Comparative Study on Molecular Epidemiology of Measles H1a Outbreak and Sporadic Cases in Shandong Province, 2013-2019

Background: Measles caused by measles virus (MeV) is a highly contagious viral disease which has also been associated with complications including pneumonia, myocarditis, encephalitis, and subacute sclerosing panencephalitis. The current study collected33 strains from 2013 to 2019 in 13 cities of Shandong province and separate them into 2 group, outbreak cases and sporadic cases. Comparative of genetic characterization between 15 outbreak strains and 18 sporadic strains was made using nucleotide sequencing of the C-terminal region of the N protein gene(N-450). Results: The results showed that all 33 stains belonged to genotype H1a. The outbreak strains and sporadic strains distribute crossly in phylogenetic tree. Sequences alignment revealed some interesting G and A transversion, which change the amino acids, on sites 1317, 1422, 1543. The nucleotide sequence and amino acid homologies of 15 Shandong outbreak isolates were 98%–100% (0–10 nucleotide variation) and 97.7%–100%, for sporadic isolations, they are 97.3%–100% and 96.6%–100% respectively. The mean evolution rate of 15 outbreak isolations and 18 sporadic isolations was 4.73× 10-3 and 2.068× 10-3 substitutions per site per year separately, which is higher than the study made before 2002. Conclusions: This report compared epidemic and genetic characteristics of outbreak strains and sporadic strains, and raise evolutionary study of sporadic cases may be helpful for discovery of the possibility of outbreak, especially in the stage of measles elimination.

PSXII-8 Mitochondrial DNA diversity within domestic reindeer in Russia

Domestic reindeer in Russia are a valuable resource of vital importance to the physical and cultural survival of the Northern indigenous minority. During the last decades, the mitochondrial (mt) genetic markers have been widely used as a molecular tool to investigate genetic structure and diversity of livestock species. Here we aimed at the assessing the mtDNA diversity of the domestic reindeer inhabiting the area from the Kola Peninsula in the west to the Chukotka region in the east. A complete cytochrome b (cytb) sequences (1,140 bp) from representatives of six populations, including Nenets (NEN, n = 16), Evenk (EVK, n = 12), Even (EVN, n = 6), Chukotka (CHU, n = 6), Chukotka-Khargin (CHUKH, n = 6) and Tuva (TUVA, n = 6) were obtained. Sequences’ alignment was conducted using MUSCLE algorithm in R package msa. In total, 34 haplotypes were identified. Median-joining network, constructed in PopART 1.7, revealed three major groups of haplotypes: the first one joined the samples of all the populations, the second one included NEN, EVN and CHUKH, and the third group was presented by the one sample of CHU. AMOVA, calculated in Arlequin 3.5.2.2, showed that only 9.58% of molecular variance could be explained by the differences between populations and 90.42% - within populations. Genetic diversity parameters calculated in DnaSP 6.12.03, demonstrated that average number of nucleotide differences (K) was highest in CHUKH (28.333) and EVN (27.409) and lowest in TUVA (4.533) and EVK (5.400). Nucleotide diversity (Pi) was 0.01238±0.00559, 0.00474±0.00091, 0.02404±0.00453, 0.01281±0.00464, 0.02485±0.00744, and 0.00398±0.00110 for NEN, EVK, EVN, CHU, CHUKH and TUVA, respectively. Our study demonstrated the lack of clear genetic structure of the studied reindeer populations in relation to cytb sequence. The level of genetic diversity was associated with census size and was lowest in the smallest Tuva population. This study was supported by RSF-21-16-00071 and Russian Ministry of Science and Higher Education-0445-2019-0024.

