Sequencing Of Fragments Research Articles

Thermolytic Synthesis of Asphaltene-like Nitrogenous Bases and Study of Their Aggregative Stability

The work is devoted to the study of the influence of nitrogenous bases on the composition of oil and the structure of asphaltenes on their colloidal stability in solution. Model petroleum systems with a basic nitrogen content of 1, 2, and 3% wt. were used as objects of study. Asphaltene-like nitrogenous bases were obtained by thermolysis of model petroleum systems with different nitrogen contents. The results were obtained using elemental analysis, non-aqueous potentiometric titration, spectrophotometry, 1H NMR spectroscopy, and liquid adsorption chromatography. It was established that the content of Nbas in asphaltenes increases by 0.3–1.3% wt. with the increase in quinoline content in petroleum components. Quinoline is incorporated into the supramolecular structure of asphaltenes and increases their average molecular weight by 650 amu. and aromaticity by 2%. The aggregative stability of asphaltenes decreases by 1.5–6 times with an increase in their average molecular weight and an increase in Nbas in their composition as a component of a dispersion medium. The colloidal stability of synthetic asphaltene-like substances, on the contrary, is due to the appearance of their molecular sequence of fragments containing Nbas in aromatic rings.

Comparison of Vaginal microbiota in HPV-negative and HPV-positive pregnant women using a culture-based approach

The purpose of this study was to conduct a comparative analysis of the composition of the dominant groups of vaginal microorganisms in healthy pregnant women and pregnant women infected with HPV using a microbiological culture-based method. The MALDI TOF MS method and 16S rRNA gene fragment sequencing were used to identify microorganisms isolated from healthy pregnant women (n=32) and pregnant women infected with HPV (n=24). It was found that vaginal secretion samples from both groups contained bacteria of 4 phyla: Bacillota, Actinomycetota, Pseudomonadota, Bacteroidota, and Ascomycota fungi. The most common microbial community in healthy pregnant women being CST I (p=0.0007), and CST V in pregnant women infected with HPV (p=0.0001). At the genus level, a total of 25 taxa were found in all samples, with Lactobacillus being the dominant genus overall. Escherichia (p<0.0001) and Prevotella (p=0.0001) concentrations were higher in HPV infected patients. When calculating the Pearson correlation coefficient for the phyla, it was found that Bacillota correlated negatively with HPV genotypes 16 and 51 (p≤0.05), but positively with HPV genotype 59 (p≤0.05), just like Actinomycetota (p≤0.05). Bacteroidota correlated positively with HPV genotype 56 (0.001<p<0.01), and Ascomycota correlated positively with HPV genotypes 39 and 51 (p≤0.05; 0.001<p<0.01). Pearson correlation coefficients between bacteria genera and HPV genotypes were statistically significant for the following genera: Lactobacillus, Streptococcus, Enterococcus, Gardnerella, Escherichia, Prevotella. The data obtained in our study indicates that the culture-based method is informative when assessing the qualitative and quantitative composition of the microbiota.

Development of Single-Nucleotide Polymorphism Markers and Population Genetic Analysis of the Hadal Amphipod Alicella gigantea across the Mariana and New Britain Trenches

Alicella gigantea, the largest amphipod scavengers found to date, play key roles in the food web of the hadal ecosystem. However, the genetic structure of A. gigantea populations among different trenches has not been reported yet. In this study, SNP (single-nucleotide polymorphism) markers were developed for three A. gigantea geographic populations collected from the southern Mariana Trench (SMT), the central New Britain Trench (CNBT), and the eastern New Britain Trench (ENBT), based on the SLAF-seq (specific locus amplified fragment sequencing) technology. A total of 570,168 filtered SNPs were screened out for subsequent population genetic analysis. Results showed that the inbreeding levels across the three geographic populations were relatively low, and the genomic inbreeding coefficients of the three populations were similar in magnitude. Based on the results of phylogenetic analysis, population structure analysis, and principal component analysis, it is believed that the three A. gigantea geographic populations belong to the same population, and the kinship relationship between the ENBT and CNBT populations is close. Moreover, the differential candidate adaptive sites on the SNPs suggest that there may be variations in metabolic rates among the three geographic populations, possibly linked to differences in food availability and sources in different trenches, ultimately resulting in different survival strategies in A. gigantea populations within distinct trenches. Compared with the Mariana Trench, the New Britain Trench has a richer organic matter input, and it is speculated that the A. gigantea Mariana Trench population may adopt a lower metabolic rate to cope with the harsher environment of nutrient deficiency.

