title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1490 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The largest European theropod dinosaurs: remains of a gigantic megalosaurid and giant theropod tracks from the Kimmeridgian of Asturias, Spain link: https://peerj.com/articles/4963 last-modified: 2018-07-05 description: The Kimmeridgian Vega, Tereñes and Lastres formations of Asturias have yielded a rich vertebrate fauna, represented by both abundant tracks and osteological remains. However, skeletal remains of theropod dinosaurs are rare, and the diversity of theropod tracks has only partially been documented in the literature. Here we describe the only non-dental osteological theropod remain recovered so far, an isolated anterior caudal vertebra, as well as the largest theropod tracks found. The caudal vertebra can be shown to represent a megalosaurine megalosaurid and represents the largest theropod skeletal remain described from Europe so far. The tracks are also amongst the largest theropod footprints reported from any setting and can be assigned to two different morphotypes, one being characterized by its robustness and a weak mesaxony, and the other characterized by a strong mesaxony, representing a more gracile trackmaker. We discuss the recently proposed distinction between robust and gracile large to giant theropod tracks and their possible trackmakers during the Late Jurassic-Berriasian. In the absence of complete pedal skeletons of most basal tetanurans, the identity of the maker of Jurassic giant theropod tracks is difficult to establish. However, the notable robustness of megalosaurine megalosaurids fits well with the described robust morphotypes, whereas more slender large theropod tracks might have been made by a variety of basal tetanurans, including allosaurids, metriocanthosaurids or afrovenatorine megalosaurids, or even exceptionally large ceratosaurs. Concerning osteological remains of large theropods from the Late Jurassic of Europe, megalosaurids seem to be more abundant than previously recognized and occur in basically all Jurassic deposits where theropod remains have been found, whereas allosauroids seem to be represented by allosaurids in Western Europe and metriacanthosaurids in more eastern areas. Short-term fluctuations in sea level might have allowed exchange of large theropods between the islands that constituted Europe during the Late Jurassic. creator: Oliver W.M. Rauhut creator: Laura Piñuela creator: Diego Castanera creator: José-Carlos García-Ramos creator: Irene Sánchez Cela uri: https://doi.org/10.7717/peerj.4963 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Rauhut et al. title: Association of circulating microRNA-122 with presence and severity of atherosclerotic lesions link: https://peerj.com/articles/5218 last-modified: 2018-07-04 description: ObjectiveMicroRNA (miR)-122 is highly expressed in the liver, where it has been implicated as a regulator of fatty-acid metabolism. A recent study reported that miR-122 plays a role in pathogenesis of atherosclerosis; however, whether it connects with severity of atherosclerotic lesion is still controversial. We therefore investigated the association between miR-122 expression and presence and severity of coronary atherosclerotic plaque.MethodsDuring January–November 2017, we included 300 patients with coronary heart disease (CHD) and 100 subjects as the control group. MiR-122 content was detected by quantitative real-time polymerase chain reaction. MiR-122 level was identified in all subjects, and the Spearman correlation between miR-122 and severity of atherosclerosis was analyzed.ResultsPatients with CHD had higher miR-122 expression than in control group (2.61, 0.91–8.86 vs. 1.62, 0.71–3.45, p < 0.001). Gensini score was significantly associated with miR-122 expression (r = 0.7964, p < 0.001). The odds ratio of miR-122 solely was 0.12 (95% CI [0.05–0.43]) and factors such as cholesterol, triglyceride together with miR-122 level were closely associated with atherosclerosis (all p < 0.001).ConclusionsThe serum level of miR-122 may be used to differentiate between mild and severe coronary atherosclerotic lesion. Use of this marker might allow non-invasive diagnosis the degree of coronary atherosclerosis. creator: Yu-Long Wang creator: Wen Yu uri: https://doi.org/10.7717/peerj.5218 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wang and Yu title: Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils link: https://peerj.com/articles/5168 last-modified: 2018-07-04 description: Catostomidae (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian “total-evidence” methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous–Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian–North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning. creator: Justin C. Bagley creator: Richard L. Mayden creator: Phillip M. Harris uri: https://doi.org/10.7717/peerj.5168 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bagley et al. title: Crystal structure of human Acinus RNA recognition motif domain link: https://peerj.com/articles/5163 last-modified: 2018-07-04 description: Acinus is an abundant nuclear protein involved in apoptosis and splicing. It has been implicated in inducing apoptotic