title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=494 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Development of the first high-density linkage map in the maize weevil, Sitophilus zeamais link: https://peerj.com/articles/15414 last-modified: 2023-06-15 description: The maize weevil, Sitophilus zeamais, is a worldwide pest that disproportionately affects subsistence farmers in developing countries. Damage from this pest threatens food security in these communities as widely available and effective control methods are lacking. With advances over the last decade in the development of genetic pest management techniques, addressing pest issues at the ecosystem level as opposed to the farm level may be a possibility. However, pest species selected for genetic management techniques require a well-characterized genome and few genomic tools have been developed for S. zeamais. Here, we have measured the genome size and developed the first genetic linkage map for this species. The genome size was determined using flow cytometry as 682 Mb and 674 Mb for females and males, respectively. The linkage map contains 11 linkage groups, which correspond to the 10 autosomes and 1 X-chromosome found in the species and it contains 1,121 SNPs. This linkage map will be useful for assembling a complete genome for S. zeamais. creator: Jennifer Fountain Baltzegar creator: Fred Gould uri: https://doi.org/10.7717/peerj.15414 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Baltzegar and Gould title: Habitat-use of the vulnerable Atlantic Nurse Shark: a review link: https://peerj.com/articles/15540 last-modified: 2023-06-15 description: Human activities have led to the loss of critical habitats for aquatic species at such an accelerated rate that habitat modification is considered a leading threat to biodiversity. Sharks and rays are considered the second most threatened group of vertebrates that have also suffered from habitat loss, especially in nursery grounds and reef-associated species. In this sense, actions toward the conservation of critical grounds for species survival are urgently needed, especially for those threatened with extinction. This study aimed to gather and provide information on the worldwide distribution and habitat association of the ‘vulnerable’ Atlantic Nurse Shark Ginglymostoma cirratum through a literature review performed at the Dimensions research database. A total of 30 studies published between 1950 and 2021 were retained since they defined at least the type of habitat in which G. cirratum was associated. Most studies covered the Floridian ecoregion, where G. cirratum is more common and abundant. Reefs, seagrass, sandy, rocky, mangrove, and macroalgae accounted for the majority of habitat associations, with a higher diversity of habitats detected within marine protected areas (MPAs). Ginglymostoma cirratum was recorded at a maximum depth of 75 m, temperatures ranging from 25 °C to 34 °C, and salinities between 31 and 38 ppt. Neonates were associated with shallower habitats (<20 m), mostly reefs, rocks, macroalgae, sandy shores, and seagrass, in an average temperature of 26 °C and salinity of 36 ppt. Breeding events and habitats were reported by 11 studies, 72.7% of them in shallow waters, mostly inside MPAs (90.9%). Our findings highlighted the key role played by MPAs in protecting essential grounds for threatened species, such as the Atlantic Nurse Shark. Major ecoregions (e.g., the Eastern Atlantic) are still underrepresented in the scientific literature as long as studies aim specifically to assess G. cirratum habitat association. Thus, further insights into the essential habitats needed to conserve the Atlantic Nurse Shark can still emerge from future studies. Considering the recent IUCN extinction risk status change in G. cirratum (i.e., Data Deficient to ‘Vulnerable’), new conservation measures that integrate habitat protection and management are urgently needed and should consider the data collected herein. creator: Vanessa Brito Bettcher creator: Ana Clara Sampaio Franco creator: Luciano Neves dos Santos uri: https://doi.org/10.7717/peerj.15540 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Bettcher et al. title: Psychological changes in athletes infected with Omicron after return to training: fatigue, sleep, and mood link: https://peerj.com/articles/15580 last-modified: 2023-06-15 description: BackgroundThis study aims to analyze the changes of approximately 1 month in fatigue, sleep, and mood in athletes after returning to training following infection with the COVID-19 Omicron strain and provide recommendations for