Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp.
The MYB-CC family is a subtype within the MYB superfamily. This family contains an MYB domain and a predicted coiled-coil (CC) domain. Several MYB-CC transcription factors are involved in the plant’s adaptability to low phosphate (Pi) stress. We identified 30, 34, and 55 MYB-CC genes in Brassica rapa, Brassica oleracea, and Brassica napus, respectively. The MYB-CC genes were divided into nine groups based on phylogenetic analysis. The analysis of the chromosome distribution and gene structure revealed that most MYB-CC genes retained the same relative position on the chromosomes and had similar gene structures during allotetraploidy. Evolutionary analysis showed that the ancestral whole-genome triplication (WGT) and the recent allopolyploidy are critical for the expansion of the MYB-CC gene family. The expression patterns of MYB-CC genes were found to be diverse in different tissues of the three Brassica species. Furthermore, the gene expression analysis under low Pi stress revealed that MYB-CC genes may be related to low Pi stress responses. These results may increase our understanding of MYB-CC gene family diversification and provide the basis for further analysis of the specific functions of MYB-CC genes in Brassica species.
Gu et al. (2022) Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp.. PeerJ 10:e12882 https://doi.org/10.7717/peerj.12882
Comparative transcriptome analysis of miRNA in hydronephrosis male children caused by ureteropelvic junction obstruction with or without renal functional injury
MicroRNAs (miRNAs or miRs) are non-coding RNAs that contribute to pathological processes of various kidney diseases. Renal function injury represents a final common outcome of congenital obstructive nephropathy and has attracted a great deal of attention. However the molecular mechanisms are still not fully established. In this study, we compared transcriptome sequencing data of miRNAs of renal tissues from congenital hydronephrosis children with or without renal functional injury, in order to better understand whether microRNAs could play important roles in renal functional injury after ureteropelvic junction obstruction. A total of 22 microRNAs with significant changes in their expression were identified. Five microRNAs were up-regulated and 17 microRNAs were down-regulated in the renal tissues of the hydronephrosis patients with renal function injury compared with those without renal function injury. MicroRNA target genes were predicted by three major online miRNA target prediction algorithms, and all these mRNAs were used to perform the gene ontology analysis and Kyoto Encyclopedia of Gene and Genomes pathway analysis. Then, twelve candidate human and rat homologous miRNAs were selected for validation using RT-qPCR in vitro and in vivo; only miR-187-3p had a trend identical to that detected by the sequencing results among the human tissues, in vivo and in vitro experimental models. In addition, we found that the change of miR-187-3p in vivo was consistent with results in vitro models and showed a decrease trend in time dependence. These results provided a detailed catalog of candidate miRNAs to investigate their regulatory role in renal injury of congenital hydronephrosis, indicating that they may serve as candidate biomarkers or therapeutic targets in the future.
Liu et al. (2022) Comparative transcriptome analysis of miRNA in hydronephrosis male children caused by ureteropelvic junction obstruction with or without renal functional injury. PeerJ 10:e12962 https://doi.org/10.7717/peerj.12962
Applications and limitations of current markerless motion capture methods for clinical gait biomechanics
Background Markerless motion capture has the potential to perform movement analysis with reduced data collection and processing time compared to marker-based methods. This technology is now starting to be applied for clinical and rehabilitation applications and therefore it is crucial that users of these systems understand both their potential and limitations. This literature review aims to provide a comprehensive overview of the current state of markerless motion capture for both single camera and multi-camera systems. Additionally, this review explores how practical applications of markerless technology are being used in clinical and rehabilitation settings, and examines the future challenges and directions markerless research must explore to facilitate full integration of this technology within clinical biomechanics. Methodology A scoping review is needed to examine this emerging broad body of literature and determine where gaps in knowledge exist, this is key to developing motion capture methods that are cost effective and practically relevant to clinicians, coaches and researchers around the world. Literature searches were performed to examine studies that report accuracy of markerless motion capture methods, explore current practical applications of markerless motion capture methods in clinical biomechanics and identify gaps in our knowledge that are relevant to future developments in this area. Results Markerless methods increase motion capture data versatility, enabling datasets to be re-analyzed using updated pose estimation algorithms and may even provide clinicians with the capability to collect data while patients are wearing normal clothing. While markerless temporospatial measures generally appear to be equivalent to marker-based motion capture, joint center locations and joint angles are not yet sufficiently accurate for clinical applications. Pose estimation algorithms are approaching similar error rates of marker-based motion capture, however, without comparison to a gold standard, such as bi-planar videoradiography, the true accuracy of markerless systems remains unknown. Conclusions Current open-source pose estimation algorithms were never designed for biomechanical applications, therefore, datasets on which they have been trained are inconsistently and inaccurately labelled. Improvements to labelling of open-source training data, as well as assessment of markerless accuracy against gold standard methods will be vital next steps in the development of this technology.
