of chlorantraniliprole.

Degradation pattern and risk assessment of carbendazim and mancozeb in mango fruits

A supervised field trial was conducted at four different agroclimatic locations in India to evaluate the dissipation pattern and risk assessment of carbendazim and mancozeb in mango fruits following foliar application of mixed formulation of carbendazim 12% and mancozeb 63% fungicide (SAAF-75WP) at recommended dose (90 + 472.5) and double the recommended dose (180 + 945 g a.i. ha(-1)). Average initial deposition of carbendazim was in the range of 1.12 to 2.7 and 1.95 to 4.09 mg kg(-1) and for mancozeb in the range of 2.25 to 2.71 and 4.17 to 5.96 mg kg(-1), given at respective doses. Residues of carbendazim and mancozeb were dissipated to the below detectable limit 7 days after spray at recommended dosage in all the locations. The fungicide degradation followed a first order kinetics with half-lives of 1-5 and 1-3 days, for carbendazim and mancozeb, respectively. The TMRC values, calculated from residue data generated from all four locations, were found to be below the MPI in mango fruit, and hence, the fungicide will not cause any adverse effect after consumption of mango fruits. This data could provide guidance for the proper and safe use of this fungicide mixture for managing disease incidence in mango in India.

Persistence behaviour of deltamethrin on tea and its transfer from processed tea to infusion

The dynamics and residues of deltamethrin in a tea grown in an open field ecosystem were investigated. The quantification was performed using gas chromatography-electron capture detection (GC-ECD) and confirmed by gas chromatograph-mass spectrometry (GC-MS) in selective ion monitoring (SIM) mode. The method was validated using blank samples spiked at three levels and the results showed that recoveries ranged from 87% to 101% with relative standard deviations (RSD) ranging of 0.7-7.1%. The residues of deltamethrin were found to dissipate following first order kinetics with half-life ranging between 3.04 and 3.54d for two different rates of foliar application. The deltamethrin residues are present in the processed tea are not transferred into the tea infusion during the infusion process, since their water solubility is extremely low. These results can be utilized in formulating the spray schedule and safety evaluation on deltamethrin tea crop.

Persistence and dissipation of flubendiamide and its risk assessment on gherkin (Cucumis sativus L.)

A supervised open field trial was conducted to evaluate the dissipation pattern and risk assessment of flubendiamide in gherkin fruits following foliar application of Fame 480 SC at 60 and 120 g a.i. ha(-1). Samples of gherkin fruits were drawn at different time intervals and quantified by HPLC-DAD. The maximum initial deposits of flubendiamide on gherkin were found to be 0.79 and 1.52 mg kg(-1), respectively, at recommended and double the recommended doses. The dissipation pattern of flubendiamide followed a first-order kinetics with half-lives of 1.87 to 2.16 days at 60 and 120 g a.i. ha(-1), respectively. The limit of quantification of flubendiamide and desiodo flubendiamide was observed to be 0.01 mg kg(-1) for gherkin fruit and soil substrates. Theoretical maximum residue contribution (TMRC) for flubendiamide was calculated and found to be well below the maximum permissible intake (MPI) on gherkin fruits. Thus, the application of flubendiamide at the recommended dose on gherkin fruits presents no human health risks and safe to consumers.

Dynamics and residues of mixed formulation of fenamidone and mancozeb in gherkin field ecosystem

The dynamics and residues of mixed formulation of fenamidone and mancozeb in a gherkin field ecosystem were investigated. The quantification was performed using gas chromatography-electron capture detection (GC-ECD) and UV-vis spectrophotometry for fenamidone and mancozeb residues, respectively. The method was validated using blank samples spiked at three levels and the results showed that recoveries ranged from 92 to 98 and 90 to 96 percent with relative standard deviations (RSD) ranging of 0.78-5.9 and 2.04-4.41 percent for fenamidone and mancozeb, respectively. The compound degradation followed a first order kinetics with half-lives of 2.8-2.82 and 2.02-2.26 days, for fenamidone and mancozeb, respectively. Pesticide residues in fruit were below the EU maximum residue level (MRL) after 10 days for fenamidone (0.02 µg/g) and just after treatment for mancozeb (2 µg/g). These results can be utilized in formulating the spray schedule and safety evaluation for these pesticides in gherkin.

