title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1109 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Integrative analysis of competitive endogenous RNA network reveals the regulatory role of non-coding RNAs in high-glucose-induced human retinal endothelial cells link: https://peerj.com/articles/9452 last-modified: 2020-06-29 description: BackgroundIncreasing evidence has suggested that non-coding RNAs (ncRNAs) play critical roles in the pathogenesis of diabetic retinopathy (DR), but their underlying mechanisms remain unclear. The purpose of this study was to determine latent key genes and to structure a competing endogenous RNA (ceRNA) regulatory network to discover the potential molecular mechanisms governing the effects of high glucose on human retinal endothelial cells (HRECs).MethodsWe obtained microarray data for long non-coding RNA (lncRNA) and mRNA of high-glucose-induced HREC samples from NCBI GEO datasets. The ceRNA network was screened using intersecting prediction results from miRcode, TargetScan, miRTarBase and miRDB. The protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes and hub genes were obtained using the cytoHubba app. The ClusterProfiler package was applied for performing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The expression of key RNAs was verified using the qRT-PCR method. A key ceRNA subnetwork was constructed based on the criticality of the genes and its binding sites were verified by luciferase reporter assay. The viability and apoptosis of HRECs were tested using the transfection of the miR-449c inhibitor.ResultsA total of 3,328 lncRNAs and 2,017 mRNAs were screened for differentially expressed (DE) profiles. The newly constructed ceRNA network was composed of 410 lncRNAs, 35 miRNAs and 122 mRNAs. The 10 hub genes were identified through the PPI network. GO and KEGG analysis revealed that DE mRNAs were mainly related to the positive regulation of the mRNA catabolic process, cell polarity, and the G1/S transition of mitotic and cell cycle signaling pathways. QRT-PCR was used to verify RNAs and the most important genes were screened out. A key ceRNA subnetwork OIP5-AS1/miR-449c/MYC was established. The binding site was verified by luciferase reporter assay. The expression levels of OIP5-AS1 and MYC increased after miR-449c inhibitor transfection, miR-449c decreased, HRECs activity increased, and apoptosis decreased, compared with the control group.ConclusionWe successfully built the key ceRNA subnetwork, OIP5-AS1/miR-449c/MYC, by applying the GEO database for data analysis and mining. The results from the ceRNA network allow us to better understand the effect of ncRNAs on HRECs under hyperglycemic conditions and the pathogenesis of DR. creator: Nan-Jue Cao creator: He-Nan Liu creator: Feng Dong creator: Wei Wang creator: Wei Sun creator: Gang Wang uri: https://doi.org/10.7717/peerj.9452 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cao et al. title: Gait characteristics in individuals with Parkinson’s disease during 1-minute treadmill walking link: https://peerj.com/articles/9463 last-modified: 2020-06-29 description: BackgroundNo previous study has examined the age-dependent characteristics of gait in individuals between 50 and 79 years simultaneously in healthy individuals and individuals with Parkinson’s disease (PD) over continuous gait cycles. This study aimed to investigate age-related differences in gait characteristics on individuals age ranged 50–79 years, including individuals with PD, during a 1-minute treadmill walking session. Additionally, we aimed to investigate the differences associated with spatiotemporal gait parameters and PD compared in age-matched individuals.MethodsThis study included 26 individuals with PD and 90 participants age ranged 50–79 years. The treadmill walking test at a self-preferred speed was performed for 1 min. The embedded inertial measurement unit sensor in the left and right outsoles-based system was used to collect gait characteristics based on tri-axial acceleration and tri-axial angular velocities.ResultsParticipants aged >60 years had a decreased gait speed and shortened stride and step, which may demonstrate a distinct shift in aging (all p < 0.005). Individuals with PD showed more of a decrease in variables with a loss of consistency, including gait asymmetry (GA), phase coordination index (PCI) and coefficient of variation (CV) of all variables, than age-matched individuals (all p < 0.001). Gait speed, stride and step length, stance phase, variability, GA and PCI were the variables that highly