The International Rice Information System. A platform for meta-analysis of rice crop data

Ambiguous germplasm identification; difficulty in tracing pedigree information; and lack of integration between genetic resources, characterization, breeding, evaluation, and utilization data are constraints in developing knowledge-intensive crop improvement programs. To address these constraints, the International Crop Information System (www.icis.cgiar.org), a database system for the management and integration of global information on genetic resources and crop improvement for any crop, was developed by genetic resource specialists, crop scientists, and information technicians associated with the Consultative Group for International Agricultural Research and collaborative partners. The International Rice Information System (www.iris.irri.org) is the rice (Oryza species) implementation of the International Crop Information System. New components are now being added to the International Rice Information System to handle the diversity of rice functional genomics data including genomic sequence data, molecular genetic data, expression data, and proteomic information. Users access information in the database through stand-alone programs and Web interfaces, which offer specialized applications and customized views to researchers with different interests.     

Predicting Species Response to Disturbance from Size Class Distributions of Adults and Saplings in a Jamaican Tropical Dry Forest

The diversity of tropical dry forests is poorly described and their regeneration ecology not well understood, however they are under severe threat of conversion and degradation. The Hellshire Hills constitute a dry limestone forest reserve on the south coast of Jamaica that is of high conservation value. In order to describe the structure and composition of this forest and assess the extent to which the population structures of its tree species do characterize their regeneration ecologies, pre-disturbance structure, floristics and seedling populations were compared with post-disturbance species responses in twelve 15 m × 15 m permanent sample plots which were laid out in a blocked design in April 1998, giving a total sample area of 0.27 ha. These plots were subjected to disturbance in April 1999 (cutting) with each of four blocks being assigned with two randomly allocated treatment plots (partially and clear cut) and one control plot (uncut). A total of 1278 trees (≥2 cm DBH) and 7863 seedlings and saplings (0–2 mm and 2–20 mm root collar diameter (RCD) respectively), comprising 60 and 52 species, respectively, were sampled in the plots prior to disturbance. The species-area curve for trees reached a maximum at 0.20 ha, and abundance was widely distributed amongst the species (26 had importance values greater than 1%); four species were notably codominant (with importance values between 7 and 8%). The forest stand structure had a reverse J-shaped curve for tree and for seedling/sapling size-class distributions, which indicated that the forest as a whole was probably regenerating adequately. From an analysis based on adult and sapling size-class distributions (SCDs), 21 species with 15 or more individuals were classified into 3 groups. Many of the species (15 of the 21), had flat adult SCDs that deviate from the whole-community reverse J-shaped SCD. However, sapling SCDs for 6 of the 15 species were strongly positive indicating the potential for their populations to be sustained by recruitment from the saplings present. No general association was found between these SCD species groupings and the actual ability of the species to recover from disturbance. Analysis of post-disturbance response revealed that for only 9 of the 21 species did adult SCDs provide adequate prediction, but for an additional 6 of the species information on sapling SCDs improved the accuracy of prediction if the ‘release’ of saplings or smaller individuals predominated recovery. However in this forest, recovery following disturbance which left stem and roots in place is predominantly by coppice regrowth, and there were no significant correlations found between adult SCDs and the species’ ability to coppice.     

Antibodies to Toxoplasma gondii in Eurasian badgers

Antibodies to Toxoplasma gondii were detected in samples collected from 90 live-trapped adult Eurasian badgers (Meles meles) sampled at three sites (two agricultural and one woodland) in southern England. Serum was tested using a qualitative latex agglutination test procedure and 63 of 90 (70%) badgers tested positive for T. gondii antibodies. Antibody prevalence varied between the sites; 67% and 77% of badgers from agricultural sites and 39% from a nonagricultural site tested positive.     

