Euler buckling and nonlinear kinking of double-stranded DNA

The bending stiffness of double-stranded DNA (dsDNA) at high curvatures is fundamental to its biological activity, yet this regime has been difficult to probe experimentally, and literature results have not been consistent. We created a ‘molecular vise’ in which base-pairing interactions generated a compressive force on sub-persistence length segments of dsDNA. Short dsDNA strands (<41 base pairs) resisted this force and remained straight; longer strands became bent, a phenomenon called ‘Euler buckling’. We monitored the buckling transition via Förster Resonance Energy Transfer (FRET) between appended fluorophores. For low-to-moderate concentrations of monovalent salt (up to ∼150 mM), our results are in quantitative agreement with the worm-like chain (WLC) model of DNA elasticity, without the need to invoke any ‘kinked’ states. Greater concentrations of monovalent salts or 1 mM Mg²⁺ induced an apparent softening of the dsDNA, which was best accounted for by a kink in the region of highest curvature. We tested the effects of all single-nucleotide mismatches on the DNA bending. Remarkably, the propensity to kink correlated with the thermodynamic destabilization of the mismatched DNA relative the perfectly complementary strand, suggesting that the kinked state is locally melted. The molecular vise is exquisitely sensitive to the sequence-dependent linear and nonlinear elastic properties of dsDNA.     

Morphological Diversity of the Rod Spherule: A Study of Serially Reconstructed Electron Micrographs

Purpose

Rod spherules are the site of the first synaptic contact in the retina’s rod pathway, linking rods to horizontal and bipolar cells. Rod spherules have been described and characterized through electron micrograph (EM) and other studies, but their morphological diversity related to retinal circuitry and their intracellular structures have not been quantified. Most rod spherules are connected to their soma by an axon, but spherules of rods on the surface of the Mus musculus outer plexiform layer often lack an axon and have a spherule structure that is morphologically distinct from rod spherules connected to their soma by an axon. Retraction of the rod axon and spherule is often observed in disease processes and aging, and the retracted rod spherule superficially resembles rod spherules lacking an axon. We hypothesized that retracted spherules take on an axonless spherule morphology, which may be easier to maintain in a diseased state. To test our hypothesis, we quantified the spatial organization and subcellular structures of rod spherules with and without axons. We then compared them to the retracted spherules in a disease model, mice that overexpress Dscam (Down syndrome cell adhesion molecule), to gain a better understanding of the rod synapse in health and disease.

Methods

We reconstructed serial EM images of wild type and Dscam^GoF (gain of function) rod spherules at a resolution of 7 nm in the X-Y axis and 60 nm in the Z axis. Rod spherules with and without axons, and retracted spherules in the Dscam^GoF retina, were reconstructed. The rod spherule intracellular organelles, the invaginating dendrites of rod bipolar cells and horizontal cell axon tips were also reconstructed for statistical analysis.

Results

Stereotypical rod (R1) spherules occupy the outer two-thirds of the outer plexiform layer (OPL), where they present as spherical terminals with large mitochondria. This spherule group is highly uniform and composed more than 90% of the rod spherule population. Rod spherules lacking an axon (R2) were also described and characterized. This rod spherule group consists of a specific spatial organization that is strictly located at the apical OPL-facing layer of the Outer Nuclear Layer (ONL). The R2 spherule displays a large bowl-shaped synaptic terminal that hugs the rod soma. Retracted spherules in the Dscam^GoF retina were also reconstructed to test if they are structurally similar to R2 spherules. The misplaced rod spherules in Dscam^GoF have a gross morphology that is similar to R2 spherules but have significant disruption in internal synapse organization.

Conclusion

We described a morphological diversity within Mus musculus rod spherules. This diversity is correlated with rod location in the ONL and contributes to the intracellular differences within spherules. Analysis of the Dscam^GoF retina indicated that their R2 spherules are not significantly different than wild type R2 spherules, but that their retracted rod spherules have abnormal synaptic organization.     

Bioinformatics as a critical prerequisite to transcriptome and proteome studies

Large-scale genomic studies rely strongly on annotations available in databases to design experimental supports such as arrays or to explain results in term of biological meaning. Most of this information originates from bioinformatic predictions. Their accuracy as well as their relevance to existing biological data are critical in avoiding the misinterpretation of experimental results.     

