title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=734 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Long non-coding RNA SPRY4-IT1 promotes proliferation and metastasis in nasopharyngeal carcinoma cell link: https://peerj.com/articles/13221 last-modified: 2022-03-30 description: BackgroundLong non-coding RNA SPRY4 intronic transcript 1 (Lnc RNA SPRY4-IT1) was aberrant-expressed in various kinds of cancer. Increasing evidence demonstrated that lnc RNAs involved in tumorigenesis and metastasis. In this study, we aimed to explore the biological role of SPRY4-IT1 on the phenotype of nasopharyngeal carcinoma (NPC) in vitro and in vivo.MethodsThe expression level of SPRY4-IT1 in NPC cell lines were measured by quantitative real-time polymerase chain reaction (qRT-PCR). Cell Counting Kit-8 (CCK-8) and colony formation assay were used to detect cell proliferation. Wound-healing assay, transwell assay and animal experiment were performed to evaluate the ability of cell migration and metastasis. Cell cycle distribution and apoptosis were determined by flow cytometry. Western blotting and immunofluorescence were employed to identify protein expression.ResultsSPRY4-IT1 was significantly up-regulated in several NPC cell lines (6-10B, CNE-2, and HONE-1) compared with human immortalized nasopharyngeal epithelial cell (NP69). Silencing of SPRY4-IT1 inhibited proliferation, migration, and metastasis, and induced significant G2/M phase arrest and apoptosis. Western blotting showed that the expression levels of cell cycle-related proteins (cyclin B1, cdc2 and p-cdc2) were down-regulated and apoptosis-associated proteins (PARP, cleaved PARP and cleaved caspase-3) were up-regulated after knockdown of SPRY4-IT1. The expression level of E-cadherin was increased and the expression of Vimentin, Snail and Twist1 were decreased after the SPRY4-IT1 knockdown.ConclusionlncRNA SPRY4-IT1 played a significant role in NPC proliferation, migration and metastasis, suggesting that SPRY4-IT1 might be a potential therapeutic target for the treatment of NPC. creator: Yanfei Li creator: Zhenpeng Liao creator: Rong Wang creator: Zibin Liang creator: Zhihe Lin creator: Shiqi Deng creator: Lei Chen creator: Zhigang Liu creator: Shaoyan Feng uri: https://doi.org/10.7717/peerj.13221 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Classifying the difficulty levels of working memory tasks by using pupillary response link: https://peerj.com/articles/12864 last-modified: 2022-03-29 description: Knowing the difficulty of a given task is crucial for improving the learning outcomes. This paper studies the difficulty level classification of memorization tasks from pupillary response data. Developing a difficulty level classifier from pupil size features is challenging because of the inter-subject variability of pupil responses. Eye-tracking data used in this study was collected while students solved different memorization tasks divided as low-, medium-, and high-level. Statistical analysis shows that values of pupillometric features (as peak dilation, pupil diameter change, and suchlike) differ significantly for different difficulty levels. We used a wrapper method to select the pupillometric features that work the best for the most common classifiers; Support Vector Machine (SVM), Decision Tree (DT), Linear Discriminant Analysis (LDA), and Random Forest (RF). Despite the statistical difference, experiments showed that a random forest classifier trained with five features obtained the best F1-score (82%). This result is essential because it describes a method to evaluate the cognitive load of a subject performing a task using only pupil size features. creator: Hugo Mitre-Hernandez creator: Jorge Sanchez-Rodriguez creator: Sergio Nava-Muñoz creator: Carlos Lara-Alvarez uri: https://doi.org/10.7717/peerj.12864 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mitre-Hernandez et al. title: Responsiveness of domesticated goats towards various stressors following long-term cognitive test exposure link: https://peerj.com/articles/12893 last-modified: 2022-03-29 description: Current evidence suggests that frequent exposure to situations in which captive animals can solve cognitive tasks may have positive effects on stress responsiveness and thus on welfare. However, confounding factors often hamper the interpretation of study results. In this study, we used human-presented object-choice tests (in form of visual discrimination and reversal learning tests and a cognitive test battery), to assess the effect of long-term cognitive stimulation (44 sessions over 4–5 months) on behavioural and cardiac responses of female domestic goats in subsequent stress tests. To disentangle whether cognitive stimulation per se or the reward associated with the human–animal interaction required for testing was affecting the stress responsiveness, we conditioned three treatment groups: goats that were isolated for participation in human-presented cognitive tests and rewarded with food (‘Cognitive’, COG treatment), goats that were isolated as for the test exposure and rewarded with food by the experimenter without being administered the object-choice tests (‘Positive’, POS treatment), and goats that were isolated in the same test room but neither received a reward nor were administered the tests (‘Isolation’, ISO treatment). All treatment groups were subsequently tested in four stress tests: a novel arena test, a novel object test, a novel human test, and a weighing test in which goats had to enter and exit a scale cage. All treatment groups weretested at the same two research sites, each using two selection lines, namely dwarf goats, not selected for production traits, and dairy goats, selected for high productivity. Analysing the data with principal component analysis and linear mixed-effects models, we did not find evidence that cognitive testing per se (COG–POS contrast) reduces stress responsiveness of goats in subsequent stress tests. However, for dwarf goats but not for dairy goats, we found support for an effect of reward-associated human–animal interactions (POS–ISO contrast) at least for some stress test measures. Our results highlight the need to consider ontogenetic and genetic variation when assessing stress responsiveness and when interacting with goats. creator: Katrina Rosenberger creator: Michael Simmler creator: Jan Langbein creator: Christian Nawroth creator: Nina Keil uri: https://doi.org/10.7717/peerj.12893 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rosenberger et al. title: Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis link: https://peerj.com/articles/12970 last-modified: 2022-03-29 description: Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3–V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis. creator: Mohd Hairul Mohd Salleh creator: Yuzine Esa creator: Mohamad Syazwan Ngalimat creator: Pelf Nyok Chen uri: https://doi.org/10.7717/peerj.12970 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mohd Salleh et al. title: Investigating effect of mutation on structure and function of G6PD enzyme: a comparative molecular dynamics simulation study link: https://peerj.com/articles/12984 last-modified: 2022-03-29 description: Several natural mutants of the human G6PD enzyme exist and have been reported. Because the enzymatic activities of many mutants are different from that of the wildtype, the genetic polymorphism of G6PD plays an important role in the synthesis of nucleic acids via ribulose-5-phosphate and formation of reduced NADP in response to oxidative stress. G6PD mutations leading to its deficiency result in the neonatal jaundice and acute hemolytic anemia in human. Herein, we demonstrate the molecular dynamics simulations of the wildtype G6PD and its three mutants to monitor the effect of mutations on dynamics and stability of the protein. These mutants are Chatham (A335T), Nashville (R393H), Alhambra (V394L), among which R393H and V394L lie closer to binding site of structural NADP+. MD analysis including RMSD, RMSF and protein secondary structure revealed that decrease in the stability of mutants is key factor for loss of their activity. The results demonstrated that mutations in the G6PD sequence resulted in altered structural stability and hence functional changes in enzymes. Also, the binding site, of structural NADP+, which is far away from the catalytic site plays an important role in protein stability and folding. Mutation at this site causes changes in structural stability and hence functional deviations in enzyme structure reflecting the importance of structural NADP+ binding site. The calculation of binding free energy by post processing end state method of Molecular Mechanics Poisson Boltzmann SurfaceArea (MM-PBSA) has inferred that ligand binding in wildtype is favorable as compared to mutants which represent destabilised protein structure due to mutation that in turn may hinder the normal physiological function. Exploring individual components of free energy revealed that the van der Waals energy component representing non-polar/hydrophobic energy contribution act as a dominant factor in case of ligand binding. Our study also provides an insight in identifying the key inhibitory site in G6PD and its mutants which can be exploited to use them as a target for developing new inhibitors in rational drug design. creator: Sadaf Rani creator: Fouzia Perveen Malik creator: Jamshed Anwar creator: Rehan Zafar Paracha uri: https://doi.org/10.7717/peerj.12984 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rani et al. title: Synergistic effects of climate and landscape change on the conservation of Amazonian lizards link: https://peerj.com/articles/13028 last-modified: 2022-03-29 description: The leading causes of the worldwide decline in biodiversity are global warming, allied with natural habitat loss and fragmentation. Here, we propose an analysis of the synergistic effects of these two factors in 63 species of Amazonian lizards. We predicted that