Replication arrests during a single round of replication of the Escherichia coli chromosome in the absence of DnaC activity

We used a flow cytometric assay to determine the frequency of replication fork arrests during a round of chromosome replication in Escherichia coli. After synchronized initiation from oriC in a dnaC(Ts) strain, non-permissive conditions were imposed, such that active DnaC was not available during elongation. Under these conditions, about 18% of the cells failed to complete chromosome replication. The sites of replication arrests were random and occurred on either arm of the bidirectionally replicating chromosome, as stalled forks accumulated at the terminus from both directions. The forks at the terminal Ter sites disappeared in the absence of Tus protein, as the active forks could then pass through the terminus to reach the arrest site, and the unfinished rounds of replication would be completed without DnaC. In a dnaC2(Ts)rep double mutant, almost all cells failed to complete chromosome replication in the absence of DnaC activity. As inactivation of Rep helicase (the rep gene product) has been shown to cause frequent replication arrests inducing double-strand breaks (DSBs) in a replicating chromosome, DnaC activity appears to be essential for replication restart from DSBs during elongation.

High affinity association of myo-inositol trisphosphates with phytase and its effect upon the catalytic potential of the enzyme

A neutral phytase from germinating mung bean (Vigna radiata) seeds dephosphorylates myo-inositol hexakisphosphate sequentially to myo-inositol. The enzyme also binds with higher affinity to myo-inositol trisphosphates (1,4,5), (2,4,5), and (1,3,4) isomers without catalysis. The high affinity complex elicits Ca(2+) mobilization in vitro from microsomes/vacuoles via the formation of a ternary complex with the receptor for Ins(1,4,5)P(3). As a sequel to our previous report, we have carried out a detailed characterization of the two sites and examined the mutual interactions between them. Presaturation of the high affinity site leads to an increase in the affinity of the enzyme for phytic acid and its rate of dephosphorylation as well. From the products of limited tryptic cleavage of phytase, two peptides, each with one activity, have been isolated. The larger peptide ( approximately 66 kDa) contains the catalytic site, and the smaller peptide ( approximately 5 kDa) has the high affinity myo-inositol trisphosphate-binding site. The interaction between the dual activities of phytase has been observed also at the level of the two peptides. A sequence homology search using N-terminal 12 amino acid residues of the 5-kDa fragment has revealed significant homology with the Homer class of proteins implicated in signaling pathways involving metabotropic glutamate receptor and myo-inositol 1,4,5-trisphosphate receptor. These results indicate a second role of phytase in Ca(2+) mobilization during germination of mung been seed via a salvage pathway that involves allosteric activation by myo-inositol trisphosphate.

Coverage of Maternal Care Services in the state of West Bengal

Evaluation of the Coverage of Maternal Care Services was conducted during the year 1999 in the entire State of West Bengal, Urban poor localities of randomly selected three Municipal Corporation areas and 'high-risk' urban wards or villages of West Bengal that had reported AFP cases in 1998. It was observed that mothers who had three or more antenatal check-ups varied between 54% to 82% in different study areas. Tetanus Toxoid coverage varied between 83.5% to 93.4% being lowest in high-risk areas. Only a very small section of mothers (12.7% to 23.7%) consumed 100 or more Iron and Folic acid tablets during pregnancy. 'Danger Signs' of pregnancy were informed to only 21.1% to 38.2% of the pregnant mothers. Proportion of home deliveries varied between 16.7% (Calcutta) to as high as 72.7% (high-risk areas). Deliveries conducted by untrained personnel were 60.8% in high risk areas, 38.1% in State clusters and between 14.2% to 29.4% in the three urban areas. Vast majority of mothers (78.8% to 88.4%) received no post-natal check-up.

