Bamboo hedgerow systems in Kerala, India: Root distribution and competition with trees for phosphorus

In a field study on bamboo (Bambusa arundinacea (Retz.) Willd.) hedgerow systems of Kerala, we tested the following three hypotheses: (1) Effective root foraging space is a function of crown spread, (2) Proximity of trees depress lateral spread of roots in mixed species systems and (3) The closer the trees are located the greater will be the subsoil root activity which in turn facilitates active absorption of nutrients from deeper layers of the soil profile. Root distribution of boundary planted bamboo and root competition with associated trees in two binary mixtures, teak (Tectona grandis)-bamboo and Malabar white pine (Vateria indica)-bamboo, were evaluated using modified logarithmic spiral trenching and ³²P soil injection techniques respectively. Excavation studies indicate that rooting intensity declined linearly with increasing lateral distance. Larger clumps manifested wider foraging zones. Eighty three per cent of the large clumps (>4.0 m dia.) extended roots beyond 8 m while only 33% of the small (<2.5 m dia.) clumps extended roots up to 8 m. Highest root counts were found in the 10–20 cm layer with nearly 30% of total roots. Although nearness of bamboo clumps depressed root activity of teak and Vateria in the surface layers of the soil profile, root activity in the deeper layers was stimulated. ³²P recovery was higher when applied at 50-cm depth than at 25-cm depth implying the safety net role of tree roots for leached down nutrients. Inter specific root competition can be regulated by planting crops 8–9 m away from the bamboo clumps and/or by canopy reduction treatments. This revised version was published online in June 2006 with corrections to the Cover Date.     

Genome size variation in three Saccharum species

Saccharum species are autopolyploids with ploidy level ranging from 5× to 16x, and are considered the most complex genomes among crop plants. In present study, the genome sizes of 28 Saccharum spontaneum accessions, 15 Saccharum officinarum accessions, 28 Saccharum robustum accessions, and 12 Saccharum hybrids spp. were analyzed using flow cytometry. The estimated genome sizes of S. officinarum accessions ranged from 7.50 to 8.55?Gb with an average size of 7.88?Gb. In S. robustum, the estimated genome sizes ranged from 7.65 to 11.78, reflecting the variation of ploidy level. In S. spontaneum, the estimated genome sizes varied widely, with a range from 3.36 to 12.64?Gb, also due to variation of ploidy level. The average monoploid genome size of S. officinarum was 985?Mb, and that of S. spontaneum was 843?Mb. The results also showed that genome sizes were correlated with chromosome numbers, and based which, that the unknown chromosome numbers of some accessions could be predicted. The estimated genome sizes of Saccharum germplasm also helped identify some mislabeled accessions and yielded information critical for sugarcane breeding and genome sequencing programs.     

Identification and fine-mapping of Xa33, a novel gene for resistance to Xanthomonas oryzae pv. oryzae

Broadening of the genetic base for identification and transfer of genes for resistance to insect pests and diseases from wild relatives of rice is an important strategy in resistance breeding programs across the world. An accession of Oryza nivara, International Rice Germplasm Collection (IRGC) accession number 105710, was identified to exhibit high level and broad-spectrum resistance to Xanthomonas oryzae pv. oryzae. In order to study the genetics of resistance and to tag and map the resistance gene or genes present in IRGC 105710, it was crossed with the bacterial blight (BB)-susceptible varieties 'TN1' and 'Samba Mahsuri' (SM) and then backcrossed to generate backcross mapping populations. Analysis of these populations and their progeny testing revealed that a single dominant gene controls resistance in IRGC 105710. The BC(1)F(2) population derived from the cross IRGC 105710/TN1//TN1 was screened with a set of 72 polymorphic simple-sequence repeat (SSR) markers distributed across the rice genome and the resistance gene was coarse mapped on chromosome 7 between the SSR markers RM5711 and RM6728 at a genetic distance of 17.0 and 19.3 centimorgans (cM), respectively. After analysis involving 49 SSR markers located between the genomic interval spanned by RM5711 and RM6728, and BC(2)F(2) population consisting of 2,011 individuals derived from the cross IRGC 105710/TN1//TN1, the gene was fine mapped between two SSR markers (RMWR7.1 and RMWR7.6) located at a genetic distance of 0.9 and 1.2 cM, respectively, from the gene and flanking it. The linkage distances were validated in a BC(1)F(2) mapping population derived from the cross IRGC 105710/SM//2 × SM. The BB resistance gene present in the O. nivara accession was identified to be novel based on its unique map location on chromosome 7 and wider spectrum of BB resistance; this gene has been named Xa33. The genomic region between the two closely flanking SSR markers was in silico analyzed for putatively expressed candidate genes. In total, eight genes were identified in the region and a putative gene encoding serinethreonine kinase appears to be a candidate for the Xa33 gene.     

