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1

Three new species of Myxobolus Butschli, 1882 from different food fishes of West Bengal, India

100%
Basu S., Haldar D. P.
Acta Protozoologica
|
2003
|
tom 42
|
nr 3
2

Description of three new myxosporean species [Myxozoa: Myxosporea: Bivalvulida] of the genera Myxobilatus Davis, 1944 and Myxobolus Butschli, 1882

100%
Basu S., Haldar D. P.
Acta Protozoologica
|
2004
|
tom 43
|
nr 4
3

Two new species of Unilobus Theodorides, Desportes and Jolivet, 1984 (Apicomplexa: Conoidasida) parasitizing tenebrionid beetles along with the remarks on the genus and Its family status

81%
Modak B. K., Adhikari R. K., Basu S., Haldar D. P.
Acta Protozoologica
|
2012
|
tom 51
|
nr 2
4

Antioxidants and stress-related metabolites in the seedlings of two indica rice varieties exposed to cadmium chloride toxicity

81%
Roychoudhury A., Basu S., Sengupta D. N.
Acta Physiologiae Plantarum
|
2012
|
tom 34
|
nr 3
We present here a comprehensive study depicting the differences in biochemical responses to increasing CdCl₂ concentrations (0.1, 0.25, 0.5 and 1.5 mM) in the two indica rice varieties, IR-29 (salt-sensitive) and Nonabokra (salt-tolerant), in order to contribute to our understanding of genotypic variation of cadmium tolerance. The oxidative damages in both the varieties enhanced with the increase in CdCl₂ concentrations, the susceptibility of IR-29 being more pronounced than Nonabokra. The detrimental effects in IR-29 were reflected in greater chlorophyll loss, higher H₂O₂and malondialdehyde content even at lower concentrations and drastically higher lipoxygenase activity, protein oxidation and putrescine accumulation, especially at higher CdCl₂ levels. The antioxidants like anthocyanin and carotenoids, antioxidative enzymes like guaiacol peroxidase (GPX) and ascorbate peroxidase (APX), osmolytes like proline, reducing sugars, spermidine and spermine, increased in both the varieties with CdCl₂ levels. While anthocyanin, reducing sugars and spermine showed greater increment in IR-29, the GPX/APX activity was more enhanced in Nonabokra; the increase in carotenoids, proline and spermidine being similar in both the varieties. However, reverse trends were noted for cysteine level and CAT activity; IR-29 showed marked decrease in cysteine content and CAT activity with increased cadmium exposure, whereas in Nonabokra, both the parameters increased, particularly at higher cadmium levels. Thus, the detoxification mechanism in the moresusceptible IR-29 was probably rendered by anthocyanin, reducing sugars and spermine in particular, as well as by GPX/APX, rather than cysteine and CAT, which showed cadmium sensitivity. Thus, the CdCl₂ stress-dependent comparative biochemical analyses displayed major differences in the two rice varieties in terms of tolerance to Cd toxicity. Our data provides evidence that Nonabokra, which is a well-known variety tolerant to sodium chloride toxicity, also shows promising tolerance to cadmium toxicity, and hints at their possible utilization in Cd remediation.
5

Effects of exogenous abscisic acid on some physiological responses in a popular aromatic indica rice compared with those from two traditional non-aromatic indica rice cultivars

81%
Roychoudhury A., Basu S., Sengupta D. N.
Acta Physiologiae Plantarum
|
2009
|
tom 31
|
nr 5
The poor productivity and local confinement of indigenous aromatic rice varieties are mostly due to their susceptibility to salinity/drought/abscisic acid (ABA)- mediated abiotic stresses. It is thus essential to study the effects of several stress factors on their physiological parameters so as to improve their tolerance mechanism and enhance their global demand. Previously, we studied the effect of salinity stress on the physiological and molecular responses of the common aromatic rice Gobindobhog. The objective of this study was to understand the influence of exogenous ABA on some biochemical parameters in Gobindobhog, and comparison with those from non-aromatic M-1-48 and Nonabokra rice. The highest endogenous hydrogen peroxide content and membrane lipid peroxidation (increased malondialdehyde and lipoxygenase activity) were found in ABA-treated Gobindobhog leaves. While the catalase activity was down regulated the most in ABA-treated Gobindobhog leaves, the guaiacol peroxidase activity was induced maximally, indicating the protective role of peroxidase rather than catalase, during ABAinduced oxidative damages. The antioxidant, anthocyanin, showed the highest level in ABA-treated Nonabokra. Enhanced cysteine, following ABA exposure and the highest levels of reducing sugars, total amino acids, proline, and polyamines (putrescine and spermidine) recorded in Gobindobhog, probably served to shield from ABAinduced stress injuries, whereas the spermine levels were comparable in ABA-treated Nonabokra and Gobindobhog. The aroma content, intensified after ABA treatment, was markedly noted in Gobindobhog. Thus, the systematic examination of ABA-mediated stress revealed the most prominent oxidative damages in Gobindobhog, even higher than M-1-48, with a concomitant enhancement in peroxidase system and particularly osmolyte or polyamine levels to ensure its sustenance.
6

