BASINS/HSPF: Model use, calibration, and validation

ABSTRACT. This article presents recommendations by model developers and the authors about calibration and validation procedures for the Hydrological Simulatio

Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life

BACKGROUND: Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular alpha-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs). METHODOLOGY/PRINCIPAL FINDINGS: We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs. While the highly reductive (approximately 1.2 MB) Rickettsia genomes range in predicted ORFs from 872 to 1512, a core of 752 OGs was identified, depicting the essential Rickettsia genes. Unsurprisingly, this core lacks many metabolic genes, reflecting the dependence on host resources for growth and survival. Additionally, we bolster our recent reclassification of Rickettsia by identifying OGs that define the AG (ancestral group), TG (typhus group), TRG (transitional group), and SFG (spotted fever group) rickettsiae. OGs for insect-associated species, tick-associated species and species that harbor plasmids were also predicted. Through superimposition of all OGs over robust phylogeny estimation, we discern between C1OGs and C2OGs, the latter depicting genes either decaying from the conserved C1OGs or acquired laterally. Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment. Interestingly, non-representative OGs, as well as OGs comprised of several gene families typically involved in microbial pathogenicity and/or the acquisition of virulence factors, fall predominantly within C2OG distributions. CONCLUSION/SIGNIFICANCE: Collectively, we determined the relative conservation and distribution of 14354 predicted ORFs from 10 rickettsial genomes across robust phylogeny estimation. The data, available at PATRIC (PathoSystems Resource Integration Center), provide novel information for unwinding the intricacies associated with Rickettsia pathogenesis, expanding the range of potential diagnostic, vaccine and therapeutic targets

A review of modelling tools for implementation of the EU Water Framework Directive in handling diffuse water pollution

A numerical catchment-scale model capable of simulating diffuse water pollution is necessary in sustainable environmental management for better implementation of the EU Water Framework Directive. This paper provides critical reviews of most popular and free models for diffuse water modelling, with detailed sources and application potential. Based upon these reviews, further work of selecting and testing the HSPF model was carried out, with a case study in the Upper Bann Catchment, Northern Ireland. The calibrated and validated HSPF model can well represent the characteristics of surface water quantity and quality. Climate change scenario evaluation in 5 years showed that when the annual mean temperature increase 3◦C the mean yearly total runoff volume will decrease by 11.1% and the mean daily river flow 11.4%. If 20% crop and pasture land is converted into forest land in the study area, the mean river concentration of nitrate, nitrite, NH4 and PO4 in 5 years will decrease by 19.4%, 33.3%, 31.3% and 31.3% respectively. When applying filter strip method in 80% crop and pasture land in the area, the reduction of the mean concentration of nitrate, nitrite, NH4 and PO4 in 5 years will be 15.3%, 33.3%, 31.3%, and 5.6% respectively. This study shows that HSPF is a suitable model in handling diffuse source water pollution, which can be introduced into the Programme of Measures in the River Basin Management Plans for better implementation of the EUWFD

Modeling pesticides and nutrients on agricultural lands /

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