title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=739 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: First fossil-leaf floras from Brunei Darussalam show dipterocarp dominance in Borneo by the Pliocene link: https://peerj.com/articles/12949 last-modified: 2022-03-24 description: The Malay Archipelago is one of the most biodiverse regions on Earth, but it suffers high extinction risks due to severe anthropogenic pressures. Paleobotanical knowledge provides baselines for the conservation of living analogs and improved understanding of vegetation, biogeography, and paleoenvironments through time. The Malesian bioregion is well studied palynologically, but there have been very few investigations of Cenozoic paleobotany (plant macrofossils) in a century or more. We report the first paleobotanical survey of Brunei Darussalam, a sultanate on the north coast of Borneo that still preserves the majority of its extraordinarily diverse, old-growth tropical rainforests. We discovered abundant compression floras dominated by angiosperm leaves at two sites of probable Pliocene age: Berakas Beach, in the Liang Formation, and Kampong Lugu, in an undescribed stratigraphic unit. Both sites also yielded rich palynofloral assemblages from the macrofossil-bearing beds, indicating lowland fern-dominated swamp (Berakas Beach) and mangrove swamp (Kampong Lugu) depositional environments. Fern spores from at least nine families dominate both palynological assemblages, along with abundant fungal and freshwater algal remains, rare marine microplankton, at least four mangrove genera, and a diverse rainforest tree and liana contribution (at least 19 families) with scarce pollen of Dipterocarpaceae, today’s dominant regional life form. Compressed leaves and rare reproductive material represent influx to the depocenters from the adjacent coastal rainforests. Although only about 40% of specimens preserve informative details, we can distinguish 23 leaf and two reproductive morphotypes among the two sites. Dipterocarps are by far the most abundant group in both compression assemblages, providing rare, localized evidence for dipterocarp-dominated lowland rainforests in the Malay Archipelago before the Pleistocene. The dipterocarp fossils include winged Shorea fruits, at least two species of plicate Dipterocarpus leaves, and very common Dryobalanops leaves. We attribute additional leaf taxa to Rhamnaceae (Ziziphus), Melastomataceae, and Araceae (Rhaphidophora), all rare or new fossil records for the region. The dipterocarp leaf dominance contrasts sharply with the family’s <1% representation in the palynofloras from the same strata. This result directly demonstrates that dipterocarp pollen is prone to strong taphonomic filtering and underscores the importance of macrofossils for quantifying the timing of the dipterocarps’ rise to dominance in the region. Our work shows that complex coastal rainforests dominated by dipterocarps, adjacent to swamps and mangroves and otherwise similar to modern ecosystems, have existed in Borneo for at least 4–5 million years. Our findings add historical impetus for the conservation of these gravely imperiled and extremely biodiverse ecosystems. creator: Peter Wilf creator: Xiaoyu Zou creator: Michael P. Donovan creator: László Kocsis creator: Antonino Briguglio creator: David Shaw creator: JW Ferry Slik creator: Joseph J. Lambiase uri: https://doi.org/10.7717/peerj.12949 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wilf et al. title: Genome-wide characterization and expression of the TLP gene family associated with Colletotrichum gloeosporioides inoculation in Fragaria × ananassa link: https://peerj.com/articles/12979 last-modified: 2022-03-24 description: BackgroundColletotrichum gloeosporioides, a soil-borne fungal pathogen, causes significant yield losses in many plants, including cultivated strawberry (Fragaria × ananassa, 2n = 8x = 56). Thaumatin-like proteins (TLPs) are a large and complex family of proteins that play a vital role in plant host defense and other physiological processes.MethodsTo enhance our understanding of the antifungal activity of F. × ananassa TLPs (FaTLP), we investigated the genome-wide identification of FaTLP gene families and their expression patterns in F. × ananassa plants upon pathogen infection. Moreover, we used RNA sequencing (RNA-seq) to detect the differences in the expression patterns of TLP genes between different resistant strawberry cultivars in response to C. gloeosporioides infection.ResultsIn total, 76 TLP genes were identified from the octoploid cultivated strawberry genome with a mean length of 1,439 bp. They were distributed on 24 F. × ananassa chromosomes. The FaTLP family was then divided into ten groups (Group I–X) according to the comparative phylogenetic results. Group VIII contained the highest number of TLP family genes. qRT-PCR analysis results indicated that FaTLP40, FaTLP41, FaTLP43, FaTLP68, and FaTLP75 were upregulated following C. gloeosporioides infection in the resistant octoploid strawberry.ConclusionsThe data showed some differences in TLP gene expression patterns across different resistant strawberry cultivars, as well as faster TLP defense responses to pathogenic