High expression of six-transmembrane epithelial antigen of prostate 3 promotes the migration and invasion and predicts unfavorable prognosis in glioma
Recent studies have suggested that ferroptosis, a form of iron-dependent regulated cell death, might play essential roles in tumor initiation and progression. Six-transmembrane epithelial antigen of prostate 3 (STEAP3) is a ferrireductase involved in the regulation of intracellular iron homeostasis. However, the clinical significance and biological function of STEAP3 in human cancers remain poorly understood. Through a comprehensive bioinformatics analysis, we found that STEAP3 mRNA and protein expression were up-regulated in GBM, LUAD, and UCEC, and down-regulated in LIHC. Survival analysis indicated that STEAP3 had prognostic significance only in glioma. Multivariate Cox regression analysis revealed that high STEPA3 expression was correlated with poor prognosis. STEAP3 expression was significantly negatively correlated with promoter methylation level, and patients with lower STEAP3 methylation level had worse prognosis than those with higher STEAP3 methylation level. Single-cell functional state atlas showed that STEAP3 regulated epithelial-to-mesenchymal transition (EMT) in GBM. Furthermore, the results of wound healing and transwell invasion assays demonstrated that knocking down STEAP3 inhibited the migration and invasion of T98G and U251 cells. Functional enrichment analysis suggested that genes co-expressed with STEAP3 mainly participated in inflammation and immune-related pathways. Immunological analysis revealed that STEAP3 expression was significantly correlated with immune infiltration cells, including macrophages and neutrophils, especially the M2 macrophages. Individuals with low STEAP3 expression were more likely to respond to immunotherapy than those with high STEAP3 expression. These results suggest that STEAP3 promotes glioma progression and highlight its pivotal role in regulating immune microenvironment.
Deng et al. (2023) High expression of six-transmembrane epithelial antigen of prostate 3 promotes the migration and invasion and predicts unfavorable prognosis in glioma. PeerJ 11:e15136 https://doi.org/10.7717/peerj.15136
Functional characterization of the GhNRT2.1e gene reveals its significant role in improving nitrogen use efficiency in Gossypium hirsutum
Background Nitrate is the primary type of nitrogen available to plants, which is absorbed and transported by nitrate transporter 2 (NRT2) at low nitrate conditions. Methods Genome-wide identification of NRT2 genes in G. hirsutum was performed. Gene expression patterns were revealed using RNA-seq and qRT-PCR. Gene functions were characterized using overexpression in A. thaliana and silencing in G. hirsutum. Protein interactions were verified by yeast two-hybrid and luciferase complementation imaging (LCI) assays. Results We identified 14, 14, seven, and seven NRT2 proteins in G. hirsutum, G. barbadense, G. raimondii, and G. arboreum. Most NRT2 proteins were predicted in the plasma membrane. The NRT2 genes were classified into four distinct groups through evolutionary relationships, with members of the same group similar in conserved motifs and gene structure. The promoter regions of NRT2 genes included many elements related to growth regulation, phytohormones, and abiotic stresses. Tissue expression pattern results revealed that most GhNRT2 genes were specifically expressed in roots. Under low nitrate conditions, GhNRT2 genes exhibited different expression levels, with GhNRT2.1e being the most up-regulated. Arabidopsis plants overexpressing GhNRT2.1e exhibited increased biomass, nitrogen and nitrate accumulation, nitrogen uptake and utilization efficiency, nitrogen-metabolizing enzyme activity, and amino acid content under low nitrate conditions. In addition, GhNRT2.1e-silenced plants exhibited suppressed nitrate uptake and accumulation, hampered plant growth, affected nitrogen metabolism processes, and reduced tolerance to low nitrate. The results showed that GhNRT2.1e could promote nitrate uptake and transport under low nitrate conditions, thus effectively increasing nitrogen use efficiency (NUE). We found that GhNRT2.1e interacts with GhNAR2.1 by yeast two-hybrid and LCI assays. Discussion Our research lays the foundation to increase NUE and cultivate new cotton varieties with efficient nitrogen use.
