PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Gene ssa-miR-301a-3p improves rainbow trout (Oncorhynchus mykiss) resistance to heat stress by targeting hsp90b2
items: G6PD and HBB polymorphisms in the Senegalese population: prevalence, correlation with clinical malaria
items: Characteristics and risk factors of infections in patients with HBV-related acute-on-chronic liver failure: a retrospective study
items: Soil mineralized carbon drives more carbon stock in coniferous-broadleaf mixed plantations compared to pure plantations
items: A comprehensive drought monitoring method integrating multi-source data
items: Telomere-to-telomere genome assembly of Phaeodactylum tricornutum
items: Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity
items: 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
items: The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents
items: Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus

Gene ssa-miR-301a-3p improves rainbow trout (Oncorhynchus mykiss) resistance to heat stress by targeting hsp90b2
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Zhe Liu
creator: Fang Ma
creator: Yujun Kang
creator: Xiaoxia Liu
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.13476
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2021-11-26
date accepted: 2022-05-01
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Zhe
author list: Agent
  family name: Ma
  given name: Fang
author list: Agent
  family name: Kang
  given name: Yujun
author list: Agent
  family name: Liu
  given name: Xiaoxia
doi: 10.7717/peerj.13476
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Liu et al.
attribution name: Liu et al.

G6PD and HBB polymorphisms in the Senegalese population: prevalence, correlation with clinical malaria
type: item
type: AcademicArticle
description: 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 correl…
format: application/pdf
format: text/html
creator: Fatou Thiam
creator: Gora Diop
creator: Cedric Coulonges
creator: Céline Derbois
creator: Babacar Mbengue
creator: Alassane Thiam
creator: Cheikh Momar Nguer
creator: Jean Francois Zagury
creator: Jean-Francois Deleuze
creator: Alioune Dieye
subject: Genetics
subject: Parasitology
subject: Epidemiology
subject: Infectious Diseases
subject: Medical Genetics
description: doi:10.7717/peerj.13487
publisher: PeerJ Inc.
rights: © 2022 Thiam et al.
abstract: 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 correl…
bibliographic citation: 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
date submitted: 2021-10-11
date accepted: 2022-05-03
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thiam
  given name: Fatou
author list: Agent
  family name: Diop
  given name: Gora
author list: Agent
  family name: Coulonges
  given name: Cedric
author list: Agent
  family name: Derbois
  given name: Céline
author list: Agent
  family name: Mbengue
  given name: Babacar
author list: Agent
  family name: Thiam
  given name: Alassane
author list: Agent
  family name: Nguer
  given name: Cheikh Momar
author list: Agent
  family name: Zagury
  given name: Jean Francois
author list: Agent
  family name: Deleuze
  given name: Jean-Francois
author list: Agent
  family name: Dieye
  given name: Alioune
doi: 10.7717/peerj.13487
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Thiam et al.
attribution name: Thiam et al.

Characteristics and risk factors of infections in patients with HBV-related acute-on-chronic liver failure: a retrospective study
type: item
type: AcademicArticle
description: 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 gr…
format: application/pdf
format: text/html
creator: Qian Zhang
creator: Baoxian Shi
creator: Liang Wu
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
description: doi:10.7717/peerj.13519
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: 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 gr…
bibliographic citation: 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
date submitted: 2021-11-30
date accepted: 2022-05-09
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Qian
author list: Agent
  family name: Shi
  given name: Baoxian
author list: Agent
  family name: Wu
  given name: Liang
doi: 10.7717/peerj.13519
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Soil mineralized carbon drives more carbon stock in coniferous-broadleaf mixed plantations compared to pure plantations
type: item
type: AcademicArticle
description: 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 h…
format: application/pdf
format: text/html
creator: Zhenzhen Hao
creator: Zhanjun Quan
creator: Yu Han
creator: Chen Lv
creator: Xiang Zhao
creator: Wenjie Jing
creator: Linghui Zhu
creator: Junyong Ma
subject: Plant Science
subject: Soil Science
subject: Climate Change Biology
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.13542
publisher: PeerJ Inc.
rights: © 2022 Hao et al.
abstract: 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 h…
bibliographic citation: 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
date submitted: 2021-03-19
date accepted: 2022-05-15
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Zhenzhen
author list: Agent
  family name: Quan
  given name: Zhanjun
author list: Agent
  family name: Han
  given name: Yu
author list: Agent
  family name: Lv
  given name: Chen
author list: Agent
  family name: Zhao
  given name: Xiang
author list: Agent
  family name: Jing
  given name: Wenjie
author list: Agent
  family name: Zhu
  given name: Linghui
author list: Agent
  family name: Ma
  given name: Junyong
doi: 10.7717/peerj.13542
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Hao et al.
attribution name: Hao et al.

