Linear Theory of Electron-Plasma Waves at Arbitrary Collisionality

The dynamics of electron-plasma waves are described at arbitrary collisionality by considering the full Coulomb collision operator. The description is based on a Hermite-Laguerre decomposition of the velocity dependence of the electron distribution function. The damping rate, frequency, and eigenmode spectrum of electron-plasma waves are found as functions of the collision frequency and wavelength. A comparison is made between the collisionless Landau damping limit, the Lenard-Bernstein and Dougherty collision operators, and the electron-ion collision operator, finding large deviations in the damping rates and eigenmode spectra. A purely damped entropy mode, characteristic of a plasma where pitch-angle scattering effects are dominant with respect to collisionless effects, is shown to emerge numerically, and its dispersion relation is analytically derived. It is shown that such a mode is absent when simplified collision operators are used, and that like-particle collisions strongly influence the damping rate of the entropy mode.Comment: 23 pages, 10 figures, accepted for publication on Journal of Plasma Physic

Formation of a Unique Cluster of G-Quadruplex Structures in the HIV-1 nef Coding Region: Implications for Antiviral Activity

G-quadruplexes are tetraplex structures of nucleic acids that can form in G-rich sequences. Their presence and functional role have been established in telomeres, oncogene promoters and coding regions of the human chromosome. In particular, they have been proposed to be directly involved in gene regulation at the level of transcription. Because the HIV-1 Nef protein is a fundamental factor for efficient viral replication, infectivity and pathogenesis in vitro and in vivo, we investigated G-quadruplex formation in the HIV-1 nef gene to assess the potential for viral inhibition through G-quadruplex stabilization. A comprehensive computational analysis of the nef coding region of available strains showed the presence of three conserved sequences that were uniquely clustered. Biophysical testing proved that G-quadruplex conformations were efficiently stabilized or induced by G-quadruplex ligands in all three sequences. Upon incubation with a G-quadruplex ligand, Nef expression was reduced in a reporter gene assay and Nef-dependent enhancement of HIV-1 infectivity was significantly repressed in an antiviral assay. These data constitute the first evidence of the possibility to regulate HIV-1 gene expression and infectivity through G-quadruplex targeting and therefore open a new avenue for viral treatment. © 2013 Perrone et al

Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions

Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), one of the top 10 causes of death worldwide in 2015. The recent emergence of strains resistant to all current drugs urges the development of compounds with new mechanisms of action. G-quadruplexes are nucleic acids secondary structures that may form in G-rich regions to epigenetically regulate cellular functions. Here we implemented a computational tool to scan the presence of putative G-quadruplex forming sequences in the genome of Mycobacterium tuberculosis and analyse their association to transcription start sites. We found that the most stable G-quadruplexes were in the promoter region of genes belonging to definite functional categories. Actual G-quadruplex folding of four selected sequences was assessed by biophysical and biomolecular techniques: all molecules formed stable G-quadruplexes, which were further stabilized by two G-quadruplex ligands. These compounds inhibited Mycobacterium tuberculosis growth with minimal inhibitory concentrations in the low micromolar range. These data support formation of Mycobacterium tuberculosis G-quadruplexes in vivo and their potential regulation of gene transcription, and prompt the use of G4 ligands to develop original antitubercular agents

Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses

G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5'-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NF\u3baB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5'-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place

Stability of casein micelles cross-linked with genipin: a physicochemical study as a function of pH

Chemical or enzymatic cross-linking of casein micelles (CMs) increases their stability against dissociating agents. In this paper, a comparative study of stability between native CMs and CMs cross-linked with genipin (CMs-GP) as a function of pH is described. Stability to temperature and ethanol were investigated in the pH range 2.0-7.0. The size and the charge ($\zeta$-potential) of the particles were determined by dynamic light scattering. Native CMs precipitated below pH 5.5, CMs-GP precipitated from pH 3.5 to 4.5, whereas no precipitation was observed at pH 2.0-3.0 or pH 4.5-7.0. The isoelectric point of CMs-GP was determined to be pH 3.7. Highest stability against heat and ethanol was observed for CMs-GP at pH 2, where visible coagulation was determined only after 800 s at 140 $^\circ$C or 87.5% (v/v) of ethanol. These results confirmed the hypothesis that cross-linking by GP increased the stability of CMs.Comment: 5 pages, 2 figures, International Dairy Journal, 201

