title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=405 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Calcareous dinoflagellate blooms during the Late Cretaceous ‘greenhouse’ world—a case study from western Ukraine link: https://peerj.com/articles/16201 last-modified: 2023-10-05 description: The Late Cretaceous was a unique period in the history of the Earth characterized by elevated sea levels, reduced land area, and significantly high concentrations of atmospheric CO2 resulting in increased temperatures across the globe—a ‘Greenhouse World’. During this period, calcareous dinoflagellate cysts (c-dinocysts) flourished and became a ubiquitous constituent of calcifying plankton around the world. An acme in calcareous dinocysts during the Albian to the Turonian coincided with the highest recorded seawater surface temperatures and was possibly linked to conditions that favored calcification and a highly oligotrophic system in European shelf seas. This study examines the potential applicability of c-dinocysts as a proxy for paleoenvironmental conditions based on their assemblage changes plotted against foraminiferal occurrences and microfacies analysis. The material was extracted from the upper Turonian chalk of the Dubivtsi region in western Ukraine. An inverse correlation was observed between species diversity and the number of c-dinocyst specimens. Nutrient availability gradients apparently determined important changes in the calcareous dinocysts distribution. These trophic changes were likely caused by the interplay of eustatic sea-level fluctuations and Subhercynian tectonic activity leading to changeable nutrient inputs from the nearby land. creator: Agnieszka Ciurej creator: Zofia Dubicka creator: Andriy Poberezhskyy uri: https://doi.org/10.7717/peerj.16201 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ciurej et al. title: Genome sequence analysis of Malayan pangolin (Manis javanica) forensic samples reveals the presence of Paraburkholderia fungorum sequences link: https://peerj.com/articles/16002 last-modified: 2023-10-04 description: BackgroundThe Malayan pangolin (Manis javanica) is a placental mammal and is listed as Critically Endangered on the IUCN Red List of Threatened Species. Most previous attempts to breed pangolins in captivity have met with little success because of dietary issues, infections, and other complications, although a previous study reported breeding pangolins in captivity to the third generation. In our previous pangolin genome sequencing data analysis, we obtained a considerable amount of bacterial DNA from a pregnant female Malayan pangolin (named “UM3”), which was likely infected by Paraburkholderia fungorum—an agent of biodegradation and bioremediation in agriculture.MethodologyHere, we further confirmed and characterized this bacterial species using PCR, histological staining, whole-genome sequencing, and bioinformatics approaches. PCR assays with in-house designed primer sets and 16S universal primers showed clear positive bands in the cerebrum, cerebellum, lung, and blood of UM3 suggesting that UM3 might have developed septicaemia. Histological staining showed the presence of Gram-negative rod-shaped bacteria in the pangolin brain and lungs, indicating the colonization of the bacteria in these two organs. In addition, PCR screening of UM3’s fetal tissues revealed the presence of P. fungorum in the gastrocnemius muscle, but not in other tissues that we examined. We also sequenced and reconstructed the genome of pangolin P. fungorum, which has a genome size of 7.7 Mbps.ConclusionOur study is the first to present detailed evidence of the presence of P. fungorum in a pangolin and her fetus (although preliminary results were presented in our previous article). Here, we raise the concern that P. fungorum may potentially infect humans, especially YOPI (young, old, pregnant, and immunocompromised) people. Therefore, caution should be exercised when using this bacterial species as biodegradation or bioremediation agents in agriculture. creator: Ka Yun Tan creator: Siwei Deng creator: Tze King Tan creator: Ranjeev Hari creator: Frankie Thomas Sitam creator: Rofina Yasmin Othman creator: Kum Thong Wong creator: Taznim Begam Mohd Mohidin creator: Siew Woh Choo uri: https://doi.org/10.7717/peerj.16002 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tan et al. title: Food and light availability induce plastic responses in fire salamander larvae from contrasting environments link: https://peerj.com/articles/16046 last-modified: 2023-10-04 description: Phenotypic plasticity has been proposed as a mechanism facilitating the colonisation and adaptation to novel environments, such as caves. However, phenotypic plasticity in subterranean environments remains largely unexplored. Here, we test for plasticity in growth and development of fire salamander larvae (Salamandra salamandra) from subterranean and surface habitats, in response to contrasting food availability and light conditions. We hypothesized that: (i) low food availability and absence of light decrease larval growth and delay metamorphosis, (ii) light conditions mediate the effects of food availability on growth and time to metamorphosis, and (iii) larval response to contrasting light and food conditions is shaped