Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective
Background There have been extensive debates on the interrelationships among the four major classes of Myriapoda—Chilopoda, Symphyla, Diplopoda, and Pauropoda. The core controversy is the position of Pauropoda; that is, whether it should be grouped with Symphyla or Diplopoda as a sister group. Two recent phylogenomic studies separately investigated transcriptomic data from 14 and 29 Myriapoda species covering all four groups along with outgroups, and proposed two different topologies of phylogenetic relationships. Methods Building on these studies, we extended the taxon sampling by investigating 39 myriapods and integrating the previously available data with three new transcriptomic datasets generated in this study. Our analyses present the phylogenetic relationships among the four major classes of Myriapoda with a more abundant taxon sampling and provide a new perspective to investigate the above-mentioned question, where visual genes’ identification were conducted. We compared the appearance pattern of genes, grouping them according to their classes and the visual pathways involved. Positive selection was detected for all identified visual genes between every pair of 39 myriapods, and 14 genes showed positive selection among 27 pairs. Results From the results of phylogenomic analyses, we propose that Symphyla is a sister group of Pauropoda. This stance has also received strong support from tree inference and topology tests.
Wang et al. (2021) Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective. PeerJ 9:e12691 https://doi.org/10.7717/peerj.12691
ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences
The massively parallel nature of next-generation sequencing technologies has contributed to the generation of massive sequence data in the last two decades. Deciphering the meaning of each generated sequence requires multiple analysis tools, at all stages of analysis, from the reads stage all the way up to the whole-genome level. Homology-based approaches based on related reference sequences are usually the preferred option for gene and transcript prediction in newly sequenced genomes, resulting in the popularity of a variety of BLAST and BLAST-based tools. For organelle genomes, a single-reference–based gene finding tool that uses grouping parameters for BLAST results has been implemented in the Genome Search Plotter (GSP). However, this tool does not accept multiple and user-customized reference sequences required for a broad homology search. Here, we present multiple Reference–based Gene Search and Plot (ReGSP), a simple and convenient web tool that accepts multiple reference sequences for homology-based gene search. The tool incorporates cPlot, a novel dot plot tool, for illustrating nucleotide sequence similarity between the query and the reference sequences. ReGSP has an easy-to-use web interface and is freely accessible at https://ds.mju.ac.kr/regsp.
Ejigu et al. (2021) ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences. PeerJ 9:e12707 https://doi.org/10.7717/peerj.12707
Identifying biomarkers for evaluating wound extent and age in the contused muscle of rats using microarray analysis: a pilot study
Wound age estimation is still one of the most important and significant challenges in forensic practice. The extent of wound damage greatly affects the accuracy and reliability of wound age estimation, so it is important to find effective biomarkers to help diagnose wound degree and wound age. In the present study, the gene expression profiles of both mild and severe injuries in 33 rats were assayed at 0, 1, 3, 24, 48, and 168 hours using the Affymetrix microarray system to provide biomarkers for the evaluation of wound age and the extent of the wound. After obtaining thousands of differentially expressed genes, a principal component analysis, the least absolute shrinkage and selection operator, and a time-series analysis were used to select the most predictive prognostic genes. Finally, 15 genes were screened for evaluating the extent of wound damage, and the top 60 genes were also screened for wound age estimation in mild and severe injury. Selected indicators showed good diagnostic performance for identifying the extent of the wound and wound age in a Fisher discriminant analysis. A function analysis showed that the candidate genes were mainly related to cell proliferation and the inflammatory response, primarily IL-17 and the Hematopoietic cell lineage signalling pathway. The results revealed that these genes play an essential role in wound-healing and yield helpful and valuable potential biomarkers for further targeted studies.
