Surface phosphomonoesterase activity of a natural immobilized system: Chroococcidiopsis in an Antarctic desert rock

The phosphomonoesterase activity of a microbialcommunity dominated by Chroococcidiopsis in arock sample from the Antarctic dry desert was comparedwith that of a non-axenic culture of thecyanobacterium isolated from the same rock in order toestablish whether the organism differed in itsproperties when immobilized in the rock. The pHoptimum (9.5) was the same, but the response totemperature and light both differed. In the case oftemperature, the optimum was much higher in culture. Light flux at the low value of 8 mol photonm^-2 s^-1 was slightly inhibitory for acrushed rock sample, but enhanced activity of thecultured material. Although materials both showeda typical (apparent) Michaelis-Menten relationship,the values for Km and V_max differed. Itis suggested that study of natural immobilized systemsis important for the development of procedures to useimmobilized phototrophs for practical purposes.     

Leishmania donovani affects antigen presentation of macrophage by disrupting lipid rafts

Leishmania donovani-infected splenic macrophages and P388D1 (P388D1(I)) failed to activate T cells in response to low dose of exogenous peptide. The membrane fluidity of P388D1(I) was greater than that of the normal counterpart P388D1(N), but could be reduced either by exposing the cell below phase transition point or by loading cholesterol into membrane (L-P388D1(I)), and this was associated with enhanced Ag-presenting ability of P388D1(I). Presentation of endogenous leishmanial Ag, kinetoplastid membrane protein-11, was also defective, but could be corrected by loading cholesterol into membrane. Because membrane rafts are important for Ag presentation at a low peptide dose, raft architecture of P388D1(I) was studied using raft (CD48 and cholera toxin-B) and non-raft (CD71) markers in terms of their colocalization with I-A(d). Binding of anti-CD48 mAb and cholera toxin B subunit decreased significantly in P388D1(I), and consequently, colocalization with I-A(d) was not seen, but this could be restored in L-P388D1(I). Conversely, colocalization between I-A(d) and CD71 remained unaffected regardless of the presence or the absence of intracellular parasites. P388D1(N) and L-P388D1(I), but not P388D1(I), formed peptide-dependent synapse with T cells quite efficiently and this was found to be corroborated with both intracellular Ca2+ mobilization in T cells and IL-2 production. This indicated that intracellular parasites disrupt the membrane rafts, possibly by increasing the membrane fluidity, which could be corrected by making the membrane rigid. This may be a strategy that intracellular L. donovani adopts to evade host immune system.     

Testing the Hypothesis that System y<Superscript>+</Superscript>L Accounts for High- and Low-Transport Phenotypes in Chicken Erythrocytes Using <Emphasis Type="SmallCaps">L</Emphasis>-Leucine as Substrate

Experiments were carried out to test the hypothesis that system y⁺L accounts for the high (HT) and low (LT) amino-acid transport phenotypes in chicken erythrocytes and to explain the different effect of selective breeding on lysine and leucine fluxes. L-Leucine transport was characterized in individuals which had been separated into two groups (HT and LT) according to their capacity to transport L-lysine across the erythrocyte membrane. Whereas lysine influx (1 μM) in the two groups differed by 32-fold (HT/LT), leucine influx was not significantly different. Average rates (nmol/ L cells/ min) were: 227 (HT) and 7.0 (LT) for L-lysine, and 8.9 (HT) and 7.1 (LT) for L-leucine. The differential ability of L-lysine and L-leucine fluxes to discriminate between the HT and LT phenotypes was shown to be consistent with the interactions of these substrates with system y⁺L and to vary depending on the conditions of the assay. It is shown that the two phenotypes can be clearly discriminated by measuring L-leucine influx in the presence of Li⁺. These results support the hypothesis that the HT and LT phenotypes reflect alterations in the function of system y⁺L and illustrate that the choice of the appropriate substrate and medium composition must be carefully considered when investigating the consequences of either experimental or natural alterations of broad-scope transporters.     

