Pangenome variation graphs (PVGs) are powerful tools for studying genomic variations in populations, as they represent genomic diversity through multiple genome alignments. However, current tools often lack integration and efficiency, and require format conversions to be used, which hinders their usability. Here, we introduce GraTools, a fast and user-friendly command-line tool for manipulating PVGs using the original GFA file, which is part of the GraSuite [1]. After a one-time graph import, GraTools enables the rapid extraction of subgraphs, retrieval of FASTA sequences, and the performance of comprehensive analyses, including the calculation of the core/dispensable genome ratio or the identification of group-specific segments. Importing the data results in conversion to standard formats (BAM/BED), enabling the reuse of well-optimised existing tools and allowing efficient storage and querying of large, complex PVG data structures. Scalability is ensured by a modular architecture that supports parallel processing and asynchronous I/O operations. GraTools supports coordinates defined on the primary reference and alternative genomes within the graph without re-import, and its outputs can be easily visualised or manipulated using external tools. Using an Asian rice pangenome graph comprising 13 accessions, we demonstrate GraTools' ability to easily extract subgraphs, compute depth statistics and identify subspecies-specific segments. Its intuitive command-line interface, real-time execution feedback, and detailed logging system make this tool suitable for a wide range of applications, from population genetics to breeding and genomic medicine, for biologists and bioinformaticians alike. Through its unified graph manipulation interface, GraTools offers an interesting alternative to existing tools for manipulating PVGs, facilitating rapid, efficient, and flexible downstream analyses. GraTools is available as an open-source tool (GNU GPLv3), and its documentation can be found at https://gratools.readthedocs.io.
Air pollution has become a serious problem in densely populated urban areas in recent years. The Po-210 activity (a toxic radionuclide) and trace heavy element concentrations in 24 aerosol samples from Hanoi, Vietnam, were measured . Po-210 activity ranged from 92.2 to 3500 mu Bq.m(-3). Notably, Po-210 activity in roadside samples was much higher compared to global reference values. Among the trace heavy metals analyzed, Co showed the lowest concentrations, while Al had the highest. Most metal levels in roadside areas were higher than those in residential areas. Enrichment factor analysis indicated that metals such as Li, Al, Ti, V, Mn, Fe, Co, and Ba mainly came from crustal sources. In contrast, Cr, Ni, Cu, Zn, Cd, Sb, and Pb were linked to vehicle emissions such as fossil fuel combustion. The relationship between Po-210 and these metals revealed factors affecting its presence in urban air. In residential areas,Po-210 negatively correlated with Ni and positively with Al, indicating a crustal origin. By contrast, its strong positive correlation with Cr and Ni in roadside areas suggests fossil fuel combustion as main source. Despite the diverse Po-210 sources in Hanoi, the findings suggest that its presence in aerosols is largely determined by local characteristics and supply on-site.
This study investigated the contributions of soil organic matter (SOM), clay, and various forms of Fe and Al oxides to the cation exchange capacity (CEC) of highly weathered tropical soils in central southwestern Nigeria. Soils representing major types in the region-Typic Paleustults, Rhodic Kandiustults, and Typic Haplustults-were sampled by genetic horizon. SOM was removed using hydrogen peroxide, and parallel subsamples underwent selective extractions targeting crystalline (dithionite-citrate-bicarbonate), poorly crystalline (acid ammonium oxalate), and organically complexed (sodium pyrophosphate) Fe and Al oxides. Changes in CEC following each treatment were used to assess the functional roles of the removed components. SOM removal resulted in substantial reductions in CEC across all soils, accounting for 38%-47% of total CEC in surface horizons, confirming SOM as the dominant source of exchangeable charge. Removal of oxides produced variable responses depending on the form and soil depth. In many subsurface horizons, CEC increased, indicating that these oxides often mask clay exchange sites. Conversely, decreases in CEC observed in some surface horizons indicate that oxides can also contribute pH-dependent charge or stabilize organic functional groups. Clay fractions exhibited modest intrinsic CEC, consistent with kaolinitic mineral dominance. These findings demonstrate that CEC in these highly weathered tropical soils is controlled primarily by SOM and the degree to which Fe and Al oxides regulate access to clay exchange sites. Enhancing organic matter and managing oxide-induced masking are therefore key strategies for improving nutrient retention and soil fertility in tropical agroecosystems.
Plastic pollution is a global One Health crisis, yet research has focused largely on marine environments. The Amazon—the world’s largest drainage basin and second most plastic-polluted river—has received limited scientific attention. This scoping review is the first to apply a systematic protocol (PRISMA-ScR) to assess plastic contamination across Amazonian ecosystems. We reviewed 52 peer-reviewed studies reporting plastic litter and fragments in terrestrial and aquatic environments of the biome. Most evidence concerns microplastics in Brazilian sites along the main Amazon River, with a focus on fish. However, plastics were also found in sediments, plants, and diverse fauna including birds, reptiles, and mammals. No studies reported nanoplastics. The contamination of key food and water sources poses a major One Health risk for traditional populations. We identify urgent research gaps—especially in non-fish fauna, tributaries, and other Amazonian countries—and highlight the need for targeted mitigation through waste management and education.
This paper synthesizes the conclusions of the research group on the applicability and improvement of forest inventory results, using auxiliary data from ALS technology, compared to a traditional inventory with field data obtained by sampling with plots. ALS data are a great advance for the improvement of knowledge about forests and forest variables, this improvement of knowledge does not mean that the field work and therefore the costs of a forest inventory are decreased. When the smaller units are considered, ALS methods appear as more advantageous alternatives than those based on classical inventory. True progress in forest management involves maintaining sampling efforts, in some cases reaching the intensity of a traditional inventory, to obtain acceptable estimates of the aggregate variables (V, B, G, Dg, Ho, N) in the AOI (Areas Of Interest), into which the forest can be divided for management. On the other hand, this also allows improving the estimates of the diameter distribution in the total forest and subpopulations (forest or management units) of the area where the sampling was designed.
