Taurine stimulation of planarian motility: a role for the dopamine receptor pathway
Taurine, a normal dietary component that is found in many tissues, is considered important for a number of physiological processes. It is thought to play a particular role in eye development and in the maturation of both the muscular and nervous systems, leading to its suggested use as a therapeutic for Alzheimer’s and Parkinson’s diseases. Taurine increases metabolism and has also been touted as a weight loss aid. Due to its possible benefits to health and development, taurine is added as a supplement to a wide array of products, including infant formula and energy drinks. Despite its pervasive use as a nutritional additive and implied physiological actions, there is little consensus on how taurine functions. This is likely because, mechanistically, taurine has been demonstrated to affect multiple metabolic pathways. Simple models and straightforward assay systems are required to make headway in understanding this complexity. We chose to begin this work using the planarian because these animals have basic, well-understood muscular and nervous systems and are the subjects of many well-tested assays examining how their physiology is influenced by exposure to various environmental, nutritional, and therapeutic agents. We used a simple behavioral assay, the planarian locomotor velocity test (pLmV), to gain insight into the stimulant properties of taurine. Using this assay, we observed that taurine is a mild stimulant that is not affected by sugars or subject to withdrawal. We also provide evidence that taurine makes use of the dopamine D1 receptor to mediate this stimulant effect. Given the pervasiveness of taurine in many commercial products, our findings using the planarian system provide needed insight into the stimulant properties of taurine that should be considered when adding it to the diet.
Livengood et al. (2024) Taurine stimulation of planarian motility: a role for the dopamine receptor pathway. PeerJ 12:e18671 https://doi.org/10.7717/peerj.18671
Motor competence of children in Singapore using Movement ABC-2 test
Introduction The Movement Assessment Battery for Children, 2nd Edition (MABC-2) test is a valuable tool for identifying motor delays in children globally. However, there has been a lack of data for children in Singapore. Methods This study compared 175 children in Singapore (SG) aged 3–6 years to MABC-2 data based on the United Kingdom (UK) population, using statistical tests to analyze age, country, and gender effects on motor competence. Results The results showed a positive age effect across all tasks, with SG children excelling in balance but lagging in aiming and catching tasks compared to UK children. The interaction between age and country yielded mixed results, favoring different groups at various ages. Additionally, girls displayed better manual dexterity and static balance than boys. Conclusion Encouraging more physical activities, especially those involving object manipulation, is crucial for SG children. Establishing local norms for the MABC-2 in Singapore and considering country-specific factors in motor competence evaluations can enhance early intervention strategies. These findings emphasize the importance of tailored approaches to address motor skill development in SG children.
Tan et al. (2024) Motor competence of children in Singapore using Movement ABC-2 test. PeerJ 12:e18446 https://doi.org/10.7717/peerj.18446
Nonadjacent dependencies and sequential structure of chimpanzee action during a natural tool-use task
Many of the complex behaviours of humans involve the production of nonadjacent dependencies between sequence elements, which in part can be generated through the hierarchical organization of sequences. To understand how these structural properties of human behaviours evolved, we can gain valuable insight from studying the sequential behaviours of nonhuman animals. Among the behaviours of nonhuman apes, tool use has been hypothesised to be a domain of behaviour which likely involves hierarchical organization, and may therefore possess nonadjacent dependencies between sequential actions. However thus far, evidence supporting hierarchical organization of great-ape tool use comes from methodologies which have been criticised in their objectivity. Additionally, the extent to which nonadjacent dependencies appear in primate action sequences during tool use has not been formally investigated. We used estimations of mutual information (MI)—a measure of dependency strength between sequence elements—to evaluate both the extent to which wild chimpanzees produce nonadjacent dependencies during a naturalistic tool-use task (nut cracking), as well as how sequences of actions are likely organized during tool use. Half of adult chimpanzees produced nonadjacent dependencies at significantly greater sequential distances than comparable, nonhierarchical Markov models once repeated actions had been accounted for. Additionally, for the majority of chimpanzees, MI decay with increasing sequential distance included a power-law relationship, which is a key indicator that the action sequences produced by chimpanzees likely entail some degree of hierarchical organization. Our analysis offered the greatest support for a system of organization where short subroutines of actions (2–8 actions long) are hierarchically arranged into longer sequences—a finding which is consistent with previous qualitative descriptions of ape tool-use behaviours. Interindividual variability was detected within our analysis in both the maximum distance dependencies were detected, and the most likely structuring mechanism for sequential action organization. We discuss these results in light of possible interindividual variation in the systems of action organization used by chimpanzees during tool use, in addition to methodological considerations for applications of MI estimations to sequential behaviours. Moreover, we discuss our main findings alongside hypotheses for the coevolution of complex syntax in language and tool-action across hominin evolutionary history.
