Multi-way modeling of hydro-chemical data of an alluvial river system--a case study

A large data set pertaining to water quality of an alluvial river was analyzed using multi-way data analysis methods with a view to extract the hidden information, spatial and temporal variation trends in the river water quality. Four-way data (8 monitoring sites x 22 water quality variables x 10 monitoring years x 12 sampling months) analysis was performed using PARAFAC and Tucker3 models. A two component PARAFAC model, although explained 35.1% of the data variance, could not fit to the data set. Tucker3 model of optimum complexity (2,3,1,3) explaining 39.7% of the data variance, allowed interpretation of the data information in four modes. The model explained spatial and temporal variation trends in terms of water quality variables during the study period and revealed that sampling sites in mid-stretch of the river were dominated mainly by the variables of anthropogenic origin. The results delineated the mid stretch of the river as critical from pollution point of view and also identified summer months as having high influence on river water quality in this stretch. The information regarding spatial and temporal variations in water quality generated by the four-way modeling of data would be useful in developing long-term water resources management strategies in the river basin.

Distribution of metals in the edible plants grown at Jajmau, Kanpur (India) receiving treated tannery wastewater: relation with physico-chemical properties of the soil

The implications of metal contamination of agricultural soils due to long term irrigation with treated industrial wastewater and their subsequent accumulation in the vegetables/crops growing on such soils has been assessed in an area of industrial complex, Jajmau, Kanpur (India). Physico-chemical properties of the soil were also studied. The soil and vegetables/crops were sampled from an area of 2100 acre agricultural land and analyzed for physico-chemical properties and metal accumulation in different parts of the plants. The comparison of the data of physico-chemical properties of control and contaminated soil showed that salinity, electrical conductivity, available phosphorous, sodium and potassium content (both water soluble and exchangeable) were found high in contaminated soil. The analysis of plant available metal content in the soil showed the highest level of Fe, which ranged from 529.02 to 2615 microg g(-1) dw and lowest level of Ni (3.12 to 10.51 microg g(-1) dw). The analysis of the results revealed that accumulation of toxic metal Cr in leafy vegetables was found more than fruit bearing vegetables/crops. Thus, it is recommended that the leafy vegetables are unsuitable to grow in such contaminated sites. It is important to note that toxic metal, Ni was not detected in all the plants. The edible part of the vegetables (under ground) such as, garlic (19.27 microg g(-1) dw), potato (11.81 microg g(-1) dw) and turmeric (20.86 microg g(-1) dw) has accumulated lowest level of toxic metal, Cr than leafy and fruit bearing vegetables. In some fruit part of vegetables such as, bitter gourd, egg plant, jack tree, maize and okra, the accumulation of Cr was not detected and may be grown in this area.

Variability in Indian isolates of Arthrobotrys dactyloides Drechsler: a nematode-trapping fungus

Five isolates of Arthrobotrys dactyloides (A, B, C, D, and E) were isolated from different locations of India. Their variability in relation to morphology, radial growth, and nematode capturing or trap-forming ability was observed. All of the five isolates produced two-celled slender conidia, whereas wider two- and three-celled conidia were produced by isolates A, C, D, and E only. The wider two- and three-celled conidia were not observed in cultures of isolate B. The isolate B produced macroconidia as well as microconidia. The microconidia were produced on separate conidiophores of smaller size. Macroconidia and microconidia were never produced on the same conidiophore, but the two types of conidiophores were produced on same or different hyphae. Similar to macroconidia, the microconidia also produced constricting rings of smaller size in presence of Meloidogyne graminicola. The constricting rings formed on microconidia did not capture second-stage juveniles of M. graminicola because of their smaller size. Among all the isolates, isolate B showed slow growth and higher nematode-capturing ability or trap-forming ability.

Diversity of flowering and fruiting phenology of trees in a tropical deciduous forest in India

BACKGROUND AND AIMS

In the dry tropics, vegetative phenology varies widely with tree characteristics and soil conditions. The present work aims to document the phenological diversity of flowering and fruiting with reference to leafing events in Indian dry-tropical tree species.

