title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=736 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Comparison of changes in fecal microbiota of calves with and without dam link: https://peerj.com/articles/12826 last-modified: 2022-04-01 description: In pastoral areas and semi-agricultural and semi-pastoral areas of Sichuan, beef cattle breeding mode is mainly dependent on nature to raise livestock. On the one hand, owing to the shortage of forage grass in spring, cows suffer from malnutrition. On the other hand, competition for milk between human and livestock further deepens the malnutrition of newborn calves, and the mortality rate even exceeds 40%, resulting in serious waste of beef cattle source resources. The objective of this study was to investigate the effect of different cultivation methods (calves with and without dam) and age on calves hindgut microbiome. Sixteen healthy calves (Yak ♂ × Pian cattle ♀, with similar birthday 0 ± 2 d and body weight 13.1 ± 1.13 kg), were selected and randomly divided into two groups. The control group was cultivated with heifers, whereas the treatment group was cultivated without heifers and was fed milk replacer during the whole 95 days formal experimental period. Fecal samples were collected on 35, 65 and 95 days of age for high-throughput sequencing. The α-diversity was different between the two groups on day 35; however, the bacterial species richness and diversity was almost not different on day 95. Principal coordinates analysis revealed significant difference between the two groups on all the three time points, and the timepoints of day 65 and 95 were closer and separated from the timepoints of day 35 in calves with dam, whereas the timepoints of day 35 and 65 were closer and separated from day 95 in calves without dam. As time passed, the abundance of Firmicutes increased, while Proteobacteria and Actinobacteria decreased in calves with dam. But in calves without dam, the abundance of Bacteroidetes and Proteobacteria increased on day 65 and then decreased on day 95. In genus level, the relative abundance of Bacteroides decreased in calf with dam while its abundance increased first and then decreased in calf without dam but both resulted in the range of 3.5~4.5%. The relative abundance of Lactobacillus decreased, whereas Ruminococcaceae UCG-005 increased in both groups as the calf grew up. It was concluded that the richness and evenness of the microbial communities was higher in calves with dam than without dam, and a stable gut microbiome in calve with dam is established earlier than calf without dam. creator: Mengya Li creator: Zhisheng Wang creator: Lizhi Wang creator: Bai Xue creator: Rui Hu creator: Huawei Zou creator: Siqiang Liu creator: Ali Mujtaba Shah creator: Quanhui Peng uri: https://doi.org/10.7717/peerj.12826 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Comparison of surface wind speed and wind speed profiles in the Taklimakan Desert link: https://peerj.com/articles/13001 last-modified: 2022-04-01 description: Near-surface (10 m) wind speed (NWS) plays a crucial role in many areas, including the hydrological cycle, wind energy production, and the dispersion of air pollution. Based on wind speed data from Tazhong and the northern margins of the Taklimakan Desert in Xiaotang in spring, summer, autumn, and winter of 2014 and 2015, statistical methods were applied to determine the characteristics of the diurnal changes in wind speed near the ground and the differences in the wind speed profiles between the two sites. The average wind speed on a sunny day increased slowly with height during the day and rapidly at night. At heights below 4 m the wind speed during the day was higher than at night, whereas at 10 m the wind speed was lower during the day than at night. The semi-empirical theory and Monin–Obukhov (M–O) similarity theory were used to fit the NWS profile in the hinterland of the Tazhong Desert. A logarithmic law was applied to the neutral stratification wind speed profile, and an exponential fitting correlation was used for non-neutral stratification. The more unstable the stratification, the smaller the n. Using M–O similarity theory, the “linear to tens of” law was applied to the near-neutral stratification. According to the measured data, the distribution of φM with stability was obtained. The γm was obtained when the near-surface stratum was stable in the hinterland of Tazhong Desert and the βm was obtained when it was unstable. In summer, γm and βm were 5.84 and 15.1, respectively, while in winter, γm and βm were 1.9 and 27.1, respectively. creator: Xinchun Liu creator: Yongde Kang creator: Hongna Chen creator: Hui Lu