A novel gene signature related to oxidative stress predicts the prognosis in clear cell renal cell carcinoma
Clear cell renal cell carcinoma (ccRCC) is considered to be related to the worse prognosis, which might in part be attributed to the early recurrence and metastasis, compared with other type of kidney cancer. Oxidative stress refers to an imbalance between production of oxidants and antioxidant defense. Accumulative studies have indicated that oxidative stress genes contribute to the tumor invasion, metastasis and drug sensitivity. However, the biological functions of oxidative stress genes in ccRCC remain largely unknown. In this study, we identified 1,399 oxidative stress genes from GeneCards with a relevance score ≥7. Data for analysis were accessed from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) database, and were utilized as training set and validation set respectively. Univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox were employed to construct a prognostic signature in ccRCC. Finally, a prognostic signature including four different oxidative stress genes was constructed from 1,399 genes, and its predictive performance was verified through Kaplan-Meier survival analysis and the receiver operating characteristic (ROC) curve. Interestingly, we found that there was significant correlation between the expression of oxidative stress genes and the immune infiltration and the sensitivity of tumor cells to chemotherapeutics. Moreover, the highest hazard ratio gene urocortin (UCN) was chosen for further study; some necessary vitro experiments proved that the UCN could promote the ability of ccRCC proliferation and migration and contribute to the degree of oxidative stress. In conclusion, it was promising to predict the prognosis of ccRCC through the four oxidative stress genes signature. UCN played oncogenic roles in ccRCC by influencing proliferation and oxidative stress pathway, which was expected to be the novel therapeutic target for ccRCC.
Ma et al. (2023) A novel gene signature related to oxidative stress predicts the prognosis in clear cell renal cell carcinoma. PeerJ 11:e14784 https://doi.org/10.7717/peerj.14784
Feeding ecology of the Terciopelo pit viper snake (Bothrops asper) in Ecuador
Thoroughly documenting prey items and diet composition is crucial for understanding a predator’s role in the ecosystem. In gape restricted predators, such as snakes, documenting and analyzing the type and size of the prey is important to interpret their ecological role. We describe the diet patterns of a species of venomous snake, the Terciopelo pit viper (Bothrops asper), from its Ecuadorian populations. Examining the gastrointestinal contents of museum specimens collected over an extensive area of the Pacific lowlands of Ecuador, we encountered 69 identifiable prey items from four major taxonomic groups (amphibians, centipedes, mammals, and reptiles). We evaluated the observed composition of prey to check for differences between sexes and size-classes. To complement our observations of the Terciopelo species complex throughout their distribution, we carried out a systematic literature review. Our data show an ontogenetic shift in diet, with a transition from more diverse diet in juveniles towards a mammal-specialized diet in adults, and distinct proportion of prey taxa between the sexes in the juvenile size class.
Loaiza-Lange et al. (2023) Feeding ecology of the Terciopelo pit viper snake (Bothrops asper) in Ecuador. PeerJ 11:e14817 https://doi.org/10.7717/peerj.14817
Occurrence of microplastics in freshwater gastropods from a tropical river U-Taphao, southern Thailand
Background Microplastics (MPs) are pollutants in rivers and marine environments. Rivers can be sources and sinks of MPs that enter the biota. Previous studies focusing on freshwater species are quite limited, especially for gastropods. Freshwater gastropods are essential to aquatic ecosystems because they are food to other aquatic animals, such as fish, shrimp, and crabs. They are a crucial link in the food chain between water resources and human food. Therefore, this study aimed to investigate MP accumulation in freshwater gastropods, commonly known as snails (Filopaludina sumatrensis speciosa and Pomacea canaliculata), in a river flowing into a shallow coastal lagoon. Method In this study, snail tissue samples were digested with 30% hydrogen peroxide. The mixture was heated at 60 °C for 24 h. MP particles were identified, counted, and characterized (shape, size, and color) by visual identification under a stereomicroscope. Furthermore, polymer-type identification was performed using Fourier transform infrared spectroscopy (FTIR). Analysis of variance (ANOVA) was applied for the statistical analysis. Results The MPs found were as follows: 4.76 particles/individual were found in F. sumatrensis speciosa upstream, 5.20 particles/individual were found in F. sumatrensis speciosa downstream, 7.28 particles/individual were found in P. canaliculata upstream, and 4.00 particles/individual were found in P. canaliculata downstream. It was found in the two-way ANOVA that the accumulation of MPs in gastropods was affected by species and study sites (upstream and downstream). There was a significant difference in the amount of MPs in P. canaliculata between upstream and downstream sites (p = 0.003). Fibers were the most common MPs in both species. Moreover, P. canaliculata upstream had the most significant amount of MPs. The smallest amount of MPs was recorded for P. canaliculata downstream, but there was great diversity in shape, size, and polymer type. MPs sized 500 μm–1 mm were the most common in both species. Fourier transform infrared spectroscopy revealed six polymers: poly (ethylene terephthalate), polypropylene, rayon, polyethyleneimine, polyamine, and poly (propylene: ethylene). The occurrence of MPs in gastropods is alarming for food security in Thailand. The results of this study can be used to support baseline data on MP accumulation among freshwater gastropods.