Sparse Coding Predicts Optic Flow Specificities of Zebrafish Pretectal Neurons

Zebrafish pretectal neurons exhibit specificities for large-field optic flow patterns associated with rotatory or translatory body motion. We investigate the hypothesis that these specificities reflect the input statistics of natural optic flow. Realistic motion sequences were generated using computer graphics simulating self-motion in an underwater scene. Local retinal motion was estimated with a motion detector and encoded in four populations of directionally tuned retinal ganglion cells, represented as two signed input variables. This activity was then used as input into one of two learning networks: a sparse coding network (competitive learning) and backpropagation network (supervised learning). Both simulations develop specificities for optic flow which are comparable to those found in a neurophysiological study (Kubo et al. 2014), and relative frequencies of the various neuronal responses are best modeled by the sparse coding approach. We conclude that the optic flow neurons in the zebrafish pretectum do reflect the optic flow statistics. The predicted vectorial receptive fields show typical optic flow fields but also "Gabor" and dipole-shaped patterns that likely reflect difference fields needed for reconstruction by linear superposition.Comment: Published Conference Paper from ICANN 2018, Rhode

Action Recognition with a Bio--Inspired Feedforward Motion Processing Model: The Richness of Center-Surround Interactions

International audienceHere we show that reproducing the functional properties of MT cells with various center--surround interactions enriches motion representation and improves the action recognition performance. To do so, we propose a simplified bio--inspired model of the motion pathway in primates: It is a feedforward model restricted to V1-MT cortical layers, cortical cells cover the visual space with a foveated structure, and more importantly, we reproduce some of the richness of center-surround interactions of MT cells. Interestingly, as observed in neurophysiology, our MT cells not only behave like simple velocity detectors, but also respond to several kinds of motion contrasts. Results show that this diversity of motion representation at the MT level is a major advantage for an action recognition task. Defining motion maps as our feature vectors, we used a standard classification method on the Weizmann database: We obtained an average recognition rate of 98.9%, which is superior to the recent results by Jhuang et al. (2007). These promising results encourage us to further develop bio--inspired models incorporating other brain mechanisms and cortical layers in order to deal with more complex videos

Undamped electrostatic plasma waves

Electrostatic waves in a collision-free unmagnetized plasma of electrons with fixed ions are investigated for electron equilibrium velocity distribution functions that deviate slightly from Maxwellian. Of interest are undamped waves that are the small amplitude limit of nonlinear excitations, such as electron acoustic waves (EAWs). A deviation consisting of a small plateau, a region with zero velocity derivative over a width that is a very small fraction of the electron thermal speed, is shown to give rise to new undamped modes, which here are named {\it corner modes}. The presence of the plateau turns off Landau damping and allows oscillations with phase speeds within the plateau. These undamped waves are obtained in a wide region of the $(k,\omega_{_R})$ plane ($\omega_{_R}$ being the real part of the wave frequency and $k$ the wavenumber), away from the well-known `thumb curve' for Langmuir waves and EAWs based on the Maxwellian. Results of nonlinear Vlasov-Poisson simulations that corroborate the existence of these modes are described. It is also shown that deviations caused by fattening the tail of the distribution shift roots off of the thumb curve toward lower $k$-values and chopping the tail shifts them toward higher $k$-values. In addition, a rule of thumb is obtained for assessing how the existence of a plateau shifts roots off of the thumb curve. Suggestions are made for interpreting experimental observations of electrostatic waves, such as recent ones in nonneutral plasmas.Comment: 11 pages, 10 figure