Nutrient dynamics and seasonal variation of phytoplankton assemblages in the coastal waters of southwest Bay of Bengal.

In order to understand the phytoplankton community structure and its relationship with the environmental variables in the near shore waters of Kalpakkam, east coast of India, observations were carried out during 2008-2009. Phytoplankton population was comprised of 219 species, and the density was higher during the southwest monsoon (SWM) and inter-monsoon seasons than that of north east monsoon (NEM) season. The nutrient status on a temporal and spatial scale indicated the impact of point sources carrying anthropogenic runoff. Comparison of ambient nutrient ratios with the Redfield ratio (N/P/Si = 16:1:16) showed a clear temporal variation in the factors that regulate the phytoplankton growth. SWM and inter-monsoon season was evident to have an acute N-limitation of algal growth (~76%) whereas P-limitation was encountered during the NEM season (~75%). Interestingly, a sizable population of cyanobacteria (Trichodesmium erythraeum) were noticed during NEM season when there was an exponential increase in nitrogen concentration, probably due to nitrogen fixation. No significant impact of temperature on phytoplankton proliferation was observed in situ during the study period.

Larval abundance and its relation to macrofouling settlement pattern in the coastal waters of Kalpakkam, southeastern part of India.

The present work revealed that salinity, water temperature, and food availability were the most crucial factors affecting the abundance of larvae and their settlement as macrofouling community in the coastal waters of Kalpakkam. Quantitative as well as qualitative results showed that late post-monsoon (April-May) and pre-monsoon (June-September) periods were found to be suitable periods for larval growth, development, and survival to adult stages for most of the organisms. Clustering of physico-chemical and biological (including larval and adult availability) data yielded two major clusters; one formed by northeast (NE) monsoon months (October-January) and the other by post-monsoon/summer (February-May) months, whereas; pre-monsoon months (June-September) were distributed between these two clusters. Among all the major macrofouler groups, only bivalves established a successful relationship between its larval abundance and adult settlement. Principal component analysis indicated good associations of bivalve larvae with polychaete larvae and adult bivalves with adult barnacles. However, biotic relation between ascidians and bryozoans was observed both in the larval as well as adult community.

Profilin oligomerization and its effect on poly (L-proline) binding and phosphorylation.

Profilin is a cytoskeletal protein that interacts specifically with actin, phosphoinositides and poly (l-proline). Experimental results and in silico studies revealed that profilin exists as dimer and tetramer. Profilin oligomers possess weak affinity to poly (l-proline) due to unavailability of binding sites in dimers and tetramers. Phosphorylation studies indicate that profilin dimers are not phosphorylated while teramers are preferentially phosphorylated over monomers. In silico studies revealed that PKC phosphorylation site, S137 is buried in dimer while it is accessible in tetramer.

Escherichia coli RNA polymerase mutations located near the upstream edge of an RNA:DNA hybrid and the beginning of the RNA-exit channel are defective for transcription antitermination by the N protein from lambdoid phage H-19B.

Transcription antitermination is an important mechanism that can control regulation of gene expression. The N protein of lambdoid phages modifies the transcription elongation complex (EC) and helps it to overcome downstream terminators. In this modified EC, the C-terminal domain of N makes specific interactions with RNA polymerase (RNAP). The interacting surface of RNAP for N is unknown. Here, we report five mutations in the beta (G1045D) and beta' (P251S, P254L, R270C and G336S) subunits of RNAP that are specifically defective for antitermination by N protein of the lambdoid phage, H-19B. A mutation in the C-terminal domain of N, L108F, suppresses the defect of beta'-P254L. Purified mutant holoenzymes exhibit less processive antitermination. The amino acid substitutions in the mutant RNAPs cluster very close to the RNA:DNA hybrid at the beginning of the RNA-exit channel of the EC. We suggest that the action of H-19B N is exerted through the region defined by these amino acids. Wild-type N stabilizes the EC at terminator sites and in this modified EC a part of the terminator hairpin may form but appears to be unstable. We propose that the action of N close to the active center alters the RNAP-nucleic acid interactions around the RNA:DNA hybrid, which impairs proper folding of the terminator hairpin or stabilizes the weak RNA:DNA hybrid, or both.

Design, synthesis, and evaluation of mixed imine-amine pyrrolobenzodiazepine dimers with efficient DNA binding affinity and potent cytotoxicity.

Synthesis of mixed imine-amine pyrrolobenzodiazepine (PBD) dimers that are comprised of DC-81 and secondary amine (N10) of DC-81 subunits tethered to their C8 positions through alkanedioxy linkers (comprised of three and five carbons) is described. These noncross-linking unsymmetrical molecules exhibit significant DNA minor groove binding ability and one of them 5b linked through the pentanedioxy chain exhibits efficient DNA binding ability (DeltaTm=11.0 degrees C) when compared to naturally occurring DC-81, 1 (DeltaTm=0.7 degrees C). The imine-amine PBD dimers exhibit promising in vitro antitumor activity in a number of human cancer cell lines.

Altered gene expression pattern in cultured human breast cancer cells treated with hepatocyte growth factor/scatter factor in the setting of DNA damage.

