N-acetyl-L-tryptophan attenuates hepatic ischemia-reperfusion injury via regulating TLR4/NLRP3 signaling pathway in rats
The aim of this study was to investigate the changes of TLR4/NLRP3 signal during hepatic ischemia-reperfusion injury (HIRI) and to verify whether N-acetyl-L-tryptophan (L-NAT) protected hepatocytes by regulating the activation of TLR4/NLRP3 signal. We have established the rat HIRI model and H2O2-induced cell damage model to simulate ischemia-reperfusion injury and detect the corresponding indicators. Compared with the sham group, Suzuki score and the level of serum ALT increased after HIRI, accompanied by an increased expression of NLRP3, ASC, Caspase-1, IL-1β, TLR4, and NF-κB. While L-NAT pretreatment reversed the above-mentioned changes. Compared with the control group, cells in the H2O2 treated group became smaller in cell volume and round in shape with unclear boundaries. Similar to the phenotypes in vivo, H2O2 treatment also induced significant increase in expression of pyroptosis-related proteins (NLRP3, ASC, Caspase-1 and IL-1β) and inflammatory factors (TLR4 and NF-κB). While L-NAT pretreatment attenuated injuries caused by H2O2. In conclusion, the present findings demonstrate that L-NAT alleviates HIRI by regulating activation of NLRP3 inflammasome, which may be related to the TLR4/NF-κB signaling pathway.
Pan et al. (2021) N-acetyl-L-tryptophan attenuates hepatic ischemia-reperfusion injury via regulating TLR4/NLRP3 signaling pathway in rats. PeerJ 9:e11909 https://doi.org/10.7717/peerj.11909
Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition
Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800–3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2–3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. During a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial ecological resilience was demonstrated with a return to pre-drought structure and abundance after snowmelt rewetting the following year. These results show similar decomposition processes across a 700 m elevation gradient and reveal the sensitivity but resilience of soil microbial ecology to low moisture conditions.
Leonard et al. (2021) Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition. PeerJ 9:e11926 https://doi.org/10.7717/peerj.11926
The nutritional applications of garlic (Allium sativum) as natural feed additives in animals
Garlic (Allium sativum) is an essential vegetable that has been widely utilized as seasoning, flavoring, culinary and in herbal remedies. Garlic contains several characteristic organosulfur compounds, such as diallyl sulfide, allicin (diallyl thiosulphate), γ-glutamylcysteine, and S-allyl cysteine (alliin) and ajoene, which garlic has beneficial effects on inflammation, oxidative stress markers, hypertension, hyperlipidaemia and endothelial function in vitro or in animal model. These bioactive molecules are also playing pivotal role in livestock and fisheries production apart from its application in humans. Supplementation of animal feed with garlic and its related products is consistent with the modern agricultural concept of organic animal husbandry. This review compiles the information describing the effects of feeding garlic and its extracts on selected performance parameters in animals (chicken, rabbits, ruminants, pigs and fish). This review may provide reference for scientists and entrepreneurs to investigate the applications of feeds added with garlic and allicin by-products for the improvement of animal husbandry and aquatic production.
Chen et al. (2021) The nutritional applications of garlic (Allium sativum) as natural feed additives in animals. PeerJ 9:e11934 https://doi.org/10.7717/peerj.11934
The association of reactive balance control and spinal curvature under lumbar muscle fatigue
Background Although low back fatigue is an important intervening factor for physical functioning among sedentary people, little is known about its possible significance in relation to the spinal posture and compensatory postural responses to unpredictable stimuli. This study investigates the effect of lumbar muscle fatigue on spinal curvature and reactive balance control in response to externally induced perturbations. Methods A group of 38 young sedentary individuals underwent a perturbation-based balance test by applying a 2 kg load release. Sagittal spinal curvature and pelvic tilt was measured in both a normal and Matthiass standing posture both with and without a hand-held 2 kg load, and before and after the Sørensen fatigue test. Results Both the peak anterior and peak posterior center of pressure (CoP) displacements and the corresponding time to peak anterior and peak posterior CoP displacements significantly increased after the Sørensen fatigue test (all at p < 0.001). A lumbar muscle fatigue led to a decrease of the lumbar lordosis in the Matthiass posture while holding a 2 kg load in front of the body when compared to pre-fatigue conditions both without a load (p = 0.011, d = 0.35) and with a 2 kg load (p = 0.000, d = 0.51). Also the sacral inclination in the Matthiass posture with a 2 kg additional load significantly decreased under fatigue when compared to all postures in pre-fatigue conditions (p = 0.01, d = 0.48). Contrary to pre-fatigue conditions, variables of the perturbation-based balance test were closely associated with those of lumbar curvature while standing in the Matthiass posture with a 2 kg additional load after the Sørensen fatigue test (r values in range from −0.520 to −0.631, all at p < 0.05). Conclusion These findings indicate that lumbar muscle fatigue causes changes in the lumbar spinal curvature and this is functionally relevant in explaining the impaired ability to maintain balance after externally induced perturbations. This emphasizes the importance for assessing both spinal posture and reactive balance control under fatigue in order to reveal their interrelations in young sedentary adults and predict any significant deterioration in later years.