chromatin condensation and DNA fragmentation during programmed cell death. Acinus undergoes activation by proteolytic cleavage that produces a truncated p17 form that comprises only the RNA recognition motif (RRM) domain. We have determined the crystal structure of the human Acinus RRM domain (AcRRM) at 1.65 Å resolution. It shows a classical four-stranded antiparallel β-sheet fold with two flanking α-helices and an additional, non-classical α-helix at the C-terminus, which harbors the caspase-3 target sequence that is cleaved during Acinus activation. In the structure, the C-terminal α-helix partially occludes the potential ligand binding surface of the β-sheet and hypothetically shields it from non-sequence specific interactions with RNA. Based on the comparison with other RRM-RNA complex structures, it is likely that the C-terminal α-helix changes its conformation with respect to the RRM core in order to enable RNA binding by Acinus. creator: Humberto Fernandes creator: Honorata Czapinska creator: Katarzyna Grudziaz creator: Janusz M. Bujnicki creator: Martyna Nowacka uri: https://doi.org/10.7717/peerj.5163 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Fernandes et al. title: Identification of SNPs potentially related to immune responses and growth performance in Litopenaeus vannamei by RNA-seq analyses link: https://peerj.com/articles/5154 last-modified: 2018-07-04 description: Litopenaeus vannamei is one of the most important shrimp species for worldwide aquaculture. Despite this, little genomic information is available for this penaeid and other closely related taxonomic crustaceans. Consequently, genes, proteins and their respective polymorphisms are poorly known for these species. In this work, we used the RNA sequencing technology (RNA-seq) in L. vannamei shrimp evaluated for growth performance, and exposed to the White Spot Syndrome Virus (WSSV), in order to investigate the presence of Single Nucleotide Polymorphisms (SNPs) within genes related to innate immunity and growth, both features of great interest for aquaculture activity. We analyzed individuals with higher and lower growth rates; and infected (unhealthy) and non-infected (healthy), after exposure to WSSV. Approximately 7,000 SNPs were detected in the samples evaluated for growth, being 3,186 and 3,978 exclusive for individuals with higher and lower growth rates, respectively. In the animals exposed to WSSV we found about 16,300 unique SNPs, in which 9,338 were specific to non-infected shrimp, and 7,008 were exclusive to individuals infected with WSSV and symptomatic. In total, we describe 4,312 unigenes containing SNPs. About 60% of these unigenes returned GO blastX hits for Biological Process, Molecular Function and Cellular Component ontologies. We identified 512 KEGG unique KOs distributed among 275 pathways, elucidating the majority of metabolism roles related to high protein metabolism, growth and immunity. These polymorphisms are all located in coding regions, and certainly can be applied in further studies involving phenotype expression of complex traits, such as growth and immunity. Overall, the set of variants raised herein enriches the genomic databases available for shrimp, given that SNPs originated from nextgen are still rare for this relevant crustacean group, despite their huge potential of use in genomic selection approaches. creator: Camilla A. Santos creator: Sónia C.S. Andrade creator: Patrícia D. Freitas uri: https://doi.org/10.7717/peerj.5154 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Santos et al. title: Speciation among sympatric lineages in the genus Palythoa (Cnidaria: Anthozoa: Zoantharia) revealed by morphological comparison, phylogenetic analyses and investigation of spawning period link: https://peerj.com/articles/5132 last-modified: 2018-07-04 description: Zoantharians are sessile marine invertebrates and colonial organisms possessing sexual and asexual reproductive ability. The zooxanthellate zoantharian genus Palythoa is widely distributed in coral reef ecosystems. In the Ryukyu Archipelago, Japan, sympatric Palythoa tuberculosa and P. mutuki are the dominant species of this genus in the intertidal zone. Previous phylogenetic analyses have shown that these two species are closely related, and additionally revealed a putative sympatric hybrid species (designated as Palythoa sp. yoron). In this study, we attempted to delineate Palythoa species boundaries and to clarify the relationships among these three groups plus another additional putative sympatric species (P. aff. mutuki) by multiple independent criteria. The morphology of these four lineages was clearly different; for example the number of tentacles was significantly different for each species group in all pairwise comparisons. From observations of gonadal development conducted in 2010 and 2011, P. sp. yoron and P. aff. mutuki appear to be reproductively isolated from P. tuberculosa. In the phylogenetic tree resulting from maximum likelihood analyses of the ITS-rDNA sequence alignment, P. tuberculosa and P. sp. yoron formed a very well supported monophyletic clade (NJ = 100%, ML = 95%, Bayes = 0.99). This study demonstrates that despite clear morphological and/or reproductive differences, P. tuberculosa and P. sp. yoron