Environmental Contamination and Remediation
Jitkaew et al. (2023) Occurrence of microplastics in freshwater gastropods from a tropical river U-Taphao, southern Thailand. PeerJ 11:e14861 https://doi.org/10.7717/peerj.14861
Integrated metabolomic and transcriptomic analysis reveal the effect of mechanical stress on sugar metabolism in tea leaves (Camellia sinensis) post-harvest
Sugar metabolites not only act as the key compounds in tea plant response to stress but are also critical for tea quality formation during the post-harvest processing of tea leaves. However, the mechanisms by which sugar metabolites in post-harvest tea leaves respond to mechanical stress are unclear. In this study, we aimed to investigate the effects of mechanical stress on saccharide metabolites and related post-harvest tea genes. Withered (C15) and mechanically-stressed (V15) for 15 min Oolong tea leaves were used for metabolome and transcriptome sequencing analyses. We identified a total of 19 sugar metabolites, most of which increased in C15 and V15. A total of 69 genes related to sugar metabolism were identified using transcriptome analysis, most of which were down-regulated in C15 and V15. To further understand the relationship between the down-regulated genes and sugar metabolites, we analyzed the sucrose and starch, galactose, and glycolysis metabolic pathways, and found that several key genes of invertase (INV), α-amylase (AMY), β-amylase (BMY), aldose 1-epimerase (AEP), and α-galactosidase (AGAL) were down-regulated. This inhibited the hydrolysis of sugars and might have contributed to the enrichment of galactose and D-mannose in V15. Additionally, galactinol synthase (Gols), raffinose synthase (RS), hexokinase (HXK), 6-phosphofructokinase 1 (PFK-1), and pyruvate kinase (PK) genes were significantly upregulated in V15, promoting the accumulation of D-fructose-6-phosphate (D-Fru-6P), D-glucose-6-phosphate (D-glu-6P), and D-glucose. Transcriptome and metabolome association analysis showed that the glycolysis pathway was enhanced and the hydrolysis rate of sugars related to hemicellulose synthesis slowed in response to mechanical stress. In this study, we explored the role of sugar in the response of post-harvest tea leaves to mechanical stress by analyzing differences in the expression of sugar metabolites and related genes. Our results improve the understanding of post-harvest tea’s resistance to mechanical stress and the associated mechanism of sugar metabolism. The resulting treatment may be used to control the quality of Oolong tea.
