A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic

Cytochrome b and D-loop nucleotide sequences were used to study patterns of molecular evolution and phylogenetic relationships between the pheasants and the partridges, which are thought to form two closely related monophyletic galliform lineages. Our analyses used 34 complete cytochrome b and 22 partial D-loop sequences from the hypervariable domain I of the D-loop, representing 20 pheasant species (15 genera) and 12 partridge species (5 genera). We performed parsimony, maximum likelihood, and distance analyses to resolve these phylogenetic relationships. In this data set, transversion analyses gave results similar to those of global analyses. All of our molecular phylogenetic analyses indicated that the pheasants and partridges arose through a rapid radiation, making it difficult to establish higher level relationships. However, we were able to establish six major lineages containing pheasant and partridge taxa, including one lineage containing both pheasants and partridges (Gallus, Bambusicola and Francolinus). This result, supported by maximum likelihood tests, indicated that the pheasants and partridges do not form independent monophyletic lineages.     

Speculations on the origin and evolution of metabolism

An autotrophic origin of metabolism is described, which requires clays, transition state metals, disulfide and dithiols, U.V. and cyanide ion. A general scheme is proposed, involving the fixation of CO2 and N2, for the evolution of intermediary metabolism based on the evolution of a complex system from a simple one. The basic conclusion is that metabolism could have evolved from a simple environment rather than from a complex one.     

Speculations on the origin and evolution of the genus Leishmania

Recently two hypotheses have been proposed for the evolution of Leishmania involving respectively a Neotropical or Paleartic origin for the species. Here an alternative proposal on the phylogeny of Leishmania based on the major divisions within the genus is presented. In this hypothesis a Neotropic origin is retained for L. (Viannia) and Paraleishmania, a recently described section within the genus Leishmania, while an African origin is proposed for L. (Leishmania) and possibly Sauroleishmania. The current distribution of Leishmania in the Neotropics is explained as the product of multiple introductions of Leishmania parasites into the New World. Problems with organismal identity in Sauroleishmania and the use of molecular sequence data in inferring phylogenies are also discussed.     

On the origin and evolution of thermophily: reconstruction of functional precambrian enzymes from ancestors of Bacillus

Thermophily is thought to be a primitive trait, characteristic of early forms of life on Earth, that has been gradually lost over evolutionary time. The genus Bacillus provides an ideal model for studying the evolution of thermophily as it is an ancient taxon and its contemporary species inhabit a range of thermal environments. The thermostability of reconstructed ancestral proteins has been used as a proxy for ancient thermal adaptation. The reconstruction of ancestral "enzymes" has the added advantages of demonstrable activity, which acts as an internal control for accurate inference, and providing insights into the evolution of enzymatic catalysis. Here, we report the reconstruction of the structurally complex core metabolic enzyme LeuB (3-isopropylmalate dehydrogenase, E. C. 1.1.1.85) from the last common ancestor (LCA) of Bacillus using both maximum likelihood (ML) and Bayesian inference. ML LeuB from the LCA of Bacillus shares only 76% sequence identity with its closest contemporary homolog, yet it is fully functional, thermophilic, and exhibits high values for k(cat), k(cat)/K(M), and ΔG(?) for unfolding. The Bayesian version of this enzyme is also thermophilic but exhibits anomalous catalytic kinetics. We have determined the 3D structure of the ML enzyme and found that it is more closely aligned with LeuB from deeply branching bacteria, such as Thermotoga maritima, than contemporary Bacillus species. To investigate the evolution of thermophily, three descendents of LeuB from the LCA of Bacillus were also reconstructed. They reveal a fluctuating trend in thermal evolution, with a temporal adaptation toward mesophily followed by a more recent return to thermophily. Structural analysis suggests that the determinants of thermophily in LeuB from the LCA of Bacillus and the most recent ancestor are distinct and that thermophily has arisen in this genus at least twice via independent evolutionary paths. Our results add significant fluctuations to the broad trend in thermal adaptation previously proposed and demonstrate that thermophily is not exclusively a primitive trait, as it can be readily gained as well as lost. Our findings also demonstrate that reconstruction of complex functional Precambrian enzymes is possible and can provide empirical access to the evolution of ancient phenotypes and metabolisms.     

The role of water in the origin of life and its function in the primitive gene

A brief outline is presented of the structure of clays and of modern views on the structure of water. The interactions between clays and water are discussed, together with the effect of hydration on the adsorption and catalytic properties of clays.From these considerations an attempt is made to show that the hydrated silica surfaces of clay-water systems could have provided the necessary environment for the abiogenesis of primitive macromolecules.The transfer of catalytic functions to abiopolymers is outlined, and a possible route to growing, dividing coacervate droplets is described.Finally, attention is drawn to analogies between the clay-water system and living matter, and the suggestion is made that the structural properties of water could be the basis for the cellular communication network on which life depends.     

Suitable microscopic entropy for the origin of microbial life: Microbiological methods are challenges

A hypothesis is proposed that the first living microbial cell(s) on Earth assembled about 3.6-4 billion years ago when an environmental microscopic entropy (balance between order and disorder; suitable amount of randomness) was within a range suitable for the origin of microbial cell(s) in a hydrogel environment. An earlier origin of microbial life was not possible as the elements, molecules and entropy conditions necessary for life were not available at the microscopic level. Methodology limitations to study postulated past origin of microbial life events and to mimic these events in the laboratory, are still obstacles to understanding the origin of life.     

