title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=272 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines link: https://peerj.com/articles/17797 last-modified: 2024-08-28 description: Numerous aspects of cellular signaling are regulated by the kinome—the network of over 500 protein kinases that guides and modulates information transfer throughout the cell. The key role played by both individual kinases and assemblies of kinases organized into functional subnetworks leads to kinome dysregulation driving many diseases, particularly cancer. In the case of pancreatic ductal adenocarcinoma (PDAC), a variety of kinases and associated signaling pathways have been identified for their key role in the establishment of disease as well as its progression. However, the identification of additional relevant therapeutic targets has been slow and is further confounded by interactions between the tumor and the surrounding tumor microenvironment. In this work, we attempt to link the state of the human kinome, or kinotype, with cell viability in treated, patient-derived PDAC tumor and cancer-associated fibroblast cell lines. We applied classification models to independent kinome perturbation and kinase inhibitor cell screen data, and found that the inferred kinotype of a cell has a significant and predictive relationship with cell viability. We further find that models are able to identify a set of kinases whose behavior in response to perturbation drive the majority of viability responses in these cell lines, including the understudied kinases CSNK2A1/3, CAMKK2, and PIP4K2C. We next utilized these models to predict the response of new, clinical kinase inhibitors that were not present in the initial dataset for model devlopment and conducted a validation screen that confirmed the accuracy of the models. These results suggest that characterizing the perturbed state of the human protein kinome provides significant opportunity for better understanding of signaling behavior and downstream cell phenotypes, as well as providing insight into the broader design of potential therapeutic strategies for PDAC. creator: Matthew E. Berginski creator: Madison R. Jenner creator: Chinmaya U. Joisa creator: Gabriela Herrera Loeza creator: Brian T. Golitz creator: Matthew B. Lipner creator: Jack R. Leary creator: Naim Rashid creator: Gary L. Johnson creator: Jen Jen Yeh creator: Shawn M. Gomez uri: https://doi.org/10.7717/peerj.17797 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Berginski et al. title: Investigating the influence of eco-friendly approaches on saline soil traits and growth of common bean plants (Phaseolus vulgaris L.) link: https://peerj.com/articles/17828 last-modified: 2024-08-28 description: Soil salinization significantly impacts agricultural lands and crop productivity in the study area. Moreover, freshwater scarcity poses a significant obstacle to soil reclamation and agricultural production. Therefore, eco-friendly strategies must be adopted for agro-ecosystem sustainability under these conditions. A study conducted in 2022 and 2023 examined the interaction effects of various soil mulching materials (unmulched, white plastic, rice straw, and sawdust) and chitosan foliar spray application (control, 250 mg L−1 of normal chitosan, 125 mg L−1 of nano chitosan, and 62.5 mg L−1 of nano chitosan) on the biochemical soil characteristics and productivity of common beans in clay-saline soil. Higher organic matter, available nutrient content, and total bacteria count in soils were found under organic mulching treatments (rice straw and sawdust). In contrast, the white plastic mulching treatment resulted in the lowest values of soil electrical conductivity (EC) and the highest soil water content. Conversely, chitosan foliar spray treatments had the least impact on the chemical properties of the soil. Plants sprayed with 62.5 mg L−1 of nano chitosan exhibited higher chlorophyll content, plant height, fresh weight of shoots and roots, seed yield, and nutrient content compared to other chitosan foliar spray applications. All treatments studied led to a significant reduction in fungal communities and Na% in plants. The combined effect of organic mulch materials and foliar spray application of 62.5 mg L−1 nano chitosan appeared to enhance biochemical saline soil properties and common bean productivity. creator: Tamer Khalifa creator: Nasser Ibrahim Abdel-Kader creator: Mohssen Elbagory creator: Mohamed ElSayed Ahmed creator: Esraa Ahmed Saber creator: Alaa El-Dein