Anthropogenic disturbances and plant biodiversity in forests of Uttaranchal,central Himalaya

Eight forest types varying in disturbance frequencies were identified along an elevational gradient in Uttaranchal, central Himalaya. Low elevation forests were close to human habitation and had high disturbance frequency, while high elevation forests were situated far from the human habitation and had low disturbance. The dominant tree species at low elevation were Pinus roxburghii and Quercus leucotrichophora, while Q. floribunda and Q. semecarpifolia dominated the high elevation forests. Pyracantha crenulata was the shrub present in all the forests except in Q. semecarpifolia forest and Anaphalis contorta, a herb species, was present in all the forests. Disturbance decreased the dominance of single species and increased the plant biodiversity by mixing species of different successional status. Species richness and diversity for all the vegetation layers were higher in low elevation–high disturbance forests. Mean tree density decreased from high to moderate and increased in low disturbance. The shrub density decreased from high to low disturbance while the reverse occured for herbs. High proportion of early successional species in disturbed forests indicated that disturbance induces succession. The mean number of young individuals increasing from high to low disturbance indicates that disturbance adversely affects regeneration. But, however, the high number of young individuals of Coriaria nepalensis, a small non-leguminous nitrogen fixing tree, in disturbed forests shows that the forest is regenerating. This species could be helpful in the re-establishment of original vegetation through triggering the regeneration of these forests. High elevation–low disturbed forests separated from low elevation–high disturbed forests. Forest type and elevation may have more influence on tree richness while shrub and herb richness may be more sensitive to disturbance and forest types.     

Cytomorphologic and morphometric limitations of the assessment of atypia in fibroadenoma of the breast

OBJECTIVE: To investigate the relevance of nuclear morphometry in separating the categories of "fibroadenoma" and "fibroadenoma with atypia." STUDY DESIGN: Thirty consecutive breast lumps, on which a fine needle aspiration (FNA) diagnosis of fibroadenoma was followed by excision and histopathologic confirmation of the diagnosis, were included. Atypia on cytology was based on cell overlap, nuclear enlargement and cell dyscohesion. Nuclear morphometric comparison was carried out between the categories of fibroadenoma, fibroadenoma with atypia and grade 1 ductal carcinoma cases that formed part of an earlier study. The parameters employed were area, roundness, diameter, perimeter and grey level. RESULTS: Among the 30 cases of fibroadenoma reported on FNA, an additional component of atypia was noted in 5. On subsequent histopathology, atypia was not confirmed in any of the cases. On morphometric analysis, a significant difference was noted between fibroadenoma and fibroadenoma with atypia categories, as between fibroadenoma and grade 1 ductal carcinoma cases. However, no significant difference was noted between fibroadenoma with atypia and grade 1 ductal carcinoma cases. CONCLUSION: FNA assessment of atypia in cases of fibroadenoma is difficult. Even conventional nuclear morphometry, though supporting the initial impression of atypia, does not help with this assessment. Also, based on morphometry alone, there may be difficulty separating fibroadenomas with atypia and grade 1 ductal carcinomas. Larger studies, employing other morphometric parameters, such as chromatin texture and fractal dimension, may shed further light on the subject.     

One step flow-through adsorptive purification of tubulin from tissue homogenate

Tubulin, a potential target for anti-cancer drugs, has been purified in one step and obtained as flow-through fraction directly from an extract of a mammalian brain tissue by adsorption chromatography on H-CELBEADS, an indigenously developed rigid, superporous cross-linked cellulose based weakly hydrophobic adsorbent. The fibrous polymerized tubulin mass passed through the H-CELBEADS bed while the associated proteins were separated by adsorption. The final tubulin preparation was obtained free from other proteins as seen on SDS-PAGE. Purified tubulin was obtained in a yield of about 29 mg/100 g brain, and its bioactivity, evaluated through its ability to bind colchicine, was found to be preserved.     

Thermal inactivation of the reductase domain of cytochrome P450 BM3

Although the reductase domain of cytochrome P450 BM3 (BMR) catalyzes the reduction of cytochrome c and 2,6-dichlorophenolindophenol, we observed a catalytically independent loss of activity. By varying the incubation time for the enzyme prior to reaction initiation, we measured an inactivation rate of 0.22 min(-1). We hypothesized that either an active BMR dimer dissociates to an inactive monomer or BMR undergoes denaturation. We were not able to trap or destabilize a dimer, and BMR inactivation proved to be irreversible. Addition of excess FMN only slightly decreased the rate of inactivation from 0.22 to 0.13 min(-1), indicating inactivation likely does not reflect loss of flavin. When inactivation rates as a function of temperature were fit to the Arrhenius equation, the energy required to inactivate BMR was 9.9 kcal mol(-1)--equivalent to a few hydrogen bonds. The potential instability of BMR under certain conditions raises concerns for the use of BMR as a model or surrogate P450 reductase in other systems.     