uri: https://doi.org/10.7717/peerj.13001 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: A spotlight on non-host resistance to plant viruses link: https://peerj.com/articles/12996 last-modified: 2022-03-31 description: Plant viruses encounter a range of host defenses including non-host resistance (NHR), leading to the arrest of virus replication and movement in plants. Viruses have limited host ranges, and adaptation to a new host is an atypical phenomenon. The entire genotypes of plant species which are imperceptive to every single isolate of a genetically variable virus species are described as non-hosts. NHR is the non-specific resistance manifested by an innately immune non-host due to pre-existing and inducible defense responses, which cannot be evaded by yet-to-be adapted plant viruses. NHR-to-plant viruses are widespread, but the phenotypic variation is often not detectable within plant species. Therefore, molecular and genetic mechanisms of NHR need to be systematically studied to enable exploitation in crop protection. This article comprehensively describes the possible mechanisms of NHR against plant viruses. Also, the previous definition of NHR to plant viruses is insufficient, and the main aim of this article is to sensitize plant pathologists to the existence of NHR to plant viruses and to highlight the need for immediate and elaborate research in this area. creator: Avanish Rai creator: Palaiyur N. Sivalingam creator: Muthappa Senthil-Kumar uri: https://doi.org/10.7717/peerj.12996 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rai et al. title: Potential roles of melatonin and ABA on apple dwarfing in semi-arid area of Xinjiang China link: https://peerj.com/articles/13008 last-modified: 2022-03-31 description: Dwarfing is a typic breeding trait for mechanical strengthening and relatively high yield in modern apple orchards. Clarification of the mechanisms associated with dwarfing is important for use of molecular technology to breed apple. Herein, we identified four dwarfing apple germplasms in semi-arid area of Xinjiang, China. The internodal distance of these four germplasms were significantly shorter than non-dwarfing control. Their high melatonin (MT) contents are negatively associated with their malondialdehyde (MDA) levels and oxidative damage. In addition, among the detected hormones including auxin (IAA), gibberellin (GA), brassinolide (BR), zeatin-riboside (ZR), and abscisic acid (ABA), only ABA and ZR levels were in good correlation with the dwarfing phenotype. The qPCR results showed that the expression of melatonin synthetic enzyme genes MdASMT1 and MdSNAT5, ABA synthetic enzyme gene MdAAO3 and degradative gene MdCYP707A, ZR synthetic enzyme gene MdIPT5 all correlated well with the enhanced levels of MT, ABA and the reduced level of of ZR in the dwarfing germplasms. Furthermore, the significantly higher expression of ABA marker genes (MdRD22 and MdRD29) and the lower expression of ZR marker genes (MdRR1 and MdRR2) in all the four dwarf germplasms were consistent with the ABA and ZR levels. Considering the yearly long-term drought occurring in Xinjiang, China, it seems that dwarfing with high contents of MT and ABA may be a good strategy for these germplasms to survive against drought stress. This trait of dwarfing may also benefit apple production and breeding in this semi-arid area. creator: Tianci Yan creator: Chuang Mei creator: Handong Song creator: Dongqian Shan creator: Yanzhao Sun creator: Zehui Hu creator: Lin Wang creator: Tong Zhang creator: Jixun Wang creator: Jin Kong uri: https://doi.org/10.7717/peerj.13008 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yan et al. title: Dietary fatty acid patterns and risk of oesophageal squamous cell carcinoma link: https://peerj.com/articles/13036 last-modified: 2022-03-31 description: BackgroundTo characterize and examine the associations between dietary fatty acid intake patterns and the risk of oesophageal squamous cell carcinoma (ESCC).MethodsA total of 422 patients and 423 controls were recruited. Dietary fatty acids were entered into a factor analysis. Multivariable logistic regression and restricted cubic spline were used to evaluate the risk of ESCC specific for different dietary fatty acid patterns (FAPs). A forest plot was applied to show the association between FAPs and ESCC risk after stratification by lifestyle exposure factors (tobacco smoking, alcohol drinking, pickled food, fried food, hot food, hard food).ResultsThe factor analysis generated four major fatty acid patterns: a medium- and long-chain SFA (MLC-SFA) pattern; an even-chain unsaturated fatty acid (EC-UFA) pattern, a saturated fatty acid (SFA) pattern