Analysis of slipped sequences in EST projects.
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Slippage is an important sequencing problem that can occur in EST projects. However, very few studies have addressed this. We propose three new methods to detect slippage artifacts: arithmetic mean method, geometric mean method, and echo coverage method. Each method is simple and has two different strategies for processing sequences: suffix and subsequence. Using the 291,689 EST sequences produced in the SUCEST project, we performed comparative tests between our proposed methods and the SUCEST method. The subsequence strategy is better than the suffix strategy, because it is not anchored at the end of the sequence, so it is more flexible to find slippage at the beginning of the EST. In a comparison with the SUCEST method, the advantage of our methods is that they do not discard the majority of the sequences marked as slippage, but instead only remove the slipped artifact from the sequence. Based on our tests the echo coverage method with subsequence strategy shows the best compromise between slippage detection and ease of calibration. (+info)
N-fertilizer saving by the inoculation of Gluconacetobacter diazotrophicus and Herbaspirillum sp. in micropropagated sugarcane plants.
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Colonization of micropropagated sugarcane plants by Gluconacetobacter diazotrophicus and Herbaspirillum sp. was confirmed by a dot-immunoblot assay. In all, a 45-day short-term and 180-day long-term experiments conducted on micropropagated sugarcane plants of Co 86032, a sugar rich popular variety in South India, indicated the usefulness of these diazotrophs as plant growth promoting bacteria. Co-inoculation of these two bacteria enhanced the biomass considerably under N-limited condition in the short duration experiment. In the long-term experiment, the establishment of inoculated Herbaspirillum sp. remained stable with the age of the crop up to 180 days, while there was a reduction in population of G. diazotrophicus for the same period. The total bio-mass and leaf N were higher in plants inoculated with G. diazotrophicus and Herbaspirillum sp. without N fertilization and also in plants with 50% of the recommended N (140 kg ha(-1)) than the plants fertilized with recommended dose of inorganic N (280 kg ha(-1)). This experiment showed that inoculation with these bacteria in sugarcane variety Co 86032 could mitigate fertilizer N application considerably in sugarcane cultivation. (+info)
Effect of low quality effluent from wastewater stabilization ponds to receiving bodies, case of Kilombero sugar ponds and Ruaha river, Tanzania.
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A study was conducted in a sewage system at Kilombero Sugar Company to review its design, configuration, effectiveness and the quality of influent and effluent discharged into the Ruaha river (receiving body). The concern was that, the water in the river, after effluent has joined the river, is used as drinking water by villages located downstream of the river. Strategic sampling at the inlet of the oxidation pond, at the outlet and in the river before and after the effluent has joined the receiving body (river) was undertaken. Samples from each of these locations were taken three times, in the morning, noon and evening. The sample were then analysed in the laboratory using standard methods of water quality analysis. The results showed that the configuration and or the layout of the oxidation ponds (treatment plant) were not in accordance with the acceptable standards. Thus, the BOD5 of the effluent discharged into the receiving body (Ruaha River) was in the order of 41 mg/l and therefore not meeting several standards as set out both by Tanzanian and international water authorities. The Tanzanian water authorities, for example, requires that the BOD5 of the effluent discharged into receiving bodies be not more that 30 mg/l while the World Health Organization (WHO) requires that the effluent quality ranges between 10 - 30 mg/l. The paper concludes that proper design of treatment plants (oxidation ponds) is of outmost importance especially for factories, industries, camps etc located in rural developing countries where drinking water from receiving bodies like rivers and lakes is consumed without thorough treatment. The paper further pinpoint that both owners of treatment plants and water authorities should establish monitoring/management plan such that treatment plants (oxidation ponds) could be reviewed regarding the change on quantity of influent caused by population increase. (+info)
Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize.
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In a previous study, nitrogen-fixing isolates were recovered from the rhizosphere of maize and from surface-sterilized leaves of sugar cane cultivated in Rio de Janeiro, Brazil. On the basis of 16S rRNA gene sequence similarities, these isolates were identified as belonging to the genus Burkholderia, and whole-cell-protein profiles demonstrated that they are closely related to each other. In the present study, novel isolates were recovered from the roots of different sugar-cane varieties cultivated in diverse geographical regions of Brazil. Twenty-one nitrogen-fixing isolates were analysed using polyphasic taxonomy criteria, including DNA-DNA relatedness, 16S rRNA gene sequence similarities, fatty acid profiles, whole-cell-protein patterns and multilocus enzyme electrophoresis profiles, as well as morphological, physiological and biochemical characterization. The analysis confirmed that these isolates belong to a novel species within the genus Burkholderia, for which the name Burkholderia silvatlantica sp. nov. is proposed. The type strain, SRMrh-20(T) (=LMG 23149(T)=ATCC BAA-1244(T)), was isolated from the rhizosphere of maize var. Avantis A2345 cultivated in Seropedica, Rio de Janeiro. (+info)
Genetic segregation of microsatellite markers in Saccharum officinarum and S. spontaneum.
