Browsing by Author "Ranka, Renate"
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Item Development of a real-time PCR method for rapid diagnosis of canine babesiosis and anaplasmosis(2021-12) Kivrane, Agnija; Namina, Agne; Seleznova, Maija; Akopjana, Sarmite; Capligina, Valentina; Ranka, RenateBackground: Canine babesiosis and anaplasmosis, caused by Babesia canis and Anaplasma phagocytophilum, respectively, are significant tick-borne diseases in Baltic countries. Both diseases can be diagnosed on the basis of clinicopathological findings, by direct pathogen detection in blood smears or by indirect pathogen detection; however, because of high selectivity and specificity, molecular methods may be advantageous. The goal of this study was to develop a duplex real-time polymerase chain reaction (RT-PCR) method for the detection of B. canis and A. phagocytophilum in canine clinical samples. Methods: Sequence-based polymorphism analysis of genes encoding B. canis-specific merozoite surface protein Bc28.1 (Bc28.1) and A. phagocytophilum malate dehydrogenase (mdh) was performed on pathogen isolates present in Latvian domestic dogs. The obtained results were used to design a species-specific duplex RT-PCR assay. Results: The presence of three B. canis Bc28.1 gene sequence types was revealed in canine samples with a nonuniform geographical distribution, and two types of A. phagocytophilum mdh genes were detected. The novel duplex RT-PCR assay provided correct classification of samples positive and negative for B. canis and A. phagocytophilum. The analytical sensitivity of this assay was ten gene copies/ reaction for both pathogens. Conclusions: A novel duplex RT-PCR molecular method was developed for the detection of B. canis and A. phagocytophilum in canine clinical samples. Sequence variability of Bc28.1 and mdh genes indicated the genetic variability of B. canis and A. phagocytophilum isolates occurring in Latvian domestic dogs. Graphic Abstract: [Figure not available: see fulltext.].Item Development of rapid antigen test prototype for detection of SARS-CoV-2 in saliva samples(2022-02-25) Kivrane, Agnija; Igumnova, Viktorija; Liepina, Elza Elizabete; Skrastina, Dace; Leonciks, Ainars; Rudevica, Zanna; Kistkins, Svjatoslavs; Reinis, Aigars; Zilde, Anna; Kazaks, Andris; Ranka, Renate; Rīga Stradiņš UniversityBackground: The development of easy-to-perform diagnostic methods is highly important for detecting current coronavirus disease (COVID-19). This pilot study aimed at developing a lateral flow assay (LFA)- based test prototype to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in saliva samples. Methods: Mice were immunized using the recombinant receptor-binding domain (rRBD) of SARS-CoV-2 virus spike protein. The combinations of the obtained mouse anti-receptor-binding domain (RBD) polyclonal antibodies (PAbs) and several commercial antibodies directed against the SARS-CoV-2 spike protein were used for enzyme-linked immunosorbent assay (ELISA) to select antibody pairs for LFA. The antibody pairs were tested in a LFA format using saliva samples from individuals with early SARS-CoV-2 infection (n = 9). The diagnostic performance of the developed LFA was evaluated using saliva samples from hospitalized COVID-19 patients (n = 111); the median time from the onset of symptoms to sample collection was 10 days (0-24 days, interquartile range (IQR): 7-13). The reverse transcription-polymerase chain reaction (rRT-PCR) was used as a reference method. Results: Based on ELISA and preliminary LFA results, a combination of mouse anti-RBD PAbs (capture antibody) and rabbit anti-spike PAbs (detection antibody) was chosen for clinical analysis of sample. When compared with rRT-PCR results, LFA exhibited 26.5% sensitivity, 58.1% specificity, 50.0% positive prediction value (PPV), 33.3% negative prediction value (NPV), and 38.7% diagnostic accuracy. However, there was a reasonable improvement in assay specificity (85.7%) and PPV (91.7%) when samples were stratified based on the sampling time. Conclusion: The developed LFA assay demonstrated a potential of SARS-CoV-2 detection in saliva samples. Further technical assay improvements should be made to enhance diagnostic performance followed by a validation study in a larger cohort of both asymptomatic and symptomatic patients in the early stage of infection.Item The effect of glaucoma filtration surgery on structural and functional eye parameters in a short-term study(2017-04) Baumane, Kristine; Ranka, Renate; Laganovska, Guna; Rīga Stradiņš UniversityGlaucoma filtration surgery (trabeculectomy) is an effective glaucoma treatment method that provides significant intraocular pressure (IOP) reduction. Indications for this method are in cases where other forms of therapy, like medicines or lasers, have failed, other forms of therapy are not suitable (compliance or side-effects are a