New heterodont odontocetes from the Oligocene Pysht Formation in Washington State, U.S.A., and a reevaluation of Simocetidae (Cetacea, Odontoceti)
Odontocetes first appeared in the fossil record by the early Oligocene, and their early evolutionary history can provide clues as to how some of their unique adaptations, such as echolocation, evolved. Here, three new specimens from the early to late Oligocene Pysht Formation are described further increasing our understanding of the richness and diversity of early odontocetes, particularly for the North Pacific. Phylogenetic analysis shows that the new specimens are part of a more inclusive, redefined Simocetidae, which now includes Simocetus rayi, Olympicetus sp. 1, Olympicetus avitus, O. thalassodon sp. nov., and a large unnamed taxon (Simocetidae gen. et sp. A), all part of a North Pacific clade that represents one of the earliest diverging groups of odontocetes. Amongst these, Olympicetus thalassodon sp. nov. represents one of the best known simocetids, offering new information on the cranial and dental morphology of early odontocetes. Furthermore, the inclusion of CCNHM 1000, here considered to represent a neonate of Olympicetus sp., as part of the Simocetidae, suggests that members of this group may not have had the capability of ultrasonic hearing, at least during their early ontogenetic stages. Based on the new specimens, the dentition of simocetids is interpreted as being plesiomorphic, with a tooth count more akin to that of basilosaurids and early toothed mysticetes, while other features of the skull and hyoid suggest various forms of prey acquisition, including raptorial or combined feeding in Olympicetus spp., and suction feeding in Simocetus. Finally, body size estimates show that small to moderately large taxa are present in Simocetidae, with the largest taxon represented by Simocetidae gen. et sp. A with an estimated body length of 3 m, which places it as the largest known simocetid, and amongst the largest Oligocene odontocetes. The new specimens described here add to a growing list of Oligocene marine tetrapods from the North Pacific, further promoting faunistic comparisons across other contemporaneous and younger assemblages, that will allow for an improved understanding of the evolution of marine faunas in the region.
Velez-Juarbe (2023) New heterodont odontocetes from the Oligocene Pysht Formation in Washington State, U.S.A., and a reevaluation of Simocetidae (Cetacea, Odontoceti). PeerJ 11:e15576 https://doi.org/10.7717/peerj.15576
Biostimulant red seaweed (Gracilaria tenuistipitata var. liui) extracts spray improves yield and drought tolerance in soybean
Drought has a deleterious impact on the growth, physiology, and yield of various plants, including soybean. Seaweed extracts are rich in various bioactive compounds, including antioxidants, and can be used as biostimulants for improving yield and alleviating the adverse effect of drought stress. The purpose of this study was to evaluate the effect of soybean growth and yield with different concentrations (0.0%, 5.0%, and 10.0% v/v) of water extracts of the red seaweed Gracilaria tenuistipitata var. liui under well-watered (80% of field capacity (FC) and drought (40% of FC)) conditions. Drought stress decreased soybean grain yield by 45.58% compared to well-watered circumstances but increased the water saturation deficit by 37.87%. It also decreased leaf water, chlorophyll content, plant height, and the fresh weight of the leaf, stem, and petiole. Drought stress decreased soybean grain yield by 45.58% compared to well-watered circumstances but increased the water saturation deficit by 37.87%. It also decreased leaf water, chlorophyll content, plant height, and the fresh weight of the leaf, stem, and petiole. Under both drought and well-watered situations, foliar application of seaweed extracts dramatically improved soybean growth and production. Under drought and well-watered situations, 10.0% seaweed extract increased grain yield by 54.87% and 23.97%, respectively in comparison to untreated plants. The results of this study suggest that red seaweed extracts from Gracilaria tenuistipitata var. liui may be used as a biostimulant to improve soybean yield and drought tolerance in the presence of insufficient water. However, the actual mechanisms behind these improvements need to be further investigated in field conditions.
