Molecular phylogeny and evolution of <i>Parabasalia</i> with improved taxon sampling and new protein markers of actin and elongation factor-1α

Background: Inferring the evolutionary history of phylogenetically isolated, deep-branching groups of taxa—in particular determining the root—is often extraordinarily difficult because their close relatives are unavailable as suitable outgroups. One of these taxonomic groups is the phylum Parabasalia, which comprises morphologically diverse species of flagellated protists of ecological, medical, and evolutionary significance. Indeed, previous molecular phylogenetic analyses of members of this phylum have yielded conflicting and possibly erroneous inferences. Furthermore, many species of Parabasalia are symbionts in the gut of termites and cockroaches or parasites and therefore formidably difficult to cultivate, rendering available data insufficient. Increasing the numbers of examined taxa and informative characters (e.g., genes) is likely to produce more reliable inferences. Principal Findings: Actin and elongation factor-1a genes were identified newly from 22 species of termite-gut symbionts through careful manipulations and seven cultured species, which covered major lineages of Parabasalia. Their protein sequences were concatenated and analyzed with sequences of previously and newly identified glyceraldehyde-3-phosphate dehydrogenase and the small-subunit rRNA gene. This concatenated dataset provided more robust phylogenetic relationships among major groups of Parabasalia and a more plausible new root position than those previously reported. Conclusions/Significance: We conclude that increasing the number of sampled taxa as well as the addition of new sequences greatly improves the accuracy and robustness of the phylogenetic inference. A morphologically simple cell is likely the ancient form in Parabasalia as opposed to a cell with elaborate flagellar and cytoskeletal structures, which was defined as most basal in previous inferences. Nevertheless, the evolution of Parabasalia is complex owing to several independent multiplication and simplification events in these structures. Therefore, systematics based solely on morphology does not reflect the evolutionary history of parabasalids

Ketone Hydrogenation with Iridium Complexes with “non N–H” Ligands: The Key Role of the Strong Base

Ferrocenyl phosphine thioether ligands (PS), not containing deprotonatable functions, efficiently support the iridium catalyzed ketone hydrogenation in combination with a strong base co-catalyst. Use of an internal base ([Ir(OMe)(COD)]2 in place of [IrCl(COD)]2) is not sufficient to insure activity and a strong base is still necessary, suggesting that the active catalyst is an anionic hydride complex. Computational investigations that include solvent effects demonstrate the thermodynamically accessible generation of the tetrahydrido complex [IrH4(PS)]-and suggest an operating cycle via a [Na+(MeOH)3∙∙∙Ir-H4(PS)] contact ion pair with an energy span of 18.2 kcal/mol. The cycle involves an outer sphere stepwise H-/H+ transfer, the proton originating from H2 after coordination and heterolytic activation. The base plays the dual role of generating the anionic complex and providing the Lewis acid co-catalyst for ketone activation. The best cycle for the neutral system, on the other hand, requires an energy span of 26.3 kcal/mol. This work highlights, for the first time, the possibility of outer sphere hydrogenation in the presence of non deprotonatable ligands and the role of the strong base in the activation of catalytic systems with such type of ligands

Individual and collective dynamics of self-propelled soft particles

Deformable self-propelled particles provide us with one of the most important nonlinear dissipative systems, which are related, for example, to the motion of microorganisms. It is emphasized that this is a subject of localized objects in non-equilibrium open systems. We introduce a coupled set of ordinary differential equations to study various dynamics of individual soft particles due to the nonlinear couplings between migration, spinning and deformation. By introducing interactions among the particles, the collective dynamics and its collapse are also investigated by changing the particle density and the interaction strength. We stress that assemblies of self-propelled particles also exhibit a variety of non-equilibrium localized patterns

Soft deformable self-propelled particles

In this work we investigate the collective behavior of self-propelled particles that deform due to local pairwise interactions. We demonstrate that this deformation alone can induce alignment of the velocity vectors. The onset of collective motion is analyzed. Applying a Gaussian-core repulsion between the particles, we find a transition to disordered non-collective motion under compression. We here explain that this reflects the reentrant fluid behavior of the general Gaussian-core model now applied to a self-propelled system. Truncating the Gaussian potential can lead to cluster crystallization or more disordered cluster states. For intermediate values of the Gaussian-core potential we for the first time observe laning for deformable self-propelled particles. Finally, without the core potential, but including orientational noise, we connect our description to the Vicsek approach for self-propelled particles with nematic alignment interactions.Comment: 6 pages, 7 figure

Highly effective yet simple transmembrane anion transporters based upon ortho-phenylenediamine bis-ureas