depended on age and PD.DiscussionOlder adults could be considered those older than 60 years of age when gait alterations begin, such as a decreased gait speed as well as shortened stride and step length. On the other hand, a loss of consistency in spatiotemporal parameters and a higher GA and PCI could be used to identify individuals with PD. Thus, the CV of all spatiotemporal parameters, GA and PCI during walking could play an important role and be useful in identifying individuals with PD.ConclusionThis study provided the notable aging pattern characteristics of gait in individuals >50 years, including individuals with PD. Increasing age after 60 years is associated with deterioration in spatiotemporal parameters of gait during continuous 1-minute treadmill walking. Additionally, GA, PCI and the CV of all variables could be used to identify PD which would be placed after 70 years of age. It may be useful to determine the decline of gait performance in general and among individuals with PD. creator: Byungjoo Noh creator: Changhong Youm creator: Myeounggon Lee creator: Sang-Myung Cheon uri: https://doi.org/10.7717/peerj.9463 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Noh et al. title: Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios link: https://peerj.com/articles/9482 last-modified: 2020-06-29 description: BackgroundCOVID-19 pandemics has challenged emergency response systems worldwide, with widespread reports of essential services breakdown and collapse of health care structure. A critical element involves essential workforce management since current protocols recommend release from duty for symptomatic individuals, including essential personnel. Testing capacity is also problematic in several countries, where diagnosis demand outnumbers available local testing capacity.PurposeThis work describes a machine learning model derived from hemogram exam data performed in symptomatic patients and how they can be used to predict qRT-PCR test results.MethodsHemogram exams data from 510 symptomatic patients (73 positives and 437 negatives) were used to model and predict qRT-PCR results through Naïve-Bayes algorithms. Different scarcity scenarios were simulated, including symptomatic essential workforce management and absence of diagnostic tests. Adjusts in assumed prior probabilities allow fine-tuning of the model, according to actual prediction context.ResultsProposed models can predict COVID-19 qRT-PCR results in symptomatic individuals with high accuracy, sensitivity and specificity, yielding a 100% sensitivity and 22.6% specificity with a prior of 0.9999; 76.7% for both sensitivity and specificity with a prior of 0.2933; and 0% sensitivity and 100% specificity with a prior of 0.001. Regarding background scarcity context, resources allocation can be significantly improved when model-based patient selection is observed, compared to random choice.ConclusionsMachine learning models can be derived from widely available, quick, and inexpensive exam data in order to predict qRT-PCR results used in COVID-19 diagnosis. These models can be used to assist strategic decision-making in resource scarcity scenarios, including personnel shortage, lack of medical resources, and testing insufficiency. creator: Eduardo Avila creator: Alessandro Kahmann creator: Clarice Alho creator: Marcio Dorn uri: https://doi.org/10.7717/peerj.9482 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Avila et al. title: Phylogenetic comparison between Type IX Secretion System (T9SS) protein components suggests evidence of horizontal gene transfer link: https://peerj.com/articles/9019 last-modified: 2020-06-26 description: Porphyromonas gingivalis is one of the major bacteria that causes periodontitis. Chronic periodontitis is a severe form of periodontal disease that ultimately leads to tooth loss. Virulence factors that contribute to periodontitis are secreted by Type IX Secretion System (T9SS). There are aspects of T9SS protein components that have yet to be characterised. Thus, the aim of this study is to investigate the phylogenetic relationship between members of 20 T9SS component protein families. The Bayesian Inference (BI) trees for 19 T9SS protein components exhibit monophyletic clades for all major classes under Bacteroidetes with strong support for the monophyletic clades or its subclades that is consistent with phylogeny exhibited by the constructed BI tree of 16S rRNA. The BI tree of PorR is different from the 19 BI trees of T9SS protein components as it does not exhibit monophyletic clades for all major classes under