Nitrate removal using Brevundimonas diminuta MTCC 8486 from ground water

Brevundimonas diminuta MTCC 8486, isolated from marine soil of coastal area of Trivandrum, Kerala, was used for biological removal of nitrate from ground water collected from Kar village of Pali district, Rajasthan. The organism was found to be resistance for nitrate up to 10,000 mg L(-1). The optimum growth conditions for biological removal of nitrate were established in batch culture. The effect of carbon sources on nitrate removal was investigated using mineral salt medium (MSM) containing 500 mg L(-1) of nitrate to select the most effective carbon source. Among glucose and starch as carbon source, glucose at 1% concentration increased the growth (182+/-8.24 x 10(4) CFU mL(-1)) and induced maximum nitrate reduction (86.4%) at 72 h. The ground water collected from Kar village, Pali district of Rajasthan containing 460+/-5.92 mg L(-1) of nitrate was subjected to three different treatment processes in pilot scale (T1 to T3). Higher removal of nitrate was observed in T2 process (88%) supplemented with 1% glucose. The system was scaled up to 10 L pilot scale treatment plant. At 72 h the nitrate removal was observed to be 95% in pilot scale plant. The residual nitrate level (23+/-0.41 mg L(-1)) in pilot scale treatment process was found to be below the permissible limit of WHO.

Preservation of kombucha tea-effect of temperature on tea components and free radical scavenging properties

Kombucha tea is sugared black tea fermented with a consortium of acetic acid bacteria and yeasts (tea fungus) for 14 days. The tea tastes slightly sweet and acidic. The formation of tea fungal biofilms during storage is a big problem when kombucha tea is being stored and commercialized. Various thermal treatments have been tried for long-term storage of kombucha tea. The present study revealed the influence of heat on the biochemical constituents and the free radical scavenging properties of kombucha tea. Heat treatment at 60, 65, and 68 degrees C for 1 min controlled biofilm formation in kombucha tea without changing its clarity, taste, and flavor. However, tea polyphenols and black tea quality parameters showed varying stability during the storage period. A decrease in free radical scavenging properties was also found during the storage period. Because the biological activities of kombucha tea depended on the biochemical constituents, it was concluded that heat treatment was not a suitable method for kombucha tea preservation.

Bio-separation of toxic arsenate ions from dilute solutions by native and pretreated biomass of Aspergillus fumigatus in batch and column mode: effect of biomass pretreatment

The sorption of As(V) from aqueous solution onto live and pretreated biomass of Aspergillus fumigatus was studied. The studies on optimization of contact time, adsorbent dosage and pH showed that the FeCl(3) treated and FeSO(4) treated biomass had the maximum capacity to adsorb As(V) while acid treated biomass was found to be minimum. Adsorption parameters were determined using both Langmuir and Freundlich isotherm models. The maximum adsorption capacity of 0.054 mg/g was observed in FeCl(3) treated and FeSO(4) treated biomasses. Column mode studies were conducted using FeSO(4) treated biomass to compare its efficacy with batch mode to adsorb As(V). Batch mode experiments proved to be efficient. Desorption studies were also carried out with dilute sodium hydroxide to recover both the adsorbent and adsorbate.

Determination of kinetic constants of hybrid textile wastewater treatment system

The present study is related to treatment of textile wastewater in microaerophilic-aerobic hybrid reactor. The study showed the effectiveness of biological treatment of wastewater involving appropriate microorganism and suitable reactors. COD and color were reduced to 82-94%, and 99% respectively for textile wastewater. The reactor was operated at highest loading of 16.4 g COD g l(-1)d(-1) and obtained 80% COD and 72% color removal. Biokinetic models were applied to data obtained from experimental studies in continuously operated hybrid reactor. Treatment efficiencies of the reactor were investigated at different hydraulic retention times (2.3-9.1d) and organic loading rates (2.6-16.4 g COD l(-1)d(-1)). Second-order and a Stover-Kincannon models were best fitted to the hybrid column reactor. The second-order substrate removal rate constant (k(2(S))) was found as 41.44 d(-1) for hybrid reactor. Applying the modified Stover-Kincannon model to the hybrid reactor, the maximum removal rate constant (U(max)) and saturation value constant (K(B)) were found to be 212 g l(-1)d(-1) and 22.89 g l(-1)d(-1), respectively.

