Genome-wide identification, evolution, expression, and alternative splicing profiles of peroxiredoxin genes in cotton
Peroxiredoxin (PRX) is a ubiquitous thioredoxin-dependent peroxidase that can eliminate excessive free radicals produced by stress and protect cells from oxidative damage. PRXs are also involved in reactive oxygen species (ROS)- and redox-dependent signaling by performing redox interactions with other proteins and modify their redox status. At present, PRX family identification, evolution and regulation research has been conducted in some plants; however, systematic research about this family is lacking in cotton. In this study, a total of 44 PRXs were identified in the cotton genome. Phylogenetic and conserved active site analyses showed that the PRXs were divided into six subfamilies according to the conserved site (PxxxTxxC…S…W/F) and conserved cysteinyl residues positions. Segmental duplication and polyploid events were the main methods for PRX family expansion, and the PRXs of diploid G. arboreum were the donors of PRXs in the D subgenomes of allotetraploid G. hirsutum and G. barbadense during the evolution of the PRX family. qRT-PCR analysis confirmed that cis-acting elements play important roles in regulating the expression of PRXs. Alternative splicing events occurred in GhPRX14-D that can increased the complexity of transcripts in G. hirsutum. Subcellular localization showed that most PRX members were located in chloroplasts, the cytoplasmic membrane and the nucleus. Our results provide systematic support for a better understanding of PRXs in cotton and a starting point for further studies of the specific functions of PRXs in cotton.
Feng et al. (2021) Genome-wide identification, evolution, expression, and alternative splicing profiles of peroxiredoxin genes in cotton. PeerJ 9:e10685 https://doi.org/10.7717/peerj.10685
Coding potential of circRNAs: new discoveries and challenges
The circular (circ)RNAs are a newly recognized group of noncoding (nc)RNAs. Research to characterize the functional features of circRNAs has uncovered distinctive profiles of conservation, stability, specificity and complexity. However, a new line of evidence has indicated that although circRNAs can function as ncRNAs, such as in the role of miRNA sponges, they are also capable of coding proteins. This discovery is no accident. In the last century, scientist detected the ability of translate in some virus and artificial circRNAs. Artificial circRNA translation products are usually nonfunctional, whereas natural circRNA translation products are completely different. Those new proteins have various functions, which greatly broadens the new ideas and research direction for our research. These series findings also raise questions about whether circRNA is still classified as non-coding RNA. Here, we summarize the evidence concerning translation potential of circRNAs, including synthetic and endogenous circRNA translation ability, and discuss the mechanisms of circRNA translation.
Miao et al. (2021) Coding potential of circRNAs: new discoveries and challenges. PeerJ 9:e10718 https://doi.org/10.7717/peerj.10718
Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result of major selection constraints
Background Codon usage bias analysis is a suitable strategy for identifying the principal evolutionary driving forces in different organisms. Delphinium grandiflorum L. is a perennial herb with high economic value and typical biological characteristics. Evolutionary analysis of D. grandiflorum can provide a rich resource of genetic information for developing hybridization resources of the genus Delphinium. Methods Synonymous codon usage (SCU) and related indices of 51 coding sequences from the D. grandiflorum chloroplast (cp) genome were calculated using Codon W, Cups of EMBOSS, SPSS and Microsoft Excel. Multivariate statistical analysis combined by principal component analysis (PCA), correspondence analysis (COA), PR2-plot mapping analysis and ENC plot analysis was then conducted to explore the factors affecting the usage of synonymous codons. Results The SCU bias of D. grandiflorum was weak and codons preferred A/T ending. A SCU imbalance between A/T and G/C at the third base position was revealed by PR2-plot mapping analysis. A total of eight codons were identified as the optimal codons. The PCA and COA results indicated that base composition (GC content, GC3 content) and gene expression were important for SCU bias. A majority of genes were distributed below the expected curve from the ENC plot analysis and up the standard curve by neutrality plot analysis. Our results showed that with the exception of notable mutation pressure effects, the majority of genetic evolution in the D. grandiflorum cp genome might be driven by natural selection. Discussions Our results provide a theoretical foundation for elucidating the genetic architecture and mechanisms of D. grandiflorum, and contribute to enriching D. grandiflorum genetic resources.
