title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=587 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Chinese striped-neck turtles vocalize underwater and show differences in peak frequency among different age and sex groups link: https://peerj.com/articles/14628 last-modified: 2023-01-13 description: BackgroundTurtle vocalizations play an important role throughout their lives by expressing individual information (position, emotion, or physiological status), reflecting mating preferences, and synchronizing incubation. The Chinese striped-neck turtle (Mauremys sinensis) is one of the most widely distributed freshwater turtles in China, whose wild population is critically endangered. However, its vocalization has not been studied, which can be the basis for behavioral and ecological studies.MethodsFive different sex–age groups of turtles were recorded underwater in a soundproof room. Cluster analysis and principal component analysis for classification of Chinese striped-neck turtle calls were unreasonable. The turtle calls were manually sought using visual and aural inspection of the recordings in Raven Pro 1.5 software and classified according to differences perceived through auditory inspection and the morphological characteristics of the spectrograms. The results of similarity analysis verified the reliability of manual classification. We compared the peak frequency of the calls among different age and sex groups.ResultsWe identified ten M. sinensis call types, displayed their spectra and waveforms, and described their auditory characteristics. Most calls produced by the turtles were low-frequency. Some high-frequency call types, that are common in other turtle species were also produced. Similar to other turtles, the Chinese striped-neck turtle generates harmonic vocalizations. Courtship behaviors were observed when one of the call types occurred in the mixed-sex group. Adult females produced more high-frequency call types, and subadult males had higher vocalizations than other groups. These results provide a basis for future research on the function of vocalizations, field monitoring, and conservation of this species. creator: Lu Zhou creator: Jinhong Lei creator: Xiaofei Zhai creator: Haitao Shi creator: Jichao Wang uri: https://doi.org/10.7717/peerj.14628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhou et al. title: Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber link: https://peerj.com/articles/14637 last-modified: 2023-01-13 description: BackgroundThe calmodulin-like (CML) protein is a crucial Ca2+-binding protein that can sense and conduct the Ca2+ signal in response to extracellular stimuli. The CML protein families have been identified and characterized in many species. Nevertheless, scarce information on cucumber CML is retrievable.MethodsIn this study, bioinformatic analyses, including gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny, were comprehensively performed to identify and characterize CsCML gene members. Spatiotemporal expression analysis in different organs and environment conditions were assayed with real-time quantitative polymerase chain reaction (qRT-PCR).ResultsForty-four CsCMLs family members were well characterized, and the results showed that the 44 CsCML proteins contained one to four EF-hand domains without other functional domains. Most of the CsCML proteins were intron-less and unevenly distributed on seven chromosomes; two tandemly duplicated gene pairs and three segmentally duplicated gene pairs were identified in the cucumber genome. Cis-acting element analysis showed that the hormone, stress, and plant growth and development-related elements were in the promotor regions. In addition, spatiotemporal expression analysis revealed distinctive expression patterns for CsCML genes in different tissues and environmental conditions, and a putative protein interaction network also confirmed their potential role in responding to various stimuli. These results provide a foundation for understanding CsCMLs and provide a theoretical basis for further study of the physiological functions of CsCMLs. creator: Yunfen Liu creator: Feilong Yin creator: Lingyan Liao creator: Liang Shuai uri: https://doi.org/10.7717/peerj.14637 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies link: https://peerj.com/articles/14642 last-modified: 2023-01-13 description: The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms’ shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundances of (i) cofactor, (ii) carrier, and (iii) vitamin biosynthesis, associated with survival metabolism. Additionally, there was the presence of secondary metabolic pathways and defense mechanisms in extreme conditions. Competitive or inhibitory relationships and metabolic patterns were influenced by the physicochemical characteristics of the environments (mainly sulfate concentration) and by human