An examination of protist diversity in serpentinization-hosted ecosystems of the Samail Ophiolite of Oman

In the Samail Ophiolite of Oman, the geological process of serpentinization produces reduced, hydrogen rich, hyperalkaline (pH > 11) fluids. These fluids are generated through water reacting with ultramafic rock from the upper mantle in the subsurface. On Earth’s continents, serpentinized fluids can be expressed at the surface where they can mix with circumneutral surface water and subsequently generate a pH gradient (∼pH 8 to pH > 11) in addition to variations in other chemical parameters such as dissolved CO2, O2, and H2. Globally, archaeal and bacterial community diversity has been shown to reflect geochemical gradients established by the process of serpentinization. It is unknown if the same is true for microorganisms of the domain Eukarya (eukaryotes). In this study, using 18S rRNA gene amplicon sequencing, we explore the diversity of microbial eukaryotes called protists in sediments of serpentinized fluids in Oman. We demonstrate that protist community composition and diversity correlate significantly with variations in pH, with protist richness being significantly lower in sediments of hyperalkaline fluids. In addition to pH, the availability of CO2 to phototrophic protists, the composition of potential food sources (prokaryotes) for heterotrophic protists and the concentration of O2 for anaerobic protists are factors that likely shape overall protist community composition and diversity along the geochemical gradient. The taxonomy of the protist 18S rRNA gene sequences indicates the presence of protists that are involved in carbon cycling in serpentinized fluids of Oman. Therefore, as we evaluate the applicability of serpentinization for carbon sequestration, the presence and diversity of protists should be considered

Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

L). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote–eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have <21, 000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph. © 2012 Macmillan Publishers Limited. All rights reserved

An evidence-based exploration into the effect of language-pair specificity in English-Chinese simultaneous interpreting

Whether and how language-pair specificity affects the process and product of interpreting is a recurring implicit topic of debate in interpreting studies. Previous discussions have touched upon this issue in Japanese/English and German/English interpreting, with little attention to its role in Chinese/English interpreting. This study focuses on the effect of structural asymmetry between English and Chinese on English-Chinese simultaneous interpreting performance, which is exemplified by right-branching structures in English and left-branching structures in Chinese. Based on a naturalistic observation of three professional interpreters’ on-site simultaneous interpretations of the same speech, it investigates two major questions: a) Does structural asymmetry between English and Chinese constitute particular difficulties in the interpreters’ interpreting performance? b) If yes, how does such language-pair specificity affect their interpreting product? While previous interpreting studies generally consider that the interpreting product is shaped by three major variables including the interpreter’s interpreting competence, cognitive conditions on the site and norms of interpreting, findings of the present study suggest that language-pair specificity functions as another variable in English-Chinese interpreting. It implies the necessity of considering it in the theoretical account of interpreting between languages such as English and Chinese that involve significant contrasts in linguistic structure and cultural conceptualization

The Fayum Primate Forest Revisited

In Oligocene times, the Fayum area of northern Egypt was a subtropical to tropical lowland coastal plain with damp soils and seasonal rainfall that supported an abundance and variety of vegetation, including lianes (large vines), tall trees, and possibly mangroves, and a large and varied vertebrate fauna. The Oligocene marine strandline was close by and principal Jebel Qatrani Formation streams were probably brackish several kilometers inland due to tidal incursions. Sediments of the Jebel Qatrani Formation were deposited by several large meandering streams, associated with minor but sometimes extensive flood basin ponds. These rocks provide no evidence for the former existence, in early Tertiary time, of a Proto-Nile River. Large accumulations of silicified fossil logs in the Jebel Qatrani Formation are autochthonous and the logs were transported only a short distance before burial. The Oligocene higher primates Argyplopithecus, , Propliopithecus, Parapithecus, and Apidium lived in this paleoenvironment and postcranial remains of Aegyptopithecus and Apidium demonstrate that these animals were arboreal. This scenario for the paleoenvironment of the Fayum area in Oligocene times differs greatly from the nearly treeless, sparsely vegetated, semiarid sahtlien Oligocene Fayum paleoenvironment populated by terrestrial primates that ,vas recently proposed by Kortlandt (1980)