Wade et al. (2022) Applications and limitations of current markerless motion capture methods for clinical gait biomechanics. PeerJ 10:e12995 https://doi.org/10.7717/peerj.12995
Profiles of anemia in adolescent students with sports club membership in an outpatient clinic setting: a retrospective study
Background Anemia is a common health issue among adolescents. Anemic conditions could affect physical performance; however, the actual profiles of anemia in adolescent students in sports clubs have not been well documented. Methods We conducted a retrospective chart review of individuals aged 13–22 years who belonged to sports clubs in schools and visited an outpatient clinic between August 1, 2016, and August 31, 2020. The medical and laboratory records, including serum levels of ferritin, folate, vitamin B12, and creatinine kinase at their first visit were assessed. Results A total of 485 individuals (231 male (48%) and 254 female (52%) patients) were eligible for the study. The most common club activity was track and field (n = 171 (35%)). The overall prevalence of the World Health Organization-defined anemia was 16.5% (95% CI [13.1–20.4]; 9.0% [5.4–13.8] and 23.1% [17.8–29.2] in males and females, respectively) after excluding pre-treated individuals. Hypoferritinemia and elevation of serum creatinine kinase levels were identified as independent contributors to anemia in both sexes (odds ratios: 13.2 (95% CI [4.2–41.1]), p < 0.001 and 14.7 (95% CI [1.8–118.4]), p = 0.012, respectively for males; odds ratios: 6.6 (95% CI [1.3–13.9]), p < 0.001 and 2.7 (95% CI [1.4–5.5]), p = 0.004, respectively for females). Discussion Anemia is prevalent in both male and female adolescent students in sports clubs. Iron deficiency and excessive training indicated by elevated creatinine kinase levels may contribute to the risk of anemia. Physicians should assess the amount of exercise, and not merely iron storage, in clinical practice.
Yamamoto et al. (2022) Profiles of anemia in adolescent students with sports club membership in an outpatient clinic setting: a retrospective study. PeerJ 10:e13004 https://doi.org/10.7717/peerj.13004
Effects of long-term nitrogen & phosphorus fertilization on soil microbial, bacterial and fungi respiration and their temperature sensitivity on the Qinghai-Tibet Plateau
Background The microbial decomposition of soil organic carbon (SOC) is a major source of carbon loss, especially in ecologically fragile regions (e.g., the Tibetan Plateau), which are also affected by global warming and anthropogenic activities (e.g., fertilization). The inherent differences between bacteria and fungi indicate that they are likely to play distinct roles in the above processes. However, there still have been no reports on that, which is restricting our knowledge about the mechanisms underlying SOC decomposition. Methods A long-term nitrogen (N) and phosphorus (P) addition field experiment was conducted to assess their effects on soil microbial, fungal, and bacterial respiration (RM, RF, and RB, respectively) and temperature sensitivity (Q10; at 15 °C, 25 °C, and 35 °C) using cycloheximide and streptomycin to inhibit the growth of fungi and bacteria. Results We found that N suppressed RM and RF at all temperatures, but RB was only suppressed at 15 °C, regardless of the addition of P. The addition of N significantly decreased the ratio of RF/RM at 35 °C, and the combined NP treatment increased the Q10 of RB but not that of RF. Results of the redundancy analysis showed that variations in soil respiration were linked with NO3−-N formation, while the variations in Q10 were linked with SOC complexity. Long-term N addition suppressed RM by the formation of NO3−-N, and this was mediated by fungi rather than bacteria. The contribution of fungi toward SOC decomposition was weakened by N addition and increasing temperatures. Combined NP addition increased the Q10 of RB due to increased SOC complexity. The present study emphasizes the importance of fungi and the soil environment in SOC decomposition. It also highlights that the role of bacteria and SOC quality will be important in the future due to global warming and increasing N deposition.
