Analyses of domains and domain fusions in human proto-oncogenes

Background: Understanding the constituent domains of oncogenes, their origins and their fusions may shed new light about the initiation and the development of cancers. Results: We have developed a computational pipeline for identification of functional domains of human genes, prediction of the origins of these domains and their major fusion events during evolution through integration of existing and new tools of our own. An application of the pipeline to 124 well-characterized human oncogenes has led to the identification of a collection of domains and domain pairs that occur substantially more frequently in oncogenes than in human genes on average. Most of these enriched domains and domain pairs are related to tyrosine kinase activities. In addition, our analyses indicate that a substantial portion of the domain-fusion events of oncogenes took place in metazoans during evolution. Conclusion: We expect that the computational pipeline for domain identification, domain origin and domain fusion prediction will prove to be useful for studying other groups of genes. Originally published BMC Bioinformatics, Vol. 10, No. 88, Mar 200

Quantitatively assessing ecological stress of urbanization on natural ecosystems by using a landscape-adjacency index

Urban spatial expansion poses a threat to regional ecosystems and biodiversity directly through altering the size, shape, and interconnectivity of natural landscapes. Monitoring urban spatial expansion using traditional area-based metrics from remote sensing provides a feasible way to quantify this regional ecological stress. However, variation in landscape-adjacency relationships (i.e., the adjacency between individual landscape classes) caused by urban expansion is often overlooked. In this study, a novel edge-based index (landscape-adjacency index, LAdI) was proposed based on the spatial-adjacency relationship between landscape patches to measure the regional ecological stress of urban expansion on natural landscapes. Taking the entire Yangtze River Delta Urban Agglomerations (YRD) as a study area, we applied the LAdI for individual landscape classes (Vi) and landscape level (LV) to quantitatively assess change over time in the ecological stress of YRD from 1990 to 2015 at two spatial scales: municipal scale and 5 km-grid scale. The results showed that the vulnerable zones (LV ≥ 0.6) were mainly distributed in the north of the YRD, and cultivated land was the most vulnerable natural landscape (Vi ≥ 0.6) at the 5 km-grid scale. The most vulnerable landscape at the municipal scale was cultivated land in 19 of 26 cities in each period, and that in the remaining 7 cities varied at distinct urbanization stages. We used scatter diagrams and Pearson correlation analysis to compare the edge-based LAdI with an area-based index (percent of built-up area, PB) and found that: LV and PB had a significant positive correlation at both the municipal scale and 5 km-grid scale. But there were multiple LVs with different values corresponding to one PB with the same value at the 5 km-grid scale. Both indexes could represent the degree of urban expansion; however, the edge-based metric better quantified ecological stress under different urban-sprawl patterns sharing the same percent of built-up area. As changes in land use affect both the size and edge effect among landscape patches, the area-based PB and the edge-based LAdI should be applied together when assessing the ecological stress caused by urbanization

Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed

Brassica napus (AACC, 2n=38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large-scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7 and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double-low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double-low and double-high), accompanied by an increase in genetic load in the double-low group. This study demonstrates distinctive genomic footprints and deleterious SNP (Single Nucleotide Polymorphism) variants for local adaptation by recent intra- and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid cro

Revisiting the two-side optimization problem in satellite pursuit-evasion

In the present paper two-side optimization problem where the intercepting satellite pursuits the target satellite was studied. In the pursuit-evasion game the continuous thruster and the simple central gravity with J2 perturbation were involved for two satellites. With applying the functional extremum condition, the optimal control outputs of both side satellites were obtained by building the systems Hamilton function. Further, the two side optimal problem was transformed to the TPBVP, which contributed the solution with the mixed numerical method. Finally, the proposed method was validated by the numerical simulation, where the optimal interception and escaping trajectories were illustrated

Revisiting the two-side optimization problem in satellite pursuit-evasion

In the present paper two-side optimization problem where the intercepting satellite pursuits the target satellite was studied. In the pursuit-evasion game the continuous thruster and the simple central gravity with J2 perturbation were involved for two satellites. With applying the functional extremum condition, the optimal control outputs of both side satellites were obtained by building the systems Hamilton function. Further, the two side optimal problem was transformed to the TPBVP, which contributed the solution with the mixed numerical method. Finally, the proposed method was validated by the numerical simulation, where the optimal interception and escaping trajectories were illustrated

Spatial Distribution, Pollution, and Ecological Risk Assessment of Metal(loid)s in Multiple Spheres of the Shennongjia Alpine Critical Zone, Central China

The development of Earth’s critical zone concept has strengthened the capacity of environmental science to better solve real-world problems, such as metal(loid) pollution in the remote alpine areas. The selected metal(loid) contents in soil, moss, and water were investigated to explore the geochemical distribution patterns, pollution levels, and potential ecological risks of metal(loid)s in the Shennongjia (SNJ) alpine critical zone of central China. The distribution of metal(loid)s in different spheres had horizontal and vertical differences. The maximum V, Ni, and Zn contents in water occurred at the sampling sites close to the Hohhot–Beihai Highway, while Dajiuhu Lake had the maximum Cu, Cr, and Mn contents. Most metal(loid) contents in the mosses showed an increasing trend from the northeast low-altitude area to the southwest high-altitude area, while As, Co, V, Ni, Cr, and Zn in soil decreased significantly with altitude and were enriched near the service areas and the highway. The contents of water Co and Ni, soil Cu and Mn, and moss As were evenly distributed and showed no significant differences with altitude. The enrichment factors, pollution index, Nemerow integrated pollution index, geo-accumulation index, heavy metal pollution index, contamination factor, and potential ecological risk index (PERI) were used to assess the pollution levels and ecological risks of SNJ soil, water, and atmosphere. The overall pollution levels of SNJ soil, moss, and water were low to moderate, low, and low, respectively. Soil V, Cu, Zn, moss As, Co, V, and Dajiuhu Lake water Mn were the main pollution factors. The ecological risks in the three spheres of the SNJ alpine critical zone were low to moderate, and As, Co, and V were the most critical potential ecological risk factors. The metal(loid)s pollution problem caused by the continuous development of tourism needs further attention

Meloidogyne aberrans sp. nov. (Nematoda: Meloidogynidae), a new root-knot nematode parasitizing kiwifruit in China.

High infection rates of roots of wild kiwifruit (Actinidia chinensis Planch) and soil infestation by a root-knot nematode were found in Anshun, GuiZhou Province, China. Morphology, esterase phenotype and molecular analyses confirmed that this nematode was different from previously described root-knot nematodes. In this report, the species is described, illustrated and named Meloidogyne aberrans sp. nov. The new species has a unique combination of characters. A prominent posterior protuberance, round and faint perineal pattern and a medium-length stylet (13.6-15.5 μm) characterized the females. Second-stage juveniles (J2) were characterized by a smooth lip region with distinctly protruded medial lips and a depression in outline at the oral aperture, a relatively long stylet (15.9-16.8 μm), four incisures in the lateral field and a very short, even poorly defined, hyaline tail terminus (2.2-5.5 μm). More incisures (11-15) existed in the lateral field of males, and the stylet and spicules of males were 18.2-19.6 μm and 22.7-36.8 μm long respectively. Egg masses were typically produced within the roots of kiwifruit. The new species had a rare Est phenotype, S2. Phylogenetic trees inferred from SSU, LSU D2D3, ITS, and partial coxII-16S rRNA revealed that M. aberrans sp. nov. was within the Meloidogyne clade and was distinguished from all described root-knot nematodes. Moreover, from histopathological observations, M. aberrans sp. nov. induced the formation of multinucleate giant cells