Journal of Biosciences

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[125I] gonadotropin binding to the ovary of an Indian major carp, Catla catla, at different stages of reproductive cycle.
(1993-09) Manna, Pulak Ranjan; Bhattacharya, Samir
At different stages of the annual reproductive cycle of Catla catla, a major Indian carp, specific binding of gonadotropic hormone to the plasma membrane receptors was demonstrated. Maximum specific binding of [125I] Catla gonadotropic hormone was obtained at 30°C and pH 7·5 during 2 h of incubation. Catla gonadotropic hormone binding was saturable with high affinity. Competitive inhibition experiment showed that binding site was specifically occupied by piscine gonadotropic hormone, Catla gonadotropic hormone and murrel gonadotropic hormone, human chorionic gonadotropin was a weak competitor while bovine thyroid stimulating hormone, bovine prolactin and ovine follicle stimulating hormone had no effect. Scatchard analysis of Catla gonadotropic hormone binding to the plasma membrane preparation from the carp oocytes of different reproductive stages showed that the range of dissociation constant (Kd) varied from 0·78 to 0·97 × 10-10 M. However, maximum binding capacity (B-max) varied remarkably between the different stages of reproductive cycle, it was 6·11 ± 0·36 fmol/mg protein in the preparatory stage which increased to about three-fold in prespawning stage of reproductive cycle (17·0 ± 0·29 fmol/mg protein) and spawning (18·7 ± 0·17 fmol/mg protein) and lowest in postspawning stage of reproductive cycle (5·28 ± 0·28 fmol/mg protein). Fluctuation in the number of gonadotropic hormone binding site at different stages of annual reproductive cycle was found to be coincided well with the pattern of ovarian steroidogenesis in response to Catla gonadotropic hormone as determined by the formation of progesterone from pregnenolone.
14-3-3 proteins mediate the localization of Centrin2 to centrosome
(Indian Academy of Sciences, 2019-06) Boseh, Arunabha; Dalal, Sorab N
14-3-3e and 14-3-3c localize to the centrosome and regulate centrosome duplication, by inhibiting cdc25C function. As14-3-3c and 14-3-3e form a complex with centrosomal proteins, we asked if this ability was required to regulate centrosomeduplication. The results in this report demonstrate that 14-3-3e and 14-3-3c form a complex with Centrin2 and that thebinding site is located in the N-terminal EF hand in Centrin2, EF1. A Centrin2 mutant that does not form a complex with14-3-3 proteins displays a punctate cytoplasmic localization and does not localize to the centrosome. These results suggestthat in addition to negatively regulating centrosome duplication as previously reported, 14-3-3 proteins might also berequired for centriole biogenesis by regulating the localization of Centrin2 at the centrosome.
2′-O-methyl nucleotide modified DNA substrates influence the cleavage efficiencies of BamHI and BglII.
(2014-09) Tong, Zhaoxue; Zhao, Bin; Zhao, Guojie; Shang, Hong; Guan, Yifu
Induction of endonucleolytic DNA cleavage is an essential event that links the initiating stimuli to the final effects of cells. The cleavage efficiency and thus the final yield could be affected by many factors, including structures of DNA substrates, composite structures of enzymes–substrates or enzymes–nucleic analogs and so on. However, it is not clear whether a nucleotide derivative-substituted in DNA substrates can influence the efficiency of enzymatic cleavage. To investigate the effect of sugar pucker conformation on DNA–protein interactions, we used 2′-O-methyl modified nucleotides (OMeN) to modify DNA substrates of isocaudemers BamHI and BglII in this study, and used FRET assay as an efficient method for analysis of enzyme cleavage. Experimental results demonstrated that OMeN-substituted recognition sequences influenced the cleavage rates significantly in a position-dependent manner. OMeN substitutions can reduce the cleavage as expected. Surprisingly, OMeN substitutions can also enhance the cleavage rates. The kinetics parameters of Vmax and Km have been obtained by fitting the Michaelis-Menten kinetic equation. These 2'- OMe nucleotides could behave as a regulatory element to modulate the enzymatic activity in vitro, and this property could enrich our understanding about the endonuclease cleavage mechanism and enhance our ability to regulate the enzymatic cleavage efficiency for applications in synthetic biology.
[31P] -Nuclear magnetic resonance spin lattice relaxation in lecithin reverse micelles.