Decrease of rice plant resistance and induction of hormesis and carboxylesterase titre in brown planthopper, Nilaparvata lugens (Stål) by xenobiotics

The brown planthopper (BPH), Nilaparvata lugens (Stål) is a serious threat to the rice production throughout Asia. The indiscriminate application of various xenobiotics in rice ecosystem is perceived as one of the factors for the frequent outbreak of BPH. The present study has critically analysed the secondary effects of some xenobiotics used in rice field on certain plant and insect parameters that subsequently favour BPH outbreak. Application of 2,4-D, carbendazim, deltamethrin and urea reduced the innate BPH resistance of PTB 33 rice variety due to favourable alterations in rice free amino acid and sucrose content. Similarly, these chemicals also induced hormesis and enhanced feeding in BPH. Alternatively, soil amendment with neem seed powder and Calotropis gigantea leaves improved plant innate resistance and showed no sign of hormesis or enhanced feeding in BPH. In addition, deltamethrin has the ability to stimulate BPH carboxylesterase titre. Native PAGE analysis of esterases from whole body homogenate of BPH revealed at least five esterase isozyme bands, prominent being E1 and E2. However, no difference in BPH esterase banding pattern was observed between different xenobiotic treatments. All these esterase bands are classified under carboxylesterase based on their inhibition by class specific esterase inhibitors.     

Prion protein in sheep urine.

The misfolded form of cellular prion protein (PrP(C)) is the main component of the infectious agent of transmissible spongiform encephalopathies and the validated biomarker for these diseases. The expression of PrP(C) is highest in the central nervous system and has been found in peripheral tissues. Soluble PrP(C) has been detected in cerebrospinal fluid, urine, serum, milk, and seminal plasma. In this study, attempts were made to characterize prion protein in urine samples from normal and scrapie-infected sheep. Urine samples from scrapie-infected sheep and age-matched healthy sheep were collected and analyzed by Western blot following concentration. A protease K-sensitive protein band with a molecular weight of approximately 27-30 kDa was visualized after immunoblotting with anti-PrP monoclonal antibodies to a C-terminal part of PrP(C), but not after immunoblotting with monoclonal antibodies to an N-terminal epitope of PrP(C) or with secondary antibodies only. The amount of PrP(C) in the urine of 49 animals (control group: n = 16; naturally scrapie-infected group: n = 33) was estimated by comparison with known amounts of ovine recombinant PrP in the immunoblot. Background concentration of PrP(C) in urine was found to be 0-0.16 ng/ml (adjusted to the initial nonconcentrated volume of the urine samples). Seven out of 33 naturally scrapie-infected animals had an elevated level (0.3-4.7 ng/ml) of PrP(C) in urine. The origin of PrP(C) in urine and the reason for the increased level of PrP(C) in scrapie-infected sheep urine has yet to be explored.     

Direct shoot organogenesis from leaf explants of Embelia ribes Burm. f.: a vulnerable medicinal plant

An efficient system was developed for direct plant regeneration from in vitro-derived leaf explants of Embelia ribes Burm. f., a vulnerable medicinal woody climber of the Western Ghats of India. The in vitro procedure involved three steps that included induction of shoot initials from leaf tissue, regeneration and elongation of shoots from the shoot initials, and rooting of shoots. The induction of shoot initials was achieved on Murashige and Skoog (MS) solid medium supplemented with different concentrations of thidiazuron (TDZ). The best medium for shoot induction was MS with 0.272 μM TDZ. Numerous shoot primordia developed within 2–3 weeks on the leaf margin as well as on the midrib region, without any callus phase. In the second step, the shoot clumps separated from the leaf explant on transfer to MS basal medium, resulting in the differentiation of 90% of the shoot initials into well-developed shoots. The 2- to 3-cm-long shoots rooted on half-strength MS basal medium supplemented with 4.90 μM indole-3-butyric acid (IBA) and 3% (w/v) sucrose in the third stage. The rooted plants could be established in soil with 70% success. This protocol could be utilized for in vitro propagation and conservation of this important threatened medicinal plant.     

