Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms
Real-time quantitative PCR (RT-qPCR) is a widely applied technique for relative quantification of gene expression. In this context, the selection of a suitable reference gene (RG) is an essential step for obtaining reliable and biologically relevant RT-qPCR results. The present study aimed to determine the expression stability of commonly used RGs in mouse skeletal muscle tissue. The expression pattern of eight RGs (ACTB, GAPDH, HPRT, YWHAZ, B2M, PPIA, TUBA and 18S) were evaluated by RT-qPCR in different sample groups classified based on genetic background, muscle tissue type, and growth stage, as well as in a C2C12 myoblast cell line model. Five computational programs were included in the study (comparative ΔCq value, NormFinder, BestKeeper, geNorm, RefFinder) to evaluate the expression stability of RGs. Furthermore, the normalization effects of RGs in soleus (SOL) and gastrocnemius (GAS) muscle tissue were evaluated. Collectively, ACTB, HPRT and YWHAZ were shown to be the most stable RGs, while GADPH and 18S were the least stable. Therefore, the combined use of ACTB, HPRT and YWHAZ is recommended for the normalization of gene expression results in experiments with murine skeletal muscle. The results discussed herein provide a foundation for gene expression analysis by RT-qPCR in mammalian skeletal muscle.
Ma et al. (2022) Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms. PeerJ 10:e14221 https://doi.org/10.7717/peerj.14221
Effects of jasmonic acid in foliar spray and an humic acid amendment to saline soils on forage sorghum plants’ growth and antioxidant defense system
Salinity is one of the primary abiotic stresses that cause negative physiological and biochemical changes due to the oxidative stress caused by the generation of reactive oxygen species (ROS). The effect of jasmonic acid (JA) as foliar spray and humic acid (HA) as soil amendment on the growth and biochemical attributes of forage sorghum plants exposed to salinity stress was investigated. Soil treated with NaCl at levels of 0, 2, and 4 g NaCl kg−1 dry soil (designated as S0, S1, and S2) and soil amendment with humic acid at 0, 3, and 6 g HA kg−1 dry soil (designated as HA0, HA1, and HA2). The plants were sprayed with three JA levels, including 0, 5, and 10 mM JA. Salinity stress increased carotenoid and soluble protein content, superoxide dismutase (SOD) activity, and malondialdehyde (MDA) content. In contrast, salinity stress reduced plant height, leaf area, relative growth rate, proline content, and the activity of peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX). At the S2 salinity level, HA2 rate increased plant high by 9.7%, relative growth rate by 70.8% and CAT by 45.5, while HA1 increased leaf area by 12.5%, chlorophyll content by 22.3%, carotenoid content by 38.1%, SOD activity by 20.9%, MDA content by 18.0%, POD activity by 24.6% and APX value by 21.7%. At the S2 salinity level, the highest plant height, chlorophyll content, soluble protein content and APX value were recorded at 5 mM JA, while the highest leaf area, the content of carotenoid, proline, and MDA, and the activity of POD and CAT were achieved at 10 mM JA. Generally, 10 mM JA and 3 g HA kg−1 dry soil produced the best positive effects on forage sorghum plants physiological responses. Our study suggested that jasmonic acid and humic acid at appropriate rates can successfully mitigate the adverse effects of salinity stress on forage sorghum.
