title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=486 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: In silico identification and in vitro assessment of a potential anti-breast cancer activity of antimicrobial peptide retrieved from the ATMP1 Anabas testudineus fish peptide link: https://peerj.com/articles/15651 last-modified: 2023-07-19 description: A previous study has shown that synthetic antimicrobial peptides (AMPs) derived from Anabas testudineus (ATMP1) could in-vitro inhibit the progression of breast cancer cell lines. In this study, we are interested in studying altered versions of previous synthetic AMPs to gain some insight into the peptides functions. The AMPs were altered and subjected to bioinformatics prediction using four databases (ADP3, CAMP-R3, AMPfun, and ANTICP) to select the highest anticancer activity. The bioinformatics in silico analysis led to the selection of two AMPs, which are ATMP5 (THPPTTTTTTTTTTTYTAAPATTT) and ATMP6 (THPPTTTTTTTTTTTTTAAPARTT). The in silico analysis predicted that ATMP5 and ATMP6 have anticancer activity and lead to cell death. The ATMP5 and ATMP6 were submitted to deep learning databases (ToxIBTL and ToxinPred2) to predict the toxicity of the peptides and to (AllerTOP & AllergenFP) check the allergenicity. The results of databases indicated that AMPs are non-toxic to normal human cells and allergic to human immunoglobulin. The bioinformatics findings led to select the highest active peptide ATMP5, which was synthesised and applied for in-vitro experiments using cytotoxicity assay MTT Assay, apoptosis detection using the Annexin V FTIC-A assay, and gene expression using Apoptosis PCR Array to evaluate the AMP’s anticancer activity. The antimicrobial activity is approved by the disc diffusion method. The in-vitro experiments analysis showed that ATMP5 had the activity to inhibit the growth of the breast cancer cell line (MDA-MB-231) after 48 h and managed to arrest the cell cycle of the MDA-MB-231, apoptosis induction, and overexpression of the p53 by interaction with the related apoptotic genes. This research opened up new opportunities for developing potential and selective anticancer agents relying on antimicrobial peptide properties. creator: Douglas Law creator: Ahmed Abdulkareem Najm creator: Jia Xuan Chong creator: Joelene Zi Ying K’ng creator: Mas Amran creator: Huey Lih Ching creator: Rui Rui Wong creator: May Ho Leong creator: Ibrahim Mahmood Mahdi creator: Shazrul Fazry uri: https://doi.org/10.7717/peerj.15651 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Law et al. title: Effects of salt stress on seed germination and respiratory metabolism in different Flueggea suffruticosa genotypes link: https://peerj.com/articles/15668 last-modified: 2023-07-19 description: The selection and utilization of ornamental plants that are highly tolerant to salt are helpful for landscape construction and the ecological protection of coastal and arid areas. To evaluate salt tolerance, one of the most used methods is the observation of seed germination under salt stress. Therefore, this work aimed to evaluate the influence of different concentrations of NaCl in water absorption, germination, and respiratory metabolism in seeds of different Flueggea suffruticosa genotypes. P2 and P27, salt-sensitive and salt-tolerant line s of F. suffruticosa, were chosen for treatment with 0, 40, 80, 120, 160, 200, and 240 mM NaCl. F. suffruticosa under salt stress exhibited inhibition of seed germination. The seeds of F. suffruticosa have different times for the physiological phases of water absorption with different NaCl concentrations. Salt stress retarded the seed water absorption process, and it depended on seed genotypes for F. suffruticosa. Soluble sugars accumulated in both P2 and P27 under salt stress. Meanwhile, the activities of hexokinase, 6-phosphofructokinase, pyruvate kinase, pyruvate dehydrogenase, citrate synthase, and glucose-6-phosphate dehydrogenase were overall increased in P27 after salt treatment, which caused increases in pyruvic acid and citric acid. The citrate synthase and glucose-6-phosphate dehydrogenase activities decreased in P2. These results suggest that the respiratory metabolism of salt-tolerant F. suffruticosa was enhanced, compared with the salt-sensitive line, to ameliorate the repression of seed germination under salt stress. The different changes in respiratory metabolism could influence the degree of salt tolerance. creator: Ningwei Xu creator: Bin Lu creator: Yang Wang creator: Xiaoyue Yu creator: Nan Yao creator: Qijuan Lin creator: Xingyou Xu creator: Bingshe Lu uri: https://doi.org/10.7717/peerj.15668 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Xu et al. title: Whistle characterization of long-beaked common dolphin (Delphinus delphis bairdii) in La Paz Bay, Gulf of California link: https://peerj.com/articles/15687 last-modified: 2023-07-19 description: Long-beaked common dolphin (Delphinus delphis bairdii) distribution is limited to the Eastern North Pacific Ocean. Its whistle repertoire is poorly investigated, with no studies in the Gulf of California. The aim of the present study is to characterize the whistles of this species and compare their parameters with different populations. Acoustic monitoring was conducted in