Effect of long-term cold exposure on antioxidant enzyme activities in a small mammal

Aerobic organisms continually face exposure to reactive oxygen species (ROS) and many have evolved sophisticated antioxidant systems to effectively remove them. Any increase in ROS production or weakening in this defense system may ultimately lead to oxidative stress and cellular damage. We investigated whether long-term cold exposure, which is known to lead to an elevation in metabolic rate, increased the activities of the ROS-scavenging enzymes, catalase (CAT), selenium-dependent glutathione peroxidase (GPx), and total superoxide dismutase (Total-SOD) in liver, cardiac muscle, kidney, skeletal muscle (vastus lateralis), and duodenum of short-tailed field voles (Microtus agrestis), born and maintained at either 8 +/- 3 degrees C or 22 +/- 3 degrees C. CAT, GPx, and Total-SOD activities were determined at age 61 +/- 1.9 days. An increase in CAT activity in voles maintained at 8 +/- 3 degrees C was observed in skeletal muscle (71%) and kidney (20%), with both CAT and GPx activities significantly elevated (by 40 and 43%, respectively) in cardiac muscle, when compared to voles at 22 +/- 3 degrees C. Total-SOD activity and protein content did not differ significantly between groups in any tissue. We suggest that the compensatory increases in CAT (skeletal muscle, cardiac muscle, kidney) and GPx (cardiac muscle), but not Total-SOD activities, resulting from long-term cold exposure may reflect the elevated metabolic rate, and possibly also increased ROS production, at this time.     

Plasma lipid profiling across species for the identification of optimal animal models of human dyslipidemia

In an attempt to understand the applicability of various animal models to dyslipidemia in humans and to identify improved preclinical models for target discovery and validation for dyslipidemia, we measured comprehensive plasma lipid profiles in 24 models. These included five mouse strains, six other nonprimate species, and four nonhuman primate (NHP) species, and both healthy animals and animals with metabolic disorders. Dyslipidemic humans were assessed by the same measures. Plasma lipoprotein profiles, eight major plasma lipid fractions, and FA compositions within these lipid fractions were compared both qualitatively and quantitatively across the species. Given the importance of statins in decreasing plasma low-density lipoprotein cholesterol for treatment of dyslipidemia in humans, the responses of these measures to simvastatin treatment were also assessed for each species and compared with dyslipidemic humans. NHPs, followed by dog, were the models that demonstrated closest overall match to dyslipidemic humans. For the subset of the dyslipidemic population with high plasma triglyceride levels, the data also pointed to hamster and db/db mouse as representative models for practical use in target validation. Most traditional models, including rabbit, Zucker diabetic fatty rat, and the majority of mouse models, did not demonstrate overall similarity to dyslipidemic humans in this study.     

New mechanistic explanation for the localization of ulcers in the rat duodenum: role of iron and selective uptake of cysteamine

Cysteamine, a coenzyme A metabolite, induces duodenal ulcers in rodents. Our recent studies showed that ulcer formation was aggravated by iron overload and diminished in iron deficiency. We hypothesized that cysteamine is selectively taken up in the duodenal mucosa, where iron absorption primarily occurs, and is transported by a carrier-mediated process. Here we report that cysteamine administration in rats leads to cysteamine accumulation in the proximal duodenum, where the highest concentration of iron in the gastrointestinal tract is found. In vitro, iron loading of intestinal epithelial cells (IEC-6) accelerated reactive oxygen species (ROS) production and increased [(14)C]cysteamine uptake. [(14)C]Cysteamine uptake by isolated gastrointestinal mucosal cells and by IEC-6 was pH-dependent and inhibited by unlabeled cysteamine. The uptake of [(14)C]cysteamine by IEC-6 was Na(+)-independent, saturable, inhibited by structural analogs, H(2)-histamine receptor antagonists, and organic cation transporter (OCT) inhibitors. OCT1 mRNA was markedly expressed in the rat duodenum and in IEC-6, and transfection of IEC-6 with OCT1 siRNA decreased OCT1 mRNA expression and inhibited [(14)C]cysteamine uptake. Cysteamine-induced duodenal ulcers were decreased in OCT1/2 knockout mice. These studies provide new insights into the mechanism of cysteamine absorption and demonstrate that intracellular iron plays a critical role in cysteamine uptake and in experimental duodenal ulcerogenesis.     