Spironolactone for poorly controlled hypertension in type 2 diabetes: conflicting effects on blood pressure, endothelial function, glycaemic control and hormonal profiles

AIMS/HYPOTHESIS

Aldosterone antagonism improves endothelial function (and reduces deaths) in chronic heart failure. It is not known whether similar effects occur in other high-risk groups such as patients with diabetes and hypertension. We therefore assessed the full effects of aldosterone blockade in poorly controlled hypertensive patients with type 2 diabetes, focussing on blood pressure, endothelial function, glycaemic control and key hormones.

METHODS

We performed a randomised, placebo-controlled, double-blind, crossover study on 50 patients with type 2 diabetes and treated but poorly controlled hypertension, comparing spironolactone versus placebo. Patients had their endothelial function assessed by standard forearm venous occlusion plethysmography.

RESULTS

There was no significant improvement in endothelium-dependent vasodilatation in response to acetylcholine, despite highly significant reductions in systolic and diastolic blood pressure. However, spironolactone significantly worsened glycaemic control, plasma angiotensin II and cortisol.

CONCLUSIONS/INTERPRETATION

Spironolactone is highly effective in lowering blood pressure in patients with type 2 diabetes and poorly controlled hypertension on standard treatment, but does not improve vascular endothelial function in this group. We speculate that any tendency for the spironolactone-induced lowering of blood pressure to improve endothelial function is offset by its tendency to worsen glycaemic control and increase the levels of angiotensin II and even possibly cortisol.

Arsenic adsorption by polyvinyl pyrrolidone K25 coated cassava peel carbon from aqueous solution

Sorption of arsenic from aqueous solution was carried out using polyvinyl pyrrolidone K25 coated cassava peel carbon (PVPCC). Batch experiments were conducted to determine the effect of contact time, initial concentration, pH and desorption. Batch sorption data's were fitted to Lagergren kinetic studies. Column studies were also conducted using PVPCC as adsorbent. The optimized flow rate of 2.5 mL min(-1) and bed height 10 cm were used to determine the effect of metal ion concentration on removal of As(V). BDST model was applied to calculate the adsorption capacity (N(0)) of column. The N(0) value of 2.59 x 10(-5), 4.21 x 10(-5), 4.05 x 10(-5), 4.26 x 10(-5) and 3.2 x 10(-5) mg g(-1) were obtained for 0.5, 1.0, 1.5, 2.0 and 2.5 mg L(-1) of As(V), respectively. The batch sorption proved to be more efficient than the column sorption. The sorption of As(V) and the nature of the adsorbent was examined by Fourier transmission infrared spectroscopy (FTIR) and X-ray diffraction (XRD) studies, respectively.

Comparative studies on removal of Congo red by native and modified mycelial pellets of Trametes versicolor in various reactor modes

Aerated and rotated mode adsorption experiments were carried out for the removal of Congo red from aqueous solution using native and pre-treated mycelial pellets/biomass of Trametes versicolor. The effect of process parameters like contact time, dosage of adsorbent, adsorbate concentration and pH on adsorption was investigated. Higher the dye concentration lower was the adsorption. Equilibrium time was attained at 90 min. Increase in biomass dosage increased the adsorption. Experimental data were analyzed by the Langmuir and Temkin isotherms. Adsorption capacity (Q(0)) of autoclaved biomass was 51.81 mg/g, which was higher than other biomass studied. The second order kinetic model by Ho and Mckay described well the experimental data. Acidic pH was favorable for the adsorption of Congo red. Studies on pH effect and desorption show that chemisorption seems to play a major role in the adsorption process. Among the native and pre-treated biomass studied, autoclaved biomass showed a better adsorption capacity. Utilization of autoclaved biomass is much safer as it does not pose any threat to environment. Aerated mode showed a better adsorption capacity when compared to rotated mode.

