title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=696 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Determination of muscle strength and function in plesiosaur limbs: finite element structural analyses of Cryptoclidus eurymerus humerus and femur link: https://peerj.com/articles/13342 last-modified: 2022-06-03 description: BackgroundThe Plesiosauria (Sauropterygia) are secondary marine diapsids. They are the only tetrapods to have evolved hydrofoil fore- and hindflippers. Once this specialization of locomotion had evolved, it remained essentially unchanged for 135 Ma. It is still controversial whether plesiosaurs flew underwater, rowed, or used a mixture of the two modes of locomotion. The long bones of Tetrapoda are functionally loaded by torsion, bending, compression, and tension during locomotion. Superposition of load cases shows that the bones are loaded mainly by compressive stresses. Therefore, it is possible to use finite element structure analysis (FESA) as a test environment for loading hypotheses. These include muscle reconstructions and muscle lines of action (LOA) when the goal is to obtain a homogeneous compressive stress distribution and to minimize bending in the model. Myological reconstruction revealed a muscle-powered flipper twisting mechanism. The flippers of plesiosaurs were twisted along the flipper length axis by extensors and flexors that originated from the humerus and femur as well as further distal locations.MethodsTo investigate locomotion in plesiosaurs, the humerus and femur of a mounted skeleton of Cryptoclidus eurymerus (Middle Jurassic Oxford Clay Formation from Britain) were analyzed using FE methods based on the concept of optimization of loading by compression. After limb muscle reconstructions including the flipper twisting muscles, LOA were derived for all humerus and femur muscles of Cryptoclidus by stretching cords along casts of the fore- and hindflippers of the mounted skeleton. LOA and muscle attachments were added to meshed volumetric models of the humerus and femur derived from micro-CT scans. Muscle forces were approximated by stochastic iteration and the compressive stress distribution for the two load cases, “downstroke” and “upstroke”, for each bone were calculated by aiming at a homogeneous compressive stress distribution.ResultsHumeral and femoral depressors and retractors, which drive underwater flight rather than rowing, were found to exert higher muscle forces than the elevators and protractors. Furthermore, extensors and flexors exert high muscle forces compared to Cheloniidae. This confirms a convergently evolved myological mechanism of flipper twisting in plesiosaurs and complements hydrodynamic studies that showed flipper twisting is critical for efficient plesiosaur underwater flight. creator: Anna Krahl creator: Andreas Lipphaus creator: P. Martin Sander creator: Ulrich Witzel uri: https://doi.org/10.7717/peerj.13342 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Krahl et al. title: Quercetin prevents chronic kidney disease on mesangial cells model by regulating inflammation, oxidative stress, and TGF-β1/SMADs pathway link: https://peerj.com/articles/13257 last-modified: 2022-06-02 description: BackgroundChronic kidney disease (CKD) happens due to decreasing kidney function. Inflammation and oxidative stress have been shown to result in the progression of CKD. Quercetin is widely known to have various bioactivities including antioxidant, anticancer, and anti-inflammatory activities.ObjectiveTo evaluate the activity of quercetin to inhibit inflammation, stress oxidative, and fibrosis on CKD cells model (mouse mesangial cells induced by glucose).Methods and MaterialThe SV40 MES 13 cells were plated in a 6-well plate with cell density at 5,000 cells/well. The medium had been substituted for 3 days with a glucose-induced medium with a concentration of 20 mM. Quercetin was added with 50, 10, and 5 µg/mL concentrations. The negative control was the untreated cell. The levels of TGF-β1, TNF-α, and MDA were determined using ELISA KIT. The gene expressions of the SMAD7, SMAD3, SMAD2, and SMAD4 were analyzed using qRT-PCR.ResultsGlucose can lead to an increase in inflammatory cytokines TNF-α, TGF-β1, MDA as well as the expressions of the SMAD2, SMAD3, SMAD4, and a decrease in SMAD7. Quercetin caused the reduction of TNF-α, TGF-β1, MDA as well as the expression of the SMAD2, SMAD3, SMAD4, and increased SMAD7.ConclusionQuercetin has anti-inflammation, antioxidant, antifibrosis activity in the CKD cells model. Thus, quercetin is a promising substance for CKD therapy and further research is needed to prove this in CKD animal model. creator: Wahyu Widowati creator: Sijani Prahastuti creator: Rita Tjokropranoto creator: Philips Onggowidjaja creator: Hanna Sari Widya Kusuma creator: Ervi Afifah creator: Seila Arumwardana creator: Muhamad Aldi Maulana creator: Rizal Rizal uri: https://doi.org/10.7717/peerj.13257 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Widowati et al. title: Withasomniferol