A Host YB-1 Ribonucleoprotein Complex Is Hijacked by Hepatitis C Virus for the Control of NS3-Dependent Particle Production

Hepatitis C virus (HCV) orchestrates the different stages of its life cycle in time and space through the sequential participation of HCV proteins and cellular machineries; hence, these represent tractable molecular host targets for HCV elimination by combination therapies. We recently identified multifunctional Y-box-binding protein 1 (YB-1 or YBX1) as an interacting partner of NS3/4A protein and HCV genomic RNA that negatively regulates the equilibrium between viral translation/replication and particle production. To identify novel host factors that regulate the production of infectious particles, we elucidated the YB-1 interactome in human hepatoma cells by a quantitative mass spectrometry approach. We identified 71 YB-1-associated proteins that included previously reported HCV regulators DDX3, heterogeneous nuclear RNP A1, and ILF2. Of the potential YB-1 interactors, 26 proteins significantly modulated HCV replication in a gene-silencing screening. Following extensive interaction and functional validation, we identified three YB-1 partners, C1QBP, LARP-1, and IGF2BP2, that redistribute to the surface of core-containing lipid droplets in HCV JFH-1-expressing cells, similarly to YB-1 and DDX6. Importantly, knockdown of these proteins stimulated the release and/or egress of HCV particles without affecting virus assembly, suggesting a functional YB-1 protein complex that negatively regulates virus production. Furthermore, a JFH-1 strain with the NS3 Q221L mutation, which promotes virus production, was less sensitive to this negative regulation, suggesting that this HCV-specific YB-1 protein complex modulates an NS3-dependent step in virus production. Overall, our data support a model in which HCV hijacks host cell machinery containing numerous RNA-binding proteins to control the equilibrium between viral RNA replication and NS3-dependent late steps in particle production.     

Effect of trophic conditions on aspartate transamination in wheat plants

The enzymatic transamination reactions between aspartic and α-ketoglutaric acid and between aspartic and pyruvic acid were studied in fresh dialysed extracts of young wheat plants cultivated under various trophical conditions, in mineral solution (Knop), in the solution of an soil organic substance (potassium humate) and without nutrients (H₂O). Simultaneously, the level of endogenic aspartic acid, glutamic acid and the growth values were determined. The enzymatic reactions were characterized by determining the optimum pH, the time course, and the effect of coenzyme and of inhibitors. The activity of the aspartate-glutamate transaminase from the root system of plants was considerably higher than the activity of the overground organs. The enzymatic activity from both parts of the plant was inversely proportional to the growth rate: intensive growth of the plants from the Knop variant was connected with their low enzymatic activity; the level of endogenic glutamic acid was high. The slow growth of the plants without nutrients was connected with a higher enzymatic activity; the level of endogenic glutamic acid was low. The plants from the potassium humate variant had an intermediate position between these two variants from the point of view of growth as well as from that of enzymatic activity. The plants with insufficient nutrition (slow growth, low level of endogenic glutamic acid) apparently have a low capacity for supplementing the glutamic acid deficit, which is essential for the metabolic processes, by increasing the activity of the reactions leading to glutamic acid synthesis (Asp-Glu) and, on the other hand, by decreasing the reactions utilizing it (Glu-Ala). For wheat plants the active aspartate-glutamate reaction is obviously physiologically more important than the direct reaction glutamate-aspartate and the reaction aspartate-alanine which in all cases had a very low activity.     

Influence of the soya meal fractions on gibberellic acid and gibberellin A production in submerse cultivation ofGibberella fujikuroi

The relationship of different soya meal components to gibberellin (GA) production was studied. Fluorometric assay confirmed that under the given fermentation conditions, only gibberellic acid (GA₃) was synthesized on medium containing corn steep. On substituting soya flour for corn steep, the same amount of GA₃ was produced and in addition gibberellin A (GA₁) was formed. The GA₃: GA₁ ratio was 1∶1. The course of fermentation in media containing the soya meal protein fraction (fraction I), the soya meal amino acid complex, the corn steep amino acid complex and individual amino acids (γ-aminobutyric acid or tryptophane) was the same as in the control medium containing soya meal. The soya meal fraction II, which is characterized by a high cellulose and carbohydrate content, raised GA production by 25% as compared with production in medium containling soya meal; it simultaneously stimulated GA₃ production, so that the final GA₃: GA₁ ratio was 4∶1.     