(1982-12) Tibarewala, D N; Ganguli, S
[31P] -Nuclear magnetic resonance (NMR) spin lattice relaxation times (T1) have been measured for lecithin-nonpolar solvent-water as a function of added water for three solvents, namely, benzene, carbon tetrachloride and cyclohexane. In benzene and carbon tetrachloride systems, where spherical reverse micelles are formed, [31P]-NMR T1, values increase linearly with added water. However, in cyclohexane, the trends in the [31P]-T1 values indicate very different micellisation processes. Even at the lowest concentration of added water, the [31P]-T1 values in this solvent are substantially larger than the corresponding values in benzene and carbon tetrachloride, which is attributed to the intramolecular chlorinephosphate interaction being the weakest in cyclohexane. At a higher water content of six mols of water per mol of lecithin in cyclohexane solvent, the [31Ρ]-T1 values show a sharp decrease indicating a sudden change in the dynamics of the phosphate group, and this confirms the on set of 'reverse micelle-to-liquid crystalline' phase transition observed in this system by other spectroscopic and physical techniques.
33-kDa C-terminal heparin binding fragment of fibronectin promotes attachment and spreading of hepatocytes.
(1992-12) Kumar, N Anil; Sudhakaran, P R
The possibility of interaction of hepatocytes with the heparin binding domain of Fibronectin was examined. Rat hepatocytes adhered to coverslips coated with the 33- kDa heparin binding fragment of the C-terminal region of plasma fibronectin. When different concentrations of the heparin binding fragment were used to coat coverslips and used as substratum, cell attachment showed saturation kinetics. Half the maximum attachment was observed at 30–40 min after seeding of cells. The cells became flat after 2–3 h indicating that they spread on the heparin binding domain as they do on intact fibronectin. Among the different glycosaminoglycans tested, maximum inhibition of attachment was observed for heparin. However it was not possible to completely inhibit attachment even at high concentrations. These results indicate that hepatocytes interact with fibronectin not only through the Arg–Gly–Asp-containing cell binding fragment, but also through the heparin binding domain of fibronectin and, further, that there exist heparin-dependent and heparin-independent mechanisms of interaction of cells with the 33- kDa heparin binding fragment of fibronectin.
5-Azacytidine and trichostatin A enhance the osteogenic differentiation of bone marrow mesenchymal stem cells isolated from steroid-induced avascular necrosis of the femoral head in rabbit
(Indian Academy of Sciences, 2019-09) Zhang, Peng; Tao, Fulin; Qinghu, Li; Shuai, Wu; Baisheng, Fu; Ping, Liu
5-Methylcytosine content and methylation status in six millet DNAs.
(1990-03) Kumar, Lalitha S; Hendre, R R; Ranjekar, P K
High performance liquid chromatographic analysis of the total nuclear DNAs of 6 millets plant species indicates that the 5-methylcytosine content ranges from 3% in barn yard millet to 9·6% in great millet while the fraction of cytosines methylated varies between 14% in little millet to 31 % in pearl millet. Digestion of millet DNAs with MspI/HpaII suggests that CpG methylation is more in great millet DNA while CpC methylation is more in the other 5 millet DNAs. Digestion of millet DNAs with MboI, Sau3AI and DpnI indicates that some of the 5’ GATC3’ sequences are methylated at adenine and/or cytosine residues except in little millet where adenine methylation of the 5’GATC3’ sequences is insignificant and there is a predominance of cytosine methylation in these sequences.
A23187—Channel behaviour: Fluorescence study.
(1994-09) Jyothi, G; Surolia, A; Easwaran, K R K
Pyranine entrapped soylipid liposomes have been used as a model system to study the proton transport across membrane in the presence of A23187, a carboxylic ionophore specific for electroneutral exchange of divalent cations. An apparent rate constant (kapp) for transport of protons has been determined from the rate of change of fluorescence intensity of pyranine by stopped flow rapid kinetics in the presence of proton gradient The variation of kapp has been studied as a function of ionophore concentration and the results have been compared with gramicidin—a well known channel former under the similar experimental conditions. The rates thus obtained showed that A23187 is not only a simple carrier but also shows channel behaviour at high concentration of ionophore.
Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER.
