The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species
The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is a huge genus comprising about 800–1,500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 available chloroplast genomes retrieved from NCBI RefSeq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of Dendrobium plastomes, which can also provide valuable information on their mutational events and sequence divergence.
Konhar et al. (2019) The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species. PeerJ 7:e7756 https://doi.org/10.7717/peerj.7756
Off-line and on-line optical monitoring of microalgal growth
The growth of Chlamydomonas reinhardtii microalgae cultures was successfully monitored, using classic off-line optical techniques (optical density and fluorescence) and on-line analysis of digital images. In this study, we found that the chlorophyll fluorescence ratio F685/F740 has a linear correlation with the logarithmic concentration of microalgae. By using digital images, the biomass concentration correlated with the luminosity of the images through an exponential equation and the length of penetration of a super luminescent blue beam (λ = 440 nm) through an inversely proportional function. The outcomes of this study are useful to monitor both research and industrial microalgae cultures.
Lazcano-Hernández et al. (2019) Off-line and on-line optical monitoring of microalgal growth. PeerJ 7:e7956 https://doi.org/10.7717/peerj.7956
TransPrise: a novel machine learning approach for eukaryotic promoter prediction
As interest in genetic resequencing increases, so does the need for effective mathematical, computational, and statistical approaches. One of the difficult problems in genome annotation is determination of precise positions of transcription start sites. In this paper we present TransPrise—an efficient deep learning tool for prediction of positions of eukaryotic transcription start sites. Our pipeline consists of two parts: the binary classifier operates the first, and if a sequence is classified as TSS-containing the regression step follows, where the precise location of TSS is being identified. TransPrise offers significant improvement over existing promoter-prediction methods. To illustrate this, we compared predictions of TransPrise classification and regression models with the TSSPlant approach for the well annotated genome of Oryza sativa. Using a computer equipped with a graphics processing unit, the run time of TransPrise is 250 minutes on a genome of 374 Mb long. The Matthews correlation coefficient value for TransPrise is 0.79, more than two times larger than the 0.31 for TSSPlant classification models. This represents a high level of prediction accuracy. Additionally, the mean absolute error for the regression model is 29.19 nt, allowing for accurate prediction of TSS location. TransPrise was also tested in Homo sapiens, where mean absolute error of the regression model was 47.986 nt. We provide the full basis for the comparison and encourage users to freely access a set of our computational tools to facilitate and streamline their own analyses. The ready-to-use Docker image with all necessary packages, models, code as well as the source code of the TransPrise algorithm are available at (http://compubioverne.group/). The source code is ready to use and customizable to predict TSS in any eukaryotic organism.
Pachganov et al. (2019) TransPrise: a novel machine learning approach for eukaryotic promoter prediction. PeerJ 7:e7990 https://doi.org/10.7717/peerj.7990
A biomechanical analysis of the stand-up paddle board stroke: a comparative study
Background Stand-up paddle boarding (SUP) is a rapidly growing global aquatic sport, with increasing popularity among participants within recreation, competition and rehabilitation. To date, few scientific studies have focused on SUP. Further, there is no research examining the biomechanics of the SUP paddle stroke. The purpose of this study was to investigate whether variations in kinematics existed among experienced and inexperienced SUP participants using three-dimensional motion analysis. This data could be of significance to participants, researchers, coaches and health practitioners to improve performance and inform injury minimization strategies. Methods A cross-sectional observational design study was performed with seven experienced and 19 inexperienced paddlers whereby whole-body kinematic data were acquired using a six-camera Vicon motion capture system. Participants paddled on a SUP ergometer while three-dimensional range of motion (ROM) and peak joint angles were calculated for the shoulders, elbows, hips and trunk. Mann–Whitney U tests were conducted on the non-normally distributed data to evaluate differences between level of expertise. Results Significant differences in joint kinematics were found between experienced and inexperienced participants, with inexperienced participants using greater overall shoulder ROM (78.9° ± 24.9° vs 56.6° ± 17.3°, p = 0.010) and less hip ROM than the experienced participants (50.0° ± 18.5° vs 66.4° ± 11.8°, p = 0.035). Experienced participants demonstrated increased shoulder motion at the end of the paddle stoke compared to the inexperienced participants (74.9° ± 16.3° vs 35.2° ± 28.5°, p = 0.001 minimum shoulder flexion) and more extension at the elbow (6.0° ± 9.2° minimum elbow flexion vs 24.8° ± 13.5°, p = 0.000) than the inexperienced participants. Discussion The results of this study indicate several significant kinematic differences between the experienced and inexperienced SUP participants. These variations in technique were noted in the shoulder, elbow and hip and are evident in other aquatic paddling sports where injury rates are higher in these joints. These finding may be valuable for coaches, therapists and participants needing to maximize performance and minimize injury risk during participation in SUP.