Duan et al. (2021) Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result of major selection constraints. PeerJ 9:e10787 https://doi.org/10.7717/peerj.10787
Prediction of state anxiety by machine learning applied to photoplethysmography data
Background As the human behavior is influenced by both cognition and emotion, affective computing plays a central role in human-machine interaction. Algorithms for emotions recognition are usually based on behavioral analysis or on physiological measurements (e.g., heart rate, blood pressure). Among these physiological signals, pulse wave propagation in the circulatory tree can be assessed through photoplethysmography (PPG), a non-invasive optical technique. Since pulse wave characteristics are influenced by the cardiovascular status, which is affected by the autonomic nervous activity and hence by the psychophysiological state, PPG might encode information about emotional conditions. The capability of a multivariate data-driven approach to estimate state anxiety (SA) of healthy participants from PPG features acquired on the brachial and radial artery was investigated. Methods The machine learning method was based on General Linear Model and supervised learning. PPG was measured employing a custom-made system and SA of the participants was assessed through the State-Trait Anxiety Inventory (STAI-Y) test. Results A leave-one-out cross-validation framework showed a good correlation between STAI-Y score and the SA predicted by the machine learning algorithm (r = 0.81; p = 1.87∙10−9). The preliminary results suggested that PPG can be a promising tool for emotions recognition, convenient for human-machine interaction applications.
Perpetuini et al. (2021) Prediction of state anxiety by machine learning applied to photoplethysmography data. PeerJ 9:e10448 https://doi.org/10.7717/peerj.10448
Municipal waste landfill as a source of polychlorinated biphenyls releases to the environment
This study aimed to investigate the impact of municipal waste landfill on polychlorinated biphenyls (PCBs) release to the environment concerning groundwater flow directions. The contents of polychlorinated biphenyls in soils, plants and water were analysed at various distances from the landfill. Thanks to low solubility PCBs in water groundwater flow direction, under the landfill, have an influence on PCBs concentration in groundwater. Strong PCBs’ sorption to organic matter caused that no affect groundwater flow directions on PCB content in soils and plants’ tissues was observed. The largest PCBs deposition zone was located 50 m from the contamination source (landfill). Tri-CB and tetra-CB homologues were capable of migration deep into the soil profile, which could be related to the geological material from which the soils under study were developed, as well as to the properties of the PCB homologues.
Environmental Contamination and Remediation
Gabryszewska et al. (2021) Municipal waste landfill as a source of polychlorinated biphenyls releases to the environment. PeerJ 9:e10546 https://doi.org/10.7717/peerj.10546
Vision of conspecifics decreases the effectiveness of ethanol on zebrafish behaviour
Aquatic organisms in pharmacology and toxicology research are often exposed to compounds in isolation prior to physiological or behavioural testing. Recent evidence suggests that the presence of conspecifics during a stressful event can modulate behavioural outcomes (called ‘social buffering’) when testing occurs within the same context. It is unknown, however, whether the social environment during exposure interacts with the efficacy of anxiety-altering substances when subsequently tested in the absence of conspecifics. In this study, zebrafish were individually exposed to habitat water or ethanol (1.0% vol/vol) while untreated conspecifics were visually present or absent during dosing. Using the novel object approach test, a validated test of boldness and anxiety-like behaviour, we observed significantly greater effects of ethanol in isolated fish, compared to fish with a view of conspecifics during dosing. These results were not explained by altered locomotion during exposure, which might otherwise increase drug uptake. This highlights the need to consider the social environment during exposure when conducting and interpreting behavioural research involving drug or toxicant exposure.
