Nuclear Magnetic Resonance Spectroscopic Studies on the Microbial Degradation of Mononitrophenol Isomers

The biochemical pathways followed by a mixed bacterial culture and one of its constituent strains, Sarcina maxima, MTCC 5216 (hitherto unreported) during the degradation of mononitrophenol isomers was studied using extensive nuclear magnetic resonance (NMR) spectroscopy (One- and Two-Dimensional Heteronuclear Multiple Quantum Coherence Transfer-2D HMQCT NMR). NMR investigations revealed that o-nitrophenol (ONP) could be degraded by the consortium to metabolites such as catechol, cis, cis-muconic acid, γ-hydroxymuconic semialdehyde, maleylacetate and β-ketoadipate. The spectra of ONP reaction mixture degraded by S.␣maxima showed that formation of maleylacetate from γ-hydroxymuconic semialdehyde should go through a new metabolite γ-hydroxymaleylacetate, hitherto unreported. The consortium could breakdown m-nitrophenol (MNP) to 4-aminocatechol indicating that it came from 3-hydroxyaminophenol. However, S. maxima MTCC 5216, could convert MNP to hitherto unreported 2-nitrohydroquinone and the subsequent 2-hydroxylaminohydroquinone to 1,2,4-benzenetriol along with γ-hydroxymuconic semialdehyde, muconolactone and maleylacetate. The pathway followed by the consortium during p-nitrophenol (PNP) degradation was by the formation of 4-nitrocatechol, maleylacetate and β-ketoadipate. PNP reaction mixture of S.␣maxima, MTCC 5216 on the other hand, showed that the pathway could proceed through the formation of p-hydroquinone as the initial metabolite. The present study conclusively established the nitrophenol-degrading ability of both the consortium and S. maxima MTCC 5216, including exhibiting slight deviations from the pathways followed by the other reported microorganisms.     

Fractional modeling dynamics of HIV and CD4<Superscript>+</Superscript> T-cells during primary infection

In this paper, we introduce fractional-order into a model of HIV-1 infection of CD4⁺ T cells. We study the effect of the changing the average number of viral particles N with different sets of initial conditions on the dynamics of the presented model. Generalized Euler method (GEM) will be used to find a numerical solution of the HIV-1 infection fractional order model.     

Degradation of 3-chlorobenzoate and phenol singly and in mixture by a mixed culture of two ortho-pathway-following <Emphasis Type="Italic">Pseudomonas</Emphasis> strains

The compatibility and efficiency of two ortho-cleavage pathway-following pseudomonads viz. the 3-chlorobenzoate (3-CBA)-degrader, Pseudomonas aeruginosa 3mT (3mT) and the phenol-degrader, P. stutzeri SPC-2 (SPC-2) in a mixed culture for the degradation of these substrates singly and simultaneously in mixtures was studied. Another phenol-degrading strain, Pseudomonas sp. SoPC-5 (SoPC-5) that utilizes a meta-cleavage mode also was tried in co-culture with 3mT. The former combination was found to be a better degrader of both the substrates when present alone. But, with inoculum levels of 0.15 mg cell dry wt each of 3mT/SPC-2 or 3mT/SoPC-5 growth with 2 mM each of 3-CBA and phenol was slow with a lag of 24 h and degradation being incomplete. However, with higher inocula in the ratios 1:1, 1:2, and 2:1, i.e., 0.3 + 0.3, 0.3 + 0.6, and 0.6 + 0.3 mg cell dry wt of 3mT and SPC-2, respectively complete degradation of both the substrates occurred. Degradation of 3-CBA was complete with the release of stoichiometric amounts of chloride (Cl⁻) when concentrations of phenol/3-CBA were varied as 2:2, 2:4, and 4:2 mM, i.e., even when the concentration of the more toxic co-substrate 3-CBA was higher than phenol effective simultaneous degradation occurred at the inoculums ratio of 1:1 (0.3 mg dry cell wt. of each strain). These studies clearly indicated the better suitability of ortho-cleavage-utilizing strains as partners in a mixed culture than those follow different modes.     

Chronic gamma-irradiation results in increased cell killing and chromosomal aberration with specific breakpoints in fibroblast cell strains derived from non-Hodgkin's lymphoma patients.

