Combo: a whole genome comparative browser

SUMMARY: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats. AVAILABILITY: Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs on multiple platforms and is freely available for download at http://www.broad.mit.edu/annotation/argo/.     

The Vertical Pattern of Rooting and Nutrient Uptake at Different Altitudes of a South Ecuadorian Montane Forest

The vertical pattern of root length densities (RLD) of fine roots (<2 mm in diameter) and nitrogen (N) uptake potential were determined at different altitudes (1,900, 2,400, and 3,000 m a.s.l.) of a tropical montane forest in order to improve our knowledge about the depth distribution of nutrient uptake in this ecosystem. At higher altitudes, precipitation rate and frequency of fog were higher than at lower altitudes while mean annual air temperature decreased with increasing altitude. Soils were always very acid with significantly lower pH at a depth of 0.0–0.3 m in mineral soil at 3,000 m (2.8–2.9) than at 1,900 and 2,400 m (3.1–3.5). The vertical distribution of RLD was very similar both during the dry and the rainy season. During the dry season the percentage of root length in the organic layer increased from 51% at 1,900 m to 61% at 2,400 m and 76% at 3,000 m. At 3,000 m, RLD was markedly higher in the upper 0.05 m than in the remaining organic layer, whereas at 1,900 m and 2,400 m RLD were similar in all depths of the organic layer. In mineral soil, RLD decreased to a greater degree with increasing soil depth at the upper two study sites than at 1,900 m. The relative N uptake potential from different soil layers (RNUP) was determined by ¹⁵N enrichment of leaves after application of ¹⁵N enriched ammonium sulphate at various soil depths. RNUP closely followed fine root distribution confirming the shallower pattern of nutrient uptake at higher altitudes. RNUP was very similar for trees, shrubs and herbs, but shallower for saplings which obtained N only from the organic layer at both altitudes. Liming and fertilizing (N, P, K, Mg) of small patches in mineral soil had no significant impact on fine root growth. We conclude that the more superficial nutrient uptake ability at higher altitudes may be partly related to increased nutrient input from canopy by leaching. However, the specific constraints for root growth in the mineral soil of tropical montane forests warrant further investigations.     

Root Morphology and Anchorage of Six Native Tree Species from a Tropical Montane Forest and an Elfin Forest in Ecuador

Root architecture of tree species was investigated at two different altitudes in tropical forests in Ecuador. Increasing altitude was accompanied by higher wind speeds and more shallow soils, while slope angles of both sites were comparable (20–50°). Three tree species typical for the montane forest at 1900 m (Graffenrieda emarginata (Ruiz & Pav.) Triana (Melastomataceae), Clethra revoluta (Ruiz & Pav.) Spreng. (Clethraceae), Vismia tomentosa Ruiz & Pav. (Clusiaceae)) and for the elfin forest at 3000 m (Weinmannia loxensis Harling (Cunoniaceae), Clusia spec. (Clusiacaea) Styrax foveolaria Perkins (Styraceae)) were examined. At 1900 m, 92% of the trees grew upright, in comparison to 52% at 3000 m. At 3000 m, 48% of the trees were inclined, lying or even partly uprooted. At this altitude, all trees with tap roots or with shoots connected by coarse rhizomes, 83% of the trees with stilt roots, and 50% of the trees in which stems or roots were supported by other trees grew upright, suggesting that these characteristics were relevant for tree stability. Root system morphology differed markedly between altitudes. In contrast to 1900 m, where 20% of structural roots originated in the deeper mineral soil, root origin at 3000 m was restricted to the forest floor. The mean ratio of root cross sectional area to tree height decreased significantly from 6.1 × 10⁻³ m² m⁻¹ at 1900 m to 3.2 × 10⁻³ m² m⁻¹ at 3000 m. The extent of root asymmetry increased significantly from 0.29 at 1900 m to 0.62 at 3000 m. This was accompanied by a significantly lower number of dominant roots at 3000 m (2.3 compared to 3.8 at 1900 m). In conclusion, native tree species growing in tropical montane and elfin forests show a variety of root traits that improve tree stability. Root system asymmetry is less important for tree stability where anchorage is provided by a deep and solid root–soil plate. When deep rooting is impeded, root traits improving the horizontal extension of the root–soil plate are more pronounced or occur more frequently. Furthermore, mutual mechanical support of roots and stems of neighboring trees seems to be an appropriate mechanism to provide anchorage in soils with low bulk density and in environments with high wind speeds.     