returning to training after infection.MethodsTwo hundred and thirty professional athletes who had returned to training after being infected with COVID-19 in December 2022 were recruited to participate in three tests conducted from early January 2023. The second test was completed approximately 1 week after the first, and the third was completed about 2 weeks after the second. Each test consisted of completing scales and the exercise-induced fatigue measure. The scales included a visual analog scale, the Athens Insomnia Scale for non-clinical application, and the Depression-Anxiety-Stress scale. The exercise task was a six-minute stair climb test, and athletes evaluated subjective fatigue levels before and after exercise using another Visual Analog Scale and the Karolinska Sleepiness Scale.ResultsAfter returning to training, athletes’ physical fatigue decreased initially but increased as training progressed. Cognitive fatigue did not change significantly. The exercise task led to elevated levels of physical fatigue after a longer duration of training. Sleep quality problems decreased rapidly after the start of training but remained stable with prolonged training. Depression levels continued to decline, while anxiety levels only reduced after a longer duration of training. Stress levels decreased rapidly after the start of training but did not change with prolonged training.ConclusionAthletes who return to training after recovering from COVID-19 experience positive effects on their fatigue, sleep, and mood. It is important to prioritize anxiety assessment and interventions during the short period after returning and to continue monitoring fatigue levels and implementing recovery interventions over a longer period of time. creator: Chenhao Tan creator: Jinhao Wang creator: Guohuan Cao creator: Yelei He creator: Jun Yin creator: Yudan Chu creator: Zhizhong Geng creator: Longji Li creator: Jun Qiu uri: https://doi.org/10.7717/peerj.15580 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tan et al. title: Medium-term acoustic monitoring of small cetaceans in Patagonia, Chile link: https://peerj.com/articles/15292 last-modified: 2023-06-14 description: Coastal dolphins and porpoises such as the Chilean dolphin (Cephalorhynchus eutropia), the Peale’s dolphin (Lagenorhynchus australis), and the Burmeister’s porpoise (Phocoena spinipinnis) inhabit the remote areas of Chilean Patagonia. Human development is growing fast in these parts and may constitute a serious threat to such poorly known species. It is thus urgent to develop new tools to try and study these cryptic species and find out more about their behavior, population levels, and habits. These odontocetes emit narrow-band high-frequency (NBHF) clicks and efforts have been made to characterize precisely their acoustic production. Passive acoustic monitoring is a common way to study these animals. Nevertheless, as the signal frequency is usually higher than 100 kHz, storage problems are acute and do not allow for long-term monitoring. The solutions for recording NBHF clicks are usually twofold: either short duration, opportunistic recording from a small boat in presence of the animals (short-term monitoring) or long-term monitoring using devices including a click detector and registering events rather than sound. We suggest, as another possibility, medium-term monitoring, arguing that today’s devices have reached a level of performance allowing for a few days of continual recording even at these extremely high frequencies and in difficult conditions, combined with a long-term click detector. As an example, during 2021, we performed a quasi-continuous recording for one week with the Qualilife High-Blue recorder anchored in a fjord near Puerto Cisnes, Region de Aysen, Chile. We detected more than 13,000 clicks, grouped in 22 periods of passing animals. Our detected clicks are quite similar to precedent results but, due to the large number of clicks recorded, we find a larger variability of parameters. Several rapid sequences of clicks (buzz) were found in the recordings and their features are consistent with previous studies: on average they have a larger bandwidth and a lower peak frequency than the usual clicks. We also installed in the same place a click detector (C-POD) and the two devices compare well and show the same number and duration of periods of animals presence. Passages of odontocetes were happening on average each three hours. We thus confirm the high site fidelity for the species of dolphins emitting NBHF clicks present in this zone. Finally, we confirm that the combined use of recording and