Exploitation of Trichoderma harzianum mycelial waste for the removal of rhodamine 6G from aqueous solution

The harvested mycelial waste of Trichoderma harzianum was used as an adsorbent for the removal of rhodamine 6G and was studied in batch mode. The effects of agitation time and initial dye concentration, adsorbent dosage and pH were examined. The study revealed that the amount of dye adsorbed (mgg(-1)) increased with increase in agitation time and reached equilibrium after 120 min, for dye concentrations of 10-50 mg L(-1). The adsorbent dosage of 1.0 g/50 mL and pH of 8.0 were found to be optimum for maximum dye removal. The batch mode adsorption data followed both the Langmuir and Freundlich isotherms. The pseudo first- and second-order rate kinetics were applied to the adsorbent system. The adsorption kinetics of rhodamine 6G showed that the pseudo-second-order kinetic model provided the best correlation of the equilibrium data. The study implies that it is possible to develop a dye removal system by using T. harzianum biomass, which occurs as sludge in waste stream of fermentation industries.

Microbially-influenced degradation of solidified/stabilized metal waste

In the present study, a refined microbially-influenced degradation method was used to evaluate the stability of a solidified synthetic waste containing chromium salt, cement and fly ash in two different proportions. The experimental samples showed evidence of microbial growth by leaching of sulfate. Chromium leached by Thiobacillus thiooxidans from the experimental samples 'C1' (10.26% CrCl3 .6H2O; 89.74% cement) and 'FC1' (10.26% CrCl3 .6H2O; 10% fly ash; 79.74% cement), after 30 days of exposure was 14.53 mg/g and 9.53 mg/g, respectively. The corresponding concentration of chromium in the leachate was 0.189 mg/l and 0.124 mg/l, respectively, which was lower than the toxicity characteristic leaching procedure (TCLP), regulatory limit (5 mg/l). Replacement of cement by 10% fly ash in FC1 restricted the leaching of chromium more effectively. Model equations based on two shrinking core models namely, acid dissolution and bulk diffusion model, were used to analyze the kinetics of microbial degradation. Of the two approaches, the bulk diffusion model fit the data better than the acid dissolution model as indicated by the correlation coefficients of >0.97.

Purification, potency and immunogenicity analysis of Vero cell culture-derived rabies vaccine: a comparative study of single-step column chromatography and zonal centrifuge purification

Continuous Vero cell lines are more suitable for large-scale production of rabies vaccine. The purification of Vero cell-derived rabies vaccine is critical because of the residual cellular DNA and serum proteins. The perfection of techniques using column chromatography with different matrix material, gel filtration and zonal centrifugation is of paramount importance for the optimal purification of rabies vaccine, leaving minimal residual cellular DNA, below the permissible level of 100 pg per dose and serum protein content of 1 ppm. In this study the potency, immunogenicity and safety of Vero cell-derived rabies vaccines were compared following purification by densely or loosely packed DEAE-sepharose CL-6B columns with different bed heights or by zonal centrifugation. The optimal virus recovery and maximum removal of substrate DNA and serum proteins were achieved only when the sepharose CL-6B column bed height was maintained at a thickness of 2-2.5 cm. The rabies virus material was purified by layering over the matrix without applying pressure. DEAE-sepharose CL-6B column purification using a simplified, cost effective technique as described in this study enhances the antigen yield by 50% in comparison with zonal purification.