The physicochemical and phylogenetic properties of twelve spike glycoprotein models for SARS-CoV-2 from China, Iran, and Tunisia

Background The coronavirus spike glycoprotein is a trimeric structural surface protein that facilitates the viral adhesion through attaching receptors on the human cell surface. This study aims to analyse and compare the genomic and phylogenetic properties of these spike glycoproteins from China, Iran, and Tunisia. Methods This is a descriptive cross-sectional comparative study for the different properties of S glycoprotein from 12 SARS-CoV-2 specimens from GenBank. Clustal Omega was used to study model sequences alignment, residual conservation, phylogeny, and identity matrix. SWISS-MODEL developed and validated the 3D models for three protein sequences with the highest model quality. The different physicochemical characteristics of different models were assessed by ExPASy proteomics. Results The Chinese and the Iranian sequences share 100% identity, although they have a different amino acids number, and 25-29.27% identity to the Tunisian sequences. The 12 models are monophyletic, with varying stages of evolutionary divergence. There are six fully, three highly, and five lowly conserved residues across the sequences. The resulting three highly reliable 3D models were of different global qualities, being the lowest for the Tunisian, and the highest for the Iranian models. All the models are highly hydrophilic. The Tunisian models were unstable in comparison to the relatively stable other models with different physicochemical characteristics. Conclusion The models had different N-terminal residues and side groups polarity and charge. The S glycoproteins are not identical nor unique in model structure nor the physicochemical profiles in different parts of the world. The Tunisian models are drastically biodiverse from the Chinese and Iranian models.

FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots

Motivation Multiple sequence alignment (MSA) is important and challenging problem of computational biology. Most of the existing methods can only provide a short length multiple alignments in an acceptable time. Nevertheless, when the researchers confront the genome size in the multiple alignments, the process has required a huge processing space/time. Accordingly, using the method that can align genome size rapidly and precisely has a great effect, especially on the analysis of the very long alignments. Herein, we have proposed an efficient method, called FAME, which vertically divides sequences from the places that they have common areas; then they are arranged in consecutive order. Then these common areas are shifted and placed under each other, and the subsequences between them are aligned using any existing MSA tool. Results The results demonstrate that the combination of FAME and the MSA methods and deploying minimizer are capable to be executed on personal computer and finely align long length sequences with much higher sum-of-pair (SP) score compared to the standalone MSA tools. As we select genomic datasets with longer length, the SP score of the combinatorial methods is gradually improved. The calculated computational complexity of methods supports the results in a way that combining FAME and the MSA tools leads to at least four times faster execution on the datasets. Availability and implementation The source code and all datasets and run-parameters are accessible free on http://github.com/naznoosh/msa. Supplementary information Supplementary data are available at Bioinformatics online.

Polymorphism of two wheat degydrines genes

Aim. The aim of this work is to study the nucleotide sequences variability of two genes encoding wheat dehydrins. One of them belong to K-2 group, the other refers to K-3 type (respectively, TaDHN18 and TaDHN19.3 according to the classification of Wang et al.). These loci sre interesting due to their's genes participation in protection of plants from the various adverse abioti ecffects. Methods. Polymorphism of two genes encoding dehydrins was investigated using 6 wheat varieties as examples, among which were spring and winter varieties with different cold resistance, using PCR-based cloning, sequencing, and data processing softwares. Results. An analysis of the obtained nucleotide and hypothetical protein sequences alignment showed that the locus under study in the genomes of different wheat varieties, both spring and winter, is characterized by a high identity degree. Conclusions. The high conservatism of two loci encoding K-2 and K-3 dehydrins was demonstrated. Keywords: wheat, dehydrins, polymorphism.

Identification and expression analysis of c-type and g-type lysozymes genes after Aeromonas hydrophila infection in African catfish