METHODS

Nine tree species, including one leaf-exchanging and eight deciduous showing varying leafless periods, were studied. Monthly counts of leaves, flowers and fruits were made on 160 tagged twigs on ten individuals of each species for initiation, completion and duration of different phenological events through two annual cycles.

KEY RESULTS

Variation in flowering relative to leaf flushing (which occurred just prior to or during a hot, dry summer) revealed five flowering types: summer flowering (on foliated shoots), rainy-season flowering (on foliated shoots following significant rains), autumn flowering (on shoots with mature leaves), winter flowering (on shoots undergoing leaf fall) and dry-season flowering (on leafless shoots). Duration of the fruiting phenophase was shortest (3-4 months) in dry-season and winter-flowering species, 6-9 months in rainy-and autumn-flowering species, and maximum (11 months) in summer-flowering species. A wide range of time lag (<1 to >8 months) between the start of vegetative (first-leaf flush) and reproductive (first-visible flower) phases was recorded in deciduous species; this time lag was correlated with the extent of the leafless period. A synthesis of available phenological information on 119 Indian tropical trees showed that summer-flowering species were most abundant (56 % of total species) amongst the five types recognized.

CONCLUSIONS

The wide diversity of seasonal flowering and fruiting with linkages to leaf flush time and leafless period reflect the fact that variable reproductive and survival strategies evolved in tree species under a monsoonic bioclimate. Flowering periodicity has evolved as an adaptation to an annual leafless period and the time required for the fruit to develop. The direct relationship between leafless period (inverse of growing period) and time lag between onset of vegetative and reproductive phases reflects the partitioning of resource use for supporting these phases. Predominance of summer flowering coupled with summer leaf flushing seems to be a unique adaptation in trees to survive under a strongly seasonal tropical climate.

Evaluation of groundwater quality in northern Indo-Gangetic alluvium region

The northern Indo-Gangetic alluvium region is known for intensive agricultural and industrial activities. Groundwater is the main source used for drinking, irrigation and industrial purposes in this region. Groundwater quality assessment is an essential component for its safer use. Thus, the measurements on various water quality parameters were carried out on surface water and groundwater samples of dug wells, bore wells and hand pumps at different sites spread over an area of about 2150 km(2). Influence of soil on hydrochemistry of groundwater was investigated through analyzing soil characteristics at selected sites in the region. Water quality classification was investigated through calculating the base-exchange, meteoric genesis, Langelier saturation and Ryznar stability indices. Groundwater sources were evaluated according to various criteria for their drinking and domestic, irrigation (salinity, chlorinity and sodicity), and industrial (saturation index) uses. Soil-water interactions and impact on groundwater quality was evaluated using ion flux coefficient (cf). Results of this study show that the groundwater in the study region is mainly of Na-HCO(3) and shallow meteoric water percolation type. Low cf values observed for NO(3), PO(4), Ca and metals indicate their lower mobility from soil matrix to groundwater. About 4-19% of the groundwater samples showed levels of TDS, hardness, alkalinity, Cl, F, SO(4), Ca, Mn, Pb, Cr and Fe above their respective permissible limits. Majority of samples violating the drinking water guidelines belong to shallow depth aquifer. Correlations between various parameters lead to interpretation of the results of analysis and suggesting the ionic species present in the groundwater sources. Contamination of some groundwater aquifers with F, Pb and Cr indicates natural and anthropogenic influences.

Screening of Different Media and Substrates for Cultural Variability and Mass Culture of Arthrobotrys dactyloides Drechsler

Variability in growth and sporulation of five isolates of Arthrobotrys dactyloides was studied on five agar, 6 bran and 5 grain media. Potato dextrose agar (PDA) supported maximum growth of isolate A, C and E, while growth of isolate B and D was significantly lower on this medium. On Czapek's agar and yeast glucose agar media the differentiation in the isolates in relation to growth was poor than PDA. The other two media showed much poorer differentiation. On Czapek's agar medium, sporulation was recorded in isolate B only, whereas other isolates showed rare sporulation. Among the bran media, pea bran agar medium supported maximum growth of all the isolates except isolate B. Gram and rice bran agar media were next best. However, the growth of isolate B on the gram bran agar medium was more or less equal as other isolates. On pigeon pea bran agar medium, isolate E failed to grow while other isolates recorded poor growth. On lentil bran agar medium, only isolate B and D recorded little growth, whereas other isolates failed to grow. All the isolates recorded good sporulation on bran agar media except pigeon pea and lentil bran agar media. The grain agar media supported moderate to very good growth of all the isolates. In general isolate B remained slow growing on these media except gram grain and sorghum grain agar media on which growth of this isolate was comparable to other isolates. Sporulation in general, was good on all the grain agar media. Among different substrates screened, barley grain and pea bran were found superior to others for mass culture of isolate A of A. dactyloides.