Dean et al. (2021) Vision of conspecifics decreases the effectiveness of ethanol on zebrafish behaviour. PeerJ 9:e10566 https://doi.org/10.7717/peerj.10566
Hyperglycemia in severe traumatic brain injury patients and its association with thirty-day mortality: a prospective observational cohort study in Uganda
Background Traumatic brain injury (TBI) is a growing public health concern that can be complicated with an acute stress response. This response may be assessed by monitoring blood glucose levels but this is not routine in remote settings. There is a paucity of data on the prevalence of hyperglycemia and variables associated with mortality after severe TBI in Uganda. Objective We aimed to determine the prevalence of hyperglycemia in patients with severe TBI and variables associated with 30-day mortality at Mulago National Referral Hospital in Uganda. Methods We consecutively enrolled a cohort 99 patients patients with severe TBI. Serum glucose levels were measured at admission and after 24 h. Other study variables included: mechanism of injury, CT findings, location and size of hematoma, and socio-demographics. The main outcome was mortality after 30 days of management and this was compared in patients with hyperglycemia more than 11.1 mmol/L to those without. Results Most patients (92.9%) were male aged 18–30 years (47%). Road Traffic Collisions were the most common cause of severe TBI (64.7%) followed by assault (17.1%) and falls (8.1%). Nearly one in six patients were admitted with hyperglycemia more than 11.1 mmol/L. The mortality rate in severe TBI patients with hyperglycemia was 68.8% (OR 1.47; 95% CI [0.236–9.153]; P = 0.063) against 43.7% in those without hyperglycemia. The presence of hypothermia (OR 10.17; 95% CI [1.574–65.669]; P = 0.015) and convulsions (OR 5.64; 95% CI [1.541–19.554]; P = 0.009) were significant predictors of mortality. Conclusion Hypothermia and convulsions at admission were major predictors of mortality in severe TBI. Early hyperglycemia following severe TBI appears to occur with a tendency towards high mortality. These findings justify routine glucose monitoring and could form the basis for establishing a blood sugar control protocol for such patients in remote settings.
Matovu et al. (2021) Hyperglycemia in severe traumatic brain injury patients and its association with thirty-day mortality: a prospective observational cohort study in Uganda. PeerJ 9:e10589 https://doi.org/10.7717/peerj.10589
Effectiveness of modifications to preadjusted appliance prescriptions based on racial dental characteristics assessed by the ABO Cast-Radiograph Evaluation: A propensity score matching study
Background Because racial discrepancies in dental characteristics are known to exist, designing preadjusted appliances according to racial normal occlusion data would be expected to improve treatment results. However, whether modifications based on racial characteristics can improve treatment outcomes in the clinic remains to be investigated. Methods To study the influence of prescription type on treatment outcomes, 91 patients treated with Chinese or Roth prescription appliances were selected as an initial sample. Two groups of patients were selected by propensity score matching (1:1) to limit the effects of confounding factors, including age, sex, case complexity, and extraction plan. Discrepancy Index and cervical vertebral maturation values were used to quantify case complexity and patient age, respectively. After matching, the final sample of 60 patients consisted of two groups of 30 patients each: group 1 had been treated with a Chinese prescription appliance and group 2 had been treated with a Roth prescription appliance. ABO casts and radiograph evaluation (CR-Eval) and lateral cephalograms were utilized to compare the treatment outcomes of the two groups. Results The total ABO scores of groups 1 and 2 were 22.03 and 23.87, respectively. There were no significant differences between the two groups in total ABO score or in seven other sub-scores; however, there was a significant difference between the two groups in mandibular canine alignment score. Conclusions There are no significant differences in overall treatment outcomes between the Chinese and Roth prescription appliances. The Chinese prescription yielded better alignment results in the mandibular canine for Chinese patients.