fungi in resistant cultivars. This study will aid in the characterization of TLP gene family members found in octoploid strawberries and their potential biological functions in plants’ defenses against pathogenic fungi. creator: Yuchao Zhang creator: Lixiang Miao creator: Xiaofang Yang creator: Guihua Jiang uri: https://doi.org/10.7717/peerj.12979 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: A prognostic risk model based on DNA methylation levels of genes and lncRNAs in lung squamous cell carcinoma link: https://peerj.com/articles/13057 last-modified: 2022-03-24 description: BackgroundRecurrence is a risk factor for the prognosis of lung squamous carcinoma (LUSC). DNA methylation levels of RNAs are also associated with LUSC prognosis. This study aimed to construct a prognostic model with high performance in predicting LUSC prognosis using the methylation levels of lncRNAs and genes.MethodsThe differentially expressed RNAs (DERs) and differentially methylated RNAs (DMRs) between the recurrent and non-recurrent LUSC tissues in The Cancer Genome Atlas (TCGA; training dataset) were identified. Weighted correlation network analysis was performed to identify co-methylation networks. Differentially methylated genes and lncRNAs with opposite expression-methylation levels were used for the screening of prognosis-associated RNAs. The prognostic model was constructed and its performance was validated in the GSE39279 dataset.ResultsA total of 664 DERs and 981 DMRs (including 972 genes) in recurrent LUSC tissues were identified. Three co-methylation modules, including 226 differentially methylated genes, were significantly associated with LUSC. Among prognosis-associated RNAs, 18 DERs/DMRs with opposite methylation-expression levels were included in the methylation prognostic risk model. LUSC patients with high risk scores had a poor prognosis compared with patients who had low risk scores (TCGA: HR = 3.856, 95% CI [2.297–6.471]; GSE39279: HR = 3.040, 95% CI [1.435–6.437]). This model had a high accuracy in predicting the prognosis (AUC = 0.903 and 0.800, respectively), equivalent to the nomogram model inclusive of clinical variables.ConclusionsReferring to the methylation levels of the 16-RNAs might help to predict the survival outcomes in LUSC. creator: Weiqing Wang creator: Ming Xiang creator: Hui Liu creator: Xiao Chu creator: Zhaoyun Sun creator: Liang Feng uri: https://doi.org/10.7717/peerj.13057 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Development of a Japanese version of the Psychological Ownership Scale link: https://peerj.com/articles/13063 last-modified: 2022-03-24 description: The present study addresses the need for a valid instrument for measuring dimensions of psychological ownership, including that of owned and non-owned objects, for use in the language and culture of Japan. Although the theory of psychological ownership has expanded self-extension theory, the most widely used scale of psychological ownership does not measure the extent to which one feels that it (the owned object) is a part of them. Thus, the present study aimed to develop a Japanese version of the Psychological Ownership Scale (POS-J) and examine its reliability and validity. Study 1 measured the POS-J of an owned object, finding the POS-J to have a two-factor structure (possession-self link and feeling of ownership) and its internal consistency and reliability to be adequate. Moreover, POS-J scores were positively correlated with perceived control and self-extension tendency, but not monetary value, indicating that conceptual validity was generally supported. To confirm whether the POS-J could be used for a non-owned object, Study 2 rephrased the expressions of item descriptions and examined the effect of imagining touching a non-owned object on the POS-J scores, showing that doing so increased the POS-J scores for the object. Our findings suggest that the POS-J is a reliable and valid measure of the psychological ownership of owned and non-owned objects for use in Japan. creator: Sayo Iseki creator: Kyoshiro Sasaki creator: Shinji Kitagami uri: https://doi.org/10.7717/peerj.13063 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Iseki et al. title: Increased cortisol levels caused by acute resistance physical exercise impair memory and learning ability link: https://peerj.com/articles/13000 last-modified: 2022-03-23 description: Acute physical exercise works as an activator of the responses of the human organism to stress. This is based on the activation of the hypothalamic–pituitary–adrenal (HPA) axis, affecting physical, physiological and psychological levels. This study aimed to analyse the effects of a single bout of high-intensity resistance exercise on cognitive-behavioural responses: visuo-spatial path learning and memory, as well as physiological responses (salivary cortisol levels). Nineteen healthy male military-trained powerlifting subjects were tested in a within-subject design on two experimental days with an interval of 48 h. The stress and cognitive variables were measured by cortisol levels and Ruff–Light trail-learning test (RULIT) test scores, respectively. The results showed the immediate influence of acute exercise on cortisol, with