A comprehensive drought monitoring method integrating multi-source data
type: item
type: AcademicArticle
description: 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 st…
format: application/pdf
format: text/html
creator: Xiaoliang Shi
creator: Hao Ding
creator: Mengyue Wu
creator: Mengqi Shi
creator: Fei Chen
creator: Yi Li
creator: Yuanqi Yang
subject: Ecohydrology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13560
publisher: PeerJ Inc.
rights: © 2022 Shi et al.
abstract: 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 st…
bibliographic citation: Shi et al. (2022) A comprehensive drought monitoring method integrating multi-source data. PeerJ 10:e13560 https://doi.org/10.7717/peerj.13560
date submitted: 2022-03-10
date accepted: 2022-05-19
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Xiaoliang
author list: Agent
  family name: Ding
  given name: Hao
author list: Agent
  family name: Wu
  given name: Mengyue
author list: Agent
  family name: Shi
  given name: Mengqi
author list: Agent
  family name: Chen
  given name: Fei
author list: Agent
  family name: Li
  given name: Yi
author list: Agent
  family name: Yang
  given name: Yuanqi
doi: 10.7717/peerj.13560
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Shi et al.
attribution name: Shi et al.

Telomere-to-telomere genome assembly of Phaeodactylum tricornutum
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Daniel J. Giguere
creator: Alexander T. Bahcheli
creator: Samuel S. Slattery
creator: Rushali R. Patel
creator: Tyler S. Browne
creator: Martin Flatley
creator: Bogumil J. Karas
creator: David R. Edgell
creator: Gregory B. Gloor
subject: Bioinformatics
subject: Genomics
subject: Marine Biology
subject: Plant Science
subject: Synthetic Biology
description: doi:10.7717/peerj.13607
publisher: PeerJ Inc.
rights: © 2022 Giguere et al.
abstract: 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.
bibliographic citation: Giguere et al. (2022) Telomere-to-telomere genome assembly of Phaeodactylum tricornutum. PeerJ 10:e13607 https://doi.org/10.7717/peerj.13607
date submitted: 2021-05-11
date accepted: 2022-05-27
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giguere
  given name: Daniel J.
author list: Agent
  family name: Bahcheli
  given name: Alexander T.
author list: Agent
  family name: Slattery
  given name: Samuel S.
author list: Agent
  family name: Patel
  given name: Rushali R.
author list: Agent
  family name: Browne
  given name: Tyler S.
author list: Agent
  family name: Flatley
  given name: Martin
author list: Agent
  family name: Karas
  given name: Bogumil J.
author list: Agent
  family name: Edgell
  given name: David R.
author list: Agent
  family name: Gloor
  given name: Gregory B.
doi: 10.7717/peerj.13607
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Giguere et al.
attribution name: Giguere et al.

Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Jirakrit Saetang
creator: Niran Roongsawang
creator: Surasak Sangkhathat
creator: Supayang Piyawan Voravuthikunchai
creator: Natnaree Sangkaew
creator: Napat Prompat
creator: Teerapol Srichana
creator: Varomyalin Tipmanee
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Translational Medicine
description: doi:10.7717/peerj.13626
publisher: PeerJ Inc.
rights: © 2022 Saetang et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-03-15
date accepted: 2022-06-02
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saetang
  given name: Jirakrit
author list: Agent
  family name: Roongsawang
  given name: Niran
author list: Agent
  family name: Sangkhathat
  given name: Surasak
author list: Agent
  family name: Voravuthikunchai
  given name: Supayang Piyawan
author list: Agent
  family name: Sangkaew
  given name: Natnaree
author list: Agent
  family name: Prompat
  given name: Napat
author list: Agent
  family name: Srichana
  given name: Teerapol
author list: Agent
  family name: Tipmanee
  given name: Varomyalin
doi: 10.7717/peerj.13626
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Saetang et al.
attribution name: Saetang et al.

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
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Priya Antony
creator: Amie Jobe
creator: Ranjit Vijayan
subject: Bioinformatics
subject: Computational Biology
subject: COVID-19
description: doi:10.7717/peerj.13680
publisher: PeerJ Inc.
rights: © 2022 Antony et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-03-28
date accepted: 2022-06-14
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Antony
  given name: Priya
author list: Agent
  family name: Jobe
  given name: Amie
author list: Agent
  family name: Vijayan
  given name: Ranjit
doi: 10.7717/peerj.13680
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Antony et al.
attribution name: Antony et al.

The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Akihiro Masuyama
creator: Takahiro Kubo
creator: Hiroki Shinkawa
creator: Daichi Sugawara
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.13687
publisher: PeerJ Inc.
rights: © 2022 Masuyama et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-03-25
date accepted: 2022-06-15
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Masuyama
  given name: Akihiro
author list: Agent
  family name: Kubo
  given name: Takahiro
author list: Agent
  family name: Shinkawa
  given name: Hiroki
author list: Agent
  family name: Sugawara
  given name: Daichi
doi: 10.7717/peerj.13687
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Masuyama et al.
attribution name: Masuyama et al.

Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus
type: item
type: AcademicArticle
description: 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).
format: application/pdf
format: text/html
creator: Zhaokui Du
creator: Weida Lin
creator: Jinxing Zhu
creator: Junmin Li
subject: Agricultural Science
subject: Biochemistry
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.13689
publisher: PeerJ Inc.
rights: © 2022 Du et al.
abstract: 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).
bibliographic citation: 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
date submitted: 2021-08-31
date accepted: 2022-06-16
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Zhaokui
author list: Agent
  family name: Lin
  given name: Weida
author list: Agent
  family name: Zhu
  given name: Jinxing
author list: Agent
  family name: Li
  given name: Junmin
doi: 10.7717/peerj.13689
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Du et al.
attribution name: Du et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359