Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress
Background The rubber tree (Hevea brasiliensis) is the only species capable of producing high-quality natural rubber for commercial use, and is often subjected to various abiotic stresses in non-traditional rubber plantation areas. Superoxide dismutase (SOD) is a vital metalloenzyme translated by a SOD gene family member and acts as a first-line of protection in plant cells by catalysing the disproportionation of reactive oxygen species (ROS) to produce H2O2 and O2. However, the SOD gene family is not reported in rubber trees. Methods Here, we used hidden markov model (HMM) and BLASTP methods to identify SOD genes in the H. brasiliensis genome. Phylogenetic tree, conserved motifs, gene structures, cis elements, and gene ontology annotation (GO) analyses were performed using MEGA 6.0, MEME, TBtools, PlantCARE, and eggNOG database, respectively. HbSOD gene expression profiles were analysed using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results We identified nine HbSOD genes in the rubber tree genome, including five HbCSDs, two HbFSDs, and two HbMSDs. Phylogenetic relationship analysis classified the SOD proteins from the rubber tree and other related species into three subfamilies. The results of gene structure and conserved motif analysis illustrated that most HbSOD genes have similar exon-intron numbers and conserved motifs in the same evolutionary branch. Five hormone-related, four stress-related, and light-responsive elements were detected in the HbSODs’ promoters. HbSODs were expressed in different tissues, gradually increased with leaf development, and were abundantly expressed in mature leaves. HbCSD2 and HbCSD4 was significantly upregulated under low and high temperatures, and salt stress, except for HbCSD2, by heat. Furthermore, most HbSOD genes were significantly upregulated by drought, except HbMSD2. These findings imply that these genes may play vital roles in rubber tree stress resistance. Our results provide a basis for further studies on the functions of HbSOD genes in rubber trees and stress response mechanisms.
Yu et al. (2022) Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress. PeerJ 10:e14251 https://doi.org/10.7717/peerj.14251
Scientists’ warning of the impacts of climate change on mountains
Mountains are highly diverse in areal extent, geological and climatic context, ecosystems and human activity. As such, mountain environments worldwide are particularly sensitive to the effects of anthropogenic climate change (global warming) as a result of their unique heat balance properties and the presence of climatically-sensitive snow, ice, permafrost and ecosystems. Consequently, mountain systems—in particular cryospheric ones—are currently undergoing unprecedented changes in the Anthropocene. This study identifies and discusses four of the major properties of mountains upon which anthropogenic climate change can impact, and indeed is already doing so. These properties are: the changing mountain cryosphere of glaciers and permafrost; mountain hazards and risk; mountain ecosystems and their services; and mountain communities and infrastructure. It is notable that changes in these different mountain properties do not follow a predictable trajectory of evolution in response to anthropogenic climate change. This demonstrates that different elements of mountain systems exhibit different sensitivities to forcing. The interconnections between these different properties highlight that mountains should be considered as integrated biophysical systems, of which human activity is part. Interrelationships between these mountain properties are discussed through a model of mountain socio-biophysical systems, which provides a framework for examining climate impacts and vulnerabilities. Managing the risks associated with ongoing climate change in mountains requires an integrated approach to climate change impacts monitoring and management.
Knight (2022) Scientists’ warning of the impacts of climate change on mountains. PeerJ 10:e14253 https://doi.org/10.7717/peerj.14253
Rolling circle amplification (RCA) -based biosensor system for the fluorescent detection of miR-129-2-3p miRNA
Herein, a versatile fluorescent bioanalysis platform for sensitive and specific screening of target miRNA (miR-129-2-3p) was innovatively designed by applying target-induced rolling circle amplification (RCA) for efficient signal amplification. Specifically, miR-129-2-3p was used as a ligation template to facilitate its ligation with padlock probes, followed by an RCA reaction in the presence of phi29 DNA polymerase. The dsDNA fragments and products were stained by SYBR Green I and then detected by fluorescence spectrophotometry. As a result, miR-129-2-3p concentrations as low as 50 nM could be detected. Furthermore, the expression of miR-129-2-3p in breast cancer patients was about twice that in healthy people. Therefore, the results indicated that the RCA-based biosensor system could be a valuable platform for miRNA detection in clinical diagnosis and biomedical study.
