title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=652
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Effects of exogenous calcium on the drought response of the tea plant (Camellia sinensis (L.) Kuntze)
link: https://peerj.com/articles/13997
last-modified: 2022-08-29
description: BackgroundDrought is one of the major factors reducing the yield of many crops worldwide, including the tea crop (Camellia sinensis (L.) Kuntze). Calcium participates in most of cellular signaling processes, and its important role in stress detection and triggering a response has been shown in many crops. The aim of this study was to evaluate possible effects of calcium on the tea plant response to drought.MethodsExperiments were conducted using 3-year-old potted tea plants of the best local cultivar Kolkhida. Application of ammonium nitrate (control treatment) or calcium nitrate (Ca treatment) to the soil was performed before drought induction. Next, a 7-day drought was induced in both groups of plants. The following physiological parameters were measured: relative electrical conductivity, pH of cell sap, and concentrations of cations, sugars, and amino acids. In addition, relative expression levels of 40 stress-related and crop quality–related genes were analyzed.ResultsUnder drought stress, leaf electrolyte leakage differed significantly, indicating greater damage to cell membranes in control plants than in Ca-treated plants. Calcium application resulted in greater pH of cell sap; higher accumulation of tyrosine, methionine, and valine; and a greater Mg2+ content as compared to control plants. Drought stress downregulated most of the quality-related genes in both groups of tea plants. By contrast, significant upregulation of some genes was observed, namely CRK45, NAC26, TPS11, LOX1, LOX6, Hydrolase22, DREB26, SWEET2, GS, ADC, DHN2, GOLS1, GOLS3, and RHL41. Among them, three genes (LOX1, RHL41, and GOLS1) showed 2–3 times greater expression in Ca-treated plants than in control plants. Based on these results, it can be speculated that calcium affects galactinol biosynthesis and participates in the regulation of stomatal aperture not only through activation of abscisic-acid signaling but also through jasmonic-acid pathway activation. These findings clarify calcium-mediated mechanisms of drought defense in tree crops. Thus, calcium improves the drought response in the tea tree.
creator: Lyudmila S. Malyukova
creator: Natalia G. Koninskaya
creator: Yuriy L. Orlov
creator: Lidiia S. Samarina
uri: https://doi.org/10.7717/peerj.13997
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Malyukova et al.

title: The redescription of the holotype of Nothosaurus mirabilis (Diapsida, Eosauropterygia)—a historical skeleton from the Muschelkalk (Middle Triassic, Anisian) near Bayreuth (southern Germany)
link: https://peerj.com/articles/13818
last-modified: 2022-08-26
description: In 2009, the historical mount of the holotype of Nothosaurus mirabilis from the Upper Muschelkalk of Oschenberg (Laineck Mountain Range, near Bayreuth, southern Germany) was disassembled and the original postcranial skeleton was reworked and remounted in find position. Its morphology is described and figured for the first time in detail. Further on, a thorough overview of the sedimentary environment and the historical activities around the Upper Muschelkalk quarries in the vicinity of Bayreuth is given. The holotype of N. mirabilis is one out of only two fairly complete nothosaur skeletons known from the Bayreuth Upper Muschelkalk and greatly emends our knowledge of the morphology of the species and the genus. It will further allow an assignment of isolated elements to this taxon. The specimen consists of an articulated and complete neck and anterior trunk vertebral column as well as several articulated parts of the anterior tail region. The sacral region is partially preserved but disarticulated. Besides vertebrae, ribs and gastral fragments, both humeri, the right femur, few zeugopodial and autopodial elements, and the right pelvic girdle are preserved. The very high neural spines of the holotype are stabilized by a supersized zygosphene-zygantrum articulation reaching far dorsally. Together with the large intercentral spaces this character suggests lateral undulation of the trunk region during fast swimming whereas propelling with the broad and wing-shaped humerus and the flat ulna was used during slower swimming. The total body length for this not fully grown individual is reconstructed as between 290 to 320 cm. Preservation, degree of completeness, and articulation of the individual is unique. The skull and shoulder girdle are both lost, whereas articulated strings of the vertebral column have turned and appendicular bones have shifted posteriorly or anteriorly, respectively, indicating water movements and possibly also scavenging.
creator: Nicole Klein
creator: Stefan Eggmaier
creator: Hans Hagdorn
uri: https://doi.org/10.7717/peerj.13818
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Klein et al.