A generalized protein identification method for novel and diverse sequencing technologies.

Protein sequencing is a rapidly evolving field with much progress towards the realization of a new generation of protein sequencers. The early devices, however, may not be able to reliably discriminate all 20 amino acids, resulting in a partial, noisy and possibly error-prone signature of a protein. Rather than achieving de novo sequencing, these devices may aim to identify target proteins by comparing such signatures to databases of known proteins. However, there are no broadly applicable methods for this identification problem. Here, we devise a hidden Markov model method to study the generalized problem of protein identification from noisy signature data. Based on a hypothetical sequencing device that can simulate several novel technologies, we show that on the human protein database (N = 20181) our method has a good performance under many different operating conditions such as various levels of signal resolvability, different numbers of discriminated amino acids, sequence fragments, and insertion and deletion error rates. Our results demonstrate the possibility of protein identification with high accuracy on many early experimental devices. We anticipate our method to be applicable for a wide range of protein sequencing devices in the future.

Culturable yeast community associated with grape must and honey bees sampled from apiaries located in the vineyards.

In this study, we investigated culturable yeast community, present in grape must sampled from vineyards with apiaries on the borders, and in honey bees collected in these apiaries. To this aim, yeasts isolated from spontaneously fermented grapes randomly collected in two vineyards (P1 and P2) with apiaries on the borders (A1 and A2) were compared to those isolated from spontaneously fermented grapes collected from a vineyard without apiary (P4). At the same time, yeast community was analyzed on bees collected in each apiary placed in the vineyards, in comparison to yeasts isolated from an apiary (A3) located far from the vineyards. The analysis was performed for two consecutive years (2021 and 2022). The isolated yeasts were identified by restriction analysis of amplified ITS region, followed by sequencing of ITS fragment.Our research showed that the presence of apiaries seems to increase yeast counts of grape must, in particular of Saccharomyces cerevisiae; furthermore, the permanence of apiaries in the vineyards allowed the recovering of these yeasts also from bees. Our findings seem to corroborate the role of bees as vectors and reservoirs of oenologically relevant yeasts, such as a source of non-conventional yeasts with potential biotechnological applications.

S100A1's single cysteine is an indispensable redox switch for the protection against diastolic calcium waves in cardiomyocytes.

