Biochemical and structural characterization of hepatitis A virus 2C reveals an unusual ribonuclease activity on single-stranded RNA

The HAV nonstructural protein 2C is essential for virus replication; however, its precise function remains elusive. Although HAV 2C shares 24–27% sequence identity with other 2Cs, key motifs are conserved. Here, we demonstrate that HAV 2C is an ATPase but lacking helicase activity. We identified an ATPase-independent nuclease activity of HAV 2C with a preference for polyuridylic single-stranded RNAs. We determined the crystal structure of an HAV 2C fragment to 2.2 Å resolution, containing an ATPase domain, a region equivalent to enterovirus 2C zinc-finger (ZFER) and a C-terminal amphipathic helix (PBD). The PBD of HAV 2C occupies a hydrophobic pocket (Pocket) in the adjacent 2C, and we show the PBD–Pocket interaction is vital for 2C functions. We identified acidic residues that are essential for the ribonuclease activity and demonstrated mutations at these sites abrogate virus replication. We built a hexameric-ring model of HAV 2C, revealing the ribonuclease-essential residues clustering around the central pore of the ring, whereas the ATPase active sites line up at the gaps between adjacent 2Cs. Finally, we show the ribonuclease activity is shared by other picornavirus 2Cs. Our findings identified a previously unfound activity of picornavirus 2C, providing novel insights into the mechanisms of virus replication.     

Synthesis and physicochemical studies of amyloidogenic hexapeptides derived from human cystatin C

Human cystatin C (hCC) is a low molecular mass protein that belongs to the cystatin superfamily. It is an inhibitor of extracellular cysteine proteinases, present in all human body fluids. At physiological conditions, hCC is a monomer, but it has a tendency to dimerization. Naturally occurring hCC mutant, with leucine in position 68 substituted by glutamine (L68Q), is directly involved in the formation of amyloid deposits, independently of other proteins. This process is the primary cause of hereditary cerebral amyloid angiopathy, observed mainly in the Icelandic population. Oligomerization and fibrillization processes of hCC are not explained equally well, but it is proposed that domain swapping is involved in both of them. Research carried out on the fibrillization process led to new hypothesis about the existence of a steric zipper motif in amyloidogenic proteins. In the hCC sequence, there are 2 fragments which may play the role of a steric zipper: the loop L1 region and the C‐terminal fragment. In this work, we focused on the first of these. Nine hexapeptides covering studied hCC fragment were synthesized, and their fibrillogenic potential was assessed using an array of biophysical methods. The obtained results showed that the studied hCC fragment has strong profibrillogenic propensities because it contains 2 fragments fulfilling the requirements for an effective steric zipper located next to each other, forming 1 super‐steric zipper motif. This hCC fragment might therefore be responsible for the enhanced amyloidogenic properties of dimeric or partially unfolded hCC.     

Novel tool in rheumatoid arthritis diagnosis—The usage of urease flap region peptidomimetics

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease. Early diagnosis can prevent joint erosion. However, available biomarkers do not always allow for clear distinction between RA and non‐RA individuals. It has become known that bacteria/viruses are among the environmental triggers that initiate RA via multiple molecular mechanisms. Thus, to better understand the role of bacteria in RA, we synthetized 6 peptidomimetics of bacterial ureases' flap region. These peptides were then used to distinguish RA patients from healthy people sera by immunoblotting. Most patients' sera were bound to peptidomimetic characteristic for Enterobacter sp. and Klebsiella sp. flap urease. We also found similarities between peptidomimetic sequence and human proteins connected with RA. This pilot study suggests that bacteria may trigger RA via mechanism of molecular mimicry of urease to host proteins and ureases flap peptidomimetics may be potential candidate as a new additional diagnostic test.     

Impact of environmental diversity of hunting complexes in the Lublin region on ontogenetic quality indicators in roe deer (<Emphasis Type="Italic">Capreolus capreolus</Emphasis>)

Populations of game are not confined to single ecosystems but function within higher-order units, e.g. ecological landscape. The basis for the establishment of the hunting complexes was the assumption that the existing game hunting grounds, i.e. the basic units implementing game management, are too small and do not cover the natural areas inhabited by game populations. Roe deer are flexible species and easily adapt to various site conditions, so they inhabit many different habitats, from large forest complexes, through small in-field tree stands and shrubs, to treeless grounds and field monocultures. The aim of the study was to determine a possible impact of environmental conditions prevailing in the hunting complexes of the Regional Directorate of State Forests (RDLP in Lublin) on the ontogenetic quality of roe deer. The study was conducted on 518 European roe deer (Capreolus capreolus) aged from 4 to 7 years (379 bucks and 139 does) harvested within hunting seasons 2010/2011–2013/2014. The results have shown that animals originating from areas with greater forest cover and denser stands are characterised by lower values of the mean ontogenetic quality parameters (carcase weight, kidney fat index, chest girth, weight of antlers) in comparison with animals from typical agricultural areas with fragmented forest complexes. These results indicate that, even in the case of such a eurytopic species as the roe deer, the ontogenetic quality differs between individual hunting complexes. The study has proved that strategies for hunting management of the roe deer should take into account the impact of the landscape structure, which provides a rationale behind creation of hunting complexes.     

