Screening of high-risk deleterious missense variations in the CYP1B1 gene implicated in the pathogenesis of primary congenital glaucoma: A comprehensive in silico approach
Background Primary congenital glaucoma (PCG) is the most common subtype of glaucoma caused by defects in the cytochrome P450 1B1 (CYP1B1) gene. It is developing among infants in more than 80% of cases who exhibit impairments in the anterior chamber angle and the trabecular meshwork. Thus, a comprehensive in silico approach was performed to evaluate the effect of high-risk deleterious missense variations in the CYP1B1 gene. Material and methods All the information for CYP1B1 missense variants was retrieved from the dbSNP database. Seven different tools, namely: SIFT, PolyPhen-2, PROVEAN, SNAP2, PANTHER, PhD-SNP, and Predict-SNP, were used for functional annotation, and two packages, which were I-Mutant 2.0 and MUpro, were used to predict the effect of the variants on protein stability. A phylogenetic conservation analysis using deleterious variants was performed by the ConSurf server. The 3D structures of the wild-type and mutants were generated using the I-TASSER tool, and a 50 ns molecular dynamic simulation (MDS) was executed using the GROMACS webserver to determine the stability of mutants compared to the native protein. Co-expression, protein-protein interaction (PPI), gene ontology (GO), and pathway analyses were additionally performed for the CYP1B1 in-depth study. Results All the retrieved data from the dbSNP database was subjected to functional, structural, and phylogenetic analysis. From the conducted analyses, a total of 19 high-risk variants (P52L, G61E, G90R, P118L, E173K, D291G, Y349D, G365W, G365R, R368H, R368C, D374N, N423Y, D430E, P442A, R444Q, F445L, R469W, and C470Y) were screened out that were considered to be deleterious to the CYP1B1 gene. The phylogenetic analysis revealed that the majority of the variants occurred in highly conserved regions. The MD simulation analysis exhibited that all mutants’ average root mean square deviation (RMSD) values were higher compared to the wild-type protein, which could potentially cause CYP1B1 protein dysfunction, leading to the severity of the disease. Moreover, it has been discovered that CYP1A1, VCAN, HSD17B1, HSD17B2, and AKR1C3 are highly co-expressed and interact with CYP1B1. Besides, the CYP1B1 protein is primarily involved in the metabolism of xenobiotics, chemical carcinogenesis, the retinal metabolic process, and steroid hormone biosynthesis pathways, demonstrating its multifaceted and important roles. Discussion This is the first comprehensive study that adds essential information to the ongoing efforts to understand the crucial role of genetic signatures in the development of PCG and will be useful for more targeted gene-disease association studies.
Shahid et al. (2022) Screening of high-risk deleterious missense variations in the CYP1B1 gene implicated in the pathogenesis of primary congenital glaucoma: A comprehensive in silico approach. PeerJ 10:e14132 https://doi.org/10.7717/peerj.14132
PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2
The optimization of resources for research in developing countries forces us to consider strategies in the wet lab that allow the reuse of molecular biology reagents to reduce costs. In this study, we used linear regression as a method for predictive modeling of coverage depth given the number of MinION reads sequenced to define the optimum number of reads necessary to obtain >200X coverage depth with a good lineage-clade assignment of SARS-CoV-2 genomes. The research aimed to create and implement a model based on machine learning algorithms to predict different variables (e.g., coverage depth) given the number of MinION reads produced by Nanopore sequencing to maximize the yield of high-quality SARS-CoV-2 genomes, determine the best sequencing runtime, and to be able to reuse the flow cell with the remaining nanopores available for sequencing in a new run. The best accuracy was −0.98 according to the R squared performance metric of the models. A demo version is available at https://genomicdashboard.herokuapp.com/.