Two new species of Gregarina Dufour, 1828 [Apicomplexa: Conoidasida] from orthopteran insects of Westt Bengal, India

81%
Modak B. K., Basu S., Haldar D. P.
Acta Protozoologica
|
2008
|
tom 47
|
nr 3
269-278
7

Description of two new species of Phleobum Halder and Chakraborty, 1974 along with a major taxonomic revision of the genus

81%
Modak B. K., Basu S., Haldar D. P.
Acta Protozoologica
|
2011
|
tom 50
|
nr 2
8

Two new species of Myxobolus Butschli, 1882 [Myxozoa: Myxosporea: Bivalvulida] from food fishes of West Bengal, India - a light and scanning electron microscopy study

81%
Basu S., Modak B. K., Haldar D. P.
Acta Protozoologica
|
2009
|
tom 48
|
nr 1
83-89
9

Comparative analysis of some biochemical responses of three indica rice varieties during polyethylene glycol-mediated water stress exhibits distinct varietal differences

81%
Basu S., Roychoudhury A., Saha P. P., Sengupta D. N.
Acta Physiologiae Plantarum
|
2010
|
tom 32
|
nr 3
Extensive investigation into plant response and adaptation to diverse osmotic stresses like high salt/dehydration/low temperature, involving a broad spectrum of cellular physiological and biochemical changes, is essential to unravel intrinsic mechanism to mitigate against such stresses. In our previous communications, we conducted biochemical analyses of indica rice varieties, subjected to exogenous salt/abscisic acid-mediated oxidative stress. The aim of this study was to compare differential biochemical responses of the salt-sensitive (IR-29), salt-tolerant (Pokkali) and aromatic (Pusa Basmati or PB) rice varieties during polyethylene glycol (PEG)-induced dehydration stress. The greater susceptibility of IR-29 and PB, to water scarcity, was reflected by the higher toxic Na⁺ and putrescine accumulation, considerable decrease in (reduced/oxidized) glutathione, maximal increment in protease activity and greater downregulation of nitrate reductase activity. On the other hand, Pokkali appeared to suffer lesser damages as evidenced from much lower endogenous Na⁺ but higher K⁺, Ca²⁺ and Mg²⁺ accumulation, registering the highest levels of osmolytes like glycinebetaine and higher polyamines (spermidine and spermine) accounting to improved relative water content, higher (reduced/oxidized) glutathione, maximal induction of the enzyme phenylalanine ammonia-lyase and practically unhindered nitrate reductase activity, following PEG treatment. The highest induction of sugars and proline in IR-29 and PB probably played the osmoprotective/antioxidative functions, enabling to a certain extent to heighten their lipoxygenase inhibition or H₂O₂ scavenging potential, more than Pokkali, to ward off oxidative damages and sustain survival under critical dehydrated situations. Thus, the salt-tolerant Pokkali also showed prominent dehydration-tolerance properties, whereas the aromatic rice PB, almost identical in their biochemical responses to IR-29, showed greater sensitivity to PEG-mediated water deficit.
10
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Micropropagation of Dipcadi montanum (Dalz.) Baker (Asparagaceae): a rare scapigerous herb

81%
Basu S., Islam E., Chakraborty D.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
|
2024
|
tom 105
|
nr 2
11

Two new species of the genus Quadruspinospora Sarkar et Chakravarty, 1969 [Apicomplexa, Conoidasida] from grasshoppers [Insecta, Orthoptera]

81%
Modak B. K., Basu S., Haldar D. P.
Acta Parasitologica
|
2008
|
tom 53
|
nr 4
Descriptions of structures and life histories of two new species of septate gregarines (Apicomplexa, Conoidasida) are given. These are: Quadruspinospora cloptoni sp. nov. and Quadruspinospora caudata sp. nov. from the midguts of Oxya hyla hyla Serville and Gesonula punctiformes (Stal.) (Insecta, Orthoptera, Acrididae), respectively. Trophozoites of Q. cloptoni attain a maximum length of 944 μm and their epimerites are either a simple knob or cauliflower-like without any digitiform process; gamonts are solitary and, spherical gametocysts, 390 μm, release ovoid oocysts by a simple rupture, the latter being provided with four characteristic spines, two at each pole. Trophozoites of Q. caudata are much smaller, 578 μm in maximum length, and the epimerite in this gregarine is short and cone like. Spherical gametocysts, 365 μm, also dehisce by a simple rupture releasing ovoid oocysts having four typical spines, characteristic of the genus Quadruspinospora Sarkar et Chakravarty, 1969. The validity of Quadruspinospora as a distinct genus is discussed.
12