the high-climatic suitability areas of species would be significantly impacted by different deforestation scenarios and the resultant landscape structure and considered that forest-dwelling species would be especially susceptible to deforestation scenarios. We also pointed out species threatened by both drivers and suggested critical areas for their future conservation. According to our results, most species will face future reductions in suitable areas for their occurrence according to five different patterns, two of which represent significant risks for 15 species. Some of these species already deal with severe habitat loss and fragmentation of their current distribution ranges, whereas others will suffer a considerable area reduction related to future range shifts. We emphasize the importance of protected areas (PAs), especially indigenous lands, and the need to plan combined strategies involving PAs’ maintenance and possible implementation of ecological corridors. Finally, we highlight eight species of thermoconformer lizards that constitute present and future conservation concerns related to the combined effects of climate change and habitat loss and that should be carefully evaluated in extinction risk assessments. creator: Cássia de Carvalho Teixeira creator: Leonardo Carreira Trevelin creator: Maria Cristina dos Santos-Costa creator: Ana Prudente creator: Daniel Paiva Silva uri: https://doi.org/10.7717/peerj.13028 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Teixeira et al. title: Rapid parameter estimation for selective inversion recovery myelin imaging using an open-source Julia toolkit link: https://peerj.com/articles/13043 last-modified: 2022-03-29 description: BackgroundMagnetic resonance imaging (MRI) is used extensively to quantify myelin content, however computational bottlenecks remain challenging for advanced imaging techniques in clinical settings. We present a fast, open-source toolkit for processing quantitative magnetization transfer derived from selective inversion recovery (SIR) acquisitions that allows parameter map estimation, including the myelin-sensitive macromolecular pool size ratio (PSR). Significant progress has been made in reducing SIR acquisition times to improve clinically feasibility. However, parameter map estimation from the resulting data remains computationally expensive. To overcome this computational limitation, we developed a computationally efficient, open-source toolkit implemented in the Julia language.MethodsTo test the accuracy of this toolkit, we simulated SIR images with varying PSR and spin-lattice relaxation time of the free water pool (R1f) over a physiologically meaningful scale from 5% to 20% and 0.5 to 1.5 s−1, respectively. Rician noise was then added, and the parameter maps were estimated using our Julia toolkit. Probability density histogram plots and Lin’s concordance correlation coefficients (LCCC) were used to assess accuracy and precision of the fits to our known simulation data. To further mimic biological tissue, we generated five cross-linked bovine serum albumin (BSA) phantoms with concentrations that ranged from 1.25% to 20%. The phantoms were imaged at 3T using SIR, and data were fit to estimate PSR and R1f. Similarly, a healthy volunteer was imaged at 3T, and SIR parameter maps were estimated to demonstrate the reduced computational time for a real-world clinical example.ResultsEstimated SIR parameter maps from our Julia toolkit agreed with simulated values (LCCC > 0.98). This toolkit was further validated using BSA phantoms and a whole brain scan at 3T. In both cases, SIR parameter estimates were consistent with published values using MATLAB. However, compared to earlier work using MATLAB, our Julia toolkit provided an approximate 20-fold reduction in computational time.ConclusionsPresented here, we developed a fast, open-source, toolkit for rapid and accurate SIR MRI using Julia. The reduction in computational cost should allow SIR parameters to be accessible in clinical settings. creator: Nicholas J. Sisco creator: Ping Wang creator: Ashley M. Stokes creator: Richard D. Dortch uri: https://doi.org/10.7717/peerj.13043 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sisco et al. title: NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology link: https://peerj.com/articles/13056 last-modified: 2022-03-29 description: BackgroundNext Generation Sequencing (NGS) techniques dominate today’s landscape of genetics and genomics research. Though Illumina still dominates worldwide sequencing, Oxford Nanopore is one of the leading technologies currently being used by biologists, medics and geneticists across various applications. Oxford Nanopore is automated and relatively simple for conducting experiments, but generates gigabytes of raw data, to be processed by often ambiguous set of alternative bioinformatics command-line tools, and genomics frameworks which require a knowledge of bioinformatics to run.ResultsWe established an inter-collegiate