Ribosomal RNA and the major lines of evolution: a perspective

Ragan, Mark A.

doi:10.1016/0303-2647(88)90011-1

Cited by 18 publications

(5 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As we repeatedly mentioned, one gene is not enough to construct the correct tree. In fact, there are cases in which 16SrRNA gene did not lead to the correct tree (Ragan, 1988; Saruhashi et al, 2007). In addition, the bootstrap test those authors used is not appropriate to examine the correctness of a constructed tree, as mentioned above.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

Horiike

Miyata

Hamada³

et al. 2009

Gene

View full text Add to dashboard Cite

Here, we constructed a phylogenetic tree of 17 bacterial phyla covering eubacteria and archaea by using a new method and 102 carefully selected orthologs from their genomes. One of the serious disturbing factors in phylogeny construction is the existence of out-paralogs that cannot easily be found out and discarded. In our method, out-paralogs are detected and removed by constructing a phylogenetic tree of the genes in question and examining the clustered genes in the tree. We also developed a method for comparing two tree topologies or shapes, ComTree. Applying ComTree to the constructed tree we computed the relative number of orthologs that support a node of the tree. This number is called the Positive Ortholog Ratio (POR), which is conceptually and methodologically different from the frequently used bootstrap value. Our study concretely shows drawbacks of the bootstrap test. Our result of bacterial phylogeny analysis is consistent with previous ones showing that hyperthermophilic bacteria such as Thermotogae and Aquificae diverged earlier than the others in the eubacterial phylogeny studied. It is noted that our results are consistent whether thermophilic archaea or mesophilic archaea is employed for determining the root of the tree. The earliest divergence of hyperthermophilic eubacteria is supported by genes involved in fundamental metabolic processes such as glycolysis, nucleotide and amino acid syntheses.

show abstract

Section: Resultsmentioning

confidence: 99%

Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

Horiike

Miyata

Hamada³

et al. 2009

Gene

View full text Add to dashboard Cite

show abstract

“…The conventional wisdom before the introduction of nucleotide sequencing of rRNA was that procaryotic cells were more primitive than eucaryotes and evolved into them after the ingestion of one procaryote into another that had lost the external peptidoglycan cell wall common to virtually all eubacteria -the endosymbiont hypothesis (Alberts et al 1989, chapter 1;Margulis, 1975). Woese and his collaborators have argued on the basis of rRNA sequencing that there is no reason to believe that either procaryotes or eucaryotes are more primitive or ancient than the other and that the three kingdoms of cells could well have parted company from their common ancestor very early in the evolutionary history of cells (Woese & Wolfe, 1985;Woese, 1987) even as far back as 3-6-4-7 eons ago (Ragan, 1988).…”

Section: Two Scenarios For the Evolution Of Cellsmentioning

confidence: 99%

Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective

Bloom

Evans

Mouritsen

1991

Quart. Rev. Biophys.

826

615

View full text Add to dashboard Cite

The motivation for this review arises from the conviction that, as a result of the mass of experimental data and observations collected in recent years, the study of the physical properties of membranes is now entering a new stage of development. More and more, experiments are being designed to answer specific, detailed questions about membranes which will lead to a quantitative understanding of the way in which the physical properties of membranes are related to and influence their biological function.

show abstract

“…All microsporidia are obligate intracellular parasites and have no active stages outside their host cells. They are considered to be ancient organisms, evolutionarily placed as an early branch leading from prokaryotes to eukaryotes (64,65,285,362,363). Microsporidia lack some typical eukaryotic characteristics.…”

Section: Morphology Of Microsporidiamentioning

confidence: 99%

Molecular Techniques for Detection, Species Differentiation, and Phylogenetic Analysis of Microsporidia

1999

View full text Add to dashboard Cite

SUMMARY Microsporidia are obligate intracellular protozoan parasites that infect a broad range of vertebrates and invertebrates. These parasites are now recognized as one of the most common pathogens in human immunodeficiency virus-infected patients. For most patients with infectious diseases, microbiological isolation and identification techniques offer the most rapid and specific determination of the etiologic agent. This is not a suitable procedure for microsporidia, which are obligate intracellular parasites requiring cell culture systems for growth. Therefore, the diagnosis of microsporidiosis currently depends on morphological demonstration of the organisms themselves. Although the diagnosis of microsporidiosis and identification of microsporidia by light microscopy have greatly improved during the last few years, species differentiation by these techniques is usually impossible and transmission electron microscopy may be necessary. Immunfluorescent-staining techniques have been developed for species differentiation of microsporidia, but the antibodies used in these procedures are available only at research laboratories at present. During the last 10 years, the detection of infectious disease agents has begun to include the use of nucleic acid-based technologies. Diagnosis of infection caused by parasitic organisms is the last field of clinical microbiology to incorporate these techniques and molecular techniques (e.g., PCR and hybridization assays) have recently been developed for the detection, species differentiation, and phylogenetic analysis of microsporidia. In this paper we review human microsporidial infections and describe and discuss these newly developed molecular techniques.

show abstract

Ribosomal RNA and the major lines of evolution: a perspective

Cited by 18 publications

References 82 publications

Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective

Molecular Techniques for Detection, Species Differentiation, and Phylogenetic Analysis of Microsporidia

Contact Info

Product

Resources

About