detection devices is probably a good alternative to study these poorly known species in remote areas. creator: Julie Patris creator: Franck Malige creator: Madeleine Hamame creator: Hervé Glotin creator: Valentin Barchasz creator: Valentin Gies creator: Sebastian Marzetti creator: Susannah Buchan uri: https://doi.org/10.7717/peerj.15292 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Patris et al. title: Anthropogenic noise decreases activity and calling behavior in wild mice link: https://peerj.com/articles/15297 last-modified: 2023-06-14 description: BackgroundAnimals rely on sound for daily activities, and anthropogenic noise is a pollutant that alters the natural soundscape within which they are active. As human infrastructure expands, broadband anthropogenic noise increases, which can affect behaviors of nocturnal animals. Mice are nocturnal animals that produce ultrasonic calls as part of their behavioral repertoire.MethodsWe assessed effects of anthropogenic and natural noise on the behaviors of wild deer mice (Peromyscus maniculatus) and woodland jumping mice (Napaeozapus insignis), two species of mice that produce ultrasonic calls. We measured activity, foraging behavior at a foraging tray, and calling behavior to broadcasts of natural and anthropogenic noise, compared to a baseline with no broadcasting, at 25 focal areas in the Southern Appalachian Mountain Range of North Carolina, USA.ResultsDeer mice exposed to anthropogenic noise spent less time in focal areas with broadcasted anthropogenic noise. Mice took longer to begin foraging in the presence of anthropogenic noise, they spent less time at the foraging tray, and left fewer husks but consumed the same number of seeds as mice exposed to natural noise. Deer mice were less likely than woodland jumping mice to be the first to enter the focal area and approach food when in the presence of anthropogenic noise. Both species produced few ultrasonic calls in the presence of broadcasted natural and anthropogenic noise compared to their baseline level of calling. We present the first calls recorded from woodland jumping mice.ConclusionAnthropogenic noise affects activity, foraging behavior, and calling behavior of nocturnal mice. Natural noise also affects the calling behavior of mice. Mouse species respond differently to anthropogenic noise, with deer mice appearing more sensitive to anthropogenic noise than woodland jumping mice. Responses to noise could have important effects on the ecology of mice and these two species respond differently. Species differences should be considered when mitigating the effects of noise in conservation ecology. creator: Radmila Petric creator: Matina Kalcounis-Rueppell uri: https://doi.org/10.7717/peerj.15297 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2023 Petric and Kalcounis-Rueppell title: Integration of statistical shape modeling and alternating interpolation-based model tracking technique for measuring knee kinematics in vivo using clinical interleaved bi-plane fluoroscopy link: https://peerj.com/articles/15371 last-modified: 2023-06-14 description: BackgroundA 2D fluoroscopy/3D model-based registration with statistical shape modeling (SSM)-reconstructed subject-specific bone models will help reduce radiation exposure for 3D kinematic measurements of the knee using clinical alternating bi-plane fluoroscopy systems. The current study aimed to develop such an approach and evaluate in vivo its accuracy and identify the effects of the accuracy of SSM models on the kinematic measurements.MethodsAn alternating interpolation-based model tracking (AIMT) approach with SSM-reconstructed subject-specific bone models was used for measuring 3D knee kinematics from dynamic alternating bi-plane fluoroscopy images. A two-phase optimization scheme was used to reconstruct subject-specific knee models from a CT-based SSM database of 60 knees using one, two, or three pairs of fluoroscopy images. Using the CT-reconstructed model as a benchmark, the performance of the AIMT with SSM-reconstructed models in measuring bone and joint kinematics during dynamic activity was evaluated in terms of mean target registration errors (mmTRE) for registered bone poses and the mean absolute differences (MAD) for each motion component of the joint poses.ResultsThe mmTRE of the femur and tibia for one image pair were significantly greater than those for two and three image pairs without significant differences between two and three image pairs. The MAD was 1.16 to 1.22° for rotations and 1.18 to 1.22 mm for translations using one image pair. The corresponding values for two and three