Sorption of Cr(VI) from dilute solutions and wastewater by live and pretreated biomass of Aspergillus flavus

Sorption of Cr(VI) was carried out from dilute solutions using live and pretreated biomass in a batch mode. Effects of agitation time, adsorbent dosage and pH were examined. The autoclaved biomass that showed maximum adsorption capacity (Q(0)=0.335 mg g(-1)) was used as an adsorbent in column studies. The optimized flow rate of 2.5 ml min(-1) and bed height 10 cm were used to determine the effect of metal ion concentration on removal of Cr(VI). Applying the BDST model to calculate the adsorption capacity (N(0)) of column, which showed 4.56 x 10(-5), 7.28 x 10(-5), 6.89 x 10(-5), 3.07 x 10(-5), 2.80 x 10(-5)mg g(-1) for 4, 8, 12, 16 and 20 mg dm(-3) of Cr(VI), respectively. Batch sorption proved to be more efficient than the column sorption and hence batch sorption was used to remove Cr(VI) from a textile dyeing industry wastewater. The phytotoxic effect of treated and untreated wastewater was studied against Zea mays. Toxicity was reduced by 50% in the treated effluent.

Arsenic removal from groundwater by pretreated waste tea fungal biomass

Arsenic contamination in ground water poses a serious threat on human health. The tea fungus, a waste produced during black tea fermentation has been examined for its capacity to sequester the metal ions from ground water samples. Autoclaved tea fungal mat and autoclaving followed by FeCl3 pretreated tea fungal mat were exploited for removal of As(III), As(V) and Fe(II) from ground water sample collected from Kolkata, West Bengal, India. The biosorption rate tends to increase with the increase in contact time and adsorbent dosage. FeCl3 pretreated and autoclaved fungal mats removed 100% of As(III) and Fe(II) after 30 min contact time and 77% of As(V) after 90 min contact time. The optimum adsorbent dosage was 1.0 g/50 mL of water sample. The results revealed that the FeCl3 pretreated fungal mat could be used as an effective biosorbent for As(III) and As(V); autoclaved fungal mat for Fe(II) removal from ground water sample.

Supplementation of waste tea fungal biomass as a dietary ingredient for broiler chicks

The waste tea fungal biomass produced during black tea fermentation was investigated as a dietary ingredient in poultry feeds. A small portion of fungal mat was used as starter culture for the next cycle while the major portion is discarded as waste. Hence a trial study was carried out to utilize the waste fungal biomass as a supplementary diet for broiler chicks. The fungal biomass contained 179.38 g of crude protein, 120 g crude fibre, 4.82 g phosphorus, 6.56 g of calcium and 8.92 MJ metabolizable energy per kilogram of biomass. The dried tea fungus showed phytase activity of 23 IU/mg protein. The supplementation of tea fungal inclusion (TFI) at 150 g/kg concentration in poultry feed increased the feed consumption, body weight, performance efficiency factor (PEF) and the carcass characters of test broilers significantly (P=0.01) over the control. The histopathological examination of liver showed no abnormalities and the mortality rate was zero.

Growth and amylase production by Aspergillus oryzae during solid state fermentation using banana waste as substrate

Aspergillus oryzae, isolated from the starch rich litter soil, produced amylase when banana fruit stalk was used as substrate in a solid state fermentation system. The effects of incubation period, pH, temperature and various carbon sources on the production of amylase were studied. A maximum yield of 380U/mg was recorded on 96th hour of incubation. The amylase is tolerant to wide range of initial culture pH values (3 to 8) and temperature (25 to 35 degrees C), with an optimum pH of 5 and temperature of 35 degrees C. In SSF addition of starch (1%) increased the amylase production, when compared with other carbon sources used.

Implementation of national diabetes retinal screening programme is associated with a lower proportion of patients referred to ophthalmology

AIMS

To examine the impact of a new national retinal screening programme on screening attendance, technical quality of images, and referrals to the ophthalmology clinic.

METHODS

Results from the previous ad hoc retinal screening service were compared with data from the first year of the new Scottish Diabetes Retinal Screening Programme in Dundee, which was administered according to criteria recommended by the Health Technology Board Scotland.

