Nest characteristics and composition of the colonial nesting Azure-winged magpie Cyanopica cyanus in South Korea
Bird nests are crucial for reproductive success since they serve as structures to hold the eggs and nestlings safely. Therefore, the structural characteristics of bird nests have optimally evolved to maximize reproductive success, which are known to be affected by various factors. We gathered information on the nest characteristics such as nest structure and constituent materials in the colonial breeding Azure-winged magpie (Cyanopica cyanus) and investigated the relationship between ecologically relevant factors and the size and mass of the nests. The Azure-winged magpie nest can be deconstructed into an outer nest and an inner cup, and the type and mass of materials used for the construction of each part varies. Compared to the inner cup, the outer nest, which constitutes the overall shape of the nest, is composed of relatively harder materials, such as branches and soil. In contrast, the inner cup, which is the part where birds directly incubate eggs and raise nestlings, is composed of more flexible and softer materials, such as fiber and moss. We found that there was no relationship between nest characteristics and ecologically relevant factors. However, as the breeding season progressed, the volume of the inner cup decreased with increasing ambient temperatures. Our results show that Azure-winged magpies use differing materials for structurally distinct parts of the nests during construction. The results also indirectly suggest that the choice regarding the amount of insulating materials relative to changing temperatures during the breeding season may be one of the more significant adaptive strategies in the nest-building behaviors of Azure-winged magpies.
Kang et al. (2022) Nest characteristics and composition of the colonial nesting Azure-winged magpie Cyanopica cyanus in South Korea. PeerJ 10:e13637 https://doi.org/10.7717/peerj.13637
Integrated transcriptome and metabolome analyses revealed regulatory mechanisms of flavonoid biosynthesis in Radix Ardisia
Background Radix Ardisia (Jab Bik Lik Jib) is a common Miao medicine and is widely distributed in the Guizhou region of southern China. The botanical origin of Radix Ardisia includes the dry root and rhizome of Ardisia Crenata Sims (ACS) or Ardisia Crispa (Thunb.) A.DC. (AC), which are closely related species morphologically. However, the secondary metabolites in their roots are different from one another, especially the flavonoids, and these differences have not been thoroughly explored at the molecular level. This project preliminarily identified regulatory molecular mechanisms in the biosynthetic pathways of the flavonoids between ACS and AC using a multi-omics association analysis. Methods In this study, we determined the total levels of saponin, flavonoid, and phenolic in Radix Ardisia from different origins. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially expressed metabolites (DEM). We also performed conjoint analyses on DEGs and DEMs to ascertain the degree pathways, and explore the regulation of flavonoid biosynthesis. Results The total flavonoid and phenolic levels in ACS were significantly higher than in AC (P < 0.05). There were 17,685 DEGs between ACS vs. AC, 8,854 were upregulated and 8,831 were downregulated. Based on this, we continued to study the gene changes in the flavonoid biosynthesis pathway, and 100 DEGs involving flavonoid biosynthesis were differentially expressed in ACS and AC. We validated the accuracy of the RNA-seq data using qRT-PCR. Metabolomic analyses showed that 11 metabolites were involved in flavonoid biosynthesis including: Naringenin, Luteolin, Catechin, and Quercetin. A conjoint analysis of the genome-wide connection network revealed the differences in the types and levels of flavonoid compounds between ACS and AC. The correlation analysis showed that Naringenin, Luteolin, Catechin, and Quercetin were more likely to be key compounds in the flavonoid biosynthesis pathway also including 4CL, AOMT, CHS, CHI, DFR, F3’5’H, FLS, and LAR. Conclusions This study provides useful information for revealing the regulation of flavonoid biosynthesis and the regulatory relationship between metabolites and genes in the flavonoid biosynthesis pathway in Radix Ardisia from different origins.
