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
The regulating effects and mechanism of biochar and maifanite on copper and cadmium in a polluted soil-Lolium perenne L. system
Arable land polluted by copper (Cu) and cadmium (Cd) is a widespread problem. The use of biochar and/or clay mineral as a soil amendment can effectively solidify heavy metals in the soil. We applied biochar (BC), iron modified biochar (Fe-BC), maifanite (MF, a kind of clay minerals), a combination of BC with MF (BC:MF), and Fe-BC with MF (Fe-BC:MF) at a 2 wt % dose as soil amendments to study their ability to prevent Cu and Cd from accumulating in ryegrass (Lolium perenne L.). We found that after 90 days of cultivation, the Cd and Cu content both significantly decreased in ryegrass shoots from 2.06 and 209.3 mg kg−1 (control) to 1.44–2.01 and 51.50–70.92 mg kg−1, respectively, across treatments (p < 0.05). Similarly, the bioconcentration factor (BCF) for Cd/Cu was significantly smaller (P < 0.05) in all amendments versus control soil. This trend differed among the shoot, BCF, and transportation factor (TF). Combining BC:MF or Fe-BC:MF did not significantly improve the Cd/Cu stabilization in the soil compared to the corresponding single amendment (p > 0.05). Our adsorption balance experiment showed that BC, Fe-BC, and MF physically and chemically adsorbed Cd and Cu by complexation with functional groups (mesoporous nanomaterials) whose porosity measurements ranged from 0.68 to 78.57 m2 g−1. Furthermore, the amorphous crystalline iron oxide binding Cd and Cu was the key to immobilizing these metals in the soil. The amendments applied in our study show promise for enhancing immobilization of Cu and Cd in contaminated paddy soils.
Environmental Contamination and Remediation
Ding et al. (2021) The regulating effects and mechanism of biochar and maifanite on copper and cadmium in a polluted soil-Lolium perenne L. system. PeerJ 9:e11921 https://doi.org/10.7717/peerj.11921
Therapeutic effects of astragaloside IV and Astragalus spinosus saponins against bisphenol A-induced neurotoxicity and DNA damage in rats
Background Bisphenol A (BPA) is an endocrine disruptor to which humans are often subjected during daily life. This study aimed to investigate the ameliorative effect of astragaloside IV (ASIV) or saponins extracted from Astragalus spinosus (A. spinosus) against DNA damage and neurotoxic effects induced by BPA in prefrontal cortex (PFC), hippocampal and striatal brain regions of developing male rats. Materials and Methods Juvenile PND20 (pre-weaning; age of 20 days) male Sprague Dawley rats were randomly and equally divided into four groups: control, BPA, BPA+ASIV and BPA+A. spinosus saponins groups. Bisphenol A (125 mg/kg/day) was administrated orally to male rats from day 20 (BPA group) and along with ASIV (80 mg/kg/day) (BPA+ASIV group) or A. spinosus saponin (100 mg/kg/day) (BPA+ A. spinosus saponins group) from day 50 to adult age day 117. Results Increased level of nitric oxide (NO) and decreased level of glutamate (Glu), glutamine (Gln), glutaminase (GA) and glutamine synthetase (GS) were observed in the brain regions of BPA treated rats compared with the control. On the other hand, co-administration of ASIV or A. spinosus saponin with BPA considerably improved levels of these neurochemicals. The current study also revealed restoration of the level of brain derived neurotrophic factor (BDNF) and N-methyl-D-aspartate receptors (NR2A and NR2B) gene expression in BPA+ ASIV and BPA+A. spinosus saponins groups. The co-treatment of BPA group with ASIV or A. spinosus saponin significantly reduced the values of comet parameters as well as the intensity of estrogen receptors (ERs) immunoreactive cells and improved the histological alterations induced by BPA in different brain regions. Conclusion It could be concluded that ASIV or A. spinosus saponins has a promising role in modulating the neurotoxicity and DNA damage elicited by BPA.