Dissipation of flubendiamide residues in/on cabbage (Brassica oleracea L.)

Residues of fubendiamide and its metabolite desiodo flubendiamide were estimated in cabbage and soil using high-performance liquid chromatography with UV-vis detector. The initial deposits of flubendiamide residues on cabbage were found to be 0.16 and 0.31 μg g(-1) following two applications of flubendiamide 20 WG at 12.5 (standard dose) and 25 (double dose) g a.i. ha(-1) respectively at 10-days interval. The half-life values (t(1/2)) of flubendiamide on cabbage ranged from 3.4 to 3.6 days. When flubendiamide applied at both the standard and double dose, no detectable residues were found in cabbage and soil at harvest. Thus, a waiting period of 1.63 days was suggested for the safe consumption of flubendiamide-treated cabbage. These data could provide guidance for the proper and safe use of this pesticide on cabbage crops in India.

Multiresidue analysis of organochlorine pesticides in milk, egg and meat by GC-ECD and confirmation by GC-MS

A multiresidue method was developed and optimized for the quantification of organochlorine pesticides (OCPs) in milk, egg and meat samples. Sample extraction was performed by adopting QuEChERS principle and the extracts were cleaned-up dispersive solid-phase extraction with primary secondary amine after salting out with NaCl and MgSO(4). Analysis was carried out by gas chromatography coupled with electron capture detector and confirmation by gas chromatography-mass spectrometry. The performance of the method was investigated in terms of linearity, accuracy, precision, detection limit and quantification limit (LOQ). Good linearity was obtained, with correlation coefficients (r(2)) higher than 0.992. Mean recoveries were found in the ranges 72%-108%, 74%-101% and 75.27%-104.56% for the milk, egg and meat, respectively, RSD % turned out to range from 0.28% to 10.05%. The method developed was successfully tested on commercial milk, egg, and meat samples from the markets of Tamil Nadu (India), proving to be a useful tool in routine analysis of OCPs for monitoring purposes. None of the compounds of interest were observed above their respective LOQ.

Persistence behaviour of thiacloprid residues in/on green tea leaves, processed tea and tea infusion

Thiacloprid residues were estimated in green tea leaves, processed tea and tea infusion by HPLC-Diode Array detection. The average initial deposits of thiacloprid (Alanto 240 SC) on the green tea leaves were found to be 3.72 and 6.77 μg g(-1) at single and double doses, respectively. The results showed that thiacloprid dissipated faster in green tea leaves following a first order reaction kinetics at both application rates. The amount of dissipation in 14 days was 93.37% and 91.62% for single and double doses respectively. Half life (T(1/2)) for degradation of thiacloprid in green tea leaves were observed to be 3.34 and 3.58 days at single and double doses respectively. Thiacloprid residues in processed tea ranged from 0.16 to 0.63 μg g(-1) on seventh day and no residues could be detected on 14th day at single dose. Infusion study indicated that thiacloprid did not infuse into tea liquor from processed tea. The limit of determination was found to be 0.05 μg g(-1).

Assessment of flubendiamide residues in pigeon pea in different agro-climatic zones of India

Supervised field trials were conducted at the research farms of four agricultural universities located at different agro-climatic zones of India to find out the harvest time residues of flubendiamide and its des-iodo metabolite on pigeon pea (Cajanus cajan) during the year 2006-2007. Two spray applications of flubendiamide 20 WDG at 50 g (T(1)) and 100 g (T(2)) a.i./ha were given to the crop at 15-days interval. The foliage samples at different time intervals were drawn at only one location, however, the harvest time samples of pigeon pea grain, shell, and straw were drawn at all the four locations. The residues were estimated by HPLC coupled with UV-VIS variable detector. No residues of flubendiamide and its des-iodo metabolite were found at harvest of the crop at or above the LOQ level of 0.05 μg/g. On the basis of the data generated, a pre-harvest interval (PHI) of 28 days has been recommended and the flubendiamide 20 WDG has been registered for use on pigeon pea by Central Insecticide Board and Registration Committee, Ministry of Agriculture, Government of India and the MRL has been fixed by Ministry of Health and Family Welfare, Government of India under Prevention of Food and Adulteration as 0.05 μg/g on pigeon pea grains.

