Effect of ZnO and CuO nanoparticles on the growth, nutrient absorption, and potential health risk of the seasonal vegetable Medicago polymorpha L.
Background Medicago polymorpha L., a seasonal vegetable, is commonly grown in China. The increasing use of nanoparticles (NPs) such as ZnO and CuO NPs in agriculture has raised concerns about their potential risks for plant growth and for human consumption. There is a lack of research on the effects of ZnO and CuO NPs on agronomic performance of Medicago polymorpha L. and their potential risks for human health. Methods In this study, different treatment concentrations of ZnO NPs (25, 50, 100, and 200 mg kg−1) and CuO NPs (10, 25, 50, and 100 mg kg−1) were used to determine their effects on the growth and nutrient absorption of Medicago polymorpha L., as well as their potential risk for human health. Results The results showed that ZnO and CuO NPs increased the fresh weight of Medicago polymorpha L. by 5.8–11.8 and 3.7–8.1%, respectively. The best performance for ZnO NPs occurred between 25–50 mg kg−1 and the best performance for CuO NPs occurred between 10–25 mg kg−1. Compared with the control, ZnO and CuO NPs improved the macronutrients phosphorus (P), potassium (K), magnesium (Mg), and calcium (Ca). The following micronutrients were also improved: iron (Fe), nickel (Ni), copper (Cu), zinc (Zn), and manganese (Mn), with the exception of nitrogen (N) accumulation. Low treatment concentrations exhibited more efficient nutrient uptake than high treatment concentrations. A comprehensive analysis showed that the optimum concentrations were 25 mg kg−1 for ZnO NPs and 10 mg kg−1 for CuO NPs. The potential non-carcinogenic health risk of Medicago polymorpha L. treated with ZnO and CuO NPs was analyzed according to the estimated daily intake (EDI), the hazard quotient (HQ), and the cumulative hazard quotient (CHQ). Compared with the oral reference dose, the EDI under different ZnO and CuO NPs treatments was lower. The HQ and CHQ under different ZnO and CuO NPs treatments were far below 1. This indicated that Medicago polymorpha L. treated with ZnO and CuO NPs did not pose any non-carcinogenic health risk to the human body. Therefore, ZnO and CuO NPs were considered as a safe nano fertilizer for Medicago polymorpha L. production according to growth analysis and a human health risk assessment.
Ji et al. (2022) Effect of ZnO and CuO nanoparticles on the growth, nutrient absorption, and potential health risk of the seasonal vegetable Medicago polymorpha L.. PeerJ 10:e14038 https://doi.org/10.7717/peerj.14038
Physiological and biochemical responses of hybrid maize (Zea mays L.) varieties grown under heat stress conditions
Maize (Zea mays L.) is the second most commonly produced and consumed crop after wheat globally and is adversely affected by high heat, which is a significant abiotic stress factor. This study was carried out to determine the physiological and biochemical responses of hybrid corn varieties under heat stress (‘HS’) compared to control (‘C’) conditions during the 2020 and 2021 growing seasons. The experiment was conducted under natural conditions in the Southeastern region of Turkey, where the most intense temperatures are experienced. This experiment used split plots in randomized blocks with three replications, with ‘HS’ and ‘C’ growing conditions applied to the main plots and the different hybrid corn varieties (FAO 650) planted on the sub plots. Mean values of days to 50% tasseling (DT, day), grain yield (GY, kg ha−1), leaf water potential (LWP, %), chlorophyll-a (Chl-a, mg g−1), cell membrane damage (CMD, %), and total phenol content (TPC, μg g−1) were significantly different between years, growing conditions, and hybrid corn varieties. Changes in the climate played a significant role in the differences between the years and growing conditions (GC), while the genetic characteristics of the different corn varieties explained the differences in outcomes between them. The values of DT, GY, LWP, Chl-a, CMD, and TPC ranged from 49.06–53.15 days, 9,173.0–10,807.2 kg ha−1, 78.62–83.57%, 6.47–8.62 mg g−1, 9.61–13.54%, and 232.36–247.01 μg g−1, respectively. Significant correlations were recorded between all the parameters. Positive correlations were observed between all the variables except for CMD. The increased damage to cell membranes under ‘HS’ caused a decrease in the other measured variables, especially GY. In contrast, the GY increased with decreased CMD. CMD was important in determining the stress and tolerance level of corn varieties under ‘HS’ conditions. The GY and other physiological parameters of ADA 17.4 and SYM-307 candidate corn varieties surpassed the control hybrid corn cultivars. The results revealed that the ADA 17.4 and SYM-307 cultivars might have ‘HS’-tolerate genes.