title: A new species of lotic breeding salamander (Amphibia, Caudata, Hynobiidae) from Shikoku, Japan
link: https://peerj.com/articles/13891
last-modified: 2022-08-26
description: BackgroundHynobius hirosei is a lotic-breeding salamander endemic to Shikoku Island in western Japan. Significant allozymic and morphological differences have been found among the populations of this species; however, the degree and pattern of intraspecific variation have not been surveyed using a sufficient number of samples.MethodsFor the taxonomic revision of H. hirosei, we conducted genetic and morphological surveys using samples collected throughout the distribution. Phylogenetic analysis using the cytochrome b region of mitochondrial DNA and population structure analysis using single nucleotide polymorphisms were conducted to evaluate the population structure within the species and the degree of genetic differentiation. Subsequently, a morphological survey based on multivariate and univariate analyses was performed to assess the morphological variation.ResultsGenetic analyses revealed three genetic groups (Tsurugi, Central, and Nanyo) within H. hirosei, with the Nanyo group distributed allopatrically from the others, and the Tsurugi and Central groups distributed parapatrically with the formation of a hybrid zone between them. The Nanyo group was morphologically distinguishable from the remaining samples, including the topotype of H. hirosei, based on a smaller body size and several ratio values of characters to snout-vent length, longer axilla-groin distance, shorter tail length, shorter internarial distance, longer upper eyelid length, and larger medial tail width. These results support the notion that the Nanyo group is an undescribed species. However, the remaining genetically differentiated groups could not be divided in the present study. Herein, we described the Nanyo group as a new species.
creator: Sally Kanamori
creator: Kanto Nishikawa
creator: Masafumi Matsui
creator: Shingo Tanabe
uri: https://doi.org/10.7717/peerj.13891
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Kanamori et al.

title: Morphology of inner cell mass: a better predictive biomarker of blastocyst viability
link: https://peerj.com/articles/13935
last-modified: 2022-08-26
description: BackgroundTransfer of embryos at the blastocyst stage is one of the best approaches for achieving a higher success rate in In vitro fertilization (IVF) treatment as it demonstrates an improved uterine and embryonic synchrony at implantation. Despite novel biochemical and genetic markers proposed for the prediction of embryo viability in recent years, the conventional morphological grading of blastocysts remains the classical way of selection in routine practice. This study aims to investigate the association between the morphological features of blastocysts and pregnancy outcomes.MethodsThis prospective study included women undergoing single or double frozen blastocyst transfers following their autologous cycles in a period between October 2020 and September 2021. The morphological grades (A—good, B—average, and C—poor) of inner cell mass (ICM) and trophectoderm (TE) of blastocysts with known implantation were compared to assess their predictive potential of pregnancy outcome. It was further explored by measuring the relationship between the two variables using logistic regression and receiver operating characteristic (ROC) analysis.ResultsA total of 1,972 women underwent frozen embryo transfer (FET) cycles with a total of 3,786 blastocysts. Known implantation data (KID) from 2,060 blastocysts of 1,153 patients were subjected to statistical analysis, the rest were excluded. Implantation rates (IR) from transfer of ICM/TE grades AA, AB, BA, BB were observed as 48.5%, 39.4%, 23.4% and 25% respectively. There was a significantly higher IR observed in blastocysts with ICM grade A (p < 0.001) than those with B irrespective of their TE scores. The analysis of the interaction between the two characteristics confirmed the superiority of ICM over TE as a predictor of the outcome. The rank biserial correlation value for ICM was also greater compared to that of TE (0.11 vs 0.05).ConclusionThis study confirms that the morphology of ICM of the blastocyst is a stronger predictor of implantation and clinical pregnancy than that of TE and can be utilized as a biomarker of viability.
creator: Sargunadevi Sivanantham
creator: Mahalakshmi Saravanan
creator: Nidhi Sharma
creator: Jayashree Shrinivasan
creator: Ramesh Raja
uri: https://doi.org/10.7717/peerj.13935
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Sivanantham et al.