Degradation dynamics of flubendiamide in different types of soils

Residual dynamics of flubendiamide in three different types of soils were investigated under laboratory condition. Flubendiamide was applied at 5 and 10 μg g(-1) for each soil and samples drawn periodically were analyzed on HPLC. The results showed that the degradation of flubendiamide in soils were followed first-order kinetics and its average half-lives in three kinds of soils were ranged from 37.62 to 60.21 days. The persistence of flubendiamide in soils significantly increased in the order of coastal soil > red and lateritic soil > new alluvial.

Persistence and dissipation of the insecticide flubendiamide and its metabolite desiodo flubendiamide residues in tomato fruit and soil

A method for residue analysis of flubendiamide and its metabolite desiodo flubendiamide was developed using high performance liquid chromatography. This method was then used to evaluate the residual level and dissipation rate of flubendiamide and desiodo flubendiamide in the tomato fruit. The half-life of flubendiamide in tomato fruit was 1.64 and 1.98 days in recommended and double of the recommended dose, respectively. Tomato fruit and soil samples analyzed on the 10th day after the last spray revealed that flubendiamide and its metabolite desiodo flubendiamide residues at below determination level (0.01 μg g(-1)) at either dose of application.

Simultaneous determination of flubendiamide its metabolite desiodo flubendiamide residues in cabbage, tomato and pigeon pea by HPLC

A sensitive and simple method for simultaneous analysis of flubendiamide and its metabolite desiodo flubendiamide in cabbage, tomato and pigeon pea has been developed. The residues were extracted with QuEChERS method followed by dispersive solid-phase extraction with primary secondary amine sorbent to remove co extractives, prior to analysis by HPLC coupled with UV-Vis detector. The recoveries of flubendiamide and desiodo flubendiamide were ranged from 85.1 to 98.5% and 85.9 to 97.1% respectively with relative standard deviations (RSD) less than 5% and sensitivity of 0.01 μg g(-1). The method offers a less expensive and safer alternative to the existing residue analysis methods for vegetables.

Persistence and safety risk assessment of propineb in Indian tea

A supervised field trial was conducted on tea with propineb at 1,750 and 3,500 g a.i./ha at two locations (Assam and Darjeeling), applied thrice at an interval of 10 days during the year 2006-2007. Propineb residue was measured spectrophotometrically at 435 nm in terms of CS2. The initial deposit of propineb in green tea leaves were found to be in the range of 16.26-35.96 mg/kg and the residue persisted up to 10 days irrespective of doses and locations with half-life value ranging from 2.24 to 2.43 days and preharvest interval of 17.17-21.37 days. Made tea residues ranged from 9.27 to 20.86 mg kg(-1) on 7 days and no residues could be detected on 14 days. Infusion study indicated that propineb did not infuse into tea liquor from made tea. The limit of determination was found to be 0.1 mg kg(-1) in terms of propineb for green tea leaves, made tea, and tea liquor. The tea applied with the recommended dose of propineb is safe for consumption as liquor.

Assessment and occurrence of various heavy metals in surface water of Ganga river around Kolkata: a study for toxicity and ecological impact

A study was conducted during November, 2005-October, 2006 to evaluate the surface water quality of river Ganga around Kolkata. The samples were analyzed for a number of physico-chemical parameters using standard laboratory procedures and giving prime thrust to determine the heavy metal concentrations (Fe, Mn, Cu, Zn, Pb, Cd, Cr, and Ni) of surface water at four different locations of the river Ganga around Kolkata from two points (middle of the river stream and a discharge point) at each location. Out of 96 samples analyzed, Fe, Mn, Cu, Zn, and Ni were detected in 71, 47, 38, 60, and 45 samples in the concentrations ranging from 0.013 to 5.49, 0.022 to 1.78, 0.003 to 0.033, 0.005 to 0.293, and 0.045 to 0.24 mg L(-1), respectively. Cd and Pb were detected in six and 21 samples in the range of 0.005 to 0.006 and 0.05 to 0.53 mg L(-1), respectively. But Cr was not detected in any of the samples analyzed. The metals exhibited no significant variation with respect to sampling locations as well as discharge points. However, the concentration of those metals varied with season, being higher in rainy and lower in winter season.