Valencia-Valencia et al. (2022) PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2. PeerJ 10:e14425 https://doi.org/10.7717/peerj.14425
Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand
Background Ongoing outbreaks of H5N1 highly pathogenic avian influenza (HPAI) viruses and the emergence of the genetic-related hemagglutinin (HA) gene of reassortant H5Nx viruses currently circulating in wild birds and poultries pose a great global public health concern. In this study, we comprehensively analyzed the genetic evolution of Thai H5N1 HA and neuraminidase (NA) genes between 2003 and 2010. The H5N1 Thailand virus clade 2.3.4 was also genetically compared to the currently circulating clade 2.3.4.4 of H5Nx viruses. Methods Full-length nucleotide sequences of 178 HA and 143 NA genes of H5N1 viruses circulating between 2003 and 2010 were phylogenetically analyzed using maximum likelihood (ML) phylogenetic construction. Bayesian phylogenetic trees were reconstructed using BEAST analysis with a Bayesian Markov chain Monte Carlo (MCMC) approach. The maximum clade credibility (MCC) tree was determined, and the time of the most recent common ancestor (tMRCA) was estimated. The H5N1 HA nucleotide sequences of clade 2.3.4 Thailand viruses were phylogenetically analyzed using ML phylogenetic tree construction and analyzed for nucleotide similarities with various subtypes of reassortant H5Nx HA clade 2.3.4.4. Results ML phylogenetic analysis revealed two distinct HA clades, clade 1 and clade 2.3.4, and two distinct NA groups within the corresponding H5 clade 1 viruses. Bayesian phylogenetic reconstruction for molecular clock suggested that the Thai H5N1 HA and NA emerged in 2001.87 (95% HPD: 2001.34-2002.49) and 2002.38 (95% HPD: 2001.99-2002.82), respectively, suggesting that the virus existed before it was first reported in 2004. The Thai H5N1 HA clade 2.3.4 was grouped into corresponding clades 2.3.4, 2.3.4.1, 2.3.4.2, and 2.3.4.3, and shared nucleotide similarities to reassortant H5Nx clade 2.3.4.4 ranged from 92.4-96.8%. Phylogenetic analysis revealed monophyletic H5Nx clade 2.3.4.4 evolved from H5N1 clade 2.3.4. Conclusion H5N1 viruses existed, and were presumably introduced and circulated in avian species in Thailand, before they were officially reported in 2004. HA and NA genes continuously evolved during circulation between 2004 and 2010. This study provides a better understanding of genetic evolution with respect to molecular epidemiology. Monitoring and surveillance of emerging variants/reassortants should be continued.
Noisumdaeng et al. (2022) Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand. PeerJ 10:e14419 https://doi.org/10.7717/peerj.14419
Occurrence of Nosemosis in honey bee, Apis mellifera L. at the apiaries of East Kazakhstan
Nosemosis is the most common disease in honey bee Apis mellifera L., and is a major issue related to bee health worldwide. Therefore, the purpose of this research study was to determine prevalence of microsporidia parasitic infection of the genus Nosema spp. in East Kazakhstan Region (EKR). In the years of 2018 –2021, 394 honey bee samples were collected at 30 apiaries located in four districts of East Kazakhstan Region (Katon-Karagay, Urzhar, Borodulikhinsky, and Shemonaikhinsky). In order to determine the level of infestation, firstly, the presence of Nosema spp. spores was detected using optical microscopy, and then the average amount of spores per bee was counted using a hemocytometer. The degree of nosemosis prevalence was determined in points by means of a semi-quantitative method, and as a percentage from the total of samples and of the amount of positive tests. At the outcome of the study, microsporidia of the genus Nosema spp. were detected in 23.3% of cases (92 samples). Prevalence at its low degree was found in six samples (1.5%), at an average degree in 55 samples (14%), and at a high one in 31 samples (7.9%). This research study proved that microsporidia of the genus Nosema spp. are widely spread at the apiaries of East Kazakhstan Region in different orographic and climatic conditions. Notwithstanding that it was impossible to statistically determine any significant differences between the dependence of nosemosis prevalence and the apiary location, this indicator is actually higher in the mountainous regions than in the steppe. Concurrently, a close inverse correlation was recognized between the amount of spores in one bee and the level of infestation in bee families from the duration of the vegetation season at the apiary location. This gives grounds to assert that the environmental factors have an impact on formation and development of nosemosis. The results of the research presented in the article indicate the need for further research aimed at increasing the number of studied apiaries, and above all the use of molecular biology methods to distinguish the species that cause nosemosis infection (PCR).