Revisiting the cell biology of the acyl‐ACP:phosphate transacylase PlsX suggests that the phospholipid synthesis and cell division machineries are not coupled in Bacillus subtilis

PlsX is a central enzyme of phospholipid synthesis in bacteria, converting acyl‐ACP to acyl‐phosphate on the pathway to phosphatidic acid formation. PlsX has received attention because it plays a key role in the coordination of fatty acid and phospholipid synthesis. Recently, PlsX was also suggested to coordinate membrane synthesis with cell division in Bacillus subtilis. Here, we have re‐investigated the cell biology of PlsX and determined that the enzyme is uniformly distributed on the membrane of most cells, but occasionally appears as membrane foci as well. Foci and homogenous patterns seem freely interconvertible but the prevalence of the uniform staining suggests that PlsX does not need to localize to specific sites to function correctly. We also investigated the relationship between PlsX and the divisome. In contrast to previous observations, PlsX's foci showed no obvious periodicity of localization and did not colocalize with the divisome. Furthermore, depletion of PlsX did not affect cell division if phospholipid synthesis is maintained by an alternative enzyme. These results suggest that coordination between division and membrane synthesis may not require physical or functional interactions between the divisome and phospholipid synthesis enzymes.     

Microsporidia: accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi

Microsporidia are obligate intracellular parasites that have long been considered to be primitive eukaryotes, both on the basis of morphological features and on the basis of molecular, mainly ribosomal RNA-based, phylogenies. However, accumulating sequence data and the use of more sophisticated tree construction methods now seem to suggest that microsporidia share a common origin with fungi and are therefore most probably just curious fungi. In this paper, we describe the current views on the phylogenetic position of the microsporidia and present additional evidence for a close relationship between fungi and microsporidia on the basis of reanalyzed ribosomal RNA data. In this respect, the importance of incorporating detailed knowledge of the substitution pattern of sequences into phylogenetic methods is discussed.     

Chemotaxonomic evidence suggests that Eriocephalus tenuifolius is the source of Cape chamomile oil and not Eriocephalus punctulatus

The distinct blue essential oil obtained from Eriocephalus sp. (Asteraceae) is known in commerce as Cape chamomile and has become an important ingredient in flavour and fragrance formulations. To date, it is commonly accepted that Cape chamomile oil is obtained from Eriocephalus punctulatus. Samples of E. tenuifolius DC (n = 35) and E. punctulatus DC (n = 17) were collected from different localities in South Africa and Lesotho. The hydrodistilled essential oil was analysed by gas chromatography coupled to mass selective detector and flame ionisation detector (GC–MS-FID). The GC–MS data was exported to MetAlign? for spectral alignment and differentiation. The mid-infrared red (MIR) spectral data was processed using principal component analysis (PCA), partial least squares (PLS) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) algorithms. The oil from E. punctulatus showed a different profile from the commercial sample which mostly contained 1,8-cineole, piperitone, yomogi alcohol and pogostol. MetAlign? successfully discriminated between the oil obtained from the two species and this data together with multivariate analysis showed that the commercial oil was similar to E. tenuifolius oil. Using the MIR data, a three component OPLS-DA model was constructed which convincingly discriminated between E. tenuifolius and E. punctulatus oil. The developed model further predicted the botanical origin of the commercial oils to be E. tenuifolius. The statistical performance of the model was excellent with an R²X (cum) = 0.897; R²Y (cum) = 0.991 and Q²Y (cum) = 0.987.     

Evidence that the ribosomal DNA genes of yeast are not on chromosome I

Summary Several workers have reported that most of the ribosomal DNA genes (rDNA) of the yeast Saccharomyces cerevisiae are located on chromosome I. More recently, data indicating that the yeast rDNA genes are located on chromosome XII has been presented. In this report, we present additional evidence indicating that most of the yeast rDNA genes are not on chromosome I. Starting from a diploid yeast strain, we isolated ten strains which were monosomic (2n-1) for chromosome I. We found that each of these ten strains contained two copies of the rDNA-containing chromosome. In addition, we show that the earlier evidence indicating that the yeast rDNA genes were on chromosome I cannot be explained by a difference in the yeast strains which were used in the different experiments.     

Sites including those of origin and termination of replication are not freely available to single-cut restriction endonucleases in the supercompact form of simian virus 40 minichromosome.

Simian virus 40 minichromosomes, isolated from both virions (MV) and infected cells (MI), have highly compact structures in buffer containing 0.15 M NaCl and sediment with S values of about 90–100 and 115–130, respectively. Under the electron microscope, also, MI appear the more compact of the two. Only 30–35% of the sites of origin and termination of replication in MV are freely available to the restriction endonucleases $\text{Bgl}$ 1 and $\text{Bam}$ H1. MV are similarly resistant to $\text{Eco}$ R1 and $\text{Hpa}$ II. In contrast, almost no sites in MI are available to any of the above single-cut endonucleases. In 0.6 M NaCl, MV and MI change to relaxed structures of 45–55 S and 50–60 S, respectively, containing 20–24 nucleosomes per genome, and become more sensitive to $\text{Bgl}$ 1, $\text{Bam}$ H1, $\text{Eco}$ R1, and $\text{Hpa}$ II.