Impact assessment of pesticide residues in fish of Ganga river around Kolkata in West Bengal

An investigation was conducted from 2001 to 2005 for determining the residual concentration of five pesticides, viz., total-HCH, total-DDT, total-Endosulfan, Dimethoate and Malathion in fish samples collected from various points of the river Ganga. Fish samples were analyzed for pesticide residues using standard laboratory procedures by GC method. It was found that total-HCH concentration remains above the MRL values for maximum number of times in comparison to four other pesticides. The pesticide contamination to fish may be due to indiscriminate discharge of polluted and untreated sewage-sludge to the river. The pesticide contents in some places are alarming. Thus proper care, maintenance, treatment and disposal of sewage water and sludge are most vital and should be the prime thrust for the nation.

DYX1C1 functions in neuronal migration in developing neocortex

Rodent homologues of two candidate dyslexia susceptibility genes, Kiaa0319 and Dcdc2, have been shown to play roles in neuronal migration in developing cerebral neocortex. This functional role is consistent with the hypothesis that dyslexia susceptibility is increased by interference with normal neural development. In this study we report that in utero RNA interference against the rat homolog of another candidate dyslexia susceptibility gene, DYX1C1, disrupts neuronal migration in developing neocortex. The disruption of migration can be rescued by concurrent overexpression of DYX1C1, indicating that the impairment is not due to off-target effects. Transfection of C- and N-terminal truncations of DYX1C1 shows that the C-terminal TPR domains determine DYX1C1 intracellular localization to cytoplasm and nucleus. RNAi rescue experiments using truncated versions of DYX1C1 further indicate that the C-terminus of DYX1C1 is necessary and sufficient to DYX1C1's function in migration. In conclusion, DYX1C1, similar to two other candidate dyslexia susceptibility genes, functions in neuronal migration in rat neocortex.

Structure of the zinc-induced heterodimer of two calcium-free isoforms of phospholipase A2fromNaja naja sagittiferaat 2.7 Å resolution

The crystal structure of a zinc-induced heterodimer of two metal-free isoforms of a cobra venom phospholipase A(2) has been determined at 2.7 angstroms resolution. The crystals belong to space group P4(1), with unit-cell parameters a = b = 65.5, c = 58.4 angstroms, and have a single dimer in the asymmetric unit. The structure has been refined to R(cryst) and R(free) factors of 0.188 and 0.232, respectively. The two isoforms have a sequence identity of 82%. The zinc ion forms a fivefold coordination with a trigonal bipyramidal geometry involving one O atom each from Asp24 and Asn112 from molecule A and Asp24 from molecule B and two water molecules. Both molecules of the dimer are inactive. Molecule A is inactive because Arg31 (B) binds to Asp49 (A), while an acetate ion has displaced the essential water molecule and interacts with His48 (A). On the other hand, Arg31 (A) interacts with the calcium-binding loop of molecule B, resulting in an altered conformation of the loop. The absence of a calcium ion, loss of the essential water molecule and the altered conformation of the calcium-binding loop may be the reasons for the loss of activity of molecule B.

Biotinyl endothelin-1 binding to endothelin receptor and its applications

The endothelin (ET) system consists of two membrane receptor types A and B and three 21-mer isopeptides endothelin-1, endothelin-2, and endothelin-3 as ligands. This system is involved in many physiological processes such as vasomodulation, neurotransmission, embryonic development, renal function, and regulation of cell proliferation. In many pathophysiological conditions involving endothelin system, the endothelin antagonism could be a possible clinical treatment. Designing of an antagonist involves the characterization of the binding of the test compounds to the endothelin receptors. This is being carried out using radioactive ligand. A simpler and quicker method will be of great advantage. This study reports a non-radioactive method for establishing the IC50 concentrations of the ligand. This method uses biotinylated-endothelin-1 and streptavidin conjugated with horseradish peroxidase. Hydroxyl apatite gel is used for separating the bound and unbound biotin-tagged endothelin-1. This method is applicable to detergent solubilized receptors and purified recombinant receptors. The endothelin receptor type A expressed in Pichia pastoris system has been used in this study. We show that this method is applicable in Western blot analysis of endothelin-1 and its receptor complex. This can be used to localize the receptor molecules as well.

