title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1112 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification of hydatidosis-related modules and key regulatory genes link: https://peerj.com/articles/9280 last-modified: 2020-06-18 description: BackgroundEchinococcosis caused by larval of Echinococcus is prevalent all over the world. Although clinical experience showed that the presence of tapeworms could not be found in liver lesions, the repeated infection and aggravation of lesions still occur in the host. Here, this study constructed a multifactor-driven disease-related dysfunction network to explore the potential molecular pathogenesis mechanism in different hosts after E.multilocularis infection.MethodFirst, iTRAQ sequencing was performed on human liver infected with E.multilocularis. Second, obtained microRNAs(miRNAs) expression profiles of humans and canine infected with Echinococcus from the GEO database. In addition, we also performed differential expression analysis, protein interaction network analysis, enrichment analysis, and crosstalk analysis to obtain genes and modules related to E.multilocularis infection. Pivot analysis is used to calculate the potential regulatory effects of multiple factors on the module and identify related non-coding RNAs(ncRNAs) and transcription factors(TFs). Finally, we screened the target genes of miRNAs of Echinococcus to further explore its infection mechanism.ResultsA total of 267 differentially expressed proteins from humans and 3,635 differentially expressed genes from canine were obtained. They participated in 16 human-related dysfunction modules and five canine-related dysfunction modules, respectively. Both human and canine dysfunction modules are significantly involved in BMP signaling pathway and TGF-beta signaling pathway. In addition, pivot analysis found that 1,129 ncRNAs and 110 TFs significantly regulated human dysfunction modules, 158 ncRNAs and nine TFs significantly regulated canine dysfunction modules. Surprisingly, the Echinococcus miR-184 plays a role in the pathogenicity regulation by targeting nine TFs and one ncRNA in humans. Similarly, miR-184 can also cause physiological dysfunction by regulating two transcription factors in canine.ConclusionThe results show that the miRNA-184 of Echinococcus can regulate the pathogenic process through various biological functions and pathways. The results laid a solid theoretical foundation for biologists to further explore the pathogenic mechanism of Echinococcosis. creator: Jijun Song creator: Mingxin Song uri: https://doi.org/10.7717/peerj.9280 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Song and Song title: How caged salmon respond to waves depends on time of day and currents link: https://peerj.com/articles/9313 last-modified: 2020-06-18 description: Disease, pest control, and environmental factors such as water quality and carrying capacity limit growth of salmon production in existing farm areas. One way to circumvent such problems is to move production into more exposed locations with greater water exchange. Farming in exposed locations is better for the environment, but may carry unforeseen costs for the fish in those farms. Currents may be too strong, and waves may be too large with a negative impact on growth and profit for farmers and on fish welfare. This study employed two major fish monitoring methods to determine the ability of Atlantic Salmon (Salmo salar) to cope with wavy conditions in exposed farms. Echosounders were used to determine vertical distribution and horizontal preference of fish during different wave and current conditions as well as times of day. Video cameras were used to monitor shoal cohesion, swimming effort, and fish prevalence in locations of interest. The results indicate complex interacting effects of wave parameters, currents, and time of day on fish behaviour and vertical distribution. During the day, hydrodynamic conditions had stronger effects on vertical distribution than during the night. In weak currents, fish generally moved further down in taller waves, but stronger currents generally caused fish to move upwards regardless of wave conditions. Long period waves had unpredictable effects on vertical distribution with fish sometimes seeking deeper water and other times moving up to shallower water. It is unclear how much the cage bottom restricted vertical distribution and whether movement upwards in the water columns was related to cage deformation. In extreme cases, waves can reach below the bottom of a salmon cage, preventing fish from moving below the waves and cage deformation could exacerbate this situation. Farmers ought to take into consideration the many interacting effects on salmon behaviour within a cage as well as the potential for cage deformation when they design their farms for highly exposed locations. This will ensure that salmon are able to cope when storms and strong currents hit at the same time. creator: Ása Johannesen creator: Øystein Patursson creator: Jóhannus Kristmundsson creator: Signar Pæturssonur Dam creator: Pascal Klebert uri: https://doi.org/10.7717/peerj.9313 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Johannesen et al. title: Parents know best: transgenerational predator recognition through parental effects link: https://peerj.com/articles/9340 last-modified: 2020-06-18 description: In highly biodiverse systems, such as coral reefs, prey species are faced with predatory threats from numerous species. Recognition of predators can be innate, or learned, and can help increase the chance of