Schram et al. (2019) A biomechanical analysis of the stand-up paddle board stroke: a comparative study. PeerJ 7:e8006 https://doi.org/10.7717/peerj.8006
Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma
Background Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although multiple efforts have been made to understand the development of HCC, morbidity, and mortality rates remain high. In this study, we aimed to discover the mRNAs and long non-coding RNAs (lncRNAs) that contribute to the progression of HCC. We constructed a lncRNA-related competitive endogenous RNA (ceRNA) network to elucidate the molecular regulatory mechanism underlying HCC. Methods A microarray dataset (GSE54238) containing information about both mRNAs and lncRNAs was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and lncRNAs (DElncRNAs) in tumor tissues and non-cancerous tissues were identified using the limma package of the R software. The miRNAs that are targeted by DElncRNAs were predicted using miRcode, while the target mRNAs of miRNAs were retrieved from miRDB, miRTarBas, and TargetScan. Functional annotation and pathway enrichment of DEGs were performed using the EnrichNet website. We constructed a protein–protein interaction (PPI) network of DEGs using STRING, and identified the hub genes using Cytoscape. Survival analysis of the hub genes and DElncRNAs was performed using the gene expression profiling interactive analysis database. The expression of molecules with prognostic values was validated on the UALCAN database. The hepatic expression of hub genes was examined using the Human Protein Atlas. The hub genes and DElncRNAs with prognostic values as well as the predictive miRNAs were selected to construct the ceRNA networks. Results We found that 10 hub genes (KPNA2, MCM7, CKS2, KIF23, HMGB2, ZWINT, E2F1, MCM4, H2AFX, and EZH2) and four lncRNAs (FAM182B, SNHG6, SNHG1, and SNHG3) with prognostic values were overexpressed in the hepatic tumor samples. We also constructed a network containing 10 lncRNA–miRNA–mRNA pathways, which might be responsible for regulating the biological mechanisms underlying HCC. Conclusion We found that the 10 significantly overexpressed hub genes and four lncRNAs were negatively correlated with the prognosis of HCC. Further, we suggest that lncRNA SNHG1 and the SNHG3-related ceRNAs can be potential research targets for exploring the molecular mechanisms of HCC.
Liu et al. (2019) Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma. PeerJ 7:e8021 https://doi.org/10.7717/peerj.8021
New information on the early Permian lanthanosuchoid Feeserpeton oklahomensis based on computed tomography
The cave deposits of the Lower Permian Richards Spur locality in Oklahoma, USA, have produced an incredible number of terrestrial tetrapod taxa, many of which are currently only known from this locality. One of the many recent taxa to be described from the locality was the small lanthanosuchoid parareptile Feeserpeton oklahomensis. Represented by a well-preserved, near complete skull, F. oklahomensis would have been a small predatory reptile, likely preying upon arthropods, and contributes to the extensive tetrapod fauna that was present at Richards Spur. New computed tomography data of the holotype and only specimen has allowed us to visualize and describe previously obscured and inaccessible anatomy of this taxon. These areas include the mandibular ramus, the palate, the sphenethmoid, the epipterygoids, and the braincase. Furthermore, this new anatomical information allowed formerly unknown character codings to be updated, thus we also performed new phylogenetic analyses that incorporated this new information. The results of these updated phylogenetic analyses are very similar to those of past studies, with F. oklahomensis being found as the sister taxon to all other lanthanosuchoids.