Comparative leaf micromorphology and anatomy of the dragon tree group of <Emphasis Type="Italic">Dracaena</Emphasis> (Asparagaceae) and their taxonomic implications

Micromorphological features of the leaf epidermis and the inner structure of leaf tissues of eight arborescent taxa of the genus Dracaena were analysed using light and scanning electron microscopy. The plants are xeromorphic or mesomorphic. Their leaves are isobilateral and amphistomatic, and the stomata are anomocytic and tetracytic. The mesophyll in all the species is divided into an outer chlorenchyma and a central region with colourless water-storage cells, chlorophyll cells and vascular bundles. Water-storage cells have wall bands and reticulate thickenings on the walls. The article describes and illustrates several new quantitative and qualitative leaf characters of the dragon tree group. Our findings can be used to identify the dragon tree group leaves, while the shape of epidermal cells and stomata types may be useful in the identification and classification of fragments of fossil leaves. We conclude that D. ombet and D. schizantha are not two distinct species, but should be treated as subspecies of D. ombet. Leaf characters, especially stomata depth on adaxial epidermis, height of adaxial epidermal cells and the presence and thickness of hypodermal fibre bundles markedly differ between geographical groups: Macaronesian species (D. draco and D. tamaranae), the species found in East Africa and Arabian Peninsula (D. ombet subsp. ombet, D. ombet subsp. schizantha, D. serrulata and D. cinnabari) and Southeast Asian species (D. kaweesakii and D. jayniana).     

Effect of methyl jasmonate on gummosis in petioles of culinary rhubarb (<Emphasis Type="Italic">Rheum rhabarbarum</Emphasis> L.) and the determination of sugar composition of the gum

This study aimed to know the key chemical compound influencing gummosis in petioles of intact growing culinary rhubarb (Rheum rhabarbarum L.) with special emphasis on its sugar composition. The application of methyl jasmonate (JA-Me, 0.5 and 1% in lanolin, w/w) in the middle of intact petiole of growing rhubarb substantially induced gummosis in the entire petioles, below and above the treatment, within several days. JA-Me at 0.5% in lanolin greatly stimulated ethylene production in intact petiole of growing rhubarb, on the 3rd day after JA-Me treatment, ethylene level being increased five times or more. However, an ethylene-releasing compound, ethephon (2-chloroethylphosphonic acid, 1 and 2% in lanolin, w/w) alone had no effect on gummosis. Analysis of gum polysaccharides by a gel permeation chromatography with a Tosho TSK-gel G5000PW gel permeation column revealed that almost all of rhubarb gum polysaccharides were eluted near the void in this gel chromatography system, suggesting that molecular mass of rhubarb gum polysaccharides are more than 500 kDa, while precise mass has not been decided in this study. Analysis of gum sugar composition after hydrolysis revealed that rhubarb gums is rich in galactose (ca. 30%), arabinose (ca. 20%), and galacturonic acid (15–20%), although other sugars also existed in small quantities. These results suggest that the key chemical compound of gummosis in petioles of rhubarb is jasmonates rather than ethylene, and gum polysaccharides consist of not only pectic arabinogalactans but also homogalacturonans.     

Novel Interaction Mechanism of a Domain Antibody-based Inhibitor of Human Vascular Endothelial Growth Factor with Greater Potency than Ranibizumab and Bevacizumab and Improved Capacity over Aflibercept

A potent VEGF inhibitor with novel antibody architecture and antigen binding mode has been developed. The molecule, hereafter referred to as VEGF dual dAb (domain antibody), was evaluated in vitro for binding to VEGF and for potency in VEGF-driven models and compared with other anti-VEGF biologics that have been used in ocular anti-angiogenic therapeutic regimes. VEGF dual dAb is more potent than bevacizumab and ranibizumab for VEGF binding, inhibition of VEGF receptor binding assays (RBAs), and VEGF-driven in vitro models of angiogenesis and displays comparable inhibition to aflibercept (Eylea). VEGF dual dAb is dimeric, and each monomer contains two distinct anti-VEGF domain antibodies attached via linkers to a human IgG1 Fc domain. Mechanistically, the enhanced in vitro potency of VEGF dual dAb, in comparison to other anti-VEGF biologics, can be explained by increased binding stoichiometry. A consistent model of the target engagement has been built based on the x-ray complexes of each of the two isolated domain antibodies with the VEGF antigen.     

Antrodia gossypium,Phlebiopsis gigantea and Heterobasidion parviporum: in vitro growth and Norway spruce wood block decay

Polymerase chain reaction-amplified and sequenced isolates of Antrodia gossypium, Phlebiopsis gigantea and Heterobasidion parviporum from decaying Norway spruce wood blocks after three and six months, which exhibited linear growth, were investigated. P. gigantea strains showed the fastest growth, whereas A. gossypium growth was five times slower. The differences between the mean daily increment of A. gossypium and the other examined isolates (except Hp2) were statistically significant. There were also significant differences in wood decay between densities over time. These results were confirmed by the decay acceleration index (DAI) and decay activity index, which were positively correlated with wood density regardless of the fungus species. The registered P. gigantea strains (Rotstop and PG Suspension) exhibited a strong decomposition ability (28% after six months); the weight loss caused by A. gossypium after six months of decay (15.2%) was similar to the results of P. gigantea (GB) after just three months (13.2%). All tested H. parviporum isolates showed rather rapid growth and equally strong wood decay (20–25%) compared to those of P. gigantea. DAI showed that A. gossypium may significantly contribute to wood decomposition over time, particularly in less dense wood samples. The use of both saprotrophs as biological agents against root pathogens is discussed.