survival. Research suggests that parental exposure to increased predatory threats can affect the development, behaviour, and ultimately, success of their offspring. Breeding pairs of damselfish (Acanthochromis polyacanthus) were subjected to one of three olfactory and visual treatments (predator, herbivore, or control), and their developing embryos were subsequently exposed to five different chemosensory cues. Offspring of parents assigned to the predator treatment exhibited a mean increase in heart rate two times greater than that of offspring from parents in herbivore or control treatments. This increased reaction to a parentally known predator odour suggests that predator-treated parents passed down relevant threat information to their offspring, via parental effects. This is the first time transgenerational recognition of a specific predator has been confirmed in any species. This phenomenon could influence predator-induced mortality rates and enable populations to adaptively respond to fluctuations in predator composition and environmental changes. creator: Jennifer A. Atherton creator: Mark I. McCormick uri: https://doi.org/10.7717/peerj.9340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Atherton and McCormick title: Spatial patterns of bat diversity overlap with woodpecker abundance link: https://peerj.com/articles/9385 last-modified: 2020-06-18 description: Woodpecker diversity is usually higher in natural forests rich in dead wood and old trees than in managed ones, thus this group of birds is regarded as an indicator of forest biodiversity. Woodpeckers excavate cavities which can be subsequently used by several bird species. As a consequence, their abundance indicates high avian abundance and diversity in forests. However, woodpecker-made holes may be also important for other animals, for example, mammals but it has seldom been investigated so far. Here, we examine how well one species, the Great Spotted Woodpecker, predicts species richness, occurrence and acoustic activity of bats in Polish pine forests. In 2011 we conducted woodpecker and bat surveys at 63 point-count sites in forests that varied in terms of stand age, structure and amount of dead wood. From zero to five Great Spotted Woodpeckers at a point-count site were recorded. The total duration of the echolocation calls during a 10-min visit varied from 0 to 542 s and the number of bat species/species groups recorded during a visit ranged between zero to five. The local abundance of the woodpecker was positively correlated with bat species richness (on the verge of significance), bat occurrence and pooled bat activity. The occurrence of Eptesicus and Vespertilio bats and Nyctalus species was positively related with the abundance of the Great Spotted Woodpecker. The activity of Pipistrellus pygmaeus, Eptesicus and Vespertilio bats and a group of Myotis species was not associated with the woodpecker abundance, but echolocation calls of Nyctalus species, P. nathusii and P.pipistrellus were more often at sites with many Great Spotted Woodpeckers. Moreover, the probability of bat presence and the activity of bats was generally higher shortly after dusk and in middle of the summer than in late spring. We suggest that the observed correlations can be driven by similar roosting habitats (e.g., woodpeckers can provide breeding cavities for bats) or possibly by associated invertebrate food resources of woodpeckers and bats. The abundance of Great Spotted Woodpecker seems to be a good positive indicator of bat species richness, occurrence and activity, thus adding a group of relatively cryptic forest species that are indicated by the presence of the Great Spotted Woodpecker. creator: Dorota Kotowska creator: Marcin Zegarek creator: Grzegorz Osojca creator: Andrzej Satory creator: Tomas Pärt creator: Michał Żmihorski uri: https://doi.org/10.7717/peerj.9385 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kotowska et al. title: KIT is involved in melanocyte proliferation, apoptosis and melanogenesis in the Rex Rabbit link: https://peerj.com/articles/9402 last-modified: 2020-06-18 description: BackgroundMelanocytes play an extremely important role in the process of skin and coat colors in mammals which is regulated by melanin-related genes. Previous studies have demonstrated that KIT is implicated in the process of determining the color of the coat in Rex rabbits. However, the effect of KIT on the proliferation and apoptosis of melanocytes and melanogenesis has not been clarified.MethodsThe mRNA and protein expression levels of KIT were quantified in different coat colored rabbits by qRT-PCR and a Wes assay. To identify whether KIT functions by regulating of melanogenesis, KIT overexpression and knockdown was conducted in melanocytes, and KIT mRNA expression and melanin-related genes TYR, MITF, PMEL and DCT were quantified by qRT-PCR. To further confirm whether KIT influences melanogenesis in melanocytes, melanin content was quantified using NaOH lysis after overexpression and knockdown of KIT. Melanocyte proliferation was estimated using a CCK-8 assay at 0, 24, 48 and 72 h after transfection, and the rate of apoptosis of melanocytes was measured by fluorescence-activated cell sorting.ResultsKITmRNA and protein expression levels were significantly different in the skin of Rex rabbits with different color coats (P < 0.05), the greatest levels observed in those with black skin. The mRNA expression levels of KIT significantly affected the mRNA expression of the pigmentation-related genes TYR, MITF, PMEL and DCT (P < 0.01). Melanin content was evidently