Liu et al. (2022) Integrated transcriptome and metabolome analyses revealed regulatory mechanisms of flavonoid biosynthesis in Radix Ardisia. PeerJ 10:e13670 https://doi.org/10.7717/peerj.13670
Agricultural big data and methods and models for food security analysis—a mini-review
Background Big data and data analysis methods and models are important tools in food security (FS) studies for gap analysis and preparation of appropriate analytical frameworks. These innovations necessitate the development of novel methods for collecting, storing, processing, and extracting data. Methodology The primary goal of this study was to conduct a critical review of agricultural big data and methods and models used for FS studies published in peer-reviewed journals since 2010. Approximately 130 articles were selected for full content review after the pre-screening process. Results There are different sources of data collection, including but not limited to online databases, the internet, omics, Internet of Things, social media, survey rounds, remote sensing, and the Food and Agriculture Organization Corporate Statistical Database. The collected data require analysis (i.e., mining, neural networks, Bayesian networks, and other ML algorithms) before data visualization using Python, R, Circos, Gephi, Tableau, or Cytoscape. Approximately 122 models, all of which were used in FS studies worldwide, were selected from 130 articles. However, most of these models addressed only one or two dimensions of FS (i.e., availability and access) and ignored the other dimensions (i.e., stability and utilization), creating a gap in the global context. Conclusions There are certain FS gaps both worldwide and in the United Arab Emirates that need to be addressed by scientists and policymakers. Following the identification of the drivers, policies, and indicators, the findings of this review could be used to develop an appropriate analytical framework for FS and nutrition.
Ammar et al. (2022) Agricultural big data and methods and models for food security analysis—a mini-review. PeerJ 10:e13674 https://doi.org/10.7717/peerj.13674
A substantial portion of seafood is mislabeled, causing significant impacts to human health, the environment, the economy, and society. Despite the large scientific literature documenting seafood mislabeling the public’s awareness of seafood mislabeling is unknown. We conducted an online survey to assess the public’s awareness and perceptions of seafood mislabeling. Of the 1,216 respondents, 38% had never heard of seafood mislabeling and 49% were only ‘vaguely familiar’ with it. After being provided the definition of seafood mislabeling 95% had some degree of concern. Respondents were the most concerned about environmental impacts caused by seafood mislabeling and the least concerned about the social justice implications. Respondents who were also more concerned and familiar with seafood mislabeling stated that they would be more likely to purchase seafood from a vendor where the labeling was independently verified.
Ryburn et al. (2022) Public awareness of seafood mislabeling. PeerJ 10:e13486 https://doi.org/10.7717/peerj.13486
G3BP2, a stress granule assembly factor, is dispensable for spermatogenesis in mice
Background Spermatogenesis is a complex process that includes mitosis, meiosis, and spermiogenesis. During spermatogenesis, genetic factors play a vital role inthe formation of properly functioning sperm. GTPase-activating protein (SH3 domain)-binding protein 2 (G3BP2) is known to take part in immune responses, mRNA transport, and stress-granule assembly. However, its role in male fertility is unclear. Here, we generated a G3bp2 conditional knockout (cKO) mouse model to explore the function of G3BP2 in male fertility. Methods Polymerase chain reaction (PCR) and western blotting (WB) were used to confirm testis-specific G3bp2 knockout. Hematoxylin-eosin (HE) staining to observe testicular morphology and epididymal structure. Computer-aided sperm analysis (CASA) to detect sperm concentration and motility. Terminal deoxynucleotidyl transferase-dUTP nick-end labeling (TUNEL) assay was used to detect apoptotic cells. Results We found that cKO male mice are fertile with the normal morphology of the testis and sperm. Additionally, CASA of the semen from cKO mice showed that they all had a similar sperm concentration and motility. In addition, sperm from these mice exhibited a similar morphology. But the tunnel assay revealed increased apoptosis in their testes relative to the level in the wild type (WT). Conclusion Together, our data demonstrate that G3BP2 is dispensable for spermatogenesis and male fertility in mice albeit with the increased germ-cell apoptosis.