Howard-Spink et al. (2024) Nonadjacent dependencies and sequential structure of chimpanzee action during a natural tool-use task. PeerJ 12:e18484 https://doi.org/10.7717/peerj.18484
PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites
In phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming tool, PhyIN, which deletes regions in which a large proportion of sites (characters) have conflicting phylogenetic signal. It does not require inference of a phylogenetic tree, as it finds neighbouring characters that cannot agree on any possible tree. In phylogenomic data of ultraconserved elements (UCE), PhyIN effectively finds the boundaries between chaotic (conflicted) and orderly regions of alignments with data for only a single locus. Its ability to work on individual loci allows it to preserve discord between gene trees and species trees.
Maddison (2024) PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites. PeerJ 12:e18504 https://doi.org/10.7717/peerj.18504
CYP3A4 and CYP3A5: the crucial roles in clinical drug metabolism and the significant implications of genetic polymorphisms
CYP3A, a key member of the cytochrome P450 (CYP450) superfamily, is integral to drug metabolism, processing a substantial portion of medications. Their role in drug metabolism is particularly prominent, as CYP3A4 and CYP3A5 metabolize approximately 30–50% of known drugs. The genetic polymorphism of CYP3A4/5 is significant inter-individual variability in enzymatic activity, which can result in different pharmacokinetic profiles in response to the same drug among individuals. These polymorphisms can lead to either increased drug toxicity or reduced therapeutic effects, requiring dosage adjustments based on genetic profiles. Consequently, the study of the enzymatic activity of CYP3A4/5 gene variants is of great importance for the formulation of personalized treatment regimens. This article first reviews the role of CYP3A4/5 in drug metabolism in the human body, including inhibitors and inducers of CYP3A4/5 and drug-drug interactions. In terms of genetic polymorphism, it discusses the detection methods, enzymatic kinetic characteristics, and clinical guidelines for CYP3A5. Finally, the article summarizes the importance of CYP3A4/5 in clinical applications, including personalized therapy, management of drug-drug interactions, and adjustment of drug doses. This review contributes to the understanding of the functions and genetic characteristics of CYP3A4/5, allowing for more effective clinical outcomes through optimized drug therapy.
Zhang et al. (2024) CYP3A4 and CYP3A5: the crucial roles in clinical drug metabolism and the significant implications of genetic polymorphisms. PeerJ 12:e18636 https://doi.org/10.7717/peerj.18636
Effects of bamboo biochar on soil physicochemical properties and microbial diversity in tea gardens
Biochar, a carbon-rich material that has attracted considerable interest in interdisciplinary research, is produced through a process known as pyrolysis, which involves the thermal decomposition of organic material in the absence of oxygen. Bamboo biochar is a specific type of biochar, manufactured from bamboo straw through carbonisation at 800 °C and subsequent filtration through a 100-mesh sieve. There is currently a lack of research into the potential benefits of bamboo biochar in improving soil quality in tea gardens. The aim of this study was to investigate the effect of bamboo biochar on the physicochemical properties, enzymatic activity, and microbial community structure of tea garden soils. The results demonstrate that the integration of bamboo biochar into the soil significantly enhanced the soil pH, total nitrogen, available nitrogen, total phosphorus, available phosphorus, available potassium, and slowly available potassium by 15.3%, 52.0%, 91.5%, 91%, 48.4%, 94.2%, and 107.7%, respectively. In addition, soil acid phosphatase activity decreased significantly by 52.5%. In contrast, the activities of sucrase, catalase, and β-glucosidase increased substantially by 54.0%, 68.7%, and 68.4%, respectively, when organic fertilizer and bamboo biochar were applied concurrently. Additionally, the Shannon, Simpson, and Pielou diversity indices of the microbial communities were significantly enhanced. Following the incorporation of bamboo biochar in the soil samples, the relative abundance of Proteobacteria increased significantly, whereas that of Acidobacteria decreased. Various concentrations of bamboo biochar markedly influenced microbial markers in the soil. The results of this study suggest that the application of bamboo biochar to soil may modestly improve its physicochemical properties, enzyme activity, and microbial community structure. These findings provide a foundation for future investigations on soil ecological restoration.
