Detoxification Genes Research Articles

Uncovering Sex‐specific Roles of Farnesoid X Receptor in Heme Metabolism and Liver Proliferation

Nuclear receptor, Farnesoid X Receptor (FXR), regulates bile acid homeostasis and has been shown to promote liver regenerative response. Serendipitously, we uncovered a distinct role for FXR in mediating liver injury response in female compared to male mice challenged with 3,5‐diethoxycarboncyl‐1,4‐dihydrocollidine (DDC, a heme biosynthesis disruptor). As expected, the DDC diet led to liver injury as measured by elevated serum ALT and AST levels in both control and FxrKO mice. Furthermore, accumulation of bile plugs and ductular reaction was visible in the WT mice, whereas both of these histological hallmarks were dramatically reduced in FxrKO mice. Despite similar histology, the proliferative response in the hepatocytes were different between both the sexes of FxrKO animals. Loss of Fxr resulted in increased hepatocyte size and low‐grade Ki‐67 positive hepatocyte nuclei even under basal conditions. But upon DDC challenge, FxrKO female livers displayed a dramatic induction of Ki‐67 positive staining even though no bile duct injury was visible. This finding correlated well with increased expression of cyclins. On the contrary, Ki‐67 staining was comparable between male FxrKO livers fed either chow or DDC diet, which matches with lower injury. We are actively investigating the crosstalk of estrogen signaling with FXR in controlling liver proliferation. At the molecular level, genes regulating the cell cycle (Ccnd1, Ccna, Ccnb1) were induced upon injury in the male livers in an Fxr‐dependent manner, whereas this response was not observed in female livers. Expression of Cyp2b10 and Cyp3a11, which are known detoxification genes, were induced with DDC treatment. To test if the absence of bile plugs in FxrKO mice is secondary to reduced heme synthesis in these livers, we examined the heme biosynthetic pathway. We mined previously published data and found strong Fxr occupancy and binding to 6 out of the 8 genes involved in the heme synthesis pathway including Alas1, which is the rate‐limiting step in heme biosynthesis. In summary, FXR may regulate heme metabolism and modulate hepatocyte proliferation in a sex‐specific manner.Support or Funding InformationResearch Scholar Grant TBE 132315

DOES CARDIOPLEGIA PROVIDE CARDIAC PROTECTION BY INDUCING Nr‐E2 RELATED FACTOR‐2(Nrf2)

BackgroundOpen heart surgery is often an unavoidable procedure for treatment of cardiovascular disease. Myocardial ischemia‐reperfusion injury (MIRI) can occur as a result of cardiopulmonary bypass. The multifaceted mechanisms of MIRI involve the generation of proinflammatory mediators and increases in reactive oxygen species (ROS), resulting in damage to proteins, lipids, and DNA, ultimately impacting postoperative cardiac function and outcomes. Nf‐E2 related factor‐2 (Nrf2), a basic leucine zipper transcription factor, is regarded as one of the most important regulators in antioxidant pathways. Nrf2 binds to and activates the Antioxidant Response Element (ARE) in the promoters of many antioxidant and detoxification genes.PurposeWe addressed whether or not cardioplegic solutions induce the activation of Nrf2, therefore serving to protect the myocardium from MIRI. Methods. We used adult cardiomyocytes in culture to test whether or not four different types of cardioplegic solutions induce Nrf2. The conditions tested include routine laboratory cell culture at 37°C and hypothermic temperatures of 10–20°C.ResultsOur data show that certain cardioplegic solutions caused increases in Nrf2 protein levels under both cell culture and hypothermic conditions. ARE luciferase reporter assay confirmed Nrf2 activation by the cardioplegic solutions. Both High K and Del Nido showed reliable activation of Nrf2.ConclusionsOur data supports our hypothesis that cardioplegic solutions can be cardiac protective via the activation of Nrf2.Support or Funding InformationThis work is supported by research grants of NIH R01 GM125212 (QMC), NIH R01 GM126165 (QMC), Holsclaw Endowment (QMC)

Effects of Neural Gene Expressions on Grooming Behavior in Honey Bees

Grooming behavior, which is one of the behavioral resistance mechanisms based on the genetic basis in honeybees, is a defense response against parasitic mites, especially Varroa mite. In recent years, scientists and beekeepers have focused on bee breeding in terms of grooming behavior, because honey bees showing grooming behavior have the potential to can protect themselves against Varroa destructor. It is of great importance to determine the genes and gene regions related to this behavior before starting the breeding studies in terms of grooming behavior. In this respect, the right honey bee species or races can be selected and the success rate will increase. In researches, it was found that bees exhibit different grooming behaviors level according to species and races. Therefore, some species and races were found to be more successful than others. Especially in neural, developmental, detoxification and health-related gene expression studies, it has been shown that some gene expression is in direct proportion to the intensity of grooming behavior. While the genes responsible for grooming behavior are not known exactly, studies are underway to solve the genetic mechanism of this behavior. In this study, we reviewed the effects of neural gene expression on grooming behavior.