Tas (2022) Physiological and biochemical responses of hybrid maize (Zea mays L.) varieties grown under heat stress conditions. PeerJ 10:e14141 https://doi.org/10.7717/peerj.14141
High metabolic load distance in professional soccer according to competitive level and playing positions
Background High metabolic load distance provides global information about the soccer players’ total high-intensity activities. Thus, this study aimed to examine the Spanish professional soccer players’ high metabolic load distance profile, comparing competitive level and playing positions. Methods A total of 18,131 individual match observations were collected from outfield players competing during the 2018/2019 and 2019/20 seasons in the First and Second Spanish Professional Soccer Leagues (LaLiga™). High Metabolic Load Distance (HMLD; distance covered with a power consumption above 25.5 W·kg−1 and accelerations or decelerations (e.g., accelerating from 2 to 4 m·s−2 for 1 s) were included), and HMLD per minute (HMLDmin) were analyzed by the ChryonHego® video-tracking system. Players were classified according to their playing position as follows: Central Backs (CB), Full Backs (FB), Center Midfields (CM), Wide Midfields (WM), and Forwards (FW). Results No differences between competitive levels were found in any variable when all players were analyzed conjointly except for HMLDmin overall and during the second half. However, when playing positions were considered, differences between competitive levels were observed in all positions, mainly in HMLD and HMLD during the first-half variables. In addition, several differences between playing positions were observed, with CB presenting the lowest values in all variables compared to their counterparts in both competitive levels, whereas CM in First Division and WM in Second Division showed the highest values in the HMLD variables. Discussion The findings are of interest to analyze the HMLD in professional soccer players, enabling the adaptation and individualization of training in this population according to the competitive level and specific playing position of each player.
García-Calvo et al. (2022) High metabolic load distance in professional soccer according to competitive level and playing positions. PeerJ 10:e13318 https://doi.org/10.7717/peerj.13318
Context dependent prediction in DNA sequence using neural networks
One way to better understand the structure in DNA is by learning to predict the sequence. Here, we trained a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model was a neural network that obtained an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, the neural network performed significantly better than any of the alternative models by a large margin. We report on where the accuracy was obtained, first observing that the performance appeared to be uniform over the chromosomes. The models performed best in repetitive sequences, as expected, although their performance far from random in the more difficult coding sections, the proportions being ~70:40%. We further explored the sources of the accuracy, Fourier transforming the predictions revealed weak but clear periodic signals. In the human genome the characteristic periods hinted at connections to nucleosome positioning. We found similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before. On other large genomes similarly high accuracy was found, while lower predictive accuracy was observed on smaller genomes. Only in the mouse genome did we see periodic signals in the same range as in the human genome, though weaker and of a different type. This indicates that the sources of these signals are other or more than nucleosome arrangement. Interestingly, applying a model trained on the mouse genome to the human genome resulted in a performance far below that of the human model, except in the difficult coding regions. Despite the clear outcomes of the likelihood-ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures.
Grønbæk et al. (2022) Context dependent prediction in DNA sequence using neural networks. PeerJ 10:e13666 https://doi.org/10.7717/peerj.13666
Bioinformatics prediction and experimental verification of key biomarkers for diabetic kidney disease based on transcriptome sequencing in mice
Background Diabetic kidney disease (DKD) is the leading cause of death in people with type 2 diabetes mellitus (T2DM). The main objective of this study is to find the potential biomarkers for DKD. Materials and Methods Two datasets (GSE86300 and GSE184836) retrieved from Gene Expression Omnibus (GEO) database were used, combined with our RNA sequencing (RNA-seq) results of DKD mice (C57 BLKS-32w db/db) and non-diabetic (db/m) mice for further analysis. After processing the expression matrix of the three sets of data using R software “Limma”, differential expression analysis was performed. The significantly differentially expressed genes (DEGs) (—logFC— > 1, p-value < 0.05) were visualized by heatmaps and volcano plots respectively. Next, the co-expression genes expressed in the three groups of DEGs were obtained by constructing a Venn diagram. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were further analyzed the related functions and enrichment pathways of these co-expression genes. Then, qRT-PCR was used to verify the expression levels of co-expression genes in the kidney of DKD and control mice. Finally, protein-protein interaction network (PPI), GO, KEGG analysis and Pearson correlation test were performed on the experimentally validated genes, in order to clarify the possible mechanism of them in DKD. Results Our RNA-seq results identified a total of 125 DEGs, including 59 up-regulated and 66 down-regulated DEGs. At the same time, 183 up-regulated and 153 down-regulated DEGs were obtained in GEO database GSE86300, and 76 up-regulated and 117 down-regulated DEGs were obtained in GSE184836. Venn diagram showed that 13 co-expression DEGs among the three groups of DEGs. GO analysis showed that biological processes (BP) were mainly enriched inresponse to stilbenoid, response to fatty acid, response to nutrient, positive regulation of macrophage derived foam cell differentiation, triglyceride metabolic process. KEGG pathway analysis showed that the three major enriched pathways were cholesterol metabolism, drug metabolism–cytochrome P450, PPAR signaling pathway. After qRT-PCR validation, we obtained 11 genes that were significant differentially expressed in the kidney tissues of DKD mice compared with control mice. (The mRNA expression levels of Aacs, Cpe, Cd36, Slc22a7, Slc1a4, Lpl, Cyp7b1, Akr1c14 and Apoh were declined, whereas Abcc4 and Gsta2 were elevated). Conclusion Our study, based on RNA-seq results, GEO databases and qRT-PCR, identified 11 significant dysregulated DEGs, which play an important role in lipid metabolism and the PPAR signaling pathway, which provide novel targets for diagnosis and treatment of DKD.