problem), in cases where a target pressure is required to prevent clinically significant disease progression that cannot be reached with topical medications and/or laser and in cases that have such advanced glaucoma and high IOP at presentation that other forms of treatment are unlikely to be successful. The aim of this study was to evaluate the effect of glaucoma surgery on the structural and functional eye parameters at different stages of glaucoma. A total of 96 eyes of 96 patients (only one eye from each patient) with different stages of glaucoma (stages 2 to 4) who were undergoing trabeculectomy were recruited. Quadrant retinal nerve fibre layer RNFL) thickness (33 patients), cup/disc vertical and horizontal ratio (36 patients) and MD of visual fields (27 patients) were analysed up to one week before and 1 month after the successful surgery. The results show that the MD value was slightly improved in 50%, 85.7%, and 71.4% of patients with glaucoma stages 2, 3, and 4, respectively. The mean RNFL of all four optic nerve head quadrants increased slightly after the surgery for patients with glaucoma stage 2; in contrast, a decrease in the mean RNFL values for all four quadrants was observed for patients with glaucoma stage 4. Statistically significant changes in the mean values for the optic nerve horizontal c/d ratio after glaucoma surgery were observed (p = 0.033) in contrast to the vertical c/d values (p = 0.77). In total, improvement of the horizontal and vertical c/d ratio was detected in 61.1% and 55.6% of the glaucoma patients, respectively. Although the observed changes were statistically insignificant, the positive influence of glaucoma surgery on the structural and functional eye parameters was more pronounced in moderate stages than in advanced or severe stages of glaucoma.Item Effect of NAT2, GSTM1 and CYP2E1 genetic polymorphisms on plasma concentration of isoniazid and its metabolites in patients with tuberculosis, and the assessment of exposure-response relationships(2024-03) Ulanova, Viktorija; Kivrane, Agnija; Viksna, Anda; Pahirko, Leonora; Freimane, Lauma; Sadovska, Darja; Ozere, Iveta; Cirule, Andra; Sevostjanovs, Eduards; Grinberga, Solveiga; Bandere, Dace; Ranka, Renate; Research Professor (Tenured Professor) Group at the Faculty of Pharmacy; Department of Pharmaceutical ChemistryObjectives: Isoniazid is a key drug in the chemotherapy of tuberculosis (TB), however, interindividual variability in pharmacokinetic parameters and drug plasma levels may affect drug responses including drug induced hepatotoxicity. The current study investigated the relationships between isoniazid exposure and isoniazid metabolism-related genetic factors in the context of occurrence of drug induced hepatotoxicity and TB treatment outcomes. Methods: Demographic characteristics and clinical information were collected in a prospective TB cohort study in Latvia ( N = 34). Time to sputum culture conversion (tSCC) was used as a treatment response marker. Blood plasma concentrations of isoniazid (INH) and its metabolites acetylisoniazid (AcINH) and isonicotinic acid (INA) were determined at three time points (pre-dose (0 h), 2 h and 6 h after drug intake) using liquid chromatography-tandem mass spectrometry. Genetic variations of three key INH-metabolizing enzymes (NAT2, CYP2E1, and GSTM1) were investigated by application PCR- and Next-generation sequencing-based methods. Depending on variables, group comparisons were performed by Student's t-test, one-way ANOVA, Mann-Whitney-Wilcoxon, and Kruskal-Wallis tests. Pearson correlation coefficient was calculated for the pairs of normally distributed variables; model with rank transformations were used for non-normally distributed variables. Time-to-event analysis was performed to analyze the tSCC data. The cumulative probability of tSCC was obtained using Kaplan-Meier estimators. Cox proportional hazards models were fitted to estimate hazard rate ratios of successful tSCC. Results: High TB treatment success rate (94.1%) was achieved despite the variability in INH exposure. Clinical and demographic factors were not associated with either tSCC, hepatotoxicity, or INH pharmacokinetics parameters. Correlations between plasma concentrations of INH and its metabolites were NAT2 phenotype-dependent, while GSTM1 genetic variants did not showed any effects. CYP2E1*6 (T > A) allelic variant was associated with INH pharmacokinetic parameters. Decreased level of AcINH was associated with hepatotoxicity, while decreased values of INA/INH and AcINH/INH were associated with month two sputum culture positivity. Conclusion: Our findings suggest that CYP2E1, but not GSTM1, significantly affects the INH pharmacokinetics along with NAT2. AcINH plasma level could serve as a biomarker for INH-related hepatotoxicity, and the inclusion of INH metabolite screening in TB therapeutic drug monitoring could be