Molecular study of indigenous bacterial community composition on exposure to soil arsenic concentration gradient

71%
Basu S., Paul T., Yadav P., Debnath A., Sarkar K.
Polish Journal of Microbiology
|
2017
|
tom 66
|
nr 2
Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soilcontaminated with low concentration of arsenic was dominated by both Actinobacteria and Proteobacteria but a shift towards Proteobacteria was observed with increasing arsenic concentration, and number of Actinobacteria eventually decreases. PCA (Principle Component Analysis) plot of bacterial community composition indicated a distinct resemblance among high arsenic content samples, while low arsenic content samples remained separated from others. Cluster analysis of soil parameters identifies three clusters, each of them was related to the arsenic content. Further, cluster analysis of 16S rDNA based DGGE fingerprint markedly distributed the soil bacterial populations into low (< 10 ppm) and high (> 10 ppm) arsenic content subgroups. Following analysis of diversity indices shows significant variation in bacterial community structure. MDS (Multi Dimensional Scaling) plot revealed distinction in the distribution of each sample denoting variation in bacterial diversity. Phylogenetic sequence analysis of fragments excised from DGGE gel revealed the presence of γ-Proteobacteria group across the study sites. Collectively, our experiments indicated that gradient of arsenic contamination affected the shape of the soil bacterial population by significant structural shift.
13

FunPred-1: Protein function prediction from a protein interaction network using neighborhood analysis

71%
Saha S., Chatterjee P., Basu S., Kundu M., Nasipuri M.
Cellular and Molecular Biology Letters
|
2014
|
tom 19
|
nr 4
Proteins are responsible for all biological activities in living organisms. Thanks to genome sequencing projects, large amounts of DNA and protein sequence data are now available, but the biological functions of many proteins are still not annotated in most cases. The unknown function of such non-annotated proteins may be inferred or deduced from their neighbors in a protein interaction network. In this paper, we propose two new methods to predict protein functions based on network neighborhood properties. FunPred 1.1 uses a combination of three simple-yet-effective scoring techniques: the neighborhood ratio, the protein path connectivity and the relative functional similarity. FunPred 1.2 applies a heuristic approach using the edge clustering coefficient to reduce the search space by identifying densely connected neighborhood regions. The overall accuracy achieved in FunPred 1.2 over 8 functional groups involving hetero-interactions in 650 yeast proteins is around 87%, which is higher than the accuracy with FunPred 1.1. It is also higher than the accuracy of many of the state-of-the-art protein function prediction methods described in the literature. The test datasets and the complete source code of the developed software are now freely available at http://code.google.com/p/cmaterbioinfo/.
14

Magnetopriming circumvents the effect of salinity stress on germination in chickpea seeds

71%
Thomas S., Anand A., Chinnusamy V., Dahuja A., Basu S.
Acta Physiologiae Plantarum
|
2013
|
tom 35
|
nr 12
Chickpea seeds of Pusa 1053 (Mediterranean) and Pusa 256 (native) were magnetoprimed with 100 mT static magnetic field for 1 h to evaluate the effect of magnetopriming on germination of seeds under saline conditions. Enhanced rate of germination and seedling growth parameters (root and shoot length, and vigour indices) under different salinity levels indicated that magnetopriming was more effective in alleviating salinity stress at early seedling stage in Pusa 1053 as compared to Pusa 256. Dynamics of seed water absorption in magnetoprimed seeds showed increased water uptake in Pusa 1053 under non-saline as compared to saline conditions. This could have resulted in faster hydration of enzymes in primed seeds leading to higher rate of germination. Total amylase, protease and dehydrogenase activities were higher in primed seeds as compared to unprimed seeds under both non-saline and saline conditions. Production of superoxide radicals was enhanced in germinating seeds of both the genotypes under salinity irrespective of priming. Increased levels of hydrogen peroxide in germinating magnetoprimed seeds, under both the growing conditions, suggested its role in promotion of germination. Our results showed that magnetopriming of dry seeds of chickpea can be effectively used as a pre-sowing treatment for mitigating adverse effects of salinity at seed germination and early seedling growth.
15