and an n-3 long-chain polyunsaturated fatty acid (n-3 LC-PUFA) pattern. In the multivariate-adjusted model, the odds ratios (ORs) with 95% confidence intervals (CIs) of ESCC were 2.07 (1.31, 3.26) and 0.53 (0.34, 0.81) for the highest versus the lowest tertiles of the EC-UFA pattern and n-3 LC-PUFA pattern, respectively. The MLC-SFA and SFA patterns were not associated with ESCC. An association between FAPs and ESCC risk after stratification by lifestyle exposure factors was also observed.ConclusionsOur study indicates that the EC-UFA pattern and n-3 LC-PUFA pattern intake are associated with ESCC, providing a potential dietary intervention for ESCC prevention. creator: Chanchan Hu creator: Zheng Lin creator: Zhiqiang Liu creator: Xuwei Tang creator: Jianyu Song creator: Jianbo Lin creator: Yuanmei Chen creator: Zhijian Hu uri: https://doi.org/10.7717/peerj.13036 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hu et al. title: Effectiveness of digital mental health interventions for university students: an umbrella review link: https://peerj.com/articles/13111 last-modified: 2022-03-31 description: BackgroundPoor mental health among university students remains a pressing public health issue. Over the past few years, digital health interventions have been developed and considered promising in increasing psychological wellbeing among university students. Therefore, this umbrella review aims to synthesize evidence on digital health interventions targeting university students and to evaluate their effectiveness.MethodsA systematic literature search was performed in April 2021 searching PubMed, Psychology and Behavioural Science Collection, Web of Science, ERIC, and Scopus for systematic reviews and meta-analyses on digital mental health interventions targeting university students. The review protocol was registered in the International Prospective Register of Systematic Reviews PROSPERO [CRD42021234773].ResultsThe initital literature search resulted in 806 records of which seven remained after duplicates were removed and evaluated against the inclusion criteria. Effectiveness was reported and categorized into the following six delivery types: (a) web-based, online/computer-delivered interventions (b) computer-based Cognitive Behavior Therapy (CBT), (c) mobile applications and short message service (d) virtual reality interventions (e) skills training (f) relaxation and exposure-based therapy. Results indicated web-based online/computer delivered-interventions were effective or at least partially effective at decressing depression, anxiety, stress and eating disorder symptoms. This was similar for skills-training interventions, CBT-based intervention and mobile applications. However, digital mental health interventions using virtual reality and relaxation, exposure-based therapy was inconclusive. Due to the variation in study settings and inconsistencies in reporting, effectiveness was greatly dependent on the delivery format, targeted mental health problem and targeted purpose group.ConclusionThe findings provide evidence for the beneficial effect of digital mental health interventions for university students. However, this review calls for a more systematic approach in testing and reporting the effectiveness of digital mental health interventions. creator: Sophia Harith creator: Insa Backhaus creator: Najihah Mohbin creator: Huyen Thi Ngo creator: Selina Khoo uri: https://doi.org/10.7717/peerj.13111 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Harith et al. title: Insight into the cryptic diversity and phylogeography of the peculiar fried egg jellyfish Phacellophora (Cnidaria, Scyphozoa, Ulmaridae) link: https://peerj.com/articles/13125 last-modified: 2022-03-31 description: The fried egg jellyfish Phacellophora camtschatica (senso lato) is a morphologically peculiar and conspicuous species occurring mostly in the cold waters of the North Pacific. It is less common in the cold waters of the NW Atlantic, and occasionally has been reported in the Mediterranean, Arctic, East and South Pacific, and E, SW and NE Atlantic. However, sightings of this scyphozoan jellyfish have intensified during the past two to three decades in Macaronesia, the Iberian Peninsula and the Mediterranean. These jellyfish are known to be voracious predators of other jellies, but also of other taxa, including fish of commercial interest. Therefore, Phacellophora aggregations may threaten local fisheries, aquaculture, and local biodiversity structuring. We report the first known occurrences of Phacellophora in the Azores Islands, which apparently become more frequent in recent years of the past decade. We confirm, through DNA barcoding