are phylogenetically entangled and closely related to each other, as are P. mutuki and P. aff. mutuki. Additionally, no single molecular marker was able to divide these four lineages into monophyletic clades by themselves, and a marker that has enough resolution to solve this molecular phylogenetic species complex is required. In summary, the morphological and reproductive results suggest these lineages are four separate species, and that incomplete genetic lineage sorting may prevent the accurate phylogenetic detection of distinct species with the DNA markers utilized in this study, demonstrating the value of morphological and reproductive data when examining closely related lineages. creator: Masaru Mizuyama creator: Giovanni D. Masucci creator: James D. Reimer uri: https://doi.org/10.7717/peerj.5132 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mizuyama et al. title: Assessing population changes of historically overexploited black corals (Order: Antipatharia) in Cozumel, Mexico link: https://peerj.com/articles/5129 last-modified: 2018-07-04 description: Black corals (Antipatharians) are crucial structural and ecological components of many mesophotic coral ecosystems (MCEs; reefs 30–150 m depth). In Mexico, black corals are harvested for the jewellery industry, which has historically led to population depletion. Harvesting began in the early 1960s and was concentrated around Cozumel Island until 1995. Since then, harvesting permits have been granted only for the mainland coast. Here we compare Cozumel populations between 1998 and 2016 for the two black coral species targeted by the jewellery industry. We found that densities of Plumapathes pennacea in 2016 were substantially lower than in 1998. However, the 2016 P. pennacea population has shifted to be dominated by larger colonies, suggesting disproportionate juvenile mortality or recruitment failure. Low numbers of Antipathes caribbeana were recorded, and no change in population density or colony size was detected between 1998 and 2016. Despite harvesting occurring for almost 70 years in the Mexican Caribbean, no information on reproduction, recruitment and other dynamics of the targeted species is available. We advocate for harvesting permits to be based on scientific evidence, and for implementation of future restrictions to prevent total depletion of black corals in the area. creator: Erika Gress creator: Dominic A. Andradi-Brown uri: https://doi.org/10.7717/peerj.5129 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gress and Andradi-Brown title: Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs link: https://peerj.com/articles/5125 last-modified: 2018-07-04 description: Many proteins display complex dynamical properties that are often intimately linked to their biological functions. As the native state of a protein is best described as an ensemble of conformations, it is important to be able to generate models of native state ensembles with high accuracy. Due to limitations in sampling efficiency and force field accuracy it is, however, challenging to obtain accurate ensembles of protein conformations by the use of molecular simulations alone. Here we show that dynamic ensemble refinement, which combines an accurate atomistic force field with commonly available nuclear magnetic resonance (NMR) chemical shifts and NOEs, can provide a detailed and accurate description of the conformational ensemble of the native state of a highly dynamic protein. As both NOEs and chemical shifts are averaged on timescales up to milliseconds, the resulting ensembles reflect the structural heterogeneity that goes beyond that probed, e.g., by NMR relaxation order parameters. We selected the small protein domain NCBD as object of our study since this protein, which has been characterized experimentally in substantial detail, displays a rich and complex dynamical behaviour. In particular, the protein has been described as having a molten-globule like structure, but with a relatively rigid core. Our approach allowed us to describe the conformational dynamics of NCBD in solution, and to probe the structural heterogeneity resulting from both short- and long-timescale dynamics by the calculation of order parameters on different time scales. These results illustrate the usefulness of our approach since they show that NCBD is rather rigid on the nanosecond timescale, but interconverts within a broader ensemble on longer timescales, thus enabling the derivation of a coherent set of conclusions from various NMR experiments on this protein, which could otherwise appear in contradiction with each other. creator: Elena Papaleo creator: Carlo Camilloni creator: Kaare Teilum creator: Michele Vendruscolo creator: Kresten Lindorff-Larsen uri: https://doi.org/10.7717/peerj.5125 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Papaleo et al. title: Back to beaked: Zea mays subsp. mays Rostrata Group in northern Italy, refugia and revival of open-pollinated maize landraces in an intensive cropping system link: https://peerj.com/articles/5123 last-modified: 2018-07-04 description: Crop landraces are fundamental resources to increase the eroded genepool of modern crops in order to adapt agriculture to future challenges; plus, they are of immeasurable heritage