Zemková et al. (2021) The association of reactive balance control and spinal curvature under lumbar muscle fatigue. PeerJ 9:e11969 https://doi.org/10.7717/peerj.11969
Icaritin protects SH-SY5Y cells transfected with TDP-43 by alleviating mitochondrial damage and oxidative stress
Background The aim of this study was to investigate the effect of icaritin (ICT) on TAR DNA-binding protein 43 (TDP-43)-induced neuroblastoma (SH-SY5Y) cell damage and to further explore its underlying mechanisms. Methods To investigate the possible mechanism, TDP-43 was used to induce SH-SY5Y cell injury. Cell viability was evaluated by the CCK-8 assay. The mitochondrial membrane potential (MMP) was determined with JC-1. The expression levels of TDP-43 and cytochrome C (CytC) were measuring by Western blotting. Changes in adenosine 5′-triphosphate (ATP) content, total antioxidative capacity (T-AOC), glutathione peroxidase (GSH-Px) activity, superoxide dismutase (SOD) activity and malondialdehyde (MDA) content were detected with specific kits. Results The results showed that ICT reduced the cell damage induced by TDP-43. ICT reduced the expression level of TDP-43; increased ATP content and the MMP; decreased CytC expression; increased T-AOC and GSH-Px, total SOD (T-SOD), copper/zinc SOD (CuZn-SOD), and manganese SOD (Mn-SOD) activity; and decreased MDA content. Conclusions The results suggest that ICT has a protective effect on TDP-43-transfected SH-SY5Y cells that is related to reductions in TDP-43 expression and mitochondrial damage and alleviation of oxidative stress.
Zhou et al. (2021) Icaritin protects SH-SY5Y cells transfected with TDP-43 by alleviating mitochondrial damage and oxidative stress. PeerJ 9:e11978 https://doi.org/10.7717/peerj.11978
Disintegration half-life of biodegradable plastic films on different marine beach sediments
The seafloor is considered the major sink for plastic debris in the world’s oceans. Biodegradable polymers are available on the market as a substitute for conventional plastic and could potentially end up in the same environment. To gain more insight into the effects of different sediments on the degradation rate of biodegradable plastic we performed two iterative seawater tank experiments. First, to test the effect of sediment grain size, film of Mater-Bi HF03V, a blend of thermoplastic starch and biodegradable polyesters, was placed on the surface of mud as well as on four different grain size fractions of beach sand. Disintegration half-life was shortest on mud (139 days) and increased with the grain size of the beach sediment fractions (63–250 µm: 296 days; 250–500 µm: 310 days; 500–1,000 µm: 438 days; >1,000 µm: 428 days). We assume that the higher surface-to-volume ratio in fine sediment compared to coarse sediment led to a higher bacterial abundance and thus to faster disintegration rates. In a follow-up experiment, the <500 µm fraction of sediment from four different beaches around Isola d’Elba, Italy, was used to test plastic disintegration as above. Additionally, polyhydroxybutyrate (PHB, MIREL P5001) was used as a positive control and high-density polyethylene (HD-PE) as a negative control. No disintegration was observed for HD-PE. Mater-Bi HF03V and PHB disintegrated significantly differently on sediment from different sites, with half-lives of Mater-Bi HF03V ranging from 72 to 368 days and of PHB from 112 to 215 days. Here, the half-life was shortest on slightly coarser sediment and at potentially anthropogenically impacted sites. We assume that the effect of the grain size on the disintegration rate was masked by other parameters influencing the microbial community and activity. Understanding the parameters driving biodegradation is key to reliably report the range of disintegration rates occurring under the various conditions in different ecosystems.
Environmental Contamination and Remediation
Eich et al. (2021) Disintegration half-life of biodegradable plastic films on different marine beach sediments. PeerJ 9:e11981 https://doi.org/10.7717/peerj.11981
Cephalopod species identification using integrated analysis of machine learning and deep learning approaches
Background Despite the high commercial fisheries value and ecological importance as prey item for higher marine predators, very limited taxonomic work has been done on cephalopods in Malaysia. Due to the soft-bodied nature of cephalopods, the identification of cephalopod species based on the beak hard parts can be more reliable and useful than conventional body morphology. Since the traditional method for species classification was time-consuming, this study aimed to develop an automated identification model that can identify cephalopod species based on beak images. Methods A total of 174 samples of seven cephalopod species were collected from the west coast of Peninsular Malaysia. Both upper and lower beaks were extracted from the samples and the left lateral views of upper and lower beak images were acquired. Three types of traditional morphometric features were extracted namely grey histogram of oriented gradient (HOG), colour HOG, and morphological shape descriptor (MSD). In addition, deep features were extracted by using three pre-trained convolutional neural networks (CNN) models which are VGG19, InceptionV3, and Resnet50. Eight machine learning approaches were used in the classification step and compared for model performance. Results The results showed that the Artificial Neural Network (ANN) model achieved the best testing accuracy of 91.14%, using the deep features extracted from the VGG19 model from lower beak images. The results indicated that the deep features were more accurate than the traditional features in highlighting morphometric differences from the beak images of cephalopod species. In addition, the use of lower beaks of cephalopod species provided better results compared to the upper beaks, suggesting that the lower beaks possess more significant morphological differences between the studied cephalopod species. Future works should include more cephalopod species and sample size to enhance the identification accuracy and comprehensiveness of the developed model.