Effect of Fertilizers and Neem Cake Amendment in Soil on Spore Germination of Arthrobotrys dactyloides

Application of fertilizers such as urea, diammonium phosphate (DAP) and muriate of potash in soil adversely affected the spore germination of Arthrobotrys dactyloides. Amendment of soil with urea at the concentrations of 1.0%, 0.5% and 0.1% completely inhibited spore germination and direct trap formation on the conidium, whereas muriate of potash delayed and reduced the spore germination even at the lowest concentration. DAP also inhibited spore germination at 1.0% concentration, while at lower concentration the percentage of spore germination was reduced. Application of neem cake at the concentration of 0.5% also inhibited spore germination after 24 h of amendment. The inhibitory effect of neem cake was reduced after 15 days of amendment, while after 30 days after amendment the inhibitory effect was completely lost and the spore germinated by direct trap as in unamended soil. Nematodes were not attracted to ungerminated spores after 24 h of amendment. After 15 days of amendment nematodes were attracted to agar blocks containing fewer germinated spores after 24 h of incubation but after 48 h of incubation large number of nematodes were attracted and trapped by the germinated spores with direct traps. After 30 days of amendment, larger number of nematodes were attracted and trapped by direct traps.

A novel nonsteroidal antifibrotic oligo decoy containing the TGF-beta element found in the COL1A1 gene which regulates murine schistosomiasis liver fibrosis

Schistosomiasis mansoni disseminated worm eggs in mice and humans induce granulomatous inflammations and cumulative fibrosis causing morbidity and possibly mortality. In this study, intrahepatic and I.V. injections of a double-stranded oligodeoxynucleotide decoy containing the TGF-beta regulatory element found in the distal promoter of the COL1A1 gene into worm-infected mice suppressed TGF-beta1, COL1A1, tissue inhibitor of metalloproteinase-1, and decreased COL3A1 mRNAs to a lesser extent. Sequence comparisons within the mouse genome found homologous sequences within the COL3A1, TGF-beta1, and TIMP-1 5' flanking regions. Cold competition gel mobility shift assays using these homologous sequences with 5' and 3' flanking regions found in the natural COL1A1 gene showed competition. Competitive gel mobility assays in a separate experiment showed no competition using a 5-base mutated or scrambled sequence. Explanted liver granulomas from saline-injected mice incorporated 10.45 +/- 1.7% (3)H-proline into newly synthesized collagen, whereas decoy-treated mice showed no collagen synthesis. Compared with the saline control schistosomiasis mice phosphorothioate double-stranded oligodeoxynucleotide treatment decreased total liver collagen content (i.e. hydroxy-4-proline) by 34%. This novel molecular approach has the potential to be employed as a novel antifibrotic treatment modality.

Immune response and protective efficacy in sheep immunised with hydroxylamine-inactivated bluetongue virus vaccine

Vero cell adapted bluetongue virus (BTV), serotype 18 (BTV-18) was inactivated with hydroxylamine and adjuvanted with aluminium hydroxide (Al[OH](3)) gel, saponin, or Al(OH)(3) gel/saponin prior to immunisation of sheep. Group-specific non-neutralising antibodies to BTV were detected in all vaccinated sheep as soon as seven days after vaccination. However, before challenge, serotype-specific neutralising antibodies were not detected in vaccinated sheep. Upon challenge with homologous live BTV, there was a reduction in delayed type of hypersensitivity response in control sheep but not in the vaccinated animals. All vaccinated sheep had significant (P<0.01) reductions in their clinical reaction index (CRI) and duration of viraemia.