interference (application of biocides and nutrients). Our worldwide baseline study of microbial communities associated with environments of the oil and gas industry will greatly facilitate the establishment of standardized approaches to control MIC. creator: Joyce Dutra creator: Rosimeire Gomes creator: Glen Jasper Yupanqui García creator: Danitza Xiomara Romero-Cale creator: Mariana Santos Cardoso creator: Vinicius Waldow creator: Claudia Groposo creator: Rubens N. Akamine creator: Maira Sousa creator: Henrique Figueiredo creator: Vasco Azevedo creator: Aristóteles Góes-Neto uri: https://doi.org/10.7717/peerj.14642 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Dutra et al. title: Research on the application of a cement and soil aggregate for the ecological restoration of vegetation in artificial soil link: https://peerj.com/articles/14657 last-modified: 2023-01-13 description: The construction of high-speed roads has resulted in large amounts of steep and exposed cut slopes, posing more potential hazards in areas with mountains and hills. Vegetation restoration is an effective and environmentally-friendly way to restore exposed slopes using outside soil spray seeding, though it is difficult to establish a vegetation cover. Spraying artificial soil on high and steep slopes is a challenging task as it is difficult to keep the fluid mixture on sloped surfaces. Because of these challenges, this study applied different combinations of cement and soil aggregates in artificial soil, measuring final soil properties after one growing season. Experimental results showed that there were substantial differences in all basic soil parameters and in the soil quality index after different treatments. In particular, adding 5–10% cement content could improve the adhesion of artificial soil without remarkably reducing soil quality; adding 0.09% of soil aggregate was also beneficial to soil nutrient availability. These findings indicate that the combination of cement and soil aggregates could be applied in artificial soils for the ecological restoration of steep slope vegetation. Adding cement to the soil increased the alkaline levels of the soil, so it is important to reduce artificial soil pH in the future. The application of a cement and soil aggregate should be considered in the field for the ecological restoration of slope vegetation, and the impact of this addition on slope stability and vegetation growth should be explored with further research. creator: Zhuxin Mao creator: Qian Li creator: Yuchao Wang uri: https://doi.org/10.7717/peerj.14657 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mao et al. title: Systematic identification of smORFs in domestic silkworm (Bombyx mori) link: https://peerj.com/articles/14682 last-modified: 2023-01-13 description: The silkworm (Bombyx mori) is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides. However, the smORFs in silkworm had been poorly identified and studied. To further study the smORFs in silkworm, systematic genome-wide identification is essential. Here, we identified and analyzed smORFs in the silkworm using comprehensive methods. Our results showed that at least 738 highly reliable smORFs were found in B. mori and that 34,401 possible smORFs were partially supported. We also identified some differentially expressed and tissue-specific-expressed smORFs, which may be closely related to the characteristics and functions of the tissues. This article provides a basis for subsequent research on smORFs in silkworm, and also hopes to provide a reference point for future research methods for smORFs in other species. creator: Linrong Wan creator: Wenfu Xiao creator: Ziyan Huang creator: Anlian Zhou creator: Yaming Jiang creator: Bangxing Zou creator: Binbin Liu creator: Cao Deng creator: Youhong Zhang uri: https://doi.org/10.7717/peerj.14682 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wan et al. title: A new genus of dance fly (Diptera: Empidoidea: Hybotidae) from Cretaceous Spanish ambers and introduction to the fossiliferous amber outcrop of La Hoya (Castellón Province, Spain) link: https://peerj.com/articles/14692 last-modified: 2023-01-13 description: Hybotidae fly species, also known as dance flies, in Cretaceous ambers have been described from Lebanon, France, Myanmar, Russia, and Canada. Here we describe Grimaldipeza coelicagen. et sp. n., and recognize another two un-named species, in Spanish amber from the middle Albian El Soplao and lower Cenomanian La Hoya outcrops. The fore tibial gland is present in the new genus, which is characteristic of the family Hybotidae. We compare Grimaldipeza coelicagen. et sp. n. with the holotypes of Trichinites cretaceusHennig, 1970 and Ecommocydromia difficilisSchlüter, 1978, and clarify some morphological details present in the latter two species. Further taxonomic placement beyond family of the here described new genus