Ali et al. (2022) Effects of jasmonic acid in foliar spray and an humic acid amendment to saline soils on forage sorghum plants’ growth and antioxidant defense system. PeerJ 10:e13793 https://doi.org/10.7717/peerj.13793
Virulence characteristics of Blumeria graminis f. sp. tritici and its genetic diversity by EST-SSR analyses
Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (an obligate biotrophic pathogen) is a worldwide threat to wheat production that occurs over a wide geographic area in China. For monitoring genetic variation and virulence structure of Blumeria graminis f. sp. tritici in Liaoning, Heilongjiang, and Sichuan in 2015, 31 wheat lines with known Powdery mildew resistance genes and 2 EST-SSR markers were used to characterize the virulence and genetic diversity. Results indicated that 90% of all isolates were virulent on Pm3c, Pm3e, Pm3f, Pm4a, Pm5, Pm6 (Timgalen), Pm7, Pm16, Pm19, and Pm1 + 2 + 9 and 62.6% to 89.9% of isolates were virulent on Pm3a, Pm3b, Pm3d, Pm4b, Pm6 (Coker747), Pm8, Pm17, Pm20, Pm23, Pm30, Pm4 + 8, Pm5 + 6, Pm4b + mli, Pm2 + mld, Pm4 + 2X, Pm2 + 6. The Pm13 and PmXBD genes were effective against most collected isolates from Liaoning and Heilongjiang Provinces. Only Pm21 exhibited an immune infection response to all isolates. Furthermore, closely related isolates within each region were distinguished by cluster analyses using EST-SSR representing some gene exchanges and genetic relationships between the flora in Northeast China (Liaoning, Heilongjiang) and Sichuan. Only 45% of the isolates tested show a clear correlation between EST-SSR genetic polymorphisms and the frequency of virulence gene data. However, the EST-SSR polymorphism of isolated genes did not correspond to the virulence diversity of isolates in the single-gene lineage identification of hosts.
Zhang et al. (2022) Virulence characteristics of Blumeria graminis f. sp. tritici and its genetic diversity by EST-SSR analyses. PeerJ 10:e14118 https://doi.org/10.7717/peerj.14118
The correlation between illness perception, pain intensity and quality of life in elderly with low back pain in Denmark: a cross-sectional study
Background Illness perception is related to management patterns and pain intensity, but among elderly with low back pain, this relation is unclear. The aims of this study were to analyse the associations between illness perception, pain intensity and health related quality of life in a group of elderly with low back pain and explore how different illness perception profiles would cluster and differ in terms of pain, quality of life and choice of management. Method This was a cross-sectional survey based on a cohort of originally 640 Danish children. Of the 311 respondents in 2019, 69% reported low back pain within last year and were included. Associations between illness perceptions (Brief illness perception questionnaire), health related quality of life (EuroQol-5 Domain-3L) and low back pain intensity were assessed, and participants were clustered based on their perceptions using hierarchical and K-means cluster analysis. Cluster differences in pain, quality of life and use of pharmacological and non-pharmacological treatments were explored. Results Among the 213 individuals with low back pain, 33% reported severe or fluctuating pain intensity. Higher pain intensity was associated with perceiving low back pain as a greater threat. Participants reporting fluctuating pain perceived their low back pain almost as threatening as participants reporting severe pain. Two clusters were identified. Cluster 1 reported lower quality of life (difference in medians: −0.176 (95% CI [−0.233–−0.119 ])) and was more likely to report severe or fluctuating pain (37.7% vs. 4.5% [P < 0.0001]) and to use pharmacological treatments than Cluster 2 (37.7% vs. 14.9% [P < 0.001]). No association was found between clusters concerning use of non-pharmacological treatments (P = 0.134). Conclusion Based on illness perceptions, two clusters differing in pain intensity, quality of life and use of pharmacological treatments were identified. Targeting illness perceptions may be beneficial during rehabilitation or when guiding patients with low back pain in choice of management.