Bacteroidetes. There is strong support for the phylogeny exhibited by the BI tree of PorR which deviates from the phylogeny based on 16S rRNA. Hence, it is possible that the porR gene is subjected to horizontal transfer as it is known that virulence factor genes could be horizontally transferred. Seven genes (porR included) that are involved in the biosynthesis of A-LPS are found to be flanked by insertion sequences (IS5 family transposons). Therefore, the intervening DNA segment that contains the porR gene might be transposed and subjected to conjugative transfer. Thus, the seven genes can be co-transferred via horizontal gene transfer. The BI tree of UgdA does not exhibit monophyletic clades for all major classes under Bacteroidetes which is similar to the BI tree of PorR (both are a part of the seven genes). Both BI trees also exhibit similar topology as the four identified clusters with strong support and have similar relative positions to each other in both BI trees. This reinforces the possibility that porR and the other six genes might be horizontally transferred. Other than the BI tree of PorR, the 19 other BI trees of T9SS protein components also exhibit evidence of horizontal gene transfer. However, their genes might undergo horizontal gene transfer less frequently compared to porR because the intervening DNA segment that contains porR is easily exchanged between bacteria under Bacteroidetes due to the presence of insertion sequences (IS5 family transposons) that flank it. In conclusion, this study can provide a better understanding about the phylogeny of T9SS protein components. creator: Reeki Emrizal creator: Nor Azlan Nor Muhammad uri: https://doi.org/10.7717/peerj.9019 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Emrizal and Nor Muhammad title: Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma link: https://peerj.com/articles/9294 last-modified: 2020-06-26 description: Esophageal squamous cell carcinoma (ESCC) is the predominant type of esophageal cancer in the Asian region, including Japan. A previous study reported mutational landscape of Japanese ESCCs by using exome sequencing. However, somatic structural alterations were yet to be explored. To provide a comprehensive mutational landscape, we performed whole genome sequencing (WGS) analysis of biopsy specimens from 20 ESCC patients in a Japanese population. WGS analysis identified non-silent coding mutations of TP53, ZNF750 and FAT1 in ESCC. We detected six mutational signatures in ESCC, one of which showed significant association with smoking status. Recurrent structural variations, many of which were chromosomal deletions, affected genes such as LRP1B, TTC28, CSMD1, PDE4D, SDK1 and WWOX in 25%–30% of tumors. Somatic copy number amplifications at 11q13.3 (CCND1), 3q26.33 (TP63/SOX2), and 8p11.23 (FGFR1) and deletions at 9p21.3 (CDKN2A) were identified. Overall, these multi-dimensional view of genomic alterations improve the understanding of the ESCC development at molecular level and provides future prognosis and therapeutic implications for ESCC in Japan. creator: Munmee Dutta creator: Hidewaki Nakagawa creator: Hiroaki Kato creator: Kazuhiro Maejima creator: Shota Sasagawa creator: Kaoru Nakano creator: Aya Sasaki-Oku creator: Akihiro Fujimoto creator: Raúl Nicolás Mateos creator: Ashwini Patil creator: Hiroko Tanaka creator: Satoru Miyano creator: Takushi Yasuda creator: Kenta Nakai creator: Masashi Fujita uri: https://doi.org/10.7717/peerj.9294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dutta et al. title: An eye for a tooth: Thylacosmilus was not a marsupial “saber-tooth predator” link: https://peerj.com/articles/9346 last-modified: 2020-06-26 description: BackgroundSaber-toothed mammals, now all extinct, were cats or “cat-like” forms with enlarged, blade-like upper canines, proposed as specialists in taking large prey. During the last 66 Ma, the saber-tooth ecomorph has evolved convergently at least in five different mammalian lineages across both marsupials and placentals. Indeed, Thylacosmilus atrox, the so-called “marsupial saber-tooth,” is often considered as a classic example of convergence with placental saber-tooth cats such as Smilodon fatalis. However, despite its superficial similarity to saber-toothed placentals, T. atrox lacks many of the critical anatomical features related to their inferred predatory behavior—that of employing their enlarged canines in a killing head strike.MethodsHere we follow a multi-proxy approach using canonical correspondence analysis of discrete traits, biomechanical models