Essawy et al. (2021) Therapeutic effects of astragaloside IV and Astragalus spinosus saponins against bisphenol A-induced neurotoxicity and DNA damage in rats. PeerJ 9:e11930 https://doi.org/10.7717/peerj.11930
Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using docking, molecular dynamics, and 3D-QSAR
Rho-associated kinase-1 (ROCK1) has been recognized for its pivotal role in heart diseases, different types of malignancy, and many neurological disorders. Hyperactivity of ROCK phosphorylates the protein kinase-C (PKC), which ultimately induces smooth muscle cell contraction in the vascular system. Inhibition of ROCK1 has been shown to be a promising therapy for patients with cardiovascular disease. In this study, we have conducted molecular modeling techniques such as docking, molecular dynamics (MD), and 3-Dimensional structure-activity relationship (3D-QSAR) on a series of N-ethyl-4-(pyridin-4-yl)benzamide-based compounds. Docking and MD showed critical interactions and binding affinities between ROCK1 and its inhibitors. To establish the structure-activity relationship (SAR) of the compounds, 3D-QSAR techniques such as Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were used. The CoMFA (q2 = 0.774, r2 = 0.965, ONC = 6, and ${r}_{pred}^{2}$ r p r e d 2 = 0.703) and CoMSIA (q2 = 0.676, r2 = 0.949, ONC = 6, and ${r}_{pred}^{2}$ r p r e d 2 = 0.548) both models have shown reasonable external predictive activity, and contour maps revealed favorable and unfavorable substitutions for chemical group modifications. Based on the contour maps, we have designed forty new compounds, among which, seven compounds exhibited higher predictive activity (pIC50). Further, we conducted the MD study, ADME/Tox, and SA score prediction using the seven newly designed compounds. The combination of docking, MD, and 3D-QSAR studies helps to understand the coherence modification of existing molecules. Our study may provide valuable insight into the development of more potent ROCK1 inhibitors.
Ghosh et al. (2021) Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using docking, molecular dynamics, and 3D-QSAR. PeerJ 9:e11951 https://doi.org/10.7717/peerj.11951
Klebsiella variicola improves the antioxidant ability of maize seedlings under saline-alkali stress
Background Saline-alkali soil is mainly distributed in the northern and coastal areas of China. The Songnen Plain, located in the northeast of China, is a region with a relatively high concentration of saline-alkali soil and is also one of the more at-risk areas in the country. Every year, the increasing spread of saline-alkali soil areas has a serious impact on the growth of agricultural crops. The maize crop is sensitive to saline-alkali stress, which seriously affects its growth and development. Our previous study determined that Klebsiella variicola performs a variety of biological functions, as well as improves the rhizosphere microenvironment and promotes the growth and development of maize seedlings in saline-alkali soil environments. The present study further analyzed the mechanism that enables K. variicola to alleviate saline-alkali stress at the level of the antioxidant system. Methods The accumulation of O2− was observed directly via histochemical staining. The activities of several antioxidant enzymes were determined using the nitro blue tetrazolium and the guaiacol methods. The contents of non-enzymatic antioxidants were determined using the dithionitrobenzoic acid method. Results The contents of the superoxide anion and hydrogen peroxide in leaves and roots of maize seedlings increased under saline-alkali stress conditions. The higher level of reactive oxygen species increased the degree of membrane lipid peroxidation. There were differences in the degree of oxidative damage and performance of the antioxidant defence system in maize seedlings under saline-alkali stress. Following the application of increasing concentrations of K. variicola, the activity of antioxidant enzymes increased by 21.22%–215.46%, and the content of non-enzymatic antioxidants increased as well, the ratios of ASA/DHA and GSH/GSSG in leaves increased by 4.97% and 1.87 times, respectively, and those in roots increased by 3.24% and 1.60 times, respectively. The accumulation of reactive oxygen species was reduced, and the content of H2O2 decreased by 26.07%–46.97%. The content of O2− decreased by 20.18%–37.01%, which alleviated the oxidative damage to maize seedlings caused by saline-alkali stress. Conclusion K. variicola reduced ROS-induced peroxidation to membrane lipids and effectively alleviated the damage caused by saline-alkali stress by increasing the activities of antioxidant enzymes in maize seedlings, thus enhancing their saline-alkali tolerance. A bacterial concentration of 1×108 cfu/mL was optimal in each set of experiments.