regulated by the change in expression patterns of KIT (P < 0.01). In addition, KIT clearly promoted melanocyte proliferation, but inhibited apoptosis.ConclusionsOur results reveal that KIT is a critical gene in the regulation of melanogenesis, controlling proliferation and apoptosis in melanocytes, providing additional evidence for the mechanism of pigmentation of animal fur. creator: Shuaishuai Hu creator: Yang Chen creator: Bohao Zhao creator: Naisu Yang creator: Shi Chen creator: Jinyu Shen creator: Guolian Bao creator: Xinsheng Wu uri: https://doi.org/10.7717/peerj.9402 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hu et al. title: Habitual and ready positions in female table tennis players and their relation to the prevalence of back pain link: https://peerj.com/articles/9170 last-modified: 2020-06-17 description: BackgroundThe current body of knowledge shows that there is very little research into the occurrence and scale of asymmetry or postural defects in table tennis. It is interesting which regions of the spine are exposed to the greatest changes in the shape of its curvatures and whether the asymmetrical position of the shoulder and pelvic girdles in table tennis players changes when adopting the ready position. Consequently, can overload occur in certain parts of the spine and can the asymmetry deepen as a response of adopting this position? The reply to these questions may be an indication of the need for appropriate compensatory or corrective measures. Therefore, the aim of the study was to evaluate the effect of body position during play on the change in the shape of anterior–posterior spinal curvatures and trunk asymmetry in table tennis players.MethodsTo evaluate body posture the photogrammetric method based on the Moiré phenomenon with equipment by CQ electronic was applied. The study involved 22 female players practicing competitive table tennis (the age of 17 ± 4.5, with the average training experience of 7 ± 4.3 years, body mass of 47.8 ± 15.8, and body height of 161.2 ± 10.4). Each participant completed an author’s own questionnaire on spinal pain. The shape of curvatures in the sagittal and frontal plane was evaluated in the participant in the habitual standing position and in the table tennis ready position. Descriptive statistical analysis was performed and the significance of differences was tested using the Mann–Whitney U test.Results and ConclusionsThis study demonstrated the dominance of kyphotic body posture in table tennis players, which can be caused by many hours of using the ready position during playing. After adopting this position, there are significant differences in the angles of anterior and posterior spinal curvatures compared to the habitual posture. This may be the cause of overloads and pain complaints reported by the study participants. Adopting the ready position is also associated with an increase in asymmetry in the position (rotation) of the pelvis and spinous processes (frontal plane). Therefore, training programs should be extended with exercises that relieve the spine in the vertical line and exercises that improve symmetry of the work of the upper limbs, body trunk muscles and the pelvis. creator: Ziemowit Bańkosz creator: Katarzyna Barczyk-Pawelec uri: https://doi.org/10.7717/peerj.9170 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bańkosz and Barczyk-Pawelec title: Image database of Japanese food samples with nutrition information link: https://peerj.com/articles/9206 last-modified: 2020-06-17 description: BackgroundVisual processing of food plays an important role in controlling eating behaviors. Several studies have developed image databases of food to investigate visual food processing. However, few databases include non-Western foods and objective nutrition information on the foods.MethodsWe developed an image database of Japanese food samples that has detailed nutrition information, including calorie, carbohydrate, fat and protein contents. To validate the database, we presented the images, together with Western food images selected from an existing database and had Japanese participants rate their affective (valence, arousal, liking and wanting) and cognitive (naturalness, recognizability and familiarity) appraisals and estimates of nutrition.ResultsThe results showed that all affective and cognitive appraisals (except arousal) of the Japanese food images were higher than those of Western food. Correlational analyses found positive associations between the objective nutrition information and subjective estimates of the nutrition information, and between the objective calorie/fat content and affective appraisals.ConclusionsThese data suggest that by using our image database, researchers can investigate the visual processing of Japanese food and the relationships between objective nutrition information and the psychological/neural processing of food. creator: Wataru Sato creator: Kazusa Minemoto creator: Reiko Sawada creator: Yoshiko Miyazaki creator: Tohru Fushiki uri: https://doi.org/10.7717/peerj.9206 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sato et al. title: Legacy effects of historical grazing alter leaf stomatal characteristics in progeny plants link: https://peerj.com/articles/9266 last-modified: 2020-06-17 description: Grazing, one of the primary utilization modes of grassland, is the main cause of grassland degradation. Historical overgrazing results in dwarf phenotype and decreased photosynthesis of perennial plants. However, it remains unknown what the mechanism underlying of this legacy effect is, and the role