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Biomedical subjects

B K Mohanty

Publications and source records attributed to B K Mohanty.

At least 19 recordsLinked to original sources

Effect of paper mill effluent on germination of green gram (Phaseolus aureus Roxb.) and growth behaviour of it's seedlings.

Effect of paper mill effluents on Phaseolus aureus Roxb was studied. The effluent significantly inhibited germination of root and shoot length. The bio-chemical injury does not appear spontaneously but with the increase in effluent treatment there is reduction in observed biochemical parameters (chlorophyll, protein, amino acid, nuclic acids and carbohydrate) which are negatively correlated. The shoots of the seedlings were found to be resistant; whereas roots of the seedlings were susceptible to paper mill effluent treatment.

Amino Acids↗

Structural and functional analysis of a bipolar replication terminus. Implications for the origin of polarity of fork arrest.

We have delineated the amino acid to nucleotide contacts made by two interacting dimers of the replication terminator protein (RTP) of Bacillus subtilis with a novel naturally occurring bipolar replication terminus by converting RTP to a site-directed chemical nuclease and mapping its cleavage sites on the terminus. The data show a relatively symmetrical arrangement of the amino acid to base contacts, and a comparison of the bipolar contacts with that of a normal unipolar terminus suggests that the DNA-protein contacts play an important determinative role in generating polarity from structurally symmetrical RTP dimers. The amino acid to nucleotide contacts provided distance constraints that enabled us to build a three-dimensional model of the protein-DNA complex. The model is consistent with features of the bipolar Ter.RTP complex derived from mutational and cross-linking data. The bipolar terminus arrested Escherichia coli DNA replication and DnaB helicase and T7 RNA polymerase in vitro in both orientations. RTP arrested the unwinding of duplex DNA on the bipolar Ter DNA substrate regardless of the length of the duplex DNA. The latter result suggested further that the terminus arrested authentic DNA unwinding by the helicase rather than just translocation of helicase on DNA.

Bacillus subtilis↗

Polynucleotide phosphorylase functions both as a 3' right-arrow 5' exonuclease and a poly(A) polymerase in Escherichia coli.

In vitro, polynucleotide phosphorylase of Escherichia coli can both synthesize RNA by using nucleotide diphosphates as precursors and exonucleolytically degrade RNA in the presence of inorganic phosphate. However, because of the high in vivo concentration of inorganic phosphate in exponentially growing cells, it has been assumed that the enzyme works exclusively as an exonuclease. Here we demonstrate that, contrary to this prediction, polynucleotide phosphorylase not only synthesizes long, highly heteropolymeric tails in vivo, but also accounts for all of the observed residual polyadenylylation in poly(A) polymerase I deficient strains. In addition, the enzyme is responsible for adding the C and U residues that are found in poly(A) tails in exponentially growing cultures of wild type E. coli.

Base Sequence↗

Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli.

Poly(A) tails in Escherichia coli are hypothesized to provide unstructured single-stranded substrates that facilitate the degradation of mRNAs by ribonucleases. Here, we have investigated the role that such nucleases play in modulating polyadenylation in vivo by measuring total poly(A) levels, polyadenylation of specific transcripts, growth rates and cell viabilities in strains containing various amounts of poly(A) polymerase I (PAP I), polynucleotide phosphorylase (PNPase), RNase II and RNase E. The results demonstrate that both PNPase and RNase II are directly involved in regulating total in vivo poly(A) levels. RNase II is primarily responsible for degrading poly(A) tails associated with 23S rRNA, whereas PNPase is more effective in modulating the polyadenylation of the lpp and 16S rRNA transcripts. In contrast, RNase E appears to affect poly(A) levels indirectly through the generation of new 3' termini that serve as substrates for PAP I. In addition, whereas excess PNPase suppresses polyadenylation by more than 70%, the toxicity associated with increased poly(A) levels is not reduced. Conversely, toxicity is significantly reduced in the presence of excess RNase II. Overproduction of RNase E leads to increased polyadenylation and no reduction in toxicity.

