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Biology, Volume 8, Issue 4 (December 2019)

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Cover Story (view full-size image) The role of autophagy in cell survival and cell death decisions is highly dependent on its extent [...] Read more.
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Open AccessArticle
In Vitro Antidiabetic, Anti-Obesity and Antioxidant Analysis of Ocimum basilicum Aerial Biomass and in Silico Molecular Docking Simulations with Alpha-Amylase and Lipase Enzymes
Biology 2019, 8(4), 92; https://doi.org/10.3390/biology8040092 - 04 Dec 2019
Abstract
The present study explored phytochemicals, porcine pancreatic α-amylase (PPA) and lipase (PPL) inhibitory activities and antioxidant potential of polar and nonpolar extracts of the leaves and flowers of Ocimum basilicum and the in-silico mode of interaction between these enzymes and the major chemical [...] Read more.
The present study explored phytochemicals, porcine pancreatic α-amylase (PPA) and lipase (PPL) inhibitory activities and antioxidant potential of polar and nonpolar extracts of the leaves and flowers of Ocimum basilicum and the in-silico mode of interaction between these enzymes and the major chemical constituents of the herb. The hexane extract (HE) and hydro-ethanolic extract (EE) obtained sequentially were used to estimate PPA and PPL inhibitory and antioxidant activities, total phenolic content (TPC) and total flavonoid content (TFC). Chemical constituents of the essential oils and HE were determined by GC-MS (Gas Chromatography-Mass Spectrometry). For PPA inhibition, IC50 (µg/mL) of the extracts were 0.27–0.37, which were close to 0.24 of acarbose, while for PPL inhibition, IC50 (µg/mL) of the extracts were 278.40–399.65, and that of Orlistat 145.72. The flowers EE was most potent antioxidant followed by leaves EE. The leaves EE had highest TPC and TFC followed of flowers EE. The essential oil of flowers had higher estragole (55%) than linalool (37%), while the essential oil of the leaves had higher linalool (42%) than estragole (38%). The HE of the flowers contained higher estragole (42%) than linalool (23%), while of the HE of the leaves too had higher estragole (65%) than linalool (18%). The in-silico molecular docking study showed linalool and estragole to have considerable PPA and PPL binding potential, which were further investigated through molecular dynamics simulations and binding free energy calculations. The PPA and PPL inhibitory activities of O. basilicum extracts and their notable antioxidant potential propose the herb as a multi-target complimentary medicine for diabetes, obesity and oxidative stress. Full article
(This article belongs to the Section Plant Science)
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Open AccessArticle
Selection of Lactic Acid Bacteria (LAB) Antagonizing Vibrio Parahaemolyticus: The Pathogen of Acute Hepatopancreatic Necrosis Disease (AHPND) in Whiteleg Shrimp (Penaeus Vannamei)
Biology 2019, 8(4), 91; https://doi.org/10.3390/biology8040091 - 01 Dec 2019
Abstract
Acute hepatopancreatic necrosis disease (AHPND) has recently emerged as a serious disease of cultured shrimp. A total of 19 lactic acid bacteria (LAB) strains isolated from shrimp samples were characterized based on morphological characteristics, biochemical tests, sequencing analysis, and their ability to antagonize [...] Read more.
Acute hepatopancreatic necrosis disease (AHPND) has recently emerged as a serious disease of cultured shrimp. A total of 19 lactic acid bacteria (LAB) strains isolated from shrimp samples were characterized based on morphological characteristics, biochemical tests, sequencing analysis, and their ability to antagonize Vibrio parahaemolyticus, which causes AHPND in whiteleg shrimp. Results from the agar well diffusion method indicated that 3 out of 19 isolated LAB strains showed the highest antagonizing ability against AHPND V. parahaemolyticus strain with an inhibition zone diameter ranging from 18 to 20 mm. Experiments where shrimps were given feed supplemented with these LAB strains and challenged with AHPND strain showed high survival rates (approximately 80.0%), which were not significantly different as compared to those recorded in the negative control treatment (86.6%), but significantly different to those recorded in the positive control treatment (40.6%) after 16 days of the experiment. However, the histological images of shrimp hepatopancreas indicated that the infection rate significantly reduced from 60.0% to 11.1% in shrimps fed with LAB-supplemented feeds and challenged with AHPND V. parahaemolyticus strain as compared to those in the positive control treatment. A polymerase chain reaction (PCR) and 16S rRNA gene sequencing confirmed the identification of LAB strain. These results can be applied in further experiments to investigate the ability of L. plantarum in preventing AHPND in intensively cultured whiteleg shrimp. Full article
Open AccessReview
Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato
Biology 2019, 8(4), 90; https://doi.org/10.3390/biology8040090 - 25 Nov 2019
Abstract
Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries. Despite having considerably high productivity, continuous supply as per the market demand is hard to achieve, mostly because of periodic losses occurring [...] Read more.
Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries. Despite having considerably high productivity, continuous supply as per the market demand is hard to achieve, mostly because of periodic losses occurring due to biotic as well as abiotic stresses. Although tomato is a temperate crop, it is grown in almost all the climatic zones because of widespread demand, which makes it challenge to adapt in diverse conditions. Development of tomato cultivars with enhanced abiotic stress tolerance is one of the most sustainable approaches for its successful production. In this regard, efforts are being made to understand the stress tolerance mechanism, gene discovery, and interaction of genetic and environmental factors. Several omics approaches, tools, and resources have already been developed for tomato growing. Modern sequencing technologies have greatly accelerated genomics and transcriptomics studies in tomato. These advancements facilitate Quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). However, limited efforts have been made in other omics branches like proteomics, metabolomics, and ionomics. Extensive cataloging of omics resources made here has highlighted the need for integration of omics approaches for efficient utilization of resources and a better understanding of the molecular mechanism. The information provided here will be helpful to understand the plant responses and the genetic regulatory networks involved in abiotic stress tolerance and efficient utilization of omics resources for tomato crop improvement. Full article
(This article belongs to the Section Plant Science)
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Open AccessArticle
Intra-Specific Difference in the Effect of Salinity on Physiological Performance in European Perch (Perca fluviatilis) and Its Ecological Importance for Fish in Estuaries
Biology 2019, 8(4), 89; https://doi.org/10.3390/biology8040089 - 17 Nov 2019
Abstract
Changes in environmental salinity challenge fish homeostasis and may affect physiological performance, such as swimming capacity and metabolism, which are important for foraging, migration, and escaping predators in the wild. The effects of salinity stress on physiological performance are largely species specific, but [...] Read more.
Changes in environmental salinity challenge fish homeostasis and may affect physiological performance, such as swimming capacity and metabolism, which are important for foraging, migration, and escaping predators in the wild. The effects of salinity stress on physiological performance are largely species specific, but may also depend on intra-specific differences in physiological capabilities of sub-populations. We measured critical swimming speed (Ucrit) and metabolic rates during swimming and at rest at salinities of 0 and 10 in European perch (Perca fluviatilis) from a low salinity tolerance population (LSTP) and a high salinity tolerance population (HSTP). Ucrit of LSTP was significantly reduced at a salinity of 10 yet was unaffected by salinity change in HSTP. We did not detect a significant cost of osmoregulation, which should theoretically be apparent from the metabolic rates during swimming and at rest at a salinity of 0 compared to at a salinity of 10 (iso-osmotic). Maximum metabolic rates were also not affected by salinity, indicating a modest tradeoff between respiration and osmoregulation (osmo-respiratory compromise). Intra-specific differences in effects of salinity on physiological performance are important for fish species to maintain ecological compatibility in estuarine environments, yet render these sub-populations vulnerable to fisheries. The findings of the present study are therefore valuable knowledge in conservation and management of estuarine fish populations. Full article
(This article belongs to the Special Issue Fish Metabolic Physiology in Response to Stress)
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Open AccessArticle
Reproductive Biology and Ecology of the Green Mussel Perna viridis: A Multidisciplinary Approach
Biology 2019, 8(4), 88; https://doi.org/10.3390/biology8040088 - 15 Nov 2019
Abstract
A multidisciplinary approach was applied to explore deeper knowledge about the reproductive biology and ecology of the green mussel (Perna viridis) by interlinking among ecological factors, ingested gut plankton, gonad fatty acid profile, and reproductive traits. Mussels were collected throughout the [...] Read more.
A multidisciplinary approach was applied to explore deeper knowledge about the reproductive biology and ecology of the green mussel (Perna viridis) by interlinking among ecological factors, ingested gut plankton, gonad fatty acid profile, and reproductive traits. Mussels were collected throughout the year from the coastal region of the Bay of Bengal of Bangladesh, and the histological analysis of 242 mussels revealed five stages of gametogenesis with an annual spawning season from January to April. The gonadosomatic index showed a strong correlation with the water quality parameters, ingested gut plankton groups, and gonadal fatty acids, and also displayed prominent effects of seasonality. In all datasets, we performed principal component analysis in which the first two principal components showed that seasonality explained >65% of the variability, and the multivariate spaces of seasonality corresponded to the gonad development. High salinity, nutrients, chlorophyll a, and plankton abundance in the water column were positively correlated with gonad development and the spawning of mussels. During the development stage, mussel ingested more plankton, particularly Bacillariophyceae and Pyrrophyceae, which were an important source of increased n-3 polyunsaturated fatty acids content in gonads. Furthermore, gonads accumulated more lipids and saturated fatty acids during the mature and spawning stages, which were probably utilized during embryogenesis and early larval development as energy sources and constituents of the cell membrane. This research provides a model toward a better understanding of reproductive biological traits and how these traits are interrelated with the surrounding environmental variables of the green mussel, which would be helpful in marine aquaculture and the sustainable exploitation of the fishery resources. Full article
(This article belongs to the Section Marine Biology)
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Open AccessArticle
Structural Equation Modelling Reveals That Nutrients and Physicochemistry Act Additively on the Dynamics of a Microcosm-Based Biotic Community
Biology 2019, 8(4), 87; https://doi.org/10.3390/biology8040087 - 14 Nov 2019
Abstract
Anthropogenic eutrophication has caused widespread environmental problems in freshwater lakes, reducing biodiversity and disrupting the classic pelagic food chain. Increasing our understanding of the exact role of nutrients and physicochemical variables on microbial dynamics, and subsequent microalgal and cyanobacterial blooms, has involved numerous [...] Read more.