Li et al. (2021) Identifying biomarkers for evaluating wound extent and age in the contused muscle of rats using microarray analysis: a pilot study. PeerJ 9:e12709 https://doi.org/10.7717/peerj.12709
Unique spicules may confound species differentiation: taxonomy and biogeography of Melonanchora Carter, 1874 and two new related genera (Myxillidae: Poecilosclerida) from the Okhotsk Sea
Sponges are amongst the most difficult benthic taxa to properly identify, which has led to a prevalence of cryptic species in several sponge genera, especially in those with simple skeletons. This is particularly true for sponges living in remote or hardly accessible environments, such as the deep-sea, as the inaccessibility of their habitat and the lack of accurate descriptions usually leads to misclassifications. However, species can also remain hidden even when they belong to genera that have particularly characteristic features. In these cases, researchers inevitably pay attention to these peculiar features, sometimes disregarding small differences in the other “typical” spicules. The genus Melonanchora Carter, 1874, is among those well suited for a revision, as their representatives possess a unique type of spicule (spherancorae). After a thorough review of the material available for this genus from several institutions, four new species of Melonanchora, M. tumultuosa sp. nov., M. insulsa sp. nov., M. intermedia sp. nov. and M. maeli sp. nov. are formally described from different localities across the Atlanto-Mediterranean region. Additionally, all Melonanchora from the Okhotsk Sea and nearby areas are reassigned to other genera; Melonanchora kobjakovae is transferred to Myxilla (Burtonanchora) while two new genera, Hanstoreia gen. nov. and Arhythmata gen. nov. are created to accommodate Melonanchora globogilva and Melonanchora tetradedritifera, respectively. Hanstoreia gen. nov. is closest to Melonanchora, whereas Arhythmata gen. nov., is closer to Stelodoryx, which is most likely polyphyletic and in need of revision.
Santín et al. (2021) Unique spicules may confound species differentiation: taxonomy and biogeography of Melonanchora Carter, 1874 and two new related genera (Myxillidae: Poecilosclerida) from the Okhotsk Sea. PeerJ 9:e12515 https://doi.org/10.7717/peerj.12515
Development of a T-cell activation-related module with predictive value for the prognosis and immune checkpoint blockade therapy response in glioblastoma
Background Despite the rise in the use of immune checkpoint blockade drugs (ICBs) in recent years, there are no ICB drugs that are currently approved or under large-scale clinical trials for glioblastoma (GBM). T-cells, which mainly mediate adaptive immunity, are an important part of the tumor immune microenvironment. The activation of T-cells in tumors plays a key role in evaluating the sensitivity of patients to immunotherapy. Therefore, we applied bioinformatics approaches to construct a T-cell activation related risk score to study the effect of the activation of T-cells on the prognosis and ICB response of patients with GBM. Materials and Methods This study collected TCGA, CGGA, and GSE16011 glioma cohorts, as well as the IMvigor210 immunotherapy dataset, with complete mRNA expression profiles and clinical information. GraphPad Prism 8 and R 3.6.3 were used for bioinformatics analysis and plotting. Results The activation of T-cells in patients with GBM is characterized by obvious heterogeneity. We established a T-cell activation-related risk score based on five univariate Cox regression prognostic genes (CD276, IL15, SLC11A1, TNFSF4, and TREML2) in GBM. The risk score was an independent risk factor for poor prognosis. The overall survival time of patients in the high-risk group was significantly lower than in the low-risk group. Moreover, the high-risk score was accompanied by a stronger immune response and a more complex tumor immune microenvironment. “Hot tumors” were mainly enriched in the high-risk group, and high-risk group patients highly expressed inhibitory immune checkpoints (PD1, PD-L1, TIM3 etc.). By combining the risk and priming scores we obtained the immunotherapy score, which was shown to be a good evaluation index for sensitivity to GBM immunotherapy. Conclusions As an independent risk factor for poor prognosis, the T-cell activation-related risk score, combined with other clinical characteristics, could efficiently evaluate the survival of patients with GBM. The immunotherapy score obtained by combining the risk and priming scores could evaluate the ICB response of patients with GBM, providing treatment opportunities.