The EF-hand calcium (Ca2+) sensor protein S100A1 combines inotropic with antiarrhythmic potency in cardiomyocytes (CMs). Oxidative posttranslational modification (ox-PTM) of S100A1's conserved, single-cysteine residue (C85) via reactive nitrogen species (i.e., S-nitrosylation or S-glutathionylation) has been proposed to modulate conformational flexibility of intrinsically disordered sequence fragments and to increase the molecule's affinity toward Ca2+. Considering the unknown biological functional consequence, we aimed to determine the impact of the C85 moiety of S100A1 as a potential redox switch. We first uncovered that S100A1 is endogenously glutathionylated in the adult heart in vivo. To prevent glutathionylation of S100A1, we generated S100A1 variants that were unresponsive to ox-PTMs. Overexpression of wild-type (WT) and C85-deficient S100A1 protein variants in isolated CM demonstrated equal inotropic potency, as shown by equally augmented Ca2+ transient amplitudes under basal conditions and β-adrenergic receptor (βAR) stimulation. However, in contrast, ox-PTM defective S100A1 variants failed to protect against arrhythmogenic diastolic sarcoplasmic reticulum (SR) Ca2+ waves and ryanodine receptor 2 (RyR2) hypernitrosylation during βAR stimulation. Despite diastolic performance failure, C85-deficient S100A1 protein variants exerted similar Ca2+-dependent interaction with the RyR2 than WT-S100A1. Dissecting S100A1's molecular structure-function relationship, our data indicate for the first time that the conserved C85 residue potentially acts as a redox switch that is indispensable for S100A1's antiarrhythmic but not its inotropic potency in CMs. We, therefore, propose a model where C85's ox-PTM determines S100A1's ability to beneficially control diastolic but not systolic RyR2 activity.NEW & NOTEWORTHY S100A1 is an emerging candidate for future gene-therapy treatment of human chronic heart failure. We aimed to study the significance of the conserved single-cysteine 85 (C85) residue in cardiomyocytes. We show that S100A1 is endogenously glutathionylated in the heart and demonstrate that this is dispensable to increase systolic Ca2+ transients, but indispensable for mediating S100A1's protection against sarcoplasmic reticulum (SR) Ca2+ waves, which was dependent on the ryanodine receptor 2 (RyR2) nitrosylation status.

Expression of the labeled recombinant glycoprotein E2 of the classical swine fever virus in &lt;i&gt;E. Coli&lt;/i&gt;

Currently, live attenuated vaccines are used in the Russian Federation for the specific prevention of classical swine fever (CSF), but this strategy contradicts the rules for importing animal products and carries the risks of recombination with field strains. These factors exacerbate the need for further development of candidate recombinant vaccines with similar efficacy and safety. The aim of the presented work was to construct a prokaryotic expression system of the marked glycoprotein E2 of the CSF virus and to evaluate its immunochemical properties. As a result of the conducted studies, a section of the primary amino acid sequence of glycoprotein E2 of a highly pathogenic Shimen strain (subgenotype 1.1) was identified using bioinformatic analysis and a hybrid polypeptide was designed, including a non-specific (marker) part from the modified V5 epitope and a fragment of the BSA sequence. By cloning a codon-optimized fragment into the pET-28a vector, the E. coli BL21(DE3) pLysS/pET-28a/E2-V5 producing strain was constructed. During the optimization of the cultivation conditions of the producer strain, it was found that the highest yield of the target protein is achieved within 5-6 hours after the induction of expression. The immunochemical properties of chromatographically purified recombinant rE2-V5 were determined: for example, it was shown that its activity in indirect enzyme immunoassay exceeds that of native E2. The data obtained indicate the effectiveness of the developed prokaryotic expression system, which consists in proper folding, good solubility and the ability of the target protein to form specific immunocomplexes. The presence of a marker fragment in the expressed hybrid polypeptide in the future will allow using the latter as the basis of a recombinant vaccine that meets the requirements of the DIVA strategy.

Characteristics of Psychrotolerant Bacteria Isolated from Clay Organogenic Deposits of Mramorny Cave (Primorsky Territory)

A cultivated community of bacteria of the genus Pseudomonas was researched in clayey organogenic deposits of the Mramorny Cave (Primorsky Territory). The bacterial strains studied in this work are eurythermal and psychrotolerant. Their phylogenetic affiliation was found by high throughput sequencing of 16S rRNA gene fragments. It is known that bacteria of the genus Pseudomonas represent all the Earth ecological niches and, accordingly, have a wide range of adaptive functions. Using microscopy methods, a change in the nature of mobility and the cell size stability with changes in the temperatures of cultivating bacteria were established. The studied strains are of scientific and practical interest due to the enzymatic activity detection to several substrates simultaneously at different temperatures (25 and 4℃), as well as the ability to secrete cold active pectinase, protease and lipase. However, phosphate-solubilizing activity both at 4 and at 25℃ became preferable for the strains. The Mramorny Cave is karst and is characterized by carbonate karst, which explains the preference for the studied strains in calcium phosphate. An analysis of the obtained data shows that the collection of cultivated bacteria obtained by us includes both typical psychrotolerant ones, which exhibit enzymatic activity under conditions of optimal growth temperature, and unique ones, capable of synthesizing a wide range of enzymes under conditions not characteristic of its optimum growth.