by the habitat of origin. Our study showed that reduced food availability significantly delayed metamorphosis and slowed total length and body mass growth rates, while exposure to constant darkness slowed body mass growth rate. However, larvae slowed growth rates and increased time to metamorphosis without compromising size at metamorphosis. The effect of food availability on growth and time to metamorphosis did not change under different light conditions. Fire salamanders from subterranean and surface habitats responded differently only in relation to contrasting food availability conditions. Specifically, larvae from the surface habitat grew faster in high food conditions, while growth in larvae from the subterranean habitat was not influenced by food availability. Initial size also appeared to be an influential factor, since larger and heavier larvae grew slower, metamorphosed faster, and the size advantage was maintained in newly-metamorphosed juveniles. Overall, the results of our experiment suggest that plasticity and local adaptation favor the exploitation of aquatic subterranean habitats for breeding by fire salamanders, allowing successful development even under food shortage and day-length constraints, without compromising metamorphic size. Our findings have implications for conservation because they confirm that phenotypic plasticity plays a critical role in allowing fire salamanders to overcome altered environmental conditions. creator: Raluca Ioana Băncilă creator: Florina Stănescu creator: Rodica Plăiaşu creator: Ioana Nae creator: Diana Székely creator: Sabina E. Vlad creator: Dan Cogălniceanu uri: https://doi.org/10.7717/peerj.16046 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Băncilă et al. title: Sarcopenia as an important determinant for adverse outcomes in patients with pyogenic liver abscess link: https://peerj.com/articles/16055 last-modified: 2023-10-04 description: BackgroundLow muscle mass/sarcopenia has been associated with poor prognosis in many diseases, but its clinical significance in pyogenic liver abscess (PLA) remains unclear. The purpose of this study is to investigate the relationship between muscle mass and prognosis of patients with PLA.MethodsA total of 154 adult patients with PLA hospitalized at Tongji Hospital (Wuhan, Hubei, China) between October 2011 and June 2021 were included in this retrospective analysis. Muscle-fat related indicators were measured by computed tomography (CT) images at the third lumbar vertebra (L3) level. The data of patients between the sarcopenia group and non-sarcopenia group were compared. Multivariate logistic regression and receiver operating characteristic (ROC) curve analyses were performed.ResultsThe skeletal muscle index (SMI) was independently associated with adverse outcomes (95% CI [0.649–0.954], P = 0.015) of PLA in multivariate logistic regression analysis. This conclusion held true in sex-specific subgroup analysis. ROC analysis indicated that SMI may predict adverse outcomes in both male (area under the ROC curve [AUC], 0.718; cut-off, 52.59; P < 0.001) and female (AUC, 0.714; cut-off, 38.39; P = 0.017) patient populations.ConclusionsSarcopenia serves as an independent risk factor for poor prognosis in PLA and patients with sarcopenia may be more prone to adverse outcomes. creator: Li Liu creator: Shaohua Liu creator: Meng Hao creator: Song Hu creator: Tian Yu creator: Yunkai Yang creator: Zhelong Liu uri: https://doi.org/10.7717/peerj.16055 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: What I see and what I feel: the influence of deceptive visual cues and interoceptive accuracy on affective valence and sense of effort during virtual reality cycling link: https://peerj.com/articles/16095 last-modified: 2023-10-04 description: BackgroundHow we feel during exercise is influenced by exteroceptive (e.g., vision) and interoceptive (i.e., internal body signals) sensory information, and by our prior experiences and expectations. Deceptive visual cues about one’s performance during exercise can increase work rate, without negatively impacting affective valence (good/bad responses) or perceived exertion. However, what is less understood is whether the perception of the exercise experience itself can be shifted, if work rate is held constant. Here we aimed to investigate whether deceptive vision—via illusory hills in a virtual reality (VR) cycling experience—alters affective valence and perceived exertion when physical effort is controlled. We also evaluated whether the accuracy with which one detects interoceptive cues influences the extent to which deceptive visual information can shift exercise experiences.MethodsA total of 20 participants (10 female; 30.2 ± 11.2 yrs) completed three VR cycling conditions each of 10-min duration, in a randomised, counterbalanced order. Pedal resistance/cadence were individualised (to exercise intensity around ventilatory threshold) and held constant across conditions; only visual cues varied. Two conditions provided deceptive visual cues about the terrain (illusory uphill, illusory downhill; resistance did not change); one condition provided accurate visual cues (flat terrain). Ratings of affective valence (Feeling Scale) and of perceived exertion (Borg’s RPE) were obtained at standardised