title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=547 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost link: https://peerj.com/articles/14426 last-modified: 2022-12-07 description: Agaricus bisporus growth alters the lignocellulosic composition and structure of compost. However, it is difficult to differentiate the enzyme activities of A. bisporus mycelia from the wider microbial community owing to the complication of completely speareting the mycelia from compost cultures. Macrogenomics analysis was employed in this study to examine the fermentation substrate of A. bisporus before and after mycelial growth, and the molecular mechanism of substrate utilization by A. bisporus mycelia was elucidated from the perspective of microbial communities and CAZymes in the substrate. The results showed that the relative abundance of A. bisporus mycelia increased by 77.57-fold after mycelial colonization, the laccase content was significantly increased and the lignin content was significantly decreased. Analysis of the CAZymes showed that AA10 family was extremely differentiated. Laccase-producing strains associated with AA10 family were mostly bacteria belonging to Thermobifida and Thermostaphylospora, suggesting that these bacteria may play a synergistic role in lignin decomposition along with A. bisporus mycelia. These findings provide preliminary evidence for the molecular mechanism of compost utilization by A. bisporus mycelia and offer a reference for the development and utilization of strains related to lignocellulose degradation. creator: Wanqiu Chang creator: Weilin Feng creator: Yang Yang creator: Yingyue Shen creator: Tingting Song creator: Yu Li creator: Weiming Cai uri: https://doi.org/10.7717/peerj.14426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chang et al. title: Characteristics and usefulness of trunk muscle endurance tests on the Roman chair in healthy adults link: https://peerj.com/articles/14469 last-modified: 2022-12-07 description: BackgroundAdequate trunk muscle endurance is considered to be an important indicator of good low back stability; therefore, its assessment is needed when determining an individual’s risk for back pain. Optimal tests to assess each trunk muscle group separately are difficult to find. The objective of this study was to verify if two groups of trunk muscle endurance tests (standard and alternative) show comparable results in terms of muscle endurance ratios, holding times and rated perceived effort to perform each test.MethodsThe study was designed as a quasi-experimental repeated-measures design. There was a single group of participants who took part in two different trunk muscle endurance testing. Sixty-eight healthy adult volunteers, aged 20–45 years (31.9 ± 7.2 years), without recent musculoskeletal injury or disorder participated in the study. All participants finished the study. Trunk muscle endurance tests as tested on the Roman chair (B tests) were compared with standard tests as suggested by McGill (A tests). Each group of tests consisted of an endurance test for trunk extensors, trunk flexors, and lateral trunk muscles for left and right side. The order of tests’ performances was randomly assigned to each participant, whereby a participant did perform A and B tests in the same order. In each test of A and B the holding time was recorded and a perceived effort in each test performance was also assessed by participants. Post testing performance the four ratios of trunk muscles endurance comparison were calculated for each group of tests to determine if there is a good or poor ratio between muscles. Results of each participant were compared for trunk muscle endurance ratio calculations, holding times and rated perceived effort for A and B tests.ResultsResults showed comparable trunk muscle endurance ratios in the three ratios observed, except for the flexors:extensors ratio (AFL:EX: 1.2 (IQR: 0.7–1.6) vs. BFL:EX: 0.6 (IQR: 0.3–0.8); p < 0.001). As compared to A tests, holding times were significantly longer in B tests for the extensors (AEX: 125.5 s (IQR: 104.8–182.8 s) vs. BEX: 284.0 s (IQR: 213.0–342.3 s); p < 0.001) and lateral trunk muscles (AL-LM: 61.0 s (IQR: 48.3–80.8 s) vs. BL-LM: 131.5 s (IQR: 95.5–158.5 s); AR-LM: 63.5 s (IQR: 45.8–77.3 s) vs. BR-LM: 113.0 s (IQR: 86.3–148.8 s); p < 0.001), both were also rated as slightly easier to perform in the extensors (ARPE-EX: 13 (IQR: 12.0–14.0) vs BRPE-EX: 11 (IQR: 10.0–13.0); pRPE-EX < 0.001) and lateral muscles testing (ARPE-LM: 14.0 (IQR: 12.3–15.8) vs. BRPE-LM: 13.0 (IQR: 12.0–15.0); pRPE-LM = 0.001).ConclusionsA and B tests are comparable in three of four trunk muscle endurance ratios, while longer holding times and lower perceived effort to perform were observed in most of the B tests. The Roman chair tests could be used as an alternative to standard tests. creator: Maja Petrič creator: Lijana Zaletel-Kragelj creator: Renata Vauhnik uri: https://doi.org/10.7717/peerj.14469 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Petrič