beneficial in clinical studies for determination of optimal dosing strategies.Item Exploring Variability in Rifampicin Plasma Exposure and Development of Anti-Tuberculosis Drug-Induced Liver Injury among Patients with Pulmonary Tuberculosis from the Pharmacogenetic Perspective(2024-03-12) Kivrane, Agnija; Ulanova, Viktorija; Grinberga, Solveiga; Sevostjanovs, Eduards; Viksna, Anda; Ozere, Iveta; Bogdanova, Ineta; Zolovs, Maksims; Ranka, Renate; Research Professor (Tenured Professor) Group at the Faculty of Pharmacy; Department of Infectology; Statistics UnitGenetic polymorphisms can exert a considerable impact on drug pharmacokinetics (PK) and the development of adverse drug reactions (ADR). However, the effect of genetic polymorphisms on the anti-tuberculosis (anti-TB) drug, and particularly rifampicin (RIF), exposure or anti-TB drug-induced liver injury (DILI) remains uncertain. Here, we evaluated the relationship between single nucleotide polymorphisms (SNPs) detected in the RIF pharmacogenes ( AADAC, SLCO1B1, SLCO1B3, ABCB1, and NR1I2) and RIF PK parameters, as well as anti-TB treatment-associated DILI. In total, the study enrolled 46 patients with drug-susceptible pulmonary TB. The RIF plasma concentration was measured using the LC-MS/MS method in the blood samples collected pre-dose and 2 and 6 h post-dose, whilst the DILI status was established using the results from blood biochemical analysis performed before and 10-12 days after treatment onset. The genotyping was conducted using a targeted NGS approach. After adjustment for confounders, the patients carrying the rs3732357 GA/AA genotype of the NR1I2 gene were found to have significantly lower RIF plasma AUC 0-6 h in comparison to those with GG genotype, while the difference in RIF plasma C max was insignificant. None of the analyzed SNPs was related to DILI. Hence, we are the first to report NR1I2 intronic SNP rs3732357 as the genetic component of variability in RIF exposure. Regarding anti-TB treatment-associated DILI, the other preexisting factors promoting this ADR should be considered.Item Fatal Babesia canis canis infection in a splenectomized Estonian dog(2016-01-25) Tiškina, Valentina; Capligina, Valentina; Must, Külli; Berzina, Inese; Ranka, Renate; Jokelainen, Pikka; Rīga Stradiņš UniversityA previously splenectomized dog from Estonia was presented with a sudden lack of appetite and discoloration of the urine. Despite supportive therapy, its condition deteriorated dramatically during 1 day. Severe thrombocytopenia and high numbers of protozoan hemoparasites were evident in blood smears, and the hematocrit dropped from 46 to 33%. The dog was euthanized before specific antibabesial treatment was initiated. Blood samples from the dog and from two other dogs in the same household tested positive for Babesia using molecular methods, and the sequences of partial 18S rRNA gene confirmed the causative species as Babesia canis canis. The risk of severe, rapidly progressing babesiosis in splenectomized dogs merits awareness.Item Haemotropic Mycoplasma species in pet cats in Latvia : a study, phylogenetic analysis and clinical case report(2021) Berzina, Inese; Capligina, Valentina; Namina, Agne; Visocka, Alina; Ranka, RenateObjectives: The aim of this study was to evaluate whether haemotropic Mycoplasma species are detected in pet cats in Latvia, to perform a phylogenetic analysis of the detected pathogens and to report a clinical case of feline infectious anaemia. Methods: Peripheral blood samples (n = 125) from pet cats were submitted; 99 samples were adequate to test for the presence of Mycoplasma species DNA by nested PCR. A clinical case was added in the later stages of the study. Positive isolates were subjected to phylogenetic analysis. Results: The prevalence of ‘Candidatus Mycoplasma haemominutum’ was 15% (n = 15/99), that of Mycoplasma haemofelis was 5% (5/99) and that of ‘Candidatus Mycoplasma turicensis’ was 2% (n = 2/99). Cases of coinfection included ‘Candidatus M haemominutum’ + M haemofelis (4%; n = 4/99) and ‘Candidatus M haemominutum’ + ‘Candidatus M turicensis’ (1%; n = 1/99). This is the first published report of M haemofelis infection in the Baltic states. Two different ‘Candidatus M turicensis’ isolates were discovered after phylogenetic analysis. Conclusions and relevance: This report is the first of an autochthonous feline infectious anaemia case in the Baltic region. The prevalence of Mycoplasma species was similar to that in other northern European countries. Phylogenetic analysis revealed variability of the isolates; one of the ‘Candidatus M turicensis’ genotypes was detected for the first time in Europe.Item LC-MS/MS method for simultaneous quantification of the first-line anti-tuberculosis drugs and six primary metabolites in patient plasma : Implications for therapeutic drug