Hao et al. (2023) Integrated metabolomic and transcriptomic analysis reveal the effect of mechanical stress on sugar metabolism in tea leaves (Camellia sinensis) post-harvest. PeerJ 11:e14869 https://doi.org/10.7717/peerj.14869
Heat stress does not induce wasting symptoms in the giant California sea cucumber (Apostichopus californicus)
Oceanic heatwaves have significant impacts on disease dynamics in marine ecosystems. Following an extreme heatwave in Nanoose Bay, British Columbia, Canada, a severe sea cucumber wasting event occurred that resulted in the mass mortality of Apostichopus californicus. Here, we sought to determine if heat stress in isolation could trigger wasting symptoms in A. californicus. We exposed sea cucumbers to (i) a simulated marine heatwave (22 °C), (ii) an elevated temperature treatment (17 °C), or (iii) control conditions (12 °C). We measured the presence of skin lesions, mortality, posture maintenance, antipredator defences, spawning, and organ evisceration during the 79-hour thermal exposure, as well as 7-days post-exposure. Both the 22 °C and 17 °C treatments elicited stress responses where individuals exhibited a reduced ability to maintain posture and an increase in stress spawning. The 22 °C heatwave was particularly stressful, as it was the only treatment where mortality was observed. However, none of the treatments induced wasting symptoms as observed in the Nanoose Bay event. This study provides evidence that sea cucumber wasting may not be triggered by heat stress in isolation, leaving the cause of the mass mortality event observed in Nanoose unknown.
Dawson Taylor et al. (2023) Heat stress does not induce wasting symptoms in the giant California sea cucumber (Apostichopus californicus). PeerJ 11:e14548 https://doi.org/10.7717/peerj.14548
Non-avian theropod phalanges from the marine Fox Hills Formation (Maastrichtian), western South Dakota, USA
We report here the first dinosaur skeletal material described from the marine Fox Hills Formation (Maastrichtian) of western South Dakota. The find consists of two theropod pedal phalanges: one recovered from the middle part of the Fairpoint Member in Meade County, South Dakota; and the other from the Iron Lightning Member in Ziebach County, South Dakota. Comparison with pedal phalanges of other theropods suggests strongly that the Fairpoint specimen is a right pedal phalanx, possibly III-2, from a large ornithomimid. The Iron Lightning specimen we cautiously identify as an ornithomimid left pedal phalanx II-2. The Fairpoint bone comes from thinly bedded and cross-bedded marine sandstones containing large hematitic concretions and concretionary horizons. Associated fossils include osteichthyan teeth, fin spines and otoliths, and abundant teeth of common Cretaceous nearshore and pelagic chondrichthyans. Leaf impressions and other plant debris, blocks of fossilized wood, and Ophiomorpha burrows are also common. The Iron Lightning bone comes from a channel deposit composed of fine to coarse sandstone beds, some of which contain bivalves, and a disseminated assemblage of mammal teeth, chondrichthyan teeth, and fragmentary dinosaur teeth and claws. We interpret the depositional environment of the two specimens as marginal marine. The Fairpoint bone derives from a nearshore foreset setting, above wave base subject to tidal flux and storm activity. The Iron Lightning specimen comes from a topset channel infill probably related to deposition on a tidal flat or associated coastal setting. The taphonomic history and ages of the two bones differ. Orthogonal cracks in the cortical bone of the Fairpoint specimen suggest post-mortem desiccation in a dryland coastal setting prior to transport and preservation in the nearby nearshore setting described above. The pristine surface of the Iron Lightning specimen indicates little transport before incorporation into the channel deposit in which it was found. The Fairpoint bone bed most probably lies within the Hoploscaphites nicolletii Ammonite Zone of the early late Maastrichtian, and would therefore have an approximate age of 69 Ma. The Iron Lightning bone is from the overlying H. nebrascensis Ammonite Zone, and is thus about one million years younger.