Ye et al. (2022) Rolling circle amplification (RCA) -based biosensor system for the fluorescent detection of miR-129-2-3p miRNA. PeerJ 10:e14257 https://doi.org/10.7717/peerj.14257
Screening and identification of miRNAs regulating Tbx4/5 genes of Pampus argenteus
Background Silver pomfret (Pampus argenteus) is one of the most widely distributed and economically important pelagic fish species. However, an unique morphological feature of P. argenteus is the loss of pelvic fins, which can increase the energy requirement during food capture to some extent and is therefore not conducive to artificial culture. Tbx4/5 genes are highly conserved regulatory factors that regulate limb development in vertebrates and are in turn regulated by microRNAs (miRNAs). However, the miRNAs that directly regulate the Tbx4/5 genes in P. argenteus remain to be elucidated. Methods The Tbx4/5 genes of P. argenteus were first cloned, and the small RNA transcriptomes were sequenced by high-throughput sequencing during the critical period of the fin development at days 1, 7, and 13 of hatching. The miRNAs regulating the Tbx4/5 genes of P. argenteus were subsequently predicted by bioinformatics analysis, and the related miRNAs were verified in vitro using a dual fluorescence reporter system. Results A total of 662 miRNAs were identified, of which 257 were known miRNAs and 405 were novel miRNAs were identified. Compared to day 1, 182 miRNAs were differentially expressed (DE) on day 7, of which 77 and 105 miRNAs were downregulated and upregulated, respectively, while 278 miRNAs were DE on day 13, of which 136 and 142 miRNAs were downregulated and upregulated, respectively. Compared to day 13, four miRNAs were DE on day 7, of which three miRNAs were downregulated and one miRNA was upregulated. The results of hierarchical clustering of the miRNAs revealed that the DE genes were inversely expressed between days 1 and 7, and between days 1 and 13 of larval development, indicating that the larvae were in the peak stage of differentiation. However, the number of DE genes between days 7 and 13 of larval development was relatively small, suggesting the initiation of development. The potential target genes of the DE miRNAs were subsequently predicted, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of target genes were performed. The results suggested that the DE miRNAs were involved in growth, development, and signal transduction pathways, of which the Wnt and Fgfs signaling pathways are known to play important roles in the growth and development of fins. The results of dual fluorescence reporter assays demonstrated that miR-102, miR-301c, and miR-589 had a significant negative regulatory effect on the 3′-UTR of the Tbx4 gene, while miR-187, miR-201, miR-219, and miR-460 had a significant negative regulatory effect on the 3′-UTR of the Tbx5 gene. Altogether, the findings indicated that miRNAs play an important role in regulating the growth and development of pelvic fins in P. argenteus. This study provides a reference for elucidating the interactions between the miRNAs and target genes of P. argenteus in future studies.
Zhang et al. (2022) Screening and identification of miRNAs regulating Tbx4/5 genes of Pampus argenteus. PeerJ 10:e14300 https://doi.org/10.7717/peerj.14300
ArVirInd—a database of arboviral antigenic proteins from the Indian subcontinent
Background Studies on antigenic proteins for arboviruses are important for providing diagnostics and vaccine development. India and its neighboring countries have a huge burden of arboviral diseases. Data mining for country-specific sequences from existing bioinformatics databases is cumbersome and time-consuming. This necessitated the development of a database of antigenic proteins from arboviruses isolated from the countries of the Indian subcontinent. Methods Arboviral antigenic protein sequences were obtained from the NCBI and other databases. In silico antigenic characterization was performed (Epitope predictions) and data was incorporated into the database. The front end was designed and developed using HTML, CSS, and PHP. For the backend of the database, we have used MySQL. Results A database, named ArVirInd, is created as a repository of information on curated antigenic proteins. This enlists sequences by country and year of outbreak or origin of the viral strain. For each entry, antigenic information is provided along with functional sites, etc. Researchers can search this database by virus/protein name, country, and year of collection (or in combination) as well as peptide search for epitopes. It is available publicly via the Internet at http://www.arvirind.co.in. ArVirInd will be useful in the study of immune informatics, diagnostics, and vaccinology for arboviruses.
Atre et al. (2022) ArVirInd—a database of arboviral antigenic proteins from the Indian subcontinent. PeerJ 10:e13851 https://doi.org/10.7717/peerj.13851
Knowledge of safe handling, administration, and waste management of chemotherapeutic drugs among oncology nurses working at Khartoum Oncology Hospital, Sudan
Introduction Knowledge of chemotherapeutic drug (CD) handling, administration, and waste disposal are important among nurses involved in cancer therapy. Inadequate knowledge of the management of CD could cause environmental contamination and potential harm to patients and nurses. To assess the knowledge of safe handling, administration, and waste management of CD among oncology nurses working at Khartoum Oncology Hospital, Sudan. Methods A questionnaire was developed by a team of experts to assess the knowledge in three domains of oncology nursing practice (handling, administration, and disposal). The study involved 78 oncology nurses working in Khartoum Oncology Hospital in Sudan from April 2020. Results The mean CD knowledge score of nurses was 12.7 ± 3.9 out of 26 items in the questionnaire. For each domain, their knowledge showed poor scores related to safe handling (mean = 2.0 ± 1.5 out of eight knowledge items) and good scores for administration (mean = 6.2 ± 1.7 out of 10) and poor scores for waste disposal (mean = 4.4 ± 1.5 out of eight). Simple linear regression indicated that education level (β = 3.715, p = .008) and training (β = 0.969, p = .004) significantly predicted knowledge among nurses. Conclusion There is a significant need to enhance the knowledge and safe handling skills of CD among oncology nurses in Sudan. Implementation of strict guidelines to manage cytotoxic waste to reduce health risks and hospital contamination.