Soil microbiome of Plaggic Anthrosol and Calcic Cryosols in Central Yakutia

Soil microbiome makes a significant contribution to the implementation of ecosystem services, which are necessary for the sustainable functioning of ecosystems. Soils of central Yakutia develop under dynamic physical and chemical conditions (long-term freezing/thawing processes, redistribution of nutrients), which ensures the formation of a specific microbial community in natural and anthropogenically transformed areas. The object of the study was the natural, fallow, and agricultural soils of central Yakutia. The method of high-throughput sequencing of 16S rRNA gene fragment on Illumina MiSEQ sequencer was used to analyze the microbial community. As a result, in fallow lands a decrease in nutrients was revealed if compared to the lands involved in agricultural turnover. Based on the composition of the microbiome it was observed that the most common phyla are Acidobacteria, Actinobacteria, Verrucomicrobiota, Pseudomonadota (Alphaproteobacteria, Gammaproteobacteria), Bacterioidota, Chloroflexi, Planctomycetota. The presence of a core set of microorganisms for the studied soils was recorded, up to 17.8% of phylotypes are unique and up to 25.7% are common to fallow lands and background plots. Microbial communities vary depending on geographical locations and on types of natural resource use. The most distinct microbial communities are formed in hydromorphic soils with the development of gley processes, as well as in agricultural soils.

QTL mapping of downy mildew resistance in foxtail millet by SLAF‑seq and BSR-seq analysis.

Key message Three major QTLs for resistance to downy mildew were located within an 0.78 Mb interval on chromosome 8 in foxtail millet. Downy mildew, a disease caused by Sclerospora graminicola, is a serious problem that jeopardizes the yield and quality of foxtail millet. Breeding resistant varieties represents one of the most economical and effective solutions, yet there is a lack of molecular markers related to the resistance. Here, a mapping population comprising of 158 F6:7 recombinant inbred lines (RILs) was constructed from the crossing of G1 and JG21. Based on the specific locus amplified fragment sequencing results, a high-density linkage map of foxtail millet with 1031 bin markers, spanning 1041.66 cM was constructed. Based on the high-density linkage map and the phenotype data in four environments, a total of nine quantitative trait loci (QTL) associated with resistance to downy mildew were identified. Further BSR-seq confirmed the genomic regions containing the potential candidate genes related to downy mildew resistance. Interestingly, a 0.78-Mb interval between C8M257 and C8M268 on chromosome 8 was highlighted because of its presence in three major QTL, qDM8_1, qDM8_2, and qDM8_4, which contains 10 NBS-LRR genes. Haplotype analysis in RILs and natural population suggest that 9 SNP loci on Seita8G.199800, Seita8G.195900, Seita8G.198300, and Seita.8G199300 genes were significantly correlated with disease resistance. Furthermore, we found that those genes were taxon-specific by collinearity analysis of pearl millet and foxtail millet genomes. The identification of these new resistance QTL and the prediction of resistance genes against downy mildew will be useful in breeding for resistant varieties and the study of genetic mechanisms of downy mildew disease resistance in foxtail millet.

A treasure trove of 1034 actinomycete genomes.

Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences from >1000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera and 389 species, including 244 likely novel species. All genomes are from filamentous isolates of the class Actinomycetia from the NBC culture collection. The largest genus is Streptomyces with 886 genomes including 742 complete assemblies. We use this data to show that analysis of complete genomes can bring biological understanding not previously derived from more fragmented sequences or less systematic datasets. We document the central and structured location of core genes and distal location of specialized metabolite biosynthetic gene clusters and duplicate core genes on the linear Streptomyces chromosome, and analyze the content and length of the terminal inverted repeats which are characteristic for Streptomyces. We then analyze the diversity of trans-AT polyketide synthase biosynthetic gene clusters, which encodes the machinery of a biotechnologically highly interesting compound class. These insights have both ecological and biotechnological implications in understanding the importance of high quality genomic resources and the complex role synteny plays in Actinomycetia biology.

Analysis of genetic diversity by the SLAF-seq among the farmed Onychostoma macrolepis populations

ObjectiveThe objective of this study was to examine the genetic diversity within and between farmed populations of Onychostoma macrolepis, and to establish a foundation for enhancing the genetic resources of breeding groups through the introduction of new individuals and crossbreeding. A total of 49 individuals were subjected to sequencing using Specific-Locus Amplified Fragment Sequencing (SLAF-seq), one of the restriction site-associated DNA sequencing technologies. The single nucleotide polymorphisms(SNPs)were identified to conduct the analyzation of phylogeny population structure, principal component and genetic diversity.ResultsA total of 853,067 SNPs were identified. The results of the phylogenetic analysis revealed that each sample was genetically clustered into three distinct groups: ZhenPing (ZP), LanGao parents (LG), and their progeny population (LG-F1). Each population was observed to be clustered together. Analysis of population genetic diversity revealed that the observed heterozygosity (Ho) ranged from 0.200 to 0.230, the expected heterozygosity (He) ranged from 0.280 to 0.282, and the polymorphic information content (PIC) ranged from 0.228 to 0.230. These results indicate that the genetic diversity of the population is low and the signs of long-term interbreeding are obvious, but there are differences between the populations, and the genetic diversity of the population can be improved by hybridization in different regions.

Molecular tracing of Biomphalaria straminea in China

To investigate the origin of Biomphalaria straminea in China, so as to provide insights into assessment of schistosomiasis mansoni transmission risk and B. straminea control. Guanlan River, Dasha River, Shenzhen Reservoir, upper and lower reaches of Kuiyong River, and Xinzhen River in Shenzhen, China, were selected as sampling sites. Ten Biomphalaria samples were collected from each site, and genomic DNA was extracted from Biomphalaria samples. DNA samples were obtained from 15 B. straminea sampled from 5 sampling sites in Minas Gerais State, Pará State, Federal District, Pernambuco State, and Sao Paulo State in Brazil, South America. Cytochrome c oxidase I (COI) and mitochondrial 16S ribosomal RNA (16S rRNA) genes were sampled using the above DNA templates, and the amplified products were sequenced. The COI and 16S rRNA gene sequences were downloaded from GenBank, and the sampling sites were acquired. All COI and 16S rRNA gene sequences were aligned and evolutionary trees of B. straminea were created based on COI and 16S rRNA gene sequences to identify the genetic similarity and evolutionary relationship between B. straminea samples from China and South America. A total of 60 COI gene sequences with a length of 529 bp and 3 haplotypes were obtained from B. straminea sampled from China. There were 165 COI gene sequences of B. straminea retrieved from GenBank, and following alignment with the above 60 gene sequences, a total of 33 haplotypes were obtained. Phylogenetic analysis showed that the three haplotypes of B. straminea from China were clustered into one clade, among which the haplotype China11 and three B. straminea samples from Brazil retrieved from GenBank belonged to the same haplotype. Geographical evolution analysis showed that the B. straminea samples from three sampling sites along eastern coasts of Brazil had the same haplotype with China11, and B. straminea samples from other two sampling sites were closely, genetically related to China11. A total of 60 16S rDNA gene sequences with approximately 322 bp in length were amplified from B. straminea in China, with 2 haplotypes identified. A total of 70 16S rDNA gene sequences of B. straminea were captured from GenBank. Phylogenetic analysis showed that Biomphalaria snails collected from China were clustered into a clade, and the haplotype China64 and the haplotype 229BS from Brazil shared the same haplotype. The 49 16S rDNA gene sequences of B. straminea from 25 sampling sites in southern Brazil, which were captured from GenBank, were included in the present analysis, and the B. straminea from 3 sampling sites shared the same haplotype with China64 in China. Geographical evolution analysis based on COI and 16S rRNA gene sequences showed that B. straminea sampled from eastern coastal areas of Brazil shared the same haplotypes in two gene fragment sequences with Biomphalaria snails collected from China. The Biomphalaria snails in China are characterized as B. straminea, which have a low genetic diversity. The Biomphalaria snails in China have a high genetic similarity with B. straminea sampled from eastern coastal areas of Brazil, which may have originated from the eastern coastal areas of Brazil.