The cytokine hepatocyte growth factor/scatter factor (HGF/SF) protects epithelial and cancer cells against DNA-damaging agents via a pathway involving signaling from c-Met --> phosphatidylinositol-3- kinase --> c-Akt. However, the downstream alterations in gene expression resulting from this pathway have not been established. On the basis of cDNA microarray and semiquantitative RT-PCR assays, we found that MDA-MB-453 human breast cancer cells preincubated with HGF/SF and then exposed to Adriamycin (ADR), a DNA topoisomerase II inhibitor, exhibit an altered pattern of gene expression, as compared with cells treated with ADR only. [HGF/SF+ADR]-treated cells showed altered expression of genes involved in the DNA damage response, cell cycle regulation, signal transduction, metabolism, and development. Some of these alterations suggest mechanisms by which HGF/SF may exert its protective activity, e.g., up-regulation of polycystic kidney disease-1 (a survival-promoting component of cadherin-catenin complexes), down-regulation of 51C (an inositol polyphosphate-5-phosphatase), and down-regulation of TOPBP1 (a topoisomerase IIB binding protein). We showed that enforced expression of the cdc42-interacting protein CIP4, a cytoskeleton-associated protein for which expression was decreased in [HGF/SF+ADR]-treated cells, inhibited HGF/SF-mediated protection against ADR. The cDNA microarray approach may open up new avenues for investigation of the DNA damage response and its regulation by HGF/SF.

Differential gene expression associated with tumorigenicity of cultured green turtle fibropapilloma-derived fibroblasts.

Fibroblast cell lines derived from normal skin and experimentally induced fibropapillomas of green turtles (Chelonia mydas), were propagated in vitro and tested for tumorigenicity in immunodeficient mice. Differential display RT-PCR was used to identify differences in messenger RNA expression between normal and tumorigenic fibropapillomatosis (FP)-derived fibroblasts from the same individual. Four unique products that were apparently overexpresed in FP and three that were apparently underexpressed were cloned and sequenced. Differential expression was confirmed for three products by Northern blotting. Two overexpressed products showed extensive sequence matches to the known mammalian cellular genes, beta-hexosaminidase and chain termination factor. The product that was underexpressed in FP showed homology with mammalian thrombospondin, a known tumor-suppressor gene and an inhibitor of angiogenesis. All of the partial gene sequences identified are novel and will require full length cDNA sequencing to further analyze their identities. These results, however, provide the foundation for further investigation to determine the role of each of these gene products in FP pathogenesis and cellular transformation. The potential for some of these products to serve as biomarkers for FP is discussed.

Cell lines from the same cervical carcinoma but with different radiosensitivities exhibit different cDNA microarray patterns of gene expression.

Combining chemotherapy with radiotherapy has improved the cure rate among patients with cancers of the cervix. Although one-half to two-thirds of the patients can be cured by radiation alone, such patients cannot be identified at present and must therefore suffer the burden of chemotherapy. Our long-range goal is to identify those cervical cancers that are radiosensitive and could be cured by radiotherapy alone. The advent of methods that permit the simultaneous analysis of expression patterns of thousands of genes, make it feasible to attempt to identify the molecular events related to radiosensitivity and the associated regulatory pathways. We hypothesize that the sensitivity of tumor cells to ionizing radiation (IR) is determined by the level of expression of specific genes that may be identified with the aid of cDNA microarrays. As the first step in testing this hypothesis, we determined the gene expression differences between two cell lines exhibiting different degrees of radiosensitivity. These were derived from the same tumor prior to treatment from a patient with squamous cell carcinoma of the cervix. The mRNA from these cells was subjected to cDNA analysis on a microarray of 5,776 known genes and ESTs. The expression of 52 genes of the total of 5,776 was elevated (maximum 4.1 fold) in the radioresistant cells as compared to the radiosensitive cells. Ten of the 52 sequences are known genes while 42 are ESTs. Conversely, the expression of 18 genes was elevated in the sensitive cells as compared to the resistant cells. Seven of these 18 are known genes while eleven are ESTs. Among the genes expressed differentially between the resistant and sensitive cells were several known to be associated with response to IR and many more genes and ESTs that had not previously been reported to be related to radiosensitivity. The genes that showed the greatest overexpression in the radioresistant cell line were metal-regulatory transcription factor-1, cytochrome P450 CYP1B1, adenomatosis polyposis coli, translation elongation factor-1, cytochrome-c oxidase, whereas in the sensitive cell line, transcription factor NF-kappa-B, metalloproteinase inhibitor-1 precursor, superoxide dismutase-2, insulin-like growth factor binding protein-3, guanine nucleotide-binding protein and transforming growth factor beta-induced protein were overexpressed.

Effect of structure on the excretion of steroidal acids in human urine and their potential colorimetric assay as 17-oxogenic steroids.

Following the oral administration of tritiated coricosterone, cortisol, deoxycorticosterone and progesterone to human subjects, 14.9%, 12.8%, 3.4% and 2.1% of the dose was recovered in the acidic metabolite fraction of 48 h urines after conventional hydrolysis and solvent partition. Neutral and acidic 17-oxogenic steroids (17-OGS) excreted in 24 h urines were also measured with the Zimmermann color reaction. The acidic 17-IGS accounted for 14.1%, 16.4% and 12.1% of the fractionated 17-OGS in the urines of normal and pregnant females and normal males respectively. From structural considerations, it was concluded that only 17-hydroxylated steroidal acids, with a 20-hydroxy-21-oic acid side chain and derived predominantly from cortisol, would be estimated as 17-OGS after oxidation with sodium periodate. 17-Dexy steroidal acids resemble the neutral 17-deoxycorticosteroids in undergoing side chain oxication to 17-aldehydes which do not form Zimmermann chromogens. The excretion of both neutral and acidic 17-OGS was suppressible with dexamethasone administration.