Biomphalaria tenagophila: dynamics of populations of resistant and susceptible strains to Schistosoma mansoni, with or without pressure of the parasite

Resistant (Taim, RS) and susceptible albino (Joinville, SC) Biomphalaria tenagophila populations were kept together, at different proportions, throughout a 18-month-period. Some of the snail groups were submitted to Schistosoma mansoni infection. The targets of this study were (a) to analyze the populational dynamics among resistant and susceptible individuals to S. mansoni; (b) to study the resistance phenotype in descendants of cross-breeding; (c) to observe whether the parasite could exert any kind of selection in those snail populations. Throughout the experiment it could be observed that the susceptible B. tenagophila strain (Joinville) underwent a selective pressure of the parasite that was negative, since the individuals showed a high mortality rate. Although B. tenagophila (Taim) population presented a higher mortality rate without pressure of the parasite, this event was compensated by a reproductive capacity. B. tenagophila Taim was more fecund than B. tenagophila Joinville and was able to transmit the resistance character to their descendants. F1 generation obtained by cross-breeding between resistant and susceptible lineages was completely resistant to S. mansoni infection, irrespective of the Taim proportion. Moreover, less than 5% of F2 progeny were susceptible to S. mansoni infection.     

The effect of gap length on double-strand break repair in Drosophila

When a double-strand break has a gap between the broken ends, the missing information can be restored through synthesis from a homologous template. Here we address the question of how long such a gap can be before this process fails. We measured the frequency of homologous repair in the Drosophila germ line following the creation of gaps of specific sizes ranging from 3.8 to 210 kb. We found that gaps of 11 kb.     

Natural Spread of Plant Viruses by Birds

Observations made in Mali strongly suggest that Rice yellow mottle virus (RYMV) is spread by weaverbirds (Quelea quelea) below and around baobab trees (Adansonia digitata) in which they nest. Rice leaves in bird nests appeared to be infected. In Spain, an infection of Southern bean mosaic virus (SBMV) in string (climbing) beans (Phaseolus vulgaris) was apparently introduced and spread by sparrows (Passer domesticus) judging from the damage caused on flowers and bean pods. Damaged leaves and pods on SBMV‐infected plants were also found in a screenhouse visited by sparrows and bulbuls (Pycnonotus barbatus) in Morocco. These observations showed that both viruses could be spread by birds when either collecting infected leaves for nesting or feeding on infected plants.     

Administration of triclabendazole is safe and effective in controlling fascioliasis in an endemic community of the bolivian altiplano

Background

The Bolivian northern Altiplano is characterized by a high prevalence of Fasciola hepatica infection. In order to assess the feasibility, safety and efficacy of large-scale administration of triclabendazole as an appropriate public health measure to control morbidity associated with fascioliasis, a pilot intervention was implemented in 2008.

Materials and Methods

Schoolchildren from an endemic community were screened for fascioliasis and treated with a single administration of triclabendazole (10 mg/kg). Interviews to assess the occurrence of adverse events were conducted on treatment day, one week later, and one month after treatment. Further parasitological screenings were performed three months after treatment and again two months later (following a further treatment) in order to evaluate the efficacy of the intervention.

Results

Ninety infected children were administered triclabendazole. Adverse events were infrequent and mild. No serious adverse events were reported. Observed cure rates were 77.8% after one treatment and 97.8% after two treatments, while egg reduction rates ranged between 74% and 90.3% after one treatment, and between 84.2% and 99.9% after two treatments. The proportion of high-intensity infections (≥400 epg) decreased from 7.8% to 1.1% after one treatment and to 0% after two treatments.

Conclusion

Administration of triclabendazole is a feasible, safe and efficacious public health intervention in an endemic community in the Bolivian Altiplano, suggesting that preventive chemotherapy can be applied to control of fascioliasis. Further investigations are needed to define the most appropriate frequency of treatment.     

Prevalence of Overweight and Obesity in Elderly People in Spain

Objective: To estimate the prevalence of obesity and overweight in the older adult population in Spain by sex, age, and educational level. Research Methods and Procedures: A cross‐sectional study was carried out in 2001 in a sample of 4009 persons representative of the noninstitutionalized population ≥60 years of age. Anthropometric measurements (BMI and waist circumference) were obtained using standardized techniques and equipment. Overweight was considered at a BMI of 25 to 29.9 kg/m² and obesity at a BMI of ≥30 kg/m². Central obesity was considered at a waist circumference of >102 cm in men and >88 cm in women. Results: The mean BMI was 28.2 kg/m² in men and 29.3 kg/m² in women. The prevalence of overweight and obesity in men was 49% and 31.5%, respectively. The corresponding percentages in women were 39.8% and 40.8%. The prevalence of obesity was higher in persons with no education than in those with third level education (i.e., university studies), especially among women (41.8% vs. 17.5%). The prevalence of central obesity was 48.4% in men and 78.4% in women. Differences by educational level were seen in only women, in whom the prevalence of central obesity was 80.9% in those with no education and 59% in those with third‐level education. Discussion: The prevalence of overweight and obesity in the Spanish adult elderly population is very high. Some other populations show similar prevalences, especially in Mediterranean countries. Socioeconomic conditions in Spain during the years these cohorts were born may partly explain the high‐frequency of obesity.