Homology in Trivaline Complex Formation with dsDNA and ssRNA

Abstract

It has been shown by the equilibrium dialysis that at a polyU concentration above the “critical” one, the complete polymer saturation with trivaline reaches approximately 0.7 trivaline molecules per one phosphate group. i.e. at these conditions peptide dimer occupies on polyU a site of three bases (phosphates) in length. The trivaline complex with polyU at a concentration lower than the “critical” one does not reveal any noticeable fluorescence, but has rather significant positive linear dichroism at 265 and 330 nm. The trivaline-nucleic acids complex has a significant fluorescence at any dsDNA concentration while with polyU it is only so at a concentration above the “critical” one. Electron microscopy has shown that at a rather high concentration of dsDNA molecules in solution a “biduplex” structure undergoes an additional stage of compaction, during which the extended particles more than 30 nm in diameter are formed.

Schematic models for the trivaline complexes and compact structures with dsDNA and ssRNA are propose     

Developmentally Regulated Linker Histone H1c Promotes Heterochromatin Condensation and Mediates Structural Integrity of Rod Photoreceptors in Mouse Retina

Mature rod photoreceptor cells contain very small nuclei with tightly condensed heterochromatin. We observed that during mouse rod maturation, the nucleosomal repeat length increases from 190 bp at postnatal day 1 to 206 bp in the adult retina. At the same time, the total level of linker histone H1 increased reaching the ratio of 1.3 molecules of total H1 per nucleosome, mostly via a dramatic increase in H1c. Genetic elimination of the histone H1c gene is functionally compensated by other histone variants. However, retinas in H1c/H1e/H1⁰ triple knock-outs have photoreceptors with bigger nuclei, decreased heterochromatin area, and notable morphological changes suggesting that the process of chromatin condensation and rod cell structural integrity are partly impaired. In triple knock-outs, nuclear chromatin exposed several epigenetic histone modification marks masked in the wild type chromatin. Dramatic changes in exposure of a repressive chromatin mark, H3K9me2, indicate that during development linker histone plays a role in establishing the facultative heterochromatin territory and architecture in the nucleus. During retina development, the H1c gene and its promoter acquired epigenetic patterns typical of rod-specific genes. Our data suggest that histone H1c gene expression is developmentally up-regulated to promote facultative heterochromatin in mature rod photoreceptors.     

Identification of Novel Cholesterol-binding Regions in Kir2 Channels

Inwardly rectifying potassium (Kir) channels play an important role in setting the resting membrane potential and modulating membrane excitability. We have recently shown that cholesterol regulates representative members of the Kir family and that in the majority of the cases, cholesterol suppresses channel function. Furthermore, recent data indicate that cholesterol regulates Kir channels by specific sterol-protein interactions, yet the location of the cholesterol binding site in Kir channels is unknown. Using a combined computational-experimental approach, we show that cholesterol may bind to two nonanular hydrophobic regions in the transmembrane domain of Kir2.1 located between adjacent subunits of the channel. The location of the binding regions suggests that cholesterol modulates channel function by affecting the hinging motion at the center of the pore-lining transmembrane helix that underlies channel gating either directly or through the interface between the N and C termini of the channel.     

The mechanoelectrical response of the cytoplasmic membrane of Vibrio cholerae

Persistence of Vibrio cholerae in waters of fluctuating salinity relies on the capacity of this facultative enteric pathogen to adapt to varying osmotic conditions. In an event of osmotic downshift, osmolytes accumulated inside the bacterium can be quickly released through tension-activated channels. With the newly established procedure of giant spheroplast preparation from V. cholerae, we performed the first patch-clamp characterization of its cytoplasmic membrane and compared tension-activated currents with those in Esherichia coli. Saturating pressure ramps revealed two waves of activation belonging to the ∼1-nS mechanosensitive channel of small conductance (MscS)-like channels and ∼3-nS mechanosensitive channel of large conductance (MscL)-like channels, with a pressure midpoint ratio p_0.5MscS/p_0.5MscL of 0.48. We found that MscL-like channels in V. cholerae present at a density three times higher than in E. coli, and yet, these vibrios were less tolerant to large osmotic downshocks. The Vibrio MscS-like channels exhibit characteristic inward rectification and subconductive states at depolarizing voltages; they also adapt and inactivate at subsaturating tensions and recover within 2 s upon tension release, just like E. coli MscS. Trehalose, a compatible internal osmolyte accumulated under hypertonic conditions, significantly shifts activation curves of both MscL- and MscS-like channels toward higher tensions, yet does not freely partition into the channel pore. Direct electrophysiology of V. cholerae offers new avenues for the in situ analysis of membrane components critical for osmotic survival and electrogenic transport in this pathogen.     