Crystal Structure of Echicetin from Echis carinatus (Indian Saw-scaled Viper) at 2.4Å Resolution

Echicetin is a heterodimeric protein from the venom of the Indian saw-scaled viper, Echis carinatus. It binds to platelet glycoprotein Ib (GPIb) and thus inhibits platelet aggregation. It has two subunits, alpha and beta, consisting of 131 and 123 amino acid residues, respectively. The two chains are linked with a disulphide bond. The level of amino acid sequence homology between two subunits is 50%. The protein was purified from the venom of E.carinatus and crystallized using ammonium sulphate as a precipitant. The crystal structure has been determined at 2.4A resolution and refined to an R-factor of 0.187. Overall dimensions of the heterodimer are approximately 80Ax35Ax35A. The backbone folds of the two subunits are similar. The central portions of the polypeptide chains of alpha and beta-subunits move into each other to form a tight dimeric association. The remaining portions of the chains of both subunits fold in a manner similar to those observed in the carbohydrate-binding domains of C-type lectins. In echicetin, the Ca(2+)-binding sites are not present, despite being topologically equivalent to other similar Ca(2+)-binding proteins of the superfamily. The residues Ser41, Glu43 and Glu47 in the calcium-binding proteins of the related family are conserved but the residues Glu126/120 are replaced by lysine at the corresponding sites in the alpha and beta-subunits.

Structure of an acidic phospholipase A2 from Indian saw-scaled viper (Echis carinatus) at 2.6 A resolution reveals a novel intermolecular interaction

The crystal structure of an acidic phospholipase A(2) from the venom of Echis carinatus (saw-scaled viper; scPLA(2)) has been determined at 2.6 A resolution and refined to a crystallographic R factor of 0.192. Although the overall structure of scPLA(2) is essentially similar to those of other group II acidic PLA(2)s from different species, it shows unique features in several parts. Particularly noteworthy is the C-terminal part, which folds differently to those of other group II PLA(2)s. This part is considered to be responsible for inhibition of the platelet-aggregation activity. The calcium-binding loop is tightly organized with sevenfold coordination. Another striking feature of scPLA(2) is the involvement of Asn79 O(delta1) of a symmetry-related molecule in a coordination linkage with Ca(2+) of the calcium-binding loop. This is the first observation of an internal metal ion participating in an intermolecular interaction. The beta-wing of a molecule is deeply inserted into the hydrophobic channel of another molecule and forms several intermolecular interactions. This results in the formation of an infinite chain of molecules. These chains are stacked in an antiparallel arrangement in the crystals.

Crystal structure of human seminal diferric lactoferrin at 3.4 Angstrom resolution

Lactoferrin was purified from human seminal fluid obtained from the semen bank. The purified samples were saturated with Fe3+ and crystallized by microdialysis method. The crystals belong to orthorhombic space group P21212, with a = 55.9 Angstrom. b = 97.2 Angstrom, c = 156.1 Angstrom and Z = 4. The structure was determined with molecular replacement method and refined to an R factor of 18.7% for all the data to 3.4 Angstrom resolution. The overall structure of seminal lactoferrin is similar to human colostrum lactoferrin. The amino acid sequence of seminal lactoferrin shows that it has one amino acid less than human colostrum lactoferrin and the structure of its N-terminal region is far more ordered than other lactoferrins. The structure of the iron-binding site and its immediate surroundings indicate well defined features.

Expression, purification, and characterization of equine lactoferrin in Pichia pastoris

Lactoferrin is an 80kDa iron-binding glycoprotein. It is secreted by exocrine glands. Many functions such as iron sequestering, anti-bacterial activity, regulation of gene expression, and immunomodulation are attributed to it. In the present study, we report the production of recombinant equine lactoferrin (ELF) in the methylotropic yeast Pichia pastoris using pPIC9K vector. The recombinant protein was purified by one-step affinity chromatography using heparin-Sepharose column. The purified protein has a molecular weight of 80kDa and reacted with antibody raised against the native equine lactoferrin. Its N-terminal sequence was identical to that of the native ELF. The iron-binding behavior and circular dichroism studies of the purified protein indicate that it has folded properly. The recombinant protein appears to be hyperglycosylated by the host strain, GS115. This is the first heterologous expression of equine lactoferrin and also the first report of intact lactoferrin expression using P. pastoris system. An yield of 40mg/l obtained in shake-flask cultures with this system, which is higher than the reported values for other systems.

