Domain discovery method for topological profile searches in protein structures

We describe a method for automated domain discovery for topological profile searches in protein structures. The method is used in a system TOPStructure for fast prediction of CATH classification for protein structures (given as PDB files). It is important for profile searches in multi-domain proteins, for which the profile method by itself tends to perform poorly. We also present an O(C(n)k +nk2) time algorithm for this problem, compared to the O(C(n)k +(nk)2) time used by a trivial algorithm (where n is the length of the structure, k is the number of profiles and C(n) is the time needed to check for a presence of a given motif in a structure of length n). This method has been developed and is currently used for TOPS representations of protein structures and prediction of CATH classification, but may be applied to other graph-based representations of protein or RNA structures and/or other prediction problems. A protein structure prediction system incorporating the domain discovery method is available at http://bioinf.mii.lu.lv/tops/

A computer system to perform structure comparison using TOPS representations of protein structure

We describe the design and implementation of a fast topology–based method for protein structure comparison. The approach uses the TOPS topological representation of protein structure, aligning two structures using a common discovered pattern and generating measure of distance derived from an insert score. Heavy use is made of a constraint-based pattern matching algorithm for TOPS diagrams that we have designed and described elsewhere Gilbert et al. (1999). The comparison system is maintained at the European Bioinformatics Institute and is available over the Web via the at tops.ebi.ac.uk/tops. Users submit a structure description in Protein Data Bank (PDB) format and can compare it with structures in the entire PDB or a representative subset of protein domains, receiving the results by email

Distribution of HLA allele frequencies in patients with cystic and alveolar echinococcosis in Latvia

Publisher Copyright: © 2019 Sniedze Laivacuma et al., published by Sciendo 2019.The aim of this study was to assess the relationship between HLA Class II alleles in two groups of patients in Latvia: patients with cystic and alveolar echinococcosis. The study included 37 patients from the Rīga East Clinical University Hospital with echinococcosis (29 patients with cystic echinococcosis and eight patients with alveolar echinococcosis) and 100 healthy control persons without echinococcosis. HLA Class II allele genotyping was performed using Real-time polymerase chain reaction-sequence specific primer (RT-PCR-SSP). The odds ratios (OR), with 95% confidence intervals (95% CI), were calculated using statistical analysis performed with IBM SPSS Statistics for Windows, Version 22.0, to evaluate the risk of developing the disease in an individual having a particular HLA genotype. In the case of cystic echinococcosis a more severe course of a disease can be anticipated in the presence of HLA-DRB1 alleles ∗17:01 and ∗07:01, -DQB1 ∗03:02, and ∗03:01, -DQA1∗04:01 and haplotypes HLA-DRB1∗04:01/-DQB1∗03:01/ -DQA1∗03:01, HLADRB1∗11:01/ -DQB1∗03:01 /-DQA1∗05:01. However, in the group with alveolar echinococcosis it was associated with the HLA-DRB1 alleles ∗17:01 and ∗07:01, -DQB1 ∗05:01 and haplotypes HLA- DRB1∗17:01/-DQB1∗02:01-2/-DQA1∗01:01, HLA-DRB1∗11:01/ -DQB1∗03:01/-DQA1∗01:03 and HLA-DRB1∗11:01/-DQB1∗03:01/-DQA1∗03:01. HLADRB1∗15:01/-DQÂ1∗06:02-8/-DQA1∗05:01 and HLA-DRB1∗13:01/-DQB1∗02:01-2/-DQA1∗05:01 haplotypes were protective in all patient groups. The limitations of this exploratory study indicate that a broader study needs to be conducted for revealing specific risk and protective HLA Class II haplotypes for patients with cystic and alveolar echinococcosis in Latvia.publishersversionPeer reviewe

Investigation of the sugar content in wood hydrolysates with iodometric titration and UPLC-ELSD

ArticleAutohydrolysis of birch wood is a mild pretreatment process, which gives a notable yield of sugars – monosaccharides and oligosaccharides – in the aqueous hydrolysate, while a solid lignocellulose fraction can be further processed into other valuable products within a biorefinery concept. In this work two analytical methods – iodometric titration and ultra-high performance liquid chromatography with evaporative light scattering detection (UPLC-ELSD) – have been optimized and compared for the determination of the sugar content in series of birch wood hydrolysates. The results of both methods were consistent and showed that the highest yield of sugars, mostly xylose, was obtained by hydrolysis at 180 °C after 75 min

Seroprevalence of diphtheria and measles antibodies and their association with demographics, self-reported immunity, and immunogenetic factors in healthcare workers in Latvia

Funding Information: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: [Aija Leidere-Reine reports financial support was provided by European Social Fund and Latvian state budget. The study was partially funded by the project No 8.2.2.0/20/I/004 “Support for involving doctoral students in scientific research and studies”.] Publisher Copyright: © 2022 The Author(s)Latvia is among European countries with outbreaks of diphtheria and measles. Healthcare workers (HCW) are exposed to infections and can transmit them to unvaccinated patients. We assessed the seroprevalence of antibodies against diphtheria and measles and their association with demographics, self-reported immunity, the presence of the HLA-B27 allele, and level of interferon regulatory factor 5 (IRF5) in Latvian HCW. Anti-diphtheria and anti-measles IgG antibodies and the level of IRF5 in serum were tested by enzyme immunoassay. The presence of the HLA-B27 allele was detected by a real-time polymerase chain reaction. The study involved 176 HCW, including 29% doctors and 44% nurses. Among HCW, 95.5% were seropositive for diphtheria. However, only 65.9% had full seroprotection against it. The seronegativity for measles (21.6%) was higher than for diphtheria (4.5%) without differences in gender and medical staff groups. Older age was associated with waning immunity against diphtheria and a higher rate of seropositivity for measles. Considered immunogenetic factors did not affect the level of antibodies, and variability of the level of IRF5 in serum can reflect ageing processes. Self-reported vaccination status had a low informative value regarding full seroprotection against diphtheria and seropositivity for measles indicating the need for pre-vaccination IgG screening in planning the booster vaccination.publishersversionPeer reviewe