monitoring(2021-11-15) Kivrane, Agnija; Grinberga, Solveiga; Sevostjanovs, Eduards; Igumnova, Viktorija; Pole, Ilva; Viksna, Anda; Bandere, Dace; Krams, Alvils; Cirule, Andra; Pugovics, Osvalds; Ranka, Renate; Rīga Stradiņš UniversityThe pharmacokinetic profiling of drug substances and corresponding metabolites in the biological matrix is one of the most informative tools for the treatment efficacy assessment. Therefore, to satisfy the need for comprehensive monitoring of anti-tuberculosis drugs in human plasma, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for simultaneous quantification of first-line anti-tuberculosis drugs (ethambutol, isoniazid, pyrazinamide, and rifampicin) along with their six primary metabolites. Simple single-step protein precipitation with methanol was chosen as the most convenient sample pre-treatment method. Chromatographic separation of the ten analyte mixture was achieved within 10 minutes on a reverse-phase C8 column using mobile phase gradient mode. The multiple reaction monitoring mode (MRM) was used for analyte detection and quantification in patient samples. The chosen quantification ranges fully covered expected plasma concentrations. The method exhibited acceptable selectivity; the within- and between-run accuracy ranged from 87.2 to 113.6%, but within- and between-run precision was between 1.6 and 14.9% (at the LLOQ level CV < 20%). Although the response of the isonicotinic acid varied depending on the matrix source (CV 21.8%), validation results proved that such inconsistency does not affect the accuracy and precision of results. If stored at room temperature plasma samples should be processed within 4 h after collection, temporary storage at −20 °C up to 24 h is acceptable due to stability issues of analytes. The developed method was applied for the patient sample analysis (n = 34) receiving anti-tuberculosis treatment with the first-line drugs.Item The link between mitochondrial DNA hypervariable segment I heteroplasmy and ageing among genetically unrelated Latvians(2011-07) Pliss, Liana; Brakmanis, Andis; Ranka, Renate; Elferts, Didzis; Krumina, Astrida; Baumanis, ViestursVarious studies have demonstrated that mitochondrial DNA (mtDNA) heteroplasmy tends to increase with age and that the observed frequency of heteroplasmy among populations mostly depends on the way it is measured. Therefore, we investigated age-related association on the presence of mtDNA heteroplasmy within the hypervariable segment 1 (HVS-I) in a selected study group. The study group consisted of 300 maternally unrelated Latvians ranging in age from 18 to over 90. years. To determine the optimal method for mtDNA heteroplasmy detection, three approaches were used: (i) SURVEYOR Mutation Detection Kit, (ii) sequencing and (iii) denaturing gradient-gel electrophoresis (DGGE). Among the studied individuals, 30.3% were found to be heteroplasmic. The distribution of heteroplasmy statistically significantly increased with individuals' age (17%; 95% confidence interval [CI] 0.095-0.244 in the 18-40. year age group vs. 39%; [CI] 0.294-0.487 in the > 90 year age group). Heteroplasmy occurred in a total of 21 different positions within HVS-I, and was the most frequent at fast-mutated positions 16189, 16304 and 16311. The results indicate that heteroplasmy in HVS-I is relatively common and occurs in a broad spectrum of sites. The above is supported by evidence to eventual increase of the probability of heteroplasmy with age due to specific mitochondrial haplogroup background.Item Morphological characterisation and molecular sex determination of human remains from the 15th-17th centuries in Latvia(2015-04-01) Ščesnaite-Jerdiakova, Asta; Pliss, Liana; Gerhards, Guntis; Gordina, Elina Petersone; Gustiņa, Agnija; Pole, Ilva; Zole, Egija; Kimsis, Janis; Jansone, Inta; Ranka, RenateSex determination is one of the most important and initial steps in human profile identification from archaeological material. The aim of the current study was to evaluate the application of molecular approaches alongside morphological methods for sex determination in archaeological human skeletal remains. Human skeletal remains were excavated from three cemeteries: St Gertrude Old Church, Dom Square and St Peter's Church, of 15th-17th century burials in Riga, Latvia. Morphological and molecular genetic methods, including amplification of genes AMELX/Y and SRY were used to analyse seven skeletal remains. The conducted analyses of morphological features identified sex in all seven cases (two females and five males). By molecular analyses of mediaeval DNA it was possible to determine sex in five of seven (71%) samples. In all positive cases full agreement between morphological estimation and molecular genetic methods was observed. To conclude, DNA analysis can be considered for sex identification in cases with no signs of sexual dimorphism (juvenile skeletons) or partially preserved skeletons.Item