Sequence comparison of the mitochondrial genomes of Plesionika species (Caridea: Pandalidae), gene rearrangement and phylogenetic relationships of Caridea
Background Despite the Caridean shrimps’ vast species richness and ecological diversity, controversies persist in their molecular classification. Within Caridea, the Pandalidae family exemplifies significant taxonomic diversity. As of June 25, 2023, GenBank hosts only nine complete mitochondrial genomes (mitogenomes) for this family. The Plesionika genus within Pandalidae is recognized as polyphyletic. To improve our understanding of the mitogenome evolution and phylogenetic relationships of Caridea, this study introduces three novel mitogenome sequences from the Plesionika genus: P. ortmanni, P. izumiae and P. lophotes. Methods The complete mitochondrial genomes of three Plesionika species were sequenced utilizing Illumina’s next-generation sequencing (NGS) technology. After assembling and annotating the mitogenomes, we conducted structural analyses to examine circular maps, sequence structure characteristics, base composition, amino acid content, and synonymous codon usage frequency. Additionally, phylogenetic analysis was performed by integrating existing mitogenome sequences of true shrimp available in GenBank. Results The complete mitogenomes of the three Plesionika species encompass 37 canonical genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). The lengths of these mitogenomes are as follows: 15,908 bp for P. ortmanni, 16,074 bp for P. izumiae and 15,933 bp for P. lophotes. Our analyses extended to their genomic features and structural functions, detailing base composition, gene arrangement, and codon usage. Additionally, we performed selection pressure analysis on the PCGs of all Pandalidae species available in Genbank, indicating evolutionary purification selection acted on the PCGs across Pandalidae species. Compared with the ancestral Caridea, translocation of two tRNA genes, i.e., trnP or trnT, were found in the two newly sequenced Plesionika species—P. izumiae and P. lophotes. We constructed a phylogenetic tree of Caridea using the sequences of 13 PCGs in mitogenomes. The results revealed that family Pandalidae exhibited robust monophyly, while genus Plesionika appeared to be a polyphyletic group. Conclusions Gene rearrangements within the Pandalidae family were observed for the first time. Furthermore, a significant correlation was discovered between phylogenetics of the Caridea clade and arrangement of mitochondrial genes. Our findings offer a detailed exploration of Plesionika mitogenomes, laying a crucial groundwork for subsequent investigations into genetic diversity, phylogenetic evolution, and selective breeding within this genus.
Sun et al. (2024) Sequence comparison of the mitochondrial genomes of Plesionika species (Caridea: Pandalidae), gene rearrangement and phylogenetic relationships of Caridea. PeerJ 12:e17314 https://doi.org/10.7717/peerj.17314
The nematode Caenorhabditis elegans enhances tolerance to landfill leachate stress by increasing trehalose synthesis
The burgeoning issue of landfill leachate, exacerbated by urbanization, necessitates evaluating its biological impact, traditionally overshadowed by physical and chemical assessments. This study harnesses Caenorhabditis elegans, a model organism, to elucidate the physiological toxicity of landfill leachate subjected to different treatment processes: nanofiltration reverse osmosis tail water (NFRO), membrane bioreactor (MBR), and raw leachate (RAW). Our investigation focuses on the modulation of sugar metabolism, particularly trehalose—a disaccharide serving dual functions as an energy source and an anti-adversity molecule in invertebrates. Upon exposure, C. elegans showcased a 60–70% reduction in glucose and glycogen levels alongside a significant trehalose increase, highlighting an adaptive response to environmental stress by augmenting trehalose synthesis. Notably, trehalose-related genes in the NFRO group were up-regulated, contrasting with the MBR and RAW groups, where trehalose synthesis genes outpaced decomposition genes by 20–30 times. These findings suggest that C. elegans predominantly counters landfill leachate-induced stress through trehalose accumulation. This research not only provides insights into the differential impact of leachate treatment methods on C. elegans but also proposes a molecular framework for assessing the environmental repercussions of landfill leachate, contributing to the development of novel strategies for pollution mitigation and environmental preservation.
Chen et al. (2024) The nematode Caenorhabditis elegans enhances tolerance to landfill leachate stress by increasing trehalose synthesis. PeerJ 12:e17332 https://doi.org/10.7717/peerj.17332
Determining the plant-pollinator network in a culturally significant food and medicine garden in the Great Lakes region
Understanding the interactions between plants and pollinators within a system can provide information about pollination requirements and the degree to which species contribute to floral reproductive success. Past research has focused largely on interactions within monocultured agricultural systems and only somewhat on wild pollination networks. This study focuses on the culturally significant Three Sisters Garden, which has been grown and tended by many Indigenous peoples for generations in the Great Lakes Region. Here, the plant-pollinator network of the traditional Three Sisters Garden with the inclusion of some additional culturally significant plants was mapped. Important visitors in this system included the common eastern bumble bee, Bombus impatiens Cresson (Hymenoptera: Apidae), and the hoary squash bee, Xenoglossa pruinosa (Say) (Hymenoptera: Apidae), as determined by their abundances and pollinator service index (PSI) values. Understanding the key pollinators in the Three Sisters Garden links biological diversity to cultural diversity through the pollination of culturally significant plants. Further, this information could be of use in supporting Indigenous food sovereignty by providing knowledge about which wild pollinators could be supported to increase fruit and seed set within the Three Sisters Garden. Our findings can also lead to more effective conservation of important wild pollinator species.