Zhao et al. (2022) Bioinformatics prediction and experimental verification of key biomarkers for diabetic kidney disease based on transcriptome sequencing in mice. PeerJ 10:e13932 https://doi.org/10.7717/peerj.13932
Sexual dimorphism in the walrus mandible: comparative description and geometric morphometrics
The modern walrus Odobenus rosmarus is characterized by marked sexual dimorphism, related to its polygynous behavior and the aggressive competition between males during the breeding season. Previous studies treated skeletal sexual dimorphism in walruses either qualitatively or with basic quantitative measurements. The present study combines a detailed qualitative comparison of male and female walrus mandibles with quantitative two-dimensional geometric morphometrics analysis (principal component analysis, Procrustes ANOVA and a linear discriminant analysis). In addition to identifying previously recognized sexually dimorphic features (e.g., convexity of the anterior margin of the mandible in adult males), our study finds new morphological differences between males and females, such as a relative dorsal expansion of the anterior part of the mandible and an accentuated concavity between the dorsal margin and the coronoid process in adult males. Both our qualitative comparisons and quantitative analyses demonstrate that sexual dimorphism as expressed in the mandible of extant walruses is statistically significant and that (variation in) mandibular morphology can be used as tool to attribute sex with a good degree of accuracy to isolated mandibles or skeletons lacking the cranium. Sexual dimorphism in walruses is directly related to their sexual behavior, characterized as aggressive in males and linked to a polygynous reproduction system. Indeed, the difference in size of the tusks between males and females but also the use of these during intraspecific fights, can reasonably account for this great mandibular morphological disparity between adult males and females, but also among different ontogenetic stages. Finally, the results obtained in the present study may serve as a starting point for assessing sexual dimorphism more in-depth and studying inter- and intraspecific variation in the mandibles of fossil walruses by identifying quantified size and shape mandibular features.
Boisville et al. (2022) Sexual dimorphism in the walrus mandible: comparative description and geometric morphometrics. PeerJ 10:e13940 https://doi.org/10.7717/peerj.13940
Thermography in ergonomic assessment: a study of wood processing industry workers
Background Workers in the wood processing industry perform activities that demand great physical and ergonomic demands, which favors the emergence of inflammatory processes and in turn the occurrence of heat regions in the body, thus making it possible to assess the inflammatory level by means of temperature gradients. This study aimed to evaluate the use of thermography as an ergonomic analysis tool to identify regions with musculoskeletal overload in workers in a wood processing industry. Methods The study was conducted with nine workers in the central-west region of Brazil. The evaluations to obtain the thermographic images were carried out before the beginning of the workday, on Monday (day I) and on Friday (day II), in order to verify the overload regions in the accumulation of days worked. The thermal images were collected in an acclimatized room with controlled conditions where the participants remained with the upper part of their bodies bare for acclimatization, and then the lumbar and scapular regions were evaluated. The images were obtained using the FLUKE TI 400 Thermal Imager, with analysis using the SmartView software program to demarcate the body regions of interest. Results The mean temperature values obtained on day I did not significantly differ from the mean values obtained on day II. Qualitative analysis showed thermal patterns with high temperature at the same points on both evaluated days. Although the thermographic analysis performed in this study cannot provide definitive results, they generally helped to provide evidence for a more accurate diagnosis in the evaluated workers.