La Paz Bay, Gulf of California. Recordings were inspected in spectrogram view in Raven Pro, selecting good quality whistles (n = 270). In the software Luscinia, contours were manually traced to obtain whistle frequencies and duration. Number of steps, inflection points and contour type were visually determined. We calculated the descriptive statistics of the selected whistle parameters and we compared the results with a dolphins population from the Eastern Pacific Ocean. Permutational multivariate analysis of variance (PERMANOVA) was performed to test the intraspecific variation of the whistle parameters among groups. In the present study the mean values (±SD) of the whistle parameters were: maximum frequency = 14.13 ± 3.71 kHz, minimum frequency = 8.44 ± 2.58 kHz and duration = 0.44 ± 0.31 s. Whistles with the upsweep contour were the most common ones (34.44%). The coefficient of variation (CV) values for modulation parameters were high (>100%), in accordance with other studies on dolphins. Whistle parameters showed significant differences among groups. Finally, ending and maximum frequencies, duration and inflection points of the whistles recorded in the present study were lower compared with the parameters of the long-beaked common dolphins from the Eastern Pacific Ocean. This study provides the first whistle characterization of long-beaked common dolphin from the Gulf of California and it will help future passive acoustic monitoring applications in the study area. creator: Óscar Carlón-Beltrán creator: Lorena Viloria-Gómora creator: Jorge Urbán R. creator: Sergio Martínez-Aguilar creator: Simone Antichi uri: https://doi.org/10.7717/peerj.15687 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Carlón-Beltrán et al. title: Investigating the relationship between inbreeding and life expectancy in dogs: mongrels live longer than pure breeds link: https://peerj.com/articles/15718 last-modified: 2023-07-19 description: This study aimed to investigate the establishment of relationship between inbreeding and life expectancy in dogs. A dataset of N = 30,563 dogs sourced from the VetCompass™ Program, UK was made available by the Royal Veterinary College, University of London, containing information about breed and longevity and was subject to survival analysis. A Cox regression proportional hazards model was used to differentiate survivability in three groups of dogs (mongrel, cross-bred and pure breed). The model was found highly significant (p < 0.001) and we found that mongrel dog had the highest life expectancy, followed by cross-bred dogs with only one purebred ancestor and purebred dogs had the lowest life expectancy. A second Cox regression was also found highly significant (p < 0.001) differentiating the lifespan of different dog breed and correlating positively the hazard ratio and the Genetic Illness Severity Index for Dogs (GISID). The results show that survivability is higher in mongrel dogs followed by cross-bred with one of the ancestor only as a pure breed, and pure breed dog have the highest morbidity level. Higher morbidity is associated with higher GISID scores, and therefore, higher inbreeding coefficients. These findings have important implications for dog breeders, owners, and animal welfare organizations seeking to promote healthier, longer-lived dogs. creator: Fernando Mata creator: Andreia Mata uri: https://doi.org/10.7717/peerj.15718 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mata et al. title: Difference in the recruitment of intrinsic foot muscles in the elderly under static and dynamic postural conditions link: https://peerj.com/articles/15719 last-modified: 2023-07-19 description: BackgroundThe effect of foot, especially intrinsic muscles, on postural control and its related mechanisms remain unclear due to the complex structure. Therefore, this study aims to investigate the activation of intrinsic foot muscles in the elderly under static and dynamic postural tasks.MethodsTwenty-one elderly participants were included to perform different postural tests (sensory organization test (SOT), motor control test (MCT), limit of stability test (LOS), and unilateral stance test) by a NeuroCom Balance Manager System. The participants were instructed to maintain postural stability under conditions with combined different sensory inputs (vision, vestibular, and proprioception) in SOT as well as conditions with translation disturbance in MCT, and to perform an active weight-shifting tasks in LOS. During these tasks, muscle activation were simultaneously acquired from intrinsic foot muscles (abductor halluces (AbH) and flexor digitorum brevis (FDB)) and ankle muscles (anterior tibialis, medial head of gastrocnemius, lateral head of gastrocnemius, and peroneus longus). The root-mean-square amplitude of these muscles in postural tasks was calculated and normalized with the EMG activity in unilateral stance task.ResultsThe activation of intrinsic foot muscles significantly differed among different SOT tasks (p < 0.001). Post-hoc tests showed that compared with that under normal condition 1 without sensory interference, EMGs increased significantly under sensory disturbance (conditions 2–6). By contrast, compared with that under the single-sensory disturbed conditions (conditions 2–4; 2 for disturbed vision, 3 for disturbed vestibular sensation, 4 for disturbed proprioception), activation was significantly greater under the dual-sensory disturbed postural tasks (conditions 5 and 6; 5 for disturbed vision and proprioception, 6 for disturbed vestibular sensation and proprioception). In MCT, EMGs of foot muscles increased significantly under different translation speeds (p < 0.001). In LOS, moderate and significant correlations were found between muscle activations and postural stability parameters (AbH, r = 0. 