Tetradifon: an oligomycin-like inhibitor of energy-linked activities of rat liver mitochondria

Tetradifon (p-chlorophenyl-2,4,5-trichlorophenyl sulfone) at concentrations between 4.5 and 27.0 nmoles/mg mitochondrial protein provides half-maximal inhibition of the following energy-linked activities of rat liver mitochondria: ADP-stimulated respiration, DNP-stimulated ATPase activity, Mg⁺⁺-stimulated ATPase activity, and P_i-ATP exchange activity. Tetradifon has no effect on the activity of soluble ATPase purified from rat liver mitochondria. Respiration inhibited by tetradifon is restored upon addition of 2,4-dinitrophenol. It is concluded that tetradifon acts at or near the oligomycin sensitivity conferring complex located in the mitochondrial inner membrane.     

Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results

Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette. Several experimental variables were changed while measuring the unfolding/refolding kinetics, including handle lengths, trap stiffness, and modes of force applied to the molecule. In constant-force mode where the tension applied to the RNA was maintained through feedback control, the measured rate coefficients varied within 40% when the handle lengths were changed by 10-fold (1.1-10.2 Kbp); they increased by two- to threefold when the trap stiffness was lowered to one-third (from 0.1 to 0.035 pN/nm). In the passive mode, without feedback control and where the force applied to the RNA varied in response to the end-to-end distance change of the tether, the RNA hopped between a high-force folded-state and a low-force unfolded-state. In this mode, the rates increased up to twofold with longer handles or softer traps. Overall, the measured rates remained with the same order-of-magnitude over the wide range of conditions studied. In the companion article on pages 3010-3021, we analyze how the measured kinetics parameters differ from the intrinsic molecular rates of the RNA, and thus how to obtain the molecular rates.     

Helical inchworming: a novel translocation mechanism for a ring ATPase

Ring ATPases perform a variety of tasks in the cell. Their function involves complex communication and coordination among the often identical subunits. Translocases in this group are of particular interest as they involve both chemical and mechanical actions in their operation. We study the DNA packaging motor of bacteriophage φ29, and using single-molecule optical tweezers and single-particle cryo-electron microscopy, have discovered a novel translocation mechanism for a molecular motor.     

Leaf functional traits of Neotropical savanna trees in relation to seasonal water deficit

The seasonal savannas (cerrados) of Central Brazil are characterized by a large diversity of evergreen and deciduous trees, which do not show a clear differentiation in terms of active rooting depth. Irrespective of the depth of the root system, expansion of new foliage in deciduous species occurs at the end of the dry season. In this study, we examined a suite of leaf traits related to C assimilation, water and nutrients (N, P) in five deciduous and six evergreen trees that were among the dominant families of cerrado vegetation. Maximum CO₂ assimilation on a mass basis (A_mass) was significantly correlated with leaf N and P, and specific leaf area (SLA; leaf area per unit of leaf mass). The highest leaf concentrations of both nutrients were measured in the newly mature leaves of deciduous species at the end of the dry period. The differences in terms of leaf N and P between evergreen and deciduous species decreased during the wet season. Deciduous species also invested less in the production of non-photosynthetic leaf tissues and produced leaves with higher SLA and maintained higher water use efficiency. Thus, deciduous species compensated for their shorter leaf payback period by maintaining higher potential payback capacity (higher values of A_mass) and lower leaf construction costs (higher SLA). Their short leafless period and the capacity to flush by the end of the dry season may also contribute to offset the longer payback period of evergreen species, although it may involve the higher cost of maintaining a deep-root system or a tight control of plant water balance in the shallow-rooted ones.     

PhySIC_IST: cleaning source trees to infer more informative supertrees

Background  

Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene coalescence. When topological conflicts occur among source trees, liberal methods infer supertrees containing the most frequent alternative, while veto methods infer supertrees not contradicting any source tree, i.e. discard all conflicting resolutions. When the source trees host a significant number of topological conflicts or have a small taxon overlap, supertree methods of both kinds can propose poorly resolved, hence uninformative, supertrees.