Gene ssa-miR-301a-3p improves rainbow trout (Oncorhynchus mykiss) resistance to heat stress by targeting hsp90b2
Rainbow trout (Oncorhynchus mykiss) is a cold-water fish that is commonly harmed by high temperatures. MicroRNAs (miRNAs) are being investigated intensively because they act as essential metabolic regulators and have a role in the heat stress response. Although there have been numerous studies on rainbow trout heat stress, research on miRNA implicated in rainbow trout heat stress is quite restricted. Rainbow trout were sampled at 18 and 24 °C, respectively, to examine the mechanism of miRNA under heat stress, and we identified a heat stress-induced miRNA, ssa-miR-301a-3p, for further investigation based on our bioinformatics analysis of rainbow trout small RNA sequencing data. Bioinformatics research suggested that hsp90b2 is a probable target gene for ssa-miR-301a-3p. QRT-PCR was used to confirm the expression levels of ssa-miR-301a-3p and hsp90b2. Meanwhile, the dual-luciferase reporter assay was employed to validate the ssa-miR-301a-3p-hsp90b2 targeted connection. The results indicated that at 24 °C, the relative expression of ssa-miR-301a-3p was considerably lower than at 18 °C. On the other hand, hsp90b2 expression, followed the opposite pattern. The binding of ssa-miR-301a-3p to the 3′-UTR of hsp90b2 resulted in a substantial decrease in luciferase activity. The findings showed that ssa-miR-301a-3p was implicated in heat stress, and our findings provide fresh insights into the processes of miRNA in response to heat stress in rainbow trout.
Liu et al. (2022) Gene ssa-miR-301a-3p improves rainbow trout (Oncorhynchus mykiss) resistance to heat stress by targeting hsp90b2. PeerJ 10:e13476 https://doi.org/10.7717/peerj.13476
G6PD and HBB polymorphisms in the Senegalese population: prevalence, correlation with clinical malaria
Background Host genetic factors contribute to the variability of malaria phenotypes and can allow a better understanding of mechanisms involved in susceptibility and/or resistance to Plasmodium falciparum infection outcomes. Several genetic polymorphisms were reported to be prevalent among populations living in tropical malaria-endemic regions and induce protection against malaria. The present study aims to investigate the prevalence of HBB (chr11) and G6PD (chrX) deficiencies polymorphisms among Senegalese populations and their associations with the risk for severe Plasmodium falciparum malaria occurrence. Methods We performed a retrospective study with 437 samples, 323 patients recruited in hospitals located in three different endemic areas where malaria episodes were confirmed and 114 free malaria controls. The patients enrolled were classified into two groups: severe malaria (SM) (153 patients) and uncomplicated malaria (UM) (170 patients). PCR and DNA sequencing assessed host genetic polymorphisms in HBB and G6PD. Using a multivariate regression and additive model, estimates of the impact of human HBB and G6PD polymorphisms on malaria incidence were performed. Results Six frequent SNPs with minor allele frequencies (MAF) > 3% were detected in the HBB gene (rs7946748, rs7480526, rs10768683, rs35209591, HbS (rs334) and rs713040) and two in the G6PD gene (rs762515 and rs1050828 (G6PD-202 G > A). Analysis of selected HbS polymorphism showed significant association with protective effect against severe malaria with a significant p-value = 0.033 (OR 0.38, 95% CI [0.16–0.91]) for SM vs. UM comparison. Surprisingly, our study did not identify the protective effect of variant HbC polymorphism against severe malaria. Finally, we found some of the polymorphisms, like HbS (rs334), are associated with age and biological parameters like eosinophils, basophils, lymphocytes etc. Conclusion Our data report HBB and G6PD polymorphisms in the Senegalese population and their correlation with severe/mild malaria and outcome. The G6PD and HBB deficiencies are widespread in West Africa endemic malaria regions such as The Gambia, Mali, and Burkina Faso. The study shows the critical role of genetic factors in malaria outcomes. Indeed, genetic markers could be good tools for malaria endemicity prognosis.