PPI_SVM: Prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables

71%
Chatterjee P., Basu S., Kundu M., Nasipuri M., Plewczynski D.
Cellular and Molecular Biology Letters
|
2011
|
tom 16
|
nr 2
Protein-protein interactions (PPI) control most of the biological processes in a living cell. In order to fully understand protein functions, a knowledge of protein-protein interactions is necessary. Prediction of PPI is challenging, especially when the three-dimensional structure of interacting partners is not known. Recently, a novel prediction method was proposed by exploiting physical interactions of constituent domains. We propose here a novel knowledge-based prediction method, namely PPI_SVM, which predicts interactions between two protein sequences by exploiting their domain information. We trained a two-class support vector machine on the benchmarking set of pairs of interacting proteins extracted from the Database of Interacting Proteins (DIP). The method considers all possible combinations of constituent domains between two protein sequences, unlike most of the existing approaches. Moreover, it deals with both single-domain proteins and multi domain proteins; therefore it can be applied to the whole proteome in high-throughput studies. Our machine learning classifier, following a brainstorming approach, achieves accuracy of 86%, with specificity of 95%, and sensitivity of 75%, which are better results than most previous methods that sacrifice recall values in order to boost the overall precision. Our method has on average better sensitivity combined with good selectivity on the benchmarking dataset. The PPI_SVM source code, train/test datasets and supplementary files are available freely in the public domain at: http://code.google.com/p/cmater-bioinfo/.
16

Purification and characterization of avian glycolipid: beta-galactosyltransferases (GalT-4 and GalT-3): cloning and expression of truncated betaGalT-4

61%
Basu S. S., Dastgheib S., Ghosh S., Basu M., Kelly P., Basu S.
Acta Biochimica Polonica
|
1998
|
tom 45
|
nr 2
Acidic glycolipid of ganglio-(containing sialic acid) and sialyl-lactofucosyl-type, SA-Lex (containing sialic acid and fucose) are developmentally regulated and appear to be ubiqitous on neuronal and cancer cell surfaces of animals. Two glycolipid: β-galactosyltransferases, GalT-3 and GalT-4, were characterized in embryonic chicken brain (ECB). Based on substrate competition experiments, these two activities were believed to be due to expression of two gene products. A cDNA fragments (about 600 bp) encoding the catalytic domain of the GalT-4 (UDP-Gal:LcOse3Cer β1,4galactosyltransferase) from ECB and human Colo-205 were isolated. These cDNAs were expressed as a soluble glutathione-S-transferase fusion protein (48 kDa) in Eschericchia coli. Interactions between GlcNAc-, UDP-hexanolamine-, and α-lactalbumin were studied with the purified fusion protein (recombinant and truncated). Functionally it was similar to that of native GalT-4 purified (40000-fold) from 11-day-old ECB. GalT-3 (UDP-Gal:GM2β1,3galactosyltransferase) was purified from 19-day-old ECB, and a polyclonal antibody was produced against the peptide backbone for immunoscreening of a λZAP ECB cDNA expression library. Each of the GalT-3 peptides (62 and 65 kDa was analyzed by protein fingerprinting analysis indicating a similar peptide mapping pattern.
17

Hydrophobic nature of mammalian ceramide glycanases: Purified from rabbit and rat mammary tissues

51%
Basu M., Dastgheib S., Girzadas M. A., O'Donnell P. H., Westarvelt C. W., Li Z., Inokuchi J., Basu S.
Acta Biochimica Polonica
|
1998
|
tom 45
|
nr 2
The ceramide glycanase (CGase) activities, which cleave the intact oligosaccharide chain and the ceramide moiety of a glycosphingolipid, have been characterized from two mammalian sources. The enzymatic activities are almost comparable in rabbit and rat mammary tissues. The majority of the activities has been concentrated in the soluble fraction which could be partially purified using hydrophobic columns. The rabbit mammary ceramide glycanase activity has been purified up to 1438-fold using ion exchange and hydrophobic columns in tandem. The purified protein exhibited a molecular mass of 54 kDa which could be immunostained on the Western blot with clam anti-CGase polyclonal antibody. In addition, a 98 kDa protein also exhibited positive immunostain in a successive purified fraction with that antibody and is under investigation. The requirement for the optimal enzymatic activities are similar for both rabbit and rat CGase activities. The CGase activity requires the presence of detergent for optimal activity but is not dependent on the presence of any divalent cations. However, Hg2+, Zn2+, and Cu2+ are inhibitory to the enzymatic activities. It has been observed that rat as well as rabbit CGases are inhibited by both D- and L-PDMP (1-phenyl-2-decanoylamino-3-morpholino-1-propanol.HCl) and its higher analogue PPMP (1-phenyl-2-palmitoylamino-3-morpholino-1-propanol.HCl). Alkyl amines containing C12 and higher chains are also found to inhibit both rat and rabbit CGase activities. Substantial levels of CGase activities have also been observed in various human tumor cells as well as in developing avian brains. These observations are significant in view of the recent findings that ceramide, which is one of the enzymatic reaction products of CGase activity, is mediating different cellular events like signal transduction and apoptosis. The role of this enzyme in development, metastasis and cellular regulation are anticipated.
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