Yan et al. (2021) Development of a T-cell activation-related module with predictive value for the prognosis and immune checkpoint blockade therapy response in glioblastoma. PeerJ 9:e12547 https://doi.org/10.7717/peerj.12547
The metabolism and role of free fatty acids in key physiological processes in insects of medical, veterinary and forensic importance
Insects are the most widespread group of organisms and more than one million species have been described. These animals have significant ecological functions, for example they are pollinators of many types of plants. However, they also have direct influence on human life in different manners. They have high medical and veterinary significance, stemming from their role as vectors of disease and infection of wounds and necrotic tissue; they are also plant pests, parasitoids and predators whose activities can influence agriculture. In addition, their use in medical treatments, such as maggot therapy of gangrene and wounds, has grown considerably. They also have many uses in forensic science to determine the minimum post-mortem interval and provide valuable information about the movement of the body, cause of the death, drug use, or poisoning. It has also been proposed that they may be used as model organisms to replace mammal systems in research. The present review describes the role of free fatty acids (FFAs) in key physiological processes in insects. By focusing on insects of medical, veterinary significance, we have limited our description of the physiological processes to those most important from the point of view of insect control; the study examines their effects on insect reproduction and resistance to the adverse effects of abiotic (low temperature) and biotic (pathogens) factors.
Kaczmarek et al. (2021) The metabolism and role of free fatty acids in key physiological processes in insects of medical, veterinary and forensic importance. PeerJ 9:e12563 https://doi.org/10.7717/peerj.12563
Wearable technology to inform the prediction and diagnosis of cardiorespiratory events: a scoping review
Background The need for health systems that allow for continuous monitoring and early adverse event detection in individuals outside of the acute care setting has been highlighted by the global rise in chronic cardiorespiratory diseases and the recent COVID-19 pandemic. Currently, it is unclear what type of evidence exists concerning the use of physiological data collected from commercially available wrist and textile wearables to assist in clinical decision making. The aim of this review was therefore to systematically map and summarize the scientific literature surrounding the use of these wearables in clinical decision making as well as identify knowledge gaps to inform further research. Methodology Six electronic bibliographic databases were systematically searched (Ovid MEDLINE, EMBASE, CINAHL, PubMed, Scopus, and SportsDiscus). Publications from database inception to May 6, 2020 were reviewed for inclusion. Non-indexed literature relevant to this review was also searched systematically. Results were then collated, summarized and reported. Results A total of 107 citations were retrieved and assessed for eligibility with 31 citations included in the final analysis. A review of the 31 papers revealed three major study designs which included (1) observational studies (n = 19), (2) case control series and reports (n = 8), and (3) reviews (n = 2). All papers examined the use of wearable monitoring devices for clinical decisions in the cardiovascular domain, with cardiac arrhythmias being the most studied. When compared to electrocardiogram (ECG) the performance of the wearables in facilitating clinical decisions varied depending upon the type of wearable, user’s activity levels and setting in which they were employed. Observational studies collecting data in the inpatient and outpatient settings were equally represented. Eight case control series and reports were identified which reported on the use of wrist wearables in patients presenting to an emergency department or clinic to aid in the clinical diagnosis of a cardiovascular event. Two narrative reviews were identified which examined the impact of wearable devices in monitoring cardiovascular disease as well as potential challenges they may pose in the future. Conclusions To date, studies employing wearables to facilitate clinical decisions have largely focused upon the cardiovascular domain. Despite the ability of some wearables to collect physiological data accurately, there remains a need for a specialist physician to retrospectively review the raw data to make a definitive diagnosis. Analysis of the results has also highlighted gaps in the literature such as the absence of studies employing wearables to facilitate clinical decisions in the respiratory domain. The disproportionate study of wearables in atrial fibrillation detection in comparison to other cardiac arrhythmias and conditions, as well as the lack of diversity in the sample populations used prevents the generalizability of results.
