Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP,ISSR and SSR markers

Molecular markers provide novel tools to differentiate between the various grades of Basmati rice, maintain fair-trade practices and to determine its relationship with other rice groups in Oryza sativa. We have evaluated the genetic diversity and patterns of relationships among the 18 rice genotypes representative of the traditional Basmati, cross-bred Basmati and non-Basmati (indica and japonica) rice varieties using AFLP, ISSR and SSR markers. All the three marker systems generated higher levels of polymorphism and could distinguish between all the 18 rice cultivars. The minimum number of assay-units per system needed to distinguish between all the cultivars was one for AFLP, two for ISSR and five for SSR. A total of 171 (110 polymorphic), 240 (188 polymorphic) and 160 (159 polymorphic) bands were detected using five primer combinations of AFLP, 25 UBC ISSR primers and 30 well distributed, mapped SSR markers, respectively. The salient features of AFLP, ISSR and SSR marker data analyzed using clustering algorithms, principal component analysis, Mantel test and AMOVA analysis are as given below: (i) the two traditional Basmati rice varieties were genetically distinct from indica and japonica rice varieties and invariably formed a separate cluster, (ii) the six Basmati varieties developed from various indica × Basmati rice crosses and backcrosses were grouped variably depending upon the marker system employed; CSR30 and Super being more closer to traditional Basmati followed by HKR228, Kasturi, Pusa Basmati 1 and Sabarmati, (iii) AFLP, ISSR and SSR marker data-sets showed moderate levels of positive correlation (Mantel test, r = 0.42–0.50), and (iv) the partitioning of the variance among and within rice groups (traditional Basmati, cross-bred Basmati, indica and japonica) using AMOVA showed greater variation among than within groups using SSR data-set, while reverse was true for both ISSR and AFLP data-sets. The study emphasizes the need for using a combination of different marker systems for a comprehensive genetic analysis of Basmati rice germplasm. The high-level polymorphism generated by SSR, ISSR and AFLP assays described in this study shall provide novel markers to differentiate between traditional Basmati rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.The first two authors have equal contribution     

Genetic analysis of a CSR10 (indica) × Taraori Basmati F3 population segregating for salt tolerance using ISSR markers

Segregation for salinity tolerance and ISSR markers based molecular polymorphism were investigated in a F₃ plant population raised via single-seed descent method from a cross between salt-tolerant indica rice variety CSR10 and salt-susceptible premium traditional Basmati rice variety Taraori Basmati HBC19. A total of 130 F₃plants were evaluated individually for salinity tolerance on 1–9 scale on the basis of seedling growth parameters; the average score ranged between 1.7 to 8.3. Frequency distribution curve obtained using the salinity tolerance data of F₃ population and a chi-square analysis, showed a good fit to a normal distribution. Eleven plants each in the category of salt-tolerant and salt-susceptible were selected from the segregating F₃ population for ISSR marker analysis. A total of 149 bands (4–11 bands per primer) ranging from 200 to 3530 bp were scored for the two rice varieties and the selected CSR10 × HBC19 segregating F₃ plants using 26 ISSR primers. Of these, 89 were monomorphic and 60 were polymorphic. Of the 60 polymorphic bands,36 and 20 bands were specific to CSR10 andHBC19 respectively. The remaining four bands were amplified using UBC primers 810,848, 853 and 886 and present in only some of the CSR10 × HBC19 F₃ plants. Notably, ISSR primers with dinucleotide repeat motif and 5'-anchored end amplified more number of bands (7.0 bands/primer) compared to3'-anchored dinucleotide primers (5.4bands/primer), but 3'-anchored dinucleotide primers revealed higher level of polymorphism (2.6 polymorphic bands/primer) compared to 5'-anchoreddinucleotide primers (1.43 polymorphic bands/ primer). While distribution of majority of the polymorphic bands were more or less in the expected ratios in salt-tolerant and/or salt-sensitive F₃segregating plants, but some of the bands amplified using UBC ISSR primers 823, 825,826, 849, 853, 864, 866 and 884 showed highly skewed distribution. Such polymorphic bands stand greater chances of having a linkage with the genes/ QTLs for salinity tolerance and shall be the target for further studies. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effect of Water Stress on Physiological Attributes and their Relationship with Growth and Yield of Wheat Cultivars at Different Stages