Yun et al. (2022) G3BP2, a stress granule assembly factor, is dispensable for spermatogenesis in mice. PeerJ 10:e13532 https://doi.org/10.7717/peerj.13532
Longitudinal study on the effect of keratinized mucosal augmentation surrounding dental implants in preventing peri-implant bone loss
Background Dental implant therapy is a well-established method of prosthetic rehabilitation of missing teeth. To maintain the health of the surrounding tissue, management of risk factors/indicators and daily maintenance are important. It still remains controversial whether a certain amount of keratinized mucosal width is essential for maintaining the health of peri-implant tissue. The purpose of this multicenter retrospective study was to assess the correlation between bone loss around dental implant and the amount of keratinized tissue width. Methods A total of 1,644 implants were evaluated. Data was collected about participants’ general and dental history, as well as implant details. Bone resorption around implant was calculated from intra-oral radiographs taken after 1 year and more than 3 years of function. Implants were classified into three groups; received free gingival graft or apically repositioned flap surgery for increasing the keratinized mucosa ≥2 mm width (group A), keratinized mucosa width ≥2 mm (group B), and keratinized mucosa width <2 mm (group C). These data were analyzed by propensity score analysis and a generalized linear regression analysis was performed to compare the bone resorption among groups. Results Mean functional time was 55.8 months (SD = 20.5) in group A, 67.6 months (SD = 28.1) in group B, and 74.5 months (SD = 32.9) in group C. Mean bone resorption of groups A, B, and C were 0.08 mm (SD = 0.40), 0.18 mm (SD = 0.66), and 0.44 mm (SD = 0.40). Groups A and B had significantly lower bone resorption than group C. Conclusion The results in this study show the importance of keratinized mucosa in maintaining the peri-implant bone. Our findings also suggest that mucosal transplantation is useful, as opposed to narrowing of the keratinized mucosa.
Kikuchi et al. (2022) Longitudinal study on the effect of keratinized mucosal augmentation surrounding dental implants in preventing peri-implant bone loss. PeerJ 10:e13598 https://doi.org/10.7717/peerj.13598
Providing choice of feedback affects perceived choice but does not affect performance
Background Autonomy or choice can lead to improved learning in various educational domains. The purpose of this online study was to examine whether giving participants a choice regarding the frequency of their received feedback (either after each individual trial or after a block of trials) in a computerized alternate task-switching task, will affect their performance. Methods Participants (n = 148) were randomly assigned to three groups: choice group (n = 49), online feedback group (n = 51), and summary feedback group (n = 48). From those three groups we created two groups: a choice group and a no-choice group (n = 49 in each group). All participants performed eight familiarization trials, a pre-test of 24 trials, five blocks of 24 trials for practice, and a post-test of 24 trials. After completing the task, the participants were asked about their perceived feeling of choice and completed the short form of the International Positive and Negative Affect Schedule. Results The participants in the choice group had higher perceived choice compared with the participants in the no-choice group (8.41 vs 5.47 out of 10, respectively). However, this higher perceived choice did not materialize into better performance during practice or in the post-test.
Ziv et al. (2022) Providing choice of feedback affects perceived choice but does not affect performance. PeerJ 10:e13631 https://doi.org/10.7717/peerj.13631
The potential of CircRNA1002 as a biomarker in hepatitis B virus-related hepatocellular carcinoma
Background Although hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, there is a lack of effective diagnostic measures. Circular RNAs (circRNAs) can be used as biomarkers for monitoring the occurrence and development of HCC. However, a convenient and reliable serum circRNA biomarker is not currently available. Materials & Methods CircRNA expression profiles were explored using high-throughput sequencing technology, and targeted circRNAs and mRNAs were validated by quantitative reverse transcription PCR (RT-qPCR). The biological functions of circRNAs were investigated using Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Downstream miRNAs and mRNAs of dysregulated circRNAs were predicted using TargetScan, miRanda, and miRDB; then circRNA-miRNA-mRNA interaction networks were constructed based on sequencing data and the Cancer Genome Atlas (TCGA). Results A total of 50,327 circRNAs were identified, with 1,187 circRNAs significantly differentially expressed between hepatitis B virus (HBV)-related HCC and HBV asymptomatic carriers. Among these circRNAs, four (circRNA1002, circRNA7941, circRNA 39338, and circRNA44142) were validated by RT-qPCR as being statistically different either in HCC tissue or serum samples. circRNA1002 was significantly down-regulated in both HCC serum and tissue, indicating its reliability. Bioinformatics analysis showed that circRNA1002-associated genes were enriched in GO terms relating to hormone pathway and cell-cell interaction processes, which are involved in the progression of HCC. Conclusion Our circRNA analysis of HCC patients and HBV asymptomatic carriers showed that circRNA1002 may be a reliable serum biomarker for HCC. These results could provide an improved assay for the early detection of HCC.