Sargidy et al. (2022) Knowledge of safe handling, administration, and waste management of chemotherapeutic drugs among oncology nurses working at Khartoum Oncology Hospital, Sudan. PeerJ 10:e14173 https://doi.org/10.7717/peerj.14173
Spatiotemporal Bayesian estimation of the number of under-reported COVID-19 cases in Victoria Australia
Having an estimate of the number of under-reported cases is crucial in determining the true burden of a disease. In the COVID-19 pandemic, there is a great need to quantify the true disease burden by capturing the true incidence rate to establish appropriate measures and strategies to combat the disease. This study investigates the under-reporting of COVID-19 cases in Victoria, Australia, during the third wave of the pandemic as a result of variation in geographic area and time. It is aimed to determine potential under-reported areas and generate the true picture of the disease in terms of the number of cases. A two-tiered Bayesian hierarchical model approach is employed to estimate the true incidence and detection rates through Bayesian model averaging. The proposed model goes beyond testing inequality across areas by looking into other covariates such as weather, vaccination rates, and access to vaccination and testing centres, including interactions and variations between space and time. This model aims for parsimony yet allows a broader range of scope to capture the underlying dynamic of the reported COVID-19 cases. Moreover, it is a data-driven, flexible, and generalisable model to a global context such as cross-country estimation and across time points under strict pandemic conditions.
Lope et al. (2022) Spatiotemporal Bayesian estimation of the number of under-reported COVID-19 cases in Victoria Australia. PeerJ 10:e14184 https://doi.org/10.7717/peerj.14184
Ontogenetic growth in the crania of Exaeretodon argentinus (Synapsida: Cynodontia) captures a dietary shift
Background An ontogenetic niche shift in vertebrates is a common occurrence where ecology shifts with morphological changes throughout growth. How ecology shifts over a vertebrate’s lifetime is often reconstructed in extant species—by combining observational and skeletal data from growth series of the same species—because interactions between organisms and their environment can be observed directly. However, reconstructing shifts using extinct vertebrates is difficult and requires well-sampled growth series, specimens with relatively complete preservation, and easily observable skeletal traits associated with ecologies suspected to change throughout growth, such as diet. Methods To reconstruct ecological changes throughout the growth of a stem-mammal, we describe changes associated with dietary ecology in a growth series of crania of the large-bodied (∼2 m in length) and herbivorous form, Exaeretodon argentinus (Cynodontia: Traversodontidae) from the Late Triassic Ischigualasto Formation, San Juan, Argentina. Nearly all specimens were deformed by taphonomic processes, so we reconstructed allometric slope using a generalized linear mixed effects model with distortion as a random effect. Results Under a mixed effects model, we find that throughout growth, E. argentinus reduced the relative length of the palate, postcanine series, orbits, and basicranium, and expanded the relative length of the temporal region and the height of the zygomatic arch. The allometric relationship between the zygomatic arch and temporal region with the total length of the skull approximate the rate of growth for feeding musculature. Based on a higher allometric slope, the zygoma height is growing relatively faster than the length of the temporal region. The higher rate of change in the zygoma may suggest that smaller individuals had a crushing-dominated feeding style that transitioned into a chewing-dominated feeding style in larger individuals, suggesting a dietary shift from possible faunivory to a more plant-dominated diet. Dietary differentiation throughout development is further supported by an increase in sutural complexity and a shift in the orientation of microwear anisotropy between small and large individuals of E. argentinus. A developmental transition in the feeding ecology of E. argentinus is reflective of the reconstructed dietary transition across Gomphodontia, wherein the earliest-diverging species are inferred as omnivorous and the well-nested traversodontids are inferred as herbivorous, potentially suggesting that faunivory in immature individuals of the herbivorous Traversodontidae may be plesiomorphic for the clade.