Zhang et al. (2023) Functional characterization of the GhNRT2.1e gene reveals its significant role in improving nitrogen use efficiency in Gossypium hirsutum. PeerJ 11:e15152 https://doi.org/10.7717/peerj.15152
Plant-exuded chemical signals induce surface attachment of the bacterial pathogen Pseudomonas syringae
Many plant pathogenic bacteria suppress host defenses by secreting small molecule toxins or immune-suppressing proteins into host cells, processes that likely require close physical contact between pathogen and host. Yet, in most cases, little is known about whether phytopathogenic bacteria physically attach to host surfaces during infection. Here we report that Pseudomonas syringae pv. tomato strain DC3000, a Gram-negative bacterial pathogen of tomato and Arabidopsis, attaches to polystyrene and glass surfaces in response to chemical signals exuded from Arabidopsis seedlings and tomato leaves. We characterized the molecular nature of these attachment-inducing signals and discovered that multiple hydrophilic metabolites found in plant exudates, including citric acid, glutamic acid, and aspartic acid, are potent inducers of surface attachment. These same compounds were previously identified as inducers of P. syringae genes encoding a type III secretion system (T3SS), indicating that both attachment and T3SS deployment are induced by the same plant signals. To test if surface attachment and T3SS are regulated by the same signaling pathways, we assessed the attachment phenotypes of several previously characterized DC3000 mutants, and found that the T3SS master regulator HrpL was partially required for maximal levels of surface attachment, whereas the response regulator GacA, a negative regulator of T3SS, negatively regulated DC3000 surface attachment. Together, our data indicate that T3SS deployment and surface attachment by P. syringae may be co-regulated by the same host signals during infection, possibly to ensure close contact necessary to facilitate delivery of T3SS effectors into host cells.
O’Malley et al. (2023) Plant-exuded chemical signals induce surface attachment of the bacterial pathogen Pseudomonas syringae. PeerJ 11:e14862 https://doi.org/10.7717/peerj.14862
m6A reader IGF2BP1 accelerates apoptosis of high glucose-induced vascular endothelial cells in a m6A-HMGB1 dependent manner
Emerging evidence indicates that N6-methyladenosine (m6A) plays a critical role in vascular biological characteristic. In diabetes mellitus pathophysiology, high glucose (HG)-induced vascular endothelial dysfunction is associated with diabetes vascular complications. Nevertheless, the underlying mechanism of high glucose (HG)-related m6A regulation on vascular endothelial cells is still unclear. Results indicated that m6A reader insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was up-regulated in HG-treated human umbilical vascular endothelium cells (HUVECs) comparing to normal group. Functionally, results indicated that IGF2BP1 knockdown recovered the proliferation of HUVECs inhibited by HG-administration. Besides, IGF2BP1 knockdown reduced the apoptosis induced by HG-administration. Mechanistically, IGF2BP1 interacted with HMGB1 mRNA and stabilized its expression of m6A-modified RNA. Therefore, these findings provided compelling evidence demonstrating that m6A reader IGF2BP1 contributes to the proliferation and apoptosis of vascular endothelial cells in hyperglycaemia, serving as a target for development of diabetic angiopathy therapeutics.