Simple, highly fluorinated receptors are shown to function as highly effective transmembrane anion antiporters with the most active transporters rivalling the transport efficacy of natural anion transporter prodigiosin for bicarbonate

Dynamics of a deformable self-propelled domain

We investigate the dynamical coupling between the motion and the deformation of a single self-propelled domain based on two different model systems in two dimensions. One is represented by the set of ordinary differential equations for the center of gravity and two tensor variables characterizing deformations. The other is an active cell model which has an internal mechanism of motility and is represented by the partial differential equation for deformations. Numerical simulations show a rich variety of dynamics, some of which are common to the two model systems. The origin of the similarity and the difference is discussed.Comment: 6 pages, 6 figure

Highly enantioselective imine hydrogenation catalyzed by ruthenium phosphane-phosphite diamine complexes

Mildly does it: A highly enantioselective catalyst for the hydrogenation of N-aryl imines is described (see scheme). This catalyst offers practical advantages because it operates under very mild conditions and is based on an Ru complex with a diamine as the sole chiral ligand.Ministerio de Economía y Competitividad CTQ2009-11867, CSD2007-00006European Union PITN 2008-215193Junta de Andalucía 2008/FQM-383

The gut microbiota of the wood-feeding termite Reticulitermes lucifugus (Isoptera; Rhinotermitidae)

Termite gut is host to a complex microbial community consisting of prokaryotes, and in some cases flagellates, responsible for the degradation of lignocellulosic material. Here we report data concerning the analysis of the gut microbiota of Reticulitermes lucifugus (Rossi), a lower termite species that lives in underground environments and is widespread in Italy, where it causes damage to wood structures of historical and artistic monuments. A 16S rRNA gene clone library revealed that the R. lucifugus gut is colonized by members of five phyla in the domain Bacteria: Firmicutes (49 % of clones), Proteobacteria (24 %), Spirochaetes (14 %), the candidatus TG1 phylum (12 %), and Bacteroidetes (1 %). A collection of cellulolytic aerobic bacteria was isolated from the gut of R. lucifugus by enrichment cultures on different cellulose and lignocellulose substrates. Results showed that the largest amount of culturable cellulolytic bacteria of R. lucifugus belongs to Firmicutes in the genera Bacillus and Paenibacillus (67 %). These isolates are also able to grow on xylan and show the largest clear zone diameter in the Congo red test. Reticulitermes lucifugus hosts a diverse community of bacteria and could be considered an acceptable source of hydrolytic enzymes for biotechnological applications

Asymmetric Hydrogenation of 1-alkyl and 1-aryl vinyl benzoates: a broad scope procedure for the highly enantioselective synthesis of 1-substituted ethyl benzoates

The enantioselective hydrogenation of enol esters of formula CH2=C(OBz)R with rhodium catalysts based on phosphine-phosphite ligands (P-OP) has been studied. The reaction has a broad scope and it is suitable for the preparation of products possessing a wide variety of R substituents. For the cases where R is a primary alkyl high catalyst activity (S/C = 500) and enantioselectivities (95-99 % ee) were obtained with a catalyst characterized by an ethane backbone and a PPh2 fragment. In contrast, for R = tBu a catalyst possessing a benzene backbone provided the best results (97 % ee). Derivatives with a cycloalkyl R substituent were particularly difficult substrates for this reaction. A broader catalyst screening was required for these substrates, which identified a catalyst possessing a P(m-xylyl)2 fragment as the most appropriate one, affording enantioselectivities between 90 and 95 % ee. Outstanding enantioselectivities (99 % ee) and high catalyst activity (S/C = 500-1000) were also obtained in the case of substrates bearing a Ph or a fluoroaryl R substituent. In addition, the system is also appropriate for the preparation of other synthetically useful esters as those for R = benzyl, 2-phenylethyl or Nphthalimido alkyl chains. Likewise, the hydrogenation of divinyl dibenzoates proceeded with very high diastero- and enantioselectivity, generating rather low amounts of the meso isomer (3-6 %). On the other hand, substrates with Br- and MeO- substituents at the phenyl benzoate ring, suitable for further functionalization, have also been examined. The results obtained indicate no detrimental effect of these substituents in the hydrogenation. Alternatively, the methodology has been applied to the highly enantioselective synthesis of deuterium isotopomers of 1-octyl benzoate bearing CDH2, CD2H or CD3 fragments. Finally, as a practical advantage of the present system, it has been observed that the high performance of the catalysts is retained in high concentrated solutions or even in the neat substrate, then minimizing both the amount of solvent added and the volume of the reactionJunta de Andalucía 2009/FQM-4832CSIC 201480E03 1Ministerio de Ciencia e Innovación CTQ2010- 14796/BQ