Plastic collective endothermy in a complex animal society (army ant bivouacs: Eciton burchellii parvispinum)

Endothermic animals do not always have a single adaptive internal temperature; some species exhibit plastic homeostasis, adaptively allowing body temperature to drop when thermoregulatory costs are high. Like large‐bodied endotherms, some animal societies exhibit collective thermal homeostasis. We tested for plasticity of thermoregulation in the self‐assembled temporary nests (bivouacs) of army ants. We measured core bivouac temperatures under a range of environmental conditions and at different colony developmental (larval vs pupal brood) stages. Contrary to previous assertions, bivouacs were not perfect thermoregulators in all developmental stages. Instead, bivouacs functioned as superorganismal facultative endotherms, using a combination of site choice and context‐dependent metabolic heating to adjust core temperatures across an elevational cline in ambient temperature. When ambient temperature was low, the magnitude of metabolic heating was dependent on colony developmental stage: pupal bivouacs were warmer than larval bivouacs. At cooler high elevations, bivouacs functioned like some endothermic animals that intermittently lower their body temperatures to conserve energy. Bivouacs potentially conserved energy by investing less metabolic heating in larval brood because the high costs of impaired worker development may require more stringent thermoregulation of pupae. Our data also suggest that site choice played an important role in bivouac cooling under high ambient temperatures at low elevations. Climate warming may expand upper elevational range limits of Eciton burchellii parvispinum, while reducing the availability of cool and moist bivouac sites at lower elevations, potentially leading to future low‐elevation range contraction.     

Interactions of HIV-1 and HIV-2 envelope glycoproteins with sulphated polysaccharides and mannose-6-phosphate

Envelope glycoproteins of human immunodeficiency viruses (HIV-1and HIV-2) can interact with high-mannose glycans and with themannosyl or N-acetylglucosaminyl core of complex-type oligosaccharidicstructures. HIV-1 glycoproteins also specifically bind sulphatedpolysaccharides such as dextran sulphate (DS) and heparin. Here,we show that the latter property is shared by HIV-2 recombinantgp140 (rgpl40) precursor glycoprotein. Binding of rgpl40 andof corresponding rgp160 of HIV-1 to heparin- and DS-substituted(sulphated dextran beads; SDB) affinity matrices was inhibitedby the soluble specific ligand and also by fetuin, asialofetuinor the anionic simple carbohydrate derivative manncsse-6-phosphate(M6P). Interaction of HIV-1 rgpl20 subunit with the two affinitymatrices was also inhibited by M6P, but only rgpl20 bindingto heparin-agarose, and not that to SDB, was affected by fetuinand asialofetuin. These results suggest that HIV-1 and HIV-2envelope glycoproteins presumably display different sulphatedpolysaccharide and carbohydrate recognition sites. Some of thesemay be common or in close proximity: with respect to rgpl60,for example, the sites may be common on the gp41 moiety and/orin a region of gp120 which would be more accessible when expressedon rgpl60 than on processed gpl20, while they may be distincton the cleaved gpl20 subunit. Finally, because M6P is a markerof lysosomal enzymes, we verified that HIV-1 and HIV-2 envelopeglycoproteins could specifically bind in a M6P-inhibitable mannerto a representative lysosomal enzyme, bovine liver ß-glucuronidasecoupled to agarose, suggesting that they may possibly interferewith lysosomal enzyme sorting in HIV-infected cells. env glycoproteins HIV lectin mannose-6-phosphate sulphated polysaccharides     

Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 Å crystal structure of the complex

Fcabs (Fc domain with antigen-binding sites) are promising novel therapeutics. By engineering of the C-terminal loops of the CH3 domains, 2 antigen binding sites can be inserted in close proximity. To elucidate the binding mode(s) between homodimeric Fcabs and small homodimeric antigens, the interaction between the Fcabs 448 and CT6 (having the AB, CD and EF loops and the C-termini engineered) with homodimeric VEGF was investigated. The crystal structures of these Fcabs, which form polymers with the antigen VEGF in solution, were determined. However, construction of heterodimeric Fcabs (JanusFcabs: one chain Fc-wt, one chain VEGF-binding) results in formation of distinct JanusFcab–VEGF complexes (2:1), which allowed elucidation of the crystal structure of the JanusCT6–VEGF complex at 2.15 Å resolution. VEGF binding to Janus448 and JanusCT6 is shown to be entropically unfavorable, but enthalpically favorable. Structure-function relationships are discussed with respect to Fcab design and engineering strategies.     

Cell Wall Proteome of Sugarcane Young and Mature Leaves and Stems

By characterizing the cell wall proteomes of different sugarcane organs (leaves and stems) at two developmental stages (young vs mature/apical vs basal), it is possible to address unique characteristics in each of them. Four‐month‐old leaves show a higher proportion of oxido‐reductases and proteins related to lipid metabolism (LM), besides a lower proportion of proteins acting on polysaccharides, in comparison to 4‐month‐old internodes. It is possible to note that sugarcane leaves and young stems have the highest LM rate than all species, which is assumed to be linked to cuticle formation. The data generated enrich the number of cell wall proteins (CWPs) identified in sugarcane, reaching 277. To our knowledge, sugarcane has now the second higher coverage of monocot CWP in plants.