Mannan et al. (2023) Biostimulant red seaweed (Gracilaria tenuistipitata var. liui) extracts spray improves yield and drought tolerance in soybean. PeerJ 11:e15588 https://doi.org/10.7717/peerj.15588
Biomes of the world under climate change scenarios: increasing aridity and higher temperatures lead to significant shifts in natural vegetation
The global potential distribution of biomes (natural vegetation) was modelled using 8,959 training points from the BIOME 6000 dataset and a stack of 72 environmental covariates representing terrain and the current climatic conditions based on historical long term averages (1979–2013). An ensemble machine learning model based on stacked regularization was used, with multinomial logistic regression as the meta-learner and spatial blocking (100 km) to deal with spatial autocorrelation of the training points. Results of spatial cross-validation for the BIOME 6000 classes show an overall accuracy of 0.67 and R2logloss of 0.61, with “tropical evergreen broadleaf forest” being the class with highest gain in predictive performances (R2logloss = 0.74) and “prostrate dwarf shrub tundra” the class with the lowest (R2logloss = −0.09) compared to the baseline. Temperature-related covariates were the most important predictors, with the mean diurnal range (BIO2) being shared by all the base-learners (i.e.,random forest, gradient boosted trees and generalized linear models). The model was next used to predict the distribution of future biomes for the periods 2040–2060 and 2061–2080 under three climate change scenarios (RCP 2.6, 4.5 and 8.5). Comparisons of predictions for the three epochs (present, 2040–2060 and 2061–2080) show that increasing aridity and higher temperatures will likely result in significant shifts in natural vegetation in the tropical area (shifts from tropical forests to savannas up to 1.7 ×105 km2 by 2080) and around the Arctic Circle (shifts from tundra to boreal forests up to 2.4 ×105 km2 by 2080). Projected global maps at 1 km spatial resolution are provided as probability and hard classes maps for BIOME 6000 classes and as hard classes maps for the IUCN classes (six aggregated classes). Uncertainty maps (prediction error) are also provided and should be used for careful interpretation of the future projections.
Spatial and Geographic Information Science
Bonannella et al. (2023) Biomes of the world under climate change scenarios: increasing aridity and higher temperatures lead to significant shifts in natural vegetation. PeerJ 11:e15593 https://doi.org/10.7717/peerj.15593
Luteolin supplementation during porcine oocyte maturation improves the developmental competence of parthenogenetic activation and cloned embryos
Luteolin (Lut), a polyphenolic compound that belongs to the flavone subclass of flavonoids, possesses anti-inflammatory, cytoprotective, and antioxidant activities. However, little is known regarding its role in mammalian oocyte maturation. This study examined the effect of Lut supplementation during in vitro maturation (IVM) on oocyte maturation and subsequent developmental competence after somatic cell nuclear transfer (SCNT) in pigs. Lut supplementation significantly increased the proportions of complete cumulus cell expansion and metaphase II (MII) oocytes, compared with control oocytes. After parthenogenetic activation or SCNT, the developmental competence of Lut-supplemented MII oocytes was significantly enhanced, as indicated by higher rates of cleavage, blastocyst formation, expanded or hatching blastocysts, and cell survival, as well as increased cell numbers. Lut-supplemented MII oocytes exhibited significantly lower levels of reactive oxygen species and higher levels of glutathione than control MII oocytes. Lut supplementation also activated lipid metabolism, assessed according to the levels of lipid droplets, fatty acids, and ATP. The active mitochondria content and mitochondrial membrane potential were significantly increased, whereas cytochrome c and cleaved caspase-3 levels were significantly decreased, by Lut supplementation. These results suggest that Lut supplementation during IVM improves porcine oocyte maturation through the reduction of oxidative stress and mitochondria-mediated apoptosis.