Anthropogenic eutrophication has caused widespread environmental problems in freshwater lakes, reducing biodiversity and disrupting the classic pelagic food chain. Increasing our understanding of the exact role of nutrients and physicochemical variables on microbial dynamics, and subsequent microalgal and cyanobacterial blooms, has involved numerous studies ranging from replicate microcosm-based studies through to temporal studies of real lake data. In a previous experimental microcosm study, we utilised metaproteomics to investigate the functional changes of a microalgal-bacterial community under oligotrophic and eutrophic nutrient levels. Here, we analyse the time series data from this experiment with a combination of typically used univariate analyses and a more modern multivariate approach, structural equation modelling. Our aim was to test, using these modern methods, whether physicochemical variables and nutrient dynamics acted additively, synergistically, or antagonistically on the specific biotic community used in the microcosms. We found that nutrients (nitrogen and phosphorus) and temperature acted additively on the interactions between the microalgae and bacteria present, with the temperature effects elevated in the eutrophic conditions we applied. The data suggests that there may be no synergistic interaction between nutrients and temperature in the tested microcosms. Our approach demonstrates how the application of multivariate methods to existing datasets, in our case from nutrient-enriched freshwater microcosms, enables new information to be extracted, enhancing interpretations as well as allowing more reliable comparisons to similar published studies. Full article
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Open AccessArticle
Transcriptional Profiling and Molecular Characterization of the yccT Mutant Link: A Novel STY1099 Protein with the Peroxide Stress Response and Cell Division of Salmonella enterica Serovar Enteritidis
Biology 2019, 8(4), 86; https://doi.org/10.3390/biology8040086 - 13 Nov 2019
Abstract
Uncharacterized protein STY1099, encoded by the yccT gene, was previously identified as the most altered (i.e., upregulated) protein among the ZnO nanoparticle (NP) stimulon of Salmonella enterica serovar Enteritidis. Here we combined various stress response-related assays with functional genetics, global transcriptomic and proteomic [...] Read more.
Uncharacterized protein STY1099, encoded by the yccT gene, was previously identified as the most altered (i.e., upregulated) protein among the ZnO nanoparticle (NP) stimulon of Salmonella enterica serovar Enteritidis. Here we combined various stress response-related assays with functional genetics, global transcriptomic and proteomic analyses to characterize the yccT gene and its STY1099 product. Exposure of S. enterica Enteritidis to H2O2 (i.e., hydrogen peroxide) resulted in a significant (p < 0.0001) upregulation of the yccT gene, whereas exposure to paraquat (i.e., superoxide) did not alter the expression of the yccT gene. The ∆yccT mutant of S. enterica Enteritidis exposed to 0.75 mM H2O2, showed significantly reduced (p < 0.05) viability compared to the wild type strain. Further, comparative transcriptome analyses supported by Co-immunoprecipitation (Co-IP) assay revealed that STY1099 protein plays a role in redox homeostasis during the peroxide stress assault via involvement in the processes of respiratory nitrate reductase, oxidoreductase activities, cellular uptake and stress response. In addition, we found that the STY1099 protein has the monopolar subcellular location and that it interacts with key cell division proteins, MinD, and FtsH, as well as with a rod shape-determining protein MerB. Full article
(This article belongs to the Section Microbiology)
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Open AccessArticle
Cryotolerance of Stallion Spermatozoa Relies on Aquaglyceroporins rather than Orthodox Aquaporins
Biology 2019, 8(4), 85; https://doi.org/10.3390/biology8040085 - 12 Nov 2019
Abstract
Aquaporins (AQPs), a family of ubiquitous water channels divided into orthodox AQPs, aquaglyceroporins (GLPs), and superAQPs, are present in stallion spermatozoa. The aim of this study was to elucidate the functional relevance of each group of AQPs during stallion sperm cryopreservation through the [...] Read more.
Aquaporins (AQPs), a family of ubiquitous water channels divided into orthodox AQPs, aquaglyceroporins (GLPs), and superAQPs, are present in stallion spermatozoa. The aim of this study was to elucidate the functional relevance of each group of AQPs during stallion sperm cryopreservation through the use of three different inhibitors: acetazolamide (AC), phloretin (PHL) and propanediol (PDO). Sperm quality and function parameters were evaluated in the presence or absence of each inhibitor in fresh and frozen–thawed samples. In the presence of AC, different parameters were altered (p < 0.05), but not in a concentration- or time-depending manner. PHL was found to decrease sperm motility, viability, acrosome integrity, and the percentages of spermatozoa with low membrane lipid disorder, high mitochondrial membrane potential (MMP) and high intracellular levels of calcium and superoxides (p < 0.05). Finally, the sperm motility, viability, acrosome integrity, the percentages of spermatozoa with low membrane lipid disorder, high MMP and high intracellular calcium levels were higher (p < 0.05) in PDO treatments than in the control. The sperm response to AC, PHL and PDO indicates that GLPs, rather than orthodox AQPs, play a crucial role during stallion sperm cryopreservation. Furthermore, post-thaw sperm quality was higher in PDO treatments than in the control, suggesting that this molecule is a potential permeable cryoprotectant. Full article
(This article belongs to the Section Zoology)
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Open AccessArticle
Melatonin Inhibits Transforming Growth Factor-β1-Induced Epithelial–Mesenchymal Transition in AML12 Hepatocytes
Biology 2019, 8(4), 84; https://doi.org/10.3390/biology8040084 - 11 Nov 2019
Abstract
Recent studies showed that melatonin, a well-known pineal hormone that modulates the circadian rhythm, exerts beneficial effects against liver fibrosis. However, mechanisms for its protective action against the fibrotic processes remain incompletely understood. Here, we aimed to explore the effects of the hormone [...] Read more.