timepoints in each VR condition. Interoceptive accuracy was measured via a heartbeat detection test.ResultsLinear mixed effects models revealed that deceptive visual cues altered affective valence (f2 = 0.0198). Relative to flat terrain, illusory downhill reduced affective valence (Est = −0.21, p = 0.003), but illusory uphill did not significantly improve affective valence (Est = 0.107, p = 0.14). Deceptive visual cues altered perceived exertion, and this was moderated by the level of interoceptive accuracy (Condition-Interoception interaction, p = 0.00000024, f2 = 0.0307). Higher levels of interoceptive accuracy resulted in higher perceived exertion in the illusory downhill condition (vs flat), while lower interoceptive accuracy resulted in lower perceived exertion in both illusory hill conditions (vs flat) and shifts of greater magnitude.ConclusionsDeceptive visual cues influence perceptual responses during exercise when physical effort does not vary, and for perceived exertion, the weighting given to visual exteroceptive cues is determined by accuracy with which interoceptive cues are detected. Contrary to our hypotheses, deceptive visual cues did not improve affective valence. Our findings suggest that those with lower levels of interoceptive accuracy experience most benefit from deceptive visual cues, providing preliminary insight into individualised exercise prescription to promote positive (and avoid negative) exercise experiences. creator: Brendan Mouatt creator: Ashleigh E. Smith creator: Gaynor Parfitt creator: Ty Stanford creator: Jeremy McDade creator: Ross T. Smith creator: Tasha R. Stanton uri: https://doi.org/10.7717/peerj.16095 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mouatt et al. title: Diversity and structure of the root-associated bacterial microbiomes of four mangrove tree species, revealed by high-throughput sequencing link: https://peerj.com/articles/16156 last-modified: 2023-10-04 description: BackgroundRoot-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. At present, most of our understanding of mangrove root-related microbial diversity is obtained from specific mangrove species in selected geographic regions. Relatively little is known about the composition of the bacterial microbiota existing in disparate mangrove species microenvironments, particularly the relationship among different mangrove species in tropical environments.MethodsWe collected the root, rhizosphere soil, and non-rhizosphere soil of four mangrove trees (Acanthus ilicifolius, Bruguiera gymnorrhiza, Clerodendrum inerme, and Lumnitzera racemosa) and detected the 16S rRNA gene by a conventional PCR. We performed high throughput sequencing using Illumina Novaseq 6000 platform (2 × 250 paired ends) to investigate the bacterial communities related with the different mangrove species.ResultsWe analyzed the bacterial diversity and composition related to the diverse ecological niches of mangrove species. Our data confirmed distinct distribution patterns of bacterial communities in the three rhizocompartments of the four mangrove species. Microbiome composition varied with compartments and host mangrove species. The bacterial communities between the endosphere and the other two compartments were distinctly diverse independent of mangrove species. The large degree of overlap in critical community members of the same rhizocompartment across distinct mangrove species was found at the phylum level. Furthermore, this is the first report of Acidothermus found in mangrove environments. In conclusion, understanding the complicated host-microbe associations in different mangrove species could lay the foundation for the exploitation of the microbial resource and the production of secondary metabolites. creator: Jinlei Sui creator: Xiaowen He creator: Guohui Yi creator: Limin Zhou creator: Shunqing Liu creator: Qianqian Chen creator: Xiaohu Xiao creator: Jinyan Wu uri: https://doi.org/10.7717/peerj.16156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sui et al. title: Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities link: https://peerj.com/articles/16163 last-modified: 2023-10-04 description: The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2–6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10–14) characterized by acid-tolerant taxa and fruity (p < 3.03e−03), sour (p < 1.60e−01), and fermented (p < 1.47e−05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics. creator: Erin A. McKenney creator: Lauren M. Nichols creator: Samuel Alvarado creator: Shannon Hardy creator: Kristen Kemp creator: Rachael Polmanteer creator: April Shoemaker creator: Robert R. Dunn uri: https://doi.org/10.7717/peerj.16163 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 McKenney et al. title: Assessment of different factors on the influence of glass wool concentration for detection of main swine viruses in water samples link: https://peerj.com/articles/16171 last-modified: 2023-10-04 description: Viruses existed in wastewaters might pose a biosecurity risk to human and animal health. However, it is generally difficult to detect viruses in wastewater directly as they usually occur in low numbers in water. Therefore, processing large volumes of water to concentrate viruses in a much smaller final volume for detection is