Insights into structure, codon usage, repeats, and RNA editing of the complete mitochondrial genome of Perilla frutescens (Lamiaceae)

Perilla frutescens (L.) Britton, a member of the Lamiaceae family, stands out as a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in Îś-linolenic acid, holding substantial economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. To this end, the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens were hereby conducted using a combination of Illumina and PacBio data. The assembled P. frutescens mitochondrial genome spanned 299,551 bp and exhibited a typical circular structure, involving a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes. Additionally, 18 introns were observed in 8 protein-coding genes. Notably, the codons of the P. frutescens mitochondrial genome displayed a notable A/T bias. The analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Moreover, RNA editing sites preferentially produced leucine at amino acid editing sites. Furthermore, 70 sequence fragments (12,680 bp) having been transferred from the chloroplast to the mitochondrial genome were identified, accounting for 4.23% of the entire mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salviamiltiorrhiza and Platostoma chinense. Meanwhile, inter-species Ka/Ks results suggested that Ka/Ks <1\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$<1$$\\end{document} for 28 PCGs, indicating that these genes were evolving under purifying selection. Overall, this study enriches the mitochondrial genome data for P. frutescens and forges a theoretical foundation for future molecular breeding research.

Isolation and identification of a pigeonpox virus strain and study on the integration of reticuloendotheliosis virus sequence.

In order to study the integration of reticuloendotheliosis virus (REV) in pigeonpox virus (PPV), we collected suspected pigeonpox disease material, amplified the 4b core protein gene of PPV, the gp90 gene of REV, and the integrated sequence fragments from the end of the ORF201 segment of PPV to the beginning of the LTR of REV, and sequenced these genes. The results showed that a 4b core protein fragment of 332bp was amplified and identified as pigeonpox virus, which was named SX/TY/LTR 01/2023. Sequence analysis showed that the pigeonpox virus isolate belonged to genotype A2, which was the closest to the domestic CVL strain, with a identity of 99.4%. A band of 1191bp was amplified from the gp90 gene of REV, named SX/TY/PPV-REV01/2023, and sequence analysis indicated that REV belonged to genotype III. The sequence analysis showed that REV belonged to genotype III, and belonged to the same large branch as the domestic isolates JSRD0701 and LNR0801, with 99.3% identity. The integrated sequence fragment was amplified to a band of 637bp, which determined that the REV sequence was integrated in the PPV rather than a mixed infection of the two viruses. This indicates that REV was integrated in this isolation of PPV, suggesting that pigeon farms need to prevent reticuloendotheliosis at the same time when preventing pigeonpox.

Submerged cultivation and phytochemical analysis of medicinal mushrooms (Trametes sp.).