image pairs were 0.75 to 0.89° and 0.75 to 0.79 mm; and 0.57 to 0.79° and 0.6 to 0.69 mm, respectively. The MAD values for one image pair were significantly greater than those for two and three image pairs without significant differences between two and three image pairs.ConclusionsAn AIMT approach with SSM-reconstructed models was developed, enabling the registration of interleaved fluoroscopy images and SSM-reconstructed models from more than one asynchronous fluoroscopy image pair. This new approach had sub-millimeter and sub-degree measurement accuracy when using more than one image pair, comparable to the accuracy of CT-based methods. This approach will be helpful for future kinematic measurements of the knee with reduced radiation exposure using 3D fluoroscopy with clinically alternating bi-plane fluoroscopy systems. creator: Hsuan-Yu Lu creator: Cheng-Chung Lin creator: Kao-Shang Shih creator: Tung-Wu Lu creator: Mei-Ying Kuo creator: Song-Ying Li creator: Horng-Chaung Hsu uri: https://doi.org/10.7717/peerj.15371 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lu et al. title: Optimizing lettuce yields and quality by incorporating movable downward lighting with a supplemental adjustable sideward lighting system in a plant factory link: https://peerj.com/articles/15401 last-modified: 2023-06-14 description: BackgroundLettuce is a vegetable that is increasingly consumed globally, given its nutritional quality. Plant factories with artificial lighting can produce high-yield and high-quality plants. High plant density in these systems speeds up leaf senescence. Wasted energy and lower yield raised labor expenses are some of the bottlenecks associated with this farming system. In order to increase lettuce yields and quality in the plant factory, it is essential to develop cultivating techniques using artificial lighting.MethodsRomaine lettuce was grown under a developed “movable downward lighting combined with supplemental adjustable sideward lighting system” (C-S) and under a system without supplemental sideward lighting (N-S) in a plant factory. The effects of C-S on lettuce’s photosynthetic characteristics, plant yield, and energy consumption relative to plants grown under a system without N-S were studied.ResultsRomaine lettuce growth and light energy consumption in the plant factory were both influenced favorably by supplementary adjustable sideward lighting. The number of leaves, stem diameter, fresh and dry weights, chlorophyll a and b concentration, and biochemical content (soluble sugar and protein) all increased sharply. The energy consumption was substantially higher in the N-S treatment than the C-S. creator: Mulowayi Mutombo Arcel creator: Ahmed Fathy Yousef creator: Zhen Hui Shen creator: Witness Joseph Nyimbo creator: Shu He Zheng uri: https://doi.org/10.7717/peerj.15401 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mutombo Arcel et al. title: Spatial and temporal dynamics of the bacterial community under experimental warming in field-grown wheat link: https://peerj.com/articles/15428 last-modified: 2023-06-14 description: Climate change may lead to adverse effects on agricultural crops, plant microbiomes have the potential to help hosts counteract these effects. While plant–microbe interactions are known to be sensitive to temperature, how warming affects the community composition and functioning of plant microbiomes in most agricultural crops is still unclear. Here, we utilized a 10-year field experiment to investigate the effects of warming on root zone carbon availability, microbial activity and community composition at spatial (root, rhizosphere and bulk soil) and temporal (tillering, jointing and ripening stages of plants) scales in field-grown wheat (Triticum aestivum L.). The dissolved organic carbon and microbial activity in the rhizosphere were increased by soil warming and varied considerably across wheat growth stages. Warming exerted stronger effects on the microbial community composition in the root and rhizosphere samples than in the bulk soil. Microbial community composition, particularly the phyla Actinobacteria and Firmicutes, shifted considerably in response to warming. Interestingly, the abundance of a number of known copiotrophic taxa, such as Pseudomonas and Bacillus, and genera in Actinomycetales increased in the roots and rhizosphere under warming and the increase in these taxa implies that they may play a role in increasing the resilience of plants to warming. Taken together, we demonstrated that soil warming along with root proximity and plant growth status drives changes in the microbial community