(2002-02-03) Aggarwal, Gautam; Ramaswamy, Ramakrishna
We compare the annotation of three complete genomes using the ab initio methods of gene identification GeneScan and GLIMMER. The annotation given in GenBank, the standard against which these are compared, has been made using GeneMark. We find a number of novel genes which are predicted by both methods used here, as well as a number of genes that are predicted by GeneMark, but are not identified by either of the nonconsensus methods that we have used. The three organisms studied here are all prokaryotic species with fairly compact genomes. The Fourier measure forms the basis for an efficient non-consensus method for gene prediction, and the algorithm GeneScan exploits this measure. We have bench-marked this program as well as GLIMMER using 3 complete prokaryotic genomes. An effort has also been made to study the limitations of these techniques for complete genome analysis. GeneScan and GLIMMER are of comparable accuracy insofar as gene-identification is concerned, with sensitivities and specificities typically greater than 0.9. The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a significant number of cases, similar results are provided by the two techniques. This suggests that there could be some as-yet unidentified additional genes in these three genomes, and also that some of the putative identifications made hitherto might require re-evaluation. All these cases are discussed in detail.
ABCA1 C69T gene polymorphism and risk of type 2 diabetes mellitus in a Saudi population.
(2013-12) Alharbi, Khalid K; Khan, Imran Ali; Al-Daghri, Nasser M; Munshi, Anjana; Sharma, Vandana; Mohammed, Abdul Khader; Wani, Kaiser A; Al-Sheikh, Yazeed A; Al-Nbaheen, May Salem; Ansari, Mohammed Ghouse Ahmed; Syed, Rabbani
Type 2 diabetes mellitus (T2DM) is a disease induced by complex interactions between environmental factors and certain genetic factors. Genetic variants in the Adenosine Binding Cassette Transporter Proteins 1 (ABCA1) have been associated with abnormalities of serum lipid levels of high-density lipoprotein (HDL-C). Decreased serum levels of HDL-C have often been observed in T2DM cases, and this condition has been considered to be involved in the mechanism of insulin resistance (IR). Therefore, we investigated possible association between ABCA1 C69T gene polymorphism and T2DMin a Saudi population. This study was carried out with 380 healthy control subjects and 376 T2DM patients. Genotyping of ABCA1 C69T polymorphism was carried out by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism technique. We observed that the frequency of the T allele of the ABCA1 C69T gene was significantly higher in healthy subjects compared to T2DMpatients (0.28 vs 0.45; p<0.0001; OR (95% CI) = 0.4624 (0.3732–0.5729), and therefore the T allele may be a protective factor against T2DM in the Saudi population.
ABCG2 aptamer selectively delivers doxorubicin to drug-resistant breast cancer cells
(Indian Academy of Sciences, 2019-06) Hashemitabar, Shirin; Yazdian-Robati, Rezvan; Hashemi, Maryam; Ramezani, Mohammad; Abnous, Khalil; Kalalinia, Fatemeh
Chemotherapy is the most widely used treatment for cancer therapy, but its efficacy is limited by the side effects of non-specificcytotoxic drugs. Ligand-based targeting drug-delivery system is a solution to circumvent this issue. In this study, an ABCG2aptamer–doxorubicin complex was prepared, and its efficacy in targeted drug delivery to mitoxantrone-resistance breast cancer cellline (MCF7/MX) was evaluated. The formation of aptamer–doxorubicin physical complex was analyzed by fluorometric analysis.The cytotoxicities of doxorubicin and aptamer–doxorubicin complex on MCF7 and MCF7/MX cell lines were evaluated by theMTT assay, and IC50 values were obtained. Cellular uptake of aptamer–doxorubicin complex was assessed by flow cytometrycellular uptake assay. Results: Fluorometric analysis of aptamer–doxorubicin showed 1–1.5 molar ratio of the drug to the aptamercould efficiently quench Dox fluorescence. MTTassay results showed that MCF7/MX cells were more resistant to doxorubicin thanMCF7 cells (IC50 : 3.172 ± 0.536 and 1.456 ± 0.154 lM, respectively). Flow cytometry and MTT assay results showed that theaptamer–doxorubicin complex could increase the uptake and cytotoxicity of doxorubicin in MCF7/MX cell line in comparison withfree doxorubicin, while the same treatments had no effect on IC50 of Dox on MCF7 cells. The results proposed that the ABCG2aptamer–drug complex can be effectively used for specific drug delivery to ABCG2-overexpressing cells.
ABCG2 inhibition as a therapeutic approach for overcoming multidrug resistance in cancer.