Chamberlain, Jr et al. (2023) Non-avian theropod phalanges from the marine Fox Hills Formation (Maastrichtian), western South Dakota, USA. PeerJ 11:e14665 https://doi.org/10.7717/peerj.14665
Bioinformatic prediction of the molecular links between Alzheimer’s disease and diabetes mellitus
Background Alzheimer’s disease (AD) and type 2 diabetes mellitus (DM2) are chronic degenerative diseases with complex molecular processes that are potentially interconnected. The aim of this work was to predict the potential molecular links between AD and DM2 from different sources of biological information. Materials and Methods In this work, data mining of nine databases (DisGeNET, Ensembl, OMIM, Protein Data Bank, The Human Protein Atlas, UniProt, Gene Expression Omnibus, Human Cell Atlas, and PubMed) was performed to identify gene and protein information that was shared in AD and DM2. Next, the information was mapped to human protein-protein interaction (PPI) networks based on experimental data using the STRING web platform. Then, gene ontology biological process (GOBP) and pathway analyses with EnrichR showed its specific and shared biological process and pathway deregulations. Finally, potential biomarkers and drug targets were predicted with the Metascape platform. Results A total of 1,551 genes shared in AD and DM2 were identified. The highest average degree of nodes within the PPI was for DM2 (average = 2.97), followed by AD (average degree = 2.35). GOBP for AD was related to specific transcriptional and translation genetic terms occurring in neurons cells. The GOBP and pathway information for the association AD-DM2 were linked mainly to bioenergetics and cytokine signaling. Within the AD-DM2 association, 10 hub proteins were identified, seven of which were predicted to be present in plasma and exhibit pharmacological interaction with monoclonal antibodies in use, anticancer drugs, and flavonoid derivatives. Conclusion Our data mining and analysis strategy showed that there are a plenty of biological information based on experiments that links AD and DM2, which could provide a rational guide to design further diagnosis and treatment for AD and DM2.
Castillo-Velázquez et al. (2023) Bioinformatic prediction of the molecular links between Alzheimer’s disease and diabetes mellitus. PeerJ 11:e14738 https://doi.org/10.7717/peerj.14738
Effect of sulfur on pollen germination of Clemenules mandarin and Nova tangelo
This study aims to elucidate whether sulfur can inhibit citrus pollination by affecting pollen grains. For this, four sulfur-based products (inorganic sulfur, water dispersible granular sulfur, ammonium sulfate, copper sulfate) were tested to evaluate their effect on pollen germination and pollen tube growth of two citrus varieties: Clemenules mandarin (Citrus clementina) and Nova tangelo (Citrus clementina x [Citrus paradisi x Citrus reticulata]). Pollen grains were extracted from the flowers of these two varieties and subsequently placed in Petri dishes with modified BK (boron and potassium) germination medium with six concentrations of the sulfur-based products (0.2, 2, 20, 200, 2,000, 20,000 mg l−1). All the dishes were incubated and the pollen germination rate was calculated. All the sulfur products showed progressive pollen germination inhibition with a rising sulfur concentration. CTC50 (50% cytotoxicity inhibition) was around 20 mg l−1, with significant differences among treatments. Total pollen germination inhibition took place at 20,000 mg l−1. These results demonstrate that sulfur application can affect citrus pollination.
Beltrán et al. (2023) Effect of sulfur on pollen germination of Clemenules mandarin and Nova tangelo. PeerJ 11:e14775 https://doi.org/10.7717/peerj.14775
Genomic relatedness and dissemination of blaNDM-5 among Acinetobacter baumannii isolated from hospital environments and clinical specimens in Thailand
Background Acinetobacter baumannii (A. baumannii) is an important cause of nosocomial infection, especially in intensive care units (ICUs). It has the propensity to tolerate various environments and multiple classes of antibiotics. Our study aimed to characterize the comparative genomes of A. baumannii from hospital environments and clinical isolates. Methods Clinical and environmental A. baumannii isolates were collected from a university hospital. Antibiotic susceptibility testing was performed, antibiotic resistance genes (ARGs) were characterized, and repetitive element palindromic-PCR (rep-PCR) typing was performed. Eight representative A. baumannii isolated from environmental and clinical samples from the same wards were selected for whole-genome sequencing (WGS) using the Illumina platform. Results A total of 106 A. baumannii isolates were obtained from 312 