Setaria cervi: kinetic studies of filarial glutathione synthetase by high performance liquid chromatography

The bovine filarial worm Setaria cervi was found to have abundance of glutathione synthetase (GS; EC 6.3.2.3) activity, the enzyme being involved in catalysing the final step of glutathione (GSH) biosynthesis. A RP-HPLC method involving precolumn derivatization with o-phthalaldehyde has been followed for the estimation of GS activity in crude filarial preparations. Subcellular fractionation of the enzyme was undertaken and it was confirmed to be a soluble protein residing mainly in cytosolic fraction. Attempts to determine the Km value for L-gamma-glutamyl-L-cysteine gave a distinctly nonlinear double-reciprocal plot in which data obtained at relatively high dipeptide concentrations (>1 mM) extrapolate to a Km value of about 400 microM whereas data obtained at lower concentrations (<0.1 mM) extrapolate to a value of about 33 microM. Km was determined to be around 950 and 410 microM for ATP and glycine, respectively. The effect of various amino acids was studied on enzyme activity at 1mM concentration. L-cystine caused a significant enzyme inhibition of 11%. Preincubation with N-ethylmaleimide also resulted in significant inhibition of GS activity.     

High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides

DNA-polymerase-mediated incorporation of different fluorochrome-labeled nucleotides (FdNTPs) was investigated with the goals of optimizing the high-density labeling of probes and exploring DNA sequencing strategies that rely on the controlled, sequential addition of such compounds. By systematically evaluating variables--including polymerase type, buffer conditions, and fluorochrome chemistries--a rational strategy for the sequential addition of labeled nucleotides to a DNA template was demonstrated. A simple structural model of the polymerase-DNA template complex that considered the fluorochrome moiety of the FdNTPs and the linker length also guided this strategy. Complementary results that portend the use of simple photobleaching to enable the reliable quantitation of consecutive additions are presented.     

Rescuing melanoma epitope-specific cytolytic T lymphocytes from activation-induced cell death, by SP600125, an inhibitor of JNK: implications in cancer immunotherapy

Activation-induced cell death (AICD) as well as programmed cell death (PCD) serve to control the expansion of activated T cells to limit untoward side effects of continued effector responses by T cells and to maintain homeostasis. AICD of T cells in tumor immunotherapy can be counterproductive particularly if the activated T cells undergo apoptotic death after the very first secondary encounter of the specific epitope. We examined the extent to which tumor epitope-specific CTLs that are activated and expanded in an in vitro-matured dendritic cell-based primary stimulation protocol undergo AICD following their first secondary encounter of the cognate epitope. Using the MART-1(27-35) epitope as a prototype vaccine epitope, we also examined whether these CTLs could be rescued from AICD. Our results demonstrate that a substantial fraction of MART-1(27-35) epitope-specific primary CTLs undergo AICD upon the very first secondary encounter of the cognate epitope. The AICD in these CTLs is neither caspase dependent nor is it triggered by the extrinsic death signaling pathways (Fas, TNFR, etc.). These CTLs, interestingly, could be rescued from AICD by the JNK inhibitor, SP600125. We also found that SP600125 interferes with their IFN-gamma response but does not block their cytolytic function. The rescued CTLs, however, regain their capacity to synthesize IFN-gamma if continued in culture without the inhibitor. These observations have implications in tumor immunotherapy and in further studies for regulation of AICD in CTLs.     

Inhibition of hepatitis C virus-like particle binding to target cells by antiviral antibodies in acute and chronic hepatitis C

Hepatitis C virus (HCV) is a leading cause of chronic viral hepatitis worldwide. The study of antibody-mediated virus neutralization has been hampered by the lack of an efficient and high-throughput cell culture system for the study of virus neutralization. The HCV structural proteins have been shown to assemble into noninfectious HCV-like particles (HCV-LPs). Similar to serum-derived virions, HCV-LPs bind and enter human hepatocytes and hepatoma cell lines. In this study, we developed an HCV-LP-based model system for a systematic functional analysis of antiviral antibodies from patients with acute or chronic hepatitis C. We demonstrate that cellular HCV-LP binding was specifically inhibited by antiviral antibodies from patients with acute or chronic hepatitis C in a dose-dependent manner. Using a library of homologous overlapping envelope peptides covering the entire HCV envelope, we identified an epitope in the N-terminal E2 region (SQKIQLVNTNGSWHI; amino acid positions 408 to 422) as one target of human antiviral antibodies inhibiting cellular particle binding. Using a large panel of serum samples from patients with acute and chronic hepatitis C, we demonstrated that the presence of antibodies with inhibition of binding activity was not associated with viral clearance. In conclusion, antibody-mediated inhibition of cellular HCV-LP binding represents a convenient system for the functional characterization of human anti-HCV antibodies, allowing the mapping of envelope neutralization epitopes targeted by naturally occurring antiviral antibodies.