of COI and 16S mitochondrial markers, the genetic identity of Phacellophora occurring in the Azores (NE Atlantic). We reveal, with COI sequence data, three (potentially four) cryptic species within the Phacellophora camtschatica complex. Two Phacellophora species co-occur in the North Pacific. In the North Atlantic (and possibly in the Mediterranean) one or two distinct species exist. Three nominal species of the genus that are currently synonymized, with type localities in the N Pacific, NW Atlantic, and the Mediterranean, need reassessment. The morphotypes previously defined for the four putative species names given for Phacellophora might be eventually differentiated by the number and disposition of the marginal lappets of umbrellae. This morphologic character has to be further inspected in vouchers of the four genetic lineages of Phacellophora, to decide between the description of new species, and the resurrection of junior synonyms through the designation of neotypes with DNA Barcodes, to validate the identity of the cryptic taxa detected. More haplotype sampling is necessary across the distribution of the genus to further investigate the genetic diversity and phylogeographic history of Phacellophora. The high genetic relatedness of Phacellophora from the cold NW Atlantic and the sub-tropical shores of the Azores, revealed by 16S and COI sequence data, suggests a recent invasion, in terms of geologic time, of the temperate waters of the NE Atlantic (and possibly of the Mediterranean). The medusivorous habits of Phacellophora, and especially its predation on the mauve stinger (Pelagia spp.) which frequently blooms in Macaronesia and Mediterranean waters, could relate to the recent reports of Phacellophora in the Azores, Madeira, Canary Islands, and the Mediterranean.More investment, including on scientific staff, is necessary to catalog, DNA barcode and monitor jellyfish dynamics more accurately worldwide. creator: Carlos J. Moura creator: Nikolai Ropa creator: Bruno Ivo Magalhães creator: João M. Gonçalves uri: https://doi.org/10.7717/peerj.13125 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Moura et al. title: Continuous mutation of SARS-CoV-2 during migration via three routes at the beginning of the pandemic link: https://peerj.com/articles/12681 last-modified: 2022-03-30 description: BackgroundIt remains unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection started, spread worldwide, and mutated to result in the present variants. This difficulty can be attributed to the limitations associated with the analytical methodology for presenting the differences among genomic sequences. In this study, we critically analysed the early data to explain the start and spread of the pandemic.MethodsObjective analyses of the RNA sequences of earlier variants of SARS-CoV-2 (up to September 1, 2020, available in DDBJ and GISAID) were performed using Principal Component Analysis (PCA). The results were compared with information on the collection dates and location. The PCA was also conducted for 12 variants of interest to the WHO as of September 2021, and compared with earlier data.ResultsThe pandemic began in Wuhan, China. This strain was suspected to be related to other reported animal viruses; however, they had a minimal similarity. The strain then spreads via three routes while accumulating mutations. Several viral subgroups were identified along the routes, each with a large number of patients reported, indicating high infectivity to humans. These routes were only confirmed by the early data analysis, because newer variants would have more mutations, and would be preferentially be examined by PCA if they were included. On the original axes found in the early variants, the newer variants revealed that they retained previously acquired mutations, which helped to reveal the viral ancestors of the newer variants. The rate of mutation was found to be comparable to that of the influenza H1N1 virus, which causes recurrent seasonal epidemics. Another threat imposed by SARS-CoV-2 is that if the pandemic cannot be contained, new variants may emerge annually, preventing herd immunity. creator: Tomokazu Konishi uri: https://doi.org/10.7717/peerj.12681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Konishi title: Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentex link: https://peerj.com/articles/12720 last-modified: 2022-03-30 description: Fast-twitch and slow-twitch muscles are the two principal skeletal muscle types in teleost with obvious differences in metabolic and contractile phenotypes. The molecular mechanisms that control and maintain the different muscle types remain unclear yet. Pseudocaranx dentex