Camel lactoferrin, a transferrin-cum-lactoferrin: crystal structure of camel apolactoferrin at 2.6 A resolution and structural basis of its dual role

Camel lactoferrin is the first protein from the transferrin superfamily that has been found to display the characteristic functions of iron binding and release of lactoferrin as well as transferrin simultaneously. It was remarkable to observe a wide pH demarcation in the release of iron from two lobes. It loses 50 % iron at pH 6.5 and the remaining 50 % iron is released only at pH values between 4.0 and 2.0. Furthermore, proteolytically generated N and C-lobes of camel lactoferrin showed that the C-lobe lost iron at pH 6.5, while the N-lobe lost it only at pH less than 4.0. In order to establish the structural basis of this striking observation, the purified camel apolactoferrin was crystallized. The crystals belong to monoclinic space group C2 with unit cell dimensions a=175.8 A, b=80.9 A, c=56.4 A, beta=92.4 degrees and Z=4. The structure has been determined by the molecular replacement method and refined to an R-factor of 0.198 (R-free=0.268) using all the data in the resolution range of 20.0-2.6 A. The overall structure of camel apolactoferrin folds into two lobes which contain four distinct domains. Both lobes adopt open conformations indicating wide distances between the iron binding residues in the native iron-free form of lactoferrin. The dispositions of various residues of the iron binding pocket of the N-lobe of camel apolactoferrin are similar to those of the N-lobe in human apolactoferrin, while the corresponding residues in the C-lobe show a striking similarity with those in the C-lobes of duck and hen apo-ovotransferrins. These observations indicate that the N-lobe of camel apolactoferrin is structurally very similar to the N-lobe of human apolactoferrin and the structure of the C-lobe of camel apolactoferrin matches closely with those of the hen and duck apo-ovotransferrins. These observations suggest that the iron binding and releasing behaviour of the N-lobe of camel lactoferrin is similar to that of the N-lobe of human lactoferrin, whereas that of the C-lobe resembles those of the C-lobes of duck and hen apo-ovotransferrins. Hence, it correlates with the observation of the N-lobe of camel lactoferrin losing iron at a low pH (4.0-2.0) as in other lactoferrins. On the other hand, the C-lobe of camel lactoferrin loses iron at higher pH (7.0-6.0) like transferrins suggesting its functional similarity to that of transferrins. Thus, camel lactoferrin can be termed as half lactoferrin and half transferrin.

Three-dimensional structure of a new form of mare lactoferrin in 70% PEG 400 at 3.8 A resolution

Three-dimensional (3D) structure of a new form of diferric mare lactoferrin has been determined at 3.8 A resolution. The protein was crystallized in a space group P2(1)2(1)2(1) with a = 80.1 A, b = 103.7 A, c = 112.2 A with a solvent content of 57%. The structure was solved by molecular replacement method using the model of native mare lactoferrin. The structure has been refined using X-PLOR to a final R-factor of 22.6% for all the data in 15.0-3.8 A resolution range. The final refined model comprises 5281 protein atoms, 2Fe3+ and 2CO3(2-) ions. The protein folds into two globular N- and C-lobes. The two lobes are further divided into two domains N1, N2 in the N-lobe and C1, C2 in the C-lobe. The overall folding of the protein is similar to that observed for the native protein. The superposition of Calpha traces of native mare lactoferrin and the present structure gives an r.m.s shift of 0.7 A. There is a slight variation in the orientation of two lobes but the domain orientations in the present structure are identical to those observed in the native mare lactoferrin.

Sequence and crystal structure determination of a basic phospholipase A2 from common krait (Bungarus caeruleus) at 2.4 A resolution: identification and characterization of its pharmacological sites

