Search results for "phylogenetic"

The swinholide biosynthesis gene cluster from a terrestrial cyanobacterium, Nostoc sp. strain UHCC 0450

2017

ABSTRACT Swinholides are 42-carbon ring polyketides with a 2-fold axis of symmetry. They are potent cytotoxins that disrupt the actin cytoskeleton. Swinholides were discovered from the marine sponge Theonella sp. and were long suspected to be produced by symbiotic bacteria. Misakinolide, a structural variant of swinholide, was recently demonstrated to be the product of a symbiotic heterotrophic proteobacterium. Here, we report the production of swinholide A by an axenic strain of the terrestrial cyanobacterium Nostoc sp. strain UHCC 0450. We located the 85-kb trans -AT polyketide synthase (PKS) swinholide biosynthesis gene cluster from a draft genome of Nostoc sp. UHCC 0450. The swinholide …

Impact of Plasma Oxidative Stress Markers on Post-race Recovery in Ultramarathon Runners: A Sex and Age Perspective Overview

2021

Oxidative stress has been widely studied in association to ultra-endurance sports. Although it is clearly demonstrated the increase in reactive oxygen species and free radicals after these extreme endurance exercises, the effects on the antioxidant defenses and the oxidative damage to macromolecules, remain to be fully clarified. Therefore, the aim of this study was to elucidate the impact of an ultramarathon race on the plasma markers of oxidative stress of 32 runners and their post-race recovery, with especial focused on sex and age effect. For this purpose, the antioxidant enzymes glutathione peroxidase (GPx) and glutathione reductase (GR) activity, as well as the lipid peroxidation prod…

Molecular evolution methods to study HIV-1 epidemics

2018

Nucleotide sequences of HIV isolates are obtained routinely to evaluate the presence of resistance mutations to antiretroviral drugs. But, beyond their clinical use, these and other viral sequences include a wealth of information that can be used to better understand and characterize the epidemiology of HIV in relevant populations. In this review, we provide a brief overview of the main methods used to analyze HIV sequences, the data bases where reference sequences can be obtained, and some caveats about the possible applications for public health of these analyses, along with some considerations about their limitations and correct usage to derive robust and reliable conclusions.

2015

Molecular clock analyses estimate that crown-group animals began diversifying hundreds of millions of years before the start of the Cambrian period. However, the fossil record has not yielded unequivocal evidence for animals during this interval. Some of the most promising candidates for Precambrian animals occur in the Weng'an biota of South China, including a suite of tubular fossils assigned to Sinocyclocyclicus , Ramitubus , Crassitubus and Quadratitubus , that have been interpreted as soft-bodied eumetazoans comparable to tabulate corals. Here, we present new insights into the anatomy, original composition and phylogenetic affinities of these taxa based on data from synchrotron radiat…

Revision of the taxonomic status of <i>Synthesium elongatum</i> (Ozaki, 1935) (Brachycladiidae), an intestinal digenean of narrow-ridged …

2019

Synthesium elongatum (Brachycladiidae) is an intestinal digenean described from the finless porpoise (Neophocaena asiaeorientalis) in Japan. Few records of this species exist and there is a remarkable morphological similarity between S. elongatum and S. tursionis, such that a synonymy between the species has been suggested previously. However, no morphological and/or molecular analysis has been carried out to clarify the taxonomic status of S. elongatum. In this study, we collected specimens of Synthesium sp. from N. asiaeorientalis in western Japan. The specimens possess lobed testes within the third quarter of the body, a round ovary, and vitellaria extending to level of uterine field, wh…

Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits

2020

In this chapter, we describe how to use DarkHorse2.0 to search for xenologs in the genome of the cyanobacterium Synechococcus elongatus PCC 7942. DarkHorse is an implicit phylogenetic method that uses BLAST searches to identify proteins having close homologs of unexpected taxonomic affiliation. Once a set of putative xenologs are identified, Phylomizer is used to reconstruct phylogenetic trees. Phylomizer reproduces all the necessary steps to perform a basic phylogenetic analysis. The combined use of DarkHorse and Phylomizer allows the identification of genes incorporated into a given genome by HGT.

Origin of modern syphilis and emergence of a contemporary pandemic cluster

2016

AbstractSyphilis swept across the world in the 16th century as one of most prominent documented pandemics and is re-emerging worldwide despite the availability of effective antibiotics. Little is known about the genetic patterns in current infections or the evolutionary origins of the disease due to the non-cultivable and clonal nature of the causative bacterium Treponema pallidum subsp. pallidum. In this study, we used DNA capture and next generation sequencing to obtain whole genome data from syphilis patient specimens and from treponemes propagated in laboratory settings. Phylogenetic analyses indicate that the syphilis strains examined here share a common ancestor after the 15th century…

16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils

2000

Bacteria capable of denitrification are spread among phylogenetically diverse groups. In the present investigation, molecular methods (amplified ribosomal DNA restriction analysis (ARDRA) and partial 16S rDNA gene sequencing) were used to determine the genetic diversity of culturable denitrifying soil bacteria. The purpose of this work was to study the microbial density and diversity of denitrifying communities isolated from two luvisols and a rendosol. The denitrifying bacterial density was significantly higher in the two luvisols (3x10(6) and 4x10(6) bacteria g(-1) dry soil) than in the rendosol (4x10(5) bacteria g(-1) dry soil). Denitrifying isolates from soils were grouped according to …

Fire and phylogenetic structure of soil microbial communities in Mediterranean ecosystems

2017

Tesis llevada a cabo para conseguir el grado de Doctor por la Universidad de Valencia.--2018-02-21.--Sobresaliente Cum laudem

Plant-animal interactions in fire-prone ecosystems

2018

SÍNTESIS Estudiar cómo responden las interacciones ecológicas a las perturbaciones es clave para abordar la creciente pérdida de biodiversidad en diferentes ecosistemas. En la Tierra existen especies que han evolucionado ante la presencia recurrente de perturbaciones naturales, como ocurre en ecosistemas con incendios frecuentes. En ellos el fuego se originó poco después de la aparición de las primeras plantas terrestres y también algunos de los patrones de incendios característicos que todavía permanecen. Sin embargo, las actividades humanas están alterando los patrones naturales de incendios, lo que puede suponer una amenaza incluso para las especies que presentan una rápida recuperación …