Omara creator: Rehab Mohamed Mahdy uri: https://doi.org/10.7717/peerj.17828 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Khalifa et al. title: Comparative analysis of biomechanical characteristics between the new Tai Chi elastic band exercise for opening and closing movement and elastic band resistance training for the reverse fly movement link: https://peerj.com/articles/17839 last-modified: 2024-08-28 description: BackgroundThe objective of this study was to compare and analyze the representative opening and closing movement of Tai Chi elastic band exercise with the reverse fly movement of elastic band resistance training. The aim was to explore the biomechanical differences between the two exercises and provide theoretical support for the application of Tai Chi elastic band exercise in health intervention.MethodsA total of 26 male participants were recruited and randomly divided into two groups in a 1:1 ratio. There were 13 participants in each Tai Chi elastic band exercise group and elastic band resistance training group. Both groups of participants used an elastic band to perform movement in the experiment. Experimental data were collected using the Vicon infrared motion capture system and Delsys surface EMG system. The AnyBody software was utilized to simulate the creation of a musculoskeletal model for both exercises.ResultThe study found that the Tai Chi elastic band exercise group exhibited smaller horizontal abduction angle and flexion angle of the shoulder joint, as well as normalized RMS of the anterior deltoid and triceps brachii, compared to the elastic band resistance training group (P < 0.01); the Tai Chi elastic band exercise group exhibited greater elbow flexion angle, elbow flexion torque, and muscle strength of the infraspinatus, coracobrachialis, biceps brachii, brachialis and brachioradialis, compared to the elastic band resistance training group (P < 0.01); the Tai Chi elastic band exercise group exhibited smaller horizontal abduction angular velocity of the shoulder joint and a lower normalized RMS of the posterior deltoid, compared to the elastic band resistance training group (P < 0.05).Conclusion(1) The opening and closing movement of Tai Chi elastic band exercise is characterized by a large elbow flexion angle, a small shoulder joint horizontal angle and flexion angle, and a slow and uniform speed of movement. The reverse fly movement of elastic band resistance training is characterized by a large horizontal abduction angle of the shoulder joint, a large flexion angle of the shoulder joint, a small flexion angle of the elbow joint, and a fast and uneven speed. (2) The opening and closing movement exerts a greater torque on the elbow flexion, while the reverse fly movement exerts a greater torque on the shoulder joint horizontal abduction and external rotation. (3) The opening and closing movement provide greater stimulation to the infraspinatus, coracobrachialis, and elbow flexor, while the reverse fly movement provides greater stimulation to the posterior deltoid, anterior deltoid, subscapularis, and elbow extensor. In summary, the variation in joint angle, joint angular velocity, and hand position could be the factor contributing to the differences in joint torque and muscle activity between the opening and closing movement of Tai Chi elastic band exercise and the reverse fly movement of elastic band resistance training. creator: Mingyu Liu creator: Cuihan Li creator: Xiongfeng Li creator: Jianwei Zhang creator: Haojie Li creator: Yameng Li creator: Qiuyang Wei creator: Zaihao Chen creator: Jiahao Fu creator: Yanying Li creator: Meize Cui creator: Lujia Li creator: Peng Zhang creator: Yuerong Huang creator: Yuxin Ma creator: Jianan Xu creator: Shaojun Lyu creator: Yunchao Ma uri: https://doi.org/10.7717/peerj.17839 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: The role of DNA topoisomerase 1α (AtTOP1α) in regulating arabidopsis meiotic recombination and chromosome segregation link: https://peerj.com/articles/17864 last-modified: 2024-08-28 description: Meiosis is a critical process in sexual reproduction, and errors during this cell division can significantly impact fertility. Successful meiosis relies on the coordinated action of numerous genes involved in DNA replication, strand breaks, and subsequent rejoining. DNA topoisomerase enzymes play a vital role by regulating DNA topology, alleviating tension during replication and transcription. To elucidate the specific function of DNA topoisomerase 1α ($AtTOP1 \alpha$AtTOP1α) in male reproductive development of Arabidopsis thaliana, we investigated meiotic cell division in Arabidopsis flower buds. Combining cytological and biochemical techniques, we aimed to reveal the novel contribution of $AtTOP1 \alpha$AtTOP1α to meiosis. Our results demonstrate that the absence of $AtTOP1 \alpha$AtTOP1α leads to aberrant chromatin behavior during meiotic division. Specifically, the top1α1 mutant displayed altered heterochromatin distribution and clustered centromere signals at early meiotic stages. Additionally, this mutant exhibited disruptions in the distribution of 45s rDNA signals and a reduced frequency of chiasma formation during metaphase I, a crucial stage for genetic exchange. Furthermore, the atm-2×top1α1 double mutant displayed even more severe meiotic defects, including incomplete synapsis, DNA fragmentation, and the presence of polyads. These observations collectively suggest that $AtTOP1 \alpha$AtTOP1α plays a critical role in ensuring accurate meiotic progression, promoting homologous chromosome crossover formation, and potentially functioning in a shared DNA repair pathway with ATAXIA TELANGIECTASIA MUTATED (ATM) in Arabidopsis microspore mother cells. creator: Ibrahim Eid Elesawi creator: Ahmed M. Hashem creator: Li Yao creator: Mohamed Maher creator: Abdallah A. Hassanin creator: Diaa Abd El-Moneim creator: Fatmah A. Safhi creator: Nora M. Al Aboud creator: Salha Mesfer Alshamrani creator: Wael F. Shehata creator: Chen Chunli uri: https://doi.org/10.7717/peerj.17864 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Elesawi et al. title: Evolution of gene regulatory networks by means of selection and random genetic drift link: https://peerj.com/articles/17918 last-modified: 2024-08-28 description: The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. In this study, we implemented a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. The fitness effect of mutations is not constant, rather fitness of each individual is evaluated on the phenotypic level, by measuring its distance from an optimal phenotype. Each individual goes through a maturation period, where its GRN may reach an equilibrium, thus deciding its phenotype. Afterwards, individuals compete to produce the next generation. We examine properties of the GRN evolution, such as robustness against the deleterious effect of mutations and the role of genetic drift. We are able to confirm previous hypotheses regarding the effect of mutations and we provide new insights on the interplay between random genetic drift and natural selection. creator: Stefanos Papadadonakis creator: Antonios Kioukis creator: Charikleia Karageorgiou creator: Pavlos Pavlidis uri: https://doi.org/10.7717/peerj.17918 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Papadadonakis et al. title: Phylogenetic synthesis of morphological and molecular data reveals insights on the classification of diogenid hermit crabs (Crustacea: Decapoda: Anomura) link: https://peerj.com/articles/17922 last-modified: 2024-08-28 description: The family Diogenidae Ortmann, 1892 is a diverse and abundance group of hermit crabs, but their systematics and phylogenetic relationships are highly complex and unresolved. Herein, we gathered nucleotide sequence data from two mitochondrial (16S rRNA and COI) and two nuclear (NaK and PEPCK) genes for a total of 2,308 bp in length across 38 species from six extant diogenid genera. Molecular data were combined with 41 morphological characters to estimate the largest phylogeny of diogenid hermit crabs to date with the aim of testing the proposed taxonomic scheme of Diogenidae and addressing intergeneric relationships within this family. Despite conflicts between mitochondrial and nuclear DNA trees, the combined-data tree reflects the contributions of each dataset, and improves tree resolution and support for internal nodes. Contrary to traditional classification, our total evidence revealed a paraphyletic Diogenidae based on internally nested representatives of Coenobitidae Dana, 1851. Within Diogenidae, the studied diogenid hermit crabs were split between two clades with high support, which contradicts recent morphological classification scheme for Diogenidae sensu lato based on fossil records. The genus Diogenes Dana, 1851 was found nested inside Paguristes Dana, 1851, which formed a clade being separated from the remainder, pointing towards paraphyly in Paguristes. In another clade, Dardanus Paulson, 1875 occupied a basal position relative to the other