of skull function using Finite Element Analysis, and 3D dental microwear texture analysis of upper and lower postcanine teeth, to investigate the degree of evolutionary convergence between T. atrox and placental saber-tooths, including S. fatalis.ResultsCorrespondence analysis shows that the craniodental features of T. atrox are divergent from those of placental saber-tooths. Biomechanical analyses indicate a superior ability of T. atrox to placental saber-tooths in pulling back with the canines, with the unique lateral ridge of the canines adding strength to this function. The dental microwear of T. atrox indicates a soft diet, resembling that of the meat-specializing cheetah, but its blunted gross dental wear is not indicative of shearing meat.ConclusionsOur results indicate that despite its impressive canines, the “marsupial saber-tooth” was not the ecological analogue of placental saber-tooths, and likely did not use its canines to dispatch its prey. This oft-cited example of convergence requires reconsideration, and T. atrox may have had a unique type of ecology among mammals. creator: Christine M. Janis creator: Borja Figueirido creator: Larisa DeSantis creator: Stephan Lautenschlager uri: https://doi.org/10.7717/peerj.9346 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Janis et al. title: Tip dating with fossil sites and stratigraphic sequences link: https://peerj.com/articles/9368 last-modified: 2020-06-26 description: Tip dating, a method of phylogenetic analysis in which fossils are included as terminals and assigned an age, is becoming increasingly widely used in evolutionary studies. Current implementations of tip dating allow fossil ages to be assigned as a point estimate, or incorporate uncertainty through the use of uniform tip age priors. However, the use of tip age priors has the unwanted effect of decoupling the ages of fossils from the same fossil site. Here we introduce a new Markov Chain Monte Carlo (MCMC) proposal, which allows fossils from the same site to have linked ages, while still incorporating uncertainty in the age of the fossil site itself. We also include an extension, allowing fossil sites to be ordered in a stratigraphic column with age bounds applied only to the top and bottom of the sequence. These MCMC proposals are implemented in a new open-source BEAST2 package, palaeo. We test these new proposals on a dataset of early vertebrate fossils, concentrating on the effects on two sites with multiple acanthodian fossil taxa but wide age uncertainty, the Man On The Hill (MOTH) site from northern Canada, and the Turin Hill site from Scotland, both of Lochkovian (Early Devonian) age. The results show an increased precision of age estimates when fossils have linked tip ages compared to when ages are unlinked, and in this example leads to support for a younger age for the MOTH site compared with the Turin Hill site. There is also a minor effect on the tree topology of acanthodians. These new MCMC proposals should be widely applicable to studies that employ tip dating, particularly when the terminals are coded as individual specimens. creator: Benedict King creator: Martin Rücklin uri: https://doi.org/10.7717/peerj.9368 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 King and Rücklin title: Description of soft tissue artifacts and related consequences on hindlimb kinematics during canine gait link: https://peerj.com/articles/9379 last-modified: 2020-06-26 description: BackgroundSoft tissue artifacts (STAs) are a source of error in marker-based gait analysis in dogs. While some studies have revealed the existence of STAs in the canine hindlimb, STAs and their influence on kinematic gait analysis remain unclear.MethodsThirteen healthy Taiwan dogs affixed with twenty skin markers on the thigh and crus were recruited. Soft tissue artifacts and their influence on the determination of segment poses and stifle angles were assessed by simultaneously measuring marker trajectories and kinematics of the underlying bones via a model-based fluoroscopic analysis method.ResultsMarkers on the thigh showed higher STAs than those on the crus, with root-mean-square amplitudes up to 15.5 mm. None of the tested marker clusters were able to accurately reproduce the skeletal poses, in which the maximum root-mean-square deviations ranged from 3.4° to 8.1°. The use of markers resulted in overestimated stifle flexion during 40–60% of the gait cycle and underestimated stifle flexion during 80–90% of the gait cycle.ConclusionsConsiderable magnitudes and effects of STAs on the marker-based 3D gait