Recent studies showed that melatonin, a well-known pineal hormone that modulates the circadian rhythm, exerts beneficial effects against liver fibrosis. However, mechanisms for its protective action against the fibrotic processes remain incompletely understood. Here, we aimed to explore the effects of the hormone on transforming growth factor-β1 (TGF-β1)-stimulated epithelial–mesenchymal transition (EMT) in AML12 hepatocytes. Pretreatment with melatonin dose-dependently reversed downregulation of an epithelial marker and upregulation of mesenchymal markers after TGF-β1 stimulation. Additionally, melatonin dose-dependently suppressed an increased phosphorylation of Smad2/3 after TGF-β1 treatment. Besides the canonical Smad signaling pathway, an increase in phosphorylation of extracellular signal-regulated kinase 1/2 and p38 was also dose-dependently attenuated by melatonin. The suppressive effect of the hormone on EMT stimulated by TGF-β1 was not affected by luzindole, an antagonist of melatonin membrane receptors, suggesting that its membrane receptors are not required for the inhibitory action of melatonin. Moreover, melatonin suppressed elevation of intracellular reactive oxygen species (ROS) levels in TGF-β1-treated cells. Finally, TGF-β1-stimulated EMT was also inhibited by the antioxidant N-acetylcysteine. Collectively, these results suggest that melatonin prevents TGF-β1-stimulated EMT through suppression of Smad and mitogen-activated protein kinase signaling cascades by deactivating ROS-dependent mechanisms in a membrane receptor-independent manner. Full article
(This article belongs to the Section Cell Biology)
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Open AccessArticle
Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation
Biology 2019, 8(4), 83; https://doi.org/10.3390/biology8040083 - 04 Nov 2019
Abstract
A precise understanding of the molecular mechanism involved in stress conditions has great importance for crop improvement. Biomolecules, such as WRKY proteins, which are the largest transcription factor family that is widely distributed in higher plants, plays a significant role in plant defense [...] Read more.
A precise understanding of the molecular mechanism involved in stress conditions has great importance for crop improvement. Biomolecules, such as WRKY proteins, which are the largest transcription factor family that is widely distributed in higher plants, plays a significant role in plant defense response against various biotic and abiotic stressors. In the present study, an extensive homology-based three-dimensional model construction and subsequent interaction study of WRKY DNA-binding domain (DBD) in CcWRKY1 (Type I), CcWRKY51 (Type II), and CcWRKY70 (Type III) belonging to pigeonpea, a highly tolerant crop species, was performed. Evaluation of the generated protein models was done to check their reliability and accuracy based on the quantitative and qualitative parameters. The final model was subjected to investigate the comparative binding analysis of different types of WRKY–DBD with DNA-W-box (a cis-acting element) by protein–DNA docking and molecular dynamics (MD) simulation. The DNA binding specificity with WRKY variants was scrutinized through protein–DNA interaction using the HADDOCK server. The stability, as well as conformational changes of protein–DNA complex, was investigated through molecular dynamics (MD) simulations for 100 ns using GROMACS. Additionally, the comparative stability and dynamic behavior of each residue of the WRKY–DBD type were analyzed in terms of root mean square deviation (RMSD), root mean square fluctuation (RMSF)values of the backbone atoms for each frame taking the minimized structure as a reference. The details of DNA binding activity of three different types of WRKY–DBD provided here will be helpful to better understand the regulation of WRKY gene family members in plants. Full article
(This article belongs to the Section Plant Science)
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Open AccessReview
Autophagy in Cancer Cell Death
Biology 2019, 8(4), 82; https://doi.org/10.3390/biology8040082 - 29 Oct 2019
Abstract
Autophagy has important functions in maintaining energy metabolism under conditions of starvation and to alleviate stress by removal of damaged and potentially harmful cellular components. Therefore, autophagy represents a pro-survival stress response in the majority of cases. However, the role of autophagy in [...] Read more.
Autophagy has important functions in maintaining energy metabolism under conditions of starvation and to alleviate stress by removal of damaged and potentially harmful cellular components. Therefore, autophagy represents a pro-survival stress response in the majority of cases. However, the role of autophagy in cell survival and cell death decisions is highly dependent on its extent, duration, and on the respective cellular context. An alternative pro-death function of autophagy has been consistently observed in different settings, in particular, in developmental cell death of lower organisms and in drug-induced cancer cell death. This cell death is referred to as autophagic cell death (ACD) or autophagy-dependent cell death (ADCD), a type of cellular demise that may act as a backup cell death program in apoptosis-deficient tumors. This pro-death function of autophagy may be exerted either via non-selective bulk autophagy or excessive (lethal) removal of mitochondria via selective mitophagy, opening new avenues for the therapeutic exploitation of autophagy/mitophagy in cancer treatment. Full article
(This article belongs to the Special Issue Autophagy in Cancer)
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Open AccessArticle
Hormonal Regulation of Glucocorticoid Inactivation and Reactivation in αT3-1 and LβT2 Gonadotroph Cells
Biology 2019, 8(4), 81; https://doi.org/10.3390/biology8040081 - 26 Oct 2019
Abstract
The regulation of reproductive function by glucocorticoids occurs at all levels of the hypothalamo-pituitary-gonadal axis. Within the pituitary, glucocorticoids have been shown to directly alter gene expression in gonadotrophs, indicating that these cell types are sensitive to regulation by the glucocorticoid receptor. Whilst [...] Read more.