Yang et al. (2021) Klebsiella variicola improves the antioxidant ability of maize seedlings under saline-alkali stress. PeerJ 9:e11963 https://doi.org/10.7717/peerj.11963
Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato
Late blight caused by Phytophthora infestans is one of the most devastating diseases in potatoes and tomatoes. At present, several late blight resistance genes have been mapped and cloned. To better understand the transcriptome changes during the incompatible interaction process between R3a and Avr3a, in this study, after spraying DEX, the leaves of MM-R3a-Avr3a and MM-Avr3a transgenic plants at different time points were used for comparative transcriptome analysis. A total of 7,324 repeated DEGs were detected in MM-R3a-Avr3a plants at 2-h and 6-h, and 729 genes were differentially expressed at 6-h compared with 2-h. Only 1,319 repeated DEGs were found in MM-Avr3a at 2-h and 6-h, of which 330 genes have the same expression pattern. Based on GO, KEGG and WCGNA analysis of DEGs, the phenylpropanoid biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly up-regulated. Parts of the down-regulated DEGs were enriched in carbon metabolism and the photosynthesis process. Among these DEGs, most of the transcription factors, such as WRKY, MYB, and NAC, related to disease resistance or endogenous hormones SA and ET pathways, as well as PR, CML, SGT1 gene were also significantly induced. Our results provide transcriptome-wide insights into R3a and Avr3a-mediated incompatibility interaction.
Xue et al. (2021) Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato. PeerJ 9:e11965 https://doi.org/10.7717/peerj.11965
Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae)
Background The African continent is comprised of several different biomes, although savanna is the most prevalent. The current heterogeneous landscape was formed through long-term vegetation shifts as a result of the global cooling trend since the Oligocene epoch. The overwhelming trend was a shift from primarily forest, to primarily savanna. As such, faunal groups that emerged during the Paleogene/Neogene period and have species distributed in both forest and savanna habitat should show a genetic signature of the possible evolutionary impact of these biome developments. Crotaphopeltis and Philothamnus (Colubridae) are excellent taxa to investigate the evolutionary impact of these biome developments on widespread African colubrid snakes, and whether timing and patterns of radiation are synchronous with biome reorganisation. Methods A phylogenetic framework was used to investigate timing of lineage diversification. Phylogenetic analysis included both genera as well as other Colubridae to construct a temporal framework in order to estimate radiation times for Crotaphopeltis and Philothamnus. Lineage diversification was estimated in Bayesian Evolutionary Analysis Sampling Trees (BEAST), using two mitochondrial markers (cyt–b, ND4), one nuclear marker (c–mos), and incorporating one fossil and two biogeographical calibration points. Vegetation layers were used to classify and confirm species association with broad biome types (‘closed’ = forest, ‘open’ = savanna/other), and the ancestral habitat state for each genus was estimated. Results Philothamnus showed an ancestral state of closed habitat, but the ancestral habitat type for Crotaphopeltis was equivocal. Both genera showed similar timing of lineage diversification diverging from their sister genera during the Oligocene/Miocene transition (ca. 25 Mya), with subsequent species radiation in the Mid-Miocene. Philothamnus appeared to have undergone allopatric speciation during Mid-Miocene forest fragmentation. Habitat generalist and open habitat specialist species emerged as savanna became more prevalent, while at least two forest associated lineages within Crotaphopeltis moved into Afromontane forest habitat secondarily and independently. Discussion With similar diversification times, but contrasting ancestral habitat reconstructions, we show that these genera have responded very differently to the same broad biome shifts. Differences in biogeographical patterns for the two African colubrid genera is likely an effect of distinct life-history traits, such as the arboreous habits of Philothamnus compared to the terrestrial lifestyle of Crotaphopeltis.
Engelbrecht et al. (2021) Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae). PeerJ 9:e11728 https://doi.org/10.7717/peerj.11728