Soranso et al. (2022) Thermography in ergonomic assessment: a study of wood processing industry workers. PeerJ 10:e13973 https://doi.org/10.7717/peerj.13973
Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of Plukenetia volubilis
Background Plukenetia volubilis is cultivated as a valuable oilseed crop, and its mature seeds are rich in polyunsaturated fatty acids (FAs), which are widely used in food and pharmaceutical industries. Recently, next-generation sequencing (NGS) transcriptome studies in P. volubilis indicated that some candidate genes were involved in oil biosynthesis. The NGS were inaccuracies in assembly of some candidate genes, leading to unknown errors in date analyses. However, single molecular real-time (SMRT) sequencing can overcome these assembled errors. Unfortunately, this technique has not been reported in P. volubilis. Methods The total oil content of P. volubilis seed (PVS) was determined using Soxhlet extraction system. The FA composition were analyzed by gas chromatography. Combining PacBio SMRT and Illumina technologies, the transcriptome analysis of developing PVS was performed. Functional annotation and differential expression were performed by BLAST software (version 2.2.26) and RSEM software (version 1.2.31), respectively. The lncRNA-targeted transcripts were predicted in developing PVS using LncTar tool. Results By Soxhlet extraction system, the oil content of superior plant-type (SPT) was 13.47% higher than that of inferior plant-type (IPT) at mature PVS. The most abundant FAs were C18:2 and C18:3, among which C18:3 content of SPT was 1.11-fold higher than that of IPT. Combined with PacBio and Illumina platform, 68,971 non-redundant genes were obtained, among which 7,823 long non-coding RNAs (lncRNAs) and 7,798 lncRNA-targeted genes were predicted. In developing seed, the expressions of 57 TFs showed a significantly positive correlation with oil contents, including WRI1-like1, LEC1-like1, and MYB44-like. Comparative analysis of expression profiles between SPT and IPT implied that orthologs of FAD3, PDCT, PDAT, and DAGT2 were possibly important for the accumulation of polyunsaturated FAs. Together, these results provide a reference for oil biosynthesis of P. volubilis and genetic improvement of oil plants.
Fu et al. (2022) Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of Plukenetia volubilis. PeerJ 10:e13998 https://doi.org/10.7717/peerj.13998
Estuarine microbial networks and relationships vary between environmentally distinct communities
Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO3, and SiO4; only NH4 was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. Coastal networks may also be driven by shifts in the abundance of certain taxonomic or functional groups. Sustained monitoring of microbial communities over environmental gradients, both spatial and temporal, is critical to predict microbial dynamics and biogeochemistry in future marine ecosystems.
Anderson et al. (2022) Estuarine microbial networks and relationships vary between environmentally distinct communities. PeerJ 10:e14005 https://doi.org/10.7717/peerj.14005
Hepatic metabolite responses to 4-day complete fasting and subsequent refeeding in rats
Background Fasting has been widely used to improve various metabolic diseases in humans. Adaptive fasting is necessary for metabolic adaptation during prolonged fasting, which could overcome the great advantages of short-term fasting. The liver is the main organ responsible for energy metabolism and metabolic homeostasis. To date, we lack literature that describes the physiologically relevant adaptations of the liver during prolonged fasting and refeeding. For that reason, this study aims to evaluate the response of the liver of Sprague-Dawley (SD) rats to prolonged fasting and refeeding. Methods Sixty-six male SD rats were divided into the fasting groups, which were fasted for 0, 4, 8, 12, 24, 48, 72, or 96 h, and the refeeding groups, which were refed for 1, 3, or 6 days after 96 h of fasting. Serum glucose, TG, FFA, β-hydroxybutyrate, insulin, glucagon, leptin, adiponectin and FGF21 levels were assessed. The glucose content, PEPCK activity, TG concentration and FFA content were measured in liver tissue, and the expression of genes involved in gluconeogenesis (PEPCK and G6Pase), ketogenesis (PPARα, CPT-1a and HMGCS2) and the protein expression of nutrient-sensing signaling molecules (AMPK, mTOR and SIRT1) were determined by RT-qPCR and western blotting, respectively. Results Fasting significantly decreased the body weight, which was totally recovered to baseline after 3 days of refeeding. A 4-day fast triggered an energy metabolic substrate shift from glucose to ketones and caused serum hormone changes and changes in the protein expression levels of nutrient-sensing signaling molecules. Glycogenolysis served as the primary fuel source during the first 24 h of fasting, while gluconeogenesis supplied the most glucose thereafter. Serum FFA concentrations increased significantly with 48 h of fasting. Serum FFAs partly caused high serum β-hydroxybutyrate levels, which became an important energy source with the prolongation of the fasting duration. One day of refeeding quickly reversed the energy substrate switch. Nutrient-sensing signaling molecules (AMPK and SIRT1 but not mTOR signaling) were highly expressed at the beginning of fasting (in the first 4 h). Serum insulin and leptin decreased with fasting initiation, and serum glucagon increased, but adiponectin and FGF21 showed no significant changes. Herein, we depicted in detail the timing of the metabolic response and adaptation of the liver to a 4-day water-only fast and subsequent refeeding in rats, which provides helpful support for the design of safe prolonged and intermittent fasting regimens.
Sui et al. (2022) Hepatic metabolite responses to 4-day complete fasting and subsequent refeeding in rats. PeerJ 10:e14009 https://doi.org/10.7717/peerj.14009