A high-resolution radiation hybrid map of the human genome draft sequence

We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases.     

Occupancy pattern of a long-horned beetle in a variegated forest landscape: linkages between tree quality and forest cover across spatial scales

Context

Interactions between landscape-scale processes and fine-grained habitat heterogeneity are usually invoked to explain species occupancy in fragmented landscapes. In variegated landscapes, however, organisms face continuous variation in micro-habitat features, which makes necessary to consider ecologically meaningful estimates of habitat quality at different spatial scales.

Objectives

We evaluated the spatial scales at which forest cover and tree quality make the greatest contribution to the occupancy of the long-horned beetle Microplophorus magellanicus (Coleoptera: Cerambycidae) in a variegated forest landscape.

Methods

We used averaged data of tree quality (as derived from remote sensing estimates of the decay stage of single trees) and spatially independent pheromone-baited traps to model the occurrence probability as a function of multiple cross-scale combinations between forest cover and tree quality (with scales ranging between 50 and 400 m).

Results

Model support and performance increased monotonically with the increasing scale at which tree quality was measured. Forest cover was not significant, and did not exhibit scale-specific effects on the occurrence probability of M. magellanicus. The interactive effect between tree quality and forest cover was stronger than the independent (additive) effects of tree quality and particularly forest cover. Significant interactions included tree quality measured at spatial scales ≥200 m, but cross-scale interactions occurred only in four of the seven best-supported models.

Conclusions

M. magellanicus respond to the high-quality trees available in the landscape rather than to the amount of forest per se. Conservation of viable metapopulations of M. magellanicus should consider the quality of trees at spatial scales >200 m.

     

QTL mapping and analysis of epistatic interactions for grain yield and yield-related traits in <Emphasis Type="Italic">Triticum turgidum</Emphasis> L. var. <Emphasis Type="Italic">durum</Emphasis>

A quantitative trait loci (QTL) analysis of grain yield and yield-related traits was performed on 93 durum wheat recombinant inbred lines derived from the cross UC1113 × Kofa. The mapping population and parental lines were analyzed considering 19 traits assessed in different Argentine environments, namely grain yield, heading date, flowering time, plant height, biomass per plant, and spikelet number per ear, among others. A total of 224 QTL with logarithm of odds ratio (LOD) ≥ 3 and 47 additional QTL with LOD > 2.0 were detected. These QTL were clustered in 35 regions with overlapping QTL, and 12 genomic regions were associated with only one phenotypic trait. The regions with the highest number of multi-trait and stable QTL were 3BS.1, 3BS.2, 2BS.1, 1BL.1, 3AL.1, 1AS, and 4AL.3. The effects of epistatic QTL and QTL × environment interactions were also analyzed. QTL putatively located at major gene loci (Rht, Vrn, Eps, and Ppd) as well as additional major/minor QTL involved in the complex genetic basis of yield-related traits expressed in Argentine environments were identified. Interestingly, the 3AL.1 region was found to increase yield without altering grain quality or crop phenology.     

The role of feral mammals on wildlife infectious disease prevalence in two nature reserves within Mexico City limits.

Wild and feral medium-sized mammals were live trapped at two natural protected areas within the Mexico City limits to determine antibody prevalence for the most common infectious diseases (rabies, toxoplasmosis, and canine parvovirus) in dogs and cats. Mammals were trapped during the dry (March-April) and rainy seasons (July-August) of 1996 and 1997. A total of 68 individuals were captured, representing 8 species: opossums (Didelphis virginiana), ringtails (Bassariscus astutus), spotted skunks (Spilogale gracilis), weasels (Mustela frenata), rock squirrels (Spermophilus variegatus), Mexican gray squirrels (Sciurus aureogaster), feral cats (Felis catus), and feral dogs (Canis familiaris). There was marked seroprevalence for parvovirus (86.6%) and lower seroprevalences for both toxoplasma (23.9%) and rabies (17.9%). There were no significant prevalence differences among mammals in both protected areas, which were of contrasting size and isolation (i.e., small and isolated versus large and nonisolated). We suggest that high seroprevalence of these three infectious agents in wild mammals is a result of the high densities of feral dogs and cats in the two areas sampled. Feral dogs are able to maintain the infectious agents in these localities regardless of the protected area size and isolation. However, the native mammals of the small and isolated reserve are more vulnerable to infectious diseases because of small population size and genetic bottlenecks. Our results indicate that natural areas in and around Mexico City are a refugium for latent infectious agents, several of which are zoonotic. These findings suggest that conservation measures, such as eradication of feral mammals and vaccination programs, in the protected areas and surrounding areas could be beneficial.     

Development and evaluation of an enzyme-linked immunosorbent assay for the serodiagnosis of pythiosis in dogs

Pythiosis (caused by the aquatic oomycete Pythium insidiosum) is a devastating and often fatal cause of either severe transmural gastroenteritis or locally invasive subcutaneous disease in dogs living in the southeastern United States. Although early diagnosis is essential for successful treatment, tools available for this task are limited. Therefore, we developed and evaluated an enzyme-linked immunosorbent assay (ELISA) for the detection of anti-P insidiosum antibodies in canine serum. A soluble mycelial extract of P insidiosum was utilized as antigen in the ELISA, which was used to evaluate serum from 43 dogs with pythiosis, 8 dogs with lagenidiosis (another canine oomycosis), 16 dogs with nonoomycotic fungal or algal infections, 22 dogs with nonfungal gastrointestinal or skin disease, and 55 healthy dogs. Results were expressed as percent positivity (PP) relative to a strong positive control serum run on each plate. Medians and ranges for each of the 5 groups were as follows: pythiosis (81.7%, 50.6-98.5%), lagenidiosis (17.3%, 11.3-29.2%), other fungal or algal infections (8.2%, 4.7-15.4%), nonfungal gastrointestinal or skin disease (6.2%, 3.9-20.7%), and healthy dogs (6.7%, 3.0-15.2%). When using a cutoff value of 40% PP, the sensitivity and specificity of the ELISA both were 100%. In addition, ELISA values measured after successful surgical therapy in 2 dogs showed a decrease of anti-P insidiosum antibody concentrations into the normal range as early as 2 months after treatment. We conclude that the ELISA is a sensitive and specific test for the diagnosis of canine pythiosis, and may be a useful tool for monitoring response to medical or surgical therapy.     