hospital environmental samples. A high percentage of samples with A. baumannii colonization were detected from AMBU bags (77.9%), followed by bedrails (66.7%) and suction tubes (66.7%). We found that 93.4% of the environmental isolates were multidrug-resistant A. baumannii (MDRAB), and 44.7% were extremely drug-resistant A. baumannii (XDRAB). blaOXA-23 blaNDM, and blaOXA-58 were present in 80.2%, 78.3%, and 0.9% of all isolates, respectively. Sixty-one A. baumannii isolates were collected from patient specimens in the same ward. Among all A. baumannii clinical isolates, MDRAB and XDRAB accounted for 82% and 55.7%, respectively. The most dominant ARGs identified was blaOXA-23 (80.3%), followed by blaNDM (55.7%). The genetic diversity of all isolates using rep-PCR could be divided into 33 genotypes. The genome size of eight A. baumannii ranged from 3.78–4.01 Mb. We found six of eight strains to be blaNDM-5-harboring A. baumannii. Mobile genetic elements (MGEs), such as integron1 (intl1), located upstream of blaNDM-5 were observed. The phylogenomic relationship of the core and pan genomes as well as the single nucleotide polymorphism (SNP) count matrix revealed the genetic similarity of A. baumannii environmental and clinical strains obtained from the same ward. Conclusion This study confirmed that A. baumannii colonized in hospital environments were the main reservoir of nosocomial infection and provides critical information to guide the control of A. baumannii infection.
Kitti et al. (2023) Genomic relatedness and dissemination of blaNDM-5 among Acinetobacter baumannii isolated from hospital environments and clinical specimens in Thailand. PeerJ 11:e14831 https://doi.org/10.7717/peerj.14831
Change the direction: 3D optimal control simulation by directly tracking marker and ground reaction force data
Optimal control simulations of musculoskeletal models can be used to reconstruct motions measured with optical motion capture to estimate joint and muscle kinematics and kinetics. These simulations are mutually and dynamically consistent, in contrast to traditional inverse methods. Commonly, optimal control simulations are generated by tracking generalized coordinates in combination with ground reaction forces. The generalized coordinates are estimated from marker positions using, for example, inverse kinematics. Hence, inaccuracies in the estimated coordinates are tracked in the simulation. We developed an approach to reconstruct arbitrary motions, such as change of direction motions, using optimal control simulations of 3D full-body musculoskeletal models by directly tracking marker and ground reaction force data. For evaluation, we recorded three trials each of straight running, curved running, and a v-cut for 10 participants. We reconstructed the recordings with marker tracking simulations, coordinate tracking simulations, and inverse kinematics and dynamics. First, we analyzed the convergence of the simulations and found that the wall time increased three to four times when using marker tracking compared to coordinate tracking. Then, we compared the marker trajectories, ground reaction forces, pelvis translations, joint angles, and joint moments between the three reconstruction methods. Root mean squared deviations between measured and estimated marker positions were smallest for inverse kinematics (e.g., 7.6 ± 5.1 mm for v-cut). However, measurement noise and soft tissue artifacts are likely also tracked in inverse kinematics, meaning that this approach does not reflect a gold standard. Marker tracking simulations resulted in slightly higher root mean squared marker deviations (e.g., 9.5 ± 6.2 mm for v-cut) than inverse kinematics. In contrast, coordinate tracking resulted in deviations that were nearly twice as high (e.g., 16.8 ± 10.5 mm for v-cut). Joint angles from coordinate tracking followed the estimated joint angles from inverse kinematics more closely than marker tracking (e.g., root mean squared deviation of 1.4 ± 1.8 deg vs. 3.5 ± 4.0 deg for v-cut). However, we did not have a gold standard measurement of the joint angles, so it is unknown if this larger deviation means the solution is less accurate. In conclusion, we showed that optimal control simulations of change of direction running motions can be created by tracking marker and ground reaction force data. Marker tracking considerably improved marker accuracy compared to coordinate tracking. Therefore, we recommend reconstructing movements by directly tracking marker data in the optimal control simulation when precise marker tracking is required.
Nitschke et al. (2023) Change the direction: 3D optimal control simulation by directly tracking marker and ground reaction force data. PeerJ 11:e14852 https://doi.org/10.7717/peerj.14852