MacDougall et al. (2019) New information on the early Permian lanthanosuchoid Feeserpeton oklahomensis based on computed tomography. PeerJ 7:e7753 https://doi.org/10.7717/peerj.7753
A new goniopholidid crocodyliform, Hulkepholis rori sp. nov. from the Camarillas Formation (early Barremian) in Galve, Spain)
Background The neosuchian crocodyliform genus Hulkepholis constitutes the longirostral lineage of the European Goniopholididae. It comprises two species ranging from the Valanginian of southern England to the lower Albian of the northern Teruel (Spain). A new species of Hulkepholis is described based on a partially complete skull from the lower Barremian Camarillas Formation. We investigate its phylogenetic position and the palatal patterns among members of Goniopholididae and the closely related Thalattosuchia and Tethysuchia. Methods Phylogenetic relationships were investigated with two matrices using a previously published dataset as the basis: the first differed only by the addition of the new species, the second had newly discovered states for 11 characters, the new species plus several additional specimens of Hulkepholis and Anteophthalmosuchus. Both matrices were processed using TNT v. 1.1, in a heuristic analysis of maximum parsimony, with tree bisection and reconnection 1,000 random addition replicates and saving the 10 most parsimonious trees per replicate, and up to 10 suboptimal trees to calculate Bremer supports. The skull geometry of nine species from Thalattosuchia, Tethysuchia and Goniopholididae was explored to test shape variation between the rostral and postrostral modules, and to visualize the differences on the secondary palate. A set of 18 landmarks was used to delimit significant anatomical features, and the skulls were isotropically scaled using Adobe Illustrator, with the longest skull (Sarcosuchus imperator) as the baseline for comparison. Results The European lineages of goniopholidids are two clades (Nannosuchus + Goniopholis) plus (Hulkepholis + Anteophthalmosuchus). The new species, Hulkepholis rori sp. nov, shares with the latter clade the following apormorphies: a long anterolateral postorbital process, postorbital process almost reaching the anterior jugal ramus, and basioccipital tubera with lateral edges turned posteriorly. Anteophthalmosuchus was found to be monophyletic, and Hulkepholis paraphyletic due to the poor preservation of H. willetti. Hulkepholis rori is distinguished by having vascular fossae and a mid-protuberance on the ventral surface of the basioccipital, and wide internal fossae in the quadrate. Among Goniopholididae differences on the secondary palate are the presence of a palatal cleft, the narrowness of the secondary choana, and a wide foramen of the median pharyngeal tube. Conclusions The new species is the earliest Hulkepholis from the Iberian Peninsula. New characters have been recognized in the organization of the palate and in the occipital region raising unexpected questions on the evolution of Goniopholididae. The set of palatal characters is discussed as part of a singular palatogenesis in Goniopholididae. The protruding occipital areas suggest that the longirostral Hulkepholis would have had an aquatic lifestyle with particular neck and skull movements.
Arribas et al. (2019) A new goniopholidid crocodyliform, Hulkepholis rori sp. nov. from the Camarillas Formation (early Barremian) in Galve, Spain). PeerJ 7:e7911 https://doi.org/10.7717/peerj.7911
Overexpression of MdIAA9 confers high tolerance to osmotic stress in transgenic tobacco
Auxin is a plant hormone that takes part in a series of developmental and physiological processes. There are three major gene families that play a role in the early response of auxin and auxin/indole-3-acetic acid (Aux/IAA) is one of these. Although the genomic organization and function of Aux/IAA genes have been recognized in reference plants there have only been a few focused studies conducted with non-model crop plants, especially in the woody perennial species. We conducted a genomic census and expression analysis of Aux/IAA genes in the cultivated apple (Malus × domestica Borkh.). The Aux/IAA gene family of the apple genome was identified and analyzed in this study. Phylogenetic analysis showed that MdIAAs could be categorized into nine subfamilies and that these MdIAA proteins contained four whole or partially conserved domains of the MdIAA family. The spatio-specific expression profiles showed that most of the MdIAAs were preferentially expressed in specific tissues. Some of these genes were significantly induced by treatments with one or more abiotic stresses. The overexpression of MdIAA9 in tobacco (Nicotiana tabacum L.) plants significantly increased their tolerance to osmotic stresses. Our cumulative data supports the interactions between abiotic stresses and plant hormones and provides a theoretical basis for the mechanism of Aux/IAA and drought resistance in apples.