RecA-mediated rescue of Escherichia coli strains with replication forks arrested at the terminus

The recombinational rescue of chromosome replication was investigated in Escherichia coli strains with the unidirectional origin oriR1, from the plasmid R1, integrated within oriC in clockwise (intR1(CW)) or counterclockwise (intR1(CC)) orientations. Only the intR1(CC) strain, with replication forks arrested at the terminus, required RecA for survival. Unlike the strains with RecA-dependent replication known so far, the intR1(CC) strain did not require RecBCD, RecF, RecG, RecJ, RuvAB, or SOS activation for viability. The overall levels of degradation of replicating chromosomes caused by inactivation of RecA were similar in oriC and intR1(CC) strains. In the intR1(CC) strain, RecA was also needed to maintain the integrity of the chromosome when the unidirectional replication forks were blocked at the terminus. This was consistent with suppression of the RecA dependence of the intR1(CC) strain by inactivating Tus, the protein needed to block replication forks at Ter sites. Thus, RecA is essential during asymmetric chromosome replication for the stable maintenance of the forks arrested at the terminus and for their eventual passage across the termination barrier(s) independently of the SOS and some of the major recombination pathways.

Insulin alone can lead to a withdrawal of meiotic arrest in the carp oocyte

Meiotic arrest of oocyte in an Indian carp, Labeo rohita Ham. has been found for the first time to be withdrawn by insulin only. Addition of insulin to oocytes in vitro caused germinal vesicle breakdown (GVBD), one of the first visual markers to determine initiation of the final maturational process. Under the influence of insulin the germinal vesicle (GV) of the oocyte migrated towards the animal pole, reached the micropyle and then dissolved (GVBD). By using different concentrations of insulin i.e., 0.063, 0.63, 6.3 and 12.6 mM, optimum amount required was found to be 6.3 mM. Induction of GVBD by insulin could be blocked by cycloheximide (Chx), a translation inhibitor, while actinomycin D (AcD) had no effect suggesting non-involvement of transcriptional activity in this process. Addition of the maturation-inducing steroid 17alpha,20beta-dihydroxy-4-pregnen-3-one (DHP) stimulated (P<0.01) GVBD of carp oocytes and its combination with insulin showed an additive effect. Gonadotropin (GtH) caused GVBD but its effect was greatly augmented by insulin. Our results demonstrate that not only can insulin alone induce GVBD in carp oocytes, but it also augments the stimulatory effect of DHP or IGF-I or GtH on GVBD. This information will be important in hormonal manipulation during induced breeding of carp.

Chelators for radioimmunotherapy: I. NMR and ab initio calculation studies on 1,4,7,10-tetra(carboxyethyl)-1,4,7,10-tetraazacyclododecane (DO4Pr) and 1,4,7-tris(carboxymethyl)-10-(carboxyethyl)-1,4,7,10-tetraazacyclododecane (DO3A1Pr)

This work describes the modification of the chelating agent 1,4,7,10-tetraazacyclododecane-N,N',N' ',N' "-tetraacetic acid (DOTA) to improve the rate of metal loading for radioimmunotherapy applications. Previous ab initio calculations predicted that the compounds 1,4,7,10-tetra(carboxyethyl)-1,4,7,10-tetraazacyclododecane (DO4Pr) and 1,4,7-tris(carboxymethyl)-10-(carboxyethyl)-1,4,7,10-tetraazacyclododecane (DO3A1Pr) have a ca. 2000-fold improvement in yttrium metal loading rates compared to those of DOTA (Jang, Y. H.; Blanco, M.; Dasgupta, S.; Keire, D. A.; Shively, J. E.; Goddard, W. A., III. J. Am. Chem. Soc. 1999, 121, 6142-6151). In this study, we report the synthesis, purification, (1)H-NMR chemical shift assignments, pK(a) values, metal loading rate measurements, and additional ab initio calculations of these two compounds. The yttrium loading rates of DO3A1Pr are approximately twice those of DOTA, at pH 4.6 and 37 degrees C. The NMR data indicates that the DO4Pr analogue forms a stable type I complex but does not form a type II complex. The new ab initio calculations performed on DO4Pr and DO3A1Pr indicate that the rate-determining step is the deprotonation of the first macrocycle amine proton, not the second proton as assumed in the previous calculations. The new calculations predict an improvement in the rate of metal loading that more closely matches the experimentally observed change in the rate.