Effects of Plant Defence Activators on Anthracnose Disease of Cashew

The plant defence activators acibenzolar-S-methyl (Benzo[1,2,3]thiadiazole-7-carbothioic acid-S-methyl ester, ASM), 2,6-dichloro-isonicotinic acid (DCINA), salicylic acid (SA), and dibasic potassium phosphate (K₂HPO₄) were tested for their ability to protect cashew (Anacardium occidentale) seeds and leaves from anthracnose disease caused by Colletotrichum gloeosporioides. No inhibition of the early stages of pathogen development was caused by concentrations equal to or lower than 1.1mM a.i. ASM, 1.2mM a.i. DCINA, 5mM SA and 50mM K₂HPO₄. Maximum reduction of the disease in detached leaves, without phytotoxic effects, was obtained with 0.07mM a.i. ASM and DCINA, 5mM SA, and 50mM K₂HPO₄, with a time interval of at least 72h between application of the activator and inoculation with the pathogen. On attached leaves, foliar sprays were slightly more efficient than soil drench treatments, with 5mM SA being the most effective treatment, while 50mM SA as well as 0.3mM a.i. ASM and DCINA caused phytotoxic effects. In field-grown plants, protection was conferred by a soil drench of concentrations as low as 12.6M a.i. ASM and DCINA and 2.6mM SA. These concentrations were not phytotoxic suggesting that plant defence activators have potential for control of anthracnose disease in the field.     

Genetic evaluation of Prosopis alba (algarrobo) in Argentina for cloning elite trees

Algarrobo (Prosopis alba) is an important nitrogen-fixing tree adapted to the semiarid regions of northwestern Argentina. The tree provides fuelwood and dimensionally stable lumber for flooring and furniture; its pods that have a high sugar content are consumed by livestock and humans. P. alba has been one of the most heavily harvested species. This paper reports on the evaluation of a nine-year-old Prosopis alba progeny trial containing 57 half-sibling families of eight provenances in northwestern Argentina (of the 1,596 trees planted, 1,289 survived in 1999). Considering the multiple uses of P. alba, the selection criteria included: total biomass production (from basal diameter using regression equations), height, rate of pod production, and pod sensory characteristics. The family-narrow-sense-heritability was 0.487 for height. 0.548 for biomass production, and 0.244 for pod production. In 1998, 12 of the 1,289 trees were more than 4 m tall and had more than 1.75 kg pods per tree; and their pods had a sweet or very sweet non-astringent taste. Scions from these 12 trees were successfully grafted onto unselected P. alba rootstock. These are currently being used to produce rooted cuttings. The pod production, biomass, and height of the 12 clones ranged from 6.55 to 14.4, 1.57 to 13.5, and 1.29 to 1.70 times the respective population means. The genetic gains of 13.5%, 77%, and 147% for height, biomass, and pod production respectively are greater than genetic gains for other tree species and are probably due to the great genetic variability in the local population and the lack of any prior genetic improvement program.This revised version was published online in November 2005 with corrections to the Cover Date.     

Effect of single Quercus ilex trees upon spatial and seasonal changes in soil water content in dehesas of central western Spain

The spatial and temporal evolution of soil water content (θ) in Quercus ilex dehesas has been investigated to determine how trees modify the soil water dynamics and the nature of tree-grass interactions in terms of soil water use in these ecosystems. Soil physical parameters and θ were measured at different distances from the tree trunk (2–30 m) in the upper 300 cm of soil. θ was measured monthly by TDR during 2002–2005. Tree water potential was determined during the summers of 2004 and 2005. At deeper soil layers, mean θ values were higher beyond than beneath tree canopy during dry periods. θ depletion beyond tree canopy continued even in summer, when herbaceous plants dried up, suggesting that trees uptake water from the whole inter-tree space. Results have shown a high dependence of trees on deep water reserves throughout late spring and summer, which helps to avoid competition for water with herbaceous vegetation.     

Growth and development of the arborescent cactus Stenocereus queretaroensis in a subtropical semiarid environment,including effects of gibberellic acid

In Stenocereus queretaroensis (Weber) Buxbaum, an arborescent cactus cultivated in Jalisco, Mexico, for its fruits but studied here in wild populations, stem extension occurred in the autumn at the beginning of the dry season, flowering and fruiting occurred in the spring at the end of the dry season, and new roots grew in the summer during the wet season. The asynchrony of vegetative and reproductive growth reduces competitive sink effects, which may be advantageous for wild populations growing in infertile rocky soils. Seasonal patterns of sugars in the roots and especially the stems of S. queretaroensis were closely related to the main phenological stages, becoming lower in concentration during periods of major stem extension. Cessation of stem extension occurred in 100-year-old plants for which injection of GA(3) reinitiated such growth. Isolated chlorenchyma cylinders had maximum extension in a bathing solution containing 0.1 &mgr;M gibberellic acid.     

Why extensive research and development did not promote use of peach palm fruit in Latin America

Agroforestry Systems - Peach palm (Bactris gasipaes) was domesticated as a fruit crop by the first Amazonians in traditional Neotropical agroforestry systems, but research and development...