Thiam et al. (2022) G6PD and HBB polymorphisms in the Senegalese population: prevalence, correlation with clinical malaria. PeerJ 10:e13487 https://doi.org/10.7717/peerj.13487
Characteristics and risk factors of infections in patients with HBV-related acute-on-chronic liver failure: a retrospective study
Background Acute-on-chronic liver failure (ACLF) is a syndrome characterized by acute decompensation, organ failures, and high short-term mortality whose main cause in China is the Hepatitis B virus (HBV). Moreover, one of the most important causes of morbidity and mortality in HBV-ACLF patients is bacterial infection. Therefore, we investigate the clinical features, risk factors, prophylaxis and management of infections in patients with HBV-ACLF. Methods We conducted a retrospective analysis of 539 patients with HBV-ACLF in Wuhan Tongji Hospital from October 2015 to May 2018. Differences among groups were compared with Student’s t test, Mann–Whitney U test, χ2 test, or Fisher exact test as appropriate. Univariate and Multivariate logistic regression analysis was used for modeling the relationship between infection and clinical characteristics of HBV-ACLF. Results In total 58.81% (317/539) of patients with HBV-ACLF became complicated with infections, and the most common types were spontaneous bacterial peritonitis, urinary tract infection and pulmonary infection. Additionally, 32.18% (102/317) of patients suffered multi-organ infections, and 95.73% (516/539) of patients received anti-infective therapy. We detected a total of 202 isolates in all infected patients, and Escherichia coli (36.14%, 73/202) was the most common causative organism. Moreover, antibiotic susceptibility test patterns showed that 52.97% (107/202) of pathogens were MDR bacteria and 4.95% (10/202) were XDR bacteria. Univariate analysis indicated that patients with infection had a higher proportion of females, taking alcohol, diuretics, hepatic encephalopathy (HE), hepatorenal syndrome (HS), cirrhosis, a long-time in bed and mechanical ventilation, lower prothrombin activity (PTA), alanine aminotransferase (ALT), albumin, total cholesterol (TC), estimated glomerular filtration rate (eGFR), hemoglobin (Hb) and platelet (PLT) and higher age, model for end-stage liver disease (MELD) scores and ACLF grade than patients without infection. Multivariate logistic regression analysis showed that taking alcohol, HE, HS, cirrhosis, albumin and eGFR were risk factors for the development of infection. Conclusions Bacterial infections were very common in patients with HBV-ACLF. Taking alcohol, the occurrence of complications (HE, HS and cirrhosis), hypoalbuminemia and poor renal function often predict the higher prevalence of infections in patients with HBV-ACLF. It is important to focus on exploring the early recognition of infection and early intervention of those risk factors in patients with HBV-ACLF.
Zhang et al. (2022) Characteristics and risk factors of infections in patients with HBV-related acute-on-chronic liver failure: a retrospective study. PeerJ 10:e13519 https://doi.org/10.7717/peerj.13519
Soil mineralized carbon drives more carbon stock in coniferous-broadleaf mixed plantations compared to pure plantations
Forest soil carbon (C) sequestration has an important effect on global C dynamics and is regulated by various environmental factors. Mixed and pure plantations are common afforestation choices in north China, but how forest type and environmental factors interact to affect soil C stock remains unclear. We hypothesize that forest type changes soil physicochemical properties and surface biological factors, and further contributes to soil active C components, which together affect soil C sequestration capacity and C dynamic processes. Three 46-year-old 25 m × 25 m pure Pinus tabulaeformis forests (PF) and three 47-year-old 25 m × 25 m mixed coniferous-broadleaf (Pinus tabulaeformis-Quercus liaotungensis) forests (MF) were selected as the two treatments and sampled in August 2016. In 2017, soil temperature (ST) at 10 cm were measured every 30 min for the entire vegetation season. Across 0–50 cm (five soil layers, 10 cm per layer), we also measured C components and environmental factors which may affect soil C sequestration, including soil organic carbon (SOC), soil total nitrogen (STN), dissolved organic carbon (DOC), microbial biomass carbon (MBC), soil moisture (SM) and soil pH. We then incubated