Partial auxin deprivation affects endogenous cytokinins in an auxin-dependent,cytokinin-independent tobacco cell strain

The dynamics of individual endogenous cytokinins within the growth cycle (subculture interval) of an auxin-dependent and cytokinin-independent cell suspension culture ofNicotiana tabacum L. (strain VBI-0) were determined using high performance liquid chromatography and radioimmunoassay. In cells grown at an optimum auxin concentration the transient maxima of N⁶-(²-isopentenyl)adenine and N⁶-(²-isopentenyl)-adenosine correlated with the onset of cell division. Cultivation of the cells in a partially auxin-deprived medium resulted in ca. tenfold increase of all endogenous cytokinins. A very distinct maximum of N⁶-(²-sopentenyl) adenine appeared at the beginning of subculture. This indicates that a lack of auxin induced an accumulation of cytokinins predominantly in the form of the free bases, which are physiologically more active than the corresponding ribosides.Abbreviations iP N⁶-(²-isopentenyl)adenine - [9R]iP N⁶-(²-isopentenyl)adenosine - t-Z trans-zeatin - t-[9R]Z trans-zeatin riboside - IAA indole-3-acetic acid - NAA 1-naphthaleneacetic acid - 2,4-D 2,4-dichlorophenoxyacetic acid - f.w. fresh weight - SBI subculture interval - C complete medium - PAD partially auxin-deprived medium - RP-HPLC reverse phase high performance liquid chromatography - RIA radioimmunoassay - PAL L-phenylalanine ammonia lyase     

Transfer of the broad-host-range IncQ plasmid RSF1010 and other plasmid vectors to the Gram-positive methylotroph Brevibacterium methylicum by electrotransformation

Gram-positive facultative methylotrophic coryneform bacterium Brevibacterium methylicum was efficiently transformed with various plasmids using electroporation of intact cells. In addition to the plasmid vectors pEC71 and pZ6-1 constructed on the basis of cryptic plasmids from coryneform bacteria, broad-host-range plasmids pLS5 (derivative of plasmid pMV158 from Streptococcus agalactiae) and RSF1010 belonging to the incompatibility group IncQ from Gram-negative bacteria were found to be present as autonomous structurally unchanged DNA molecules in B. methylicum transformants. With the exception of pZ6-1, all these plasmids were stably maintained in B. methylicum cells grown under non-selective conditions. When plasmid DNAs isolated from B. methylicum were used, the highest efficiency of transformation (10⁵ transformants/g DNA) was achieved. Correspondence to: J. Nevera     

The effect of cytokinins on nitrate reductase activity

Cytokinins in addition to nitrate induce nitrate reductase activity (NRA) in some plants. Effects of cytokinins onNRA was investigated in stem pith parenchyma of kale, intact wheat and barley seedlings and isolated cucumber cotyledons. The most profound effect onNRA was found in barley and wheat seedlings.NRA in seedlings sprayed with 100 μM 6-benzylaminopurine (BAP) for three subsequent days was increased in leaves and decreased in roots. These changes were further enhanced in seedlings grown in nutrient solution lacking nitrate:NRA in wheat and barley leaves was increased by 57% and 202%, respectively, in plants supplied with nitrate theNRA increase was not significant: in wheat and barley leaves by 22% and 9%, respectively. Similar effect of BAP and kinetin was found in kale stem parenchyma and cucumber cotyledons. The cytokinin kinetin or BAP alone increasedNRA about twice in kale and three times in cucumber. Addition of nitrate to the medium enhanced the effect of kinetin in kale discs, but the two effects were not additive. Additive effect of nitrate and BAP onNRA was found in cucumber cotyledons in light. In general NRA was more affected by cytokinins in intact seedlings of wheat and barley as compared to explanted tissue of kale and cucumber, and lack of nitrogen made their effect more expressive.     