Effect of addition of proton carriers in culture medium on growth and secretion of hybridoma cell line OKT3

Monoclonal antibodies (MAb) constitute the centre of all in-vitro diagnostic measures and almost all in-vivo therapeutic manoeuvres now. Production emphasis for these antibodies is having a current shift from animal-based large-scale culture to in-vitro bioreactor-based high-density culture. One of the major difficulties in high-density culture is end-metabolite accumulation in batch and fed-batch cultures in the forms of H+, NH4+ etc.. thereby reducing cellular growth and secretions. In the present study, effects of added proton carries--NAD and NADP--over and above the metabolic pools of the molecules, were examined on the cellular growth and secretion kinetics. Although NADP fortification showed a remarkable improvement in cellular growth (time dependent 200-300% improvements compared to controls) and size, cumulative MAb titre was better with NAD fortification. Combined additional loads of the proton carriers would be interesting to study in high density culture conditions.

Microsatellite instability in squamous cell carcinoma of head and neck from the Indian patient population

Genomic instability in simple repeated sequences has been observed in several human cancers. We have analyzed 50 squamous cell carcinomas of the head and neck (SCCHN) and 5 pre-malignant severe dysplastic tissues from Indian patient populations for microsatellite instability in 18 different loci spread over eight different chromosomes. Among the tumors analyzed, 45% exhibited instability at two or more loci, and 15% exhibited instability at 40% of the markers tested. Similar analysis of SCCHN tumors from other populations (British, American and French) showed much less frequency of instability. SCCHN tumors in the present study did not show any instability in the mononucleotide repeat sequences. There is also a clear distinction in the nature of the instability in these tumors in comparison with colorectal tumors. These results suggest that the underlying mechanism generating this type of instability is different from those reported for colorectal tumors.

Chromatographic resolution and quantitative assay of CNS tissue sphingoids and sphingolipids

Quantitative separation of ceramide, sphingoids (dihydrosphingosine, sphingosine, psychosine), and glycosphingolipids as individual fractions was achieved with silicic acid, Dowex column chromatography, and specific solvent mixtures that have not been previously described. Purified ceramide, resolved as a single band, was assayed by thin-layer chromatography (TLC) followed by gas chromatography (GC) and high performance liquid chromatography (HPLC). Sphingoids, purified by Dowex, were assayed by GC and HPLC without mild alkaline hydrolysis, which reduces the yield by interfering with the free amino group of psychosine and dihydrosphingosine. Several less polar (than cerebroside) alkali-/acid-labile glycosphingolipids that elute with galactosylceramide were also identified. Neutral and acidic glycosphingolipids, quantitatively recovered and purified to homogeneity, were resolved by TLC. We used these techniques to determine sphingolipids and sphingoids of vertebrate central nervous system (CNS) tissue, using as little as 30-50 mg (wet weight) of tissue. In addition, phosphatidylcholine and sphingomyelin, relevant to ceramide metabolism, were quantitatively recovered in pure form and resolved by TLC. This method, used to study CNS sphingolipid content, may well be applicable to determine the sphingolipid composition of other tissues and cell culture, but further experiments are necessary to ascertain this.

Effect of myo-inositol(1,4,5)trisphosphate on the hydrolysis of phytic acid by phytase

Phytase is a monomeric enzyme of molecular mass 160 kDa which catalyzes the hydrolysis of phytic acid (D-myo inositol hexakisphosphate, InsP6) in a stepwise manner to myo-inositol. The enzyme-InsPn (n = 1-6) interaction at the catalytic site has a dissociation constant in the micro molar range. There also exists in the enzyme, a non-catalytic site specific for InsP3 with dissociation constant in the nano molar range. We have probed the effect of the high affinity InsP3 binding on the dissociation constant (Kd) of the phytase-InsP6 interaction and the kinetics of hydrolysis. These studies demonstrate the effect exerted by the high affinity InsP3 binding on the catalytic site of the enzyme.

Declining trend in routine UIP coverage

Routine UIP coverage status in the state of West Bengal and three selected Municipal Corporation areas (Calcutta, Howrah and Siliguri) were studied during 1997-98 and 1998-99. Also, UIP coverage status in the 'high risk' areas of the State (areas which reported Polio cases during 1998) was studied during 1998-99. UIP coverage in the state of West Bengal was only 54.3% in 1997-98, which further declined to 48.1% in 1998-99. In the three urban areas, UIP coverage ranged between 57.3%-70.9% in 1997-98, which further declined to 29.6%-47.1% in 1998-99. Antigenwise coverage revealed very poor performance with DPT3, OPV3, and Measles in 1997-98 and further decline in 1998-99. Dropout rate was also very high. In 1998-99 drop-out rate ranged between 30.1% to 54.2% in different studied areas. Some other studies suggested that PPI activities, which are very visible and targetted programme, may adversely affect routine UIP services. There is urgent need for further probing to identify the reasons for such poor state of affairs, keeping PPI angle in mind and to initiate remedial measure urgently.