Cultured skin fibroblast cells from 6 patients with non-Hodgkin's lymphoma (NHL) and 2 clinically normal subjects were compared for cell survival and chromosomal aberration after chronic gamma-irradiation. Fibroblasts from an ataxia telangiectasia (AT) homozygote and an AT heterozygote were used as positive controls. Following irradiation, fibroblasts from all 6 NHL patients showed an increase in both cell death and chromosomal aberration (breaks and rearrangements) compared to the normal subjects. The difference in the frequency of chromosomal aberration between the normals and the NHL patients remained virtually unchanged over a period of 24-72 h post irradiation incubation of the cells. Cell cycle analysis by flow cytometry carried out in 1 normal and 1 NHL fibroblast cell strain showed that more cells representing the NHL patient were in G2/M phase compared to the normal at various times of cytogenetic analysis. While the AT homozygote appeared to be the most radiosensitive, the AT heterozygote showed a slightly higher incidence of cell death and chromosomal aberration than the normals. The cellular and chromosomal radiosensitivity of fibroblast cell lines from the NHL patients differed slightly from that of the AT heterozygote but clearly occupied an intermediate position between the AT homozygote and the normal subjects. Cells from 3 of the NHL patients showed radiation-induced specific chromosomal breaks involving chromosomes 1, 2, 6, 8, 10 and 11 which correspond to known fragile sites. Such breakpoints associated with increased radiosensitivity may be indicative of predisposition to malignancy in the patients studied.     

Impact of patient setup error in the treatment of head and neck cancer with intensity modulated radiation therapy

PurposeTo study the impact of setup errors on the dose to the target volume and critical structures in the treatment of cancer of nasopharynx with intensity modulated radiation therapy (IMRT).Methods and materialsTwelve patients of carcinoma of nasopharynx treated by IMRT with simultaneous integrated boost technique were enrolled. The gross tumor volume, clinical target volume and low-risk nodal region were planned for 70, 59.4 and 54 Gy, respectively, in 33 fractions. Based on the constraints, treatment plans were generated. Keeping it as the base plan, the patient setup error was simulated for 3, 5 and 10 mm by shifting the isocenter in all three directions viz. anterior, posterior, superior, inferior, right and left lateral. The plans were evaluated for mean dose, maximum dose, volume of PTV receiving >110% and <93% of the prescribed dose. For both the parotids, the mean dose and the dose received by >50% of the parotid were evaluated. The maximum dose and dose received by 2 cc of spinal cord were also analyzed.ResultsThe dose to the target volume decreases gradually with increase in setup error. The superior and inferior shifts play major role in tumor under-dosage. A setup error of 3 mm along the posterior and lateral directions significantly affects the dose to the spinal cord. Similarly, setup error along lateral and anterior directions affects the dose to both parotids.ConclusionsThe isocenter position should be verified regularly to ensure that the goal of IMRT is achieved.     

Interference of thiol-compounds with dextrinizing activity assay of α-amylase by starch-iodine colour reaction: Modification of the method to eliminate this interference

Interference of Luria broth and other bacteriological media with the starch–iodine colour assay of the dextrinizing activity of -amylase (Fuwa's method) was observed, complete bleaching occurring with 0.4ml of the Luria broth. The interference was found to be due to the thiol groups present in the medium which compete with starch for iodine. Among the various metal salts tested for counteracting the interference, ZnSO₄ was found to be the best which reverted the colour to about 73–85% of that of the blank. A combination of hydrogen peroxide (10 l of 30% solution) and CuSO₄ · 5H₂O (50 l of 0.1 M solution) completely protected the starch–iodine reaction in the presence of even 0.5 ml of Luria broth and a modified assay was developed based on this finding. The colour intensity, however, was almost double than that obtained for the same amount of starch and iodine in the absence of these protective agents. Nevertheless, with different concentrations of starch as well as with varying amounts of enzymes, the modified method showed perfect linearity and could be effectively used for estimation of dextrinizing activity of -amylase in the presence of thiol groups.     

Comparative expression analysis of tRF-3001a and tRF-1003 with corresponding miRNAs (miR-1260a and miR-4521) and their network analysis with breast cancer biomarkers

Molecular Biology Reports - MicroRNAs and tRFs (tRNA-derived fragments) are small non-coding RNAs that are promising breast cancer (BC) biomarkers. miRNA sequences are found within tRFs. For...     

Cation-mediated cross-linking in natural organic matter: a review

Interactions between cations and natural organic matter (NOM) are central for the stability of organic matter, formation of supramolecular NOM structure, formation of organo-mineral associations, soil aggregation and binding of organic contaminants. The effect of multivalent cations on environmental functionalities of NOM strongly depends on the relative importance between intramolecular complexation and intermolecular cross-linking, the degree of which will be determined by the spatial arrangement of the hydrophilic functional groups in NOM. This literature review seeks to evaluate the current state of the art regarding the relevance of intermolecular cross-links via bridges of multivalent cations. Cross-linking has been suggested to explain among others aggregate stability, retarded dissolved organic matter release, reduced organic matter (OM) solubility as well as increase in degree and nonlinearity of sorption or organic chemicals to NOM. Although the cross-linking mechanism has been suggested in numerous studies, it has not yet been verified directly. The dynamics of the intermolecular cross-links, their persistence as well as their interplay with OM and their influence on stability and bioavailability of organic chemicals is up to now unknown. The major challenge in this context is the development of a suitable combination of experimental and instrumental techniques and relating the results to molecular and physicochemical models on the basis of targeted combination of spectroscopic, molecular modelling and thermoanalytical methods.