Jeong et al. (2023) Luteolin supplementation during porcine oocyte maturation improves the developmental competence of parthenogenetic activation and cloned embryos. PeerJ 11:e15618 https://doi.org/10.7717/peerj.15618
Glutathione-mediated changes in productivity, photosynthetic efficiency, osmolytes, and antioxidant capacity of common beans (Phaseolus vulgaris) grown under water deficit
Globally, salinity and drought are severe abiotic stresses that presently threaten vegetable production. This study investigates the potential exogenously-applied glutathione (GSH) to relieve water deficits on Phaseolus vulgaris plants cultivated in saline soil conditions (6.22 dS m−1) by evaluating agronomic, stability index of membrane, water satatus, osmolytes, and antioxidant capacity responses. During two open field growing seasons (2017 and 2018), foliar spraying of glutathione (GSH) at 0.5 (GSH1) or 1.0 (GSH1) mM and three irrigation rates (I100 = 100%, I80 = 80% and I60 = 60% of the crop evapotranspiration) were applied to common bean plants. Water deficits significantly decreased common bean growth, green pods yield, integrity of the membranes, plant water status, SPAD chlorophyll index, and photosynthetic capacity (Fv/Fm, PI), while not improving the irrigation use efficiency (IUE) compared to full irrigation. Foliar-applied GSH markedly lessened drought-induced damages to bean plants, by enhancing the above variables. The integrative I80 + GSH1 or GSH2 and I60 + GSH1 or GSH2 elevated the IUE and exceeded the full irrigation without GSH application (I100) treatment by 38% and 37%, and 33% and 28%, respectively. Drought stress increased proline and total soluble sugars content while decreased the total free amino acids content. However, GSH-supplemented drought-stressed plants mediated further increases in all analyzed osmolytes contents. Exogenous GSH enhanced the common bean antioxidative machinery, being promoted the glutathione and ascorbic acid content as well as up-regulated the activity of superoxide dismutase, catalase, ascorbate peroxidase, and glutathione peroxidase. These findings demonstrate the efficacy of exogenous GSH in alleviating water deficit in bean plants cultivated in salty soil.
Abd El Mageed et al. (2023) Glutathione-mediated changes in productivity, photosynthetic efficiency, osmolytes, and antioxidant capacity of common beans (Phaseolus vulgaris) grown under water deficit. PeerJ 11:e15343 https://doi.org/10.7717/peerj.15343
Early pain in females is linked to late pathological features in murine experimental osteoarthritis
Background Osteoarthritis (OA) is a progressive joint disease and a major cause of chronic pain in adults. The prevalence of OA is higher in female patients, who tend to have worse OA outcomes, partially due to pain. The association between joint pain and OA pathology is often inconclusive. Preclinical research studies have largely overlooked sex as a potential determinant in joint pain during OA. This study aimed to investigate the role of sex in joint pain in the collagenase-induced OA (CiOA) model and its link with joint pathology. Methods Multiple aspects of pain were evaluated during identically executed experiments of CiOA in male and female C57BL/6J mice. Cartilage damage, osteophyte formation, synovial thickness, and cellularity were assessed by histology on day 56. The association between pain and pathology was investigated, disaggregated by sex. Results Differences in pain behavior between sexes were found in the majority of the evaluated pain methods. Females displayed lower weight bearing ability in the affected leg compared to males during the early phase of the disease, however, the pathology at the end stage was comparable between sexes. In the second cohort, males displayed increased mechanical sensitivity in the affected joint compared to females but also showed more cartilage damage at the end stage of the model. Within this cohort, gait analysis showed varied results. Males used the affected paw less often and displayed dynamic weight-bearing compensation in the early phase of the model. These differences were not observed in females. Other evaluated parameters displayed comparable gait behavior between males and females. A detailed analysis of individual mice revealed that seven out of 10 pain measurements highly correlated with OA histopathology in females (Pearson r range: 0.642–0.934), whereas in males this measurement was only two (Pearson r range: 0.645–0.748). Conclusion Our data show that sex is a determinant in the link between pain-related behavior with OA features. Therefore, to accurately interpret pain data it is crucial to segregate data analysis by sex to draw the correct mechanistic conclusion.