Liang et al. (2023) m6A reader IGF2BP1 accelerates apoptosis of high glucose-induced vascular endothelial cells in a m6A-HMGB1 dependent manner. PeerJ 11:e14954 https://doi.org/10.7717/peerj.14954
Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific
Background The lack of barriers in the marine environment has promoted the idea of panmixia in marine organisms. However, oceanographic conditions and habitat characteristics have recently been linked to genetic structure in marine species. The Tropical Eastern Pacific (TEP) is characterized by dynamic current systems and heterogeneous oceanographic conditions. The Gulf of Panama (part of the equatorial segment for the TEP) is influenced by a complex current system and heterogeneous environment, which has been shown to limit the gene flow for shoreline species. Next Generation Sequencing (NGS) has contributed to detect genetic differences in previously reported panmictic species by the assessment of loci associated with selection and to understand how selection acts affects marine populations. Lutjanus guttatus is a species distributed in the TEP for which previous studies using mitochondrial data recovered a panmictic pattern along its distributional range. In this study, we used SNP data of L. guttatus individuals sampled along its range to evaluate population genetic structure and investigate whether oceanographic factors influence the species’ genetic architecture. Finally, we assessed the role of adaptive selection by evaluating the contribution of outlier and neutral loci to genetic divergence. Methods The RADcap method was used to obtain 24 million paired reads for 123 individuals of L. guttatus covering nearly all its distributional area. Genetic variation was assessed using both spatial and non-spatial methods by comparing three different data sets: (i) a Combined Loci (CL dataset = 2003 SNPs); a search for putative loci under selection allowed the evaluation of (ii) Neutral Loci (NL dataset = 1858 SNPs) and (iii) Outlier Loci (OL dataset = 145 SNPs). We used the estimating effective migration surface (EEMS) approach to detect possible barriers to gene flow. Results Genetic differences were found in the OL dataset, showing two clusters (Northern and Southern), whereas NL showed no differences. This result may be related to the Selection-Migration balance model. The limit between the Northern and Southern groups was in the Gulf of Panama, which has been previously identified as a barrier to gene flow for other species, mainly due to its heterogeneous oceanographic conditions. The results suggest that selection plays an important role in generating genetic differences in Lutjanus guttatus. A migration corridor was detected that coincides with the Costa Rica Coastal Current that flows from Central America to the Gulf of California, allowing the homogenization of the northern population. In the Southern cluster, a migration corridor was observed with the OL from Panama to Colombia, which could be associated with the currents found in the Gulf of Panama. Genetic variation found in the OL of Lutjanus guttatus highlights the usefulness of NGS data in evaluating the role of selection in population differentiation.
Mar-Silva et al. (2023) Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific. PeerJ 11:e15029 https://doi.org/10.7717/peerj.15029
A clinical medicine level test at Jinan University School of Medicine reveals the importance of training medical students in clinical history-taking
Backgrounds Training in the basic interview skills of clinical history-taking has always been a significant component of medical education. Purpose This study was designed to identify the factors influence medical students’ history-taking skills learning and develop a way to improve these skills. Methods We firstly analysed the academic performance of medical students at Jinan University School of Medicine in different disciplines of the Clinical Medicine Level Test (CMLT), to ensure the students have obtained comprehensive medical education prior to beginning their clinical internships. Next, we conducted a survey among the CMLT participants to seek the underlying causes and corresponding measures to improve history-taking in the future. Before these medical students entered their fifth-year clinical practice, we finally provide them with pre-internship training, including the history-taking workshops with standard patients (SP). Results The analysis of the clinical skill sections of the CMLT revealed that the students performed significantly better on clinical operations from multiple disciplines than on medical history-taking. Principal component analysis of the survey questionnaire indicated that the capability of history-taking, course assessments, and awareness of the value of medical history-taking emerged as the key factors forming a cohesive clue for sustaining history-taking implementation. The intervention workshops of employing SP had a positive impact, as evidenced by the students’ feedback and suggestions for improving their ability of history-taking. Conclusions This study suggests that strengthening of medical history-taking training is indispensable for training qualified medical students. Workshops with SP is a successful teaching strategy for practicing history-taking, allowing students to spot minute errors and training communication skills.