Baigazanov et al. (2022) Occurrence of Nosemosis in honey bee, Apis mellifera L. at the apiaries of East Kazakhstan. PeerJ 10:e14430 https://doi.org/10.7717/peerj.14430
Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye
Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is widely distributed in the high latitude areas of Eurasia. It plays an important role in grassland ecosystem maintenance, as well as being a valuable palatable forage species for livestock and wildlife. Russian wildrye germplasm has rich phenotypic and genetic diversity and has potential for improvement through crossbreeding. In this study, fifteen Russian wildrye hybrid combinations were produced and one F1 population with 123 putative hybrids was obtained by crossing two individual plants with significant differences in nutritional characteristics and reproductive tiller number. Twelve phenotypic traits of the F1 population were measured for three consecutive years, and ten of the twelve traits were in line with the genetic characteristics of quantitative traits. Hybrid superiority was revealed among F1 hybrids in both nutritional and reproductive traits. One non-recurrent parent plant with the highest PCA-synthesis score was selected and used to make a backcross with the ‘BOZOISKY SELECT’ male parent, and 143 putative BC1 hybrids were obtained. Sixteen pairs of EST-SSR primers were randomly selected from polymorphic primers derived from different expressed tiller trait related genes. Three primer pairs that amplified both the paternal and maternal characteristic band were used to assess the purity of the F1 population, and three primer pairs (with one shared primer pair) were used to identify the BC1 population. The hybrid purity was 96.75% for the F1 population and 95.80% for the BC1 population, and the results were confirmed by self-fertility test through bagging isolation. The genetic similarity coefficients between the F1 progeny and the male parent ranged from 0.500 to 0.895, and those between the BC1 progeny and the male parent ranged from 0.667 to 0.939. A subset of individuals in the BC1 population had closer genetic distance to the recurrent parent, and genetic variation within the BC1 population decreased compared to the F1 population.
Gao et al. (2022) Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye. PeerJ 10:e14442 https://doi.org/10.7717/peerj.14442
Adult intussusception: a challenge to laparoscopic surgery?
Background Intussusception can occur at any age and is common in children but less common in adults. This study aimed to evaluate our experience of 51 adult intussusception and study the etiology, clinical manifestations, diagnosis, and treatment. Methods This analysis assessed the clinical manifestations, etiology, diagnosis, and treatment of adult intussusception in 51 adult patients at the Department of Gastrointestinal Surgery of China-Japan Union Hospital of Jilin University from January 2010 to December 2020. Results The mean age of the cohort was 54.43 ± 18.21 years, and 42 patients were diagnosed by abdominal ultrasonography and abdominal computed tomography (CT). Among them, 76.5% (39/51) had abdominal pain, 11.8% (6/51) had blood in stool, and 5.9% (3/51) had a palpable abdominal mass. Of these, 62.7% had tumors: malignant accounted for 39.2% (20/51) and benign accounted for 23.5% (12/51). CT is the preferred imaging method with a sensitivity of 92.2%, while colonoscopy provides a complementary diagnosis in patients involving the colon. All patients underwent surgical treatment, including 21.6% (11/51) laparoscopic surgery, 74.5% (38/51) open surgery, and 5.9% (3/51) intussusception reduction during the operation. The average operation time of the open group was 133.27 ± 43.75 min and the average hospital stay was 16.24 ± 12.55 days, while the average operation time of the laparoscopic group was 140.50 ± 46.15 mins, and the average hospital stay was 16.60 ± 16.98 days (P > 0.05). Conclusion Adult intussusception is a rare disease in clinic. Laparoscopic surgery can be useful and safe for adult intussusception.
