Descartes, corpuscles and reductionism : mechanism and systems in Descartes' physiology

I argue that Descartes explains physiology in terms of whole systems, and not in terms of the size, shape and motion of tiny corpuscles (corpuscular mechanics). It is a standard, entrenched view that Descartes’s proper means of explanation in the natural world is through strict reduction to corpuscular mechanics. This view is bolstered by a handful of corpuscular-mechanical explanations in Descartes’s physics, which have been taken to be representative of his treatment of all natural phenomena. However, Descartes’s explanations of the ‘principal parts’ of physiology do not follow the corpuscular–mechanical pattern. Des Chene (2001) has identified systems in Descartes’s account of physiology, but takes them ultimately to reduce down to the corpuscle level. I argue that they do not. Rather, Descartes maintains entire systems, with components selected from multiple levels of organisation, in order to construct more complete explanations than corpuscular mechanics alone would allow

Iron, silicate, and light co-limitation of three Southern Ocean diatom species

The effect of combined iron, silicate, and light co-limitation was investigated in the three diatom species Actinocyclus sp. Ehrenberg, Chaetoceros dichaeta Ehrenberg, and Chaetoceros debilis Cleve, isolated from the Southern Ocean (SO). Growth of all species was co-limited by iron and silicate, reflected in a significant increase in the number of cell divisions compared to the control. Lowest relative Si uptake and drastic frustule malformation was found under iron and silicate co-limitation in C. dichaeta, while Si limitation in general caused cell elongation in both Chaetoceros species. Higher light intensities similar to SO surface conditions showed a negative impact on growth of C. dichaeta and Actinocyclus sp. and no effect on C. debilis. This is in contrast to the assumed light limitation of SO diatoms due to deep wind driven mixing. Our results suggest that growth and species composition of Southern Ocean diatoms is influenced by a sensitive interaction of the abiotic factors, iron, silicate, and light

Trans-cleaving hammerhead ribozymes with tertiary stabilizing motifs: in vitro and in vivo activity against a structured viroid RNA

Trans-cleaving hammerheads with discontinuous or extended stem I and with tertiary stabilizing motifs (TSMs) have been tested previously against short RNA substrates in vitro at low Mg2+ concentration. However, the potential of these ribozymes for targeting longer and structured RNAs in vitro and in vivo has not been examined. Here, we report the in vitro cleavage of short RNAs and of a 464-nt highly structured RNA from potato spindle tuber viroid (PSTVd) by hammerheads with discontinuous and extended formats at submillimolar Mg2+. Under these conditions, hammerheads derived from eggplant latent viroid and peach latent mosaic viroid (PLMVd) with discontinuous and extended formats, respectively, where the most active. Furthermore, a PLMVd-derived hammerhead with natural TSMs showed activity in vivo against the same long substrate and interfered with systemic PSTVd infection, thus reinforcing the idea that this class of ribozymes has potential to control pathogenic RNA replicons

Metal–organic complexation in the marine environment

We discuss the voltammetric methods that are used to assess metal–organic complexation in seawater. These consist of titration methods using anodic stripping voltammetry (ASV) and cathodic stripping voltammetry competitive ligand experiments (CSV-CLE). These approaches and a kinetic approach using CSV-CLE give similar information on the amount of excess ligand to metal in a sample and the conditional metal ligand stability constant for the excess ligand bound to the metal. CSV-CLE data using different ligands to measure Fe(III) organic complexes are similar. All these methods give conditional stability constants for which the side reaction coefficient for the metal can be corrected but not that for the ligand. Another approach, pseudovoltammetry, provides information on the actual metal–ligand complex(es) in a sample by doing ASV experiments where the deposition potential is varied more negatively in order to destroy the metal–ligand complex. This latter approach gives concentration information on each actual ligand bound to the metal as well as the thermodynamic stability constant of each complex in solution when compared to known metal–ligand complexes. In this case the side reaction coefficients for the metal and ligand are corrected. Thus, this method may not give identical information to the titration methods because the excess ligand in the sample may not be identical to some of the actual ligands binding the metal in the sample

Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs

[EN] Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.This work was supported by the Ministerio de Economia y Competitividad (grant number BFU2011-23398).Cervera Olagüe, A.; La Peña Del Rivero, MD. (2014). Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs. Molecular Biology and Evolution. 31(11):2941-2947. https://doi.org/10.1093/molbev/msu232S29412947311

Involvement of the Chloroplastic Isoform of tRNA Ligase in the Replication of Viroids Belonging to the Family Avsunviroidae

Avocado sunblotch viroid, peach latent mosaic viroid, chrysanthemum chlorotic mottle viroid, and eggplant latent viroid (ELVd), the four recognized members of the family Avsunviroidae, replicate through the symmetric pathway of an RNA-to-RNA rolling-circle mechanism in chloroplasts of infected cells. Viroid oligomeric transcripts of both polarities contain embedded hammerhead ribozymes that, during replication, mediate their self-cleavage to monomeric-length RNAs with 5'-hydroxyl and 2',3'-phosphodiester termini that are subsequently circularized. We report that a recombinant version of the chloroplastic isoform of the tRNA ligase from eggplant (Solanum melongena L.) efficiently catalyzes in vitro circularization of the plus [(+)] and minus [(-)] monomeric linear replication intermediates from the four Avsunviroidae. We also show that while this RNA ligase specifically recognizes the genuine monomeric linear (+) ELVd replication intermediate, it does not do so with five other monomeric linear (+) ELVd RNAs with their ends mapping at different sites along the molecule, despite containing the same 5'-hydroxyl and 2',3'-phosphodiester terminal groups. Moreover, experiments involving transient expression of a dimeric (+) ELVd transcript in Nicotiana benthamiana Domin plants preinoculated with a tobacco rattle virus-derived vector to induce silencing of the plant endogenous tRNA ligase show a significant reduction of ELVd circularization. In contrast, circularization of a viroid replicating in the nucleus occurring through a different pathway is unaffected. Together, these results support the conclusion that the chloroplastic isoform of the plant tRNA ligase is the host enzyme mediating circularization of both (+) and (-) monomeric linear intermediates during replication of the viroids belonging to the family Avsunviroidae.This work was supported by the Ministerio de Ciencia e Innovacion (MICINN) from Spain through grants BIO2008-01986, BIO2011-26741, and BFU2008-03154. M. A. Nohales and D. Molina-Serrano were the recipients of predoctoral fellowships from the Spanish Ministerio de Educacion y Ciencia.Nohales Zafra, MA.; Molina Serrano, D.; Flores Pedauye, R.; Daros Arnau, JA. (2012). Involvement of the Chloroplastic Isoform of tRNA Ligase in the Replication of Viroids Belonging to the Family Avsunviroidae. Journal of Virology. 86:8269-8276. https://doi.org/10.1128/JVI.00629-12S8269827686Abelson, J., Trotta, C. R., & Li, H. (1998). tRNA Splicing. 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Evaluation of gait symmetry in poliomyelitis subjects : Comparison of a conventional knee ankle foot orthosis (KAFO) and a new powered KAFO.

Background: Compared to able-bodied subjects, subjects with post polio syndrome and poliomyelitis demonstrate a preference for weight-bearing on the non-paretic limb, causing gait asymmetry. Objectives: The purpose of this study was to evaluate the gait symmetry of the poliomyelitis subjects when ambulating with either a drop- locked knee ankle foot orthosis (KAFO) or a newly developed powered KAFO. Methods: Seven subjects with poliomyelitis who routinely wore conventional KAFOs participated in this study, and received training to enable them to ambulate with the powered KAFO on level ground, prior to gait analysis. Results: There were no significant differences in the gait symmetry index (SI) of step length (P=0.085), stance time (P=0.082), double limb support time (P=0.929) or speed of walking (p=0.325) between the two test conditions. However, using the new powered KAFO improved the SI in step width (P=0.037), swing time (P=0.014), stance phase percentage (P=0.008) and knee flexion during swing phase (p≤0.001) compared to wearing the dropped locked KAFO. Conclusion: The use of a powered KAFO for ambulation by poliomyelitis subjects affects gait symmetry in the base of support, swing time, stance phase percentage and knee flexion during swing phase