Chen et al. (2022) Effects of long-term nitrogen & phosphorus fertilization on soil microbial, bacterial and fungi respiration and their temperature sensitivity on the Qinghai-Tibet Plateau. PeerJ 10:e12851 https://doi.org/10.7717/peerj.12851
Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives
The need for comprehensive and effective coral restoration projects, as part of a broader conservation management strategy, is accelerating in the face of coral reef ecosystem decline. This study aims to expand the currently limited knowledge base for restoration techniques in the Maldives by testing the performance of mid-water rope nurseries in a lagoon and a reef habitat. We examined whether different coral farming habitats impacted fragment survival, health and growth of two coral genera and how the occurrence of mutualistic fauna, predation and disease influenced coral rearing success. Two nurseries were stocked with a total of 448 Pocillopora verrucosa and 96 Acropora spp. fragments, divided into different groups (four Pocillopora groups: lagoon nursery at 5 m; reef nursery at 5, 10 and 15 m; two Acropora groups: lagoon nursery at 5 m and reef nursery at 5 m). Eight fragment replicates from the same donor colony (Pocillopora genets: N = 14, Acropora genets N = 6) were used in each group and monitored for one year. Our results show that fragment survival was high in both farming habitats (>90%), with P. verrucosa surviving significantly better in the lagoon and Acropora spp. surviving and growing significantly faster in the reef nursery. P. verrucosa growth rates were similar between reef and lagoon habitat. Different rearing depths in the reef nursery had no impact on the survival of P. verrucosa but coral growth decreased considerably with depth, reducing fragments’ ecological volume augmentation and growth rates by almost half from 5 to 15 m depth. Further, higher fish predation rates on fragments were recorded on the reef, which did not impact overall nursery performance. Mutualistic fauna, which correlated positively with fragment survival, was more frequently observed in the lagoon nursery. The occurrence of disease was noted in both habitats, even though implications for fragment health were more severe in the lagoon. Overall, our study demonstrates that lagoon and reef nurseries are suitable for rearing large numbers of coral fragments for transplantation. Nevertheless, we recommend considering the specific environmental conditions of the farming habitat, in particular water quality and year-round accessibility, in each case and to adjust the coral farming strategy accordingly. We hope that this novel research encourages the increased application of mid-water rope nurseries for ‘coral gardening’ to advance coral reef recovery and climate resilience in the Maldives.
Dehnert et al. (2022) Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives. PeerJ 10:e12874 https://doi.org/10.7717/peerj.12874
Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes
Background Wind, an important abiotic stress factor, affects forests in coastal areas, causes tree damage and timber loss. Methods Two genotypes of Eucalyptus camaldulensis-strong wind-resistant CA5 and weak wind-resistant C037 were used for RNA-seq analysis to screen for candidate wind-resistance genes and transcription factors (TFs) by comparing the transcriptome analysis of the two varieties in response to wind stress. Results It showed that 7061 differentially expressed unigenes could be annotated including 4,110 up-regulated unigenes and 2,951 down-regulated unigenes. Gene Ontology (GO) analysis revealed that six cellulose pathways were involved in response to wind stress. The unigenes in phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis pathways were found to be differentially expressed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Moreover, 37 differentially expressed genes were functionally annotated to be involved in the secondary metabolism of phenylalanine (ko00940). Seventy-eight TFs related to the regulating cellulose and lignin synthesis were expressed differently from the various treatments. The expressions of C3H, POX, MYB, NAC, Gene008307, and Gene011799 were significantly upregulated in CA5. Overall, the main response of Eucalyptus to wind stress was associated with cell wall biosynthesis; key genes of cellulose and lignin biosynthesis pathways and related TFs were involved in the tree response to wind stress.
Shang et al. (2022) Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes. PeerJ 10:e12954 https://doi.org/10.7717/peerj.12954
AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis
Ascorbic acid (AsA) is an important nutrient in celery, the conversion of D-mannose-1-P to GDP-D-mannose catalyzed by GDP-D-mannose pyrophosphorylase (GMPase) represents the first committed step in the biosynthesis of AsA. To clarify the function of the AgGMP gene of celery, the AgGMP gene was cloned from celery cv. ‘Jinnan Shiqin’ . It contains an open reading frame (ORF) with the length of 1,086 bp, encoding 361 amino acids. AgGMP protein was highly conserved among different plant species. Phylogenetic analysis demonstrated that the GMP proteins from celery and carrot belonged to the same branch. AgGMP protein was mainly composed of three α-helixes and certain random coils. No signal peptide was found in the AgGMP protein. The subcellular localization indicated that the AgGMP protein was located in the cytoplasm. The relative expression levels of AgGMP in ‘Jinnan Shiqin’ were significantly up-regulated at 2 h and 4 h under drought stress treatments. AsA contents in transgenic Arabidopsis lines hosting AgGMP gene were higher than that in wild type plants, and the root lengths were also longer in the MS medium containing 300 mM mannitol. The present study provides useful evidence for the functional involvement of AgGMP in regulating AsA accumulation and response to drought stress in celery.