(2016-06) Hasanabady, Maryam Hosseini; Kalalinia, Fatemeh
Breast cancer resistance protein (BCRP, ABCP or MXR)/ATP-binding cassette subfamily G member 2 (ABCG2) was characterized as a multidrug resistance efflux transporter in 1998. ABCG2 physiologically acts as a part of a selfdefence mechanism for the organism; it enhances eliminating of toxic xenobiotic substances and harmful agents in the intestine, as well as through the blood–brain barrier and placenta. ABCG2 recognizes and transports numerous anticancer drugs including conventional chemotherapeutic and new targeted small therapeutic molecules in clinical usage. Development of ABCG2 inhibitors for clinical usage may allow increased penetration of therapeutic agents into sanctuary sites and increases their intestinal absorption. Here we review the mechanisms that modulate MDR mediated by the ABC transporter ABCG2 in normal and cancer cells by different levels including, epigenetic modifications, transcriptional, post-transcriptional, translation and post-translational regulation. Some clinical applications of ABCG2 inhibitors are also explained.
The ABCs of molecular dynamics simulations on B-DNA, circa 2012.
(2012-07) Beveridge, David L; Cheatham, III Thomas E; Mezei, Mihaly
This article provides a retrospective on the ABC initiative in the area of all-atom molecular dynamics (MD) simulations including explicit solvent on all tetranucleotide steps of duplex B-form DNA duplex, ca. 2012. The ABC consortium has completed two phases of simulations, the most current being a set of 50–100 trajectories based on the AMBER ff99 force field together with the parmbsc0 modification. Some general perspectives on the field of MD on DNA and sequence effects on DNA structure are provided, followed by an overview our MD results, including a detailed comparison of the ff99/parmbsc0 results with crystal and NMR structures available for d(CGCGAATTCGCG). Some projects inspired by or related to the ABC initiative and database are also reviewed, including methods for the trajectory analyses, informatics of dealing with the large database of results, compressions of trajectories for efficacy of distribution, DNA solvation by water and ions, parameterization of coarse-grained models with applications and gene finding and genome annotation.
Abdominal pigmentation and growth temperature in Indian Drosophila melanogaster : Evidence for genotype-environment interaction.
(1994-06) Das, Aparup; Mohanty, Sujata; Parida, B B
Phenotypic variability for abdominal pigmentation in females of an Indian natural population of Drosophila melanogaster was studied using isofemale lines and by rearing the larvae and pupae at 4 different temperatures ranging from 20–30°C. The dark pigmented area was found to increase in all the three segments when the growth temperature decreases. A significant positive correlation was detected for the occurrence of dark pigmentation in the 5th and 6th segments in each growth temperature but for other comparisons the correlation was not regular. Analysis of variance (ANOVA) was carried out both for individual segments over different growth temperatures and also for each temperature over the three abdominal segments and in all cases found to be statistically significant. The results are quite different from the earlier observation in French Drosophila melanogaster and suggest that genes controlling pigmentation are temperature dependent; temperature could affect post-transitional events involved in pigmentation. The present findings also clearly indicate that significant genotype-environment interaction exists, responsible for the production of desired phenotype at the opportune moment during the life span of a species.
Aberrant transcription in fit mutants of Escherichia coli and its alleviation by suppressor mutations.
(1993-03) Munavar, M Hussain; Madhavi, K; Jayaraman, R
Earlier work from this laboratory had identified, mapped and characterised an intragenic suppressor (fitA24) as well as an extragenic suppressor (fitB) for the temperature-sensitive transcription defective mutation fitA76 in Escherichia coli In this communication we report the results of experiments on RNA synthesis and decay of pulse labelled RNA in strains harbouring fit Α76, fitB, fitA24, fitA76-fitA24, fitA76-fitB mutation(s) as well as in the isogenic fitA+ fitB+ strain. Taken together with earlier results, this indicates that the fitA and fitB gene products could be involved in the expression of some classes of genes including genes coding for ribosomal proteins. The implications of these results for the in vivo control of transcription in Escherichia coli are discussed.
Abnormal erythrocyte membrane phospholipid organisation in chronic myeloid leukaemia.
(1987-03) Kumar, A; Daniel, S; Agarwal, S S; Gupta, C M
The membrane phospholipid organisation in the red cells of humans suffering from chronic myeloid leukaemia has been analysed using the amino-group labelling reagent trinitrobenzenesulphonic acid and the fluid-sensing fluorophore, Merocyanine 540. Unlike the normal human erythrocytes, trinitrobenzenesulphonic acid in intact chronic myeloid leukaemia erythrocytes modified about 30% phosphatidylserine, under controlled conditions. Also, the chronic myeloid laukaemia red cells, but not the normal cells, were found to bind the fluorescent dye Merocyanine 540. These results demonstrate that loss of the transmembrane phospholipid asymmetry in chronic myeloid leukaemia erythrocytes is accompanied by an enhancement in the outer surface fluidity and, therefore, suggest that the red cells membrane phase-state asymmetry originates probably from the asymmetric arrangements of phospholipids across the membrane bilayer.