Tan et al. (2021) Cephalopod species identification using integrated analysis of machine learning and deep learning approaches. PeerJ 9:e11825 https://doi.org/10.7717/peerj.11825
Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters
Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.
Ponce et al. (2021) Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters. PeerJ 9:e11835 https://doi.org/10.7717/peerj.11835
Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana
Background Photosynthesis is a key process in plants that is compromised by the oxygenase activity of Rubisco, which leads to the production of toxic compound phosphoglycolate that is catabolized by photorespiratory pathway. Transformation of plants with photorespiratory bypasses have been shown to reduce photorespiration and enhance plant biomass. Interestingly, engineering of a single gene from such photorespiratory bypasses has also improved photosynthesis and plant productivity. Although single gene transformations may not completely reduce photorespiration, increases in plant biomass accumulation have still been observed indicating an alternative role in regulating different metabolic processes. Therefore, the current study was aimed at evaluating the underlying mechanism (s) associated with the effects of introducing a single cyanobacterial glycolate decarboxylation pathway gene on photosynthesis and plant performance. Methods Transgenic Arabidopsis thaliana plants (GD, HD, OX) expressing independently cyanobacterial decarboxylation pathway genes i.e., glycolate dehydrogenase, hydroxyacid dehydrogenase, and oxalate decarboxylase, respectively, were utilized. Photosynthetic, fluorescence related, and growth parameters were analyzed. Additionally, transcriptomic analysis of GD transgenic plants was also performed. Results The GD plants exhibited a significant increase (16%) in net photosynthesis rate while both HD and OX plants showed a non-significant (11%) increase as compared to wild type plants (WT). The stomatal conductance was significantly higher (24%) in GD and HD plants than the WT plants. The quantum efficiencies of photosystem II, carbon dioxide assimilation and the chlorophyll fluorescence-based photosynthetic electron transport rate were also higher than WT plants. The OX plants displayed significant reductions in the rate of photorespiration relative to gross photosynthesis and increase in the ratio of the photosynthetic electron flow attributable to carboxylation reactions over that attributable to oxygenation reactions. GD, HD and OX plants accumulated significantly higher biomass and seed weight. Soluble sugars were significantly increased in GD and HD plants, while the starch levels were higher in all transgenic plants. The transcriptomic analysis of GD plants revealed 650 up-regulated genes mainly related to photosynthesis, photorespiratory pathway, sucrose metabolism, chlorophyll biosynthesis and glutathione metabolism. Conclusion This study revealed the potential of introduced cyanobacterial pathway genes to enhance photosynthetic and growth-related parameters. The upregulation of genes related to different pathways provided evidence of the underlying mechanisms involved particularly in GD plants. However, transcriptomic profiling of HD and OX plants can further help to identify other potential mechanisms involved in improved plant productivity.
Abbasi et al. (2021) Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana. PeerJ 9:e11860 https://doi.org/10.7717/peerj.11860
Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress
Coreopsis tinctoria Nutt. (C. tinctoria) is a special tea ingredient that adapts to certain salt stresses and shares the functions of chrysanthemum. With annual expansion of the cultivation area of C. tinctoria in Xinjiang (China), soil salinity may become a constraint for chrysanthemum cultivation. To investigate the response of C. tinctoria to salt stress, physiological and transcriptional changes in C. tinctoria in the early stages of low (50 mM NaCl) and high (200 mM NaCl) salt stress were analyzed and identified. The results showed that the contents of osmotic regulators (free proline, soluble sugar, and soluble protein) and antioxidant enzymes (catalase and peroxidase) under salt stress increased to various extents compared with those of the control (CK) within 72 h, and the increase was higher under 200 mM NaCl treatments. De novo RNA-seq was used to analyze changes in the transcripts under 50 and 200 mM NaCl treatments for up to 48 h. In total, 8,584, 3,760, 7,833, 19,341, 13,233, and 9,224 differentially expressed genes (DEGs) were detected under 12 h, 24 h, and 48 h for 50 and 200 mM NaCl treatments, respectively. Weighted correlation network analysis (WGCNA) was used to analyze the correlations between all DEGs and physiological indexes. We found that the coexpression modules blue2 and Lightskyblue4 highly correlated with osmotic regulators and CAT and identified 20 and 30 hub genes, respectively. The results provide useful data for the further study of salt tolerance in C. tinctoria.
Jiang et al. (2021) Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress. PeerJ 9:e11888 https://doi.org/10.7717/peerj.11888