BIOMASS AS A SOURCE OF RENEWABLE ENERGY IN POLAND

Розглянуто особливості використання біомаси для збільшення обсягів виробництва відновлюваної енергії в Польщі, що є однією з основних передумов виконання вимог кліматичного пакету Європейського Союзу (до 2020 р.). Серед різноманітних видів біомаси найбільшу питому вагу у виробництві відновлюваної енергії має сектор твердого біопалива з рослинної чи тваринної сировини, з продуктів життєдіяльності організмів чи промислових відходів органічного походження, де у 2013 р. вироблено 46,4 % електроенергії та 97 % теплової енергії від загального обсягу виробництва "зеленої" енергії. Оцінено можливості збільшення обсягів виробництва енергії з біомаси у сучасній польській економіці.Рассмотрены особенности использования биомассы для увеличения выработки возобновляемой энергии в Польше, что является одним из главных условий выполнения требований климатического пакета Европейского Союза (до 2020 г.). Среди разнообразных видов биомассы наибольший удельный вес в производстве возобновляемой энергии имеет сектор твердого биотoплива из растительного или животного сырья, из продуктов жизнедеятельности организмов или органических промышленных отходов, в котором в 2013 г. произведено 46,4 % электроэнергии и 97 % тепловой энергии из общего объема производства "зеленой" энергии. Оценены возможности увеличения выработки энергии из биомассы в современной польской экономике.Preconditions for using biomass in order to increase Poland's energy production out of renewable sources as it is required by the European Union's climate package (by 2020) are considered. Among various types of biomass, the highest share in renewable energy production is kept by the sector of biofuel production out of products of either plant or animal origin, and organic industrial residues, where 46,4 % of electrical energy and 97 % of thermic energy in the total amount of "green" energy production is supplied as of 2013. Potential directions of an increase in the energy production out of biomass in the contemporary Poland's economy are discussed

Global RNA Structure Analysis of Poliovirus Identifies a Conserved RNA Structure Involved in Viral Replication and Infectivity

The genomes of RNA viruses often contain RNA structures that are crucial for translation and RNA replication and may play additional, uncharacterized roles during the viral replication cycle. For the picornavirus family member poliovirus, a number of functional RNA structures have been identified, but much of its genome, especially the open reading frame, has remained uncharacterized. We have now generated a global RNA structure map of the poliovirus genome using a chemical probing approach that interrogates RNA structure with single-nucleotide resolution. In combination with orthogonal evolutionary analyses, we uncover several conserved RNA structures in the open reading frame of the viral genome. To validate the ability of our global analyses to identify functionally important RNA structures, we further characterized one of the newly identified structures, located in the region encoding the RNA-dependent RNA polymerase, 3D(pol), by site-directed mutagenesis. Our results reveal that the structure is required for viral replication and infectivity, since synonymous mutants are defective in these processes. Furthermore, these defects can be partially suppressed by mutations in the viral protein 3C(pro), which suggests the existence of a novel functional interaction between an RNA structure in the 3D(pol)-coding region and the viral protein(s) 3C(pro) and/or its precursor 3CD(pro)

New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing.

Double stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3' non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3' NCR were identified in a single Prunus source, with 3' NCRs of 214-312 nt, a size similar to that observed in other foveaviruses, but 567-850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated

Characterization of new isolates of apricot vein clearing-associated virus and of a new prunus-infecting virus: Evidence for recombination as a driving force in Betaflexiviridae evolution

Double stranded RNAs from Prunus samples gathered from various surveys were analyzed by a deep-sequencing approach. Contig annotations revealed the presence of a potential new viral species in an Azerbaijani almond tree (Prunus amygdalus) and its genome sequence was completed. Its genomic organization is similar to that of the recently described Apricot vein clearing associated virus (AVCaV) for which two new isolates were also characterized, in a similar fashion, from two Japanese plums (Prunus salicina) from a French germplasm collection. The amino acid identity values between the four proteins encoded by the genome of the new virus have identity levels with those of AVCaV which fall clearly outside the species demarcation criteria. The new virus should therefore be considered as a new species for which the name of Caucasus prunus virus (CPrV) has been proposed. Phylogenetic relationships and nucleotide comparisons suggested that together with AVCaV, CPrV could define a new genus ( proposed name: Prunevirus) in the family Betaflexiviridae. A molecular test targeting both members of the new genus was developed, allowing the detection of additional AVCaV isolates, and therefore extending the known geographical distribution and the host range of AVCaV. Moreover, the phylogenetic trees reconstructed with the amino acid sequences of replicase, movement and coat proteins of representative Betaflexiviridae members suggest that Citrus leaf blotch virus (CLBV, type member of the genus Citrivirus) may have evolved from a recombination event involving a Prunevirus, further highlighting the importance of recombination as a driving force in Betaflexiviridae evolution. The sequences reported in the present manuscript have been deposited in the GenBank database under accession numbers KM507061-KM504070

Molecular Dynamics Simulations Identify Time Scale of Conformational Changes Responsible for Conformational Selection in Molecular Recognition of HIV-1 Transactivation Responsive RNA

The HIV-1 Tat protein and several small molecules bind to HIV-1 transactivation responsive RNA (TAR) by selecting sparsely populated but pre-existing conformations. Thus, a complete characterization of TAR conformational ensemble and dynamics is crucial to understand this paradigmatic system and could facilitate the discovery of new antivirals targeting this essential regulatory element. We show here that molecular dynamics simulations can be effectively used toward this goal by bridging the gap between functionally relevant time scales that are inaccessible to current experimental techniques. Specifically, we have performed several independent microsecond long molecular simulations of TAR based on one of the most advanced force fields available for RNA, the parmbsc0 AMBER. Our simulations are first validated against available experimental data, yielding an excellent agreement with measured residual dipolar couplings and order parameter S2. This contrast with previous molecular dynamics simulations (Salmon et al., J. Am. Chem. Soc. 2013 135, 5457-5466) based on the CHARMM36 force field, which could achieve only modest accord with the experimental RDC values. Next, we direct the computation toward characterizing the internal dynamics of TAR over the microsecond time scale. We show that the conformational fluctuations observed over this previously elusive time scale have a strong functionally oriented character in that they are primed to sustain and assist ligand binding