significantly higher cortisol levels found in subjects after completion of the acute resistance exercise. In addition, this study found a significant deterioration of memory and learning ability after a dose of intense resistance exercise. In conclusion, the study highlights the relative effects of resistance exercise on cortisol and cognitive performance depending on the intensity and type of the exercise, the moment of measurement and the cerebral areas implicated. creator: José-Luis Bermejo creator: Raúl Valldecabres creator: Israel Villarrasa-Sapiña creator: Gonzalo Monfort-Torres creator: Adrià Marco-Ahulló creator: Bruno Ribeiro Do Couto uri: https://doi.org/10.7717/peerj.13000 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bermejo et al. title: Antioxidant defense system in the prefrontal cortex of chronically stressed rats treated with lithium link: https://peerj.com/articles/13020 last-modified: 2022-03-23 description: BackgroundThis study aimed to investigate the effects of lithium treatment on gene expression and activity of the prefrontal antioxidant enzymes: copper, zinc superoxide dismutase (SOD1), manganes superoxide dismutase (SOD2), catalase (CAT), and glutathione peroxidase (GPx) in animals exposed to chronic restraint stress (CRS).MethodsThe investigated parameters were quantified using real-time RT-PCR, Western blot analyses, and assays of enzyme activities.ResultsWe found that lithium treatment decreased gene expression of SOD2, as well as the activities of SOD1 and SOD2 in chronically stressed rats to the levels found in unstressed animals. However, lithium treatment in animals exposed to CRS increased prefrontal GPx activity to the levels found in unstressed animals.ConclusionsThese findings confirm that treatment with lithium induced the modulation of prefrontal antioxidant status in chronically stressed rats. Our results may be very important in biomedical research for understanding the role of lithium in maintaining the stability of prefrontal antioxidant defense system in neuropsychiatric disorders caused by chronic stress. creator: Ljubica Gavrilović creator: Nataša Popović creator: Vesna Stojiljković creator: Snežana Pejić creator: Ana Todorović creator: Predrag Vujović creator: Snežana B. Pajović uri: https://doi.org/10.7717/peerj.13020 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gavrilović et al. title: Exploring the genome of Lactobacillaceae spp. Sy-1 isolated from Heterotrigona itama honey link: https://peerj.com/articles/13053 last-modified: 2022-03-23 description: BackgroundHoney produced by Heterotrigona itama is highly preferred among consumers due to its high-value as a functional food and beneficial lactic acid bacteria (LAB) reservoir. Fructophilic lactic acid bacteria (FLAB) are a group of LAB with unique growth characteristics and are regarded as promising producers of bioactive compounds. Hence, it is not surprising that LAB, especially FLAB, may be involved with the excellent bioactivity of H. itama honey. With the trending consumer preference for H. itama honey coupled with increasing awareness for healthy food, the genomic background of FLAB isolated from this honey must, therefore, be clearly understood. In this study, one FLAB strain designated as Sy-1 was isolated from freshly collected H. itama honey. Its FLAB behavior and genomic features were investigated to uncover functional genes that could add value to functional food.MethodsThe fructophilic characteristics of strain Sy-1 were determined, and the genome was sequenced using Illumina iSeq100 and Oxford Nanopore. The average nucleotide identity and phylogenetic analyses based on 16S rRNA, 92 core genes, and whole-genome sequence were performed to unravel the phylogenetic position of strain Sy-1. NCBI Prokaryotic Genome Annotation Pipeline annotated the genome, while the EggNOG-mapper, BLASTKoala, and GHOSTKoala were used to add functional genes and pathways information.ResultsStrain Sy-1 prefers D-fructose over D-glucose and actively metabolizes D-glucose in the presence of electron acceptors. Genomic annotation of strain Sy-1 revealed few genes involved in carbohydrate transport and metabolism, and partial deletion of adhE gene, in line with the characteristic of FLAB. The 16S rRNA gene sequence of strain Sy-1 showed the highest similarity to unknown LAB species isolated from the gut of honeybees. The phylogenetic analyses discovered that strain Sy-1 belonged to the Lactobacillaceae family and formed a separate branch closer to type strain from the genera of Acetilactobacillus and Apilactobacillus. The ANI analysis showed the similarity of the closest relative, Apilactobacillus micheneri Hlig3T. The assembled genome of Sy-1 contains 3 contigs with 2.03 Mbp and a 41% GC content. A total of 1,785 genes were identified, including 1,685 protein-coding genes, 68 tRNA, and 15 rRNA. Interestingly, strain Sy-1 encoded complete genes for the biosynthesis of folate and riboflavin. High-performance liquid chromatography analysis further confirmed the high production of folic acid (1.346 mg/L) by Sy-1.DiscussionBased on phylogenetic and biochemical characteristics, strain Sy-1 should be classified as a novel genus in the family of