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Genetic mapping techniques can be used to study the interaction between two different genomes after hybridization. This study investigated a Saccharum officinarum (Green German or GG, 2n approximately 11x approximately 110) x S. spontaneum (IND 81-146 or IND, 2n approximately 7x approximately 56) interspecific cross. Segregation of 193 microsatellite (SSR) loci was evaluated in the F(1) progeny of 169 full-sibs of the cross. Following the two-way pseudo-testcross strategy and 'cross pollination' population type, linkage groups (LG) and phases were established for each parent map, using the criteria of LOD score > or = 3.0 and a maximum recombination frequency of 0.35. Of the 193 markers analyzed, 61 were IND-specific, 106 were GG-specific, and 26 were heterozygous in both parents. About 78% of the markers segregated in a Mendelian fashion and 22% were distorted (as evaluated by chi(2)-tests, P < or = 0.01). The GG map included 91 marker loci arranged into 25 LG covering 1180 cM of the officinarum genome. The IND map consisted of 46 marker loci assembled into 10 LG, which spanned 614 cM of the spontaneum genome. A specific chromosome associated with segregation distortion was detected in the female (GG) genome only, probably as a result of double reduction. The segregation patterns of the marker loci indicated a centromere-driven distortion process with the shared allelic markers (as putative centromeres) regulating the placement and association of markers with opposite phase (coupling vs repulsion) and dosage on either side. Although incomplete, the framework maps were informative with respect to segregation distortion, chromosome fusion, rearrangements, and translocations, observed in both parental genomes as a result of their merger. (+info)
The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical.
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The helical junction region of a -1 frameshift stimulating hairpin-type mRNA pseudoknot from sugarcane yellow leaf virus (ScYLV) is characterized by a novel C27.(G7-C14) loop 2-stem 1 minor groove base triple, which is stacked on a C8+.(G12-C28) loop 1-stem 2 major groove base triple. Substitution of C27 with adenosine reduces frameshifting efficiency to a level just twofold above the slip-site alone. Here, we show that the global structure of the C27A ScYLV RNA is nearly indistinguishable from the wild-type counterpart, despite the fact that the helical junction region is altered and incorporates the anticipated isostructural A27.(G7-C14) minor groove base triple. This interaction mediates a 2.3-A displacement of C8+ driven by an A27 N6-C8+ O2 hydrogen bond as part of an A(n-1).C+.G-Cn base quadruple. The helical junction regions of the C27A ScYLV and the beet western yellows virus (BWYV) pseudoknots are essentially superimposable, the latter of which contains an analogous A25.(G7-C14) minor groove base triple. These results reveal that the global ground-state structure is not strongly correlated with frameshift stimulation and point to a reduced thermodynamic stability and/or enhanced kinetic lability that derives from an altered helical junction architecture in the C27A ScYLV RNA as a significant determinant for setting frameshifting efficiencies in plant luteoviral mRNA pseudoknots. (+info)
Survival of Trypanosoma cruzi in sugar cane used to prepare juice.
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Chagas disease can be transmitted to man by many different means, including contact with infected triatomine feces, blood transfusion, laboratory accidents, organ transplants, and congenital or oral routes. The latter mode has received considerable attention recently. In this assay, we evaluate the survival of Trypanosoma cruzi contaminating sugar cane used to prepare juice, as well as the viability and capacity for infection by the parasite after recovery. Thirty triatomines were contaminated with T. cruzi Y strain and 45 days later pieces of sugar cane were contaminated with the intestinal contents of the insects. The pieces were ground at different intervals after contamination (time=0, 1, 4, 6, 12 and 24 hours) and the juice extracted and analyzed. Different methods were used to show T. cruzi in the juice: direct analysis, hematocrit tube centrifugation and QBC, and experimental inoculation in 47 female BALB/c mice (five control mice and seven mice for each interval examined (five inoculated orally and two intraperitoneally). Positive results were found using the direct analysis and QBC methods for juice prepared up to 12 hours after initial contamination. However, by the centrifugation technique, positivity was found only up to four hours after contamination of the sugar cane. Inoculated animals showed parasitemia during a 14 day observation period, demonstrating the high survival rate of T. cruzi in sugar cane. (+info)
Lack of cholesterol-lowering efficacy of Cuban sugar cane policosanols in hypercholesterolemic persons.
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BACKGROUND: More than 50 studies have reported substantial reductions in plasma lipid concentrations in response to 2-40 mg Cuban sugar cane policosanol (SCP) mixtures/d. However, several animal and human trials conducted outside of Cuba that used non-Cuban mixtures have failed to reproduce the efficacy of policosanols observed in earlier studies. OBJECTIVE: The objective was to evaluate lipid-modulating actions of the authentic Cuban SCPs on plasma lipids in healthy hypercholesterolemic volunteers. DESIGN: Twenty-one volunteers consumed, under supervision, 10 mg SCPs/d or a placebo incorporated in margarine as an afternoon snack, for a period of 28 d with the use of a randomized, double-blind crossover study design. Subjects maintained their habitual diet and physical activity and were weighed daily throughout the study period. Blood was collected at days 1, 2, 28, and 29 of the feeding trial, and lipid concentrations were measured. RESULTS: Body weights did not vary significantly throughout the trial and did not affect plasma lipid values. No significant difference was observed between treatment and control groups in plasma total, LDL-, HDL-cholesterol, and triacylglycerol concentrations. CONCLUSION: Present results show no beneficial effects of Cuban SCPs on lipid indicators in hypercholesterolemic persons and question the clinical usefulness of policosanol mixtures as cholesterol-lowering neutraceutical agents. (+info)