355–0.636, p < 0.05; FDB, r = 0.336–0.622, p < 0.05).ConclusionIntrinsic foot muscles play a complementary role to regulate postural stability when disturbances occur. In addition, the recruitment magnitude of intrinsic foot muscles is positively correlated with the limit of stability, indicating their contribution to increasing the limits of stability in the elderly. creator: Zhangqi Lai creator: Ruiyan Wang creator: Bangguo Zhou creator: Jing Chen creator: Lin Wang uri: https://doi.org/10.7717/peerj.15719 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lai et al. title: Combined effects of dietary faba bean water extract and vitamin K3 on growth performance, textural quality, intestinal characteristics, oxidative and immune responses in grass carp link: https://peerj.com/articles/15733 last-modified: 2023-07-19 description: Faba bean water extract (FBW) and vitamin K3 (VK3) have been demonstrated to improve the muscle textural quality of fish. To better apply these two feed additives in commercial aquaculture setting, four experimental diets (control, commercial feed group; 15% FBW, 15% faba bean water extract group; 2.5% VK3, 2.5% vitamin K3 group; combined group, 15% faba bean water extract + 2.5% vitamin K3 group) were formulated to explore their combined effects of FBW and VK3 on the growth, health status, and muscle textural quality of grass carp. The growth performance, textural quality, intestinal characteristics, and oxidative and immune responses were analyzed on days 40, 80 and 120. The results showed that supplementation with higher doses of FBW and VK3 have no influence on growth-related parameters and immune parameters of grass carp. Notably, compared with the control, fish in the combined group had the highest textural qualities (hardness, chewiness and adhesiveness), followed by those in 15% FBW and 2.5% VK3 groups (P < 0.05). Also, FBW and VK3, to some extent, may lower antioxidative ability of grass carp, as illustrated by lower levels of GSH and CAT in 15% FBW, 2.5% VK3, and combined groups on day 120 (P < 0.05). In addition, enhanced lipase activity was observed in the 15% FBW group. Taken together, the combined supplementation of FBW and VK3 was demonstrated to be a more advanced option than their individual supplementation in a commercial setting owing to the resulting combined effects on both the textural quality and health status of grass carp. creator: Yichao Li creator: Bin Chen creator: Junming Zhang creator: Guangjun Wang creator: Wangbao Gong creator: Jingjing Tian creator: Hongyan Li creator: Kai Zhang creator: Yun Xia creator: Zhifei Li creator: Jun Xie creator: Ermeng Yu uri: https://doi.org/10.7717/peerj.15733 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: mRNA sequencing reveals the distinct gene expression and biological functions in cardiac fibroblasts regulated by recombinant fibroblast growth factor 2 link: https://peerj.com/articles/15736 last-modified: 2023-07-19 description: After myocardial injury, cardiac fibroblasts (CFs) differentiate into myofibroblasts, which express and secrete extracellular matrix (ECM) components for myocardial repair, but also promote myocardial fibrosis. Recombinant fibroblast growth factor 2 (FGF2) protein drug with low molecular weight can promote cell survival and angiogenesis, and it was found that FGF2 could inhibit the activation of CFs, suggesting FGF2 has great potential in myocardial repair. However, the regulatory role of FGF2 on CFs has not been fully elucidated. Here, we found that recombinant FGF2 significantly suppressed the expression of alpha smooth muscle actin (α-SMA) in CFs. Through RNA sequencing, we analyzed mRNA expression in CFs and the differently expressed genes regulated by FGF2, including 430 up-regulated genes and 391 down-regulated genes. Gene ontology analysis revealed that the differentially expressed genes were strongly enriched in multiple biological functions, including ECM organization, cell adhesion, actin filament organization and axon guidance. The results of gene set enrichment analysis (GSEA) show that ECM organization and actin filament organization are down-regulated, while axon guidance is up-regulated. Further cellular experiments indicate that the regulatory functions of FGF2 are consistent with the findings of the gene enrichment analysis. This study provides valuable insights into the potential therapeutic role of FGF2 in treating cardiac fibrosis and establishes a foundation for further research to uncover the underlying mechanisms of CFs gene expression regulated by FGF2. creator: Changye Sun creator: Mengru Bai creator: Yangyang Jia creator: Xiangqin Tian creator: Yonglong Guo creator: Xinhui Xu creator: Zhikun Guo uri: https://doi.org/10.7717/peerj.15736 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Sun