Michał Burmistrz

Distribution of polycyclic aromatic hydrocarbons in coke plant wastewater

The subject of examinations presented in this paper is the distribution of polycyclic aromatic hydrocarbons (PAHs) between solid and liquid phases in samples of raw wastewater and wastewater after treatment. The content of 16 PAHs according to the US EPA was determined in the samples of coke plant wastewater from the Zdzieszowice Coke Plant, Poland. The samples contained raw wastewater, wastewater after physico-chemical treatment as well as after biological treatment. The ΣPHA16 content varied between 255.050 μg L(-1) and 311.907 μg L(-1) in raw wastewater and between 0.940 and 4.465 μg L(-1) in wastewater after full treatment. Investigation of the distribution of PAHs showed that 71-84% of these compounds is adsorbed on the surface of suspended solids and 16-29% is dissolved in water. Distribution of individual PAHs and ΣPHA16 between solid phase and liquid phase was described with the use of statistically significant, linear equations. The calculated values of the partitioning coefficient Kp changed from 0.99 to 7.90 for naphthalene in samples containing mineral-organic suspension and acenaphthylene in samples with biological activated sludge, respectively.

Coke dust enhances coke plant wastewater treatment.

Coke plant wastewater contain many toxic pollutants. Despite physico-chemical and biological treatment this specific type of wastewater has a significant impact on environment and human health. This article presents results of research on industrial adsorptive coke plant wastewater treatment. As a sorbent the coke dust, dozen times less expensive than pulverized activated carbon, was used. Treatment was conducted in three scenarios: adsorptive after full treatment with coke dust at 15 g L(-1), biological treatment enhanced with coke dust at 0.3-0.5 g L(-1) and addition of coke dust at 0.3 g L(-1) prior to the biological treatment. The enhanced biological treatment proved the most effective. It allowed additional removal of 147-178 mg COD kg(-1) of coke dust.

Substrate profiling of Zika virus NS2B-NS3 protease.

Zika virus (ZIKV), isolated from macaques in Uganda in 1947, was not considered to be a dangerous human pathogen. However, this view has recently changed as ZIKV infections are now associated with serious pathological disorders including microcephaly and Guillain–Barré syndrome. Similar to other viruses in the Flaviviridae family, ZIKV expresses the serine protease NS3 which is responsible for viral protein processing and replication. Herein, we report the expression of an active NS3pro domain fused with the NS2B cofactor (NS2BLNNS3pro) in a prokaryotic expression system and profile its specificity for synthesized FRET‐type substrate libraries. Our findings pave way for screening potential intracellular substrates of NS3 and for developing specific inhibitors of this ZIKV protease.

The nucleocapsid protein of human coronavirus NL63.

Human coronavirus (HCoV) NL63 was first described in 2004 and is associated with respiratory tract disease of varying severity. At the genetic and structural level, HCoV-NL63 is similar to other members of the Coronavirinae subfamily, especially human coronavirus 229E (HCoV-229E). Detailed analysis, however, reveals several unique features of the pathogen. The coronaviral nucleocapsid protein is abundantly present in infected cells. It is a multi-domain, multi-functional protein important for viral replication and a number of cellular processes. The aim of the present study was to characterize the HCoV-NL63 nucleocapsid protein. Biochemical analyses revealed that the protein shares characteristics with homologous proteins encoded in other coronaviral genomes, with the N-terminal domain responsible for nucleic acid binding and the C-terminal domain involved in protein oligomerization. Surprisingly, analysis of the subcellular localization of the N protein of HCoV-NL63 revealed that, differently than homologous proteins from other coronaviral species except for SARS-CoV, it is not present in the nucleus of infected or transfected cells. Furthermore, no significant alteration in cell cycle progression in cells expressing the protein was observed. This is in stark contrast with results obtained for other coronaviruses, except for the SARS-CoV.

CRISPR-Cas Systems in Prokaryotes.