Valdrighi et al. (2023) Early pain in females is linked to late pathological features in murine experimental osteoarthritis. PeerJ 11:e15482 https://doi.org/10.7717/peerj.15482
Estimating average wind speed in Thailand using confidence intervals for common mean of several Weibull distributions
The Weibull distribution has been used to analyze data from many fields, including engineering, survival and lifetime analysis, and weather forecasting, particularly wind speed data. It is useful to measure the central tendency of wind speed data in specific locations using statistical parameters for instance the mean to accurately forecast the severity of future catastrophic events. In particular, the common mean of several independent wind speed samples collected from different locations is a useful statistic. To explore wind speed data from several areas in Surat Thani province, a large province in southern Thailand, we constructed estimates of the confidence interval for the common mean of several Weibull distributions using the Bayesian equitailed confidence interval and the highest posterior density interval using the gamma prior. Their performances are compared with those of the generalized confidence interval and the adjusted method of variance estimates recovery based on their coverage probabilities and expected lengths. The results demonstrate that when the common mean is small and the sample size is large, the Bayesian highest posterior density interval performed the best since its coverage probabilities were higher than the nominal confidence level and it provided the shortest expected lengths. Moreover, the generalized confidence interval performed well in some scenarios whereas adjusted method of variance estimates recovery did not. The approaches were used to estimate the common mean of real wind speed datasets from several areas in Surat Thani province, Thailand, fitted to Weibull distributions. These results support the simulation results in that the Bayesian methods performed the best. Hence, the Bayesian highest posterior density interval is the most appropriate method for establishing the confidence interval for the common mean of several Weibull distributions.
La-ongkaew et al. (2023) Estimating average wind speed in Thailand using confidence intervals for common mean of several Weibull distributions. PeerJ 11:e15513 https://doi.org/10.7717/peerj.15513
Estimation of genetic variation in yield, its contributing characters and capsaicin content of Capsicum chinense Jacq. (ghost pepper) germplasm from Northeast India
Capsicum chinense Jacq. (ghost pepper), a naturally occurring chili species of Northeast India is known throughout the world for its high pungency and a pleasant aroma. The economic importance is due to the high capsaicinoid levels, the main source for pharmaceutical industries. The present study focused on identifying important traits necessary for increasing the yield and pungency of ghost pepper and to determine the parameters for the selection of superior genotypes. A total of 120 genotypes with more than 1.2% capsaicin content (>1,92,000 Scoville Heat Unit, w/w on dry weight basis) collected from different northeast Indian regions were subjected to variability, divergence and correlation studies. Levene’s homogeneity test of variance studied for three environments did not show significant deviation and so homogeneity of variance was reasonably met for analysis of variance study. Genotypic and phenotypic coefficient of variation was highest for fruit yield per plant (33.702, 36.200, respectively), followed by number of fruits per plant (29.583, 33.014, respectively) and capsaicin content (25.283, 26.362, respectively). The trait number of fruits per plant had maximum direct contribution to fruit yield per plant and the trait fruit yield per plant towards capsaicin content in the correlation study. High heritability with high genetic advance, which is the most favored selection criteria was observed for fruit yield per plant, number of fruits per plant, capsaicin content, fruit length and fruit girth. The genetic divergence study partitioned the genotypes into 20 clusters, where fruit yield per plant contributed maximum towards total divergence. Principal components analysis (PCA) studied to determine the largest contributor of variation showed 73.48% of the total variability, of which the PC1 and PC2 contributed 34.59% and 16.81% respectively.