title: Differences in subjective well-being between individuals with distinct Joint Personality (temperament-character) networks in a Bulgarian sample
link: https://peerj.com/articles/13956
last-modified: 2022-08-26
description: BackgroundPersonality is the major predictor of people’s subjective well-being (i.e., positive affect, negative affect, and life satisfaction). Recent research in countries with high-income and strong self-transcendent values shows that well-being depends on multidimensional configurations of temperament and character traits (i.e., Joint Personality Networks) that regulate the way people learn to adapt their habits to be in accord with their goals and values, rather than individual traits. To evaluate the prevalence and the associations of different Joint Personality (temperament-character) Networks with well-being in a low-income country with weak self-transcendent values, we tested their association in Bulgarian adults, a population known to have strong secular-rationalist values but weak self-transcendent values.MethodThe sample consisted of 443 individuals from Bulgaria (68.70% females) with a mean age of 34 years (SD = 15.05). Participants self-reported personality (Temperament and Character Inventory), affect (Positive Affect Negative Affect Schedule), and life satisfaction (Satisfaction with Life Scale). The personality scores were used for profiling through latent profile analysis and latent class analysis based on temperament configurations (i.e., Temperament Profiles) of high/low scores of Novelty Seeking (N/n), Harm Avoidance (H/h), Reward Dependence (R/r), and Persistence (P/s); and character configurations (i.e., Character Profiles) of high/low scores of Self-Directedness (S/s), Cooperativeness (C/c), and Self-Transcendence (T/t).ResultsWe found two Temperament Profiles and two Character Profiles that clustered into two distinctive Joint Personality Networks. All individuals in Joint Personality Network 1 had a Reliable (nhRP) Temperament Profile in combination with an Organized (SCt) Character Profile (i.e., a stable temperament and a healthy character configuration). About 71.9% in Joint Personality Network 2 had an Apathetic (sct) Character Profile in combination with Methodical (nHrp) or Reliable (nhRP) Temperament Profiles, while 28.1% had a Methodical (nHrp) Temperament Profile in combination with an Organized (SCt) Character Profile. Few people with high self-expressive values (i.e., high in all three character traits; SCT) were found. Individuals with a Joint Personality Network 1 with strong secular-rationalist values reported higher levels of positive affect and life satisfaction (p < .001), while individuals with a Joint Personality Network 2 reported higher levels of negative affect (p < .001).ConclusionsAlthough a stable temperament and a healthy character were separately important for well-being, it was clear that it was the interaction between such temperament and character configuration that yielded greater levels of subjective well-being. Nevertheless, future research needs to investigate this interaction further to evaluate other cultures with variable configurations of personality traits and values.
creator: Danilo Garcia
creator: Maryam Kazemitabar
creator: Kristina Stoyanova
creator: Drozdstoy Stoyanov
creator: C. Robert Cloninger
uri: https://doi.org/10.7717/peerj.13956
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Garcia et al.

title: The efficacy of computed tomography scanning versus surface scanning in 3D finite element analysis
link: https://peerj.com/articles/13760
last-modified: 2022-08-25
description: Finite element analysis (FEA) is a commonly used application in biomechanical studies of both extant and fossil taxa to assess stress and strain in solid structures such as bone. FEA can be performed on 3D structures that are generated using various methods, including computed tomography (CT) scans and surface scans. While previous palaeobiological studies have used both CT scanned models and surface scanned models, little research has evaluated to what degree FE results may vary when CT scans and surface scans of the same object are compared. Surface scans do not preserve the internal geometries of 3D structures, which are typically preserved in CT scans. Here, we created 3D models from CT scans and surface scans of the same specimens (crania and mandibles of a Nile crocodile, a green sea turtle, and a monitor lizard) and performed FEA under identical loading parameters. It was found that once surface scanned models are solidified, they output stress and strain distributions and model deformations comparable to their CT scanned counterparts, though differing by notable stress and strain magnitudes in some cases, depending on morphology of the specimen and the degree of reconstruction applied. Despite similarities in overall mechanical behaviour, surface scanned models can differ in exterior shape compared to CT scanned models due to inaccuracies that can occur during scanning and reconstruction, resulting in local differences in stress distribution. Solid-fill surface scanned models generally output lower stresses compared to CT scanned models due to their compact interiors, which must be accounted for in studies that use both types of scans.
creator: Andre J. Rowe
creator: Emily J. Rayfield
uri: https://doi.org/10.7717/peerj.13760
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Rowe and Rayfield