diogenids, while Calcinus Dana, 1851 and Clibanarius Dana, 1852 showed sister relationships and formed a cluster with Ciliopagurus Forest, 1995. Among the morphological characters examined, carapace shield and telson were identified as phylogenetically significant for grouping diogenid genera, while phylogenetic insignificance of gill number was evidenced by its mosaic pattern in diogenid phylogeny. The present study sheds light on the controversial generic phylogeny of Diogenidae and highlights the necessity for thorough taxonomic revisions of this family as well as some genera (e.g., Paguristes) to reconcile current classifications with phylogenetic relationships. creator: Jiao Cheng creator: Wenjie Li creator: Yanrong Wang creator: Zhongli Sha uri: https://doi.org/10.7717/peerj.17922 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cheng et al. title: Lost, hidden, broken, cut-estimating and interpreting the shapes and masses of damaged assemblages of plesiosaur gastroliths link: https://peerj.com/articles/17925 last-modified: 2024-08-28 description: BackgroundGastroliths are stones of uncertain purpose that are commonly found inside the rib cages of plesiosaur fossils worldwide. Gastroliths from four Alberta (Canada) plesiosaurs were studied to determine both their shapes and masses, and their mass fractions relative to body mass. One animal’s set of gastroliths was 100% complete and fully visible, but the others showed varying degrees of loss, damage or obscuration, so estimations of their original states were needed.MethodsThe studied animals were: Albertonectes vanderveldei, Fluvionectes sloanae, Nichollssaura borealis and Wapuskanectes betsynichollsae. The animals come from three different palaeoenvironments: open marine, near shore marine, and fluvial. Gastrolith shapes were classified as either xiphoid, cylindrical, discoidal or spherical based on observed and/or estimated dimensions. Although not all methods could be applied in all cases, gastrolith shapes and masses were estimated four different ways: (1) direct measurement and weighing of a subset and predicting the properties of the remaining obscured and hidden stones; (2) measuring triaxial ellipsoid dimensions of free stones to calculate volumes and multiplying by the mass density of chert; (3) measuring two visible triaxial dimensions of embedded stones, estimating the hidden third dimension three different ways, and then determining volumes and masses by calculation; and (4) predicting the density and mass of a densely packed cluster of small gastroliths using geometrical arguments.ResultsTotal gastrolith mass never exceeded 0.2% of body mass in any plesiosaur, and is consistent with the idea that the amounts of gastroliths recovered with plesiosaurs would be ineffective as ballast. The largest plesiosaur in the sample had the largest single gastrolith and total gastrolith mass increases with body size. The shape characteristics of the gastroliths were different for different environments, but compositionally they are dominated by black cherts. A possible common source for the gastroliths was identified for the two geographically close and near-contemporanous Nichollssaura and Wapuskanectes. creator: Donald M. Henderson uri: https://doi.org/10.7717/peerj.17925 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Henderson title: The median effective concentration of ropivacaine for ultrasound-guided anterior iliopsoas muscle space block in the elderly undergoing hip surgery: a dose-finding study link: https://peerj.com/articles/17970 last-modified: 2024-08-28 description: BackgroundIn order to improve perioperative pain and reduce the adverse outcome of severe pain in elderly hip fractures, anterior iliopsoas muscle space block (AIMSB) can be used clinically to reduce pain. The aim of the study is to investigate the 50% effective concentration (EC50) of ropivacaine for ultrasound-guided anterior iliopsoas space block in elderly with hip fracture.MethodsA total of 27 patients were enrolled with aged ≥65 years, American society of Anesthesiologists (ASA) physical status classification II–III and undergoing Total Hip Arthroplasty (THA). We measured the EC50 using Dixon’s up-and-down method. Ultrasound-guided AIMSB was performed preoperatively with an initial concentration of 0.2% in the first patient. After a successful or unsuccessful postoperative analgesia, the concentration of local anesthetic was decreased or increased 0.05%, respectively in the next patient. The successful block