Endoribonucleases↗

Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism.

To help understand the role of polyadenylation in Escherichia coli RNA metabolism, we constructed an IPTG-inducible pcnB [poly(A) polymerase I, PAP I] containing plasmid that permitted us to vary poly(A) levels without affecting cell growth or viability. Increased polyadenylation led to a decrease in the half-life of total pulse-labelled RNA along with decreased half-lives of the rpsO, trxA, lpp and ompA transcripts. In contrast, the transcripts for rne (RNase E) and pnp (polynucleotide phosphorylase, PNPase), enzymes involved in mRNA decay, were stabilized. rnb (RNase II) and rnc (RNase III) transcript levels were unaffected in the presence of increased polyadenylation. Long-term overproduction of PAP I led to slower growth and irreversible cell death. Differential display analysis showed that new RNA species were being polyadenylated after PAP I induction, including the mature 3'-terminus of 23S rRNA, a site that was not tailed in wild-type cells. Quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) demonstrated an almost 20-fold variation in the level of polyadenylation among three different transcripts and that PAP I accounted for between 94% and 98.6% of their poly(A) tails. Cloning and sequencing of cDNAs derived from lpp, 23S and 16S rRNA revealed that, during exponential growth, C and U residues were polymerized into poly(A) tails in a transcript-dependent manner.

Blotting, Southern↗

Residual polyadenylation in poly(A) polymerase I (pcnB ) mutants of Escherichia coli does not result from the activity encoded by the f310 gene.

As extracts of poly(A) polymerase I (PAP I) deficient strains of Escherichia coli appeared to contain considerable residual polyadenylating activity, efforts were undertaken to identify a second poly(A) polymerase. Recently, a gene (f310 ) encoding the putative second poly(A) polymerase was cloned and sequenced. Here we have tested the ability of the F310 protein to add poly(A) tails in vivo by measuring total poly(A) levels in both f310 mutants and strains that overproduce F310. In addition, we have visualized poly(A) tails and examined ColE1 plasmid copy number in various genetic backgrounds. We also carried out direct biochemical measurements of AMP incorporation, using cell extracts after amplification of F310. All the data obtained indicate that F310 is not a poly(A) polymerase. Although the presence of two potential ATP binding domains in the F310 protein may account for its apparent ATP binding activity, its true biochemical function remains to be identified. In addition, we show that the f310 gene is transcribed, almost exclusively, during stationary phase from a sigmas promoter.

Adenosine Triphosphate↗

Hypohaptoglobinaemia as a biochemical and epidemiological marker of falciparum malaria.

OBJECTIVES: The study was conducted in two parts to find out the usefulness of hypohaptoglobinemia (Hpo) as a biochemical and epidemiological marker of malaria. Part-I study was conducted in a Medical College Hospital to find out Hpo in malaria and the time required for normalization of Hpo. Part-II study was undertaken in two endemic areas of malaria to find out the prevalence of Hpo and haptoglobin index (HI) throughout the year along with other indicators of malaria. METHODS: In Part-I study, 172 patients of malaria constituting 58, 52 and 62 patients of cerebral malaria, uncomplicated falciparum malaria and vivax malaria, respectively were enrolled. Along with routine haematological and biochemical investigations, haptoglobin (Hp) estimation was done by endoplate haptoglobin test kit on admission and at 15 days interval for 3 months. In Part-II study Hp was estimated is 305 subjects in two endemic areas of malaria. HI, parasitic index, slide positivity rate (SPR), slide falciparum rate (SFR) were estimated throughout the year and HI was compared with these epidemiological markers. RESULTS: Hpo was present in 102 (92.7%) cases of falciparum malaria which was significantly more than vivax malaria and non-malarial fever. The normalisation of Hpo took about a month or more. The incidence of Hpo was 32.1% is endemic and 4.7% in nonendemic area of malaria. The HI varied between 12.4 to 25.2% throughout the year and was found to be a better marker than other classical markers of malaria. CONCLUSION: Hypohaptoglobinemia may be considered as a useful indirect indicator of falciparum malaria. HI can be used as an epidemiological maker which is better than classical markers of malaria used at present.