was not possible and remains incertae sedis within Hybotidae until extant subfamilies are better defined. We provide new paleoecological data of the hybotids, together with paleogeographical and life paleoenvironmental notes. A table with the known Cretaceous Hybotidae is provided. Furthermore, the La Hoya amber-bearing outcrop is described in detail, filling the information gap for this deposit. creator: Mónica M. Solórzano-Kraemer creator: Bradley J. Sinclair creator: Antonio Arillo creator: Sergio Álvarez-Parra uri: https://doi.org/10.7717/peerj.14692 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Solórzano-Kraemer et al. title: A redescription of Palaeogekko risgoviensis (Squamata, Gekkota) from the Middle Miocene of Germany, with new data on its morphology link: https://peerj.com/articles/14717 last-modified: 2023-01-13 description: After its original description, the Middle Miocene gekkotan Palaeogekko risgoviensis remained an enigma for palaeontologists due to a rather poor knowledge of its osteology and relationships. Coming from a single locality in southern Germany, this gecko lived in central Europe during a period when a single gekkotan lineage (i.e., euleptine sphaerodactylids) is confidently reported to have inhabited the continent. However, it is unclear whether P. risgoviensis may represent a member of this same lineage or a second clade of Gekkota. In order to shed light on this issue, the type material of P. risgoviensis is here redescribed, refigured and extensively compared with extinct and extant geckos from Europe. A phylogenetic analysis is also conducted in order to investigate its relationships. The new observations confirm the validity of the German species as a distinct taxon, and exclude the previously-suggested chimeric status of the type material of this gecko (with the exception of a single dentary included in the type series, which clearly belong to a different lizard). Phylogenetic relationships of Palaeogekko are still unclear, though, with different positions within the gekkotan tree recovered for the taxon. Nevertheless, it is confidently supported as a non-eublepharid gekkonoid, in agreement with hypothesys presented by other scholars. creator: Andrea Villa uri: https://doi.org/10.7717/peerj.14717 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Villa title: Characteristics of muscle contraction of the rectus femoris using tensiomyography by sex in healthy college students: a cross-sectional study link: https://peerj.com/articles/14732 last-modified: 2023-01-13 description: BackgroundTensiomyography (TMG) is a non-invasive instrument for measuring mechanical muscle contraction characteristics and measuring the maximum displacement of the muscle belly in the radial direction with respect to the muscle and the time needed to achieve this from electrical stimulation. There have been only been a reports of TMG in healthy adults. A systematic review of TMG reported a low proportion of female participants, with a small sample size. Therefore, it is unclear whether there is a difference in TMG parameters according to sex and between dominant and non-dominant feet. Furthermore, the relationship between TMG parameters and evaluations commonly used in clinical practice has not been clarified. This study aimed to clarify the characteristics of muscle contraction of the rectus femoris using TMG according to sex among healthy college students and its relationship with muscle function evaluation, such as lower limb muscle mass and muscle strength.MethodsThis cross-sectional study included 91 healthy university students (18–24 years). Five tools were used: TMG, lower-limb muscle mass, rectus femoris thickness, isometric knee joint extension torque, and thigh circumference. Each parameter was compared by the generalized linear mixed model (GLMM) and Bonferroni’s multiple comparison test, with sex as the without-subject factor and dominant/non-dominant foot as the within-subject factor. The correlation between the TMG parameters and other parameters was examined using Pearson’s correlation coefficient for both males and females.ResultsThe results of the GLMM, in terms of the TMG parameters, an interaction was observed for maximum displacement (Dm); in the results of the multiple comparison test, Dm for the non-dominant leg was significantly lower in females than in males. A main effect and interaction were not observed for delay time (Td) and contraction time (Tc) by sex, dominant foot, or non-dominant foot. There was a main effect of sex on muscle function evaluation parameters (ρ ≤ 0.05). The correlation between TMG parameters for males and females and lower limb muscle mass, muscle thickness, joint torque, and thigh circumference were significantly correlated with some TMG parameters, lower limb muscle mass and muscle thickness (ρ ≤ 0.05). The absolute value of the correlation coefficient