Search results for "Tree"

Acetobacter musti sp. nov., isolated from Bobal grape must

2016

An acetic acid bacterium (strain Bo7T), obtained during a study of the microbial diversity of spontaneous fermentations of Bobal grape must, was subjected to a taxonomic study using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences allocated strain Bo7T to the genus Acetobacter, and revealed Acetobacter aceti and Acetobacter oeni to be nearest neighbours (99.57 % 16S rRNA gene sequence similarity between strain Bo7T and A. oeni CECT 5830T, and 98.76 % between strain Bo7T and A. aceti CECT 298T). Cells of strain Bo7T are Gram-negative, motile rods, catalase-positive and oxidase-negative. The DNA G+C content of strain Bo7T was 58.0 mol%. DNA–DNA hybridizations demo…

Phylogenetic variation in cortical layer II immature neuron reservoir of mammals

2020

The adult mammalian brain is mainly composed of mature neurons. A limited amount of stem cell-driven neurogenesis persists in postnatal life and is reduced in large-brained species. Another source of immature neurons in adult brains is cortical layer II. These cortical immature neurons (cINs) retain developmentally undifferentiated states in adulthood, though they are generated before birth. Here, the occurrence, distribution and cellular features of cINs were systematically studied in 12 diverse mammalian species spanning from small-lissencephalic to large-gyrencephalic brains. In spite of well-preserved morphological and molecular features, the distribution of cINs was highly heterogeneou…

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…

2020

Abstract. The new PAGES2k global compilation of temperature-sensitive proxies offers an unprecedented opportunity to study regional to global trends associated with orbitally driven changes in solar irradiance over the past 2 millennia. Here, we analyze pre-industrial long-term trends from 1 to 1800 CE across the PAGES2k dataset and find that, in contrast to the gradual cooling apparent in ice core, marine, and lake sediment data, tree rings do not exhibit the same decline. To understand why tree-ring proxies lack any evidence of a significant pre-industrial cooling, we divide those data by location (high Northern Hemisphere latitudes vs. midlatitudes), seasonal response (annual vs. summer)…

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.

Hyperion

2019

Indexes are essential in data management systems to increase the speed of data retrievals. Widespread data structures to provide fast and memory-efficient indexes are prefix tries. Implementations like Judy, ART, or HOT optimize their internal alignments for cache and vector unit efficiency. While these measures usually improve the performance substantially, they can have a negative impact on memory efficiency. In this paper we present Hyperion, a trie-based main-memory key-value store achieving extreme space efficiency. In contrast to other data structures, Hyperion does not depend on CPU vector units, but scans the data structure linearly. Combined with a custom memory allocator, Hyperion…

Efficient Online Laplacian Eigenmap Computation for Dimensionality Reduction in Molecular Phylogeny via Optimisation on the Sphere

2019

Reconstructing the phylogeny of large groups of large divergent genomes remains a difficult problem to solve, whatever the methods considered. Methods based on distance matrices are blocked due to the calculation of these matrices that is impossible in practice, when Bayesian inference or maximum likelihood methods presuppose multiple alignment of the genomes, which is itself difficult to achieve if precision is required. In this paper, we propose to calculate new distances for randomly selected couples of species over iterations, and then to map the biological sequences in a space of small dimension based on the partial knowledge of this genome similarity matrix. This mapping is then used …

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…

STREET WORKOUT: PERFIL PSICOSOCIAL DE SUS PRACTICANTES

2020

La presente investigación estudia las principales características psicológicas de los practicantes de Street Workout, una modalidad deportiva emergente y en auge en los últimos años. A través de un estudio descriptivo-correlacional, con una muestra de 107 practicantes de España, se elaboró un estudio piloto del perfil psicosocial que incluye la evaluación de los motivos de práctica, la satisfacción muscular, la cohesión y el bienestar psicológico; además de una comparación en función de si compiten. Los resultados señalan que es un deporte practicado mayoritariamente por hombres menores de 23 años, cuya principal motivación es hallar un equilibrio entre la preocupación por la salud y su asp…