Adolescent↗

Mechanistic studies on the impact of transcription on sequence-specific termination of DNA replication and vice versa.

Since DNA replication and transcription often temporally and spatially overlap each other, the impact of one process on the other is of considerable interest. We have reported previously that transcription is impeded at the replication termini of Escherichia coli and Bacillus subtilis in a polar mode and that, when transcription is allowed to invade a replication terminus from the permissive direction, arrest of replication fork at the terminus is abrogated. In the present report, we have addressed four significant questions pertaining to the mechanism of transcription impedance by the replication terminator proteins. Is transcription arrested at the replication terminus or does RNA polymerase dissociate from the DNA causing authentic transcription termination? How does transcription cause abrogation of replication fork arrest at the terminus? Are the points of arrest of the replication fork and transcription the same or are these different? Are eukaryotic RNA polymerases also arrested at prokaryotic replication termini? Our results show that replication terminator proteins of E. coli and B. subtilis arrest but do not terminate transcription. Passage of an RNA transcript through the replication terminus causes the dissociation of the terminator protein from the terminus DNA, thus causing abrogation of replication fork arrest. DNA and RNA chain elongation are arrested at different locations on the terminator sites. Finally, although bacterial replication terminator proteins blocked yeast RNA polymerases in a polar fashion, a yeast transcription terminator protein (Reb1p) was unable to block T7 RNA polymerase and E. coli DnaB helicase.

Bacillus subtilis↗

Mitoxantrone, mitomycin-C, methotrexate combination chemotherapy with radiotherapy and/or surgery in stage III (T4B, NO-2, M0) breast cancer.

Results of primary surgery with or without locoregional radiotherapy (LRRT) are poor in stage III (T4b, NO-2, M0) breast cancer. Combination of mitoxantrone, mitomycin-c and methotrexate (MMM) has been reported to be as efficacious as doxorubicin based protocols with advantages of reduced nausea, vomiting, alopecia and cardiotoxicity. We tested MMM chemotherapy with LRRT and surgery in locally advanced breast cancer (LABC) with a view to assess response, survival, breast conservation, cost and toxicity. Fifty two previously untreated patients were given Mitoxantrone: 8 mg/m sq by infusion on days 1 and 21, Mitomycin-C: 8 mg/m sq by infusion on day 1 and Methotrexate: 35 mg/m sq i.v. on days 1 and 21. Cycles were repeated every 42 days. After 3 cycles LRRT was given if lump reduced to less than 2 cms. Otherwise patients were subjected to modified radical mastectomy (MRM) or radical mastectomy (RM). Following this 3 more cycles of chemotherapy were given. Patients with soft tissue, skin or heavy nodal involvement also received LRRT. Tamoxifen 20 mg daily was prescribed at the end of chemotherapy to postmenopausal patients. Complete/partial responses were seen in 5 and 26 patients, respectively after chemotherapy giving an overall response of 59.5%. Twenty four patients each had LRRT and MRM/RM. Responses could be significantly enhanced by LRRT/and or surgery. Nineteen out of 25 relapses were at distant sites. Breast conservation was achieved in 24/52 (46%) patients. Three year disease free and overall survival was 54% and 65%, respectively. There was 1 toxic death. Severe prolonged myelosuppresion was seen in those who also received LRRT. Mucositis, alopecia, nausea and vomiting were minor problems. Overall, combination was less expensive than doxorubicin based protocols.

Adult↗

Direct physical interaction between DnaG primase and DnaB helicase of Escherichia coli is necessary for optimal synthesis of primer RNA.

The primase DnaG of Escherichia coli requires the participation of the replicative helicase DnaB for optimal synthesis of primer RNA for lagging strand replication. However, previous studies had not determined whether the activation of the primase or its loading on the template was accomplished by a helicase-mediated structural alteration of the single-stranded DNA or by a direct physical interaction between the DnaB and the DnaG proteins. In this paper we present evidence supporting direct interaction between the two proteins. We have mapped the surfaces of interaction on both DnaG and DnaB and show further that mutations that reduce the physical interation also cause a significant reduction in primer synthesis. Thus, the physical interaction reported here appears to be physiologically significant.