Removal of alpha-picoline, beta-picoline, and gamma-picoline from synthetic wastewater using low cost activated carbons derived from coconut shell fibers

In the present study the ability of activated carbons developed from coconut shell fibers to remove alpha-picoline, beta-picoline, and gamma-picoline from aqueous solution in the broad range of concentrations (1-100 mg/L) is investigated. The derived carbons are designated as FAC (activated carbon derived from coconut shell fibers without any treatment) and ATFAC (activated carbon derived from acid treated coconut shell fibers). Systematic equilibrium and kinetic adsorption studies at different pH, temperatures, particle size, and solid-to-liquid ratio were carried out to determine various parameters necessary to establish the fixed bed reactors. The Langmuir and Freundlich models were applied and the data are not fitted well by the Freundlich and Langmuir equations, but the Langmuir model has an edge over Freundlich model. The monolayer adsorption capacity (Q0) as calculated using Langmuir adsorption isotherm of the activated carbons viz., FAC and ATFAC is found to increase with an increase in temperature confirming the endothermic process. The ATFAC has a higher sorption capacity than FAC. Overall the adsorption of alpha-picoline, beta-picoline, and y-picoline on FAC and ATFAC follow the order FACalpha-picoline < ATFACalpha-picoline < FAC gamma-picoline < ATFACbeta-picoline < FACbeta picoline < ATFAC gamma-picoline. The adsorption of alpha-,beta-, and gamma-picoline followed the pseudosecond-order rate kinetics. On the basis of these studies, various parameters such as effective diffusion coefficients, activation energy, and entropy of activation were evaluated to establish the mechanisms. It was concluded that the adsorption occurred through particle diffusion at low temperatures viz., 10 degrees C and 25 degrees C (except alpha-picoline where it was film diffusion), while at 40 degrees C it occurred through film diffusion. Similarly at concentrations of 25 and 50 mg/L the adsorption was particle diffusion controlled (except for alpha-picoline where it was film diffusion), while at > 50 mg/L it was film diffusion controlled.

Morphological Variations in Conidia of Arthrobotrys oligospora on Different Media

Most commonly occurring predacious fungus Arthrobotrys oligospora showed great variation in size and shape of conidia on some media. The formation of larger conidia was recorded on beef extract and nutrient agar media. The length of conidia in Richard's YPSS, Sabouraud's, PDA and corn meal agar media was of medium size while smaller conidia were produced on Czapek's, Jensen's, Martin's medium. Maximum width of conidia was recorded on YPSS medium followed by Sabouraud's medium. The average size of spores on nematode infested corn meal agar medium was slightly increased than those on corn meal agar medium.

Status of heavy metals in water and bed sediments of river Gomti--a tributary of the Ganga River, India

The concentrations of cadmium, chromium, copper, iron, lead, manganese, nickel, and zinc in water and bed sediments of river Gomti have been studied in a fairly long stretch of 500 km from Neemsar to Jaunpur. Grab samples of water (October 2002-March 2003) and bed sediments (December 2002 and March 2003) were collected from 10 different locations following the standard methods. The river water and sediment samples were processed and analyzed for heavy metals viz., Cd, Cr, Cu, Fe, Pb, Mn, Ni, and Zn, and using ICP-AES. The heavy metals found in the river water were in the range: Cd (0.0001-0.0005 mg/L); Cr (0.0015-0.0688 mg/L); Cu (0.0013-0.0.0043 mg/L); Fe (0.0791-0.3190 mg/L); Mn (0.0038-0.0.0973 mg/L); Ni (0.0066-0.011 mg/L); Pb (0.0158-0.0276 mg/L); and Zn (0.0144-0.0298 mg/L) respectively. In the sediments the same were found in the range: Cd (0.70-7.90 /microg/g); Cr (6.105-20.595 microg/g); Cu (3.735-35.68 microg/g); Fe (5051.485-8291.485 micorg/g); Mn (134.915-320.45 microg/g); Ni (13.905-37.370 microg/g); Pb (21.25-92.15 microg/g); and Zn (1 5.72-99.35 microg/g) of dry weight respectively. Some physico-chemical parameters viz., pH, total solids, total dissolved solids, total suspended solids, dissolved oxygen, biological oxygen demand, chemical oxygen demand, hardness etc. were estimated as these have direct or indirect influence on the incidence, transport and speciation of the heavy metals. Based on the geoaccumulation indices, the Gomti river sediments from Neemsar to Jaunpur are considered to be unpolluted with respect to Cr, Cu, Fe, Mn, and Zn. It is unpolluted to moderately polluted with Pb. In case of Cd it varies from moderately polluted to highly polluted. As far as Ni is concerned the sediment is very highly polluted at Barabanki and Jaunpur D/s. No correlation was found between enrichment factor and geoaccumulation index.