et al. title: Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia link: https://peerj.com/articles/14477 last-modified: 2022-12-07 description: BackgroundOnce a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region’s reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well.MethodsDuring the annual monitoring that was performed in the period from 2013–2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers.ResultsThe level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn’t demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source population for restocking and reintroduction programmes in the region. These data combined with previously observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds should be avoided and that local birds should be used instead. creator: Slobodan Davidović creator: Saša Marinković creator: Irena Hribšek creator: Aleksandra Patenković creator: Marina Stamenković-Radak creator: Marija Tanasković uri: https://doi.org/10.7717/peerj.14477 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Davidović et al. title: Catalases in the pathogenesis of Sporothrix schenckii research link: https://peerj.com/articles/14478 last-modified: 2022-12-07 description: Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system. Hints may be found in pathogenic fungi that also inhabit the soil. In nature, the saprophyte lifestyle of fungi is also associated with predators that can induce oxidative stress upon cell damage. The natural sources of nutrients for fungi are linked to cellulose degradation, which in turn generates reactive oxygen species (ROS). Overall, the antioxidant arsenal needed to thrive both in free-living and pathogenic lifestyles in fungi is fundamental for success. In this review, we present recent findings regarding catalases and oxidative stress in fungi and how these can be in close relationship with pathogenesis. Additionally, special focus is placed on catalases of Sporothrix schenckii as a pathogenic model with a dual lifestyle. It is assumed that catalase expression is activated upon exposure to H2O2, but there are reports where this is not always the case. Additionally, it may be relevant to consider the role of catalases in S. schenckii survival in the saprophytic lifestyle and why their study can assess their involvement in the survival and therefore, in the virulence phenotype of different species of Sporothrix and when each of the three catalases are required. Also, studying antioxidant mechanisms in other isolates of pathogenic and free-living fungi may be linked to the virulence phenotype and be potential therapeutic and diagnostic targets. Thus, the rationale for this review to place focus on fungal catalases and their role in pathogenesis in addition to counteracting the effect of immune system reactive oxygen species. Fungi that thrive in soil and have mammal hosts could shed light on the importance of these enzymes in the two types of lifestyles. We look forward to encouraging more research in a myriad of areas on catalase biology with a focus on basic and applied objectives and placing these enzymes as virulence determinants. creator: Naurú Idalia Vargas-Maya creator: Vianey Olmedo-Monfil creator: Jorge Humberto Ramírez-Prado creator: Ruth Reyes-Cortés creator: Felipe Padilla-Vaca creator: Bernardo Franco uri: https://doi.org/10.7717/peerj.14478 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Vargas-Maya et al. title: Estimation of common percentile of rainfall datasets in Thailand using delta-lognormal distributions link: https://peerj.com/articles/14498 last-modified: 2022-12-07 description: Weighted percentiles in many areas can be used to investigate the overall trend in a particular context. In this article, the confidence intervals for the common percentile are constructed to estimate rainfall in Thailand. The confidence interval for the common percentile help to indicate intensity of rainfall. Herein, four new approaches for estimating confidence intervals for the common percentile of several delta-lognormal distributions are presented: the fiducial generalized confidence interval, the adjusted method of variance estimates recovery, and two Bayesian approaches using fiducial quantity and approximate fiducial distribution. The Monte Carlo simulation was used to evaluate the coverage probabilities and average lengths via the R statistical program. The proposed confidence intervals are compared in terms of their coverage probabilities and average lengths, and the results of a comparative study based on these metrics indicate that one of the Bayesian confidence intervals is better than the others. The efficacies of the approaches are also illustrated by applying them to daily rainfall datasets from various regions in Thailand. creator: Warisa Thangjai creator: Sa-Aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.14498 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Thangjai et al. title: Symbiotic association of microalgae