TMT labeled comparative proteomic analysis reveals spleen active immune responses during Clostridium perfringens type C infected piglet diarrhea
Background Clostridium perfringens (C. perfringens) type C is the principal pathogenic clostridia of swine, frequently causing hemorrhagic diarrhea, even necrotic enteritis in piglets, leading to severe economic loss for swine industr ies worldwide. However, there are no specific and effective prevention measures. Therefore, clarifying the molecular mechanisms of hosts against pathogenesis infection is very important to reduce the incidence of C. perfringens type C infected piglet diarrhea disease. Methods We performed an TMT labeling-based quantitative spleen proteomic analysis of the control group (SC), tolerance group (SR) and susceptible group (SS) to identify the differentially expressed proteins (DEPs), and screened potential molecular markers of piglet spleen tissues in response to C. perfringens type C infection. Results In this study, a total of 115, 176 and 83 DEPs were identified in SR vs SC, SS vs SC, and SR vs SC, respectively, which may play the important regulatory roles in the process of piglet spleens in response toC. perfringens type C-infected diarrhea diseases. GO enrichment analysis revealed that the DEPs were mostly significantly enriched in acute inflammatory response, defense response, antimicrobial response, transporter activity, cellular metabolic process and so on, and KEGG pathway enrichment analysis showed that the significantly enriched immune related pathways of the PPAR signaling pathway, IL-17 signaling pathway, antigen processing and presentation, which hints at the immune defense process of piglet spleen against C. perfringens infection. This study helps to elucidate the protein expressional pattern of piglet spleen against C. perfringens type C-infected diarrhea disease, which can contribute to the prevention and control for pig diarrhea disease and the further development of diarrhea resistant pig breeding.
Wang et al. (2022) TMT labeled comparative proteomic analysis reveals spleen active immune responses during Clostridium perfringens type C infected piglet diarrhea. PeerJ 10:e13006 https://doi.org/10.7717/peerj.13006
Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications
Biomedical knowledge is represented in structured databases and published in biomedical literature, and different computational approaches have been developed to exploit each type of information in predictive models. However, the information in structured databases and literature is often complementary. We developed a machine learning method that combines information from literature and databases to predict drug targets and indications. To effectively utilize information in published literature, we integrate knowledge graphs and published literature using named entity recognition and normalization before applying a machine learning model that utilizes the combination of graph and literature. We then use supervised machine learning to show the effects of combining features from biomedical knowledge and published literature on the prediction of drug targets and drug indications. We demonstrate that our approach using datasets for drug-target interactions and drug indications is scalable to large graphs and can be used to improve the ranking of targets and indications by exploiting features from either structure or unstructured information alone.
Alshahrani et al. (2022) Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications. PeerJ 10:e13061 https://doi.org/10.7717/peerj.13061
Diagnostics of tissue involved injury occurrence of top-level judokas during the competition: suggestion for prevention
Background Judo, as a high-intensity contact sport, may lead to the occurrence of injuries, especially in competitions. This work aims to assess the likelihood of soft and hard tissue injuries in top-level judokas during competition with defining factors that determine the probability of injury occurrence. Methods The injuries that occurred in 123 official international competitions from 2005–2019 were recorded by the European Judo Union (EJU) Medical Commission as a survey that was a part of the EJU Injury Registration form with internal consistency shown by a Crombach Alpha of 0.69. This survey data identified factors such as: sex, anatomical localisation of injury, type of injury, tissue involved and mechanisms of the injury. A total of 650 tissue injuries were reported correctly in terms of tissue injury definition. Results The most frequent soft tissue injury (STI) reported was a ligament STI (48.15%), closely followed by skin STI (12.15%) and muscles STI (11.38%). In turn, the most frequent hard tissue injury occurred in bones (8.56%). The highest rates of injuries occurred during the fight in the standing position (78%). Injuries in the standing position mainly occurred while executing a throw (25.85%) and followed by the attempt to throw, i.e., the action of reaching the throwing position (22.30%), grip fighting (15.07%), and during falls (14.77%). Opposite to this, fight in groundwork reached only 18.30% soft and hard tissue injuries combined. The ongoing registration of injuries during judo combat and training and the early diagnosis of risk factors for injuries are the basis for the development of effective strategies for injury prevention and further treatment.
