SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus
Background Ananas comosus var. bracteatus is an herbaceous perennial monocot cultivated as an ornamental plant for its chimeric leaves. Because of its genomic complexity, and because no genomic information is available in the public GenBank database, the complete structure of the mRNA transcript is unclear and there are limited molecular mechanism studies for Ananas comosus var. bracteatus. Methods Three size fractionated full-length cDNA libraries (1–2 kb, 2–3 kb, and 3–6 kb) were constructed and subsequently sequenced in five single-molecule real-time (SMRT) cells (2 cells, 2 cells, and 1 cell, respectively). Results In total, 19,838 transcripts were identified for alternative splicing (AS) analysis. Among them, 19,185 (96.7%) transcripts were functionally annotated. A total of 9,921 genes were identified by mapping the non-redundant isoforms to the reference genome. A total of 10,649 AS events were identified, the majority of which were intron retention events. The alternatively spliced genes had functions in the basic metabolism processes of the plant such as carbon metabolism, amino acid biosynthesis, and glycolysis. Fourteen genes related to chlorophyll biosynthesis were identified as having AS events. The distribution of the splicing sites and the percentage of conventional and non-canonical AS sites of the genes categorized in pathways related to the albino leaf phenotype (ko00860, ko00195, ko00196, and ko00710) varied greatly. The present results showed that there were 8,316 genes carrying at least one poly (A) site, which generated 21,873 poly (A) sites. These findings indicated that the quality of the gene structure and functional information of the obtained genome was greatly improved, which may facilitate further genetic study of Ananas comosus var. bracteatus.
Ma et al. (2019) SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus. PeerJ 7:e7062 https://doi.org/10.7717/peerj.7062
Isolation and functional characterization of two dioxygenases putatively involved in bixin biosynthesis in annatto (Bixa orellana L.)
Carotenoid cleavage dioxygenases (CCDs) are enzymes that have been implicated in the biosynthesis of a wide diversity of secondary metabolites with important economic value, including bixin. Bixin is the second most used pigment in the world’s food industry worldwide, and its main source is the aril of achiote (Bixa orellana L.) seeds. A recent transcriptome analysis of B. orellana identified a new set of eight CCD members (BoCCD4s and BoCCD1s) potentially involved in bixin synthesis. We used several approaches in order to discriminate the best candidates with CCDs genes. A reverse transcription-PCR (RT-qPCR) expression analysis was carried out in five developmental stages of two accessions of B. orellana seeds with different bixin contents: (P13W, low bixin producer and N4P, high bixin producer). The results showed that three BoCCDs (BoCCD4-1, BoCCD4-3, and BoCCD1-1) had an expression pattern consistent with bixin accumulation during seed development. Additionally, an alignment of the CCD enzyme family and homology models of proteins were generated to verify whether the newly proposed CCD enzymes were bona fide CCDs. The study confirmed that these three enzymes were well-preserved and belonged to the CCD family. In a second selection round, the three CCD genes were analyzed by in situ RT-qPCR in seed tissue. Results indicated that BoCCD4-3 and BoCCD1-1 exhibited tissue-specific expressions in the seed aril. To test whether the two selected CCDs had enzymatic activity, they were expressed in Escherichia coli; activity was determined by identifying their products in the crude extract using UHPLC-ESI-QTOF-MS/MS. The cleavage product (bixin aldehyde) was also analyzed by Fourier transform infrared. The results indicated that both BoCCD4-3 and BoCCD1-1 cleave lycopene in vitro at 5,6-5′,6′.
Carballo-Uicab et al. (2019) Isolation and functional characterization of two dioxygenases putatively involved in bixin biosynthesis in annatto (Bixa orellana L.). PeerJ 7:e7064 https://doi.org/10.7717/peerj.7064
Wnt signaling in liver disease: emerging trends from a bibliometric perspective
Background The Wnt signaling pathway, an evolutionarily conserved molecular transduction cascade, has been identified as playing a pivotal role in various physiological and pathological processes of the liver, including homeostasis, regeneration, cirrhosis, and hepatocellular carcinoma (HCC). In this study, we aimed to use a bibliometric method to evaluate the emerging trends on Wnt signaling in liver diseases. Methods Articles were retrieved from the Web of Science Core Collection. We used a bibliometric software, CiteSpace V 5.3.R4, to analyze the active countries or institutions in the research field, the landmark manuscripts, important subtopics, and evolution of scientific ideas. Results In total, 1,768 manuscripts were published, and each was cited 33.12 times on average. The U.S. published most of the articles, and the most active center was the University of Pittsburgh. The top 5 landmark papers were identified by four bibliometric indexes including citation, burstness, centrality, and usage 2013. The clustering process divided the whole area into nine research subtopics, and the two major important subtopics were “liver zonation” and “HCC.” Using the “Part-of-Speech” technique, 1,743 terms representing scientific ideas were identified. After 2008, the bursting phrases were “liver development,” “progenitor cells,” “hepatic stellate cells,” “liver regeneration,” “liver fibrosis,” “epithelial-mesenchymal transition,” and etc. Conclusion Using bibliometric methods, we quantitatively summarized the advancements and emerging trends in Wnt signaling in liver diseases. These bibliometric findings may pioneer the future direction of this field in the next few years, and further studies are needed.