The regulation of reproductive function by glucocorticoids occurs at all levels of the hypothalamo-pituitary-gonadal axis. Within the pituitary, glucocorticoids have been shown to directly alter gene expression in gonadotrophs, indicating that these cell types are sensitive to regulation by the glucocorticoid receptor. Whilst the major glucocorticoid metabolising enzymes, 11β-hydroxysteroid dehydrogenase (11βHSD; HSD11B1 and HSD11B2), have been described in human pituitary adenomas, the activity of these enzymes within different pituitary cell types has not been reported. Radiometric conversion assays were performed in αT3-1, LβT2 (gonadotrophs), AtT-20 (corticotrophs) and GH3 (somatolactotrophs) anterior pituitary cell lines, using tritiated cortisol, corticosterone, cortisone or 11-dehydrocorticosterone as substrates. The net oxidation of cortisol/corticosterone and net reduction of cortisone/11-dehydrocorticosterone were significantly higher in the two gonadotroph cells lines compared with the AtT-20 and GH3 cells after 4 h. Whilst these enzyme activities remained the same in αT3-1 and LβT2 cells over a 24 h period, there was a significant increase in glucocorticoid metabolism in both AtT-20 and GH3 cells over this same period, suggesting cell-type specific activity of the 11βHSD enzyme(s). Stimulation of both gonadotroph cell lines with either 100 nM GnRH or PACAP (known physiological regulators of gonadotrophs) resulted in significantly increased 11β-dehydrogenase (11βDH) and 11-ketosteroid reductase (11KSR) activities, over both 4 and 24 h. These data reveal that gonadotroph 11βHSD enzyme activity can act to regulate local glucocorticoid availability to mediate the influence of the HPA axis on gonadotroph function. Full article
(This article belongs to the Section Cell Biology)
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Open AccessArticle
Wheat Yellow Mosaic Virus NIb Interacting with Host Light Induced Protein (LIP) Facilitates Its Infection through Perturbing the Abscisic Acid Pathway in Wheat
Biology 2019, 8(4), 80; https://doi.org/10.3390/biology8040080 - 23 Oct 2019
Abstract
Positive-sense RNA viruses have a small genome with very limited coding capacity and are highly reliant on host factors to fulfill their infection. However, few host factors have been identified to participate in wheat yellow mosaic virus (WYMV) infection. Here, we demonstrate that [...] Read more.
Positive-sense RNA viruses have a small genome with very limited coding capacity and are highly reliant on host factors to fulfill their infection. However, few host factors have been identified to participate in wheat yellow mosaic virus (WYMV) infection. Here, we demonstrate that wheat (Triticum aestivum) light-induced protein (TaLIP) interacts with the WYMV nuclear inclusion b protein (NIb). A bimolecular fluorescence complementation (BIFC) assay displayed that the subcellular distribution patterns of TaLIP were altered by NIb in Nicotiana benthamiana. Transcription of TaLIP was significantly decreased by WYMV infection and TaLIP-silencing wheat plants displayed more susceptibility to WYMV in comparison with the control plants, suggesting that knockdown of TaLIP impaired host resistance. Moreover, the transcription level of TaLIP was induced by exogenous abscisic acid (ABA) stimuli in wheat, while knockdown of TaLIP significantly repressed the expression of ABA-related genes such as wheat abscisic acid insensitive 5 (TaABI5), abscisic acid insensitive 8 (TaABI8), pyrabatin resistance 1-Llike (TaPYL1), and pyrabatin resistance 3-Llike (TaPYL3). Collectively, our results suggest that the interaction of NIb with TaLIP facilitated the virus infection possibly by disturbing the ABA signaling pathway in wheat. Full article
(This article belongs to the Section Plant Science)
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Open AccessReview
Circadian Clock Regulation of Hepatic Energy Metabolism Regulatory Circuits
Biology 2019, 8(4), 79; https://doi.org/10.3390/biology8040079 - 19 Oct 2019
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Abstract
The liver is a critical organ of energy metabolism. At least 10% of the liver transcriptome demonstrates rhythmic expression, implying that the circadian clock regulates large programmes of hepatic genes. Here, we review the mechanisms by which this rhythmic regulation is conferred, with [...] Read more.
The liver is a critical organ of energy metabolism. At least 10% of the liver transcriptome demonstrates rhythmic expression, implying that the circadian clock regulates large programmes of hepatic genes. Here, we review the mechanisms by which this rhythmic regulation is conferred, with a particular focus on the transcription factors whose actions combine to impart liver- and time-specificity to metabolic gene expression. Full article
(This article belongs to the Special Issue Biological Clocks)
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Open AccessArticle
Histone H2A and Bovine Neutrophil Extracellular Traps Induce Damage of Besnoitia besnoiti-Infected Host Endothelial Cells but Fail to Affect Total Parasite Proliferation
Biology 2019, 8(4), 78; https://doi.org/10.3390/biology8040078 - 11 Oct 2019
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Abstract
Besnoitia besnoiti tachyzoites infect and develop in bovine endothelial cells in vivo and trigger the release of neutrophil extracellular traps (NETs) from bovine polymorphonuclear neutrophils (PMN). The purpose of this study was to analyze if pure B. besnoiti tachyzoite-triggered NETs would damage endothelial [...] Read more.
Besnoitia besnoiti tachyzoites infect and develop in bovine endothelial cells in vivo and trigger the release of neutrophil extracellular traps (NETs) from bovine polymorphonuclear neutrophils (PMN). The purpose of this study was to analyze if pure B. besnoiti tachyzoite-triggered NETs would damage endothelial host cells and subsequently influence intracellular development and proliferation of B. besnoiti tachyzoites in primary bovine endothelial cells. For comparison purposes, isolated A23187-induced NETs were also used. Thus, we here evaluated endothelial host cell damage triggered by histone 2A (H2A) and B. besnoiti tachyzoite-induced NET preparations and furthermore estimated the effects of PMN floating over B. besnoiti-infected endothelium under physiological flow conditions on endothelial host cell viability. Overall, all treatments (H2A, B. besnoiti-triggered NETs and floating PMN) induced endothelial cell death of B. besnoiti-infected host cells. However, though host cell damage led to significantly altered intracellular parasite development with respect to parasitophorous vacuole diameter and numbers, the total proliferation of the parasite over time was not significantly affected by these treatments thereby denying any direct effect of NETs on intracellular B. besnoiti replication. Full article
(This article belongs to the Special Issue Neutrophil Extracellular Traps)
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Open AccessArticle
Sequence Determinants of Substrate Ambiguity in a HAD Phosphosugar Phosphatase of Arabidopsis Thaliana
Biology 2019, 8(4), 77; https://doi.org/10.3390/biology8040077 - 09 Oct 2019
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Abstract
The Arabidopsis thaliana broad-range sugar phosphate phosphatase AtSgpp (NP_565895.1, locus AT2G38740) and the specific DL-glycerol-3-phosphatase AtGpp (NP_568858.1, locus AT5G57440) are members of the wide family of magnesium-dependent acid phosphatases subfamily I with the C1-type cap domain haloacid dehalogenase-like hydrolase proteins (HAD). Although both [...] Read more.