of stomata in the resulting decreased photosynthesis also remains unclear. To address these questions, differences in stomatal density, length and width on both adaxial and abaxial epidermis were compared between overgrazing and ungrazed Leymus chinensis offspring by using rhizome buds cultivated in a greenhouse, and the correlation between photosynthetic capacity and stomatal behavior was also investigated. Our results showed that historical grazing significantly impacted phenotype, photosynthesis and stomatal traits of L. chinensis. The offspring plants taken from overgrazed parents were dwarfed compared to those taken from ungrazed parents, and the photosynthesis and stomatal conductance of plants with a grazing history decreased by 28.6% and 21.3%, respectively. In addition, stomatal density and length on adaxial and abaxial leaf surfaces were significantly increased; however, stomatal width on abaxial leaf surfaces of overgrazed L. chinensis was significantly decreased compared with ungrazed individuals. Moreover, the expression patterns of eight genes related to stomatal regulation were tested: seven were down-regulated (2–18 times) and one was up-regulated (three times). Genes, involved in ABC transporter and receptor-like serine/threonine protein kinase were down-regulated. These results suggest that legacy effects of historical grazing affect the stomatal conductance by decreasing the stomatal width in progeny plants, which thus results in lower photosynthesis. Furthermore, changes of stomatal traits and function were regulated by the inhibition of ABC transporter and serine/threonine protein kinase. These findings are helpful for future exploration of the possible mechanisms underlying the response of grassland plants to long-term overgrazing. creator: Jingjing Yin creator: Xiliang Li creator: Huiqin Guo creator: Jize Zhang creator: Lingqi Kong creator: Weibo Ren uri: https://doi.org/10.7717/peerj.9266 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yin et al. title: Novel rapid identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by real-time RT-PCR using BD Max Open System in Taiwan link: https://peerj.com/articles/9318 last-modified: 2020-06-17 description: Coronavirus disease 2019 has become a worldwide pandemic. By April 7, 2020, approximately 1,279,722 confirmed cases were reported worldwide including those in Asia, European Region, African Region and Region of the Americas. Rapid and accurate detection of Severe Acute Respiratory Syndrome Virus 2 (SARS-CoV-2) is critical for patient care and implementing public health measures to control the spread of infection. In this study, we developed and validated a rapid total nucleic acid extraction method based on real‐time RT-PCR for reliable, high‐throughput identification of SARS-CoV-2 using the BD MAX platform. For clinical validation, 300 throat swab and 100 sputum clinical samples were examined by both the BD MAX platform and in-house real-time RT-PCR methods, which showed 100% concordant results. This BD MAX protocol is fully automated and the turnaround time from sample to results is approximately 2.5 h for 24 samples compared to 4.8 h by in-house real-time RT-PCR. Our developed BD MAX RT-PCR assay can accurately identify SARS-CoV-2 infection and shorten the turnaround time to increase the effectiveness of control and prevention measures for this emerging infectious disease. creator: Cherng-Lih Perng creator: Ming-Jr Jian creator: Chih-Kai Chang creator: Jung-Chung Lin creator: Kuo-Ming Yeh creator: Chien-Wen Chen creator: Sheng-Kang Chiu creator: Hsing-Yi Chung creator: Yi-Hui Wang creator: Shu-Jung Liao creator: Shih-Yi Li creator: Shan-Shan Hsieh creator: Shih-Hung Tsai creator: Feng-Yee Chang creator: Hung-Sheng Shang uri: https://doi.org/10.7717/peerj.9318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Perng et al. title: Contribution of prokaryotes and eukaryotes to CO2 emissions in the wastewater treatment process link: https://peerj.com/articles/9325 last-modified: 2020-06-17 description: Reduction of the greenhouse effect is primarily associated with the reduction of greenhouse gas (GHG) emissions. Carbon dioxide (CO2) is one of the gases that increases the greenhouse effect - it is responsible for about half of the greenhouse effect. Significant sources of CO2 are wastewater treatment plants (WWTPs) and waste management, with about 3% contribution to global emissions. CO2 is produced mainly in the aerobic stage of wastewater purification and is a consequence of activated sludge activity. Although the roles of activated sludge components in the purification process have been studied quite well, their quantitative contribution to CO2 emissions is still unknown. The emission of CO2 caused by prokaryotes and eukaryotes over the course of a year (taking into account subsequent seasons) in model sequencing batch reactors (SBR) is presented in this study. In this work, for the first time, we aimed to quantify this contribution of eukaryotic organisms to total CO2 emissions during the WWTP process. It is of the order of several or more ppm. The contribution of CO2 produced by different components of activated sludge in WWTPs can improve estimation of the emissions of GHGs in this area of human activity. creator: Katarzyna Jaromin-Gleń creator: Roman Babko creator: Tatiana Kuzmina creator: Yaroslav Danko creator: Grzegorz Łagód creator: Cezary Polakowski creator: Joanna Szulżyk-Cieplak creator: Andrzej Bieganowski uri: https://doi.org/10.7717/peerj.9325 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jaromin-Gleń et al.