Amino Acid Sequence↗

The replication initiator protein pi of the plasmid R6K specifically interacts with the host-encoded helicase DnaB.

The replication initiator protein pi of plasmid R6K is known to interact with the seven iterons of the gamma origin/enhancer and activate distant replication origins alpha and beta (ori alpha and ori beta) by pi-mediated DNA looping. Here we show that pi protein specifically interacts in vitro with the host-encoded helicase DnaB. The site of interaction of pi on DnaB has been localized to a 37-aa-long region located between amino acids 151 and 189 of DnaB. The surface of pi that interacts with DnaB has been mapped to the N-terminal region of the initiator protein between residues 1 and 116. The results suggest that during initiation of replication, the replicative helicase DnaB is first recruited to the gamma enhancer by the pi protein. In a subsequent step, the helicase probably gets delivered from ori gamma to ori alpha and ori beta by pi-mediated DNA looping.

Amino Acid Sequence↗

The relationship between sequence-specific termination of DNA replication and transcription.

In Escherichia coli and Bacillus subtilis replication fork arrest occurs in the terminus at sequence-specific sites by the binding of replication terminator proteins to the fork arrest sites. The protein-DNA complex causes polar arrest of the replication forks by inhibiting the activity of the replicative helicases in only one orientation of the terminus with respect to the replication origin. This activity has been named as polar contrahelicase. In this paper we report on a second novel activity of the terminator proteins of E.coli and B.subtilis, namely the ability of the proteins to block RNA chain elongation by several prokaryotic RNA polymerases in a polar mode. The replication terminator proteins ter and RTP of E.coli and B.subtilis respectively, impeded RNA chain elongation catalyzed by T7, SP6 and E.coli RNA polymerases in a polar mode at the replication arrest sites. The RNA chain anti-elongation and the contrahelicase activities were isopolar. Whereas one monomer of ter was necessary and sufficient to block RNA chain elongation, two interacting dimers of RTP were needed to effect the same blockage. The biological significance of the RNA chain anti-elongation activity is manifested in the functional inactivation of a replication arrest site by invasion of RNA chains from outside, and the consequent need to preserve replication arrest activity by restricting the passage of transcription through the terminus-terminator protein complex.

Bacillus subtilis↗

The contrahelicase activities of the replication terminator proteins of Escherichia coli and Bacillus subtilis are helicase-specific and impede both helicase translocation and authentic DNA unwinding.

Replication forks are arrested at sequence-specific replication termini primarily, perhaps exclusively, by polar arrest of helicase-catalyzed DNA unwinding by the terminator protein. The mechanism of this arrest is of considerable interest. This paper presents experimental evidence in support of four major points pertaining to termination of DNA replication. First, the replication terminator proteins of both Escherichia coli and Bacillus subtilis are helicase-specific contrahelicases, i.e. the proteins specifically impede the activities of helicases that are involved in symmetric DNA replication but not of those involved in conjugative DNA transfer and rolling circle replication. Second, the terminator protein (Ter) of E. coli blocks not only helicase translocation but also authentic DNA unwinding. Third, the replication terminator protein of Gram-positive B. subtilis is a polar contrahelicase of the primosomal helicase PriA of Gram-negative E. coli. Finally, the blockage of PriA-catalyzed DNA unwinding was abrogated by the passage of an RNA transcript through the replication terminator protein-terminus complex. These results are significant because of their relevance to the mechanistic aspects of replication termination.

Bacillus subtilis↗

Termination of DNA replication in vitro: requirement for stereospecific interaction between two dimers of the replication terminator protein of Bacillus subtilis and with the terminator site to elicit polar contrahelicase and fork impedance.

