Richness of ancient forest plant species indicates suitable habitats for macrofungi

Macrofungal species richness generally increases with forest continuity as does the richness of so-called ancient forest plant species (AFS). Based on this assumption, we examined the ability of AFS to indicate macrofungal diversity in six study areas covering a range of elevations and environments in the Czech Republic. In total, we used data from 106 sampling plots (2,500 m² each) distributed over six types of forest stands reflecting different intensities and temporal stages of forest management. Species composition of vascular plants and macrofungi was recorded by a single inventory and regular 2-year monitoring, respectively. In total, we found 71 AFS and 1,413 macrofungal species, of which 150 were red-listed macrofungal species. We documented that AFS show potential for being used in the prediction of macrofungi species richness, including endangered species, at the local scale (α-diversity). Additionally, we found significant differences in macrofungal species richness depending on study area and type of forest management, which did not, however, derogate the effect of AFS. Spatial congruence between species composition of AFS and macrofungi communities (β-diversity) increased with forest age and decreased with intensity of forest management. If we consider the simplicity of monitoring AFS in comparison to regular monitoring of macrofungi, we found a widely usable tool for estimating macrofungal diversity in all dominant types of managed forest in central Europe. However, we should be aware of the limited ability of AFS to capture macrofungal diversity across a broader spatial context (γ-diversity), especially in areas with a low diversity of AFS.     

Branched, tripartite-interfering RNAs silence multiple target genes with long guide strands

Structural modifications could provide classical small interfering RNA (siRNA) structure with several advantages, including reduced off-target effects and increased silencing activity. Thus, RNA interference (RNAi)-triggering molecules with diverse structural modifications have been investigated by introducing variations on duplex length and overhang structure. However, most of siRNA structural variants are based on the linear duplex structure. In this study, we introduce a branched, non-linear tripartite-interfering RNA (tiRNA) structure that could induce silencing of multiple target genes. Surprisingly, the gene silencing by tiRNA structure does not require Dicer-mediated processing into smaller RNA units, and the 38-nt-long guide strands can trigger specific gene silencing through the RNAi machinery in mammalian cells. tiRNA also shows improved gene silencing potency over the classical siRNA structure when complexed with cationic delivery vehicles due to the enhanced intracellular delivery. These results demonstrate that tiRNA is a novel RNA nanostructure for executing multi-target gene silencing with increased potency, which could be utilized as a structural platform to develop efficient anticancer or antiviral RNAi therapeutics.     

Ultrasonic cleavage of DNA in complexes with Ag(I), Cu(II), Hg(II)

We investigated a phenomenon of ultrasonic cleavage of DNA complexed with transition metal cations Ag(I), Cu(II) and Hg(II). We found the statistically significant dependence of relative intensity of cleavage on cation type and concentration. Each cation may cause two different types of distortion in the DNA double-helix depending on whether it binds to major or minor DNA groove. The intensity of ultrasonic cleavage decreases where the cation binds to the major DNA groove; the intensity of cleavage increases where the cation binds to the minor DNA groove and disturbs the hydrogen bonds of complementary base pairs or where it intercalates between bases. Both types of DNA distortion can affect the intensity of N?S intercon-version of deoxyribose.     

Characterization of protocatechuate 4,5-dioxygenase induced from p-hydroxybenzoate-cultured Pseudomonas sp. K82

Pseudomonas sp. K82 has been reported to be an aniline-assimilating soil bacterium. However, this strain can use not only aniline as a sole carbon and energy source, but can also utilize benzoate, p-hydroxybenzoate, and aniline analogues. The strain accomplishes this metabolic diversity by using different aerobic pathways. Pseudomonas sp. K82, when cultured in p-hydroxybenzoate, showed extradiol cleavage activity of protocatechuate. In accordance with those findings, our study attempted the purification of protocatechuate 4,5-dioxygenase (PCD 4,5). However the purified PCD 4,5 was found to be very unstable during purification. After Q-sepharose chromatography was performed, the crude enzyme activity was augmented by a factor of approximately 4.7. From the Q-sepharose fraction which exhibited PCD 4,5 activity, two subunits of PCD4,5 (alpha subunit and beta subunit) were identified using the N-terminal amino acid sequences of 15 amino acid residues. These subunits were found to have more than 90% sequence homology with PmdA and PmdB of Comamonas testosteroni. The molecular weight of the native enzyme was estimated to be approximately 54 kDa, suggesting that PCD4,5 exists as a heterodimer (alpha1beta1). PCD 4,5 exhibits stringent substrate specificity for protocatechuate and its optimal activity occurs at pH 9 and 15 degrees C. PCR amplification of these two subunits of PCD4,5 revealed that the alpha subunit and beta subunit occurred in tandem. Our results suggest that Pseudomonas sp. K82 induced PCD 4,5 for the purpose of p-hydroxybenzoate degradation.     

Biosynthesis of SOD by carrot hairy roots

Summary Superoxide dismutase(SOD) was produced by carrot hairy roots. After increasing in the early exponential growth phase, SOD biosynthesis decreased as the growth rate of hairy roots declined. High sucrose concentration stimulated the SOD biosynthesis, while inhibiting the growth of hairy roots. Potential inducers were tested for the enhanced production of SOD. The addition of 0.3 mM CuSO₄ to the broth showed about 6 fold increase in SOD biosynthesis compared to the results obtained with basic MS medium. Since CuSO₄ in the broth inhibited the growth of hairy roots, the addition of CuSO₄ to the broth at the late exponential growth phase led to a 12 times higher intracellular level of SOD compared to that in basic MS medium.     