RESULTS

Of 5150 patients invited for screening, 10.3% of patients did not attend. Overall, 4574 patients underwent single-field digital retinal photography and 25.4% required mydriasis for an adequate image. After screening, 1.9 and 90.5% were recalled for repeat photography at 6 months and 1 year, respectively, whilst 4.6% were ungradable and 3.0% were referred to the ophthalmology clinic. Compared with the last 18 months of the previous scheme, with the new programme a smaller proportion of patients were referred to ophthalmology (3.0 vs. 5.9%; P < 0.001, difference 2.9%: 95% confidence interval 2.1-3.7%). Moreover, the attendance was higher (89 vs. 82%; P < 0.01) and there were fewer ungradable images (4.6 vs. 7.1%; P < 0.001).

CONCLUSIONS

Introduction of a systematic retinal screening programme can reduce the proportion of patients referred to the ophthalmology clinic, and use ophthalmology services more efficiently.

Leaching of metals on stabilization of metal sludge using cement based materials

Toxicity characteristic leaching procedure(TCLP) of zinc plating sludge was carried out to assess the leaching potential of the sludge and the leachates were analyzed for heavy metals. The concentration of zinc, chromium, and lead in the leachate were 371.5 mg/L, 1.95 mg/L and 1.99 mg/L respectively. Solidification of zinc sludge was carried out using four different binder systems consisting of cement mortar, fly ash, clay and lime and cured for 28 d. The ratio of sludge added varied from 60% to 80% by volume. The solidified products were tested for metal fixing efficiency and physical strength. It was observed that the volume of sludge added that resulted in maximum metal stabilization was 60% for all the combinations, above which the metal fixation efficiency decreased resulting in high values of zinc in the leachate. Addition of 5% sodium silicate enhanced the chemical fixation of metals in all the binder systems. Among the four fixing agents studied, mixture of fly ash: lime, and cement mortar: lime stabilized zinc and other metals in the sludge effectively than other combinations. Addition of lime increased the stabilization of zinc whereas cement mortar increased the strength of the solidified product.

Comparison of decolorization of reactive microorganisms isolated from various sources

Azo dyes are among the oldest man-made chemicals and they are still widely used in the textile, printing and the food industries. About 10% - 15% of the total dyes used in the industry is released into the environment during the manufacturing and usage. Some dyes and some of their N-substituted aromatic bio-transformation products are toxic and/or carcinogenic and therefore these dyes are considered to be envionmental pollutants and health hazards. These azo dyes are degraded by physico-chemical and biological methods. Of these, biological methods are considered to be the most economical and efficient. In this work, attempts were made to degrade these dyes aerobically. The organisms which were efficient in degrading the following azo dyes-Red RB, Remazol Red, Remazol Blue, Remazol Violet, Remazol Yellow, Golden Yellow, Remazol Orange, Remazol Black- were isolated from three different sources viz., wastewater treatment plant, paper mill effluent treatment plant and tannery wastewater treatment plant. The efficiency of azo dye degradation by mixed cultures from each source was analyzed. It was found that mixed cultures from tannery treatment plant worked efficiently in decolorizing Remazol Red, Remazol Orange, Remazol Blue and Remazol Violet, while mixed cultures from the paper mill effluent worked efficiently in decolorizing Red RB, Golden Yellow and Remazol Yellow. The mixed cultures from wastewater treatment plant efficiently decolorized Remazol Black.

Decolourization of azo dyes and a dye industry effluent by a white rot fungus Thelephora sp

A white rot fungus Thelephora sp. was used for decolourization of azo dyes such as orange G (50 microM), congo red (50 microM), and amido black 10B (25 microM). Decolourization using the fungus was 33.3%, 97.1% and 98.8% for orange G, congo red and amido black 10B, respectively. An enzymatic dye decolourization study showed that a maximum of 19% orange G was removed by laccase at 15 U/ml whereas lignin peroxidase (LiP) and manganese dependent peroxidase (MnP) at the same concentration decolourized 13.5% and 10.8%, orange G, respectively. A maximum decolourization of 12.0% and 15.0% for congo red and amido black 10B, respectively, was recorded by laccase. A dye industry effluent was treated by the fungus in batch and continuous modes. A maximum decolourization of 61% was achieved on the third day in the batch mode and a maximum decolourization of 50% was obtained by the seventh day in the continuous mode. These results suggest that the batch mode of treatment using Thelephora sp. may be more effective than the continuous mode for colour removal from dye industry effluents.