Partitioning of the Escherichia coli chromosome: superhelicity and condensation

Segregation in Escherichia coli, the process of separating the replicated chromosomes into daughter progeny cells, seems to start long before the duplication of the genome reaches completion. Soon after initiation in mid-cell region, the daughter oriCs rapidly move apart to fixed positions inside the cell (quarter length positions from each pole) and are anchored there by yet unknown mechanism(s). As replication proceeds, the rest of the chromosome is sequentially unwound and then refolded. At termination, the two sister chromosomes are unlinked by decatenation and separated by supercoiling and/or condensation. Muk and Seq proteins are involved in different stages of this replication-cum-partition process and thus can be categorized as important partition proteins along with topoisomerases. E. coli strains, lacking mukB or seqA functions, are defective in segregation and cell division. The nucleoids in these mutant strains exhibit altered condensation and superhelicity as can be demonstrated by sedimentation analysis and by fluorescence microscopy. As the supercoiling of an extrachromosomal element (a plasmid DNA) was also influenced by the mukB and seqA mutations we concluded that the MukB and SeqA proteins are possibly involved in maintaining the general supercoiling activity in the cell. The segregation of E. coli chromosome might therefore be predominantly driven by factors that operate by affecting the superhelicity and condensation of the nucleoid (MukB, SeqA, topoisomerases and additional unknown proteins). A picture thus emerges in which replication and partition are no longer compartmentalized into separable stages with clear gaps (S and M phases in eukaryotes) but are parallel processes that proceed concomitantly through a cell cycle continuum.

Escherichia coli cell cycle control genes affect chromosome superhelicity

We have used ethidium bromide titration for direct measurement of the changes in the negative supercoiling of Escherichia coli chromosome caused by mutations inactivating the cell cycle functions mukB and seqA. The amounts of the intercalative agent required to relax the supercoiled chromosome in mukB and seqA mutants were lower and higher, respectively, than for the wild-type parent, confirming that these cell cycle genes modulate the topology of the E. coli chromosome. Plasmid superhelicity measured in these mutant strains showed similar effects albeit of reduced magnitude. As the effects of mukB and seqA mutations were not restricted to the chromosome alone, MukB and SeqA proteins possibly interact with factors involved in the maintenance of intracellular DNA topology. To our knowledge, this is the first direct demonstration of the influence of mukB and seqA genes on the superhelicity of the E. coli chromosome.

New genes with old modus operandi. The connection between supercoiling and partitioning of DNA in Escherichia coli

The process of partitioning bacterial sister chromosomes into daughter cells seems to be distinct from chromatid segregation during eukaryotic mitosis. In Escherichia coli, partitioning starts soon after initiation of replication, when the two newly replicated oriCs move from the cell centre to quarter positions within the cell. As replication proceeds, domains of the compact, supercoiled chromosome are locally decondensed ahead of the replication fork. The nascent daughter chromosomes are recondensed and moved apart through the concerted activities of topoisomerases and the SeqA (sequestration) and MukB (chromosome condensation) proteins, all of which modulate nucleoid superhelicity. Thus, genes involved in chromosome topology, once set aside as 'red herrings' in the search for 'true' partition functions, are again recognized as being important for chromosome partitioning in E. coli.

Role of the mukB gene in chromosome and plasmid partition in Escherichia coli

The intracellular locations of oriC and oriR1, the replication origins of the chromosome and plasmid R1, respectively, were visualized by fluorescence in situ hybridization (FISH) in exponentially growing populations of Escherichia coli. The locations of oriC and oriR1 (from a Par+ R1 plasmid) were unique and different in the wild-type host. In a mukB mutant, the positions were perturbed for both origins. The position of oriR1 from a plasmid with active partition (Par+) in the mukB host was as randomized as that of oriR1 from the Par- plasmid in a wild-type host. However, this mukB-induced randomization did not result in unstable inheritance of the Par+ plasmid, as measured by the conventional segregation assay. This might result from the preferential association of the Par+ plasmid with the bigger, decondensed nucleoid-containing daughters during cell division of MukB- cells, whereas the Par- plasmids were distributed at random and were lost by frequently ending up in anucleate cells.