Fostering molecular breeding in developing countries

Molecular breeding (MB) increases genetic gain per crop cycle, stacks favourable alleles at target loci and reduces the number of selection cycles. In the last decade, the private sector has benefitted immensely from MB, which demonstrates its efficacy. In contrast, MB adoption is still limited in the public sector, and it is hardly used in developing countries. Major bottlenecks in these countries include shortage of well-trained personnel, inadequate high-throughput capacity, poor phenotyping infrastructure, lack of information systems or adapted analysis tools or simply resource-limited breeding programmes. The emerging virtual platforms aided by the information and communication technology revolution will help to overcome some of these limitations by providing breeders with better access to genomic resources, advanced laboratory services and robust analytical and data management tools. Apart from some advanced national agricultural research systems (NARS), the implementation of large-scale molecular breeding programmes in developing countries will take time. However, the exponential development of genomic resources, including for less-studied crops, the ever-decreasing cost of marker technologies and the emergence of platforms for accessing MB tools and support services, plus the increasing public–private partnerships and needs-driven demand for improved varieties to counter the global food crisis, are all grounds to predict that MB will have a significant impact on crop breeding in developing countries. These predictions are supported by some preliminary successful examples presented in this paper.     

The Intercostal NMJ Assay: a new alternative to the conventional LD50 assay for the determination of the therapeutic potency of botulinum toxin preparations

Therapeutic botulinum neurotoxin type A preparations have found an increasing number of clinical uses for a large variety of neuromuscular disorders and dermatological conditions. The accurate determination of potency in the clinical application of botulinum toxins is critical to ensuring clinical efficacy and safety, and is currently achieved by using a lethal dose (LD50) assay in mice. Ethical concerns and operational constraints associated with this assay have prompted the development of alternative assay systems that could potentially lead to its replacement. As one such alternative, we describe the development and evaluation of a novel ex vivo assay (the Intercostal Neuromuscular Junction [NMJ] Assay), which uses substantially fewer animals and addresses ethical concerns associated with the LD50 assay. The assay records the decay of force from electrically-stimulated muscle tissue sections in response to the toxin, and thus combines the important mechanisms of receptor binding, translocation, and the enzymatic action of the toxin molecule. Toxin application leads to a time-related and dose-related reduction in contractile force. A regression model describing the relationship between the applied dose and force decay was determined statistically, and was successfully tested as able to correctly predict the potency of an unknown sample. The tissue sections used were found to be highly reproducible, as determined through the innervation pattern and the localisation of NMJs in situ. Furthermore, the efficacy of the assay protocol to successfully deliver the test sample to the cellular target sites, was critically assessed by using molecular tracer molecules.     

Relationships between lamb carcass quality traits measured by X-ray computed tomography and current UK hill sheep breeding goals

Genetic parameters were estimated between current UK hill sheep breeding goals and lamb carcass composition and muscularity traits derived using X-ray computed tomography (CT). To produce these estimates, a total of 648 lambs from two hill farms were CT scanned at weaning (ca 120 days of age), over 3 years, and total weights of carcass muscle (MUSC), fat (CFAT) and bone (BONE) and internal fat (IFAT) were predicted. Previously derived muscularity indices were also calculated for the hind leg (HLMI) and lumbar (LRMI) regions, to assess muscle shape. Data for current breeding goals (lamb performance and maternal traits) were also included from a total of 10 297 lamb records and 12 704 ewe records. Heritabilities were estimated for each trait and genetic and phenotypic correlations were calculated between each CT trait and other lamb or ewe traits. Moderate to high positive genetic correlations were found between CT-predicted tissue weights and breeding goals, which were also weights (lamb weaning weight, carcass weight, mature ewe weight, average weight of lambs reared by the ewe). CFAT was positively genetically correlated with ultrasound backfat depth at weaning (UFD) and subjective fatness grade at slaughter (MLCF), suggesting that carcass fat could be decreased using selection on any of these predictors. Ultrasound muscle depth at weaning (UMD) and subjective conformation score at slaughter (MLCC) had high genetic correlations with the muscularity indices (HLMI and LRMI), but correlations with MUSC were not significantly different from zero. This implies that selection to improve MLCC is likely to be increasing the 'roundness' of muscle shape in the high-priced carcass region, but having little impact on total lean meat yield. Correlations of CT traits with the other ewe traits (number of lambs weaned, number of lambs lost, longevity, fleece weight) were generally small or not significantly different from zero. The genetic parameters generated in this study can now be used in selection index calculations to assess the benefits of including lamb CT traits in future selection programmes for hill sheep.