Meng et al. (2023) A clinical medicine level test at Jinan University School of Medicine reveals the importance of training medical students in clinical history-taking. PeerJ 11:e15052 https://doi.org/10.7717/peerj.15052
Seed priming with essential oils for sustainable wheat agriculture in semi-arid region
Drought is one of the major constraints to global crop production. A number of sustainable systems have focused on the development of environmentally friendly innovative biotechnological interventions to prevent yield losses. The use of essential oils as a seed priming agent can make an important contribution as a natural stimulant in increasing drought stress tolerance. This study focuses on the effects of seeds coated with different doses (D0 (0%), D1 (0.01%), D2 (0.05%), D3 (0.10%) and D4 (0.25%)) of sage, rosemary and lavender essential oils on wheat germination, seedling establishment and yield parameters. Turkey’s local wheat genotype Köse was used as plant material. The impact of the seed priming on germination rate, coleoptile length, shoot length, root length, shoot fresh and dry weight, root fresh and dry weight, relative water content (RWC), proline, and chlorophyll contents was assessed in laboratory experiments. In addition, the effect of essential oil types on yield parameters and agronomic components (plant height, spike height, number of grains per spike, grain yield per spike, grain yield per unit area, thousand-grain weight) was evaluated in a field experiment during the 2019–2020 crop seasons in a semi-arid climate. According to laboratory results, the highest germination rate among all treatment doses was determined in the D2 treatment (rosemary 93.30%, sage 94.00% and lavender 92.50%), while the lowest germination rates for all essential oil types were determined in the D4 treatment (rosemary 41.70%, sage 40.90% and lavender 40.90%). Increasing treatment doses showed a similar suppressive effect on the other parameters. In the field experiment, the highest grain yield (256.52 kg/da) and thousand-grain weight (43.30 g) were determined in the rosemary treatment. However, the priming treatment has an insignificant on the number of grains per spike and the spike length. The light of these results, the effects of essential oil types and doses on yield parameters were discussed. The findings highlight the importance of using essential oils in seed priming methods for sustainable agricultural practices.
Oğuz et al. (2023) Seed priming with essential oils for sustainable wheat agriculture in semi-arid region. PeerJ 11:e15126 https://doi.org/10.7717/peerj.15126
Reconstructing the dietary habits and trophic positions of the Longipterygidae (Aves: Enantiornithes) using neontological and comparative morphological methods
The Longipterygidae are a unique clade among the enantiornithines in that they exhibit elongate rostra (≥60% total skull length) with dentition restricted to the distal tip of the rostrum, and pedal morphologies suited for an arboreal lifestyle (as in other enantiornithines). This suite of features has made interpretations of this group’s diet and ecology difficult to determine due to the lack of analogous taxa that exhibit similar morphologies together. Many extant bird groups exhibit rostral elongation, which is associated with several disparate ecologies and diets (e.g., aerial insectivory, piscivory, terrestrial carnivory). Thus, the presence of rostral elongation in the Longipterygidae only somewhat refines trophic predictions of this clade. Anatomical morphologies do not function singularly but as part of a whole and thus, any dietary or ecological hypothesis regarding this clade must also consider other features such as their unique dentition. The only extant group of dentulous volant tetrapods are the chiropterans, in which tooth morphology and enamel thickness vary depending upon food preference. Drawing inferences from both avian bill proportions and variations in the dental morphology of extinct and extant taxa, we provide quantitative data to support the hypothesis that the Longipterygidae were animalivorous, with greater support for insectivory.