Gibson et al. (2024) Determining the plant-pollinator network in a culturally significant food and medicine garden in the Great Lakes region. PeerJ 12:e17401 https://doi.org/10.7717/peerj.17401
Temperature-size responses during ontogeny are independent of progenitors’ thermal environments
Background Warming generally induces faster developmental and growth rates, resulting in smaller asymptotic sizes of adults in warmer environments (a pattern known as the temperature-size rule). However, whether temperature-size responses are affected across generations, especially when thermal environments differ from one generation to the next, is unclear. Here, we tested temperature-size responses at different ontogenetic stages and in two consecutive generations using two soil-living Collembola species from the family Isotomidae: Folsomia candida (asexual) and Proisotoma minuta (sexually reproducing). Methods We used individuals (progenitors; F0) from cultures maintained during several generations at 15 °C or 20 °C, and exposed their offspring in cohorts (F1) to various thermal environments (15 °C, 20 °C, 25 °C and 30 °C) during their ontogenetic development (from egg laying to first reproduction; i.e., maturity). We measured development and size traits in the cohorts (egg diameter and body length at maturity), as well as the egg diameters of their progeny (F2). We predicted that temperature-size responses would be predominantly determined by within-generation plasticity, given the quick responsiveness of growth and developmental rates to changing thermal environments. However, we also expected that mismatches in thermal environments across generations would constrain temperature-size responses in offspring, possibly due to transgenerational plasticity. Results We found that temperature-size responses were generally weak in the two Collembola species, both for within- and transgenerational plasticity. However, egg and juvenile development were especially responsive at higher temperatures and were slightly affected by transgenerational plasticity. Interestingly, plastic responses among traits varied non-consistently in both Collembola species, with some traits showing plastic responses in one species but not in the other and vice versa. Therefore, our results do not support the view that the mode of reproduction can be used to explain the degree of phenotypic plasticity at the species level, at least between the two Collembola species used in our study. Our findings provide evidence for a general reset of temperature-size responses at the start of each generation and highlight the importance of measuring multiple traits across ontogenetic stages to fully understand species’ thermal responses.
Martínez-De León et al. (2024) Temperature-size responses during ontogeny are independent of progenitors’ thermal environments. PeerJ 12:e17432 https://doi.org/10.7717/peerj.17432
Dental pulp stem cells ameliorate D-galactose-induced cardiac ageing in rats
Background Ageing is a key risk factor for cardiovascular disease and is linked to several alterations in cardiac structure and function, including left ventricular hypertrophy and increased cardiomyocyte volume, as well as a decline in the number of cardiomyocytes and ventricular dysfunction, emphasizing the pathological impacts of cardiomyocyte ageing. Dental pulp stem cells (DPSCs) are promising as a cellular therapeutic source due to their minimally invasive surgical approach and remarkable proliferative ability. Aim This study is the first to investigate the outcomes of the systemic transplantation of DPSCs in a D-galactose (D-gal)-induced rat model of cardiac ageing. Methods. Thirty 9-week-old Sprague-Dawley male rats were randomly assigned into three groups: control, ageing (D-gal), and transplanted groups (D-gal + DPSCs). D-gal (300 mg/kg/day) was administered intraperitoneally daily for 8 weeks. The rats in the transplantation group were intravenously injected with DPSCs at a dose of 1 × 106 once every 2 weeks. Results The transplanted cells migrated to the heart, differentiated into cardiomyocytes, improved cardiac function, upregulated Sirt1 expression, exerted antioxidative effects, modulated connexin-43 expression, attenuated cardiac histopathological alterations, and had anti-senescent and anti-apoptotic effects. Conclusion Our results reveal the beneficial effects of DPSC transplantation in a cardiac ageing rat model, suggesting their potential as a viable cell therapy for ageing hearts.