Ginnerup-Nielsen et al. (2022) The correlation between illness perception, pain intensity and quality of life in elderly with low back pain in Denmark: a cross-sectional study. PeerJ 10:e14129 https://doi.org/10.7717/peerj.14129
Fermentation characteristics of bedded pack barn dairy cattle manure on methane yield, carbon, and nitrogen content in solid-state anaerobic digestion
This study aimed to estimate the fermentation characteristics of bedded pack barn dairy cattle manure (BDCM) in terms of methane yield, fibrous material, and nitrogen content in batch solid-state anaerobic digestion (SSAD). SSAD was performed in triplicate using a 1,400 ml polypropylene bottle at a constant temperature of 39 °C until less than 1% methane was produced. The cumulative methane content of BDCM was 142.5 N mL/g volatile solids (VSs). The methane content rapidly increased for 18 days, reaching 63.4 ± 4.6% until the end of the experiment. The ultimate biodegradability and total VS removal of BDCM were 23.1 and 19.0%, respectively. The slopes of the non-fibrous and hemicellulose carbon fractions, and acid detergent insoluble carbon by digestion time were −0.174 (p < 0.001), −0.141 (p = 0.003), and −0.051 (p < 0.001), respectively. The non-fibrous and hemicellulose nitrogen fraction contents quadratically decreased during SSAD (p = 0.001 and p = 0.008). No significant decrease was observed in the acid detergent insoluble nitrogen content (p = 0.840). The results of the present study provide basic data on the digestion characteristics of BDCM and could help determine fermentation conditions in the anaerobic digestion of BDCM.
Choi et al. (2022) Fermentation characteristics of bedded pack barn dairy cattle manure on methane yield, carbon, and nitrogen content in solid-state anaerobic digestion. PeerJ 10:e14134 https://doi.org/10.7717/peerj.14134
Exogenous melatonin treatment on post-harvest jujube fruits maintains physicochemical qualities during extended cold storage
This study was conducted to investigate the visual appearance and physicochemical changes of postharvest jujube fruits (Ziziphus jujuba Mill. cv. Shucuizao) stored under 0 °C for 15 days. The fruits were dipped in 0 (control), 50, 100, 200 and 400 µM melatonin solutions after harvest. The results showed that treatment with a suitable melatonin concentration improved the rate of crisp fine fruits, delayed weight loss and firmness decline, and suppressed changes in total soluble solids (TSS) and titratable acidity (TA) contents of jujube fruits compared with the control. In addition, jujube fruits soaked with melatonin showed improved antioxidant capacity through increased ascorbic acid (AsA) content, enhanced superoxide dismutase (SOD) activity, and decreased malonaldehyde (MDA) content. As a result, 50 µM melatonin showed the greatest improvement of visual appearance and quality maintenance, and could be used as an effective treatment to preserve postharvest jujube fruit.
Wang et al. (2022) Exogenous melatonin treatment on post-harvest jujube fruits maintains physicochemical qualities during extended cold storage. PeerJ 10:e14155 https://doi.org/10.7717/peerj.14155
Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature
Pacific oysters (Crassostrea gigas) are a valuable aquaculture product that provides important ecosystem benefits. Among other threats, climate-driven changes in ocean temperature can impact oyster metabolism, survivorship, and immune function. We investigated how elevated temperature impacts larval oysters during settlement (19–33 days post-fertilization), using shotgun proteomics with data-independent acquisition to identify proteins present in the oysters after 2 weeks of exposure to 23 °C or 29 °C. Oysters maintained at elevated temperatures were larger and had a higher settlement rate, with 86% surviving to the end of the experiment; these oysters also had higher abundance trends of proteins related to metabolism and growth. Oysters held at 23 °C were smaller, had a decreased settlement rate, displayed 100% mortality, and had elevated abundance trends of proteins related to immune response. This novel use of proteomics was able to capture characteristic shifts in protein abundance that hint at important differences in the phenotypic response of Pacific oysters to temperature regimes. Additionally, this work has produced a robust proteomic product that will be the basis for future research on bivalve developmental processes.
Crandall et al. (2022) Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158
The mechanism analysis of exogenous melatonin in limiting pear fruit aroma decrease under low temperature storage
Exogenous melatonin (MT) is widely used in fruit preservation, and can increase the storage time and delay the quality deterioration. Firstly, it was found that 150 μM MT was the optimal concentration to treat ‘Xinli No.7’ under storage at 4 °C for 60 days. MT could significantly improve oxidase activity and inhibit the reduction of physiological indexes, including pulp hardness, weight loss, titratable acid and soluble solid content. MT could also reduce ethylene release and limit the reduction of fruit aroma. The average content of fruit aroma substance increased by 43.53%. A relevant RNA-Seq database was built to further explore the regulation mechanism of MT. A total of 2,761 differentially expressed genes (DEGs) were identified. DEGs were enriched in 64 functional groups and 191 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. DEGs were mainly enriched in alpha-linolenic acid metabolism, fatty acid metabolism and plant hormone signal transduction pathway. The gene pycom09g05270 belonging to long chain acyl-CoA synthetase family and participating in fatty acid metabolism pathway was identified, and its expression level was consistent with fragments per kilobase per million mapped reads (FPKM) values, implying that pycom09g05270 might play a vital role in maintaining quality during the storage process.