Mushrooms are widely available around the world and have various nutritional as well as therapeutic values. Many Asian cultures believe that medicinal mushrooms can prolong life and improve vitality. This study aims to characterize the phytochemical and polysaccharide content, mainly β-glucan content, of mycelial biomass and fruiting bodies collected from the Himalayan region, particularly Uttarakhand. Through molecular analysis of the LSU F/R-rDNA fragment sequence and phylogenetic analysis, the strain was identified as Trametes sp. We performed screening of phytochemicals and polysaccharides in mushroom and biomass extracts using high-performance liquid chromatography (HPLC) and a PC-based UV-Vis spectrophotometer. The macrofungal biomass was found to be high in saponin, anthraquinone, total phenolic, flavonoid, and β-glucan content. In biomass extract, we observed a high level of saponin (70.6µg/mL), anthraquinone (14.5µg/mL), total phenolic (12.45 µg/mL), and flavonoid (9.500 µg/mL) content. Furthermore, we examined the contents of alkaloids, tannins, terpenoids, and sterols in the biomass and mushroom extracts; the concentration of these compounds in the ethanol extract tested was minimal. We also looked for antioxidant activity, which is determined in terms of the IC50 value. Trametes sp. mushroom extract exhibits higher DPPH radical scavenging activity (62.9% at 0.5 mg/mL) than biomass extract (59.19% at 0.5 mg/mL). We also analyzed β-glucan in Trametes sp. from both mushroom and biomass extracts. The biomass extract showed a higher β-glucan content of 1.713 mg/mL than the mushroom extract, which is 1.671 mg/mL. Furthermore, β-glucan analysis was confirmed by the Megazyme β-glucan assay kit from both biomass and mushroom extract of Trametes sp. β-glucans have a promising future in cancer treatment as adjuncts to conventional medicines. Producing pure β-glucans for the market is challenging because 90-95% of β glucan sold nowadays is thought to be manipulated or counterfeit. The present study supports the recommendation of Trametes sp. as rich in β-glucan, protein, phytochemicals, and antioxidant activities that help individuals with cancer, diabetes, obesity, etc.

Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population

BackgroundCarcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET).ResultsA total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 30 SNPs were identified for seven carcass traits using the mixed linear model (MLM) (p < 1.0 × 10− 5), of which 9 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43 to 16.32%. Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found for carcass traits in pigs.ConclusionsThe GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.

Red foxes (Vulpes vulpes) and raccoon dogs (Nyctereutes procyonoides) as potential spreaders of Sarcocystis species.

Sarcocystis includes a global group of apicomplexan parasites with two-host life cycle frequently circulating in wildlife and domestic hosts, including humans. Two of the most important wild terrestrial carnivores acting as definitive hosts are the red fox and raccoon dog, due to their wide distribution in Europe and usage of wild and farmed animals as prey. This study was conducted to determine the prevalence of Sarcocystis in hunted red foxes and raccoon dogs from nine regions of the Czech Republic and to identify isolated sporocysts by molecular techniques. Approximately 5 g of the contents of large intestine from 200 animals (197 red foxes and three raccoon dogs) were examined by flotation centrifugation coprological method. Only samples of 50 red foxes and one raccoon dog positive to Sarcocystis spp. were used for the nested PCR (nPCR) method to amplify a fragment or partial sequence on the cox1 gene. Ten species-specific primer pairs for detection of Sarcocystis spp. using farm animals as intermediate hosts were utilized. In total, 38.1% of the red foxes and 66.7% of the raccoon dogs were positive to Sarcocystis by light microscopy. The molecular characterization resulted in the identification of five species in the red fox: S. arieticanis, S. capracanis, S. cruzi, S. miescheriana, and S. tenella, while the PCR was negative for the sole raccoon dog. The highest intraspecific variation was found for S. miescheriana, while S. tenella was the most prevalent. Co-infections occurred in the large intestine of the red fox. No zoonotic species were found in our samples. This is the first study where the potential role of the red fox and raccoon dogs as spreaders of Sarcocystis to farm animals in the Czech Republic is shown. The use of species-specific primers provides a fast and easy method for screening multiple samples for a particular Sarcocystis species.