Identification of amino acids required for the functional up-regulation of human dihydrofolate reductase protein in response to antifolate Treatment

Human dihydrofolate reductase (DHFR) protein levels rapidly increase upon exposure to methotrexate, a potent inhibitor of this enzyme. A model to explain this increase proposes that DHFR inhibits its own translation by binding to its cognate mRNA and that methotrexate disrupts the DHFR protein-mRNA complex allowing its translation to resume. In the present study, Chinese hamster ovary cells lacking DHFR were transfected with wild type and mutants of human DHFR to identify amino acids that are essential for increases in DHFR in response to methotrexate. Glu-30, Leu-22, and Ser-118 were involved in the up-regulation of DHFR protein levels by methotrexate and certain other antifolates. Cells transfected with E30A, L22R, and S118A mutants that did not respond to methotrexate up-regulation had higher basal levels of DHFR, consistent with the model, i.e. lack of feedback regulation of these enzymes. Although cells containing the S118A mutant enzyme had higher levels of DHFR and had catalytic activity similar to that of wild type DHFR, they had the same sensitivity to the cytotoxicity of methotrexate, as were cells with wild type DHFR. This finding provides evidence that the adaptive up-regulation of DHFR by methotrexate contributes to the decreased sensitivity to this drug. Based on these observations, a new model is proposed whereby DHFR exists in two conformations, one bound to DHFR mRNA and the other bound to NADPH. The mutants that are not up-regulated by methotrexate are unable to bind their cognate mRNA.     

Use of jute processing wastes for treatment of wastewater contaminated with dye and other organics

A study was conducted to examine the potential of jute processing waste (JPW) for the treatment of wastewater contaminated with dye and other organics generated from various activities associated with jute cultivation and fibre production. Adsorption studies in batch mode have been conducted using dye solution as an adsorbate and JPW as an adsorbent. A comparative adsorption study was made with standard adsorbents such as powdered and granular activated carbon (PAC and GAC, respectively). A maximum removal of 81.7% was obtained with methylene blue dye using JPW as compared to 61% using PAC and 40% using GAC under similar conditions. The adsorption potential of JPW was observed to be dependent on various parameters such as type of dye, initial dye concentration, pH and dosage of adsorbent. The batch sorption data conformed well to the Langmuir and Freundlich isotherms. However, lower BOD (33.3%) and COD (13.8%) removal from retting effluent was observed using JPW as compared to 75.6% BOD removal and 71.1% COD removal obtained with GAC.     

Issues in high-throughput comparative modelling: a case study using the ubiquitin E2 conjugating enzymes

Sequences of the ubiquitin-conjugating enzyme (UBC or E2) family were used as a test set to investigate issues associated with the high-throughput comparative modelling of protein structures. A semi-automatic method was initially developed with particular emphasis on producing models of a quality suitable for structural comparison. Structural and sequence features of the E2 family were used to improve the sequence alignment and the quality of the structural templates. Initially, failure to correct for subtle structural inconsistencies between templates lead to problems in the comparative analysis of the UBC electrostatic potentials. Modelling of known UBC structures using Modeller 4.0 showed that multiple templates produced, on average, no better models than the use of just one template, as judged by the root-mean-squared deviation between the comparative model and crystal structure backbones. Using four different quality-checking methods, for a given target sequence, it was not possible to distinguish the model most similar to the experimental structure. The UBC models were thus finally modelled using only the crystal structure template with the highest sequence identity to the target to be modelled, and producing only one model solution. Quality checking was used to reject models with obvious structural anomalies (e.g., bad side-chain packing). The resulting models have been used for a comparison of UBC structural features and of their electrostatic potentials. The work was extended through the development of a fully automated pipeline that identifies E2 sequences in the sequence databases, aligns and models them, and calculates the associated electrostatic potential.     