The origins and nature of the cognitive paradigm: an overview

Although cognitive science, the 'science of mind' is generally regarded as of relatively recent vintage, its origins can actually be traced back to ideas from the 1930s. The purpose of this paper is to offer a view of the essential nature of what has come to be called the cognitive paradigm--the framework around which cognitive science has come to be constructed--and about its origins and development. Of particular note is the interdisciplinarity of the field, with its strong links to psychology, linguistics, neurobiology, computer science and philosophy. As will be explained below, this interdisciplinary character is rooted in the historical development of the science itself, and can only be understood in such a context. Thus, the present article is strongly historical in spirit and content.

Quantum hopping models for kinetic processes

We propose that a quantum operator, apart from representing quantum dynamics, may also represent a dynamical (steady-state) situation of a classical system. We consider a Hamiltonian that describes hopping of single (spinless, noninteracting) bosons to nearest-neighbor sites in a hypercubic lattice and find exactly the mass distribution (in arbitrary dimension) for the ground state and the first excited state. The density shows a peak at a mass equal to the density. A variant of this Hamiltonian is shown to have an exponential mass distribution (in the ground state) that is identical with an analogous classical model.

Effect of cationic amino acid, L-lysine and its polymers on the growth and secretion of hybridoma cell line OKT-3

Apart from their pivotal roles in anabolic protein synthesis, cationic amino acids, particularly, L-lysine HCl and its oligomers, up to molecular weight 1000, showed a remarkable property of cellular growth stimulation both in vitro and in vivo. L- and D-Lysine HCl, at a maximal stimulatory concentration of 7 microg/mL of added load of the amino acid, supported a characteristic time-scaled cellular expansion in vitro, and L-lysine-mediated cell expansion in batch cultures always showed a stimulation index (S.I.) ranging up to approximately 35, compared with the matched control populations. Variable S.I. was possibly due to factors such as seeding density, type of media additives, number of passages the cells have undergone before being stimulated, etc. Beyond and before maximal stimulatory concentration of the amino acid, there is a sharp decline in the cellular growth-promoting activity of monomeric L-lysine HCl in vitro, thereby showing a clear concentration window for maximum cellular growth promotion. While the essential amino acid does not have any dedicated cell surface receptor, the monomeric and oligomeric amino acid molecule(s) possibly mediates the serum-derived growth factor-receptor binding on the cell membrane by having two cationic charge centres at two ends of the molecule. Beyond a cutoff molecular weight of 1000, oligomeric lysines did not show any positive effects on either cell division and secretion.

Plasmid R1 is present as clusters in the cells of Escherichia coli

Fluorescence microscopy was used to determine the location(s) of the replication origin of plasmid R1 in exponentially growing cells of Escherichia coli. The number of oriR1 foci per cell was smaller than the number of R1 copies per cell and was found to be the same for a copA mutant of R1 and for the wild-type plasmid. The intensities of individual foci were stronger for the cop mutant than for the wild type. We interpreted these results to imply that the plasmid DNA molecules were localized in small groups/clusters, a result that seems contrary to the earlier observations that plasmid R1 replicates randomly and segregates as a single-copy unit. The implications for the quantitative behavior of plasmid R1 in stability, incompatibility tests, replication, and partition experiments are discussed.

Troger's base molecular scaffolds in dicarboxylic acid recognition

Artificial receptors (1-5) have been designed and synthesized from simple precursors. The chain length selectivity studies of dicarboxylic acids within the cavities of new fluorescent Troger's base molecular frameworks (1-3) have been carried out with a critical examination of their role of rigidity as well as flexibility in selective binding in comparison to receptor 5. The chiral resolution of the racemic Troger's base receptors (1 and 2) by chiral recognition with (+)- camphoric acid using hydrogen-bonding interactions has been studied.