Jiang et al. (2019) Wnt signaling in liver disease: emerging trends from a bibliometric perspective. PeerJ 7:e7073 https://doi.org/10.7717/peerj.7073
Metabolomic and biochemical characterization of a new model of the transition of acute kidney injury to chronic kidney disease induced by folic acid
Background Renal diseases represent a major public health problem. The demonstration that maladaptive repair of acute kidney injury (AKI) can lead to the development of chronic kidney disease (CKD) and end-stage renal disease has generated interest in studying the pathophysiological pathways involved. Animal models of AKI–CKD transition represent important tools to study this pathology. We hypothesized that the administration of multiple doses of folic acid (FA) would lead to a progressive loss of renal function that could be characterized through biochemical parameters, histological classification and nuclear magnetic resonance (NMR) profiling. Methods Wistar rats were divided into groups: the control group received a daily intraperitoneal (I.P.) injection of double-distilled water, the experimental group received a daily I.P. injection of FA (250 mg kg body weight−1). Disease was classified according to blood urea nitrogen level: mild (40–80 mg dL−1), moderate (100–200 mg dL−1) and severe (>200 mg dL−1). We analyzed through biochemical parameters, histological classification and NMR profiling. Results Biochemical markers, pro-inflammatory cytokines and kidney injury biomarkers differed significantly (P < 0.05) between control and experimental groups. Histology revealed that as damage progressed, the degree of tubular injury increased, and the inflammatory infiltrate was more evident. NMR metabolomics and chemometrics revealed differences in urinary metabolites associated with CKD progression. The main physiological pathways affected were those involved in energy production and amino-acid metabolism, together with organic osmolytes. These data suggest that multiple administrations of FA induce a reproducible model of the induction of CKD. This model could help to evaluate new strategies for nephroprotection that could be applied in the clinic.
Perales-Quintana et al. (2019) Metabolomic and biochemical characterization of a new model of the transition of acute kidney injury to chronic kidney disease induced by folic acid. PeerJ 7:e7113 https://doi.org/10.7717/peerj.7113
A functional magnetic resonance imaging investigation of the autonomous sensory meridian response
Background Autonomous Sensory Meridian Response (ASMR) is a sensory-emotional experience in which specific stimuli (ASMR “triggers”) elicit tingling sensations on the scalp, neck, and shoulders; these sensations are accompanied by a positive affective state. In the current research, functional magnetic resonance imaging (fMRI) was used in order to delineate the neural substrates of these responses. Methods A total of 17 individuals with ASMR and 17 age- and sex-matched control participants underwent fMRI scanning while watching six 4-minute videos. Three of the videos were designed to elicit ASMR tingling and three videos were not. Results The results demonstrated that ASMR videos have a distinct effect on the neural activity of individuals with ASMR. The contrast of ASMR participants’ responses to ASMR videos showed greater activity in the cingulate gyrus as well as in cortical regions related to audition, movement, and vision. This activity was not observed in control participants. The contrast of ASMR and control participants’ responses to ASMR-eliciting videos detected greater activity in right cingulate gyrus, right paracentral lobule, and bilateral thalamus in ASMR participants; control participants showed greater activity in the lingula and culmen of the cerebellum. Conclusions Together, these results highlight the fact that ASMR videos elicit activity in brain areas related to sensation, emotion, and attention in individuals with ASMR, but not in matched control participants.
