DNA Sequence Determinants Controlling Affinity,Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequences in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. The affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.     

Simultaneous registration of rheographic and manometric parameters of the inferior esophageal sphincter in the cat

The aim of the present study was to detect simultaneously hemodynamic parietal events and intraluminal pressure of the Lower Esophageal Sphincter (LES), with particular regards to cyclic changes due to systo-diastolic cardiac activity. A probe for combined Intraluminal Manometric Plethysmography (IMP) and Intraluminal Impedence Plethysmography (IIP) was used. It was a Swan Ganz bipolar pacing catheter, modified by removing the latex balloon from the tip. The exposed side-hole (diameter smaller than 0.5 mm) was utilized as a terminal orifice for an infused manometry system. It was preliminarly essayed in bench tests. A perfusion rate of 1.75 ml/min was chosen as it did not induce significant elevations of the pressure base-line and allowed detection of pressure rise rates up to 300 mm Hg/s. The two metallic rings, originally designed for intracardiac stimulation, were used as low resistance electrodes to record impedence variations. Since very small shifts of recording electrodes induce important artifacts, the present experiments were carried out on curarized cats. In these conditions, artificial ventilation could be temporarily stopped to avoid any artifact due to respiration mechanics. The proposed method seems to be satisfactory enough for simultaneous acquisition of IIP and IMP data at LES level. Recordings of IIP allow to reveal changes in parietal blood content which could chiefly be referred to lamina propria and submucosa districts. On the other hand, IMP cyclic fluctuations would signal variations of total sphincteric tension, likely depending on hemodynamic events in all vascular beds of the wall. In our opinion, a more extensive analysis of IMP and IIP waves, as well as of reciprocal relationships between rheografic and manometric parameters, may provide very useful knowledges on sphincteric physiology.     

Body condition helps to explain metabolic rate variation in wolf spiders

1. Metabolism is the fundamental process that powers life. Understanding what drives metabolism is therefore critical to our understanding of the ecology and behaviour of organisms in nature. 2. Metabolic rate generally scales with body size according to a power law. However, considerable unexplained variation in metabolic rate remains after accounting for body mass with scaling functions. 3. We measured resting metabolic rates (oxygen consumption) of 227 field‐caught wolf spiders. Then, we tested for effects of body mass, species, and body condition on metabolic rate. 4. Metabolic rate scales with body mass to the 0.85 power in these wolf spiders, and there are metabolic rate differences between species. After accounting for these factors, residual variation in metabolic rate is related to spider body condition (abdomen:cephalothorax ratio). Spiders with better body condition consume more oxygen. 5. These results indicate that recent foraging history is an important determinant of metabolic rate, suggesting that although body mass and taxonomic identity are important, other factors can provide helpful insights into metabolic rate variation in ecological communities.     

Identification of a caleosin associated with hazelnut (Corylus avellana L.) oil bodies

• Caleosins are involved in several cellular and biological processes that are closely associated with the synthesis, degradation and stability of oil bodies (OB).
• Because of the importance and the multiple roles of these OB‐associated proteins, in silico identification of sequences corresponding to putative caleosins in the hazelnut genome has been performed, and the association with seed OB was verified using a proteomic approach.
• Five full‐length sequences (CavCLO‐H1, CavCLO‐H2, CavCLO‐H3, CavCLO‐L1, CavCLO‐L2), belonging to the two groups of caleosins (H and L), have been identified in the hazelnut genome. The number of identified caleosins is in agreement with that previously observed in other plant species, confirming that caleosins comprise small gene families in plants.
• A proteomic approach allowed us to verify only the presence of CavCLO‐H1 in hazelnut OB, suggesting that several members inside this family could have different roles during plant growth and development. In silico analysis also suggests that CavCLO‐H1 may act as a peroxygenase.

     

Rapid Migration of Inositol Phospholipids with Axonally Transported Substances in the Rabbit Optic Pathway

Following an intraocular injection of myo-[2-3H]inositol, the axonal transport of labelled water-soluble substances and inositol phospholipids was investigated. Evidence was obtained for a rapid axonal transport of a relatively small amount of labelled inositol phospholipids. In contrast to other axonally transported phospholipids, there was no significant accumulation of labelled, rapidly transported inositol phospholipids in the nerve terminal region at later time intervals following the isotope administration.     

Inactive DNMT3B Splice Variants Modulate De Novo DNA Methylation

Inactive DNA methyltransferase (DNMT) 3B splice isoforms are associated with changes in DNA methylation, yet the mechanisms by which they act remain largely unknown. Using biochemical and cell culture assays, we show here that the inactive DNMT3B3 and DNMT3B4 isoforms bind to and regulate the activity of catalytically competent DNMT3A or DNMT3B molecules. DNMT3B3 modestly stimulated the de novo methylation activity of DNMT3A and also counteracted the stimulatory effects of DNMT3L, therefore leading to subtle and contrasting effects on activity. DNMT3B4, by contrast, significantly inhibited de novo DNA methylation by active DNMT3 molecules, most likely due to its ability to reduce the DNA binding affinity of co-complexes, thereby sequestering them away from their substrate. Immunocytochemistry experiments revealed that in addition to their effects on the intrinsic catalytic function of active DNMT3 enzymes, DNMT3B3 and DNMT34 drive distinct types of chromatin compaction and patterns of histone 3 lysine 9 tri-methylation (H3K9me3) deposition. Our findings suggest that regulation of active DNMT3 members through the formation of co-complexes with inactive DNMT3 variants is a general mechanism by which DNMT3 variants function. This may account for some of the changes in DNA methylation patterns observed during development and disease.