Wei et al. (2022) The mechanism analysis of exogenous melatonin in limiting pear fruit aroma decrease under low temperature storage. PeerJ 10:e14166 https://doi.org/10.7717/peerj.14166
Genetic species identification and population structure of grouper Epinephelus coioides (Hamilton, 1822) collected from fish markets along the Persian Gulf and the Oman Sea
Many ecologically important and valuable fisheries marine species have been misidentified in terms of both the statistical data and market demand. Correct identification at the species level and the population genetic structure of the orange-spotted grouper (Epinephelus coioides), a precious fish in the Persian Gulf and the Oman Sea, was tested using mitochondrial cytochrome oxidase subunit I (DNA barcoding) and D-loop sequencing. The results revealed that the Epinephelus species found in the region, including E. coioides, E. bleekeri, E. polylepis, and E. chlorostigma were all mistakenly grouped together and identified as only E. coioides. Moreover, the analysis of molecular variance (AMOVA) of E. coioides samples using the D-loop showed a significantly unique genetic structure (ΦST = 0.068, p < 0.001) within the E. coioides population throughout the Persian Gulf and the Oman Sea, with the pairwise genetic difference between sampling locations in UAE and the Iranian coast. Moreover, D-loop sequences analysis showed two distinct haplotype groups scattered among the sampling locations, which did not correlate with the geographic distance between the sampling locations. These findings indicate that the issue of misidentification should be highlighted in the management and conservation of E. coioides. As this type of misidentification is likely to happen to other threatened marine species as well, the efficacy of using genetic markers for the correct identification, both at the species and the population level, is vital.
Tavakoli-Kolour et al. (2022) Genetic species identification and population structure of grouper Epinephelus coioides (Hamilton, 1822) collected from fish markets along the Persian Gulf and the Oman Sea. PeerJ 10:e14179 https://doi.org/10.7717/peerj.14179
biomonitoR: an R package for managing ecological data and calculating biomonitoring indices
The monitoring of biological indicators is required to assess the impacts of environmental policies, compare ecosystems and guide management and conservation actions. However, the growing availability of ecological data has not been accompanied by concomitant processing tools able to facilitate data handling and analysis. Multiple common challenges limit the usefulness of biomonitoring information across ecosystems and biological groups. Biomonitoring data analysis is currently constrained by time-consuming steps for data preparation and a data processing environment with limited integration in terms of software, biological groups, and protocols. We introduce biomonitoR, a package for the R programming language that addresses technical challenges for the management of ecological data and metrics calculation. biomonitoR implements most of the biological indices currently used or proposed in different fields of ecology and water resource management. Its combination of customizable functions aims to support a transferable and comprehensive biomonitoring workflow in a user-friendly environment. biomonitoR represents a versatile toolbox with five main assets: (i) it checks taxonomic information against reference datasets allowing for customization of trait and sensitivity scores; (ii) it supports heterogeneous taxonomic resolution allowing computations at multiple taxonomic levels; (iii) it calculates multiple biological indices, including metrics for both broad and stressor-specific ecological assessments; (iv) it enables user-friendly data visualization, helping both decision-making processes and data interpretation; and (v) it allows working with an interactive web application straight from R. Overall, biomonitoR can benefit the wide biomonitoring community, including environmental private consultants, ecologists and natural resource managers.
Laini et al. (2022) biomonitoR: an R package for managing ecological data and calculating biomonitoring indices. PeerJ 10:e14183 https://doi.org/10.7717/peerj.14183