Kinetics of anaerobic biodegradation of resorcinol catechol and hydroquinone in upflow fixed film-fixed bed reactors

Biodegradation of resorcinol, catechol and hydroquinone under anaerobic conditions was studied in identical upflow fixed film-fixed bed reactors. Kinetic constants; V(max) (maximum substrate utilization rate) and K(s) (Monod's half saturation constant) were determined for the three compounds using Lineweaver-Burk plot. V(max) for resorcinol was highest, followed by catechol and then by hydroquinone. When both resorcinol and catechol were fed to the resorcinol-acclimated reactor, resorcinol degradation was inhibited by catechol. The inhibition was of the uncompetitive type and V(max) for resorcinol was reduced by catechol.

Decolorization and degradation of H-acid and other dyes using ferrous-hydrogen peroxide system

In this study, advanced oxidation process utilizing Fenton's reaction was investigated for the decolorization and degradation of two commercial dyes viz., Red M5B, Blue MR and H-acid, a dye intermediate used in chemical industries for the synthesis of direct, reactive and azo dyes. Effect of Fe2 +, H2O2, pH, and contact time on the degradation of the dyes was studied. Maximum color and COD removal was obtained for Red MSB, H-acid and Blue MR at 10-25 mg/l of Fe2+ dose and 400-500 mg/l of H2O2 dose at pH 3.0. The initial oxidation reaction was found to fit into first order rate kinetics and the rate of oxidation of H-acid was higher than the other dyes. Release of chloride and sulfate from the Fenton's treated Red M5B dye and sulfate from H-acid and Blue MR indicates that the dye degradation proceeds through cleavage of the substituent group.

Biodegradation of p-nitrophenol in anaerobic fixed film fixed bed reactor

Biodegradation of p-nitrophenol (PNP) was studied in upflow anaerobic fixed film fixed bed reactor. The studies showed that PNP was not degraded as a sole carbon source in the reactor. Addition of glucose as co-substrate increased the degradation of PNP. A ratio of > 1 in terms of glucose to PNP could achieve 90% PNP degradation. However the total organic carbon (TOC) removals were 76.3% indicating the possibility of biotransformation of PNP.

Process standardization for optimal virus recovery and removal of substrate DNA and bovine serum proteins in Vero cell-derived rabies vaccine

Purification of a rabies vaccine by a single zonal centrifugation run was replaced by two runs with optimal standardization of the sucrose density gradient. As a result, significant reductions in the levels of substrate DNA and bovine serum protein in the Vero cell-derived human rabies vaccine were achieved. Following many trials, for the first run, loading of the 3.2-l capacity K-3 rotor with 1800 ml of 60% sucrose solution and 1400 ml of vaccine PBS buffer solution gave a satisfactory linear gradient. However, after the first run, the substrate DNA and bovine serum contents exceeded the required levels. After protamine sulphate and Tween-80 treatment of the concentrated inactivated material, a second run using the same procedure as in the first run was tried. However, these purification procedures resulted in low virus recovery. To achieve optimal virus recovery, and removal of substrate DNA and bovine serum protein, the peak fractions from the first run as indicated by the haemagglutination, sucrose concentration, and optical density values were pooled and the sucrose concentration of the pooled fractions was increased to 60%. A second (flotation) run was then carried out. Using this method, the virus recovery rate was more than 95% that of the first run, and the levels of cellular DNA and bovine serum protein were well within the acceptable limits of less than 100 pg/dose and one part per million, respectively. The substrate DNA was quantified by both radioactive labeling and non-radioactive biotin labeling methods. For the quantification of calf serum protein, a counter-immunoelectrophoresis method was developed and effectively applied. A potency assay was performed using the National Institutes of Health (NIH) and well-standardized in vitro single radial immuno diffusion (SRD) methods. Finally, an immunogenicity study was conducted with human volunteers and the results were confirmed by a rapid fluorescent focus inhibition test (RFFIT).