Description and circadian rhythms of Chandlerella sinensis Li, 1933 (Nematoda; Onchocercidae), with remarks of microfilariae effects on the host health.

During investigation of common linnet (Linaria cannabina) blood using the buffy coat method one bird with microfilariae in the blood was found. The morphometric description of adult worms corresponded to the Chandlerella sinensis. This species was found for the first time in common linnets. DNA sequences of cox1 and 28S gene fragments of adult worm recovered during necropsy was identical to that from the microfilariae in the bird blood. Phylogenetic analysis of the cox1 gene fragment clustered this parasite with Chandlerella quiscali. Histological examination revealed the presence of microfilariae in the lumen of small capillaries and other blood vessels in different organs, but no inflammations were notice. The greatest number of microfilariae was in the lungs. Even if there was no inflammation, but vessels associated with the lungs were markedly distended with blood, parabronchial walls were thickened and, in some cases, almost completely obstructing the lumen. The large number of microfilariae in lungs indicates possible disturbance of gas exchange in the lungs adversely affected the ability of the bird to exercise and made breathing difficult at rest. The investigation of circadian rhythm of the microfilariae showed that C. sinensis microfilariae in blood of common linnet were more numerous at night and morning and less numerous at midday. The survival rate of mosquitoes infected with C. sinensis microfilariae was significantly lower than that of uninfected mosquitoes.

Zoonotic human liver flukes, a type 1 biocarcinogen, in freshwater fishes: genetic analysis and confirmation of molluscan vectors and reservoir hosts in Bangladesh

BackgroundOpisthorchiid flukes, particularly Opisthorchis viverrini, Opisthorchis felineus, Clonorchis sinensis, and Metorchis spp. are the most common fish-borne zoonotic human liver flukes (hLFs). Liver fluke infections are more prevalent in resource-deprived and underprivileged areas. We herein estimated the prevalence of the metacercariae (MC) of major hLFs in common large freshwater fishes (lFWF) marketed for human consumption from some selected areas of Bangladesh along with detection of their molluscan vectors and reservoirs.MethodsThe current status of fish-borne zoonotic hLF infections in lFWF was investigated along with their molluscan vectors and mammalian reservoir hosts in Mymensingh and Kishoreganj in Bangladesh from July 2018–June 2022 using conventional and multiple molecular techniques, such as PCR, PCR-restriction fragment length polymorphism (RFLP), sequencing, and bioinformatic analyses. The infection rate of fishes was analyzed using the Z-test and the loads of MC were compared using the chi-squared (χ2) test.ResultsThe MC of C. sinensis, Opisthorchis spp., and Metorchis spp. were detected in 11 species of common and popular lFWF. In lFWF, the estimated prevalence was 18.7% and the mean load was 137.4 ± 149.8 MC per 100 g of fish. The prevalence was the highest (P < 0.05) in spotted snakehead fishes (Channa punctata, 63.6%). The highest rate of infection (P < 0.05) was observed with the MC of C. sinensis (11.8%). Metacercariae were almost equally (P > 0.05) distributed between the head and body of fishes. The infection rate was slightly higher in cultured (19.6%) fishes. The MC of C. sinensis, O. felineus, O. viverrini, and Metorchis orientalis in fishes were confirmed using PCR, PCR-RFLP and bioinformatics. The cercariae of opisthorchiid (Pleurolophocercus cercariae) flukes were only recovered from Bithynia spp. (3.9%, 42 out of 1089). The ova of hLFs from dogs (4.3%, 5 out of 116) and cats (6.0%, 6 out of 100), and adult flukes (M. orientalis) from ducks (41.1% 113 out of 275) were detected.ConclusionsThe MC of hLFs are highly prevalent in fresh water fishes in Bangladesh. Reservoir hosts, such as street dogs, cats, and ducks carried the patent infection, and residents of Bangladesh are at risk.Graphical