collaboration across experimentalists and bioinformaticians in order to provide a novel bioinformatics tool, free for academics. This tool allows people without extensive bioinformatics knowledge to simply process their raw genome sequencing data. Currently, due to ICT resources’ maintenance reasons, our server is only capable of handling small genomes (up to 15 Mb). In this paper, we introduce our tool, NanoForms: an intuitive and integrated web server for the processing and analysis of raw prokaryotic genome data, coming from Oxford Nanopore. NanoForms is freely available for academics at the following locations: http://nanoforms.tech (webserver) and https://github.com/czmilanna/nanoforms (GitHub source repository). creator: Anna Czmil creator: Michal Wronski creator: Sylwester Czmil creator: Marta Sochacka-Pietal creator: Michal Cmil creator: Jan Gawor creator: Tomasz Wołkowicz creator: Dariusz Plewczynski creator: Dominik Strzalka creator: Michal Pietal uri: https://doi.org/10.7717/peerj.13056 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Czmil et al. title: Subject specific muscle synergies and mechanical output during cycling with arms or legs link: https://peerj.com/articles/13155 last-modified: 2022-03-29 description: BackgroundUpper (UL) and lower limb (LL) cycling is extensively used for several applications, especially for rehabilitation for which neuromuscular interactions between UL and LL have been shown. Nevertheless, the knowledge on the muscular coordination modality for UL is poorly investigated and it is still not known whether those mechanisms are similar or different to those of LL. The aim of this study was thus to put in evidence common coordination mechanism between UL and LL during cycling by investigating the mechanical output and the underlying muscle coordination using synergy analysis.MethodsTwenty-five revolutions were analyzed for six non-experts’ participants during sub-maximal cycling with UL or LL. Crank torque and muscle activity of eleven muscles UL or LL were recorded. Muscle synergies were extracted using nonnegative matrix factorization (NNMF) and group- and subject-specific analysis were conducted.ResultsFour synergies were extracted for both UL and LL. UL muscle coordination was organized around several mechanical functions (pushing, downing, and pulling) with a proportion of propulsive torque almost 80% of the total revolution while LL muscle coordination was organized around a main function (pushing) during the first half of the cycling revolution. LL muscle coordination was robust between participants while UL presented higher interindividual variability.DiscussionWe showed that a same principle of muscle coordination exists for UL during cycling but with more complex mechanical implications. This study also brings further results suggesting each individual has unique muscle signature. creator: Théo Cartier creator: Laurent Vigouroux creator: Elke Viehweger creator: Guillaume Rao uri: https://doi.org/10.7717/peerj.13155 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cartier et al. title: Mechanisms and potential immune tradeoffs of accelerated coral growth induced by microfragmentation link: https://peerj.com/articles/13158 last-modified: 2022-03-29 description: Microfragmentation is the act of cutting corals into small pieces (~1 cm2) to accelerate the growth rates of corals relative to growth rates observed when maintaining larger-sized fragments. This rapid tissue and skeletal expansion technique offers great potential for supporting reef restoration, yet the biological processes and tradeoffs involved in microfragmentation-mediated accelerated growth are not well understood. Here we compared growth rates across a range of successively smaller fragment sizes in multiple genets of reef-building corals, Orbicella faveolata and Montastraea cavernosa. Our results confirm prior findings that smaller initial sizes confer accelerated growth after four months of recovery in a raceway. O. faveolata transcript levels associated with growth rate include genes encoding carbonic anhydrase and glutamic acid-rich proteins, which have been previously implicated in coral biomineralization, as well as a number of unannotated transcripts that warrant further characterization. Innate immunity enzyme activity assays and gene expression results suggest a potential tradeoff between growth rate after microfragmentation and immune investment. Microfragmentation-based restoration practices have had great success on Caribbean reefs, despite widespread mortality among wild corals due to infectious diseases. Future studies should continue to examine potential immune tradeoffs throughout the microfragmentation recovery period that may affect growout survival and disease transmission after outplanting. creator: Louis Schlecker creator: Christopher Page creator: Mikhail Matz creator: Rachel M. Wright uri: https://doi.org/10.7717/peerj.13158 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Schlecker et al.