samples for 56 days at 25 °C to monitor the C loss through CO2 release, characterized as cumulative mineralization carbon (CMC) and mineralized carbon (MC). Our results indicate that ST, pH, SM and litter thickness were affected by forest type. Average SOC stock in MF was 20% higher than in PF (MF: 11.29 kg m−2; PF: 13.52 kg m−2). Higher CMC under PF caused more soil C lost, and CMC increased 14.5% in PF (4.67 g kg−1 soil) compared to MF (4.04 g kg−1 soil) plots over the two-month incubation period. SOC stock was significantly positively correlated with SM (p < 0.001, R2 = 0.43), DOC (p < 0.001, R2 = 0.47) and CMC (p < 0.001, R2 = 0.33), and significantly negatively correlated with pH (p < 0.001, R2 = −0.37) and MC (p < 0.001, R2 = −0.32). SOC stock and litter thickness may have contributed to more DOC leaching in MF, which may also provide more C source for microbial decomposition. Conversely, lower SM and pH in MF may inhibit microbial activity, which ultimately makes higher MC and lower CMC under MF and promotes C accumulation. Soil mineralized C drives more C stock in coniferous-broadleaf mixed plantations compared to pure plantations, and CMC and MC should be considered when soil C balance is assessed.
Hao et al. (2022) Soil mineralized carbon drives more carbon stock in coniferous-broadleaf mixed plantations compared to pure plantations. PeerJ 10:e13542 https://doi.org/10.7717/peerj.13542
A comprehensive drought monitoring method integrating multi-source data
Droughts are the most expensive natural disasters on the planet. As a result of climate change and human activities, the incidence and impact of drought have grown in China. Timely and effective monitoring of drought is crucial for water resource management, drought mitigation, and national food security. In this study, we constructed a comprehensive drought index (YCDI) suitable for the Yellow River Basin using principal component analysis and the entropy weight-AHP method, which integrated a standardized precipitation evapotranspiration index (SPEI), self-calibrating Palmer drought severity index (scPDSI), vegetation condition index (VCI), and standardized water storage index (SWSI). SWSI is calculated by the terrestrial water storage anomaly (TWSA), which can more comprehensively reflect the impact of surface water resources on drought (as compared with soil moisture-based indexes). The study results showed that: (1) compared with single drought index, YCDI has stronger ability to monitor drought process. In terms of time scale and drought degree, the monitoring results based on YCDI were similar with data presented in the China Flood and Drought Bulletin and Meteorological Drought Yearbook, reaching ~87% and ~69%, respectively. The correlation between drought intensity and crop harvest area was 0.56. (2) By the combined analysis of the Mann-Kendall test and Moving T test, it was found that the abrupt change of YCDI index at the time of 2009, mainly due to the precipitation in 2009 reached the lowest value in the past 30 years in northern China and extreme high temperature weather. (3) The YCDI of Henan and Shandong provinces in the middle and lower reaches of the basin decreased more significantly, with the maximum value reaching 0.097/yr, while the index in the upper reaches showed an increasing trend with the maximum rate of 0.096/yr. (4) The frequency of mild drought, moderate drought, severe drought and extreme drought in the Yellow River basin during the study period was 15.84%, 12.52%, 4.03% and 0.97%, respectively. Among them, the highest frequency of droughts occurred in Ningxia, Inner Mongolia and central Shaanxi provinces. Drought causation in the Yellow River basin is more influenced by human activities than climate change in the middle and lower reaches, while climate change is the main factor in the upper reaches. Overall, YCDI is a reliable indicator for monitoring the spatial and temporal evolution of drought in the Yellow River basin, and it can be used for monitoring soil moisture changes and vegetation dynamics, which can provide scientific guidance for regional drought governance.
Spatial and Geographic Information Science
Shi et al. (2022) A comprehensive drought monitoring method integrating multi-source data. PeerJ 10:e13560 https://doi.org/10.7717/peerj.13560
Telomere-to-telomere genome assembly of Phaeodactylum tricornutum
Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes.