Wynd et al. (2022) Ontogenetic growth in the crania of Exaeretodon argentinus (Synapsida: Cynodontia) captures a dietary shift. PeerJ 10:e14196 https://doi.org/10.7717/peerj.14196
Telomerase reverse transcriptase promotes angiogenesis in neonatal rats after hypoxic-ischemic brain damage
Background Angiogenesis is an endogenous repair mechanism following hypoxic-ischemic brain damage (HIBD). Interestingly, recent studies have shown that angiogenesis can be regulated by telomerase reverse transcriptase (TERT), a critical component of telomerase. As telomerase reverse transcriptase can promote angiogenesis after stroke, we hypothesized that it could also promote angiogenesis after HIBD. To test this hypothesis, we developed in vivo and in vitro HIBD models in neonatal rats. Methods TERT was overexpressed by lentivirus and adenovirus infection, and levels were measured using quantitative real-time polymerase chain reaction. We used a cell counting kit to quantify the proliferation rate of brain microvascular endothelial cells (BMECs), and immunofluorescence staining to measure CD34 expression levels. A microvessel formation assay was used to evaluate angiogenesis. Blood-brain barrier (BBB) integrity was assessed using immunohistochemical staining for ZO-1 and Evans Blue staining. Lastly, the expression level of Notch-1 was measured by western blotting. Results Overexpression of TERT promoted the proliferation of BMECs after hypoxic-ischemic damage in vitro. TERT overexpression increased the formation of microvessels in the neonatal brain after HIBD both in vivo and in vitro. Overexpression of TERT improved BBB integrity in the brains of neonatal rats after HIBD. In addition, the expression level of Notch-1 was increased in BMECs following oxygen glucose deprivation, and overexpression of TERT further increased Notch-1 expression levels in BMECs following oxygen glucose deprivation. Discussion Our results reveal that telomerase reverse transcriptase promotes angiogenesis and maintains the integrity of the blood-brain barrier after neonatal hypoxic-ischemic brain damage. Furthermore, the Notch-1 signaling pathway appears to contribute to the angiogenic function of telomerase reverse transcriptase. This protective effect of telomerase reverse transcriptase opens new horizons for future investigations aimed at uncovering the full potential of telomerase reverse transcriptase as a promising new target for the treatment of hypoxic-ischemic encephalopathy.
Li et al. (2022) Telomerase reverse transcriptase promotes angiogenesis in neonatal rats after hypoxic-ischemic brain damage. PeerJ 10:e14220 https://doi.org/10.7717/peerj.14220
Effects of carbodiimide combined with ethanol–wet bonding pretreatment on dentin bonding properties: an in vitro study
Purpose This study evaluated the combined effects of Carbodiimide (EDC) and ethanol–wet bonding (EWB) pretreatment on the bond strength and resin–dentin surface. Methods Phosphoric acid-etched dentin specimens were randomly divided into five groups based on the following pretreatments: deionized water (control), EWB, 0.3M EDC in water (EDCw), EDC water solution combined EWB (EDCw + EWB), and 0.3M EDC in ethanol (EDCe). A scanning electron microscope (SEM) was used to observe the morphology of collagen fibrils on the demineralized dentin matrix in each group after pretreatment. The adhesives Prime & Bond NT (PB) (Dentsply De trey, Konstanz, Germany) or Single bond 2 (SB) (3M ESPE, St. Paul, MN, USA) was applied after pretreatments, and a confocal laser scanning microscope (CLSM) was used to evaluate the quality of resin tags. The degree of conversion (DC) of the adhesive was investigated by Fourier transform infrared spectroscopy (ATR-FTIR). The dentin was first bonded with resin and bathed in water at 37 °C for 24 h. Half of them were subjected to 10, 000 cycles in a thermocycler between 5 °C and 55 °C before a microshear bond strength (µSBS) test. The statistical methods were Analysis of Variance (ANOVA) and a Tukey post hoc test at α = 0.05. Results The µSBS was significantly affected by pretreatments (p < 0.001), adhesives (p < 0.001), and aging conditions (p < 0.001) as revealed by the three-way ANOVA. The EDCw, EDCw + EWB, and EDCe groups significantly increased the µSBS; the EDCw + EWB and EDCe groups produced the highest µSBS. In the EDC-containing groups, the SEM showed at the collagen fibrils in the dentin matrix formed a three-dimensional network structure in the tubules after cross-linking into sheets, and the hybrid layer formed thicker resin tags under a CLSM. In the EDC-containing groups, the CLSM observed an increase in the length of resin tags. PB showed a higher DC and bonding strength than SB, and the five pretreatment groups tested did not affect the DC of the two adhesives. Conclusions In etch–and–rinse bonding system, EDC combined with EWB pretreatment can improve the quality of the hybrid layer and enhance the mechanical properties of demineralized dentin matrix. Pretreatment with EDC–ethanol solution may be a new clinically friendly option for enhancing dentin bonding durability.
You et al. (2022) Effects of carbodiimide combined with ethanol–wet bonding pretreatment on dentin bonding properties: an in vitro study. PeerJ 10:e14238 https://doi.org/10.7717/peerj.14238