Prokaryotic evolution and the tree of life are two different things

Background

The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.

Results

It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes.

Conclusion

Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution.

Reviewers

This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier.     

Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm

Mapping the epitope of an antibody is of great interest, since it contributes much to our understanding of the mechanisms of molecular recognition and provides the basis for rational vaccine design. Here we present Mapitope, a computer algorithm for epitope mapping. The algorithm input is a set of affinity isolated peptides obtained by screening phage display peptide-libraries with the antibody of interest. The output is usually 1-3 epitope candidates on the surface of the atomic structure of the antigen. We have systematically tested the performance of Mapitope by assessing the effect of the algorithm parameters on the final prediction. Thus, we have examined the effect of the statistical threshold (ST) parameter, relating to the frequency distribution and enrichment of amino acid pairs from the isolated peptides and the D (distance) and E (exposure) parameters which relate to the physical parameters of the antigen. Two model systems were analyzed in which the antibody of interest had previously been co-crystallized with the antigen and thus the epitope is a given. The Mapitope algorithm successfully predicted the epitopes in both models. Accordingly, we formulated a stepwise paradigm for the prediction of discontinuous conformational epitopes using peptides obtained from screening phage display libraries. We applied this paradigm to successfully predict the epitope of the Trastuzumab antibody on the surface of the Her-2/neu receptor in a third model system.     

Identification of a new glycerol-3-phosphate acyltransferase isoenzyme, mtGPAT2, in mitochondria

Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the initial and rate-limiting step of glycerolipid synthesis. Two distinct GPAT isoenzymes had been identified in mammalian tissues, an N-ethylmaleimide (NEM)-sensitive isoform in the endoplasmic reticulum membrane (microsomal GPAT) and an NEM-resistant form in the outer mitochondrial membrane (mtGPAT). Although only mtGPAT has been cloned, the microsomal and mitochondrial GPAT isoforms can be distinguished, because they differ in acyl-CoA substrate preference, sensitivity to inhibition by dihydroxyacetone phosphate and polymixin B, temperature sensitivity, and ability to be activated by acetone. The preponderance of evidence supports a role for mtGPAT in synthesizing the precursors for triacylglycerol synthesis. In mtGPAT(-/-) mice, PCR genotyping and Northern analysis showed successful knockout of mtGPAT; however, we detected a novel NEM-sensitive GPAT activity in mitochondrial fractions and an anti-mtGPAT immunoreactive protein in liver mitochondria, but not in microsomes. Rigorous analysis using two-dimensional gel electrophoresis revealed that the anti-mtGPAT immunoreactive proteins in wild type and mtGPAT(-/-) liver mitochondria have different isoelectric points. These results suggested the presence of a second GPAT in liver mitochondria from mtGPAT(-/-) mice. Characterization of this GPAT activity in liver from mtGPAT null mice showed that, unlike the mtGPAT activity in wild type samples, activity in mtGPAT knockout mitochondria did not prefer palmitoyl-CoA, was sensitive to inactivation by NEM, was inhibited by dihydroxyacetone phosphate and polymixin B, was temperature-sensitive, and was not activated by acetone. We conclude that a novel GPAT (mtGPAT2) with antigenic epitopes similar to those of mtGPAT is detectable in mitochondria from the livers of mtGPAT(-/-) mice.     

Heat shock protein 60 activates cytokine-associated negative regulator suppressor of cytokine signaling 3 in T cells: effects on signaling, chemotaxis, and inflammation

Previously, we reported that treatment of T cells with the 60-kDa heat shock protein (HSP60) inhibits chemotaxis. We now report that treatment of purified human T cells with recombinant human HSP60 or its biologically active peptide p277 up-regulates suppressor of cytokine signaling (SOCS)3 expression via TLR2 and STAT3 activation. SOCS3, in turn, inhibits the downstream effects of stromal cell-derived-1alpha (CXCL12)-CXCR4 interaction in: 1) phosphorylation of ERK1/2, Pyk2, AKT, and myosin L chain, required for cell adhesion and migration; 2) formation of rear-front T cell polarity; and 3) migration into the bone marrow of NOD/SCID mice. HSP60 also activates SOCS3 in mouse lymphocytes and inhibits their chemotaxis toward stromal cell-derived factor-1alpha and their ability to adoptively transfer delayed-type hypersensitivity. These effects of HSP60 could not be attributed to LPS or LPS-associated lipoprotein contamination. Thus, HSP60 can regulate T cell-mediated inflammation via specific signal transduction and SOCS3 activation.     

Visual learning in multiple-object tracking

Background

Tracking moving objects in space is important for the maintenance of spatiotemporal continuity in everyday visual tasks. In the laboratory, this ability is tested using the Multiple Object Tracking (MOT) task, where participants track a subset of moving objects with attention over an extended period of time. The ability to track multiple objects with attention is severely limited. Recent research has shown that this ability may improve with extensive practice (e.g., from action videogame playing). However, whether tracking also improves in a short training session with repeated trajectories has rarely been investigated. In this study we examine the role of visual learning in multiple-object tracking and characterize how varieties of attention interact with visual learning.