Smith et al. (2019) A functional magnetic resonance imaging investigation of the autonomous sensory meridian response. PeerJ 7:e7122 https://doi.org/10.7717/peerj.7122
Molecular mechanisms linking peri-implantitis and type 2 diabetes mellitus revealed by transcriptomic analysis
Aims To explore molecular mechanisms that link peri-implantitis and type 2 diabetes mellitus (T2DM) by bioinformatic analysis of publicly available experimental transcriptomic data. Materials and methods Gene expression data from peri-implantitis were downloaded from the Gene Expression Omnibus database, integrated and differentially expressed genes (DEGs) in peri-implantitis were identified. Next, experimentally validated and computationally predicted genes related to T2DM were downloaded from the DisGeNET database. Protein–protein interaction network (PPI) pairs of DEGs related to peri-implantitis and T2DM related genes were constructed, “hub” genes and overlapping DEG were determined. Functional enrichment analysis was used to identify significant shared biological processes and signaling pathways. The PPI networks were subjected to cluster and specific class analysis for identifying “leader” genes. Module network analysis of the merged PPI network identified common or cross-talk genes connecting the two networks. Results A total of 92 DEGs overlapped between peri-implantitis and T2DM datasets. Three hub genes (IL-6, NFKB1, and PIK3CG) had the highest degree in PPI networks of both peri-implantitis and T2DM. Three leader genes (PSMD10, SOS1, WASF3), eight cross-talk genes (PSMD10, PSMD6, EIF2S1, GSTP1, DNAJC3, SEC61A1, MAPT, and NME1), and one signaling pathway (IL-17 signaling) emerged as peri-implantitis and T2DM linkage mechanisms. Conclusions Exploration of available transcriptomic datasets revealed IL-6, NFKB1, and PIK3CG expression along with the IL-17 signaling pathway as top candidate molecular linkage mechanisms between peri-implantitis and T2DM.
Yu et al. (2019) Molecular mechanisms linking peri-implantitis and type 2 diabetes mellitus revealed by transcriptomic analysis. PeerJ 7:e7124 https://doi.org/10.7717/peerj.7124
Response patterns of routinely measured inflammatory and coagulatory parameters in sepsis
Background Sepsis is characterized by a pro-inflammatory and pro-coagulatory shift which can induce life-threatening complications. Close monitoring and risk stratification of sepsis patients is crucial for proper treatment and consequently patient outcome. Therefore, this study focuses on the response patterns of inflammatory and coagulatory parameters used in clinical routines to estimate the course of sepsis. Methods A total of 1,110 patients diagnosed with sepsis were retrospectively analyzed to identify response patterns for risk stratification of routine parameters measured at the peak level of C-reactive protein. Cluster analysis was used and the differences in the patient characteristics and 28-day survival were assessed. Cox proportional hazards regression model for survival stratified by the clusters was performed. Results The analyses revealed the parameters to have five distinct response patterns. These clusters reflect the etiology as well as the course of sepsis associated with different mortalities. Here, impairment of the liver plays a crucial role in the ability to appropriately respond to sepsis. Of the routinely measured parameters, C-reactive protein and antithrombin seem to be unspecific for stratification of septic patients. Adjusted for the individual clusters, survival was associated with an increase in fibrinogen (p = 0.0042), platelets (p = 0.0003) and PT (p = 0.001) as well as a decrease in leukocytes (p = 0.034). Conclusions This study reveals that patients have distinct response patterns of inflammatory and coagulatory parameters depending on disease etiology. These patterns are associated with different mortalities although the patients have similar levels of C-reactive protein. Independently of the type of response, good coagulatory capacity seems to be crucial for patient survival.
Bachler et al. (2019) Response patterns of routinely measured inflammatory and coagulatory parameters in sepsis. PeerJ 7:e7147 https://doi.org/10.7717/peerj.7147
Diagnostic performance of clinical properties and conventional magnetic resonance imaging for determining the IDH1 mutation status in glioblastoma: a retrospective study
Background Glioblastoma (GBM), the most malignant form of gliomas, is a relatively common primary brain tumor in adults. Preoperative identification of isocitrate dehydrogenase 1 (IDH1) mutations in GBM is of critical prognostic importance. The aim of the present study was to explore the feasibility and diagnostic performance of basic patient information combined with conventional magnetic resonance imaging (MRI) findings for determination of the IDH1 status (mutant vs wild type) in patients with GBM. Methods From January 1, 2016 to December 31, 2017, a consecutive series of 50 patients with GBM was retrospectively collected. The patients were divided into two group according to their IDH1 mutation status. Basic information and MRI features were analyzed for the establishment of a diagnostic prediction model using logistic regression. A receiver operating characteristic curve was used to evaluate the diagnostic performance. Results Patients with IDH1-mutant tumors were younger than those with IDH1-wild type tumors, and exhibited a larger tumor volume. The diagnostic predictive model established by combining age and the tumor size exhibited a sensitivity and specificity of 70% and 93%, respectively. The area under the curve was 0.88, which indicated high diagnostic performance. Conclusion Patient age and tumor volume can be used as indicators of IDH1 mutation status in patients with GBM, with high diagnostic performance for simple evaluations in clinical practice. The combined use of these two indicators can further enhance the diagnostic specificity.