An enhancer trap line associated with a D-class cyclin gene in Arabidopsis

In yeast and animals, cyclins have been demonstrated to be important regulators of cell cycle progression. In recent years, a large number of A-, B-, and D-class cyclins have been isolated from a variety of plant species. One class of cyclins, the D-class cyclins, is important for progression through G1 phase of the cell cycle. In Arabidopsis, four D-class cyclins have been isolated and characterized (CYCLIN-D1;1, CYCLIN-D2;1, CYCLIN-D3;1, and CYCLIN-D4;1). In this report we describe the characterization of a fifth D-class cyclin gene, CYCLIN-D3;2 (CYCD3;2), from Arabidopsis. An enhancer trap line, line 5580, contains a T-DNA insertion in CYCD3;2. Enhancer trap line 5580 exhibits expression in young vegetative and floral primordia. In line 5580, T-DNA is inserted in the first exon of the CYCD3;2 gene; in homozygous 5580 plants CYCD3;2 RNA is not detectable. Even though CYCD3;2 gene function is eliminated, homozygous 5580 plants do not exhibit an obvious growth or developmental phenotype. Via in situ hybridization we demonstrate that CYCD3;2 RNA is expressed in developing vegetative and floral primordia. In addition, CYCD3;2 is also capable of rescuing a yeast strain that is deficient in G1 cyclin activity.

Paraganglioma of the pancreas: literature review and case report

Extraadrenal paragangliomas are very rare tumors arising from cells derived from the neural crest. These tumors are encountered only as case reports, and as a result, little is known of their natural history. We present a case of pancreatic paraganglioma and review all previously reported cases.

Crystal structure of the CDK4/6 inhibitory protein p18INK4c provides insights into ankyrin-like repeat structure/function and tumor-derived p16INK4 mutations

p18INK4c is a member of a family of INK4 proteins that function to arrest the G1 to S cell cycle transition by inhibiting the activity of the cyclin-dependent kinases 4 and 6. The X-ray crystal structure of the human p18INK4c protein to a resolution of 1.95 A reveals an elongated molecule comprised of five contiguous 32- or 33-residue ankyrin-like repeat units. Each ankyrin-like repeat contains a beta-strand helix-turn-helix extended strand beta-strand motif that associates with neighboring motifs through beta-sheet, and helical bundle interactions. Conserved ankyrin-like repeat residues function to facilitate the ankyrin repeat fold and the tertiary interactions between neighboring repeat units. A large percentage of residues that are conserved among INK4 proteins and that map to positions of tumor-derived p16INK4 mutations play important roles in protein stability. A subset of these residues suggest an INK4 binding surface for the cyclin-dependent kinases 4 and 6. This surface is centered around a region that shows structural features uncharacteristic of ankyrin-like repeat units.

Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster

PUT3 is a member of a family of at least 79 fungal transcription factors that contain a six-cysteine, two-zinc domain called a 'Zn2Cys6 binuclear cluster'. We have determined the crystal structure of the DNA binding region from the PUT3 protein bound to its cognate DNA target. The structure reveals that the PUT3 homodimer is bound asymmetrically to the DNA site. This asymmetry orients a beta-strand from one protein subunit into the minor groove of the DNA resulting in a partial amino acid-base pair intercalation and extensive direct and water-mediated protein interactions with the minor groove of the DNA. These interactions facilitate a sequence dependent kink at the centre of the DNA site and specify the intervening base pairs separating two DNA half-sites that are contacted in the DNA major groove. A comparison with the GAL4-DNA and PPR1-DNA complexes shows how a family of related DNA binding proteins can use a diverse set of mechanisms to discriminate between the base pairs separating conserved DNA half-sites.