Bystander activation involving T lymphocytes in herpetic stromal keratitis

Herpes simplex virus infection of mouse corneas can lead to the development of an immunopathological lesion, termed herpetic stromal keratitis (HSK). Such lesions also occur in TCR-transgenic mice backcrossed to SCID (TgSCID) that are unable to mount detectable HSV-specific immune responses. The present study demonstrates that lesion expression in such mice depends on continuous viral replication, whereas in immunocompetent mice, lesions occurred even if virus replication was terminated at 4 days after infection. The continuous replication in TgSCID mice was considered necessary to produce an activating stimulus to CD4(+) T cells that invade the cornea. Lesions in TgSCID were resistant to control by cyclosporin A, but were inhibited by treatment with rapamycin. This result was interpreted to indicate that T cell activation involved a non-TCR-mediated cytokine-driven bystander mechanism. Bystander activation was also shown to play a role in HSK lesions in immunocompetent mice. Accordingly, in immunocompetent DO11.10 mice, lesions were dominated by KJ1.26(+) OVA-specific CD4(+) T cells that were unreactive with HSV. In addition, KJ1.26(+) HSV nonimmune cells parked in ocularly infected BALB/c mice were demonstrable in HSK lesions. These results provide insight for the choice of new strategies to manage HSK, an important cause of human blindness.     

Pyridoxal phosphate binding sites are similar in human heme-dependent and yeast heme-independent cystathionine beta-synthases. Evidence from 31P NMR and pulsed EPR spectroscopy that heme and PLP cofactors are not proximal in the human enzyme

Two classes of cystathionine beta-synthases have been identified in eukaryotes, the heme-independent enzyme found in yeast and the heme-dependent form found in mammals. Both classes of enzymes catalyze a pyridoxal phosphate (PLP)-dependent condensation of serine and homocysteine to produce cystathionine. The role of the heme in the human enzyme and its location relative to the PLP in the active site are unknown. (31)P NMR spectroscopy revealed that spin-lattice relaxation rates of the phosphorus nucleus in PLP are similar in both the paramagnetic ferric (T(1) = 6.34 +/- 0.01 s) and the diamagnetic ferrous (T(1) = 5.04 +/- 0.06 s) enzyme, suggesting that the two cofactors are not proximal to each other. This is also supported by pulsed EPR studies that do not provide any evidence for strong or weak coupling between the phosphorus nucleus and the ferric iron. However, the (31)P signal in the reduced enzyme moved from 5.4 to 2.2 ppm, and the line width decreased from 73 to 16 Hz, providing the first structural evidence for transmission to the active site of an oxidation state change in the heme pocket. These results are consistent with a regulatory role for the heme as suggested by previous biochemical studies from our laboratory. The (31)P chemical shifts of the resting forms of the yeast and human enzymes are similar, suggesting that despite the difference in their heme content, the microenvironment of the PLP is similar in the two enzymes. The addition of the substrate, serine, resulted in an upfield shift of the phosphorus resonance in both enzymes, signaling formation of reaction intermediates. The resting enzyme spectra were recovered following addition of excess homocysteine, indicating that both enzymes retained catalytic activity during the course of the NMR experiment.     

Thyroidal regulation of different isoforms of NaKATPase in the primary cultures of neurons derived from fetal rat brain

The developmental profile of the different isoforms of NaKATPase have been investigated using primary cultures of isolated neurons initiated from 17 day old fetal rat brain. Northern blot analysis showed that the expression of three alpha isoforms (alpha(1), alpha(2) and alpha(3)) and two beta isoforms (beta(1) and beta(2)) increased progressively and reached a peak between 12 to 16 days of culture. Comparison of the mRNA levels of these isoforms in the cells maintained in thyroid hormone deficient (TH def) and thyroid hormone supplemented (TH sup) media for 6-12 days, revealed for the first time that in the neurons three alpha and two beta isoforms of NaKATPase are sensitive to TH. Furthermore immunocytochemical staining of these cells with isoform specific NaKATPase antibodies showed that the uniform distribution of alpha(2), alpha(3) and beta(2) isoforms in the neuronal processes require the presence of TH. These results establish neurons as the target cells for the regulation of NaKATPase by TH in the developing brain.