Li et al. (2022) The potential of CircRNA1002 as a biomarker in hepatitis B virus-related hepatocellular carcinoma. PeerJ 10:e13640 https://doi.org/10.7717/peerj.13640
High-resolution melting (HRM) curve analysis as a potential tool for the identification of earthworm species and haplotypes
Background Earthworm communities are an important component of soil biodiversity and contribute to a number of ecosystem functions such as soil-nutrient cycling. Taxonomic identification is an essential requirement to assess earthworm biodiversity and functionality. Although morphological identification of species is labour-intensive, it is the most commonly used method due to a lack of cost-efficient alternatives. Molecular approaches to identify earthworms at species and haplotype level such as DNA barcoding are gaining popularity in science but are rarely applied in practice. In contrast to barcoding, the differentiation of PCR products based on their thermal denaturation properties using high-resolution melting (HRM) curve analysis is a fast and cost-efficient molecular closed-tube, post-PCR tool that allows identification of taxa. Methods We developed a HRM curve assay to identify eight earthworm species common to agricultural soils in Central Europe (Allolobophora chlorotica, Aporrectodea caliginosa, Apo. limicola, Apo. longa, Apo. rosea, Lumbricus castaneus, L. rubellus, and L. terrestris). For this, a new primer pair targeting a 158-bp long subregion of the cytochrome c oxidase I (COI) gene was designed. Our HRM assay was further tested for the differentiation of COI haplotypes using 28 individuals of the earthworm species Allo. chlorotica. Furthermore, we developed a novel extraction method for DNA from earthworm tissue that is fast and requires minimal consumables and laboratory equipment. Results The developed HRM curve assay allowed identifying all eight earthworm species. Performing the assay on 28 individuals of the earthworm species Allo. chlorotica enabled the distinction among different COI haplotypes. Furthermore, we successfully developed a rapid, robust, scalable, and inexpensive method for the extraction of earthworm DNA from fresh or frozen tissue. Conclusions HRM curve analysis of COI genes has the potential to identify earthworm species and haplotypes and could complement morphological identification, especially for juvenile or damaged individuals. Our rapid and inexpensive DNA extraction method from earthworm tissue helps to reduce the costs of molecular analyses and thereby promote their application in practice.
Vaupel et al. (2022) High-resolution melting (HRM) curve analysis as a potential tool for the identification of earthworm species and haplotypes. PeerJ 10:e13661 https://doi.org/10.7717/peerj.13661
Comparative transcriptomics reveals new insights into melatonin-enhanced drought tolerance in naked oat seedlings
The growth and development of naked oat (Avena nuda L.) seedlings, a grain recognized as nutritious and healthy, is limited by drought. Melatonin plays a positive role in plants under drought stress. However, its function is unclear in naked oats. This study demonstrated that melatonin enhances drought stress tolerance in oat seedlings. Melatonin application alleviated the declining growth parameters of two naked oat varieties, Huazao No.2 (H2) and Jizhangyou No.15 (J15), under drought stress by increasing the chlorophyll content and photosynthetic rate of leaves. Melatonin pretreatment induced differential gene expression in H2 and J15 under drought stress. Subsequently, the differential gene expression responses to melatonin in the two varieties were further analyzed. The key drought response transcription factors and the regulatory effect of melatonin on drought-related transcription factors were assessed, focusing on genes encoding proteins in the ABA signal transduction pathway, including PYL, PP2C, ABF, SNRK2, and IAA. Taken together, this study provides new insights into the effect and underlying mechanism of melatonin in alleviating drought stress in naked oat seedlings.
Zhang et al. (2022) Comparative transcriptomics reveals new insights into melatonin-enhanced drought tolerance in naked oat seedlings. PeerJ 10:e13669 https://doi.org/10.7717/peerj.13669