Sun et al. (2022) Adult intussusception: a challenge to laparoscopic surgery?. PeerJ 10:e14495 https://doi.org/10.7717/peerj.14495
Trichoderma longibrachiatum TG1 increases endogenous salicylic acid content and antioxidants activity in wheat seedlings under salinity stress
Several studies have reported the deleterious effects of excessive salt stress on Triticum aestivum L. seedlings. Seed pretreatment with exogenous salicylic acid (SA) enhances plants to tolerate salt stress. Herein, the present study aims to investigate the potential of plant-growth-promoting fungus Trichoderma longibrachiatum (TG1) to increase the plant growth and enhance the salicylic acid (SA) contents and antioxidants activity in wheat seedlings under different concentrations of salt stress. Wheat seeds were pretreated in TG1 spore suspension before exposure to different salt stresses. Compared with 0, 50, 100, 150 salt stresses, the TG1 and NaCl increased the wheat seeds germination rate, germination potential and germination index significantly; the shoot height and root length were increased by an average of 39.45% and 29.73%, respectively. Compared to NaCl stress across the four concentrations (0, 50, 100, and 150 mM), the TG1 treated wheat seedlings increased SA concentration and phenylalanine ammonia-lyase activity (PAL) by an average of 55.87% and 24.10% respectively. In addition, the TG1+NaCl-treated seedlings increased superoxide dismutase (SOD), peroxidases (POD), and catalase (CAT) activities in the shoot by an average of 47.68%, 23.68%, and 38.65% respectively compared to NaCl-stressed seedlings. Significantly, the genes, SOD, CAT, and POD were relatively up-regulated in the salt-tolerant TG1-treated seedlings at all NaCl concentrations in comparison to the control. Wheat seedlings treated with TG1+NaCl increased the transcript levels of SOD, POD and CAT by 1.35, 1.85 and 1.04-fold at 50 mM NaCl concentration, respectively, compared with 0 mM NaCl concentration. Our results indicated that seeds pretreatment with TG1 could increase endogenous SA of plants and promote seedling growth under salt stress by improving enzymatic antioxidant activities and gene expression.
Boamah et al. (2022) Trichoderma longibrachiatum TG1 increases endogenous salicylic acid content and antioxidants activity in wheat seedlings under salinity stress. PeerJ 10:e12923 https://doi.org/10.7717/peerj.12923
Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential
Background Pea eggplant (Solanum torvum Swartz) commonly known as turkey berry or ‘terung pipit’ in Malay is a vegetable plant widely consumed by the local community in Malaysia. The shrub bears pea-like turkey berry fruits (TBFs), rich in phytochemicals of medicinal interest. The TBF phytochemicals hold a wide spectrum of pharmacological properties. In this study, the TBF phytochemicals’ potential inhibitory properties were evaluated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of the Coronavirus disease 2019 (COVID-19). The TBF polyphenols were screened against SARS-CoV receptors via molecular docking and the best receptor-ligand complex was validated further by molecular dynamics (MD) simulation. Method The SARS-CoV receptor structure files (viral structural components) were retrieved from the Protein Data Bank (PDB) database: membrane protein (PDB ID: 3I6G), main protease (PDB ID: 5RE4), and spike glycoproteins (PDB ID: 6VXX and 6VYB). The receptor binding pocket regions were identified by Discovery Studio (BIOVIA) for targeted docking with TBF polyphenols (genistin, kaempferol, mellein, rhoifolin and scutellarein). The ligand and SARS-CoV family receptor structure files were pre-processed using the AutoDock tools. Molecular docking was performed with the Lamarckian genetic algorithm using AutoDock Vina 4.2 software. The best pose (ligand-receptor complex) from the molecular docking analysis was selected based on the minimum binding energy (MBE) and extent of structural interactions, as indicated by BIOVIA visualization tool. The selected complex was validated by a 100 ns MD simulation run using the GROMACS software. The dynamic behaviour and stability of the receptor-ligand complex were evaluated by the root mean square displacement (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), solvent accessible surface volume (SASV) and number of hydrogen bonds. Results At RMSD = 0, the TBF polyphenols showed fairly strong physical interactions with SARS-CoV receptors under all possible combinations. The MBE of TBF polyphenol-bound SARS CoV complexes ranged from −4.6 to −8.3 kcal/mol. Analysis of the structural interactions showed the presence of hydrogen bonds, electrostatic and hydrophobic interactions between the receptor residues (RR) and ligands atoms. Based on the MBE values, the 3I6G-rhoifolin (MBE = −8.3 kcal/mol) and 5RE4-genistin (MBE = −7.6 kcal/mol) complexes were ranked with the least value. However, the latter showed a greater extent of interactions between the RRs and the ligand atoms and thus was further validated by MD simulation. The MD simulation parameters of the 5RE4-genistin complex over a 100 ns run indicated good structural stability with minimal flexibility within genistin binding pocket region. The findings suggest that S. torvum polyphenols hold good therapeutics potential in COVID-19 management.