This is the first phospholipase A2 (PLA2) structure from the family of kraits. The protein was isolated from Bungarus caeruleus (common krait) and the primary sequence was determined using cDNA approach. Three-dimensional structure of this presynaptic neurotoxic PLA2 from group I has been determined by molecular replacement method using the model of PLA2 component of beta2-bungarotoxin (Bungarus multicinctus) and refined using CNS package to a final R-factor of 20.1 % for all the data in resolution range 20.0-2.4 A. The final refined model comprises 897 protein atoms and 77 water molecules. The overall framework of krait phospholipase A2 with three long helices and two short antiparallel beta-strands is extremely similar to those observed for other group I PLA2s. However, the critical parts of PLA2 folding are concerned with its various functional loops. The conformations of these loops determine the efficiency of enzyme action and presence/absence of various pharmacological functions. In the present structure calcium-binding loop is occupied by a sodium ion with a 7-fold co-ordination. The conformation of loop 55-75 in krait PLA2 corresponds to a very high activity of the enzyme. A comparison of its sequence with multimeric PLA2s clearly shows the absence of critical residues such as Tyr3, Trp61 and Phe64, which are involved in the multimerization of PLA2 molecules. The protein shows anticoagulant and neurotoxic activities.

Structure of buffalo lactoferrin at 3.3 A resolution at 277 K

The three-dimensional structure of diferric buffalo lactoferrin has been determined at 3.3 A resolution. The structure was solved by molecular replacement using the coordinates of diferric human lactoferrin as a search model and was refined by simulated annealing (X-PLOR). The final model comprises 5316 protein atoms for all 689 residues, two Fe(3+) and two CO(3)(2-) ions. The final R factor was 21.8% for 11 711 reflections in the resolution range 17.0-3.3 A. The folding of buffalo lactoferrin is essentially similar to that of the other members of the transferrin family. The significant differences are found in the dimensions of the binding cleft and the interlobe orientation. The interlobe interactions are predominantly hydrophobic in nature, thus facilitating the sliding of two lobes owing to external forces. The interdomain interactions are comparable in the N and C lobes.

Structure of buffalo lactoferrin at 2.5 A resolution using crystals grown at 303 K shows different orientations of the N and C lobes

The structure of buffalo lactoferrin has been determined at 303 K. The crystals belong to orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 77.5, b = 91.0, c = 131.5 A and Z = 4. The structure has been refined to an R factor of 0.187. The overall structure of the protein is similar to its structure determined at 277 K in a different crystal form. However, the lobe orientations in the two structures differ by 9.0 degrees, suggesting significant inter-lobe flexibility in this family of proteins. The inter-lobe interactions are predominantly hydrophobic and could act as a cushion for a change in orientation under the influence of external conditions. On the other hand, the domain arrangements are found to be similar in 277 and 303 K crystal structures, with orientations differing by 1.5 and 1.0 degrees in the N and C lobes, respectively. The results of these investigations suggest that the increase in temperature helps in the production of better quality crystals.

Three-dimensional structure of mare diferric lactoferrin at 2.6 A resolution

Lactoferrin is a monomeric glycoprotein with a molecular mass of approximately 80 kDa. The three-dimensional structure of mare diferric lactoferrin (mlf) has been determined at 2.6 A resolution. The protein crystallizes in the space group P 212121with a=85.2 A, b=99.5 A, c=103.1 A with a solvent content of 55 % (v/v). The structure was solved by the molecular replacement method using human diferric lactoferrin as the model. The structure has been refined using XPLOR to a final R -factor of 0.194 for all data in the 15-2.6 A resolution range. The amino acid sequence of mlf was determined using a cDNA method. The final refined model comprises 5281 protein atoms, 2 Fe3+, 2 CO32-and 112 water molecules. The overall folding of mlf is similar to that of other proteins of the transferrin family. The protein folds into two globular lobes, N and C. The lobes are further divided into two domains, N1 and N2, and C1 and C2. The iron-binding cleft is situated between the domains in each lobe. The N lobe appears to be well ordered and is more stable than the C lobe in mlf unlike in other lactoferrins, where the C lobe is the more stable. The opening of the binding cleft in the N lobe of mlf is narrower than those in other proteins of the transferrin family. This is very unusual and is found only in mare lactoferrin. Apart from certain hydrophobic interactions at the mouth of the cleft, one salt-bridge (Lys301 . . . . . . . . Glu216) crosses between the two walls of the cleft. The two lobes are connected covalently by a three-turn alpha-helix involving residues 334-344. The N lobe displays a highly ordered structure with appreciably low temperature factors. The iron coordination is more symmetrical in the N lobe than in the C lobe. There are only 16 intermolecular hydrogen bonds in the structure of mlf.