The Arabidopsis thaliana broad-range sugar phosphate phosphatase AtSgpp (NP_565895.1, locus AT2G38740) and the specific DL-glycerol-3-phosphatase AtGpp (NP_568858.1, locus AT5G57440) are members of the wide family of magnesium-dependent acid phosphatases subfamily I with the C1-type cap domain haloacid dehalogenase-like hydrolase proteins (HAD). Although both AtSgpp and AtGpp have a superimporsable α/β Rossmann core active site, they differ with respect to the loop-5 of the cap domain, accounting for the differences in substrate specificity. Recent functional studies have demonstrated the essential but not sufficient role of the signature sequence within the motif-5 in substrate discrimination. To better understand the mechanism underlying the control of specificity, we explored additional sequence determinants underpinning the divergent evolutionary selection exerted on the substrate affinity of both enzymes. The most evident difference was found in the loop preceding the loop-5 of the cap domain, which is extended in three additional residues in AtSgpp. To determine if the shortening of this loop would constrain the substrate ambiguity of AtSgpp, we deleted these three aminoacids. The kinetic analyses of the resulting mutant protein AtSgpp3Δ (ΔF53, ΔN54, ΔN55) indicate that promiscuity is compromised. AtSgpp3Δ displays highest level of discrimination for D-ribose-5-phosphate compared to the rest of phosphate ester metabolites tested, which may suggest a proper orientation of D-ribose-5-phosphate in the AtSgpp3Δ active site. Full article
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Open AccessArticle
Cytotoxic Potential of the Coelomic Fluid Extracted from the Sea Cucumber Holothuria tubulosa against Triple-Negative MDA-MB231 Breast Cancer Cells
Biology 2019, 8(4), 76; https://doi.org/10.3390/biology8040076 - 09 Oct 2019
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Abstract
Growing evidence has demonstrated that the extracts of different holothurian species exert beneficial effects on human health. Triple negative breast cancers (TNBC) are highly malignant tumors that present a poor prognosis due to the lack of effective targeted therapies. In the attempt to [...] Read more.
Growing evidence has demonstrated that the extracts of different holothurian species exert beneficial effects on human health. Triple negative breast cancers (TNBC) are highly malignant tumors that present a poor prognosis due to the lack of effective targeted therapies. In the attempt to identify novel compounds that might counteract TNBC cell growth, we studied the effect of the exposure of the TNBC cell line MDA-MB231 to total and filtered aqueous extracts of the coelomic fluid obtained from the sea cucumber Holoturia tubulosa, a widespread species in the Mediterranean Sea. In particular, we examined cell viability and proliferative behaviour, cell cycle distribution, apoptosis, autophagy, and mitochondrial metabolic/cell redox state. The results obtained indicate that both total and fractionated extracts are potent inhibitors of TNBC cell viability and growth, acting through both an impairment of cell cycle progression and mitochondrial transmembrane potential and a stimulation of cellular autophagy, as demonstrated by the increase of the acidic vesicular organelles and of the intracellular protein markers beclin-1, and total LC3 and LC3-II upon early exposure to the preparations. Identification of the water-soluble bioactive component(s) present in the extract merit further investigation aiming to develop novel prevention and/or treatment agents efficacious against highly metastatic breast carcinomas. Full article
(This article belongs to the Special Issue Autophagy in Cancer)
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Open AccessArticle
Development of a Novel Quinoline Derivative as a P-Glycoprotein Inhibitor to Reverse Multidrug Resistance in Cancer Cells
Biology 2019, 8(4), 75; https://doi.org/10.3390/biology8040075 - 01 Oct 2019
Viewed by 242
Abstract
Multidrug resistance (MDR) is one of conventional cancer chemotherapy’s limitations. Our group previously synthesized a series of quinoline-based compounds in an attempt to identify novel anticancer agents. With a molecular docking analysis, the novel compound 160a was predicted to target p-glycoprotein, an MDR [...] Read more.
Multidrug resistance (MDR) is one of conventional cancer chemotherapy’s limitations. Our group previously synthesized a series of quinoline-based compounds in an attempt to identify novel anticancer agents. With a molecular docking analysis, the novel compound 160a was predicted to target p-glycoprotein, an MDR candidate. The purpose of this study is to evaluate 160a’s MDR reversal effect and investigate the underlying mechanism at the molecular level. To investigate 160a’s inhibitory effect, we used a series of parental cancer cell lines (A549, LCC6, KYSE150, and MCF-7), the corresponding doxorubicin-resistant cell lines, an MTS cytotoxicity assay, an intracellular doxorubicin accumulation test, and multidrug resistance assays. The Compusyn program confirmed, with a combination index (CI) value greater than 1, that 160a combined with doxorubicin exerts a synergistic effect. Intracellular doxorubicin accumulation and transported calcein acetoxymethyl (AM) (a substrate for p-glycoprotein) were both increased when cancer cells with MDR were treated with compound 160a. We also showed that compound 160a’s MDR reversal effect can persist for at least 1 h. Taken together, these results suggest that the quinoline compound 160a possesses high potential to reverse MDR by inhibiting p-glycoprotein-mediated drug efflux in cancer cells with MDR. Full article
(This article belongs to the Section Cell Biology)
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Open AccessArticle
The H2S–Nrf2–Antioxidant Proteins Axis Protects Renal Tubular Epithelial Cells of the Native Hibernator Syrian Hamster from Reoxygenation-Induced Cell Death
Biology 2019, 8(4), 74; https://doi.org/10.3390/biology8040074 - 30 Sep 2019
Viewed by 278
Abstract
During hibernation, repeated cycles of ischemia-reperfusion (I-R) leave vital organs without injury. Studying this phenomenon may reveal pathways applicable to improving outcomes in I-R injury-induced human diseases. We evaluated whether the H2S–nuclear factor erythroid 2-like 2 (Nrf2)–antioxidant proteins axis protects renal [...] Read more.