necessary. Glass wool has been recognized as an effective material to concentrate multiple in water, and in this study, we assessed the use of glass wools on concentrating pseudorabies virus (PRV), African swine fever virus (ASFV), and porcine epidemic diarrhea virus (PEDV) in water samples. The influence of pH values, water matrix, water volume, filtration rate, temperature on the effect of the method concentrating these viruses for detection was evaluated in laboratory. Our results revealed that glass wool was suitable for the concentration of above-mentioned viruses from different water samples, and demonstrated a good application effect for water with pH between 6.0–9.0. Furthermore, glass wool also showed a good recovery effect on concentrating viral nucleic acids and viral particles, as well as living viruses. In addition, combining use of glass wool with skim milk, polyethylene glycol (PEG)-NaCl, or ultracentrifuge had good effects on concentrating ASFV, PRV, and PEDV. Detection of wastewater samples (n = 70) collected from 70 pig farms in 13 regions across Hubei Province in Central China after glass-wool-concentration determined one sample positive for ASFV, eighteen samples positive for PRV, but no sample positive for PEDV. However, these positive samples were detected to be negative before glass wool enrichment was implemented. Our results suggest that glass wool-based water concentration method developed in this study represents an effective tool for detecting viruses in wastewater. creator: Jie Fan creator: Hongjian Chen creator: Wenbo Song creator: Hao Yang creator: Rui Xie creator: Mengfei Zhao creator: Wenqing Wu creator: Zhong Peng creator: Bin Wu uri: https://doi.org/10.7717/peerj.16171 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Fan et al. title: SaPt-CNN-LSTM-AR-EA: a hybrid ensemble learning framework for time series-based multivariate DNA sequence prediction link: https://peerj.com/articles/16192 last-modified: 2023-10-04 description: Biological sequence data mining is hot spot in bioinformatics. A biological sequence can be regarded as a set of characters. Time series is similar to biological sequences in terms of both representation and mechanism. Therefore, in the article, biological sequences are represented with time series to obtain biological time sequence (BTS). Hybrid ensemble learning framework (SaPt-CNN-LSTM-AR-EA) for BTS is proposed. Single-sequence and multi-sequence models are respectively constructed with self-adaption pre-training one-dimensional convolutional recurrent neural network and autoregressive fractional integrated moving average fused evolutionary algorithm. In DNA sequence experiments with six viruses, SaPt-CNN-LSTM-AR-EA realized the good overall prediction performance and the prediction accuracy and correlation respectively reached 1.7073 and 0.9186. SaPt-CNN-LSTM-AR-EA was compared with other five benchmark models so as to verify its effectiveness and stability. SaPt-CNN-LSTM-AR-EA increased the average accuracy by about 30%. The framework proposed in this article is significant in biology, biomedicine, and computer science, and can be widely applied in sequence splicing, computational biology, bioinformation, and other fields. creator: Wu Yan creator: Li Tan creator: Li Meng-Shan creator: Sheng Sheng creator: Wang Jun creator: Wu Fu-an uri: https://doi.org/10.7717/peerj.16192 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yan et al. title: Exploring the relationship between environmental DNA concentration and biomass in Asian giant softshell turtle (Pelochelys cantorii) link: https://peerj.com/articles/16218 last-modified: 2023-10-04 description: In recent years, environmental DNA (eDNA) technology has become an accepted approach for investigating rare and endangered species because of its economic efficiency, high sensitivity, and non-invasiveness. The Asian giant softshell turtle (Pelochelys cantorii) is a first-class protected aquatic animal in China, and traditional resource survey methods have not identified its natural populations for many years. In this study, primers and a TaqMan probe targeting ND5 were designed, reaction conditions were optimized, a standard curve was constructed using synthetic DNA, and an eDNA quantitative PCR (qPCR) detection method was established. The eDNA detection technology for P. cantorii revealed that the number of species in the experimental pools showed a significant linear relationship with the eDNA concentration (p < 0.05). The eDNA concentration was negatively correlated with the length of time after the removal of P. cantorii and retention in the water body for 9 days. The qPCR detection method for P. cantorii eDNA established in this study can be applied to the qualitative detection of P. cantorii in water bodies, as well as to preliminary evaluation of its relative biomass. This can serve as a baseline for the investigation of natural P. cantorii population and the evaluation of its wild release effects. creator: Xiaoyou Hong creator: Kaikuo Wang creator: Liqin Ji creator: Xiaoli Liu creator: Lingyun Yu creator: Jie Wei creator: Yakun Wang creator: Chengqing Wei creator: Wei Li creator: Xinping Zhu uri: https://doi.org/10.7717/peerj.16218 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hong et al.