Wang et al. (2019) Diagnostic performance of clinical properties and conventional magnetic resonance imaging for determining the IDH1 mutation status in glioblastoma: a retrospective study. PeerJ 7:e7154 https://doi.org/10.7717/peerj.7154
Initial decomposition of floating leaf blades of waterlilies: causes, damage types and impacts
The initial decomposition of large floating-leaved macrophytes, such as waterlilies, can be studied by following changes in leaf damage and area loss of leaf blades tagged in their natural environment. This approach was taken in the present study to examine the initial decomposition patterns of floating leaf blades of Nuphar lutea (L.) Sm., Nymphaea alba L. and Nymphaea candida C. Presl at three freshwater sites differing in nutrient status, alkalinity and pH. Floating leaf blades of the three plant species were tagged and numbered within established replicate plots and the leaf length, percentages and types of damage and decay of all tagged leaves were recorded weekly during the growing season. Microbial decay, infection by phytopathogenic fungi (Colletotrichum nymphaeae) and oomycetes (Pythium sp.), consumption by pond snails, and mechanical factors were the most important causes of leaf damage. Several types of succession comprising different causes of damage were distinguished during the season. For example, young floating leaves are affected by more or less specialized invertebrate species consuming leaf tissue, followed by non-specialized invertebrate species feeding on the damaged floating leaves. In the two investigated hardwater lakes the seasonal patterns of initial decomposition differed between Nymphaea and Nuphar.
Klok et al. (2019) Initial decomposition of floating leaf blades of waterlilies: causes, damage types and impacts. PeerJ 7:e7158 https://doi.org/10.7717/peerj.7158
Isisfordia molnari sp. nov., a new basal eusuchian from the mid-Cretaceous of Lightning Ridge, Australia
The Australian Mesozoic crocodyliform record is sparse in comparison to other Gondwanan localities. A single formally-named taxon is known from this interval; Isisfordia duncani (Winton Formation, Albian–Turonian, Queensland). We present a previously undescribed crocodyliform braincase from the Griman Creek Formation (Cenomanian), New South Wales, which we assign to Isisfordia molnari sp. nov. Assignment to the genus is based on the possession of a newly-defined autapomorphy of Isisfordia: a broadly exposed prootic within the supratemporal foramen. A second autapomorphy of I. duncani (maximum diameter of the caudal aperture of the cranioquadrate siphonium approximately one-third the mediolateral width of the foramen magnum, with the lateral wall of the caudal aperture formed exclusively by the quadrate) may also be present in I. molnari; however, definitive recognition of this feature is marred by incomplete preservation. The new taxon is differentiated from I. duncani based on the absence of a median ridge on the parietal, and the lack of characteristic ridges on the parietal that form the medial margin of the supratemporal foramina. Reanalysis of a second specimen (the former holotype of the nomen dubium,‘Crocodylus (Bottosaurus) selaslophensis’) allows for its referral to the genus Isisfordia. Crucial to this reappraisal is the reinterpretation of the specimen as a partial maxilla, not the dentary as previously thought. This maxillary fragment possesses specific characteristics shared only with I. duncani; namely an alveolar groove. However, several key features differentiate the maxillary fragment from I. duncani, specifically the presence of continuous alveolar septa, the thickening of the medial alveolar rim, and the alveolar and crown base morphology. These findings constitute the first evidence of Isisfordia outside of the type locality and indicate its widespread occurrence on the freshwater floodplains along the eastern margin of the epeiric Eromanga Sea during the Albian–Cenomanian.
Hart et al. (2019) Isisfordia molnari sp. nov., a new basal eusuchian from the mid-Cretaceous of Lightning Ridge, Australia. PeerJ 7:e7166 https://doi.org/10.7717/peerj.7166