The effects of water stress on physiological attributes of drought‐sensitive (Kalyansona) and drought‐tolerant (C‐306) wheat cultivars were studied in a pot experiment. Water stress was imposed by withholding irrigation at boot and anthesis stages. Leaf water potential, leaf osmotic potential and leaf turgor potential (measured with pressure chamber and osmometer), as well as leaf diffusive resistance, leaf transpiration rate and leaf‐to‐air transpiration gradient (measured with a steady‐state porometer) were measured diurnally. Growth and yield parameters were recorded after harvesting of the crop. Triplicate data were analysed using a completely randomized design and correlations amongst these parameters were computed. Water stress was found to reduce diurnal leaf water potential and leaf osmotic potential in both the genotypes but leaf osmotic potential was significantly higher in the drought‐tolerant cultivar C‐306 than in the drought‐sensitive cultivar Kalyansona. Positive turgor was recorded in both the genotypes under water stress and non‐stress conditions. Water‐stressed plants showed significantly lower turgor potential than control plants. In diurnal observations, water‐stressed plants exhibited significantly higher leaf diffusive resistance in both genotypes at both stages. The diffusive resistance of C‐306 was predominantly higher than that of Kalyansona. Water stress decreased leaf transpiration rate at both stages but the reduction was higher at the anthesis stage. The leaf‐to‐air temperature gradient was much higher in C‐306 than in Kalyansona at the boot stage but at the anthesis stage genotypic variation was non‐significant. The capacity to maintain cooler foliage was lower at the anthesis stage than at the boot stage in both the cultivars. Shoot dry weight, number of grains, test weight, grain yield, biological yield and harvest index decreased to a greater extent when water stress was imposed at the anthesis stage, while imposition of water stress at the boot stage caused a greater reduction in plant height and number of tillers. Similarly, water stress caused a smaller reduction in growth, yield and yield attributes in C‐306 than in Kalyansona. In general, the correlation coefficient of grain and biological yield with water potential and its components was positive and highly significant. Similarly, turgor potential was also correlated positively and significantly with grain yield at both the stages, but with biological yield it was significant only at the anthesis stage. A negative and significant correlation was obtained for diffusive resistance and leaf‐to‐air temperature gradient with grain yield at the boot and anthesis stages. The rate of transpiration was also positively and significantly correlated to grain and biological yields at both the stages. Amongst the yield attributes, number of leaves and number of tillers were positively correlated at the anthesis stage, whereas leaf area and shoot dry weight were significantly correlated with grain and biological yields at both the stages.     

Pre-Treatment of Currency Printing Ink Wastewater through Coagulation-Flocculation Process

Attempt has been made to study the treatability of printing ink wastewatergenerated from an Indian currency printing press using coagulation-flocculation process. Coagulant agents, viz. ferrous sulphate, ferric chloride, aluminium sulphate and polyaluminium chloride were studied to select the most suitablecoagulant for effective treatment, and attain the optimum coagulant concentration. Cationic polyeletrolyte in conjunction with the most effective coagulant was also studied to assess its effect on floc settleability. Polyaluminium chloride (PAC) was found to be the most efficient coagulant, achieving removals of colour, suspended solids (SS), biochemical oxygen demand (BOD) and chemical oxygen demand (COD) of 95.9–96.5%, 96.5–97.0%, 61.3–65.8%and 54.8–61.8%, respectively at an optimum concentration of 1500 mg L^-1. Other coagulants, viz. ferrous sulphate, ferric chloride and aluminium sulphate did not show substantial removals of colour, BOD and COD, except suspended solids in comparison to the performance of PAC. Cationic ploylectrolyte in combination with PAC at an optimum concentration of 1500 mg L^-1 of PAC and 1.0 mg L^-1 of polyelectrolyte further improved the removal efficiency of various parameters studied, in addition to improving the floc settling rate, and reduction in quantity of sludge generation.Effect of rapid mixing intensity expressed as mean temporal velocity gradient (G), and mixing time (t) on flocculation was also investigated. Rapid mixing at an impeller rotational speed (n) of 300 rpm and mixing time (t) of 60 sec indicated good floc formation, which resulted in achieving velocity gradient of 821 s^-1, and was found to be an optimum combination. This was also indicated by relatively high settling velocity of sludge formed and low residual colour in the supernatant. However, slow mixing beyond 5 min, adopted after initial optimum rapid mixing, indicated negligible effect on flocculation.     

Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells

A strain of Halomonas bacteria, GFAJ-1, has been claimed to be able to use arsenate as a nutrient when phosphate is limiting and to specifically incorporate arsenic into its DNA in place of phosphorus. However, we have found that arsenate does not contribute to growth of GFAJ-1 when phosphate is limiting and that DNA purified from cells grown with limiting phosphate and abundant arsenate does not exhibit the spontaneous hydrolysis expected of arsenate ester bonds. Furthermore, mass spectrometry showed that this DNA contains only trace amounts of free arsenate and no detectable covalently bound arsenate.     