Giguere et al. (2022) Telomere-to-telomere genome assembly of Phaeodactylum tricornutum. PeerJ 10:e13607 https://doi.org/10.7717/peerj.13607
Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity
Background Interleukin-18 (IL-18) is prone to form multimers resulting in inactive aggregates, making this cytokine unstable for clinical use. Therefore, mutations have been introduced into recombinant IL-18 to overcome this issue. Methods To prevent the formation of disulfide bonds between the IL-18 molecules, multiple mutations targeting surface cysteines (C38, C68, C76, and C127) were introduced into our previously modified human IL-18 double mutant E6K+T63A (IL-18 DM) by direct gene synthesis. The open reading frames of IL-18 wild-type (WT), IL-18 DM, and IL-18 multiple mutant E6K+T63A+C38S+C68S+C76S+C127S (IL-18 DM1234) were inserted in the pET28a expression vector and transformed into Escherichia coli Rosetta2 (DE3) pLysS cells for protein production. The inclusion bodies of WT and mutated IL-18 were extracted by sonication and refolded by stepwise dialysis using 8 M urea as the starting concentration. The refolded IL-18 proteins were tested for aggregation using the ProteoStat protein aggregation assay. Their activity was also investigated by treating NK-92MI cells with each IL-18 at concentrations of 75, 150, and 300 ng/ml with 0.5 ng/ml of human IL-12 and interferon-gamma (IFN-γ) levels in the supernatant were evaluated using ELISA. The structure of modified IL-18 was visualized using molecular dynamics (MD) simulations. Results IL-18 DM1234 exhibited the lowest aggregation signal, approximately 1.79- and 1.63-fold less than that of the WT and IL-18 DM proteins. Additionally, the IFN-γ inducing activity of IL-18 DM1234 was about 10 and 2.8 times higher than that of the WT and IL-18 DM, respectively. MD simulations revealed that binding site I of IL-18 DM1234 was altered mainly due to surface cysteine replacement with serine (C-to-S substitution). This is the first report showing that C-to-S substitutions in IL-18 improved its activity and stability, suggesting the use of this modified IL-18 for medical purposes in the future.
Saetang et al. (2022) Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity. PeerJ 10:e13626 https://doi.org/10.7717/peerj.13626
Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2
Background The COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions. Methods To gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein’s receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics—generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant. Results Though mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2’s N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface.
Antony et al. (2022) Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2. PeerJ 10:e13680 https://doi.org/10.7717/peerj.13680
The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents
Background Extensive literature revealed the relations of depression with behavioral inhibition system (BIS) and behavioral activation system (BAS) as vulnerability and with resilience separately. Besides, the concept of resilience is still broad and ambiguous. Thus, this study aimed to reveal the mediation of two aspects of resilience: trait and process, in the relations of BIS and BAS to depression among adolescents. Methods The data set used in this study was a cross-sectional survey among 965 adolescents. The obtained data from the self-reported questionnaires used in this study were as below: Depression Serf-Rating Scale for Children (DSRS-C), Behavioral Inhibition and Behavioral Activation System Scale (BIS/BASS), and Bidimensional Resilience Scale (BRS). Structural equation modeling (SEM) was conducted to verify the hypothesized relations among BIS/BAS, trait and behavior resilience, and depressive symptoms. Results The obtained indices of fit from SEM were good or sufficient (χ2 = 562.911, df = 96, p < 0.001; CFI = 0.925; NFI = 0.913; RMSEA = 0.073, 90% CI [0.067, 0.079]; SRMR = 0.066). And the modeling showed that both BIS/BAS directly and indirectly influenced to depression. The indirect effects of BIS/BAS were mediated only trait resilience except the indirect effect of BIS via behavioral resilience. Discussion Our results suggested that trait resilience played a significant mediation role in the relationships between BIS/BAS and depression. Trait but not process resilience could be considered suitable as an intervention target in line with decreasing depression.
Masuyama et al. (2022) The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents. PeerJ 10:e13687 https://doi.org/10.7717/peerj.13687
Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus
Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
Du et al. (2022) Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus. PeerJ 10:e13689 https://doi.org/10.7717/peerj.13689