analysis of dogs were demonstrated. The results indicate that the development of error-compensation techniques based on knowledge regarding STAs is warranted for more accurate gait analysis. creator: Cheng-Chung Lin creator: Shi-Nuan Wang creator: Ming Lu creator: Tzu-Yi Chao creator: Tung-Wu Lu creator: Ching-Ho Wu uri: https://doi.org/10.7717/peerj.9379 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Lin et al. title: Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis link: https://peerj.com/articles/9408 last-modified: 2020-06-26 description: BackgroundSeveral examples have emerged of enzymes where slow conformational changes are of key importance for function and where low populated conformations in the resting enzyme resemble the conformations of intermediate states in the catalytic process. Previous work on the subtilisin protease, Savinase, from Bacillus lentus by NMR spectroscopy suggested that this enzyme undergoes slow conformational dynamics around the substrate binding site. However, the functional importance of such dynamics is unknown.MethodsHere we have probed the conformational heterogeneity in Savinase by following the temperature dependent chemical shift changes. In addition, we have measured changes in the local stability of the enzyme when the inhibitor phenylmethylsulfonyl fluoride is bound using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finally, we have used X-ray crystallography to compare electron densities collected at cryogenic and ambient temperatures and searched for possible low populated alternative conformations in the crystals.ResultsThe NMR temperature titration shows that Savinase is most flexible around the active site, but no distinct alternative states could be identified. The HDX shows that modification of Savinase with inhibitor has very little impact on the stability of hydrogen bonds and solvent accessibility of the backbone. The most pronounced structural heterogeneities detected in the diffraction data are limited to alternative side-chain rotamers and a short peptide segment that has an alternative main-chain conformation in the crystal at cryo conditions. Collectively, our data show that there is very little structural heterogeneity in the resting state of Savinase and hence that Savinase does not rely on conformational selection to drive the catalytic process. creator: Shanshan Wu creator: Tam T.T.N. Nguyen creator: Olga V. Moroz creator: Johan P. Turkenburg creator: Jens E. Nielsen creator: Keith S. Wilson creator: Kasper D. Rand creator: Kaare Teilum uri: https://doi.org/10.7717/peerj.9408 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu et al. title: Highly diverse root endophyte bacterial community is driven by growth substrate and is plant genotype-independent in common bean (Phaseolus vulgaris L.) link: https://peerj.com/articles/9423 last-modified: 2020-06-26 description: The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet with an essential role in sustainable agriculture mostly based on the symbiotic relationship established between this legume and rhizobia, a group of bacteria capable of fixing atmospheric nitrogen in the roots nodules. Moreover, root-associated bacteria play an important role in crop growth, yield, and quality of crop products. This is particularly true for legume crops forming symbiotic relationships with rhizobia, for fixation of atmospheric N2. The main objective of this work is to assess the substrate and genotype effect in the common bean (Phaseolus vulgaris L.) root bacterial community structure. To achieve this goal, we applied next-generation sequencing coupled with bacterial diversity analysis. The analysis of the bacterial community structures between common bean roots showed marked differences between substrate types regardless of the genotype. Also, we were able to find several phyla conforming to the bacterial community structure of the common bean roots, mainly composed by Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes. Therefore, we determined that the substrate type was the main factor that influenced the bacterial community structure of the common bean roots, regardless of the genotype, following a substrate-dependent pattern. These guide us to develop efficient and sustainable strategies for crop field management based on the soil characteristics and the bacterial community that it harbors. creator: Aarón Barraza creator: Juan Carlos Vizuet-de-Rueda creator: Raúl Alvarez-Venegas uri: https://doi.org/10.7717/peerj.9423 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Barraza et al.