Detection of Rabies Virus Genes by <Emphasis Type="Italic">In-Situ</Emphasis> Polymerase Chain Reaction

Rabies is diagnosed by FAT in the impression smears of brain tissues. In this study, an attempt was made to diagnose rabies using in situ polymerase chain reaction (ISPCR). A digoxigenin-labelled double-stranded probe specific for a portion of the ‘N’ gene of rabies virus was used. Positive signals were identified as blue dots in the intraneuronal and neuropil areas.     

Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment

With the objective of identifying SSR markers that can distinguish parental lines of rice hybrids, we characterized 10 each of cytoplasmic male sterile (CMS) and restorer (R) lines along with 10 popular Indian rice varieties using a set of 48 hyperpolymorphic SSRs distributed uniformly across the rice genome. All the SSR markers were polymorphic, amplifying a total of 163 alleles, with an average of 3.36 ± 1.3 allelic variants per locus. Twenty-seven SSR markers showed amplification of an allele, which was very specific and unique to a particular parental line and not amplified in any other rice genotype tested. Through multiplex PCR, SSR marker combinations that were unique to a particular parental line or hybrid were also identified. With a set of 10 SSR markers, all the public bred Indian rice hybrids along with their parental lines could be clearly distinguished. To utilize these SSR markers effectively for detection of impurities in parental lines, a two dimensional bulked DNA sampling strategy involving a 20 × 20 grow-out matrix has been designed and used for detection of contaminants in a seed-lot of the popular CMS line IR58025A. We have also designed a multiplex PCR strategy involving single tube analysis using 2–3 markers for hybrid seed purity assessments and demonstrate its superiority over single marker analysis in accurate detection of impurities in hybrids. Implications of parental and hybrid specific SSR markers and strategies to utilize the informative SSR markers for detection of contaminants in a cost effective manner are discussed.     

Infrasound at long range from saturn v, 1967

Two distinct groups of infrasonic waves from Saturn V, 1967, were recorded at Palisades, New York, 1485 kilometers from the launch site. The first group, of 10-minute duration, began about 70 minutes after launch time; the second, having more than twice the amplitude and a duration of 9 minutes, commenced 81 minutes after launch time. From information on the Saturn V trajectory and analysis of recorded data, it is established that the first group represents sound emitted either by the first stage reentry or by the second stage when its elevation was above 120 kilometers. The second, more intense wave group represents the sound from the powered first stage. A reversal of signal occurs because the rocket outran its own sound. Fourier analyses indicate that the energy extends to relatively long periods-10 seconds for the first stage and 7 seconds for the second. Trapping of sound in the upper atmospheric sound channel can be the cause of the separation of the signal into two distinct groups.     

Prediction of heterosis for grain yield in rice using 'key' informative EST-SSR markers

This study was undertaken to assess the comparative potential of 25 Expressed Sequence Tag derived simple sequence repeats (EST-SSRs) and 25 genomic SSRs in the prediction of grain yield heterosis using a set of nine cytoplasmic male sterile (CMS) lines and 32 restorer lines of rice. EST-SSRs and genomic SSRs exhibited an average Polymorphism Information Content value of 0.37 and 0.45, respectively. The coefficient of marker polymorphism among parental lines with respect to a set of hypervariable EST and genomic SSRs was correlated with standard heterosis for grain yield of six public bred rice hybrids. EST-SSRs gave a better correlation (r = 0.75) as compared with genomic SSRs (r = 0.09). When 10 'key' informative EST-SSR markers which showed a higher positive correlation with grain yield heterosis were validated in a new set of 14 experimental hybrids, the markers exhibited a higher correlation (r = 0.79), indicating the predictive value of these EST-SSRs. We recommend these 10 'key' informative EST-SSR markers for analysis of genetic diversity of parental lines and prediction of heterosis in hybrid rice breeding programmes.