Huang et al. (2019) Overexpression of MdIAA9 confers high tolerance to osmotic stress in transgenic tobacco. PeerJ 7:e7935 https://doi.org/10.7717/peerj.7935
A genomic-clinical nomogram predicting recurrence-free survival for patients diagnosed with hepatocellular carcinoma
Liver resection surgery is the most commonly used treatment strategy for patients diagnosed with hepatocellular carcinoma (HCC). However, there is still a chance for recurrence in these patients despite the survival benefits of this procedure. This study aimed to explore recurrence-related genes (RRGs) and establish a genomic-clinical nomogram for predicting postoperative recurrence in HCC patients. A total of 123 differently expressed genes and three RRGs (PZP, SPP2, and PRC1) were identified from online databases via Cox regression and LASSO logistic regression analyses and a gene-based risk model containing RRGs was then established. The Harrell’s concordance index (C-index), receiver operating characteristic (ROC) curves and calibration curves showed that the model performed well. Finally, a genomic-clinical nomogram incorporating the gene-based risk model, AJCC staging system, and Eastern Cooperative Oncology Group performance status was constructed to predict the 1-, 2-, and 3-year recurrence-free survival rates (RFS) for HCC patients. The C-index, ROC analysis, and decision curve analysis were good indicators of the nomogram’s performance. In conclusion, we identified three reliable RRGs associated with the recurrence of cancer and constructed a nomogram that performed well in predicting RFS for HCC patients. These findings could enrich our understanding of the mechanisms for HCC recurrence, help surgeons predict patients’ prognosis, and promote HCC treatment.
Kong et al. (2019) A genomic-clinical nomogram predicting recurrence-free survival for patients diagnosed with hepatocellular carcinoma. PeerJ 7:e7942 https://doi.org/10.7717/peerj.7942
Appendicular anatomy of the artiopod Emeraldella brutoni from the middle Cambrian (Drumian) of western Utah
The non-biomineralized artiopod Emeraldella brutoni Stein, Church & Robison, from the middle Cambrian (Drumian) Wheeler Formation in Utah represents the only confirmed occurrence of the genus Emeraldella outside of the stratigraphically older (Wuliuan) Burgess Shale Konservat-Lagerstätte in British Columbia. The hitherto known sole specimen of this species is preserved in dorsal view and lacks critical information on the ventral appendages. Here, we redescribe E. brutoni based on a new completely articulated specimen that illustrates the appendage organization in exceptional detail. The main body consists of a cephalic region covered by a semicircular head shield, a trunk including 10 tergites with expanded pleurae plus a cylindrical terminal segment, and a long articulated tailspine. The head carries a pair of elongate and flexible antennae, a pair of lateral eyes, and three pairs of post-antennal appendages. We report the presence of eyes in Emeraldella for the first time. The first post-antennal limb solely consists of an endopod with well-developed paired spiniform endites. The remaining cephalic appendages and those associated with all but the last trunk segments possess exopods terminating in paddle-shaped, distal lobes fringed with robust setae. The cylindrical terminal segment bears a pair of posteriorly oriented caudal flaps reminiscent of trunk exopods, and a styliform, possibly uniarticulate tailspine longer than the main body. The new data on E. brutoni suggests an exopodal origin for the paired caudal structures in Vicissicaudata, and improve our understanding of the fundamental organization of this major clade within Artiopoda.
© 2019 Lerosey-Aubril and Ortega-Hernández
Lerosey-Aubril et al. (2019) Appendicular anatomy of the artiopod Emeraldella brutoni from the middle Cambrian (Drumian) of western Utah. PeerJ 7:e7945 https://doi.org/10.7717/peerj.7945