title: Evolution of pathogenicity in obligate fungal pathogens and allied genera
link: https://peerj.com/articles/13794
last-modified: 2022-08-25
description: Obligate fungal pathogens (ascomycetes and basidiomycetes) and oomycetes are known to cause diseases in cereal crop plants. They feed on living cells and most of them have learned to bypass the host immune machinery. This paper discusses some of the factors that are associated with pathogenicity drawing examples from ascomycetes, basidiomycetes and oomycetes, with respect to their manifestation in crop plants. The comparisons have revealed a striking similarity in the three groups suggesting convergent pathways that have arisen from three lineages independently leading to an obligate lifestyle. This review has been written with the intent, that new information on adaptation strategies of biotrophs, modifications in pathogenicity strategies and population dynamics will improve current strategies for breeding with stable resistance.
creator: Moytri RoyChowdhury
creator: Jake Sternhagen
creator: Ya Xin
creator: Binghai Lou
creator: Xiaobai Li
creator: Chunnan Li
uri: https://doi.org/10.7717/peerj.13794
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 RoyChowdhury et al.

title: Readiness of the primary health care units and associated factors for the management of hypertension and type II diabetes mellitus in Sidama, Ethiopia
link: https://peerj.com/articles/13797
last-modified: 2022-08-25
description: BackgroundIn low-income nations such as Ethiopia, noncommunicable diseases (NCDs) are becoming more common. The Ethiopian Ministry of Health has prioritized NCD prevention, early diagnosis, and management. However, research on the readiness of public health facilities to address NCDs, particularly hypertension and type II diabetes mellitus, is limited.MethodsThe study used a multistage cluster sampling method and a health facility-based cross-sectional study design. A total of 83 health facilities were evaluated based on WHO’s Service Availability and Readiness Assessment (SARA) tool to investigate the availability of services and the readiness of the primary health care unit (PHCU) to manage type II diabetes and Hypertension. Trained data collectors interviewed with PHCU head or NCD focal persons. The study tried to investigate (1) the availability of basic amenities and the four domains: staff and guidelines, basic equipment, diagnostic materials, and essential medicines used to manage DM and HPN, (2) the readiness of the PHCU to manage DM and HPN. The data were processed by using SPSS version 24. Descriptive statistics, including frequency and percentage, inferential statistics like the chi-square test, and logistic regression models were used to analyze the data.ResultsOf the 82 health facilities, only 29% and 28% of the PHCU identified as ready to manage HPN and DM. Facility type, facility location, presence of guidelines, trained staff, groups of antihypertensive and antidiabetic medicines had a significant impact (P < 0.05) on the readiness of the PHCU to manage HPN and DM at a 0.05 level of significance. Facilities located in urban were 8.2 times more likely to be ready to manage HPN cases than facilities located in rural (AOR = 8.2, 95% CI [2.4–28.5]) and P < 0.05.Conclusion and recommendationThe results identified comparatively poor and deprived readiness to offer HPN and DM services at lower-level health facilities(health centers). Equipping the lower-level health facilities with screening and diagnostic materials, essential medicines, and provision of basic training for the health care providers and NCD guidelines should be available, especially in the lower health care facilities.
creator: Tigist Kebede Mulugeta
creator: Dejene Hailu Kassa
uri: https://doi.org/10.7717/peerj.13797
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Mulugeta and Kassa

