1,804 research outputs found
Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins
Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding of the evolution of both bacteria and eukaryotes. All phylogenetic dating in the Proterozoic and before is difficult: Significant debates surround potential fossil calibration points based on the interpretation of the Precambrian microbial fossil record, and strict molecular clock methods cannot be expected to yield accurate dates over such vast timescales because of strong heterogeneity in rates. Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating. However, endosymbiosis events and gene duplications provide some additional information that has never been exploited in dating; namely, that certain nodes on a gene tree must represent the same events, and thus must have the same or very similar dates, even if the exact date is uncertain. We devised techniques to exploit this information: cross-calibration, in which node date calibrations are reused across a phylogeny, and cross-bracing, in which node date calibrations are formally linked in a hierarchical Bayesian model. We apply these methods to proteins with ancient duplications that have remained associated and originated from plastid and mitochondrial endosymbionts: the α and ÎČ subunits of ATP synthase and its relatives, and the elongation factor thermo unstable. The methods yield reductions in dating uncertainty of 14â26% while only using date calibrations derived from phylogenetically unambiguous Phanerozoic fossils of multicellular plants and animals. Our results suggest that primary plastid endosymbiosis occurred âŒ900 Mya and mitochondrial endosymbiosis occurred âŒ1,200 Mya
Effects of Aneuploidy on Genome Structure, Expression, and Interphase Organization in Arabidopsis thaliana
Aneuploidy refers to losses and/or gains of individual chromosomes from the
normal chromosome set. The resulting gene dosage imbalance has a noticeable
affect on the phenotype, as illustrated by aneuploid syndromes, including Down
syndrome in humans, and by human solid tumor cells, which are highly aneuploid.
Although the phenotypic manifestations of aneuploidy are usually apparent,
information about the underlying alterations in structure, expression, and
interphase organization of unbalanced chromosome sets is still sparse. Plants
generally tolerate aneuploidy better than animals, and, through colchicine
treatment and breeding strategies, it is possible to obtain inbred sibling
plants with different numbers of chromosomes. This possibility, combined with
the genetic and genomics tools available for Arabidopsis
thaliana, provides a powerful means to assess systematically the
molecular and cytological consequences of aberrant numbers of specific
chromosomes. Here, we report on the generation of Arabidopsis
plants in which chromosome 5 is present in triplicate. We compare the global
transcript profiles of normal diploids and chromosome 5 trisomics, and assess
genome integrity using array comparative genome hybridization. We use live cell
imaging to determine the interphase 3D arrangement of transgene-encoded
fluorescent tags on chromosome 5 in trisomic and triploid plants. The results
indicate that trisomy 5 disrupts gene expression throughout the genome and
supports the production and/or retention of truncated copies of chromosome 5.
Although trisomy 5 does not grossly distort the interphase arrangement of
fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations
between transgene alleles. Our analysis reveals the complex genomic changes that
can occur in aneuploids and underscores the importance of using multiple
experimental approaches to investigate how chromosome numerical changes
condition abnormal phenotypes and progressive genome instability
Bayesian analysis of congruence of core genes in Prochlorococcus and Synechococcus and implications on horizontal gene transfer
It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. âUniversal proteinsâ have been used to infer the organismal phylogeny, but have been criticized as being only the âtree of one percent.â Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees â a âtreecloudâ â for each, as well as for a concatenated dataset based on putative âuniversal proteins.â We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the âtree of one percentâ is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence
Effect of Ceftazidime on Systemic Cytokine Concentrations in Rats
The effect of a single dose of ceftazidime on circulating concentrations of interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) in a rat model of sepsis was studied. IL-6 concentrations were significantly elevated (100 to 200 times the baseline) 6 h after ceftazidime administration in both septic and nonseptic (control) rats. TNF-α concentrations increased significantly in nonseptic (âŒ40 times the baseline) rats but not septic (âŒ2 to 3 times the baseline) rats. Ceftazidime administration was not associated with an increase in endotoxin concentrations. These findings suggest that ceftazidime modulation of proinflammatory cytokine concentrations may be independent of its antimicrobial properties
Effects of confinement and crowding on folding of model proteins
We perform molecular dynamics simulations for a simple coarse-grained model
of crambin placed inside of a softly repulsive sphere of radius R. The
confinement makes folding at the optimal temperature slower and affects the
folding scenarios, but both effects are not dramatic. The influence of crowding
on folding are studied by placing several identical proteins within the sphere,
denaturing them, and then by monitoring refolding. If the interactions between
the proteins are dominated by the excluded volume effects, the net folding
times are essentially like for a single protein. An introduction of
inter-proteinic attractive contacts hinders folding when the strength of the
attraction exceeds about a half of the value of the strength of the single
protein contacts. The bigger the strength of the attraction, the more likely is
the occurrence of aggregation and misfolding
"Because it is the Right Thing to Do'': Taking Stock of the Peer Reviewersâ Openness Initiative
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