et al. title: Leaf nutrient resorption of two life-form tree species in urban gardens and their response to soil nutrient availability link: https://peerj.com/articles/15738 last-modified: 2023-07-19 description: BackgroundLeaf nutrient resorption is a key strategy in plant conservation that minimizes nutrient loss and enhances productivity. However, the differences of the nutrient resorption among garden tree species in urban ecosystems were not clearly understood, especially the differences of nitrogen resorption efficiency (NRE) and phosphorous resorption efficiency (PRE) between evergreen and deciduous trees.MethodsWe selected 40 most generally used garden tree specie belonged two life forms (evergreen and deciduous) and investigated the nitrogen (N) and phosphorus (P) concentrations in green and senesced leaves and soil nutrient concentrations of nine samples trees for each species. Then, the nutrient concentrations and resorption efficiency were compared, and the soil nutrients utilization strategies were further analyzed.ResultsThe results showed that the N concentration was significantly higher in the green and senesced leaves of deciduous trees than in the leaves of evergreen trees. The two life-form trees were both N limited and evergreen trees were more sensitive to N limitation. The NRE and PRE in the deciduous trees were significantly higher than those in the evergreen trees. The NRE was significantly positively correlated with the PRE in the deciduous trees. As the soil N and P concentrations increased, the nutrient resorption efficiency (NuRE) of the evergreen trees increased, but that of the deciduous trees decreased. Compared with the deciduous trees, the evergreen trees were more sensitive to the feedback of soil N and P concentrations. These findings reveal the N and P nutrient resorption mechanism of evergreen and deciduous trees and fill a gap in the understanding of nutrient resorption in urban ecosystems. creator: Ruyuan Hu creator: Tairui Liu creator: Yunxiang Zhang creator: Rongrong Zheng creator: Jinping Guo uri: https://doi.org/10.7717/peerj.15738 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hu et al. title: Optimal tillage depths for enhancing rice yield, quality and lodging resistance in the rice production systems of northeast China link: https://peerj.com/articles/15739 last-modified: 2023-07-19 description: Long-term shallow tillage leads to poor development of root system and deterioration of soil quality. Field experiments were conducted during 2019–2021 to explore the effects of different tillage depths on rice root system, stem lodging resistance, rice yield and quality. The experimental treatments were comprised of four tillage depths i.e., 14 cm (TD 14) as the control, 17 cm (TD17), 20 cm (TD20), and 23 cm (TD23) by using a tractor- mounted hydraulic-adjustable. Results indicated that the TD17 treatment substantially improved the breaking resistance by 39.45–72.37% and decreased the lodging index by 11.73–29.94% of first to third node attribute, increased the stem diameter and unit length dry weight and decreased the internode length, compared with control. The TD17 treatment also reduced the chalkiness, chalkiness rate by 26.23% and 32.30%, respectively. Moreover, the viscosity value and cooking and eating quality of rice in TD17 treatment were improved 27.30% and 12.33%, respectively, compared to control. Moreover, the TD20 treatment enhanced the grain yield by 9.18% owing to the higher panicle number and grain number per panicle. The highest photosynthetic rate was also found in the TD20 treatment, which was significant higher 15.57% than TD14 treatment. Overall, the 17–20 cm was found the optimum tillage depth and therefore recommended to the farmers to get improved rice yield with minimum lodging in the rice production systems of the Northeast China. creator: Diankai Gong creator: Guijin Dai creator: Ying Chen creator: Guangxing Yu uri: https://doi.org/10.7717/peerj.15739 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gong et al. title: Prediction of sea ice area based on the CEEMDAN-SO-BiLSTM model link: https://peerj.com/articles/15748 last-modified: 2023-07-19 description: This article proposes a combined prediction model based on a bidirectional long short-term memory (BiLSTM) neural network optimized by the snake optimizer (SO) under complete ensemble empirical mode decomposition with adaptive noise. First, complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) was used to decompose the sea ice area time series data into a series of eigenmodes and perform noise reduction to enhance the stationarity and smoothness of the time series. Second, this article used a bidirectional long short-term memory neural network optimized by the snake optimizer to fully exploit the characteristics of each eigenmode of the time series to achieve the prediction of each. Finally, the predicted values of each mode are superimposed and reconstructed as the final prediction values. Our model achieves a good score of RMSE: 1.047, MAE: 0.815, and SMAPE: 3.938 on the test set. creator: Qiao Guo creator: Haoyu Zhang creator: Yuhao Zhang creator: Xuchu Jiang uri: https://doi.org/10.7717/peerj.15748 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guo et al.