Clark et al. (2023) Reconstructing the dietary habits and trophic positions of the Longipterygidae (Aves: Enantiornithes) using neontological and comparative morphological methods. PeerJ 11:e15139 https://doi.org/10.7717/peerj.15139
Association between ACE and ACTN3 genes polymorphisms and athletic performance in elite and sub-elite Chinese youth male football players
Background Previous studies have shown controversial relationships between ACE I/D and ACTN3 R577x polymorphisms and athletic performance. Therefore, the aim of this study was to assess athletic performance indicators of Chinese youth male football players with different ACE and ACTN3 gene profiles. Methods and Materials This study recruited 73 elite (26 13-year-olds, 28 14-year-olds, and 19 15-year-olds) and 69 sub-elite (37 13-year-olds, 19 14-year-olds, and 13 15-year-olds) and 107 controls (63 13-year-olds, and 44 14-year olds aged 13–15 years, all participants were of Chinese Han origin. We measured height, body mass, thigh circumference, speed, explosive power, repeat sprints ability, and aerobic endurance in elite and sub-elite players. We used single nucleotide polymorphism technology to detect controls elite and sub-elite players’ ACE and ACTN3 genotypes, Chi-squared (χ2) tests were employed to test for Hardy-Weinberg equilibrium. χ2 tests were also used to observe the association between the genotype distribution and allele frequencies between controls and elite and sub-elite players. The differences in parameters between the groups were analyzed using one-way analysis of variance and a Bonferroni’s post-hoc test, with statistical significance set at p ≤ 0.05. Results (1) The genotype distribution of the ACE I/D and ACTN3 R577x polymorphisms in controls, elite and sub-elite football players were consistent with Hardy-Weinberg equilibrium, except for the ACE genotype distribution of sub-elite players. (2) The RR and DD genotypes were significantly different between elite and sub-elite players (p = 0.024 and p = 0.02, respectively). (3) Elite players were more likely to have the RR genotype and less likely to have the DD genotype compared with sub-elite players. (4) Both elite and sub-elite RR players’ Yo-yo intermittent recovery level 1 (YYIR1) running distance was significantly longer than that of RX players (p = 0.05 and p = 0.025, respectively). However, there was no significantly different in YYIR1 running distance between elite and sub-elite RR players. (5) Elite XX players’ VO2 max was significantly higher than that of RX and sub-elite players. Conclusion These results indicate that ACE I/D and ACTN3 R577x polymorphisms are not associated with muscle power in Chinese elite and sub-elite players. The XX genotype of ACTN3 is associated with the aerobic endurance of elite players.
Yang et al. (2023) Association between ACE and ACTN3 genes polymorphisms and athletic performance in elite and sub-elite Chinese youth male football players. PeerJ 11:e14893 https://doi.org/10.7717/peerj.14893
Economic costs of invasive rodents worldwide: the tip of the iceberg
Background Rodents are among the most notorious invasive alien species worldwide. These invaders have substantially impacted native ecosystems, food production and storage, local infrastructures, human health and well-being. However, the lack of standardized and understandable estimation of their impacts is a serious barrier to raising societal awareness, and hampers effective management interventions at relevant scales. Methods Here, we assessed the economic costs of invasive alien rodents globally in order to help overcome these obstacles. For this purpose, we combined and analysed economic cost data from the InvaCost database—the most up-to-date and comprehensive synthesis of reported invasion costs—and specific complementary searches within and beyond the published literature. Results Our conservative analysis showed that reported costs of rodent invasions reached a conservative total of US$ 3.6 billion between 1930 and 2022 (annually US$ 87.5 million between 1980 and 2022), and were significantly increasing through time. The highest cost reported was for muskrat Ondatra zibethicus (US$ 377.5 million), then unspecified Rattus spp. (US$ 327.8 million), followed by Rattus norvegicus specifically (US$ 156.6 million) and Castor canadensis (US$ 150.4 million). Of the total costs, 87% were damage-related, principally impacting agriculture and predominantly reported in Asia (60%), Europe (19%) and North America (9%). Our study evidenced obvious cost underreporting with only 99 documents gathered globally, clear taxonomic gaps, reliability issues for cost assessment, and skewed breakdowns of costs among regions, sectors and contexts. As a consequence, these reported costs represent only a very small fraction of the expected true cost of rodent invasions (e.g., using a less conservative analytic approach would have led to a global amount more than 80-times higher than estimated here). Conclusions These findings strongly suggest that available information represents a substantial underestimation of the global costs incurred. We offer recommendations for improving estimates of costs to fill these knowledge gaps including: systematic distinction between native and invasive rodents’ impacts; monetizing indirect impacts on human health; and greater integrative and concerted research effort between scientists and stakeholders. Finally, we discuss why and how this approach will stimulate and provide support for proactive and sustainable management strategies in the context of alien rodent invasions, for which biosecurity measures should be amplified globally.
Diagne et al. (2023) Economic costs of invasive rodents worldwide: the tip of the iceberg. PeerJ 11:e14935 https://doi.org/10.7717/peerj.14935