Single‐molecule real‐time sequencing reveals diverse allelic variations in carotenoid biosynthetic genes in pepper (Capsicum spp.)

The diverse colours of mature pepper (Capsicum spp.) fruit result from the accumulation of different carotenoids. The carotenoid biosynthetic pathway has been well elucidated in Solanaceous plants, and analysis of candidate genes involved in this process has revealed variations in carotenoid biosynthetic genes in Capsicum spp. However, the allelic variations revealed by previous studies could not fully explain the variation in fruit colour in Capsicum spp. due to technical difficulties in detecting allelic variation in multiple candidate genes in numerous samples. In this study, we uncovered allelic variations in six carotenoid biosynthetic genes, including phytoene synthase (PSY1, PSY2), lycopene β‐cyclase, β‐carotene hydroxylase, zeaxanthin epoxidase and capsanthin‐capsorubin synthase (CCS) genes, in 94 pepper accessions by single‐molecule real‐time (SMRT) sequencing. To investigate the relationship between allelic variations in the candidate genes and differences in fruit colour, we performed ultra‐performance liquid chromatography analysis using 43 accessions representing each allelic variation. Different combinations of dysfunctional mutations in PSY1 and CCS could explain variation in the compositions and levels of carotenoids in the accessions examined in this study. Our results demonstrate that SMRT sequencing technology can be used to rapidly identify allelic variation in target genes in various germplasms. The newly identified allelic variants will be useful for pepper breeding and for further analysis of carotenoid biosynthesis pathways.     

Analysis of foreign epitope inserts in HBcAg. Approaches to solving the problem of core particle self-assembly

The hepatitis B virus core antigen (HBcAg) is a promising protein carrier for exposing the epitopes of various human and animal pathogens. HBcAg-based chimeric proteins can be used in creating highly efficient vaccines; however, not all chimeric HBcAg with foreign epitope inserts are capable of assembly into virus-like particles. Using computer programs ProAnalyst, SALIX, and QSARPro, we examined the relationship between the self-assembly capability of chimeric HBcAg and the physicochemical properties of the inserts. The self-assembly was found to be impaired when the inserted peptides contained highly hydrophobic and bulky residues tending to form β-structures; this especially concerned the C-proximal residues in the insert. Recommendations were elaborated for constructing foreign epitopes that would ensure correct self-assembly of chimeric HBcAg particles.     

Interferon-inducible ubiquitin E2, Ubc8, is a conjugating enzyme for protein ISGylation

Protein ISGylation is unique among ubiquitin-like conjugation systems in that the expression and conjugation processes are induced by specific stimuli, mainly via the alpha/beta interferon signaling pathway. It has been suggested that protein ISGylation plays a special role in the immune response, because of its interferon-signal dependency and its appearance only in higher eukaryotic organisms. Here, we report the identification of an ISG15-conjugating enzyme, Ubc8. Like other components of the protein ISGylation system (ISG15, UBE1L, and UBP43), Ubc8 is an interferon-inducible protein. Ubc8 clearly mediates protein ISGylation in transfection assays. The reduction of Ubc8 expression by small interfering RNA causes a decrease in protein ISGylation in HeLa cells upon interferon treatment. Neither UbcH7/UbcM4, the closest homologue of Ubc8 among known ubiquitin E2s, nor the small ubiquitin-like modifier E2 Ubc9 supports protein ISGylation. These findings strongly suggest that Ubc8 is a major ISG15-conjugating enzyme responsible for protein ISGylation upon interferon stimulation. Furthermore, we established an assay system to detect ISGylated target proteins by cotransfection of ISG15, UBE1L, and Ubc8 together with a target protein to be analyzed. This method provides an easy and effective way to identify new targets for the ISGylation system and will facilitate related studies.     

Survivin silencing and TRAIL expression using oncolytic adenovirus increase anti-tumorigenic activity in gemcitabine-resistant pancreatic cancer cells

In this study, we demonstrated that survivin downregulation with TRAIL expression greatly enhanced the cytotoxic death of pancreatic cancer cells after gemcitabine treatment. Using real-time RT-PCR, we analyzed five survivin shRNAs to identify the best target sequence for suppression of human survivin, with the goal of treating gemcitabine-resistant pancreatic cancer cells. Survivin shRNA 5, corresponding to target 5, showed the greatest reduction in survivin mRNA levels. Furthermore, combined treatment with survivin shRNA-expressing adenovirus with gemcitabine plus TRAIL decreased uncleaved PARP and increased consequent PARP cleavage, which was correlated with the greatest levels of survivin downregulation and cell death. These results indicate that survivin functions as a common mediator of gemcitabine- and TRAIL-induced cell death. Using a nude mouse model implanted with MiaPaCa-2 pancreatic cancer cells, we observed tumor regression induced by an oncolytic adenovirus expressing survivin shRNA and TRAIL plus gemcitabine. Together, our findings provide a strong rationale for treating pancreatic cancer patients with both gemcitabine and oncolytic adenovirus armed with survivin shRNA and TRAIL.