The termination of DNA replication at a sequence-specific replication terminus in Bacillus subtilis is catalyzed by a dimeric replication terminator protein (RTP) of subunit mol. wt 14,500. RTP has become an attractive protein with which to study the molecular mechanism of termination because its crystal structure has now been solved and the previous lack of an in vitro replication system has been largely overcome by our discovery that the protein terminates replication in vivo and in vitro in the well-studied Gram-negative Escherichia coli system. We have exploited the surrogate in vitro system to show that RTP acts as a polar contrahelicase to DnaB helicase of E. coli only when two RTP dimers are bound co-operatively to overlapping core and auxiliary sequences comprising the terminus. A core sequence by itself binds one dimer of RTP, but elicits no contrahelicase activity. Binding of two RTP dimers to a tandem head-to-tail core repeat also elicits no contrahelicase activity, thus suggesting that a specific stereochemical interaction between two RTP dimers and with the terminator site is essential for termination. RTP blocks unwinding of DNA substrates containing heteroduplex regions that include the terminus and are in the size range of approximately 50 to > 1000 bp in length. Thus, the protein blocks authentic helicase-catalyzed unwinding rather than just the translocation of the helicase on DNA.

Bacillus subtilis↗

The replication terminator protein of the gram-positive bacterium Bacillus subtilis functions as a polar contrahelicase in gram-negative Escherichia coli.

The replication terminator protein (RTP) of Bacillus subtilis is a dimer with a monomeric molecular mass of 14.5 kDa. The protein terminates DNA replication at a specific binding site. Although the protein has been crystallized and its crystal structure has been solved, the lack of an in vitro replication system in B. subtilis has been a serious impediment to the analysis of the mechanism of action of this protein. We have discovered that the protein is functional in the Gram-negative bacterium Escherichia coli in vivo and in vitro. RTP blocked replication forks initiated from a ColE1 replication origin at the cognate DNA-binding site (BS3) in a polar mode. The protein did not block rolling circle replication initiated from the pT181 origin in cell extracts of Staphylococcus aureus. RTP antagonized the helicase activity of DnaB but not that of helicase II of E. coli. Thus, RTP functioned as a polar contrahelicase blocking a helicase that participates in symmetric DNA replication but it did not impede rolling circle replication nor the action of a helicase involved in DNA repair.

Adenosine Triphosphatases↗

A novel way to generate nonspecifically radiolabeled proteins for use as molecular-weight markers.

A method for labeling proteins using radioactive nucleotides in the presence of divalent cations such as Cu2+, Zn2+ and Cd2+ is described. Small amounts of marker proteins can be rapidly labeled using the method and they can be used for molecular-weight determination of radioactive proteins of unknown molecular weights, as for example, any protein labeled with 35S-methionine in vivo or any protein radiolabeled by 32P in protein phosphorylation experiments. The gels in which the labeled markers and the proteins of unknown molecular weight are electrophoresed could be directly exposed to X-ray films and comparisons made from a single autoradiogram, avoiding a two step procedure of Coomassie blue staining followed by autoradiography and aligning of the two sets of bands. This metal-ion-mediated labeling of proteins described in the present communication is not by any site-specific interaction of the nucleotide with the proteins and the protein is denatured after the complex formation. The adducts, once formed, are stable under conditions of SDS-PAGE or EDTA treatment. It is suggested that proteins labeled under conditions described in this communication are ternary complexes involving aromatic residues of the proteins, nucleotides and the divalent cations.

Cadmium↗

Effect of a mercurial ayurvedic drug (kajyoli) on the ion concentration and respiratory activity in brain, liver and kidney of the albino rat.

The effect of a mercurial ayurvedic drug (kajyoli), on the concentration of Na+, K+ and Ca2+ in rat liver, kidney and brain, and on the respiratory activity of these tissues is reported. The doses used were 20 mg and 40 mg X day-1 X kg-1 body wt. daily for 30 days, the lower level being equivalent to the human dose. A marked dose-dependent decrease in respiratory activity occurred in the three tissues. The only significant changes seen in the ion concentration were a decrease in Na+ at the higher dose level in the kidney and a dose-dependent decrease in Ca2+ in the liver.

Animals↗