effect was defined as no sensation to pinprick in the area with femoral nerve, obturator nerve, and lateral femoral cutaneous nerve in 30 min. Meanwhile, the EC50 of ropivacaine was determined by using linear model, linear-logarithmic model, probit regression model, and centered isotonic regression.ResultsA total of 12 patients (48%) had a successful block. All patients with a successful block had a postoperative visual analog scale score of <4 in the 12 h. The estimated EC50 values in linear model, linear-logarithmic model, probit regression model, and centered isotonic regression (a nonparametric method) were 0.268%, 0.259%, 0.277%, and 0.289%. The residual standard error of linear model was the smallest (0.1245).ConclusionThe EC50 of ropivacaine in anterior iliopsoas space block under ultrasound guidance is 0.259–0.289%. creator: Peng Ma creator: Rui Zeng creator: Jiang Peng creator: Juan Zhu creator: Zhaojun Jing creator: Yu Han uri: https://doi.org/10.7717/peerj.17970 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ma et al. title: Assessing the opportunity for selection to impact morphological traits in crosses between two Solanum species link: https://peerj.com/articles/17985 last-modified: 2024-08-28 description: Within biology, there have been long-standing goals to understand how traits impact fitness, determine the degree of adaptation, and predict responses to selection. One key step in answering these questions is to study the mode of gene action or genetic architecture of traits. The genetic architecture underlying a trait will ultimately determine whether selection can lead to a change in the phenotype. Theoretical and empirical research have shown that additive architectures are most responsive to selection. The genus Solanum offers a unique system to quantify the genetic architecture of traits. Crosses between Solanum pennellii and S. lycopersicum, which have evolved unique adaptive traits for very different environments, offer an opportunity to investigate the genetic architecture of a variety of morphological traits that often are not variable within species. We generated cohorts between strains of these two Solanum species and collected phenotypic data for eight morphological traits. The genetic architectures underlying these traits were estimated using an information-theoretic approach to line cross analysis. By estimating the genetic architectures of these traits, we were able to show a key role for maternal and epistatic effects and infer the accessibility of these traits to selection. creator: Jorja Burch creator: Crystal Nava creator: Heath Blackmon uri: https://doi.org/10.7717/peerj.17985 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Burch et al. title: Intervention effect of exercise on working memory in patients with depression: a systematic review link: https://peerj.com/articles/17986 last-modified: 2024-08-28 description: BackgroundThis article aims to systematically evaluate the intervention effect of exercise on working memory in patients with depression.MethodsSix Chinese and English databases were searched for randomized controlled trials (RCTs) about exercise on working memory in patients with depression. PEDro scale was adopted to evaluate the methodological quality of the included articles, GRADEpro scale was employed to evaluate the level of evidence for outcomes, and the Metafor Package in R 4.4.1 was used to analyze the combined effect size, subgroup analyses and publication bias.ResultsA total of 15 studies were included. The meta-analysis indicated that exercise had a statistically significant effect on working memory in patients with depression, with an effect size of 0.16 (95% CI [0.03–0.28], p = 0.02). Exercise type (F(3,34) = 1.99, p = 0.13), intervention content (F(1,36) = 1.60, p = 0.22), and exercise duration (F(1,36) = 0.05, p = 0.83) did not moderate the effect, whereas exercise intensity showed a moderating effect (F(2,35) = 8.83, p < 0.01). There was evidence of publication bias in the study results (t = 2.52, p = 0.02).ConclusionExercise can improve the working memory of patients with depression, and its moderating effect is the best when having low-intensity and moderate-intensity. Research plan was registered in international system evaluation platform PROSPERO (https://www.crd.york.ac.uk/PROSPERO/) (CRD42023475325). creator: Cong Liu creator: Rao Chen creator: So Mang Yun creator: Xing Wang uri: https://doi.org/10.7717/peerj.17986 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al.