Prokaryotic organisms possess numerous strategies that enable survival in hostile conditions. Among others, these conditions include the invasion of foreign nucleic acids such as bacteriophages and plasmids. The clustered regularly interspaced palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) system provides the majority of bacteria and archaea with adaptive and hereditary immunity against this threat. This mechanism of immunity is based on short fragments of foreign DNA incorporated within the hosts genome. After transcription, these fragments guide protein complexes that target foreign nucleic acids and promote their degradation. The aim of this review is to summarize the current status of CRISPR-Cas research, including the mechanisms of action, the classification of different types and subtypes of these systems, and the development of new CRISPR-Cas-based molecular biology tools.

Stability of infectious human coronavirus NL63

Abstract The human coronavirus NL63 was identified in 2004 and subsequent studies showed its worldwide distribution. Infection with this pathogen is associated with upper and lower respiratory tract diseases of mild to moderate severity. Furthermore, HCoV-NL63 is the main cause of croup in children. Within this study an optimal protocol for freeze-drying that allows safe and effective preservation of HCoV-NL63 infectious material was developed. Lyophilized virus preparations can be stored either at ambient temperature or at +4°C. In the latter case samples may be stored for at least two months. Surprisingly, conducted analysis showed that HCoV-NL63 virions are exquisitely stable in liquid media and can be stored also without preservatives at ambient temperature for up to 14 days.

Structural Characterization of Human Coronavirus NL63 N Protein.

ABSTRACT Coronaviruses are responsible for upper and lower respiratory tract infections in humans. It is estimated that 1 to 10% of the population suffers annually from cold-like symptoms related to infection with human coronavirus NL63 (HCoV-NL63), an alphacoronavirus. The nucleocapsid (N) protein, the major structural component of the capsid, facilitates RNA packing, links the capsid to the envelope, and is also involved in multiple other processes, including viral replication and evasion of the immune system. Although the role of N protein in viral replication is relatively well described, no structural data are currently available regarding the N proteins of alphacoronaviruses. Moreover, our understanding of the mechanisms of RNA binding and nucleocapsid formation remains incomplete. In this study, we solved the crystal structures of the N- and C-terminal domains (NTD, residues 10 to 140, and CTD, residues 221 to 340, respectively) of the N protein of HCoV-NL63, both at a 1.5-Å resolution. Based on our structure of NTD solved here, we proposed and experimentally evaluated a model of RNA binding. The structure of the CTD reveals the mode of N protein dimerization. Overall, this study expands our understanding of the initial steps of N protein-nucleic acid interaction and may facilitate future efforts to control the associated infections. IMPORTANCE Coronaviruses are responsible for the common cold and other respiratory tract infections in humans. According to multiple studies, 1 to 10% of the population is infected each year with HCoV-NL63. Viruses are relatively simple organisms composed of a few proteins and the nucleic acids that carry the information determining their composition. The nucleocapsid (N) protein studied in this work protects the nucleic acid from the environmental factors during virus transmission. This study investigated the structural arrangement of N protein, explaining the first steps of its interaction with nucleic acid at the initial stages of virus structure assembly. The results expand our understanding of coronavirus physiology and may facilitate future efforts to control the associated infections.

07.14 Novel polymorphism of peptidylarginine deiminase from p. gingivalis augments bacterial pathogenicity and severity of periodontitis