Liu et al. (2022) AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis. PeerJ 10:e12976 https://doi.org/10.7717/peerj.12976
Biomarkers of non-communicable chronic disease: an update on contemporary methods
Chronic diseases constitute a major global burden with significant impact on health systems, economies, and quality of life. Chronic diseases include a broad range of diseases that can be communicable or non-communicable. Chronic diseases are often associated with modifications of normal physiological levels of various analytes that are routinely measured in serum and other body fluids, as well as pathological findings, such as chronic inflammation, oxidative stress, and mitochondrial dysfunction. Identification of at-risk populations, early diagnosis, and prediction of prognosis play a major role in preventing or reducing the burden of chronic diseases. Biomarkers are tools that are used by health professionals to aid in the identification and management of chronic diseases. Biomarkers can be diagnostic, predictive, or prognostic. Several individual or grouped biomarkers have been used successfully in the diagnosis and prediction of certain chronic diseases, however, it is generally accepted that a more sophisticated approach to link and interpret various biomarkers involved in chronic disease is necessary to improve our current procedures. In order to ensure a comprehensive and unbiased coverage of the literature, first a primary frame of the manuscript (title, headings and subheadings) was drafted by the authors working on this paper. Second, based on the components drafted in the preliminary skeleton a comprehensive search of the literature was performed using the PubMed and Google Scholar search engines. Multiple keywords related to the topic were used. Out of screened papers, only 190 papers, which are the most relevant, and recent articles were selected to cover the topic in relation to etiological mechanisms of different chronic diseases, the most recently used biomarkers of chronic diseases and finally the advances in the applications of multivariate biomarkers of chronic diseases as statistical and clinically applied tool for the early diagnosis of chronic diseases was discussed. Recently, multivariate biomarkers analysis approach has been employed with promising prospect. A brief discussion of the multivariate approach for the early diagnosis of the most common chronic diseases was highlighted in this review. The use of diagnostic algorithms might show the way for novel criteria and enhanced diagnostic effectiveness inpatients with one or numerous non-communicable chronic diseases. The search for new relevant biomarkers for the better diagnosis of patients with non-communicable chronic diseases according to the risk of progression, sickness, and fatality is ongoing. It is important to determine whether the newly identified biomarkers are purely associations or real biomarkers of underlying pathophysiological processes. Use of multivariate analysis could be of great importance in this regard.
Al-hadlaq et al. (2022) Biomarkers of non-communicable chronic disease: an update on contemporary methods. PeerJ 10:e12977 https://doi.org/10.7717/peerj.12977
Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard
High levels of within-individual variation (WIV) in reiterative components in plants such as leaves, flowers, and fruits have been shown to increase individual fitness by multiple mechanisms including mediating interactions with natural enemies. This relationship between WIV and fitness has been studied almost exclusively in plant systems. While animals do not exhibit conspicuous reiterative components, they have traits that can vary at the individual level such as erythrocyte size. It is currently unknown if WIV in animals can influence individual fitness by mediating the outcome of interactions with natural enemies as it has been shown in plants. To address this issue, we tested for a relationship between WIV in erythrocyte size, hemoparasite infection status, and body condition (a proxy for fitness) in a Caribbean anole lizard. We quantified the coefficient of variation of adult erythrocytes size in $n = 95$ infected and $n = 107$ non-infected lizards. We found higher degrees of erythrocyte size variation in infected lizards than in non-infected individuals. However, we found no significant relationship between infection status or erythrocyte size variation, and lizard body condition. These results suggest that higher WIV in erythrocyte size in infected lizards is not necessarily adaptive but likely a consequence of the host response to infection. Many hemoparasites destroy their host cells as part of their life cycle. To compensate, the host lizard may respond by increasing production of erythrocytes resulting in higher WIV. Our results emphasize the need to better understand the role of within-animal variation as a neglected driver or consequence of ecological and evolutionary interactions.
Cruz et al. (2022) Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard. PeerJ 10:e12761 https://doi.org/10.7717/peerj.12761