During hibernation, repeated cycles of ischemia-reperfusion (I-R) leave vital organs without injury. Studying this phenomenon may reveal pathways applicable to improving outcomes in I-R injury-induced human diseases. We evaluated whether the H2S–nuclear factor erythroid 2-like 2 (Nrf2)–antioxidant proteins axis protects renal proximal tubular epithelial cells (RPTECs) of the native hibernator, the Syrian hamster, from reperfusion-induced cell death. To imitate I-R, the hamsters’, and control mice’s RPTECs were subjected to warm anoxia, washed, and then subjected to reoxygenation in fresh culture medium. Whenever required, the H2S-producing enzymes inhibitor aminooxyacetate or the lipid peroxidation inhibitor α-tocopherol were used. A handmade H2S detection methylene blue assay, a reactive oxygen species (ROS) detection kit, a LDH release cytotoxicity assay kit, and western blotting were used. Reoxygenation upregulated the H2S-producing enzymes cystathionine beta-synthase, cystathionine γ-lyase, and 3-mercaptopyruvate sulfurtransferase in the hamster, but not in mouse RPTECs. As a result, H2S production increased only in the hamster RPTECs under reoxygenation conditions. Nrf2 expression followed the alterations of H2S production leading to an enhanced level of the antioxidant enzymes superoxide dismutase 3 and glutathione reductase, and anti-ferroptotic proteins ferritin H and cystine-glutamate antiporter. The upregulated antioxidant enzymes and anti-ferroptotic proteins controlled ROS production and rescued hamster RPTECs from reoxygenation-induced, lipid peroxidation-mediated cell death. In conclusion, in RPTECs of the native hibernator Syrian hamster, reoxygenation activates the H2S–Nrf2–antioxidant proteins axis, which rescues cells from reoxygenation-induced cell death. Further studies may reveal that the therapeutic activation of this axis in non-hibernating species, including humans, may be beneficial in I-R injury-induced diseases. Full article
(This article belongs to the Section Cell Biology)
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Open AccessArticle
Effects of Pulsed Electric Field on the Cell Wall and Infection Activity of Rhizoctonia solani
Biology 2019, 8(4), 73; https://doi.org/10.3390/biology8040073 - 26 Sep 2019
Viewed by 238
Abstract
This paper adopts the Design-Expert software to design an orthogonal experiment with a pulse voltage amplitude of 30 kV, processing time of three minutes, and a pulse width of 45 μs as the center points, in order to study the effects of the [...] Read more.
This paper adopts the Design-Expert software to design an orthogonal experiment with a pulse voltage amplitude of 30 kV, processing time of three minutes, and a pulse width of 45 μs as the center points, in order to study the effects of the pulsed electric field on the cell wall and infection activity of Rhizoctonia solani. High-voltage pulse power was used to treat the bacteria solution with the pulsed electric field. Untreated Rhizoctonia solani were used as the control group. Transmission electron microscope images were used to analyze the cell wall damage. ANOVA was performed on the experimental results and the fitting degree of the model was good (F>>1). Response surface analysis was used to optimize the parameters based on chitin content and polygalacturonase activity. The optimal treatment conditions were obtained as a pulse voltage amplitude of 25 kV, processing time of 2.54 min, and a pulse width of 34.35 μs. On this basis, experiments were designed to verify the optimized conditions. The results demonstrated that, under the optimal processing conditions, the damage index of the cell wall of Rhizoctonia solani was 9.59% lower in chitin content and 83.05% lower in polygalacturonase activity compared with those of the control group. All indexes were significantly different (P < 0.001), which is consistent with the parameter optimization results. The results provide a theoretical basis for the pulsed electric field assisted sterilization and reference for the design of plant protection machinery in the latter stage. Full article
(This article belongs to the Section Biophysics)
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Open AccessArticle
In Vitro Propagation of Rheophytic Orchid, Epipactis flava Seidenf.—A Comparison of Semi-Solid, Continuous Immersion and Temporary Immersion Systems
Biology 2019, 8(4), 72; https://doi.org/10.3390/biology8040072 - 24 Sep 2019
Viewed by 263
Abstract
Epipactis flava Seidenf. is an endangered Thai rheophytic orchid that has recently shown a rapid decrease in its natural habitat, prompting an urgent need for conservation using ex situ reintroduction methods. Temporary immersion system (TIS) has been successfully applied for large-scale propagation in [...] Read more.