Revised Systematics of Holospora-Like Bacteria and Characterization of “Candidatus Gortzia infectiva”, a Novel Macronuclear Symbiont of Paramecium jenningsi

The genus Holospora (Rickettsiales) includes highly infectious nuclear symbionts of the ciliate Paramecium with unique morphology and life cycle. To date, nine species have been described, but a molecular characterization is lacking for most of them. In this study, we have characterized a novel Holospora-like bacterium (HLB) living in the macronuclei of a Paramecium jenningsi population. This bacterium was morphologically and ultrastructurally investigated in detail, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and developed a specific probe for fluorescence in situ hybridization experiments. A new taxon, “Candidatus Gortzia infectiva”, was established for this HLB according to its unique characteristics and the relatively low DNA sequence similarities shared with other bacteria. The phylogeny of the order Rickettsiales based on 16S rRNA gene sequences has been inferred, adding to the available data the sequence of the novel bacterium and those of two Holospora species (Holospora obtusa and Holospora undulata) characterized for the purpose. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and showed a possible pattern of evolution for some of their features. We suggested to classify inside the family Holosporaceae only HLBs, excluding other more distantly related and phenotypically different Paramecium endosymbionts.     

New records of the chaetiferous leech-like annelid Paracanthobdella livanowi (Epshtein, 1966) (Annelida: Clitellata: Acanthobdellida) from Kamchatka, Russia

Acanthobdellidans are unique in their organisation and phylogenetic relationships due to having transitional characters that combine features of oligochaetous and achaetous annelids. Alongside the relatively well-studied Acanthobdella peledina Grube, 1851, there is another member of the group, Paracanthobdella livanowi (Epshtein, 1966), with five rows of chaetae and an anterior sucker. It appears that the anterior sucker is weakly developed in small juveniles but acquires a deep cavity in adults. Smaller individuals of P. livanowi can be distinguished from A. peledina, which does not possess an anterior sucker, by the varying breadth of their chaetae. The mid-body segment consists of two doubled annuli in juveniles and is quadri-annulate in large individuals. In Kamchatka freshwaters, hosts of P. livanowi mostly include Salvelinus spp. and more rarely Gasterosteus aculeatus, Oncorhynchus mykiss and O. kisutch. New information on the distribution and the biology of P. livanowi is presented.     

Membrane shape changes at initial stage of membrane fusion under the action of proteins inducing spontaneous curvature

This paper studies change of membrane shape at the initial stage of the fusion process due to the fusion proteins inducing spontaneous curvature in the membrane. As protein inclusions are embedded into the membrane, a highly curved surface forms in the center of the membrane; it facilitates the formation of short-lived hydrophobic defects and leads to the merger of the contact monolayers of the membranes. Membrane is considered as continuous liquid-crystal medium subject to elastic deformations. One deformational mode of splay is taken into account; energy is calculated in the quadratic approximation on this deformation. In case of positive spontaneous curvature induced by the protein there is no bulge on the top of the membrane despite high deviation of membrane shape from the equilibrium state. In case of negative spontaneous curvature a bulge is formed and its height and curvature increase with the increase of the membrane curvature in the initial state.     

Nanoscale Elastic Changes in 2D Ti3C2Tx (MXene) Pseudocapacitive Electrodes

Designing sustainable electrodes for next generation energy storage devices relies on the understanding of their fundamental properties at the nanoscale, including the comprehension of ions insertion into the electrode and their interactions with the active material. One consequence of ion storage is the change in the electrode volume resulting in mechanical strain and stress that can strongly affect the cycle life. Therefore, it is important to understand the changes of dimensions and mechanical properties occurring during electrochemical reactions. While the characterization of mechanical properties via macroscopic measurements is well documented, in situ characterization of their evolution has never been achieved at the nanoscale. It is reported here with in situ imaging, combined with density functional theory of the elastic changes of a 2D titanium carbide (Ti₃C₂T_x) based electrode in direction normal to the basal plane (electrode surface) during alkaline cation intercalation/extraction. 2D carbides, known as MXenes, are promising new materials for supercapacitors and various kinds of batteries, and understanding the coupling between their mechanical and electrochemical properties is therefore necessary. The results show a strong correlation between the cations content and the out‐of‐plane elastic modulus. This strategy enables identifying the preferential intercalation pathways within a single particle, which is important for understanding ionic transport in these materials.     

Tree diversity and species identity effects on soil fungi,protists and animals are context dependent

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.