and plants in a deep water culture system link: https://peerj.com/articles/14536 last-modified: 2022-12-07 description: In this study, microalgae culture (Chlorella vulgaris) and mint seedlings (Mentha spp.) were combined in a hydroponic system to improve plant growth. Mint seedlings were grown both in microalgae-containing and in microalgae-free trial groups, and both groups were subjected to aerated and non-aerated conditions to show the effect of aeration and microalgae co-cultivation on the mint weight and height. The plant quality was also determined with color measurements of the mint leaves. The increase in the weight of the plants was the highest in microalgae-containing and aerated group (0.47 g) and the lowest in microalgae-free and non-aerated group (0.22 g). On the other hand, the variation in the plant height was not significant between the groups, the growth was lateral. The best quality mint leaves were also produced in microalgae-containing and aerated group. Our results have revealed the symbiotic life of the mint plant placed in the hydroponic system with microalgae and demonstrated improved mint growth and quality. This co-cultivation system is also potentially more environmentally friendly compared to growing microalgae and mint independently because of lower cost of aeration and mixing for microalgae cultivation, higher nutrient consumption efficiency, and reduced nutrient outflow. creator: Gülsüm Ebru Özer Uyar creator: Nurdan Mısmıl uri: https://doi.org/10.7717/peerj.14536 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Özer Uyar and Mısmıl title: N-mixture model-based estimate of relative abundance of sloth bear (Melursus ursinus) in response to biotic and abiotic factors in a human-dominated landscape of central India link: https://peerj.com/articles/13649 last-modified: 2022-12-06 description: Reliable estimation of abundance is a prerequisite for a species’ conservation planning in human-dominated landscapes, especially if the species is elusive and involved in conflicts. As a means of population estimation, the importance of camera traps has been recognized globally, although estimating the abundance of unmarked, cryptic species has always been a challenge to conservation biologists. This study explores the use of the N-mixture model with three probability distributions, i.e., Poisson, negative binomial (NB) and zero-inflated Poisson (ZIP), to estimate the relative abundance of sloth bears (Melursus ursinus) based on a camera trapping exercise in Sanjay Tiger Reserve, Madhya Pradesh from December 2016 to April 2017. We used environmental and anthropogenic covariates to model the variation in the abundance of sloth bears. We also compared null model estimates (mean site abundance) obtained from the N-mixture model to those of the Royle-Nichols abundance-induced heterogeneity model (RN model) to assess the application of similar site-structured models. Models with Poisson distributions produced ecologically realistic and more precise estimates of mean site abundance (λ = 2.60 ± 0.64) compared with other distributions, despite the relatively high Akaike Information Criterion value. Area of mixed and sal forest, the photographic capture rate of humans and distance to the nearest village predicted a higher relative abundance of sloth bears. Mean site abundance estimates of sloth bears obtained from the N-mixture model (Poisson distribution) and the RN model were comparable, indicating the overall utility of these models in this field. However, density estimates of sloth bears based on spatially explicit methods are essential for evaluating the efficacy of the relatively more cost-effective N-mixture model. Compared to commonly used index/encounter-based methods, the N-mixture model equipped with knowledge on governing biotic and abiotic factors provides better relative abundance estimates for a species like the sloth bear. In the absence of absolute abundance estimates, the present study could be insightful for the long-term conservation and management of sloth bears. creator: Sankarshan Chaudhuri creator: Rajasekar Rajaraman creator: Sankar Kalyanasundaram creator: Sambandam Sathyakumar creator: Ramesh Krishnamurthy uri: https://doi.org/10.7717/peerj.13649 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chaudhuri et al. title: Hypoxia-induced factor and its role in liver fibrosis link: https://peerj.com/articles/14299 last-modified: 2022-12-06 description: Liver fibrosis develops as a result of severe liver damage and is considered a major clinical concern throughout the world. Many factors are crucial for liver fibrosis progression. While advancements have been made to understand this disease, no effective pharmacological drug and treatment strategies have been established that can effectively prevent liver fibrosis or even could halt the fibrotic process. Most of those advances in curing liver fibrosis have been aimed towards mitigating the causes of fibrosis, including the development of