Uniparental Genetic Heritage of Belarusians: Encounter of Rare Middle Eastern Matrilineages with a Central European Mitochondrial DNA Pool

Ethnic Belarusians make up more than 80% of the nine and half million people inhabiting the Republic of Belarus. Belarusians together with Ukrainians and Russians represent the East Slavic linguistic group, largest both in numbers and territory, inhabiting East Europe alongside Baltic-, Finno-Permic- and Turkic-speaking people. Till date, only a limited number of low resolution genetic studies have been performed on this population. Therefore, with the phylogeographic analysis of 565 Y-chromosomes and 267 mitochondrial DNAs from six well covered geographic sub-regions of Belarus we strove to complement the existing genetic profile of eastern Europeans. Our results reveal that around 80% of the paternal Belarusian gene pool is composed of R1a, I2a and N1c Y-chromosome haplogroups – a profile which is very similar to the two other eastern European populations – Ukrainians and Russians. The maternal Belarusian gene pool encompasses a full range of West Eurasian haplogroups and agrees well with the genetic structure of central-east European populations. Our data attest that latitudinal gradients characterize the variation of the uniparentally transmitted gene pools of modern Belarusians. In particular, the Y-chromosome reflects movements of people in central-east Europe, starting probably as early as the beginning of the Holocene. Furthermore, the matrilineal legacy of Belarusians retains two rare mitochondrial DNA haplogroups, N1a3 and N3, whose phylogeographies were explored in detail after de novo sequencing of 20 and 13 complete mitogenomes, respectively, from all over Eurasia. Our phylogeographic analyses reveal that two mitochondrial DNA lineages, N3 and N1a3, both of Middle Eastern origin, might mark distinct events of matrilineal gene flow to Europe: during the mid-Holocene period and around the Pleistocene-Holocene transition, respectively.     

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem

Background  

The protein folding problem is a fundamental problems in computational molecular biology and biochemical physics. Various optimisation methods have been applied to formulations of the ab-initio folding problem that are based on reduced models of protein structure, including Monte Carlo methods, Evolutionary Algorithms, Tabu Search and hybrid approaches. In our work, we have introduced an ant colony optimisation (ACO) algorithm to address the non-deterministic polynomial-time hard (NP-hard) combinatorial problem of predicting a protein's conformation from its amino acid sequence under a widely studied, conceptually simple model – the 2-dimensional (2D) and 3-dimensional (3D) hydrophobic-polar (HP) model.     

Entrainment of Spontaneously Hypertensive Rat Fibroblasts by Temperature Cycles

The functional state of the circadian system of spontaneously hypertensive rats (SHR) differs in several characteristics from the functional state of normotensive Wistar rats. Some of these changes might be due to the compromised ability of the central pacemaker to entrain the peripheral clocks. Daily body temperature cycles represent one of the important cues responsible for the integrity of the circadian system, because these cycles are driven by the central pacemaker and are able to entrain the peripheral clocks. This study tested the hypothesis that the aberrant peripheral clock entrainment of SHR results from a compromised peripheral clock sensitivity to the daily temperature cycle resetting. Using cultured Wistar rat and SHR fibroblasts transfected with the circadian luminescence reporter Bmal1-dLuc, we demonstrated that two consecutive square-wave temperature cycles with amplitudes of 2.5°C are necessary and sufficient to restart the dampened oscillations and entrain the circadian clocks in both Wistar rat and SHR fibroblasts. We also generated a phase response curve to temperature cycles for fibroblasts of both rat strains. Although some of the data suggested a slight resistance of SHR fibroblasts to temperature entrainment, we concluded that the overall effect it too weak to be responsible for the differences between the SHR and Wistar in vivo circadian phenotype.