and cultural value. Between the 1940s and the 1960s open-pollinated varieties (OPVs) of flint and semi-flint maize in Europe were almost completely replaced by high-yielding hybrid dent cultivars selected in North America. No comprehensive assessment was performed after the 1950s to understand which maize genetic resources survived genetic erosion in northern Italy, an area characterized by a high degree of landraces extinction and introgression, intensive hybrid dent monocultures, as well as being one of the hotspots of maize cultivation at a continental level. Among these landraces, beaked maize represents a peculiar case study for assessing the survival of OPVs in intensive cropping systems. By means of ethnobotanical and literature surveys, the history of Zea mays subsp. mays Rostrata Group and its current distribution were reconstructed. It emerged that beaked maize originated in the study area and it is one of the oldest genepools available not subjected to formal crop improvement. We identified 28 landraces of beaked maize currently cultivated, 18 here recorded for the first time. The cultivation of more than half of the 28 landraces has continued throughout the last 80 years in a few fragmented localities that can be regarded as “refugia”. The survival of these landraces from substitution with high-yielding cultivars and unidirectional introgression has been mainly due to active on-farm conservation performed by custodian farmers and secondarily to cultivation in isolated areas (e.g., mountain valleys). After decades of genetic erosion, beaked maize has since the late 1990s experienced a revival, in terms of an increasing number of cultivation localities and the level of product commercialization. This process is mostly spontaneous and only occasionally mediated by governmental institutions; it is linked to the rediscovery of local food products, in this case mainly polenta, a dish made of corn flour, which used to be the staple food across northern Italy. The ex situ conservation of beaked maize and on-farm measures put in place by the farmers to prevent introgression are also assessed. Further research and collecting missions are needed to provide an inventory of open-pollinated landraces of other landrace groups that have survived genetic erosion in Europe. To meet this aim, extensive ethnobotanical surveys, such as the one performed here, are very powerful tools in detecting these genetic resources. creator: Nicola Maria Giuseppe Ardenghi creator: Graziano Rossi creator: Filippo Guzzon uri: https://doi.org/10.7717/peerj.5123 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ardenghi et al. title: Preliminary study on phosphate solubilizing Bacillus subtilis strain Q3 and Paenibacillus sp. strain Q6 for improving cotton growth under alkaline conditions link: https://peerj.com/articles/5122 last-modified: 2018-07-04 description: BackgroundLow phosphorus availability limits crop production in alkaline calcareous soils in semi-arid regions including Pakistan. Phosphate solubilizing bacteria may improve crop growth on alkaline calcareous soils due to their ability to enhance P availability.MethodsTwenty rhizobacterial isolates (Q1–Q20) were isolated from rhizosphere of cotton and characterized for their growth promoting attributes in vitro. The selected phosphate solubilizing isolates were further screened for their ability to improve cotton growth under axenic conditions (jar trial). The phosphorus solubilization capacities of selected strains were quantified and these strains were identified through 16S rDNA sequencing.ResultsIsolates Q2, Q3, Q6, Q7, Q8, Q13 and Q14 were able to solubilize phosphate from insoluble sources. Most of these isolates also possessed other traits including catalase activity and ammonia production. The growth promotion assay showed that Q3 was significantly better than most of the other isolates followed by Q6. Maximum root colonization (4.34 × 106 cfu g−1) was observed in case of isolate Q6 followed by Q3. The phosphorus solubilization capacities of these strains were quantified, showing a maximum phosphorus solubilization by Q3 (optical density 2.605 ± 0.06) followed by the Q6 strain. The strain Q3 was identified as Bacillus subtilis (accession # KX788864) and Q6 as Paenibacillus sp. (accession # KX788865) through 16S rDNA sequencing.DiscussionThe bacterial isolates varied in their abilities for different growth promoting traits. The selected PGPR Bacillus subtilis strain Q3 and Paenibacillus sp. strain Q6 have multifarious growth promoting traits including ability to grow at higher EC and pH levels, and phosphorus solubilizing ability. These strains can efficiently colonize cotton roots under salt affected soils and help plants in phosphorus nutrition. It is concluded that both strains are potential candidates for promoting cotton growth under alkaline conditions, however further investigation is required to determine their potential for field application. creator: Maqshoof Ahmad creator: Iqra Ahmad creator: Thomas H. Hilger creator: Sajid M. Nadeem creator: Muhammad F. Akhtar creator: Moazzam Jamil creator: Azhar Hussain creator: Zahir A. Zahir uri: https://doi.org/10.7717/peerj.5122 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ahmad et al.