Social interactions dominate speed control in poising natural flocks near criticality.

Flocks of birds exhibit a remarkable degree of coordination and collective response. It is not just that thousands of individuals fly, on average, in the same direction and at the same speed, but that even the fluctuations around the mean velocity are correlated over long distances. Quantitative measurements on flocks of starlings, in particular, show that these fluctuations are scale-free, with effective correlation lengths proportional to the linear size of the flock.

Time-lapse microscopy and fluorescence resonance energy transfer to analyze the dynamics and interactions of nucleolar proteins in living cells.

The dynamics of proteins play a key role in the organization and control of nuclear functions. Techniques were developed recently to observe the movement and interactions of proteins in living cells; time-lapse microscopy using fluorescent-tagged proteins gives access to observations of nuclear protein trafficking over time, and fluorescence resonance energy transfer (FRET) is used to investigate protein interactions in the time-lapse mode. In this chapter, we describe the application of these two approaches to follow the recruitment of nucleolar processing proteins at the time of nucleolar assembly.

Adsorption of phenylacetylene on Si(100)-2 x 1: kinetics and structure of the adlayer.

Direct adsorption of phenylacetylene on clean silicon surface Si(100)-2 x 1 is studied in ultrahigh vacuum (UHV). The combination of scanning tunnel microscopy (STM) and surface differential reflectance spectroscopy (SDRS) with Monte Carlo calculations are put together to draw a realistic kinetic model of the evolution of the surface coverage as a function of the molecular exposure. STM images of weakly covered surfaces provide evidence of two very distinct adsorption geometries for phenylacetylene, with slightly different initial sticking probabilities.

Heterologous expression of a plant uracil transporter in yeast: improvement of plasma membrane targeting in mutants of the Rsp5p ubiquitin protein ligase.

Plasma membrane proteins involved in transport processes play a crucial role in cell physiology. On account of these properties, these molecules are ideal targets for development of new therapeutic and agronomic agents. However, these proteins are of low abundance, which limits their study.

Chromatin remodeling: RSC Motors along the DNA.

Single-molecule experiments show that the chromatin-remodeling complex RSC, a member of the SNF2 ATPase family, induces formation of a negatively supercoiled DNA loop by active translocation.

Compartmentation of the nucleolar processing proteins in the granular component is a CK2-driven process.

To analyze the compartmentation of nucleolar protein complexes, the mechanisms controlling targeting of nucleolar processing proteins onto rRNA transcription sites has been investigated. We studied the reversible disconnection of transcripts and processing proteins using digitonin-permeabilized cells in assays capable of promoting nucleolar reorganization. The assays show that the dynamics of nucleolar reformation is ATP/GTP-dependent, sensitive to temperature, and CK2-driven.

Structure, surface interactions, and compressibility of bacterial S-layers through scanning force microscopy and the surface force apparatus.

Two-dimensional crystalline bacterial surface layers (S-layers) are found in a broad range of bacteria and archaea as the outermost cell envelope component. The self-assembling properties of the S-layers permit them to recrystallize on solid substrates. Beyond their biological interest as S-layers, they are currently used in nanotechnology to build supramolecular structures.

Probing the Si-Si dimer breaking of Si(100)2x1 surfaces upon molecule adsorption by optical spectroscopy.

The adsorption of atoms and molecules of several gases of the Si(100)2x1 silicon reconstructed surface is investigated by surface differential reflectance spectroscopy. This UV-visible optical spectroscopy makes possible the discrimination between two adsorption modes, depending on whether or not the adsorption leads to breaking the Si-Si dimers. The observation of two different optical features is assigned to the bonding on dangling bonds or to the breaking of dimers, and gives access to the adsorption mode of hydrogen, water, oxygen, and pyridine.

Tracking the interactions of rRNA processing proteins during nucleolar assembly in living cells.

Reorganization of the nuclear machinery after mitosis is a fundamental but poorly understood process. Here, we investigate the recruitment of the nucleolar processing proteins in the nucleolus of living cells at the time of nucleus formation. We question the role of the prenucleolar bodies (PNBs), during migration of the processing proteins from the chromosome periphery to sites of rDNA transcription.

Dynamics and compartmentation of the nucleolar processing machinery.

In active nucleoli, machineries involved in the biogenesis of ribosomal RNAs (rRNAs) are compartmentalized. The late rRNA processing proteins are localized in the granular component (GC). Here we investigate the behavior of these proteins when production of 28S is impaired and when this blockage is reversed.

Nucleolus in the spotlight.

The recent contributions on chromatid segregation at the metaphase/anaphase transition demonstrate two distinct pathways in budding yeast. While segregation of most of the genome is a direct consequence of cohesin cleavage by separase, rDNA segregation requires a novel pathway involving Cdc14 phosphatase activation. This activation induces targeting of condensin to rDNA which in association with Aurora B kinase modulates rDNA compaction during anaphase.

Ubiquitin and endocytic internalization in yeast and animal cells.

Endocytosis is involved in a wide variety of cellular processes, and the internalization step of endocytosis has been extensively studied in both lower and higher eukaryotic cells. Studies in mammalian cells have described several endocytic pathways, with the main emphasis on clathrin-dependent endocytosis. Genetic studies in yeast have underlined the critical role of actin and actin-binding proteins, lipid modification, and the ubiquitin conjugation system.

Raft partitioning of the yeast uracil permease during trafficking along the endocytic pathway.

Lipid rafts, formed by the lateral association of sphingolipids and cholesterol in the external membrane leaflet, have been implicated in membrane traffic and cell signaling in mammalian cells. Yeast plasma membranes were also recently shown to contain lipid raft microdomains consisting of sphingolipids and ergosterol, and containing several plasma membrane proteins, including Gas1p, a GPI-anchored protein, and the [H+] ATPase Pma1p. In this study, we investigated whether lipid rafts were involved in the intracellular trafficking of a yeast transporter, uracil permease, which undergoes ubiquitin-dependent endocytosis.

Mutants defective in secretory/vacuolar pathways in the EUROFAN collection of yeast disruptants.

We have screened the EUROFAN (European Functional Analysis Network) deletion strain collection for yeast mutants defective in secretory/vacuolar pathways and/or associated biochemical modifications. We used systematic Western immunoblotting to analyse the electrophoretic pattern of several markers of the secretory/vacuolar pathways, the soluble alpha-factor, the periplasmic glycoprotein invertase, the plasma membrane GPI-anchored protein Gas1p, and two vacuolar proteins, the soluble carboxypeptidase Y and the membrane-bound alkaline phosphatase, which are targeted to the vacuole by different pathways. We also used colony immunoblotting to monitor the secretion of carboxypeptidase Y into the medium, to identify disruptants impaired in vacuolar targeting.

Membrane transport: ubiquitylation in endosomal sorting.

In yeast, membrane proteins from the biosynthetic and endocytic pathways must be ubiquitylated for sorting to inward-budding vesicles in late endosomes, which give rise to multivesicular bodies. A conserved protein complex containing the yeast Vps23p or its mammalian counterpart Tsg101 may act as the ubiquitin receptor.

6-Substituted 2-oxo-2H-1-benzopyran-3-carboxylic acid as a core structure for specific inhibitors of human leukocyte elastase.

Pyridyl esters of 6-substituted 2-oxo-2H-1-benzopyran-3-carboxylic acid were designed as mechanism-based inhibitors of human leukocyte elastase. Compounds of series 4 specifically inhibited this enzyme. Several of the tested compounds (series 2 and 3) acted as powerful time-dependent inhibitors of both human leukocyte elastase and alpha-chymotrypsin; some compounds of these series inhibited thrombin.