Baruah et al. (2023) Estimation of genetic variation in yield, its contributing characters and capsaicin content of Capsicum chinense Jacq. (ghost pepper) germplasm from Northeast India. PeerJ 11:e15521 https://doi.org/10.7717/peerj.15521
Comparative analysis of flavonoids, polyphenols and volatiles in roots, stems and leaves of five mangroves
Mangrove plants contain a variety of secondary metabolites, including flavonoids, polyphenols, and volatiles, which are important for their survival and adaptation to the coastal environment, as well as for producing bioactive compounds. To reveal differences in these compounds among five mangrove species’ leaf, root, and stem, the total contents of flavonoids and polyphenols, types and contents of volatiles were determined, analyzed and compared. The results showed that Avicennia marina leaves contained the highest levels of flavonoids and phenolics. In mangrove parts, flavonoids are usually higher than phenolic compounds. A total of 532 compounds were detected by a gas chromatography-mass spectrometry (GC-MS) method in the leaf, root, and stem parts of five mangrove species. These were grouped into 18 classes, including alcohols, aldehydes, alkaloids, alkanes, etc. The number of volatile compounds in A. ilicifolius (176) and B. gymnorrhiza (172) was lower than in the other three species. The number of volatile compounds and their relative contents differed among all three parts of five mangrove species, where the mangrove species factor had a greater impact than the part factor. A total of 71 common compounds occurring in more than two species or parts were analyzed by a PLS-DA model. One-way ANOVA revealed 18 differential compounds among mangrove species and nine differential compounds among parts. Principal component analysis and hierarchical clustering analysis showed that both unique and common compounds significantly differed in composition and concentration between species and parts. In general, A. ilicifolius and B. gymnorrhiza differed significantly from the other species in terms of compound content, while the leaves differed significantly from the other parts. VIP screening and pathway enrichment analysis were performed on 17 common compounds closely related to mangrove species or parts. These compounds were mainly involved in terpenoid pathways such as C10 isoprenoids and C15 isoprenoids and fatty alcohols. The correlation analysis showed that the content of flavonoids/phenolics, the number of compounds, and the content of some common compounds in mangroves were correlated with their salt and waterlogging tolerance levels. These findings will help in the development of genetic varieties and medicinal utilization of mangrove plants.
Wu et al. (2023) Comparative analysis of flavonoids, polyphenols and volatiles in roots, stems and leaves of five mangroves. PeerJ 11:e15529 https://doi.org/10.7717/peerj.15529
Silencing of TRAF5 enhances necroptosis in hepatocellular carcinoma by inhibiting LTBR-mediated NF-κB signaling
Background Hepatocellular carcinoma (HCC) is a common malignancy with poor prognosis and high mortality. This study aimed to explore the oncogenic mechanisms of TRAF5 in HCC and provide a novel therapeutic strategy for HCC. Methods Human HCC cell lines (HepG2, HuH7, SMMC-LM3, and Hep3B), normal adult liver epithelial cells (THLE-2), and human embryonic kidney cells (HEK293T) were utilized. Cell transfection was performed for functional investigation. qRT-PCR and western blotting were used to detect mRNA expression of TRAF5, LTBR, and NF-κB and protein expression of TRAF5, p-RIP1(S166)/RIP1, p-MLKL(S345)/MLKL, LTBR, and p-NF-κB/NF-κB. Cell viability, proliferation, migration, and invasion were evaluated using CCK-8, colony formation, wound healing, and Transwell assays. Cell survival, necrosis, and apoptosis were assessed using flow cytometry and Hoechst 33342/PI double staining. Co-immunoprecipitation and immunofluorescence were performed to determine the interaction between TRAF5 and LTBR. A xenograft model was established to validate the role of TRAF5 in HCC. Results TRAF5 knockdown inhibited HCC cell viability, colony formation, migration, invasion, and survival but enhanced necroptosis. Additionally, TRAF5 is correlated with LTBR and TRAF5 silencing down-regulated LTBR in HCC cells. LTBR knockdown inhibited HCC cell viability, while LTBR overexpression eliminated the effects of TRAF5 deficiency on inhibiting HCC cell proliferation, migration, invasion, and survival. LTBR overexpression abolished the promotive function of TRAF5 knockdown on cell necroptosis. LTBR overexpression undid the suppressive effect of TRAF5 knockdown on NF-κB signaling in HCC cells. Moreover, TRAF5 knockdown suppressed xenograft tumor growth, inhibited cell proliferation, and promoted tumor cell apoptosis. Conclusions TRAF5 deficiency facilitates necroptosis in HCC by suppressing LTBR-mediated NF-κB signaling.
Wu et al. (2023) Silencing of TRAF5 enhances necroptosis in hepatocellular carcinoma by inhibiting LTBR-mediated NF-κB signaling. PeerJ 11:e15551 https://doi.org/10.7717/peerj.15551