The needs of cancer patients during the COVID-19 pandemic—psychosocial, ethical and spiritual aspects—systematic review
The COVID-19 pandemic resulted in unprecedented changes in the functioning of the health care system, which were connected with the occurrence of new challenges for both the health care system’s employees and for the patients. The purpose of the present article is to analyze the needs of persons with oncological diseases. Taking into account the multiple aspects of the term health, psychological, social, and existential needs of the patients were analyzed. This article is directed mainly at persons who remain in a direct therapeutic relation with a patient. It is to facilitate recognizing the needs of ill people and to increase sensitivity to the issue of maintaining or improving the well-being of patients which requires paying special attention to their psychological, social, and existential needs during the period of hindered access to the health care system. This systematic review takes advantage of quantitative and qualitative methods of text analysis with phenomenological analysis factored in. The COVID-19 pandemic resulted in the appearance of new problems in the population of oncological patients or it made the existing problems more severe. As a consequence, it made it significantly more difficult to meet their needs on various levels and sometimes it even made it impossible. It seems necessary to determine and introduce strategies to ensure that patients with oncological diseases have access to psychological and spiritual support in the period of the pandemic.
Zapała et al. (2022) The needs of cancer patients during the COVID-19 pandemic—psychosocial, ethical and spiritual aspects—systematic review. PeerJ 10:e13480 https://doi.org/10.7717/peerj.13480
The effect of age and sexual maturation on thermal preferences of honey bee drones
The thermal preferences of Apis mellifera carnica drones (male individuals) are poorly understood, though their reproductive quality affects the quality of the inseminated queen and the whole honey bee colony. Therefore, the aim of this study was to determine the thermal preferences of individual drones according to their age and sexual maturity. Drones at the ages of 1, 5, 10, 15, 20 and 25 days were tested. The drones were placed on a platform in a temperature gradient in the range 20 °C and 46 °C. The thermal preferences of the drones were measured with the use of a thermal-imaging camera. Drones significantly differed with their choice of a preferred temperature. The one-day-old and the 25-day-old drones preferred the lowest temperatures. A slightly higher temperature was preferred by the 5-day-old drones, and the highest temperature was chosen by the drones at the ages of 10, 15, and 20 days. The changes in the thermal preferences of drones correspond to physiological changes occurring with age and connected with the rate of sexual maturation.
Czekońska et al. (2022) The effect of age and sexual maturation on thermal preferences of honey bee drones. PeerJ 10:e13494 https://doi.org/10.7717/peerj.13494
Genetic diversity analysis for wild and cultivated accessions of Cymbopogon citratus (D.C.) Stapf using phytochemical and molecular markers
Background Genetic diversity is being lost because of increasing urbanization and decreasing cultivation land, which leads to the abrupt use of wild resources of medicinally aromatic plants (MAPs). Cymbopogon citratus is a morphologically diverse MAP that is largely exploited in the food, cosmetics, and pharmaceutical industries. However, the intraspecific phytochemical and molecular diversity of C. citratus has yet to be explored. Methodology The germplasm was obtained from four different countries representing Pakistan, India, Bangladesh, and the United States. Oil extraction was performed by hydro distillation, and metabolic profiles of different accessions were generated by GC–MS. Seventeen functional molecular markers based on three genes encoding cytochrome P450, uridyl diphosphate glycosyltransferase and the 5S rRNA gene family were used to explore genetic diversity. Principal component analysis (PCA) and heatmaps were constructed using R software with the help of the gg-plot R package v1.0.5 for data validation. Results Among the 208 identified metabolites, citral was maximal, with a phytochemical contribution (1.92–27.73%), α-pinene (0.82–15.57%), verbenol (0.24–22.84%), neral (0.23–21.31%) and geranial acetate (0.43–15.65%). In the majority of accessions, citral was the dominant component. The highest concentration of citral was detected in 384541 (27.74%), 384527 (27.52%) belonging to Pakistan and one USA-based accession 38456 (27.71%). Region-specific grouping revealed a relationship between genetic diversity and geographical location. Pakistani accessions 384518, 38452, and 384544 genetically and 384535, 384518, and 384510 were phytochemically diverse. Conclusion The genetic diversity was more pronounced in cultivated accessions than in wild accessions. Moreover, it was observed that phytochemical diversity correlated with the altitude and temperature of the region.