Background Periodontitis (PD) is the most common chronic inflammatory disease caused by bacterial infection resulting in alveolar bone resorption and tooth loss.1,2 A main causative agent of PD is Porphyromonas gingivalis (Pg). 3,4 This periodontopathogen produces peptidylarginine deiminase (PPAD) catalysing conversion of arginine to citrulline.5,6 PD shares common mechanism and risk factors with rheumatoid arthritis (RA). Due to the presence of pathogenic autoantibodies reactive with citrullinated proteins in RA, citrullination of host and bacterial proteins by PPAD was proposed as a mechanistic link between PD and RA.7–9 The aim of this study was to investigate the impact of a novel polymorphism identified in the PPAD gene on bacterial virulence and PD clinical status. Materials and methods Gingival crevicular fluid (GCF) from 20 patients with PD was plated on blood agar and Pg colonies re-cultured to isolate individual strains of the bacterium. From each strain the PPAD gene was cloned, sequenced and analysed. The native PPAD gene in the reference Pg ATCC33277 strain was substituted with the polymorphic gene. The phenotype of clinical isolates harbouring polymorphism, the mutated and native ATCC33277 strains was examined. Further, periodontal clinical parameters were compared amongst patients infected by Pg expressing PPAD with and w/o polymorphism. Results A three amino acid polymorphism (G231N, E232T, N235D) was identified in the vicinity of the PPAD catalytic His residue in Pg isolates obtained from 30% of PD patients. The PPAD activity of clinical strains with polymorphism and the ATCC33277 mutant was 2-fold higher in comparison to the reference strain. Gingival fibroblasts infection with strains carrying polymorphic PPAD caused significantly higher upregulation of cyclooxygenase 2 (COX-2) than infection with native ATCC33277. Probing pocket depth (PPD) and clinical attachment level (CAL) assessment revealed that patients infected with Pg expressing polymorphic PPAD suffered from more severe disease than those carrying ‘classical’ Pg w/o polymorphism. Conclusions A three amino acid polymorphism of PPAD augments the virulence of Pg and severity of periodontitis apparently due to higher PPAD activity. The increased citrullination of bacterial and/or host proteins by Pg with the characterised PPAD genotype can trigger autoimmune response in RA. Acknowledgments National Science Centre, Poland (2012/07/B/NZ6/03524, K.G.), Foundation for Polish Science (TEAM, DPS/424-329/10, J.P.). References 1. Petersen PE, Bourgeois D, Ogawa H, et al.The global burden of oral diseases and risks to oral health. Bull World Health Organ 2003;83:661–69. 2. Eke PI, Dye BA, Wei L, et al.CDC Periodontal Disease Surveillance workgroup and representatives of the American Academy of Periodontology. Prevalence of periodontitis in adults in the United States: 2009 and 2010. J Dent Res 2012;91:914–20. 3. Socransky SS, Haffajee AD, Smith C, et al.Relation of counts of microbial species to clinical status at the sampled site. J Clin Periodontol 1991;18:766–75. 4. Holt SC, Ebersole J, Felton J, et al.Implantation of Bacteroides gingivalis in nonhuman primates initiates progression of periodontitis. Science 1998;239:55–57. 5. McGraw WT, Potempa J, Farley D, et al.Purification, characterisation, and sequence analysis of a potential virulence factor from Porphyromonas gingivalis, peptidylarginine deiminase. Infect Immun 1999;67:3248–56. 6. Rodriguez SB, Stitt BL, Ash DE.Expression of peptidylarginine deiminase from Porphyromonas gingivalis in Escherichia coli: enzyme purification and characterisation. Arch Biochem Biophys 2009;488:14–22. 7. Wegner N, Wait R, Sroka A, et al.Peptidylarginine deiminase from Porphyromonas gingivalis citrullinates human fibrinogen and α-enolase: implications for autoimmunity in rheumatoid arthritis. Arthritis Rheum 2010;62:2662–72. 8. Lundberg K, Kinloch A, Fisher BA, et al.Antibodies to citrullinated alpha-enolase peptide 1 are specific for rheumatoid arthritis and cross-react with bacterial enolase. Arthritis Rheum 2008;58:3009–19. 9. Quirke AM, Lugli EB, Wegner N, et al.Heightened immune response to autocitrullinated Porphyromonas gingivalis peptidylarginine deiminase: a potential mechanism for breaching immunologic tolerance in rheumatoid arthritis. Ann Rheum Dis 2014;73:263–69.