Dynamics of collagen, MMP and TIMP gene expression during the granulomatous, fibrotic process induced by Schistosoma mansoni eggs

In schistosomiasis mansoni, granulomatous inflammation and fibrotic resolution are the major pathogenetic factors. The outcome of fibrosis is influenced by the deposition of collagen and degradation mediated by matrix metalloproteinases (MMP). There is a dearth of data on the expression of MMP and the tissue inhibitors of metalloproteinase (TIMP) during the fibrosis associated with schistosomiasis. In this study, the dynamics of collagen, MMP and TIMP gene expression were analysed during murine Schistosoma mansoni infection. Expression within the granulomatous liver tissue of the genes coding for collagen of types I, III and IV was up-regulated at the onset of granuloma development, and the dominant type-I expression peaked at the chronic, fibrotic stage. The amount of deposited hepatic collagen increased with the chronicity of the infection, indicating cumulative fibrosis. Collagenase, gelatinase, stromelysin, matrilysin-specific gene activities were similarly up-regulated, but only MMP-8 (collagenase-2) expression peaked at the height of fibrosis. TIMP-1 gene expression gradually increased during the course of the disease and, along with TIMP-2, peaked at the chronic, fibrotic stage. Granuloma myofibroblasts expressed both MMP and TIMP-1 genes. In ELISA of the splenic cytokines, high levels of fibrogenic interleukin-13 and moderate production of transforming growth factor-beta were found to be concurrent with fibrosis. These data indicate that an imbalance in MMP:TIMP expression and fibrogenic cytokine production are associated with cumulative fibrosis.

Multivariate statistical techniques for the evaluation of spatial and temporal variations in water quality of Gomti River (India)--a case study

This case study reports different multivariate statistical techniques applied for evaluation of temporal/spatial variations and interpretation of a large complex water-quality data set obtained during monitoring of Gomti River in Northern part of India. Water quality of the Gomti River, a major tributary of the Ganga River was monitored at eight different sites selected in relatively low, moderate and high pollution regions, regularly over a period of 5 years (1994-1998) for 24 parameters. The complex data matrix (17,790 observations) was treated with different multivariate techniques such as cluster analysis, factor analysis/principal component analysis (FA/PCA) and discriminant analysis (DA). Cluster analysis (CA) showed good results rendering three different groups of similarity between the sampling sites reflecting the different water-quality parameters of the river system. FA/PCA identified six factors, which are responsible for the data structure explaining 71% of the total variance of the data set and allowed to group the selected parameters according to common features as well as to evaluate the incidence of each group on the overall variation in water quality. However, significant data reduction was not achieved, as it needed 14 parameters to explain 71% of both the temporal and spatial changes in water quality. Discriminant analysis showed the best results for data reduction and pattern recognition during both temporal and spatial analysis. Discriminant analysis showed five parameters (pH, temperature, conductivity, total alkalinity and magnesium) affording more than 88% right assignations in temporal analysis, while nine parameters (pH, temperature, alkalinity, Ca-hardness, DO, BOD, chloride, sulfate and TKN) to afford 91% right assignations in spatial analysis of three different regions in the basin. Thus, DA allowed reduction in dimensionality of the large data set, delineating a few indicator parameters responsible for large variations in water quality. This study presents necessity and usefulness of multivariate statistical techniques for evaluation and interpretation of large complex data sets with a view to get better information about the water quality and design of monitoring network for effective management of water resources.