C, a new potential SARS-CoV-2 main protease inhibitor from the Withania somnifera plant proposed by in silico approaches link: https://peerj.com/articles/13374 last-modified: 2022-06-02 description: Exploring potent herbal medicine candidates is a promising strategy for combating a pandemic in the present global health crisis. In Ayurveda (a traditional medicine system in India), Withania somnifera (WS) is one of the most important herbs and it has been used for millennia as Rasayana (a type of juice) for its wide-ranging health benefits. WS phytocompounds display a broad spectrum of biological activities (such as antioxidant, anticancer and antimicrobial) modulate detoxifying enzymes, and enhance immunity. Inspired by the numerous biological actions of WS phytocompounds, the present investigation explored the potential of the WS phytocompounds against the SARS-CoV-2 main protease (3CLpro). We selected 11 specific withanolide compounds, such as withaphysalin, withasomniferol, and withafastuosin, through manual literature curation against 3CLpro. A molecular similarity analysis showed their similarity with compounds that have an established inhibitory activity against the SARS-CoV-2. In silico molecular docking and molecular dynamics simulations elucidated withasomniferol C (WS11) as a potential candidate against SARS-CoV-2 3CLpro. Additionally, the present work also presents a new method of validating docking poses using the AlteQ method. creator: Shivananada Kandagalla creator: Hrvoje Rimac creator: Krishnamoorthy Gurushankar creator: Jurica Novak creator: Maria Grishina creator: Vladimir Potemkin uri: https://doi.org/10.7717/peerj.13374 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kandagalla et al. title: A new hybodontiform shark (Strophodus Agassiz 1838) from the Lower Cretaceous (Valanginian-Hauterivian) of Colombia link: https://peerj.com/articles/13496 last-modified: 2022-06-02 description: The vertebrate marine faunas that inhabited northern South America during the Cretaceous are still poorly known. This study is a contribution to a growing wave of new studies on Lower Cretaceous vertebrates from Colombia. Here we report and describe a new species of a hybodontiform shark of the genus Strophodus, which we named Strophodus rebecae sp. nov., based on isolated teeth, that were collected in Valanginian-Hauterivian rocks of the Rosa Blanca Formation (Carrizal and El Sapo Members) near the town of Zapatoca, Santander Department, Andes of Colombia. In addition, we describe two other fragmented teeth assigned to Strophodus sp. from the Rosa Blanca Fm. The new species from Colombia represents the only Cretaceous record of Strophodus from Gondwana, offering new insights into the paleogeographic distribution of the genus, as well as increasing the knowledge about the scarce hybodontiform paleodiversity known from South America. The presence of Strophodus in the Rosa Blanca Formation suggests that these durophagous (shell-crushing) fishes played an important role as predators of the abundant and diverse invertebrate fauna present in these ancient tropical coastal ecosystems of Gondwana. creator: Jorge D. Carrillo-Briceño creator: Edwin-Alberto Cadena uri: https://doi.org/10.7717/peerj.13496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Carrillo-Briceño and Cadena title: A new species of deep-sea grunt, Rhonciscus pauco (Lutjaniformes: Haemulidae), from Puerto Rico link: https://peerj.com/articles/13502 last-modified: 2022-06-02 description: A fourth species of the genus Rhonciscus (Lutjaniformes: Haemulidae) is described from various specimens collected by small-scale fishers from the insular upper slope of western Puerto Rico. The new species was molecularly recovered as sister to the Eastern Pacific R. branickii, to which it bears many morphological similarities. It is distinguished from other Rhonciscus species by the number of scale rows between the dorsal fin and the lateral line (7), larger and thus fewer scales along the lateral line (48–50), large eyes (9.4–10.4 times in SL), longer caudal peduncle (15.2–20% of SL), larger sized penultimate (14.7–19.1% in SL) and last (7.4–9.5% in SL) dorsal fin spines which translates to a less deeply notched dorsal fin, and its opalescent silver with golden specks live coloration. This grunt, only now recognized by ichthyologists, but well known by local fishers that target snappers and groupers between 200 and 500 m in depth, occurs in far deeper waters than any western Atlantic grunt. creator: Jose Tavera creator: Michelle T. Schärer-Umpierre creator: Arturo Acero P. uri: https://doi.org/10.7717/peerj.13502 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tavera et al. title: Calotropin and corotoxigenin 3-O-glucopyranoside from the desert milkweed Asclepias subulata inhibit the Na+/K+-ATPase activity link: https://peerj.com/articles/13524 last-modified: 2022-06-02 description: Na+/K+-ATPase is an essential transmembrane enzyme found in all mammalian cells with critical functions for cell ion