A Guide to Phylogenomic Inference.

Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs.

CFD-based design optimization of ducted hydrokinetic turbines.

Hydrokinetic turbines extract kinetic energy from moving water to generate renewable electricity, thus contributing to sustainable energy production and reducing reliance on fossil fuels. It has been hypothesized that a duct can accelerate and condition the fluid flow passing the turbine blades, improving the overall energy extraction efficiency. However, no substantial evidence has been provided so far for hydrokinetic turbines.

New insights into plant natriuretic peptide evolution: From the lysogenic conversion in Xanthomonas to the lateral transfer to the whitefly Bemisia tabaci.

Plant natriuretic peptide-like (PNP) are signaling molecules related to adaptive responses to stress. The Arabidopsis thaliana PNP (AtPNP-A) is capable of modulating catalase 2 (CAT2) and rubisco activase (RCA) activity in some circumstances. Interestingly, many plant-pathogens co-opted PNP-like molecules to their benefit.

Acetyl-CoA Synthetase Is Essential for Parasite Intraerythrocytic Development and Chromatin Modification.

The malaria parasite possesses a unique Acetyl-CoA Synthetase (PfACS), which provides acetyl moieties for different metabolic and regulatory cellular pathways. We characterized PfACS and studied its role focusing on epigenetic modifications using the gene family as reporter genes. For this, mutant lines to modulate plasmodial ACS expression by degron-mediated protein degradation and ribozyme-induced transcript decay were created.

Genomic Characterization of -Producing Recovered From Human Infections in São Paulo, Brazil.

Polymyxins are one of most important antibiotics available for multidrug-resistant Gram-negative infections. Diverse chromosomal resistance mechanisms have been described, but the polymyxin resistance phenotype is not yet completely understood. The objective of this study was to characterize colistin resistant -producing strains isolated from human infections over one year in a hospital setting (Hospital das Clínicas, São Paulo, Brazil).

Monolithic Approach for Next-Generation Aircraft Design Considering Airline Operations and Economics.

Traditional approaches to design and optimization of a new system often use a system-centric objective that does not consider how the operator will use this new system alongside other existing systems. When the new system design is incorporated into the broader group of systems, the performance of the operator-level objective can be sub-optimal due to the unmodeled interaction between the new system and the other systems. Among the few available references that describe attempts to address this disconnect, most follow an MDO-motivated sequential decomposition approach of first designing an optimal system and then providing this system to the operator who decides the best way to use this new system along with the existing systems.

Carcinoma of the gallbladder presenting as haemorrhagic cholecystitis.

Gallbladder carcinoma has several atypical presentations, but one of the rarest is intraluminal haemorrhage, which occurs in 1% of patients. We report a case of gallbladder cancer diagnosed by an emergency cholecystectomy, performed for acute cholecystitis caused by a hemocholecyst.

Analyses of Seven New Genomes of pv. Strains, Causative Agents of Citrus Canker B and C, Show a Reduced Repertoire of Pathogenicity-Related Genes.

pv. pathotype B (XauB) and pathotype C (XauC) are the causative agents respectively of citrus canker B and C, diseases of citrus plants related to the better-known citrus canker A, caused by pv. .

Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses.

Background: Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and A are more restricted both in hosts and in geography.

Phylogenomics.

Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. The abundance of genomic data for an enormous variety of organisms has enabled phylogenomic inference of many groups, and this has motivated the development of many computer programs implementing the associated methods. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs.

The Candidatus Liberibacter-Host Interface: Insights into Pathogenesis Mechanisms and Disease Control.

"Candidatus Liberibacter" species are associated with economically devastating diseases of citrus, potato, and many other crops. The importance of these diseases as well as the proliferation of new diseases on a wider host range is likely to increase as the insects vectoring the "Ca. Liberibacter" species expand their territories worldwide.

Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses.

is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five complete genomes from the United Kingdom, South Korea, Brazil, and the United States revealed four novel large-scale structural variations of at least 2,000 bp. A comparative phylogenomic study including 2,483 core genes of 38 taxa from eight countries showed conflicting phylogenetic signal among sites.

Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity.

Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains.

Phylogenetic relationships in genus Arachis based on ITS and 5.8S rDNA sequences.

Background: The genus Arachis comprises 80 species and it is subdivided into nine taxonomic sections (Arachis, Caulorrhizae, Erectoides, Extranervosae, Heteranthae, Procumbentes, Rhizomatosae, Trierectoides, and Triseminatae). This genus is naturally confined to South America and most of its species are native to Brazil. In order to provide a better understanding of the evolution of the genus, we reconstructed the phylogeny of 45 species using the variation observed on nucleotide sequences in internal transcribed spacer regions (ITS1 and ITS2) and 5.

Bathing waters: new directive, new standards, new quality approach.

Bathing water quality is an important public health issue, mainly because of fecal contamination. In 2006, the European Commission (EC) adopted a new directive with respect to recreational bathing waters that calls for stricter standards and reduces the number of laboratory tests done in routine beach monitoring from nineteen to two bacterial indicators, namely, Escherichia coli and intestinal enterococci, replacing policies of the EC Bathing Water Directive that have existed since 1976. Our practice in Portugal is in line with this international development, and this study demonstrates the equivalency of the new bacteriological parameters with the old.

Paleodistributions and comparative molecular phylogeography of leafcutter ants (Atta spp.) provide new insight into the origins of Amazonian diversity.

The evolutionary basis for high species diversity in tropical regions of the world remains unresolved. Much research has focused on the biogeography of speciation in the Amazon Basin, which harbors the greatest diversity of terrestrial life. The leading hypotheses on allopatric diversification of Amazonian taxa are the Pleistocene refugia, marine incursion, and riverine barrier hypotheses.