Lactobacillaceae and a new member of FLAB. The genome information coupled with experimental studies supported the ability of strain Sy-1 to produce high folic acid. Our collective findings support the suitable application of FLAB strain Sy-1 in the functional food and pharmaceutical industries. creator: Syariffah Nuratiqah Syed Yaacob creator: Fahrul Huyop creator: Mailin Misson creator: Roswanira Abdul Wahab creator: Nurul Huda uri: https://doi.org/10.7717/peerj.13053 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Syed Yaacob et al. title: Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity link: https://peerj.com/articles/13084 last-modified: 2022-03-23 description: BackgroundThe horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community.ResultsWe performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes.ConclusionsOur metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome. creator: Rachel Gilroy creator: Joy Leng creator: Anuradha Ravi creator: Evelien M. Adriaenssens creator: Aharon Oren creator: Dave Baker creator: Roberto M. La Ragione creator: Christopher Proudman creator: Mark J. Pallen uri: https://doi.org/10.7717/peerj.13084 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gilroy et al. title: Reference values for bone density and bone mineral content from 5 to 80 years old in a province of Chile link: https://peerj.com/articles/13092 last-modified: 2022-03-23 description: BackgroundThe assessment of bone health throughout the life cycle is essential to determine fracture risk. The objectives of the work were (a) compare bone mineral density and content with international references from the United States, (b) determine maximum bone mass, (c) propose references for bone health measurements from ages 5 to 80 years old.MethodsResearch was carried out on 5,416 subjects. Weight and height were measured. Body Mass Index (BMI) was calculated. The total body was scanned using dual energy X-ray absorptiometry (DXA). Information was extracted from the bone health measures (bone mineral density (BMD) and bone mineral content (BMC)) for both sexes, according to pediatric and adult software.Results and DiscussionDifferences were identified between the mean values of Chilean and American men for BMD (~0.03 to 0.11 g/cm2) and BMC (~0.15 to 0.46 g). Chilean females showed average values for BMD similar to the US references (~−0.01 to 0.02 g/cm2). At the same time, they were relatively higher for BMC (~0.07 to 0.33 g). The cubic polynomial regression model reflected a relationship between BMD and BMC with chronological age in both sexes. For males, R2 was higher (R2 = 0.72 and 0.75) than for females (R2 = 0.59 and 0.66). The estimate of maximum bone mass (MBM) for males emerged at 30 years old (1.45 ± 0.18 g/cm2 of BMD and 3.57 ± 0.60 g of BMC) and for females at age 28 (1.22 ± 0.13 g/cm2 of BMD and 2.57 ± 0.44 g of BMC). The LMS technique was used to generate smoothed percentiles for BMD and BMC by age and sex. Results showed that maximum bone mass occurred in females at age 28 and in males at 30. Reference values obtained from this research may be used to evaluate bone health, diagnose bone fragility and osteoporosis in individuals and regional population groups. creator: Marco Cossio-Bolanos creator: Rubén Vidal-Espinoza creator: Jose Fuentes-Lopez creator: Luis Felipe Castelli Correia de Campos creator: Cynthia Lee Andruske creator: Camilo Urra-Albornoz creator: Fernando Alvear Vasquez creator: Rossana Gomez-Campos uri: https://doi.org/10.7717/peerj.13092 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cossio-Bolanos et al. title: A flexible and accurate method for electroencephalography rhythms extraction based on circulant singular spectrum analysis link: https://peerj.com/articles/13096 last-modified: 2022-03-23 description: Rhythms extraction from electroencephalography (EEG) signals can be used to monitor the physiological and pathological states of the brain and has attracted much attention in recent studies. A flexible and accurate method for EEG rhythms extraction was proposed by incorporating a novel circulant singular spectrum analysis (CiSSA). The EEG signals are decomposed into the sum of a set of orthogonal reconstructed components (RCs) at known frequencies. The frequency bandwidth of each RC is limited to a particular brain rhythm band, with no frequency mixing between different RCs. The RCs are then grouped flexibly to extract the desired EEG rhythms based on the known frequencies. The extracted brain rhythms are accurate and no mixed components of other rhythms or artifacts are included. Simulated EEG data based on the Markov Process Amplitude EEG model and experimental EEG data in the eyes-open and eyes-closed states were used to verify the CiSSA-based method. The results showed that the CiSSA-based method is flexible in alpha rhythms extraction and has a higher accuracy in distinguishing between the eyes-open and eyes-closed states, compared with the basic SSA method, the wavelet decomposition method, and the finite impulse response filtering method. creator: Hai Hu creator: Zihang Pu creator: Peng Wang uri: https://doi.org/10.7717/peerj.13096 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hu et al.