ABSTRACTLysozymes play an important role in the first line of defense in fish and potentially used as an immunity status biomarker and immune responses evaluation in fish, which often found in two types, i.e. chicken-type and goose-type (c- and g-type, respectively). To recent, the information related to the sequences and the expression analysis of the c- and g-type lysozyme genes in African catfish is still limited. In the present study, we report a partial cloning and mRNA expression analysis of c-type and g-type lysozymes in African catfish Clarias gariepinus. We have successfully cloned and partially identify the c-type, and g-type lysozyme genes of C. gariepinus, which consist of 594 and 560 of coding sequences, respectively. Catalytic and other conserved residues were identified by multiple sequences alignment and they showed high similarity with other teleost fish species. mRNA levels of the genes were analyzed by using qPCR method and their expressions in the spleen, liver, and head kidney were rapidly modulated after Aeromonas hydrophila injection, with different patterns were observed in each organ. These results confirmed that c- and g-type lysozymes played an important role in non-specific immunity against A. hydrophila infection. This study provided valuable information that can be used to understand the African catfish immune systems for better disease and stress management in C. gariepinus culture.Keywords: lysozymes, gene identification, gene expression, bacterial infection, African catfish ABSTRAKLisozim berperan dalam sistem pertahanan dini pada ikan dan sangat potensial digunakan sebagai marka status imunitas dalam evaluasi respons imun. Lisozim umum ditemukan dalam dua tipe pada ikan: tipe-ayam (tipe-c) dan tipe-angsa (tipe-g). Informasi terkait sekuens gen dan ekspresi gen kedua tipe lisozim pada ikan lele dumbo sangat terbatas. Pada penelitian ini, kami melaporkan kloning gen secara parsial, dan analisis ekspresi gen dari kedua tipe lisozim pada ikan lele dumbo C. gariepinus. Sekuens parsial gen lisozim tipe-c dan tipe-g yang berhasil diidentifikasi adalah sepanjang 594 dan 560 pasang basa. Situs katalitik dan residu khas memiliki tingkat kesamaan yang tinggi dengan spesies ikan yang lain. Analisis mRNA dilakukan dengan metode quantitative PCR (qPCR). Ekspresi kedua gen di jaringan ginjal depan, limpa, dan hati dengan cepat terinduksi pasca infeksi bakteri A. hydrophila dengan pola yang berbeda. Hasil ini menunjukkan bahwa lisozim tipe-c dan tipe-g memiliki peran yang sangat penting dalam sistem imun ikan lele dumbo terhadap infeksi A. hydrophila. Penelitian ini menghasilkan informasi penting yang dapat digunakan untuk mempelajari sistem imun ikan lele dumbo dan sebagai acuan dalam penanganan dan manajemen penyakit pada budidaya ikan lele dumbo.Kata kunci: lisozim, identifikasi gen, ekspresi gen, infeksi bakteri, ikan lele dumbo

Non-Mammalian Prdx6 Enzymes (Proteins with 1-Cys Prdx Mechanism) Display PLA2 Activity Similar to the Human Orthologue

Mammalian peroxiredoxin class 6 (Prdx6) are bifunctional enzymes. Non-mammalian Prdx6 enzymes display Cys-based peroxidase activity, but to date their putative phospholipase A2 (PLA2 activities) has not been experimentally investigated. Initially, we observed that five non-mammalian Prdx6 enzymes (enzymes from Arabidopsis thaliana (AtPER1), Triticum aestivum (TaPER1), Pseudomonas aeruginosa (PaLsfA) and Aspergillus fumigatus (AfPrx1 and AfPrxC)) present features compatible with PLA2 activities in mammalian Prdx6 by amino acid sequences alignment and tertiary structure modeling. Employing unilamellar liposomes with tracer amounts of [3H]-1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and thin layer chromatography, all the tested non-mammalian Prdx6 enzymes displayed PLA2 activities, with values ranging from 3.4 to 6.1 nmol/min/mg protein. It was previously shown that Thr177 phosphorylation of human Prdx6 increases its PLA2 activity, especially at neutral pH. Therefore, we investigated if human Erk2 kinase could also phosphorylate homologous Thr residues in non-mammalian Prdx6 proteins. We observed phosphorylation of the conserved Thr in three out of the five non-mammalian Prdx enzymes by mass spectrometry. In the case of the mitochondrial Prdx6 from A. fumigatus (AfPrxC), we also observed phosphorylation by western blot, and as a consequence, the PLA2 activity was increased in acidic and neutral conditions by the human Erk2 kinase treatment. The possible physiological meanings of these PLA2 activities described open new fields for future research.