Abnormalities in the fine structure of the spermatids of rats injected with cadmium.
(1980-12) Dutt, N H Gopal; Kobayashi, Kan
The degenerative changes in the spermatids as measured by changes in fine structure abnormalities increased with time following injection of Cd2+ into rat testis. The spermatids in the twelve hours group appear as peculiarly club shaped and elongated structures with one or two small but perceptible vacuoles. The subacrosomal area and the space between the nucleus and the middle piece are seen abnormally dilated. In the 30 day group, the central filaments are the most susceptible unit of 9+2 axoneme complex. The plasma membrane, the cytoplasmic matrix, the mitochondria of the middle piece and the fibrous sheath appear shrunken, discontinuous and degenerative.
Absence of kinetic barrier for transfer of protons from aqueous phase to membrane-water interface.
(1995-12) Maity, H P; Krishnamoorthy, G
The kinetics of interfacial proton transfer reaction is an important factor in proton transport across membranes. The following experimental system was designed in order to measure this kinetics. Sonicated liposomes having the protonophore SF6847 was suspended in Tris buffer. Application of a temperature jump (in ~ 3 μs) caused a drop in the aqueous phase pH which was subsequently sensed by the membrane-bound SF6847. The kinetics of this interfacial proton transfer reaction was monitored on μs timescales. The estimated bimolecular rate constant of 2×1011 Μ–1 s–1 for this process show that there is no kinetic barrier for the transfer of protons from the aqueous phase to the membrane-water interface.
Accelerated fat cell aging links oxidative stress and insulin resistance in adipocytes.
(2013-03) Monickaraj, Finny; Aravind, Sankaramoorthy; Nandhini, Pichamoorthy; Prabu, Paramasivam; Sathishkumar, Chandrakumar; Mohan, Viswanathan; Balasubramanyam, Muthuswamy
Telomere shortening is emerging as a biological indicator of accelerated aging and aging-related diseases including type 2 diabetes. While telomere length measurements were largely done in white blood cells, there is lack of studies on telomere length in relation to oxidative stress in target tissues affected in diabetes. Therefore, the aim of this study is to induct oxidative stress in adipocytes and to test whether these adipocytes exhibit shortened telomeres, senescence and functional impairment. 3T3-L1 adipocytes were subjected to oxidative stress and senescence induction by a variety of means for 2 weeks (exogenous application of H2O2, glucose oxidase, asymmetric dimethylarginine (ADMA) and glucose oscillations). Cells were probed for reactive oxygen species generation (ROS), DNA damage, mRNA and protein expression of senescent and pro-inflammatory markers, telomere length and glucose uptake. Compared to untreated cells, both ROS generation and DNA damage were significantly higher in cells subjected to oxidative stress and senescence. Adipocytes subjected to oxidative stress also showed shortened telomeres and increased mRNA and protein expression of p53, p21, TNFα and IL-6. Senescent cells were also characterized by decreased levels of adiponectin and impaired glucose uptake. Briefly, adipocytes under oxidative stress exhibited increased ROS generation, DNA damage, shortened telomeres and switched to senescent/pro-inflammatory phenotype with impaired glucose uptake.
Accelerated processing of solitary and clustered abasic site DNA damage lesions by APE1 in the presence of aqueous extract of Ganoderma lucidum.
(2016-06) Kumari, Bhavini; Das, Prolay; Kumari, Rekha
The stimulatory effect of the aqueous extract of G. lucidum, a basidiomycetes class fungus in the APE1-enzyme-mediated processing of solitary and bistranded clustered abasic sites DNA damages is presented. Abasic sites are considered the most common type of DNA damage lesions. Our study shows enhanced activity of APE1 in the processing of abasic sites in the presence of the polysaccharides fraction of G. lucidum. Remarkable increase in the amount of single-strand breaks (SSBs) and double-strand breaks (DSBs) from solitary and bistranded clustered abasic sites respectively with APE1 in the presence of the extract was found. This trend is maintained when abasic sites in DNA oligomers are exposed to fibroblast cell extracts in the presence of the extract. While DNA conformational alteration is negligible, APE1 enzyme shows characteristic changes in the alpha helix and beta strand ratio after incubation with G. lucidum extract. The enhanced reactivity of APE1 at the molecular level in the presence of G. lucidium is attributed to this effect. This study potentially amplifies the scope of the use of G. lucidum, which was earlier shown to have only reactive oxygen species (ROS) scavenging properties with regards to DNA damage inhibition.

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