homeostasis. The inhibition of this enzyme by several cardiotonic steroids (CTS) has been associated with the cytotoxic effect on cancer cell lines of phytochemicals such as ouabain and digitoxin. This study evaluated the inhibitory capacity of cardenolides calotropin and corotoxigenin 3-O-glucopyranoside (C3OG) from Asclepias subulata over the Na+/K+-ATPase activity in vitro and silico. The inhibitory assays showed that calotropin and C3OG decreased the Na+/K+-ATPase activity with IC50 values of 0.27 and 0.87 μM, respectively. Furthermore, the molecules presented an uncompetitive inhibition on Na+/K+-ATPase activity, with Ki values of 0.2 μM to calotropin and 0.5 μM to C3OG. Furthermore, the molecular modeling indicated that calotropin and C3OG might interact with the Thr797 and Gln111 residues, considered essential to the interaction with the Na+/K+-ATPase. Besides, these cardenolides can interact with amino acid residues such as Phe783, Leu125, and Ala323, to establish hydrophobic interactions on the binding site. Considering the results, these provide novel evidence about the mechanism of action of cardenolides from A. subulata, proposing that C3OG is a novel cardenolide that deserves further consideration for in vitro cellular antiproliferative assays and in vivo studies as an anticancer molecule. creator: Salvador E. Meneses-Sagrero creator: Luisa A. Rascón-Valenzuela creator: Juan C. García-Ramos creator: Wagner Vilegas creator: Aldo A. Arvizu-Flores creator: Rogerio R. Sotelo-Mundo creator: Ramon E. Robles-Zepeda uri: https://doi.org/10.7717/peerj.13524 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Meneses-Sagrero et al. title: High-throughput sequencing reveals rhizosphere fungal community composition and diversity at different growth stages of Populus euphratica in the lower reaches of the Tarim River link: https://peerj.com/articles/13552 last-modified: 2022-06-02 description: BackgroundPopulus euphratica is one of the most ancient and primitive tree species of Populus spp and plays an important role in maintaining the ecological balance in desert areas. To decipher the diversity, community structure, and relationship between rhizosphere fungi and environmental factors at different growth stages of P. euphratica demands an in-depth investigation.MethodsIn this study, P. euphratica at different growth stages (young, medium, overripe, and decline periods) was selected as the research object, based on the determination of the physicochemical properties of its rhizosphere soil, the fungal community structure and diversity of P. euphratica and their correlation with soil physicochemical properties were comprehensively analyzed through high-throughput sequencing technology (internal transcribed spacer (ITS)) and bioinformatics analysis methods.ResultsAccording to the analysis of OTU annotation results, the rhizosphere soil fungal communities identified in Populus euphratica were categorized into10 phyla, 36 classes, 77 orders, 165 families, 275 genera and 353 species. The alpha diversity analysis showed that there was no obvious change between the different growth stages, while beta diversity analysis showed that there were significantly differences in the composition of rhizosphere soil fungal communities between mature and overripe trees (R2 = 0.31, P = 0.001), mature and deadwood (R2 = 0.28, P = 0.001). Ascomycota and Basidiomycota were dominant phyla in the rhizosphere fungal community and the dominant genera were Geopora, Chondrostereum and unidentified_Sordariales_sp. The relative abundance of the top ten fungi at each classification level differed greatly in different stages. Canonical correspondence analysis (CCA) and Spearman’s correlation analysis showed that conductivity (EC) was the main soil factor affecting the composition of Populus euphratica rhizosphere soil fungal community (P < 0.01), followed by total dissolvable salts (TDS) and available potassium (AK) (P < 0.05).ConclusionsOur data revealed that the rhizosphere fungal communities at the different growth stages of P. euphratica have differences, conductivity (EC) was the key factor driving rhizosphere fungi diversity and community structure, followed by total dissolvable salts (TDS) and available potassium (AK). creator: Yuanyuan Li creator: Hanli Dang creator: Xinhua Lv creator: Zhongke Wang creator: Xiaozhen Pu creator: Li Zhuang uri: https://doi.org/10.7717/peerj.13552 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Nitric oxide production rather than oxidative stress and cell death is associated with the onset of coral bleaching in Pocillopora acuta link: https://peerj.com/articles/13321 last-modified: 2022-06-01 description: Elevated seawater temperatures associated with climate change lead to coral bleaching. While the ultimate causes of bleaching are well understood, the proximate physiological mechanisms underlying the bleaching response are not as well defined. Here we measured nitric oxide synthase activity, oxidative stress, and cell death in algal symbionts (Symbiodinaceae) freshly isolated from the reef-building coral Pocillopora acuta collected in the field under natural non-bleaching conditions and from corals experimentally exposed to elevated temperatures. Nitric oxide synthase activity in the algal symbionts was >3 orders of magnitude higher than that of the host and increased dramatically with increasing temperature and time of exposure (up to 72 h), consistent with the onset of bleaching for these corals. Oxidative stress and cell death among the algal symbionts were highest in coral holobionts exposed to intermediate as opposed to maximal temperatures, suggesting that these mechanisms are not proximal triggers for bleaching in this species. Our results point to nitric oxide production by the algal symbionts, rather than symbiont dysfunction, as a more important driver of coral bleaching under acute thermal stress in this coral. creator: Christopher P. Jury creator: Brian M. Boeing creator: Henry Trapido-Rosenthal creator: Ruth D. Gates creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.13321 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jury et al. title: Assessment of a developed pig cadaver model for teaching crown lengthening surgical procedures link: https://peerj.com/articles/13421 last-modified: 2022-06-01 description: BackgroundInformation regarding using a pig cadaver model for teaching purposes in dentistry is limited, especially for periodontal surgery procedures. The aim of this study was to assess the feasibility and efficacy of teaching crown lengthening surgical procedures using a prepared pig cadaver model.MethodsMandibles of slaughtered pigs with subgingival crown fracture defects on two premolars and two molars on each side were prepared as periodontal surgery teaching cases. A resident group (n = 20) and an instructor group (n = 18) participated in assessing the efficacy of the model by completing questionnaires before and after training sessions. Data was either assessed descriptively or analyzed statistically with Wilcoxon signed-rank test with the significance level at α = 0.05.ResultsResults revealed that all the knowledge points showed statistically significant improvements (p < 0.05) except for the procedure to determine the quantity of bone removal during osteotomy procedures. Most residents rated the efficacy of the model obtained with 9.0 out of 10 scale. The data of effectiveness of the pig cadaver model from the instructor group ranged from 7.4 ± 1.4 to 9.0 ± 1.0.ConclusionResults of this study support feasibility in using prepared pig cadaver models to teach crown lengthening surgical procedures to postgraduates. creator: Jinsheng Zhong creator: Dong Shi creator: Cui Wang creator: Min Zhen creator: Yiping Wei creator: Ziyao Han creator: Wenjie Hu creator: Kwok-Hung Chung uri: https://doi.org/10.7717/peerj.13421 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhong et al. title: First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird’s) tapir (Tapirus bairdii) link: https://peerj.com/articles/13440 last-modified: 2022-06-01 description: Baird’s tapir, or the Central American Tapir Tapirus bairdii (family Tapiridae), is one of the largest mammals native to the forests and wetlands of southern North America and Central America, and is categorized as ‘endangered’ on the 2014 IUCN Red List of Threatened Species. This study reports, for the first time, the complete mitochondrial genome of T. bairdii and examines the phylogenetic position of T. bairdii amongst closely related species in the same family and order to which it belongs using mitochondrial protein-coding genes (PCG’s). The circular, double-stranded, A-T rich mitochondrial genome of T. bairdii is 16,697 bp in length consisting of 13 protein-coding genes (PCG’s), two ribosomal RNA genes (rrnS (12s ribosomal RNA and rrnL (16s ribosomal RNA)), and 22 transfer RNA (tRNA) genes. A 33 bp long region was identified to be the origin of replication for the light strand (OL), and a 1,247 bp long control region (CR) contains the origin of replication for the heavy strand (OH). A majority of the PCG’s and tRNA genes are encoded on the positive, or heavy, strand. The gene order in T. baiirdi is identical to that of T. indicus and T. terrestris, the only two other species of extant tapirs with assembled mitochondrial genomes. An analysis of Ka/Ks ratios for all the PCG’s show values <1, suggesting that all these PCGs experience strong purifying selection. A maximum-likelihood phylogenetic analysis supports the monophyly of the genus Tapirus and the order Perissodactyla. The complete annotation and analysis of the mitochondrial genome of T. bairdii will contribute to a better understanding of the population genomic diversity and structure of this species, and it will assist in the conservation and protection of its dwindling populations. creator: Caroline C. Ennis creator: Jorge Ortega creator: J. Antonio Baeza uri: https://doi.org/10.7717/peerj.13440 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ennis et al.