was low overall (0.20–0.38).ConclusionIn healthy college students, TMG parameters for the rectus femoris showed sex differences in Dm, and there was a weak correlation between TMG parameters and lower limb muscle mass. TMG parameter evaluation may indicate a different function compared to the traditional muscle function assessment used in clinical practice. When using the Dm of the TMG as an evaluation battery for the rectus femoris muscle, it is important to consider sex-related differences. creator: Yasuaki Kusumoto creator: Hayato Goto creator: Kohei Chiba creator: Sakiko Oonishi creator: Junko Tsuchiya uri: https://doi.org/10.7717/peerj.14732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kusumoto et al. title: Blooming plant species diversity patterns in two adjacent Costa Rican highland ecosystems link: https://peerj.com/articles/14445 last-modified: 2023-01-12 description: The Costa Rican Paramo is a unique ecosystem with high levels of endemism that is geographically isolated from the Andean Paramos. Paramo ecosystems occur above Montane Forests, below the permanent snow level, and their vegetation differs notably from that of adjacent Montane Forests. We compared the composition and beta diversity of blooming plant species using phenological data from functional plant groups (i.e., insect-visited, bird-visited and insect + bird-visited plants) between a Paramo and a Montane Forest site in Costa Rica and analyzed seasonal changes in blooming plant diversity between the rainy and dry seasons. Species richness was higher in the Montane Forest for all plant categories, except for insect-visited plants, which was higher in the Paramo. Beta diversity and blooming plant composition differed between both ecosystems and seasons. Differences in species richness and beta diversity between Paramo and the adjacent Montane Forest are likely the result of dispersal events that occurred during the last glacial period and subsequent isolation, as climate turned to tropical conditions after the Pleistocene, and to stressful abiotic conditions in the Paramo ecosystem that limit species establishment. Differences in blooming plant composition between both ecosystems and seasons are likely attributed to differential effects of climatic cues triggering the flowering events in each ecosystem, but phylogenetic conservatism cannot be discarded. Analyses of species composition and richness based on flowering phenology data are useful to evaluate potential floral resources for floral visitors (insects and birds) and how these resources change spatially and temporarily in endangered ecosystems such as the Paramo. creator: E. Jacob Cristóbal-Pérez creator: Gilbert Barrantes creator: Alfredo Cascante-Marín creator: Ruth Madrigal-Brenes creator: Paul Hanson creator: Eric J. Fuchs uri: https://doi.org/10.7717/peerj.14445 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cristóbal-Pérez et al. title: Primate tooth crown nomenclature revisited link: https://peerj.com/articles/14523 last-modified: 2023-01-12 description: Cusp patterning on living and extinct primate molar teeth plays a crucial role in species diagnoses, phylogenetic inference, and the reconstruction of the evolutionary history of the primate clade. These studies rely on a system of nomenclature that can accurately identify and distinguish between the various structures of the crown surface. However, studies at the enamel-dentine junction (EDJ) of some primate taxa have demonstrated a greater degree of cusp variation and expression at the crown surface than current systems of nomenclature allow. In this study, we review the current nomenclature and its applicability across all the major primate clades based on investigations of mandibular crown morphology at the enamel-dentine junction revealed through microtomography. From these observations, we reveal numerous new patterns of lower molar accessory cusp expression in primates. We highlight numerous discrepancies between the expected patterns of variation inferred from the current academic literature, and the new patterns of expected variation seen in this study. Based on the current issues associated with the crown nomenclature, and an incomplete understanding of the precise developmental processes associated with each individual crown feature, we introduce these structures within a conservative, non-homologous naming scheme that focuses on simple location-based categorisations. Until there is a better insight into the developmental and phylogenetic origin of these crown features, these categorisations are the most practical way of addressing these structures. Until then, we also suggest the cautious use of accessory cusps for studies of taxonomy and phylogeny. creator: Simon A. Chapple creator: Matthew M. Skinner uri: https://doi.org/10.7717/peerj.14523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chapple and Skinner