Soil organic phosphorus fractions in response to long-term fertilization with composted manures under rice–wheat cropping system

Present investigation evaluates the effect of organic fertilization (OF), integrated nutrient management (INM) practice, and recommended dose of chemical fertilization (CF) on changes in soil organic phosphorus (P) and its fractions under rice (Oryza sativa L.)–wheat (Triticum aestivum L.) cropping system. The 4-year experiment (2009–2013), under split-plot design, showed that OF did not increase the total P or total organic P content of soil under either of the test crops. However, OF maintained the higher level of labile organic P and moderately labile organic P in soil under wheat the moderately stable organic P and highly stable organic P was highest in paddy soil under CF practices (11.34 and 7.77 μg g^?1, respectively) followed by wheat. The P concentration in organically grown rice or wheat grain was increased significantly compared with their CF counterparts. The productivity economics for rice and wheat crops showed INM fertilization to be more economical than OF.     

A keratoprosthesis prototype for the dog

Objective  To describe the technique for implantation of a novel keratoprosthesis (KP) prototype and evaluate its application for the treatment of corneal blindness in dogs.
Animals studied  Seven dogs, all of them being clinically blind before surgery as a result of severe corneal endothelial disease (5/7) or chronic superficial keratitis (2/7) that were unresponsive to prior therapy.
Procedures  A silicone KP was implanted unilaterally, just anterior to Descemet's membrane, after creating a stromal pocket by deep stromal lamellar dissection.
Results  Implantation of the KP was accomplished without complication in six of seven operated dogs. In the remaining case, an intra-operative complication (perforation of Descemet's membrane) was associated with extrusion of the KP 8 weeks postoperatively. All operated eyes regained limited vision after surgery. Three to six months after implantation purulent keratitis occurred in all five eyes with endothelial disease, necessitating surgical removal of the KP 6 months postoperatively in 5/7 eyes.
Conclusions  This KP prototype shows promise as a treatment for certain blinding corneal diseases. However, changes in the design of this KP, allowing improved stromal integration, will be necessary before its clinical application can be approved.     

Genetic diversity analysis in date palm (Phoenix dactylifera L.): a comparative assessment using ISSR and RAPD marker assays

SUMMARY

A comparative study was conducted to evaluate genetic diversity in 45 genotypes of date palm (Phoenix dactylifera L.), including both male and female plants, employing RAPD and ISSR marker systems. The data were analysed to calculate the total number of bands, the number of polymorphic bands, the percentage polymorphism, the average number of bands per primer, the effective multiplex ratio (EMR), the polymorphic information content (PIC), the marker index (MI), and genetic similarity coefficients. The 37 RAPD and 53 ISSR primers used generated 363 and 608 scorable amplified products, respectively, of which 95.0% and 90.9% were polymorphic. The ISSR markers produced more information than the RAPD markers due to their higher EMR and MI values. Jaccard similarity values among male plants, female plants, and between all male and all female plants varied between 0.72 – 0.80. The results indicate the effectiveness of these two marker systems for demonstrating genetic relationships among date palm genotypes.     

Estimating Velocity for Processive Motor Proteins with Random Detachment

We show that, for a wide range of models, the empirical velocity of processive motor proteins has a limiting Pearson type VII distribution with finite mean but infinite variance. We develop maximum likelihood inference for this Pearson type VII distribution. In two simulation studies, we compare the performance of our MLE with the performance of standard Student’s t-based inference. The studies show that incorrectly assuming normality (1) can lead to imprecise inference regarding motor velocity in the one-sample case, and (2) can significantly reduce power in the two-sample case. These results should be of interest to experimentalists who wish to engineer motors possessing specific functional characteristics.     

Hydrogenated Vegetable Oil Industry Wastewater Treatment using UASB Reactor System with Recourse to Energy Recovery

The investigation was carried out on laboratory scale to assess the feasibility of upflow anaerobic sludge blanket reactor system as a pretreatment for hydrogenated vegetable oil industry wastewater with recourse to energy recovery. The reactor system operated at 35°C, resulted in COD removal efficiency in the range 98.9–80.1% at organic loading varying in the range 1.33–10 kgCOD/m³ day. The specific methane yield varied from 0.295–0.345 m³CH₄/kgCOD_r. Hydraulic retention time, substrate concentrations, pH, and temperature were also varied to study the influence of operating parameters on reactor performance. The methane content decreased with increase in substrate loading rate, and varied from 53–66.7% under varying operating conditions. Impulse loading studies in terms of hydraulic, organic, and pH though resulted in destabilization of the reactor; however, the reactor rapidly achieved stable performance after steady operation.