Govender et al. (2022) Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential. PeerJ 10:e14168 https://doi.org/10.7717/peerj.14168
Supplementation of banana peel powder for the development of functional broiler nuggets
Banana peel powder is considered one of the most nutritive and effective waste product to be utilized as a functional additive in the food industry. This study aimed to determine the impact of banana peel powder at concentrations of 2%, 4%, and 6% on the nutritional composition, physicochemical parameters, antioxidant potential, cooking properties, microbial count, and organoleptic properties of functional nuggets during storage at refrigeration temperature for 21 days. Results showed a significant increase in nutritional content including ash and crude fiber ranging from 2.52 ± 0.017% to 6.45 ± 0.01% and 0.51 ± 0.01% to 2.13 ± 0.01%, respectively, whereas a significant decrease was observed in crude protein and crude fat ranging from 13.71 ± 0.02% to 8.92 ± 0.02% and 9.25 ± 0.02% to 4.51 ± 0.01%, respectively. The incorporation of banana peel powder significantly improved the Water Holding Capacity from 5.17% to 8.37%, cooking yield from 83.20 ± 0.20% to 87.73 ± 0.16% and cooking loss from 20.19 ± 0.290% to 13.98 ± 0.15%. Antioxidant potential was significantly improved as TPC of functional nuggets increased ranging from 3.73 ± 0.02 mg GAE/g to 8.53 ± 0.02 mg GAE/g while a decrease in TBARS (0.18 ± 0.02 mg malonaldehyde/kg to 0.14 ± 0.02 mg malonaldehyde/kg) was observed. Furthermore, functional broiler nuggets depicted a significantly reduced total plate count (3.06–4.20 × 105 CFU/g) than control, which is likely due to high amounts of phenolic compounds in BPP. Broiler nuggets supplemented with 2% BPP (T1) received the greatest sensory scores in terms of flavour, tenderness, and juiciness. Results of current study revealed the potential of BPP to be utilized as an effective natural source of fibre supplementation in food products along with enhanced antioxidant and anti-microbial properties.
Akram et al. (2022) Supplementation of banana peel powder for the development of functional broiler nuggets. PeerJ 10:e14364 https://doi.org/10.7717/peerj.14364
Correlation between religion, spirituality and perception of healthcare services utilisation in Poland during COVID-19 pandemic
Background The worldwide transmission of SARS CoV-2 caused the COVID-19 pandemic and had an impact on healthcare provision. The disruption of reliance on the health system during the COVID-19 pandemic posed a clear threat to public trust. Religiosity, like spirituality, is believed to have a positive influence on people’s lives, enabling them to cope with illness, stress, and sudden life changes. In practice, although the terms religiosity and spirituality have similar meanings and are related, they are not identical concepts. The aim of this study is to compare the perceptions of the accessibility and quality of healthcare services provided before and during the COVID-19 pandemic in Poland by religious/spiritual people compared to those for whom religion and spirituality have little or no importance in their lives. Methodology This cross-sectional study was based on the authors’ questionnaire, carried out during the third wave of the COVID-19 pandemic in Poland. Participants in the study were people living in various regions of Poland over 18 who were willing to complete the questionnaire voluntarily. The number of people sampled was two hundred and sixty-four. Convenience sampling method was used for this study. Statistical calculations were performed using Statistica 13 software from TIBCO and PQStat from PQStat Software and were based on the Kruskal-Wallis test, multiple regression model, the chi2 test of independence or the Mann-Whitney test. The result was considered statistically significant when p < α. The significance level was taken as α = 0.05. Results Two hundred and sixty-three respondents answered the questionnaire. Among them, 181 (69%) were women, and 82 (31%) were men. It was shown that religion is more important for women than for men and women who report a high role of religion in their lives rated the quality of healthcare services better before and during the COVID-19 pandemic. It was also concluded that religious people for whom religion played a major role and those who were helped by spiritual life rated accessibility and quality higher both before and during the pandemic. Conclusions Religious/spiritual people, through their more positive attitudes towards the world, were thought to rate access and quality of healthcare services better. Regardless of religious affiliation, the help of spiritual life during the pandemic or the importance of religion in life in all respondents, perception of healthcare services utilisation were decreased by the pandemic. This prompts thoughts on the implementation of spiritual assistance as a supportive measure to mitigate the effects of the pandemic.
Tuczyńska et al. (2022) Correlation between religion, spirituality and perception of healthcare services utilisation in Poland during COVID-19 pandemic. PeerJ 10:e14376 https://doi.org/10.7717/peerj.14376