Blach et al. (2022) Diagnostics of tissue involved injury occurrence of top-level judokas during the competition: suggestion for prevention. PeerJ 10:e13074 https://doi.org/10.7717/peerj.13074
Biochemical composition and function of subalpine shrubland and meadow soil microbiomes in the Qilian Mountains, Qinghai–Tibetan plateau, China
Microorganisms participate in the soil biogeochemical cycle. Therefore, investigating variations in microbial biomass, composition, and functions can provide a reference for improving soil ecological quality due to the sensitivity of microorganisms to vegetation coverage changes. However, the differences in soil microorganisms between shrubland and meadow have not been investigated in ecologically vulnerable subalpine areas. This study aimed to investigate the biochemical composition and functions of the soil microbial community under two shrublands and a meadow at high altitudes (3,400–3,550 m). Three sites under two shrublands, Rhododendron thymifolium (RHO) and Potentilla fruticosa (POT), and one meadow dominated by Kobresia myosuroides (MEA), were selected on the southern slope of the Qilian Mountains on the northeastern edge of the Qinghai–Tibetan Plateau, China. Soil physicochemical properties, the microbial community composition expressed by the phospholipid fatty acid (PLFA) biomarker, and enzyme activities were analyzed as well as their relationships. The results showed that water holding capacity and the soil carbon, nitrogen, and potassium content in RHO and POT were higher than those in the MEA. Moreover, the soil active carbon, dissolved organic carbon, total nitrogen, and dissolved total nitrogen content in RHO were higher than those in POT. The abundance of total PLFAs, bacteria, and fungi beneath the shrublands was considerably higher than that in the MEA. The PLFA abundance in RHO was significantly higher than that in POT. The fungal-to-bacterial ratio of RHO and POT was significantly higher than that in the MEA. The activities of β-glucosidase, cellobiohydrolase, and leucine aminopeptidase were the highest in RHO among the three vegetation types, followed by POT and MEA. The redundancy analysis indicated that the biochemical composition of the soil microorganisms and enzyme activities were driven by total nitrogen, dissolved organic carbon, water holding capacity, and soil organic carbon. Therefore, shrublands, which have higher biomass, can improve soil moisture status, increase soil carbon and nitrogen content (especially active carbon and active nitrogen), and further increase the abundance of total PLFAs, bacteria, and fungi. The increase of microbial biomass indirectly enhances the activity of relevant soil enzymes. The variations in PLFA abundance and enzyme activities can be attributed to shrub species, especially evergreen shrubs, which create more favorable conditions for soil microorganisms. This study provides a theoretical basis for investigating the soil biogeochemical cycle and a scientific basis for soil management and vegetation restoration in the subalpine regions.
Fan et al. (2022) Biochemical composition and function of subalpine shrubland and meadow soil microbiomes in the Qilian Mountains, Qinghai–Tibetan plateau, China. PeerJ 10:e13188 https://doi.org/10.7717/peerj.13188
Comparison of changes in fecal microbiota of calves with and without dam
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.
Li et al. (2022) Comparison of changes in fecal microbiota of calves with and without dam. PeerJ 10:e12826 https://doi.org/10.7717/peerj.12826
Comparison of surface wind speed and wind speed profiles in the Taklimakan Desert
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.
Environmental Contamination and Remediation
Liu et al. (2022) Comparison of surface wind speed and wind speed profiles in the Taklimakan Desert. PeerJ 10:e13001 https://doi.org/10.7717/peerj.13001
A spotlight on non-host resistance to plant viruses
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.
Rai et al. (2022) A spotlight on non-host resistance to plant viruses. PeerJ 10:e12996 https://doi.org/10.7717/peerj.12996
Potential roles of melatonin and ABA on apple dwarfing in semi-arid area of Xinjiang China
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.
Yan et al. (2022) Potential roles of melatonin and ABA on apple dwarfing in semi-arid area of Xinjiang China. PeerJ 10:e13008 https://doi.org/10.7717/peerj.13008
Dietary fatty acid patterns and risk of oesophageal squamous cell carcinoma
Background To characterize and examine the associations between dietary fatty acid intake patterns and the risk of oesophageal squamous cell carcinoma (ESCC). Methods A 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). Results The 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. Conclusions Our 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.
Hu et al. (2022) Dietary fatty acid patterns and risk of oesophageal squamous cell carcinoma. PeerJ 10:e13036 https://doi.org/10.7717/peerj.13036
Effectiveness of digital mental health interventions for university students: an umbrella review
Background Poor 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. Methods A 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]. Results The 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. Conclusion The 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.
Harith et al. (2022) Effectiveness of digital mental health interventions for university students: an umbrella review. PeerJ 10:e13111 https://doi.org/10.7717/peerj.13111