Zhang et al. (2024) Effects of bamboo biochar on soil physicochemical properties and microbial diversity in tea gardens. PeerJ 12:e18642 https://doi.org/10.7717/peerj.18642
A computational framework for processing time-series of earth observation data based on discrete convolution: global-scale historical Landsat cloud-free aggregates at 30 m spatial resolution
Processing large collections of earth observation (EO) time-series, often petabyte-sized, such as NASA’s Landsat and ESA’s Sentinel missions, can be computationally prohibitive and costly. Despite their name, even the Analysis Ready Data (ARD) versions of such collections can rarely be used as direct input for modeling because of cloud presence and/or prohibitive storage size. Existing solutions for readily using these data are not openly available, are poor in performance, or lack flexibility. Addressing this issue, we developed TSIRF (Time-Series Iteration-free Reconstruction Framework), a computational framework that can be used to apply diverse time-series processing tasks, such as temporal aggregation and time-series reconstruction by simply adjusting the convolution kernel. As the first large-scale application, TSIRF was employed to process the entire Global Land Analysis and Discovery (GLAD) ARD Landsat archive, producing a cloud-free bi-monthly aggregated product. This process, covering seven Landsat bands globally from 1997 to 2022, with more than two trillion pixels and for each one a time-series of 156 samples in the aggregated product, required approximately 28 hours of computation using 1248 Intel® Xeon® Gold 6248R CPUs. The quality of the result was assessed using a benchmark dataset derived from the aggregated product and comparing different imputation strategies. The resulting reconstructed images can be used as input for machine learning models or to map biophysical indices. To further limit the storage size the produced data was saved as 8-bit Cloud-Optimized GeoTIFFs (COG). With the hosting of about 20 TB per band/index for an entire 30 m resolution bi-monthly historical time-series distributed as open data, the product enables seamless, fast, and affordable access to the Landsat archive for environmental monitoring and analysis applications.
Spatial and Geographic Information Science
Consoli et al. (2024) A computational framework for processing time-series of earth observation data based on discrete convolution: global-scale historical Landsat cloud-free aggregates at 30 m spatial resolution. PeerJ 12:e18585 https://doi.org/10.7717/peerj.18585
Identification and validation of apoptosis-related genes in acute myocardial infarction based on integrated bioinformatics methods
Background Acute myocardial infarction (AMI) is one of the most serious cardiovascular diseases. Apoptosis is a type of programmed cell death that causes DNA degradation and chromatin condensation. The role of apoptosis in AMI progression remains unclear. Methods Three AMI-related microarray datasets (GSE48060, GSE66360 and GSE97320) were obtained from the Gene Expression Omnibus database and combined for further analysis. Differential expression analysis and enrichment analysis were performed on the combined dataset to identify differentially expressed genes (DEGs). Apoptosis-related genes (ARGs) were screened through the intersection of genes associated with apoptosis in previous studies and DEGs. The expression pattern of ARGs was studied on the basis of their raw expression data. Three machine learning algorithms, Least Absolute Shrinkage and Selection Operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and Random Forest (RF) were utilized to screen crucial genes in these ARGs. Immune infiltration was estimated by single sample gene set enrichment analysis (ssGSEA). Corresponding online databases were used to predict miRNAs, transcription factors (TFs) and therapeutic agents of crucial genes. A nomogram clinical prediction model of the crucial genes was constructed and evaluated. The Mendelian randomization analysis was employed to investigate whether there is a causal relationship between apoptosis and AMI. Finally, an AMI mouse model was established, and apoptosis in the hearts of AMI mice was assessed via TUNEL staining. qRT-PCR was employed to validate these crucial genes in the hearts of AMI mice. The external dataset GSE59867 was used for further validating the crucial genes. Results Fifteen ARGs (GADD45A, DDIT3, FEZ1, PMAIP1, IER3, IFNGR1, CDKN1A, GNA15, IL1B, EREG, BCL10, JUN, EGR3, GADD45B, and CD14) were identified. Six crucial genes (CDKN1A, BCL10, PMAIP1, IL1B, GNA15, and CD14) were screened from ARGs by machine learning. A total of 102 miRNAs, 13 TFs and 23 therapeutic drugs were predicted targeting these crucial genes. The clinical prediction model of the crucial genes has shown good predictive capability. The Mendelian randomization analysis demonstrated that apoptosis is a risk factor for AMI. Lastly, the expression of CDKN1A, CD14 and IL1B was verified in the AMI mouse model and external dataset. Conclusions In this study, ARGs were screened by machine learning algorithms, and verified by qRT-PCR in the AMI mouse model. Finally, we demonstrated that CDKN1A, CD14 and IL1B were the crucial genes involved in apoptosis in AMI. These genes may provide new target for the recognition and intervention of apoptosis in AMI.