Next-Generation Sequencing and Bioinformatics-Based Protocol for the Full-Length CYP2E1 Gene Polymorphism Analysis(2022) Igumnova, Viktorija; Kivrane, Agnija; Viksna, Anda; Norvaisa, Inga; Ranka, Renate; Department of Pharmaceutical Chemistry; Department of InfectologyIntroduction: Pharmacogenetics studies provide clinically relevant information on the identified associations between genetic variants and individual variability in drug response, which, in turn, offers great promise for guiding personalized drug therapy and clinical trial design. However, there is a lack of information concerning the evidence-based clinical annotations of specific CYP2E1 genetic variants. Aim: To design and evaluate the next-generation sequencing-based method for full-length CYP2E1 gene polymorphism analysis. Materials and Methods: Seven gene-specific oligonucleotide primer pairs targeting overlapping CYP2E1 gene fragments spanning all nine gene exons with interleaving introns, untranslated (UTR) and intergenic regions were designed. Human DNA samples (n = 3) were used as a training set to check the primer performance and to optimize the PCR conditions. The effectiveness of the developed target amplification and sequencing protocol was evaluated using the test set comprising human DNA samples (n = 3) obtained from tuberculosis patients. Sequencing data analysis was performed on the Galaxy online-based platform. Results: The sequencing data quality was sufficient for the detection of genetic variants dispersed throughout the CYP2E1 gene with a high degree of confidence in fully covered regions achieving optimal reading depth of the targeted fragment with high base call accuracy. Conclusion: Developed protocol can be applied in subpopulation-level association studies to determine whether single nucleotide variants (SNVs) or variant combinations from multiple regions of the CYP2E1 gene are of clinical significance.Item The postmedieval Latvian oral microbiome in the context of modern dental calculus and modern dental plaque microbial profiles(2021-02) Kazarina, Alisa; Petersone‐Gordina, Elina; Kimsis, Janis; Kuzmicka, Jevgenija; Zayakin, Pawel; Griškjans, Žans; Gerhards, Guntis; Ranka, Renate; Rīga Stradiņš UniversityRecent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16–17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral micro-biome patterns in historic samples and compared the microbial composition of historic dental cal-culus, modern human dental plaque, modern human dental calculus samples and burial soil micro-biota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the micro-biome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.Item Structural characterization of CspZ, a complement regulator factor H and FHL-1 binding protein from Borrelia burgdorferi(2014-06) Brangulis, Kalvis; Petrovskis, Ivars; Kazaks, Andris; Bogans, Janis; Otikovs, Martins; Jaudzems, Kristaps; Ranka, Renate; Tars, Kaspars; Rīga Stradiņš UniversityBorrelia burgdorferi is the causative agent of Lyme disease and is found in two different types of hosts in nature - Ixodes ticks and various mammalian organisms. To initiate disease and survive in mammalian host organisms, B. burgdorferi must be able to transfer to a new host, proliferate, attach to different tissue and resist the immune response. To resist the host's immune response, B. burgdorferi produces at least five different outer surface proteins that can bind complement regulator factor H (CFH) and/or factor H-like protein 1 (CFHL-1). The crystal structures of two uniquely folded complement binding proteins, which belong to two distinct gene families and are not found in other bacteria, have been previously described. The crystal structure of the CFH and CFHL-1 binding protein CspZ (also known as BbCRASP-2 or BBH06) from B. burgdorferi, which belongs to a third gene family, is reported in this study. The structure reveals that the overall fold is different from the known structures of the other complement binding proteins in B. burgdorferi or other bacteria; this structure does not resemble the fold of any known protein deposited in the Protein Data Bank. The N-terminal part of the CspZ protein forms a four-helix bundle and has features similar to the FAT domain (focal adhesion targeting domain) and a related domain found in the vinculin/α-catenin family. By combining our findings from the crystal structure of CspZ with previous mutagenesis studies, we have identified a likely binding surface on CspZ for CFH and CFHL-1.Item Tracing microbial communities associated with archaeological human samples in Latvia, 7–11th centuries AD(2023-10) Ķimsis, Jānis; Pokšāne, Alise; Kazarina, Alisa; Vilcāne, Antonija; Petersone-Gordina, Elina; Zayakin, Pawel; Gerhards, Guntis; Ranka, RenateIn the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7–11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.