Phylogenetic analysis of bluetongue virus genome segment 6 (encoding VP5) from different serotypes

Full-length cDNAs were sequenced for genome segment 6 from representative isolates of all 24 bluetongue virus (BTV) serotypes. Segment 6 is 1635 to 1645 nucleotides in length with a single open reading frame in all isolates. The deduced VP5 protein sequence is 526 amino acids long for most BTVs, except BTV-15 (isolate number RSArrrr/15), which is 527 amino acids long, and BTV-12 (isolate number RSArrrr/12) and BTV-22 (isolate number Nig1982/11), which were 529 amino acids long. Sequence comparisons have revealed the level of genetic diversity in segment 6, between different BTV serotypes and between isolates within a single serotype. The resulting sequences can be used to design RT-PCR primers for amplification and identification of segment 6 from new BTV isolates, providing potentially valuable diagnostic and research tools. These data are available on the international databases and accession numbers are listed on the website of the Institute for Animal Health (iah.bbsrc.ac.uk/dsRNA_virus_proteins/ btv_sequences.htm).

Development of reverse transcriptase-polymerase chain reaction-based assays and sequencing for typing European strains of bluetongue virus and differential diagnosis of field and vaccine strains

Bluetongue virus (BTV) is a double-stranded (ds) RNA virus, classified within the genus Orbivirus, family Reoviridae, which causes bluetongue (BT), an infectious, non-contagious disease of ruminants. The virus exists as 24 distinct serotypes, which are currently identified by virus isolation and serum neutralisation assays. The most variable outer capsid protein VP2 (encoded by genome segment 2), is the primary determinant of BTV serotype. Reverse transcriptase-polymerase chain reaction (RT-PCR) assays, based on amplification of segment 2, have been developed for identification of the five European BTV types (BTV-1, BTV-2, BTV-4, BTV-9 and BTV-16). Primer pairs were designed that are specific for each BTV serotype. The resulting RT-PCR assay was both sensitive and specific, providing BTV typing within 24 h. Perfect agreement was recorded between the RT-PCR and virus neutralisation assays. The primers for each serotype could successfully amplify the BTV isolates of that serotype from different regions and showed no cross-amplification of the most closely related BTV serotypes. RT-PCR primers were also developed for the discrimination of field and vaccine strains of BTV serotypes currently circulating in Europe. The primer pairs which could amplify field and vaccine strains of BTV-1, BTV-2, BTV-4 and BTV-9 were validated with several isolates of each serotype from various geographic origins around the world and their type specificity was again tested with the most closely related serotypes. Overall, these RT-PCR assays provide a rapid and reliable method for the identification and differentiation of field and vaccine strains of different BTV types. The primers used in this study are listed on the website of the Institute for Animal Health, Pirbright.

Bluetongue virus replication, molecular and structural biology

The icosahedral bluetongue virus (BTV) particle (~80 nm diameter) is composed of three distinct protein layers. These include the subcore shell (VP3), core-surface layer (VP7) and outer capsid layer (VP2 and VP5). The core also contains ten dsRNA genome segments and three minor proteins (VP1[Pol], VP4[CaP]and VP6[Hel]), which form transcriptase complexes. The atomic structure of the BTV core has been determined by X-ray crystallography, demonstrating how the major core proteins are assembled and interact. The VP3 subcore shell assembles at an early stage of virus morphogenesis and not only determines the internal organisation of the genome and transcriptase complexes, but also forms a scaffold for assembly of the outer protein layers. The BTV polymerase (VP1) and VP3 have many functional constraints and equivalent proteins have been identified throughout the Reoviridae, and even in some other families of dsRNA viruses. Variations in these highly conserved proteins can be used to identify members of different genera (e.g. by comparing the polymerase) and different virus species (serogroups) within the genus Orbivirus (e.g. by comparison of VP3). This has helped to identify three new genera within the Reoviridae and two new Orbivirus species. In contrast, sequences of the BTV outer capsid proteins (involved in interactions with neutralising antibodies) are much more variable (particularly VP2) and comprehensive sequence analyses for the 24 types demonstrate that they can be used to identify BTV serotype. The 21 species (158 serotypes) currently recognised within the genus Orbivirus are listed, along with 11 unassigned viruses.