Zhu et al. (2024) Identification and validation of apoptosis-related genes in acute myocardial infarction based on integrated bioinformatics methods. PeerJ 12:e18591 https://doi.org/10.7717/peerj.18591
Use of integrated population models for assessing density-dependence and juvenile survival in Northern Bobwhites (Colinus virginianus)
Management of wildlife populations is most effective with a thorough understanding of the interplay among vital rates, population growth, and density-dependent feedback; however, measuring all relevant vital rates and assessing density-dependence can prove challenging. Integrated population models have been proposed as a method to address these issues, as they allow for direct modeling of density-dependent pathways and inference on parameters without direct data. We developed integrated population models from a 25-year demography dataset of Northern Bobwhites (Colinus virginianus) from southern Georgia, USA, to assess the demographic drivers of population growth rates and to estimate the strength of multiple density-dependent processes simultaneously. Furthermore, we utilize a novel approach combining breeding productivity and post-breeding abundance and age-and-sex ratio data to infer juvenile survival. Population abundance was relatively stable for the first 14 years of the study but began growing after 2012, showing that bobwhite populations may be stable or exhibit positive population growth in areas of intensive management. Variation in breeding and non-breeding survival drove changes in population growth in a few years; however, population growth rates were most affected by productivity across the entire study duration. A similar pattern was observed for density-dependence, with relatively stronger negative effects of density on productivity than on survival. Our novel modeling approach required an informative prior but was successful at updating the prior distribution for juvenile survival. Our results show that integrated population models provide an attractive and flexible method for directly modeling all relevant density-dependent processes and for combining breeding and post-breeding data to estimate juvenile survival in the absence of direct data.
Lewis et al. (2024) Use of integrated population models for assessing density-dependence and juvenile survival in Northern Bobwhites (Colinus virginianus). PeerJ 12:e18625 https://doi.org/10.7717/peerj.18625
DNA shuffling to improve crude-water interfacial activity in biosurfactants with OmpA protein of Escherichia coli
Surfactants are molecules derived primarily from petroleum that can reduce the surface tension at interfaces. Their slow degradation is a characteristic that could cause environmental issues. This and other factors contribute to the allure of biosurfactants today. Progress has been made in this area of research, which aims to satisfy the need for effective surfactants that are not harmful to the environment. In previous studies, we demonstrated the surface tension activity of the Escherichia coli transmembrane protein OmpA. Here, we carried out DNA shuffling on ompA to improve its interfacial activity. We evaluated changes in interfacial tension when exposing mutants to a water-oil interface to identify the most promising candidates. Two mutants reached an interfacial tension value lower (9.10 mN/m and 4.24 mN/m) than the original protein OmpA (14.98 mN/m). Since predicted isoelectric point values are far from neutral pH, the charge of the protein was a crucial factor in explaining the migration of proteins towards the interface. Low molecular weight mutants did not exhibit a significant difference in their migration to the interface.
Nuñez Velez et al. (2024) DNA shuffling to improve crude-water interfacial activity in biosurfactants with OmpA protein of Escherichia coli. PeerJ 12:e17239 https://doi.org/10.7717/peerj.17239