Methodology/Principal Findings

Participants first conducted attentive tracking on trials with repeated motion trajectories for a short session. In a transfer phase we used the same motion trajectories but changed the role of tracking targets and nontargets. We found that compared with novel trials, tracking was enhanced only when the target subset was the same as that used during training. Learning did not transfer when the previously trained targets and nontargets switched roles or mixed up. However, learning was not specific to the trained temporal order as it transferred to trials where the motion was played backwards.

Conclusions/Significance

These findings suggest that a demanding task of tracking multiple objects can benefit from learning of repeated motion trajectories. Such learning potentially facilitates tracking in natural vision, although learning is largely confined to the trajectories of attended objects. Furthermore, we showed that learning in attentive tracking relies on relational coding of all target trajectories. Surprisingly, learning was not specific to the trained temporal context, probably because observers have learned motion paths of each trajectory independently of the exact temporal order.     

Anaerobic ammonia-oxidizing bacteria and related activity in Baltimore inner harbor sediment

The discovery of bacteria capable of anaerobic ammonia oxidation (anammox) has generated interest in understanding the activity, diversity, and distribution of these bacteria in the environment. In this study anammox activity in sediment samples obtained from the Inner Harbor of Baltimore, Md., was detected by (15)N tracer assays. Anammox-specific oligonucleotide primer sets were used to screen a Planctomycetales-specific 16S rRNA gene library generated from sediment DNA preparations, and four new anammox bacterial sequences were identified. Three of these sequences form a cohesive new branch of the anammox group, and the fourth sequence branches separately from this group. Denaturing gradient gel electrophoresis analysis of sediment incubated with anammox-specific media confirmed the presence of the four anammox-related 16S rRNA gene sequences. Evidence for the presence of anammox bacteria in Inner Harbor sediment was also obtained by using an anammox-specific probe in fluorescence in situ hybridization studies. To our knowledge, this is the first report of anammox activity and related bacterial 16S rRNA gene sequences from the Chesapeake Bay basin area, and the results suggest that this pathway plays an important role in the nitrogen cycle of this estuarine environment. Furthermore, the presence of these bacteria and their activity in sediment strengthen the contention that anammox-related Plactomycetales are globally distributed.     

Bile acids. LXXII. High-performance liquid chromatographic analysis of bile acid coenzyme A derivatives

The mobilities of coenzyme A and coenzyme A derivatives of cholate, chenodeoxycholate, deoxycholate, lithocholate, and their 5 alpha analogs were studied in reversed-phase high-performance liquid chromatography. With a C18 Radial-PAK A cartridge (10-micron particles) and a solvent mixture of 2-propanol/10 mM phosphate buffer (pH 7.0, 140:360), separation of the chenodeoxycholyl and deoxycholyl coenzyme A derivatives was not observed. An increase in ionic strength of the buffer to 50 mM afforded separation, which was markedly augmented with a C18 Radial-PAK A cartridge with 5-micron particles. Lowering the pH of the buffer to 5.5 did not materially change the separations regardless of the ionic strength. Quantitation was carried out to a lower level of 8.5 X 10(-12) mol.     

Coevolution of cells and virus as a mechanism for the persistence of lymphotropic minute virus of mice in L-cells.

Infection of L-cells with minute virus of mice (i), a lymphotropic strain of minute virus of mice, resulted in the emergence of host range mutant viruses capable of a lytic infection that destroys the initially restrictive parental cells. Despite that, the culture was not lysed completely; instead, a persistent infection resulted which lasted at least 150 days. Throughout the persistent infection, extensive changes occurred in both the tissue tropism of the progeny virus and in the phenotypic properties of the cells. Mutant cells were selected which were increasingly restrictive to the replication of the resident virus, but concomitant changes in the virus enabled it to replicate in a subpopulation of the restrictive cells. The persistent infection could be reconstructed by infection of mutant cells with mutant virus; in contrast, neither infection of parental cells with mutant virus nor infection of mutant cells with parental virus led to persistence. On the basis of these results, we suggest that virus-cell coevolution provides the primary mechanism for the initiation and the maintenance of the persistent infection.     

Wound-induced and naturally occurring regenerative differentiation of xylem in Zea mays L.

The regenerative differentiation of xylem, both around a wound in the stem and at the root junction was studied in seedlings of maize. The regeneration of vessels around a wound was very small, being limited to the very young internodes and sharply declining basipetally. There were more regenerative vessel elements and they differentiated faster above the wound than below it. The regenerative vessel elements around the wound were characterized by helical or annular pattern of secondary wall thickenings. Wounding also resulted in the development of additional vascular anastomoses in the leaf immediately above the wound, and in differentiation of discontinuous vessels in adjacent bundles. Regenerative vessel elements were very common where the adventitious roots connected with the stem internodes, and exhibited pitted or reticulated secondary wall thickenings.