is a highly mobile active pelagic fish with distinctly differentiated fast-twitch and slow-twitch muscles. Meanwhile, P. dentex has become a potential target species for deep-sea aquaculture because of its considerable economic value. To elucidate the molecular characteristics in the two muscle types of P. dentex, we generated 122 million and 130 million clean reads from fast-twitch and slow-witch muscles using RNA-Seq, respectively. Comparative transcriptome analysis revealed that 2,862 genes were differentially expressed. According to GO and KEGG analysis, the differentially expressed genes (DEGs) were mainly enriched in energy metabolism and skeletal muscle structure related pathways. Difference in the expression levels of specific genes for glycolytic and lipolysis provided molecular evidence for the differences in energy metabolic pathway between fast-twitch and slow-twitch muscles of P. dentex. Numerous genes encoding key enzymes of mitochondrial oxidative phosphorylation pathway were significantly upregulated at the mRNA expression level suggested slow-twitch muscle had a higher oxidative phosphorylation to ensure more energy supply. Meanwhile, expression patterns of the main skeletal muscle developmental genes were characterized, and the expression signatures of Sox8, Myod1, Calpain-3, Myogenin, and five insulin-like growth factors indicated that more myogenic cells of fast-twitch muscle in the differentiating state. The analysis of important skeletal muscle structural genes showed that muscle type-specific expression of myosin, troponin and tropomyosin may lead to the phenotypic structure differentiation. RT-qPCR analysis of twelve DEGs showed a good correlation with the transcriptome data and confirmed the reliability of the results presented in the study. The large-scale transcriptomic data generated in this study provided an overall insight into the thorough gene expression profiles of skeletal muscle in a highly mobile active pelagic fish, which could be valuable for further studies on molecular mechanisms responsible for the diversity and function of skeletal muscle. creator: Huan Wang creator: Busu Li creator: Long Yang creator: Chen Jiang creator: Tao Zhang creator: Shufang Liu creator: Zhimeng Zhuang uri: https://doi.org/10.7717/peerj.12720 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Oviducal gland transcriptomics of Octopus maya through physiological stages and the negative effects of temperature on fertilization link: https://peerj.com/articles/12895 last-modified: 2022-03-30 description: BackgroundElevated temperatures reduce fertilization and egg-laying rates in the octopus species. However, the molecular mechanisms that control the onset of fertilization and egg-laying in the octopus’ oviducal gland are still unclear; and the effect of temperature on the expression of key reproductive genes is unknown. This study aims to better understand the molecular bases of octopus fertilization and egg-laying, and how they are affected by elevated temperatures.MethodRNA-seq of oviducal glands was performed for samples before, during, and after fertilization and their transcriptomic profiles were compared. Also, at the fertilization stage, the optimal and thermal-stress conditions were contrasted. Expression levels of key reproductive genes were validated via RT-qPCR.ResultsIn mated females before egg-laying, genes required for the synthesis of spermine, spermidine, which may prevent premature fertilization, and the myomodulin neuropeptide were upregulated. Among the genes with higher expression at the fertilization stage, we found those encoding the receptors of serotonin, dopamine, and progesterone; genes involved in the assembly and motility of the sperm flagellum; genes that participate in the interaction between male and female gametes; and genes associated with the synthesis of eggshell mucoproteins. At temperatures above the optimal range for reproduction, mated females reduced the fertilization rate. This response coincided with the upregulation of myomodulin and APGW-amide neuropeptides. Also, genes associated with fertilization like LGALS3, VWC2, and Pcsk1 were downregulated at elevated temperatures. Similarly, in senescent females, genes involved in fertilization were downregulated but those involved in the metabolism of steroid hormones like SRD5A1 were highly expressed. creator: Oscar E. Juárez creator: Lousiana Arreola-Meraz creator: Edna Sánchez-Castrejón creator: Omar Hernando Avila-Poveda creator: Laura L. López-Galindo creator: Carlos Rosas creator: Clara E. Galindo-Sánchez uri: https://doi.org/10.7717/peerj.12895 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Juárez et al.