title: Diagnosis and potential invasion risk of Thrips parvispinus under current and future climate change scenarios
link: https://peerj.com/articles/13868
last-modified: 2022-08-25
description: Background and ObjectiveInvasive thrips, Thrips parvispinus Karny recently reported in India, causing a widespread severe infestation in more than 0.4 million ha of chilli (Capsicum annum L.) growing areas. This species is native to Thailand and most prevalent in other South East Asian countries. Large scale cultivation of the major host plants (chilli and papaya), and favourable climatic conditions in India and other countries similar to native range of Thrips parvispinus expected to favour its further spread and establishment to new areas.Materials and MethodsThe present study was undertaken to confirm invasive thrips species identity through both morphological and molecular approaches and predict its potential invasion using the maximum entropy (MaxEnt) algorithm.ResultsThe model predicted species range in respect of discrimination of suitable and unsuitable areas for its occurrence both in current and future climatic scenarios. The model provided a good fit for species distribution with a high value of area under the curve (0.957). The jackknife test indicated annual mean temperature and precipitation were found to be the most important bioclimatic variable in determining the distribution of T. parvispinus. High suitability areas were predicted in the countries wherever its occurrence was reported with high discrimination ability of suitable and unsuitable areas. Key distinguishing morphological characters of T. parvispinus were illustrated through high-resolution scanning electron microscopic images.ConclusionThe identity of the thrips causing wide spread damage in chilli confirmed through morphological and molecular approaches. Key identifying characters were described through high resolution scanning electron microscopic images for accurate identification of the species. MaxEnt model identified high suitability regions for the potential establishment of T. parvispinus in India and other parts of the world. This study facilitates forecasting of further spread and also suggests imposing strict domestic quarantine measures to curtail its establishment in the new areas.
creator: Timmanna Hulagappa
creator: Gundappa Baradevanal
creator: Shwetha Surpur
creator: Devaramane Raghavendra
creator: Sagar Doddachowdappa
creator: Pathour R. Shashank
creator: Kumaranag Kereyagalahalli Mallaiah
creator: Jamuna Bedar
uri: https://doi.org/10.7717/peerj.13868
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Hn et al.

title: Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria)
link: https://peerj.com/articles/13886
last-modified: 2022-08-25
description: Molecular phylogenetic studies that have included sirenians from the genera Trichechus, Dugong, and Hydrodamalis have resolved their interrelationships but have yielded divergence age estimates that are problematically discordant. The ages of these lineage splits have profound implications for how to interpret the sirenian fossil record—including clade membership, biogeographic patterns, and correlations with Earth history events. In an effort to address these issues, here we present a total evidence phylogenetic analysis of Sirenia that includes living and fossil species and applies Bayesian tip-dating methods to estimate their interrelationships and divergence times. In addition to extant sirenians, our dataset includes 56 fossil species from 106 dated localities and numerous afrotherian outgroup taxa. Genetic, morphological, temporal, and biogeographic data are assessed simultaneously to bring all available evidence to bear on sirenian phylogeny. The resulting time-tree is then used for Bayesian geocoordinates reconstruction analysis, which models ancestral geographic areas at splits throughout the phylogeny, thereby allowing us to infer the direction and timing of dispersals. Our results suggest that Pan-Sirenia arose in North Africa during the latest Paleocene and that the Eocene evolution of stem sirenians was primarily situated in the Tethyan realm. In the late Eocene, some lineages moved into more northern European latitudes, an area that became the source region for a key trans-Atlantic dispersal towards the Caribbean and northern-adjacent west Atlantic. This event led to the phylogenetic and biogeographic founding of crown Sirenia with the Dugongidae-Trichechidae split occurring at the Eocene-Oligocene boundary (~33.9 Ma), temporally coincident with the onset of dropping global sea levels and temperatures. This region became the nexus of sirenian diversification and supported taxonomically-rich dugongid communities until the earliest Pliocene. The Dugonginae-Hydrodamalinae split occurred near Florida during the early Miocene (~21.2 Ma) and was followed by a west-bound dispersal that gave rise to the Pacific hydrodamalines. The late middle Miocene (~12.2 Ma) split of Dugong from all other dugongines also occurred near Florida and our analyses suggest that the Indo-Pacific distribution of modern dugongs is the result of a trans-Pacific dispersal. From at least the early Miocene, trichechid evolution was based entirely in South America, presumably within the Pebas Wetlands System. We infer that the eventual establishment of Amazon drainage into the South Atlantic allowed the dispersal of Trichechus out of South America no earlier than the mid-Pliocene. Our analyses provide a new temporal and biogeographic framework for understanding major events in sirenian evolution and their possible relationships to oceanographic and climatic changes. These hypotheses can be further tested with the recovery and integration of new fossil evidence.
creator: Steven Heritage
creator: Erik R. Seiffert
uri: https://doi.org/10.7717/peerj.13886
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Heritage and Seiffert