Shamsheer et al. (2022) Genetic diversity analysis for wild and cultivated accessions of Cymbopogon citratus (D.C.) Stapf using phytochemical and molecular markers. PeerJ 10:e13505 https://doi.org/10.7717/peerj.13505
A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest
Monitoring biodiversity change is key to effective conservation policy. While it is difficult to establish in situ biodiversity monitoring programs at broad geographical scales, remote sensing advances allow for near-real time Earth observations that may help with this goal. We combine periodical and freely available remote sensing information describing temperature and precipitation with curated biological information from several groups of animals and plants in the Brazilian Atlantic rainforest to design an indirect remote sensing framework that monitors potential loss and gain of biodiversity in near-real time. Using data from biological collections and information from repeated field inventories, we demonstrate that this framework has the potential to accurately predict trends of biodiversity change for both taxonomic and phylogenetic diversity. The framework identifies areas of potential diversity loss more accurately than areas of species gain, and performs best when applied to broadly distributed groups of animals and plants.
Spatial and Geographic Information Science
Paz et al. (2022) A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest. PeerJ 10:e13534 https://doi.org/10.7717/peerj.13534
Fungal diversity in shade-coffee plantations in Soconusco, Mexico
Background As forested natural habitats disappear in the world, traditional, shade-coffee plantations offer an opportunity to conserve biodiversity and ecosystem services. Traditional coffee plantations maintain a diversity of tree species that provide shade for coffee bushes and, at the same time, are important repositories for plants and animals that inhabited the original cloud forest. However, there is still little information about shade-coffee plantation’s fungal diversity despite their relevance for ecosystem functioning as decomposers, symbionts and pathogens. Specifically, it is unknown if and what mycorrhizae-forming fungi can be found on the branches and trunks of coffee bushes and trees, which hold a diversity of epiphytes. Here, we evaluate fungal communities on specific plant microsites on both coffee bushes and shade trees. We investigate the ecological roles played by this diversity, with a special focus on mycorrhizae-forming fungi that may enable the establishment and development of epiphytic plants. Methods We collected 48 bark samples from coffee bushes and shade trees (coffee; tree), from four plant microsites (upper and lower trunks, branches and twigs), in two shade-coffee plantations in the Soconusco region in southern Mexico, at different altitudes. We obtained ITS amplicon sequences that served to estimate alpha and beta diversity, to assign taxonomy and to infer the potential ecological role played by the detected taxa. Results The bark of shade trees and coffee bushes supported high fungal diversity (3,783 amplicon sequence variants). There were no strong associations between community species richness and collection site, plant type or microsite. However, we detected differences in beta diversity between collection sites. All trophic modes defined by FUNGuild database were represented in both plant types. However, when looking into guilds that involve mycorrhizae formation, the CLAM test suggests that coffee bushes are more likely to host taxa that may function as mycorrhizae. Discussion We detected high fungal diversity in shade-coffee plantations in Soconusco, Chiapas, possibly remnants of the original cloud forest ecosystem. Several mycorrhiza forming fungi guilds occur on the bark of coffee bushes and shade trees in this agroecosystem, with the potential of supporting epiphyte establishment and development. Thus, traditional coffee cultivation could be part of an integrated strategy for restoration and conservation of epiphytic populations. This is particularly relevant for conservation of threatened species of Orchidaceae that are highly dependent on mycorrhizae formation.
Zarza et al. (2022) Fungal diversity in shade-coffee plantations in Soconusco, Mexico. PeerJ 10:e13610 https://doi.org/10.7717/peerj.13610
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