THE EVALUATION OF STABLE ISOTOPIC RATIOS 13C AND 15N IN HUMIC ACIDS ALONG A FEN PEAT PROFILE

Mires are known as consistent environmental archives, but humic acids are the fraction of peat that is most recalcitrant and refractory to organic matter degradation, thus data on environmental changes during mire development can be recorded into them. This work was focused on the studies of stable isotopic ratios delta carbon-13 and delta nitrogen-15, and their distribution in humic acids within fen peat layers of different depths and peat composition. The variations in delta carbon-13 reflect isotopic variations in peat-forming plants over time and can be considered as a function of photosynthetic pathway that is being used to fix carbon dioxide. At the same time, variations in delta nitrogen-15 show nitrogen fixation in peat-forming plants and can be traced along with peat decomposition degree and depth. Properties of humic acids were studied in 2018 at 3 fens located in Latvia and Southern Finland, and comparatively they show properties. The method used for the determination of stable isotopes was the isotope-ratio mass spectrometry that was performed in the Faculty of Chemistry, University of Latvia. Results on delta carbon-13 indicate signal of C3 peat-forming plants, while signal of C4 peat-forming plants is not evident, which can be explained by non-efficient carbon dioxide fixation in fen vegetation. Results on delta nitrogen-15 show variations in nitrogen fixation in fen vegetation. Data show nitrogen fixation in terrestrial plants, however significant shifts in absolute isotope values indicate dependence on variations in peat decomposition degree and botanical composition. Data suggest that differences in peat botanical composition, decomposition degree and site dependent characteristics reflect in differences in delta carbon-13 and delta nitrogen-15 variation

History of Academic Neurology in Latvia

Peer reviewe

Retrospective serological evidence of high exposure of globally relevant zoonotic parasite toxoplasma gondii in the Latvian Population

Funding Information: This study was partly funded by the European Regional Development Fund “1.1.1.2. “Post-doctoral research aid” project “One Health multidisciplinary approaches for epidemiology and prevention of selected parasitic zoonosis (OMEPPAZ)” (1.1.1.2/VIAA/1/16/204). Publisher Copyright: © 2019 Gunita Deksne et al., published by Sciendo 2019.Toxoplasmosis is an important infection caused by the single-celled parasite Toxoplasma gondii, which is a zoonotic parasite causing widespread human and animal diseases, mostly involving the central nervous system. Humans can acquire toxoplasmosis by ingestion of raw or undercooked meat containing T. gondii tissue cysts, ingestion of oocysts shed by infected felids via contaminated food or water, and by vertical transmission to the fetus through the placenta from the mother during pregnancy. The aim of the present study was to determine the seroprevalence of specific anti-T. gondii IgG and IgM antibodies using a large set of clinical diagnostic laboratory data obtained over a 14-year period. In total, 25 069 unique patients were included in the present study. The overall specific anti-T. gondii IgG prevalence were 36.3%, which was significantly (p < 0.01) higher than IgM prevalence (2.4%). Mean age for IgG antibody-positive patients was 33.7 ± 12.2 years. A significant positive correlation (r = 0.99; p < 0.01) was observed between age group and anti-T. gondii IgG antibody prevalence, which ranged from 4.2% to 66.7%. The most prevalent (69.9%; 95% CI 69.2-70.7) comorbidities of patients tested for presence of anti-T. gondii IgG and IgM antibodies were classified as factors affecting health status which includes also monitoring of normal pregnancy.publishersversionPeer reviewe

Gene Duplication Models and Reconstruction of Gene Regulatory Network Evolution from Network Structure

In this paper we study evolution of gene regulatory networks from the graph-theoretic perspective. We consider two gene duplication models that are based on those studied before, but are more general and/or mathematically more precise than previously published schemes. Our aims are to assess the biological appropriateness of the proposed models and to study the possibilities of reconstruction of the evolution history of networks solely on the basis of network topology. For one of the proposed models, which is fully deterministic, we provide an exact algorithm for reconstruction of evolutionary history of the network. The algorithm is applicable in real time to networks with up to 200 genes, which is comparable to sizes of real biological networks. The other proposed model involves random deletions of gene interactions. In this case a heuristic modification of the algorithm can be used to identify a large subset of genes that have been duplicated during the last duplication event. The methods have been tested for analysis of yeast gene regulatory network and have been able to identify several biologically confirmed pairs of duplicated genes. Similarity between inferred pairs of gene duplicates is shown to be above average, thus indicating that traces from gene duplications, which have occurred long time ago, can still be detected from the network topology alone.The work was supported by Latvian Council of Science grant 258/2012 and Latvian State Research programme project NexIT (2014-2017)