potent antivirals to inhibit the hepatitis virus. It is not practicable for many individuals; however, a liver transplant becomes the only suitable alternative. A liver transplant is an expensive procedure. Thus, there is a significant need to identify potential targets of liver fibrosis and the development of such agents that can effectively treat or reverse liver fibrosis by targeting them. Researchers have identified hypoxia-inducible factors (HIFs) in the last 16 years as important transcription factors driving several facets of liver fibrosis, making them possible therapeutic targets. The latest knowledge on HIFs and their possible role in liver fibrosis, along with the cell-specific activities of such transcription factors that how they play role in liver fibrosis progression, is discussed in this review. creator: Jan Mohammad Omar creator: Yang Hai creator: Shizhu Jin uri: https://doi.org/10.7717/peerj.14299 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mohammad Omar et al. title: Stiffness and thickness of the upper trapezius muscle increase after repeated climbing bouts in male climbers link: https://peerj.com/articles/14409 last-modified: 2022-12-06 description: BackgroundIndoor climbing involves overloading the shoulder girdle, including the rotator cuff and upper trapezius muscles. This on the field study aimed to investigate the effects of repeated climbing bouts on morphological and mechanical measures of the upper trapezius muscle.Materials and MethodsFifteen experienced male climbers participated in the study. Rate of perceived exertion (RPE), blood lactate concentration ([La−]b), and stiffness and thickness over four points of the upper trapezius were assessed before and after a repeated climbing exercise. The procedure for the climbing exercise consisted of five climbs for a total time of 5-minutes per climb, followed by a 5-minute rest.ResultsThe analysis showed an increase from baseline to after the 3rd climb (p ≤ 0.01) for RPE and after the 5th climb for [La−]b (p ≤ 0.001). Muscle stiffness and thickness increased at all points (1–2–3–4) after the 5th climb (p ≤ 0.01). We found spatial heterogeneity in muscle stiffness and thickness; muscle stiffness was the highest at Point 4 (p ≤ 0.01), while muscle thickness reached the highest values at points 1–2 (both p ≤ 0.01). Moreover, the analysis between the dominant and non-dominant shoulder showed greater stiffness after the 1st climb at Point 1 (p = 0.004) and after the 5th climb at Point 4 (p ≤ 0.001).ConclusionsFor muscle thickness, the analysis showed significant changes in time and location between the dominant and the non-dominant shoulder. Bilateral increases in upper trapezius muscle stiffness and thickness, with simultaneous increases in RPE and blood lactate in response to consecutive climbs eliciting fatigue. creator: Sebastian Klich creator: Adam Kawczyński creator: Klaudia Sommer creator: Natalia Danek creator: César Fernández-de-las-Peñas creator: Lori A. Michener creator: Pascal Madeleine uri: https://doi.org/10.7717/peerj.14409 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Klich et al. title: Multi-dimensional feature recognition model based on capsule network for ubiquitination site prediction link: https://peerj.com/articles/14427 last-modified: 2022-12-06 description: Ubiquitination is an important post-translational modification of proteins that regulates many cellular activities. Traditional experimental methods for identification are costly and time-consuming, so many researchers have proposed computational methods for ubiquitination site prediction in recent years. However, traditional machine learning methods focus on feature engineering and are not suitable for large-scale proteomic data. In addition, deep learning methods are mostly based on convolutional neural networks and fuse multiple coding approaches to achieve classification prediction. This cannot effectively identify potential fine-grained features of the input data and has limitations in the representation of dependencies between low-level features and high-level features. A multi-dimensional feature recognition model based on a capsule network (MDCapsUbi) was proposed to predict protein ubiquitination sites. The proposed module consisting of convolution operations and channel attention was used to recognize coarse-grained features in the sequence dimension and the feature map dimension. The capsule network module consisting of capsule vectors was used to identify fine-grained features and classify ubiquitinated sites. With ten-fold cross-validation, the MDCapsUbi achieved 91.82% accuracy, 91.39% sensitivity, 92.24% specificity, 0.837 MCC, 0.918 F-Score and 0.97 AUC. Experimental results indicated that the proposed method outperformed other ubiquitination site prediction technologies. creator: Weimin Li creator: Jie Wang creator: Yin Luo creator: Tsigabu Teame Bezabih uri: https://doi.org/10.7717/peerj.14427 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al.