El-Akabawy et al. (2024) Dental pulp stem cells ameliorate D-galactose-induced cardiac ageing in rats. PeerJ 12:e17299 https://doi.org/10.7717/peerj.17299
Awareness and attitudes towards eye donation among medical and allied health students in Jeddah, Saudi Arabia
Background Many national studies in Saudi Arabia have revealed a lack of knowledge about eye donation. The current study assessed awareness and attitudes towards eye donation among health faculty students in Jeddah, Saudi Arabia. It aims to increase their awareness as future healthcare providers are expected to raise general awareness to attain more local corneal donations. Methods A cross-sectional study including 1,060 health faculty students was conducted at King Abdulaziz University. Data were collected through an online questionnaire that covered participants’ demographics, academic year, knowledge, and attitudes regarding eye donation. Results Thirty-five percent of students had heard about eye donation, with the most common sources of information being social media (29%) and health workers (24%). Most respondents, 61% (n = 643), indicated willingness to donate their eyes after death. Of these respondents, 93% (n = 986), 6.8% (n = 72), and 0.2% (n = 2) had poor, fair, and good knowledge levels, respectively. A total of 66% (n = 696) and 34% (n = 364) had negative and positive attitudes, respectively. Conclusion Students in this study showed low levels of knowledge and negative attitudes about eye donation. Students should be adequately educated about the significance of eye donation.
Showail et al. (2024) Awareness and attitudes towards eye donation among medical and allied health students in Jeddah, Saudi Arabia. PeerJ 12:e17334 https://doi.org/10.7717/peerj.17334
Estimates on age, growth, and mortality of Leuciscus chuanchicus (Kessler 1876) in the Ningxia section of the upper reaches of the Yellow River, China
To investigate the age structure, growth pattern, mortality and exploitation rates of Leuciscus chuanchicus in the upstream Ningxia section of the Yellow River, four sampling surveys were conducted between 2022 and 2023. A total of 472 individuals were measured for their total length (TL) and body weight (W). Age determination was performed using otoliths. The collected samples had a range of total lengths from 4.52 to 37.45 cm, body weights ranging from 0.68 to 552.43 g, and ages ranging from 1 to 7 years old. The relationship between total length and body weight was expressed as W = 0.0052 L3.19 for all samples, which indicates that the growth of L. chuanchicus adheres to allometry. The Von Bertalanffy growth equation revealed that the fish had an asymptotic total length (L∞) of approximately 37.9 cm with a growth coefficient (K) value of approximately 0.461 yr−1. Using the age-based catch curve method, the calculated total instantaneous mortality rate (Z) for all samples was determined as being equal to approximately 1.1302 yr−1. Additionally, three methods were used to estimate the average instantaneous rate of natural mortality (M), resulting in an approximate value of 0.7167 yr−1 for all samples. Furthermore, the instantaneous rate of fishing mortality (F) for all samples was calculated as 0.4134 yr−1, leading us to determine that the exploitation rate (E) is 0.3658. It was concluded that the growth rate of L. chuanchicus in the upstream of the Yellow River is relatively fast, and L. chuanchicus has not been subjected to excessive exploitation, yet its relatively high natural mortality rate underscores the need for targeted management measures aimed at preserving its habitat.
Xiong et al. (2024) Estimates on age, growth, and mortality of Leuciscus chuanchicus (Kessler 1876) in the Ningxia section of the upper reaches of the Yellow River, China. PeerJ 12:e17351 https://doi.org/10.7717/peerj.17351
Measuring multi-year changes in the Symbiodiniaceae algae in Caribbean corals on coral-depleted reefs
Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.
Cunning et al. (2024) Measuring multi-year changes in the Symbiodiniaceae algae in Caribbean corals on coral-depleted reefs. PeerJ 12:e17358 https://doi.org/10.7717/peerj.17358
Pseudotargeted lipidomics analysis of scoparone on glycerophospholipid metabolism in non-alcoholic steatohepatitis mice by LC-MRM-MS
As the inflammatory subtype of nonalcoholic fatty liver disease (NAFLD), the progression of nonalcoholic steatohepatitis (NASH) is associated with disorders of glycerophospholipid metabolism. Scoparone is the major bioactive component in Artemisia capillaris which has been widely used to treat NASH in traditional Chinese medicine. However, the underlying mechanisms of scoparone against NASH are not yet fully understood, which hinders the development of effective therapeutic agents for NASH. Given the crucial role of glycerophospholipid metabolism in NASH progression, this study aimed to characterize the differential expression of glycerophospholipids that is responsible for scoparone’s pharmacological effects and assess its efficacy against NASH. Liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS) was performed to get the concentrations of glycerophospholipids, clarify mechanisms of disease, and highlight insights into drug discovery. Additionally, pathologic findings also presented consistent changes in high-fat diet-induced NASH model, and after scoparone treatment, both the levels of glycerophospholipids and histopathology were similar to normal levels, indicating a beneficial effect during the observation time. Altogether, these results refined the insights on the mechanisms of scoparone against NASH and suggested a route to relieve NASH with glycerophospholipid metabolism. In addition, the current work demonstrated that a pseudotargeted lipidomic platform provided a novel insight into the potential mechanism of scoparone action.
Song et al. (2024) Pseudotargeted lipidomics analysis of scoparone on glycerophospholipid metabolism in non-alcoholic steatohepatitis mice by LC-MRM-MS. PeerJ 12:e17380 https://doi.org/10.7717/peerj.17380
Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.)
The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.
Ye et al. (2024) Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.). PeerJ 12:e17388 https://doi.org/10.7717/peerj.17388