composition and function in the wheat root zone. creator: Jing Wang creator: Shuaimin Chen creator: Ruibo Sun creator: Binbin Liu creator: Tatoba Waghmode creator: Chunsheng Hu uri: https://doi.org/10.7717/peerj.15428 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Detection of Echinococcus multilocularis in repurposed environmental DNA samples from river water link: https://peerj.com/articles/15431 last-modified: 2023-06-14 description: Environmental DNA (eDNA) is an increasingly popular tool in biological and ecological studies. As a biproduct of its increasing use, large number of eDNA samples are being collected and stored, that potentially contain information of many non-target species. One potential use for these eDNA samples is a surveillance and early detection of pathogens and parasites that are otherwise difficult to detect. Echinococcus multilocularis is such a parasite with serious zoonotic concern, and whose range has been expanding. If eDNA samples from various studies can be repurposed in detecting the parasite, it can significantly reduce the costs and efforts in surveillance and early detection of the parasite. We designed and tested a new set of primer-probe for detecting E. multilocularis mitochondrial DNA in environmental medium. Using this primer-probe set, we conducted real-time PCR on repurposed eDNA samples collected from three streams flowing through an area of Japan endemic to the parasite. We detected the DNA of E. multilocularis in one of the 128 samples (0.78%). The discovery suggests that while detecting E. multilocularis using eDNA samples is possible, the rate of detection appear to be very low. However, given the naturally low prevalence of the parasite among wild hosts in endemic areas, the repurposed eDNAs may still be a valid option for surveillance in newly introduced areas with the reduced cost and efforts. Further work is needed to assess and improve the effectiveness of using eDNA for detection of E. multilocularis. creator: Kensuke Mori creator: Akio Imamura creator: Itsuki Hirayama creator: Toshifumi Minamoto uri: https://doi.org/10.7717/peerj.15431 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mori et al. title: Physiological response and transcriptome analyses of leguminous Indigofera bungeana Walp. to drought stress link: https://peerj.com/articles/15440 last-modified: 2023-06-14 description: ObjectiveIndigofera bungeana is a shrub with high quality protein that has been widely utilized for forage grass in the semi-arid regions of China. This study aimed to enrich the currently available knowledge and clarify the detailed drought stress regulatory mechanisms in I. bungeana, and provide a theoretical foundation for the cultivation and resistance breeding of forage crops.MethodsThis study evaluates the response mechanism to drought stress by exploiting multiple parameters and transcriptomic analyses of a 1-year-old seedlings of I. bungeana in a pot experiment.ResultsDrought stress significantly caused physiological changes in I. bungeana. The antioxidant enzyme activities and osmoregulation substance content of I. bungeana showed an increase under drought. Moreover, 3,978 and 6,923 differentially expressed genes were approved by transcriptome in leaves and roots. The transcription factors, hormone signal transduction, carbohydrate metabolism of regulatory network were observed to have increased. In both tissues, genes related to plant hormone signaling transduction pathway might play a more pivotal role in drought tolerance. Transcription factors families like basic helix-loop-helix (bHLH), vian myeloblastosis viral oncogene homolog (MYB), basic leucine zipper (bZIP) and the metabolic pathway related-genes like serine/threonine-phosphatase 2C (PP2C), SNF1-related protein kinase 2 (SnRK2), indole-3-acetic acid (IAA), auxin (AUX28), small auxin up-regulated rna (SAUR), sucrose synthase (SUS), sucrosecarriers (SUC) were highlighted for future research about drought stress resistance in Indigofera bungeana.ConclusionOur study posited I. bungeana mainly participate in various physiological and metabolic activities to response severe drought stress, by regulating the expression of the related genes in hormone signal transduction. These findings, which may be valuable for drought resistance breeding, and to clarify the drought stress regulatory mechanisms of I. bungeana and other plants. creator: Shuang Ma creator: Haiying Hu creator: Hao Zhang creator: Fenghua Ma creator: Zhihao Gao creator: Xueying Li uri: https://doi.org/10.7717/peerj.15440 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ma et al.