Khundaqji et al. (2021) Wearable technology to inform the prediction and diagnosis of cardiorespiratory events: a scoping review. PeerJ 9:e12598 https://doi.org/10.7717/peerj.12598
Effects of short-term nitrogen and phosphorus addition on leaf stoichiometry of a dominant alpine grass
The effects of increasing nitrogen (N) and phosphorus (P) deposition on the nutrient stoichiometry of soil and plant are gaining improving recognition. However, whether and how the responses of N cycle coupled with P of the soil–plant system to external N and P deposition in alpine grassland is still unclear. A short-term external N and P addition experiment was conducted in an alpine grazing grassland in the KunLun Mountain to explore the effects of short-term N and P addition on the nutrient stoichiometry in soil and plant. Different rates of N addition (ranging from 0.5 g N m−2 yr−1 to 24 g N m−2 yr−1) and P addition (ranging from 0.05 g N m−2 yr−1 to 3.2 g P m−2 yr−1) were supplied, and the soil available N, P, leaf N and P stoichiometry of Seriphidium rhodanthum which dominant in the alpine ecosystem were measured. Results showed that N addition increased soil inorganic N, leaf C, leaf N, and leaf N:P ratio but decreased soil available P and leaf C:P. Furthermore, P addition increased soil available P, leaf P, soil inorganic N, leaf N, and leaf C and reduced leaf C:N, C:P, and N:P ratios. Leaf N:P was positively related to N addition gradient. Leaf C:P and leaf N:P were significantly negatively related to P addition gradient. Although external N and P addition changed the value of leaf N:P, the ratio was always lower than 16 in all treatments. The influences of P addition on soil and plant mainly caused the increase in soil available P concentration. In addition, the N and P cycles in the soil–plant system were tightly coupled in P addition but decoupled in N addition condition. The nutrient stoichiometry of soil and leaf responded differently to continuous N and P addition gradients. These data suggested that the alpine grazing grassland was limited by P rather than N due to long-term N deposition and uniform fertilization. Moreover, increasing P addition alleviated P limitation. Therefore, the imbalanced N and P input could change the strategy of nutrient use of the grass and then change the rates of nutrient cycling in the alpine grassland ecosystem in the future.
Liu et al. (2021) Effects of short-term nitrogen and phosphorus addition on leaf stoichiometry of a dominant alpine grass. PeerJ 9:e12611 https://doi.org/10.7717/peerj.12611
Identification of HMMR as a prognostic biomarker for patients with lung adenocarcinoma via integrated bioinformatics analysis
Background Lung adenocarcinoma (LUAD) is the most prevalent tumor in lung carcinoma cases and threatens human life seriously worldwide. Here we attempt to identify a prognostic biomarker and potential therapeutic target for LUAD patients. Methods Differentially expressed genes (DEGs) shared by GSE18842, GSE75037, GSE101929 and GSE19188 profiles were determined and used for protein-protein interaction analysis, enrichment analysis and clinical correlation analysis to search for the core gene, whose expression was further validated in multiple databases and LUAD cells (A549 and PC-9) by quantitative real-time PCR (qRT-PCR) and western blot analyses. Its prognostic value was estimated using the Kaplan-Meier method, meta-analysis and Cox regression analysis based on the Cancer Genome Atlas (TCGA) dataset and co-expression analysis was conducted using the Oncomine database. Gene Set Enrichment Analysis (GSEA) was performed to illuminate the potential functions of the core gene. Results A total of 115 shared DEGs were found, of which 24 DEGs were identified as candidate hub genes with potential functions associated with cell cycle and FOXM1 transcription factor network. Among these candidates, HMMR was identified as the core gene, which was highly expressed in LUAD as verified by multiple datasets and cell samples. Besides, high HMMR expression was found to independently predict poor survival in patients with LUAD. Co-expression analysis showed that HMMR was closely related to FOXM1 and was mainly involved in cell cycle as suggested by GSEA. Conclusion HMMR might be served as an independent prognostic biomarker for LUAD patients, which needs further validation in subsequent studies.
Li et al. (2021) Identification of HMMR as a prognostic biomarker for patients with lung adenocarcinoma via integrated bioinformatics analysis. PeerJ 9:e12624 https://doi.org/10.7717/peerj.12624
3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.
Tross et al. (2021) 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves. PeerJ 9:e12628 https://doi.org/10.7717/peerj.12628