Epipactis flava Seidenf. is an endangered Thai rheophytic orchid that has recently shown a rapid decrease in its natural habitat, prompting an urgent need for conservation using ex situ reintroduction methods. Temporary immersion system (TIS) has been successfully applied for large-scale propagation in various plants species. Propagation efficiency of E. flava using TIS was investigated and compared with conventional semi-solid system (SSS) and liquid continuous immersion system (CIS). The highest percentage of new shoot and shoot bud formation was obtained from TIS, followed by CIS and SSS, respectively. Growth parameters as indicated by number of new shoots, shoot buds, shoot height and leaves per explant were significantly higher using TIS than with SSS and CIS. Moreover, the maximum number of new shoots and shoot buds per replication were reliably obtained from TIS higher than SSS and CIS. After acclimatization, the highest survival percentage of plantlets was observed in TIS (76.7%), with 60% surviving after eight weeks of transplantation in artificial stream. TIS was determined as the most suitable culture system for in vitro mass propagation of E. flava compared to CIS and SSS. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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Open AccessReview
Autophagy and Its Relationship to Epithelial to Mesenchymal Transition: When Autophagy Inhibition for Cancer Therapy Turns Counterproductive
Biology 2019, 8(4), 71; https://doi.org/10.3390/biology8040071 - 24 Sep 2019
Viewed by 351
Abstract
The manipulation of autophagy for cancer therapy has gained recent interest in clinical settings. Although inhibition of autophagy is currently being used in clinical trials for the treatment of several malignancies, autophagy has been shown to have diverse implications for normal cell homeostasis, [...] Read more.
The manipulation of autophagy for cancer therapy has gained recent interest in clinical settings. Although inhibition of autophagy is currently being used in clinical trials for the treatment of several malignancies, autophagy has been shown to have diverse implications for normal cell homeostasis, cancer cell survival, and signaling to cells in the tumor microenvironment. Among these implications and of relevance for cancer therapy, the autophagic process is known to be involved in the regulation of protein secretion, in tumor cell immunogenicity, and in the regulation of epithelial-to-mesenchymal transition (EMT), a critical step in the process of cancer cell invasion. In this work, we have reviewed recent evidence linking autophagy to the regulation of EMT in cancer and normal epithelial cells, and have discussed important implications for the manipulation of autophagy during cancer therapy. Full article
(This article belongs to the Special Issue Autophagy in Cancer)
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Open AccessArticle
Extraction, Storage Duration, and Storage Temperature Affect the Activity of Ascorbate Peroxidase, Glutathione Reductase, and Superoxide Dismutase in Rice Tissue
Biology 2019, 8(4), 70; https://doi.org/10.3390/biology8040070 - 24 Sep 2019
Viewed by 276
Abstract
In experimental plant science, research often faces large numbers of tissue samples resulting from sequential harvests of a larger number of genotypes and treatments combinations. Analyses of biological processes such as enzyme kinetics are often time-consuming or need specific sample preparation procedures before [...] Read more.
In experimental plant science, research often faces large numbers of tissue samples resulting from sequential harvests of a larger number of genotypes and treatments combinations. Analyses of biological processes such as enzyme kinetics are often time-consuming or need specific sample preparation procedures before the actual measurements can be done. Time is thus often the critical factor and the possibility to store plant samples either as tissue or as extracts increases the available timeframe for analyses. Biological molecules such as enzymes often change their activities when stored and thus do not reflect the processes occurring in living tissue. We investigated the effect of different storage methods such as freeze-drying, freezing at −20 °C, and freezing at −80 °C on the activity of three enzymes known as antioxidants, namely ascorbate peroxidase, glutathione reductase, and superoxide dismutase from two rice varieties. Varieties differed in enzyme activity in extracts of fresh material from leaf blades, leaf sheaths, and roots. When subjected to different storage methods, there were no differences between varieties, but strong effects of the different storage methods on enzyme activities were found. The effects of the storage methods on enzyme activity strongly differed between extracts from stored tissue samples or extracts stored from freshly sampled material. We propose enzyme-specific storage methods and durations that allow for expanding the window for analyses in large experimental studies involving destructive samplings for enzyme kinetics. Full article
(This article belongs to the Section Physiology)
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Open AccessArticle
The Role of Lipopolysaccharide-Induced Extracellular Vesicles in Cardiac Cell Death
Biology 2019, 8(4), 69; https://doi.org/10.3390/biology8040069 - 23 Sep 2019
Viewed by 322
Abstract
Exosomes play a crucial role in the progression of infectious diseases, as exosome release and biogenesis are affected by external factors, such as pathogenic infections. Pyrogens may aide in the progression of diseases by triggering inflammation, endothelial cell injury, and arterial plaque rupture, [...] Read more.
Exosomes play a crucial role in the progression of infectious diseases, as exosome release and biogenesis are affected by external factors, such as pathogenic infections. Pyrogens may aide in the progression of diseases by triggering inflammation, endothelial cell injury, and arterial plaque rupture, all of which can lead to acute coronary disease, resulting in cardiac tissue death and the onset of a cardiac event (CE). To better understand the effects of Gram-negative bacterial infections on exosome composition and biogenesis, we examined exosome characteristics after treatment of AC16 human cardiomyocytes with lipopolysaccharide (LPS), which served as a model system for Gram-negative bacterial infection. Using increasing doses (0, 0.1, 1, or 10 µg) of LPS, we showed that treatment with LPS substantially altered the composition of AC16-derived exosomes. Both the relative size and the quantity (particles/mL) of exosomes were decreased significantly at all tested concentrations of LPS treatment compared to the untreated group. In addition, LPS administration reduced the expression of exosomal proteins that are related to exosomal biogenesis. Conversely, we observed an increase in immunomodulators present after LPS administration. This evaluation of the impact of LPS on cardiac cell death and exosome composition will yield new insight into the importance of exosomes in a variety of physiological and pathological processes as it relates to disease progression, diagnosis, and treatment. Full article
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