Chu et al. (2021) Effectiveness of modifications to preadjusted appliance prescriptions based on racial dental characteristics assessed by the ABO Cast-Radiograph Evaluation: A propensity score matching study. PeerJ 9:e10605 https://doi.org/10.7717/peerj.10605
Comparison of the effects of two laser photobiomodulation techniques on bio-physical properties of Zea mays L. seeds
Background Laser applications in agriculture have recently gained much interest due to improved plant characteristics following laser treatment before the sowing of seeds. In this study, maize seeds were exposed to different levels of laser treatment prior to sowing to improve their field performance. The aim of this study is to evaluate the impact of pre-sowing laser photobiomodulation on the field emergence and growth of treated maize seeds. Methods The maize seeds were first photobiomodulated with two lasers: 1) a helium-neon (He–Ne) red laser (632.8 nm), and 2) a neodymium-doped yttrium aluminum garnet (Nd:YAG) green laser (532 nm). Following three replications of randomized complete block design (RCBD), four irradiation treatments were applied (45 s, 65 s, 85 s, and 105 s) at two power intensities (2 mW/cm2 and 4 mW/cm2). Results Based on the results, maize seeds pretreated with a green laser and 2 mW/cm2 power intensity for 105 s exhibited the highest rate of seed emergence (96%) compared to the untreated control seeds with a lower seed emergence rate (62.5%). Furthermore, maize seeds treated with a red laser for 45 s showed an increased vigor index compared to the other treatment options and the control (P < 0.01). The treatment groups also showed statistically significant differences in seedling growth characteristics compared to the control group p < 0.01. The green laser produced a significant enhancement of about 24.20 cm in seedling length, 8.2 leaves/plant, and 3.4 cm in stem diameter compared to the untreated seeds. Moreover, the green laser treatment showed 57.4 days to anthesis, which was earlier than the untreated seeds (61.4 days). The results showed that the protein, oil, and starch contents of the seeds irradiated with the green laser were 17.54%, 6.18%, and 73.32%, respectively, compared to the seeds irradiated by the red laser with 16.51%, 6.33%, and 71.05%, respectively. Conclusions The photo biomodulation of maize seeds using a green laser light can improve the field emergence, seedling growth, and seed quality of the treated seed compared to the red laser treatment.
Hasan et al. (2021) Comparison of the effects of two laser photobiomodulation techniques on bio-physical properties of Zea mays L. seeds. PeerJ 9:e10614 https://doi.org/10.7717/peerj.10614
Gene signatures with predictive and prognostic survival values in human osteosarcoma
Osteosarcoma is a common malignancy seen mainly in children and adolescents. The disease is characterized by poor overall prognosis and lower survival due to a lack of predictive markers. Many gene signatures with diagnostic, prognostic, and predictive values were evaluated to achieve better clinical outcomes. Two public data series, GSE21257 and UCSC Xena, were used to identify the minimum number of robust genes needed for a predictive signature to guide prognosis of patients with osteosarcoma. The lasso regression algorithm was used to analyze sequencing data from TCGA-TARGET, and methods such as Cox regression analysis, risk factor scoring, receiving operating curve, KMplot prognosis analysis, and nomogram were used to characterize the prognostic predictive power of the identified genes. Their utility was assessed using the GEO osteosarcoma dataset. Finally, the functional enrichment analysis of the identified genes was performed. A total of twenty-gene signatures were found to have a good prognostic value for predicting patient survival. Gene ontology analysis showed that the key genes related to osteosarcoma were categorized as peptide–antigen binding, clathrin-coated endocytic vesicle membrane, peptide binding, and MHC class II protein complex. The osteosarcoma related genes in these modules were significantly enriched in the processes of antigen processing and presentation, phagocytosis, cell adhesion molecules, Staphylococcus aureus infection. Twenty gene signatures were identified related to osteosarcoma, which would be helpful for predicting prognosis of patients with OS. Further, these signatures can be used to determine the subtypes of osteosarcoma.
Qiu et al. (2021) Gene signatures with predictive and prognostic survival values in human osteosarcoma. PeerJ 9:e10633 https://doi.org/10.7717/peerj.10633