Transcriptional response of zebrafish larvae exposed to lindane reveals two detoxification genes of ABC transporter family (abcg5 and abcg8)

Lindane is a highly toxic organochlorine pesticide and widely exist in water with harmful effects on fish. Although some genes have been found to be regulated by lindane in fish, the transcriptional response of fish exposed to lindane is still unknown. In this research, the transcriptional changes of zebrafish larvae exposed to 0.2 mg/L lindane from 96 to 120 hpf were studied by RNA sequencing. Our transcriptome identified 554 up-regulated and 118 down-regulated genes and the differentially expressed genes were closely related to the neuromast development, RNA silencing genes, ion transport, and response to estrogen. In addition, we characterized two sensitive and novel lindane-induced ABCG (ATP binding cassette G subfamily) transporter genes- abcg5 and abcg8. Abcg5 and abcg8 genes are located on chromosome 13 of zebrafish and contain 1956/2024 bp open reading frame. The polypeptide deduced by CDS amplification contains 652/676 amino acids and has most of the functional domains and key residues defined in human and mouse ABCG5/Abcg5 or ABCG8/Abcg8. Only when the co-expression of Abcg5 and Abcg8 enable them to transport to the cell membrane surface in 293T cells. In addition, lindane can induce the transcriptional expression of abcg5 and abcg8 genes, and overexpression of Abcg5 and Abcg8 significantly reduced the toxicity of lindane to zebrafish larvae, which means that zebrafish Abcg5 and Abcg8 are potential efflux transporters of lindane. Therefore, these findings provide useful insights for further understanding the zebrafish larvae's transcriptional response and detoxification ability after acute exposure to lindane.

Protective Mechanisms of Avocado Oil Extract Against Ototoxicity

Despite the excellent antimicrobial activity of aminoglycoside antibiotics, permanent inner ear damage associated with the use of these drugs has resulted in the need to develop strategies to address the ototoxic risk given their widespread use. In a previous study, we showed that avocado oil protects ear hair cells from damage caused by neomycin. However, the detailed mechanism by which this protection occurs is still unclear. Here, we investigated the auditory cell-protective mechanism of enhanced functional avocado oil extract (DKB122). RNA sequencing followed by pathway analysis revealed that DKB122 has the potential to enhance the expression of detoxification and antioxidant genes associated with glutathione metabolism (Hmox4, Gsta4, Mgst1, and Abcc3) in HEI-OC1 cells. Additionally, DKB122 effectively decreased ROS levels, resulting in the inhibition of apoptosis in HEI-OC1 cells. The expression of the inflammatory genes that encode chemokines and interleukins was also downregulated by DKB122 treatment. Consistent with these results, DKB122 significantly inhibited p65 nuclear migration induced by TNF-α or LPS in HEI-OC1 cells and THP-1 cells and the expression of inflammatory chemokine and interleukin genes induced by TNF-α was significantly reduced. Moreover, DKB122 treatment increased LC3-II and decreased p62 in HEI-OC1 cells, suggesting that DKB122 increases autophagic flux. These results suggest that DKB122 has otoprotective effects attributable to its antioxidant activity, induction of antioxidant gene expression, anti-inflammatory activity, and autophagy activation.

The Thyromimetic Sobetirome (GC-1) Alters Bile Acid Metabolism in a Mouse Model of Hepatic Cholestasis

Chronic cholestasis results from bile secretory defects or impaired bile flow with few effective medical therapies available. Thyroid hormone triiodothyronine and synthetic thyroid hormone receptor agonists, such as sobetirome (GC-1), are known to impact lipid and bile acid (BA) metabolism and induce hepatocyte proliferation downstream of Wnt/β-catenin signaling after surgical resection; however, these drugs have yet to be studied as potential therapeutics for cholestatic liver disease. Herein, GC-1 was administered to ATP binding cassette subfamily B member 4 (Abcb4-/-; Mdr2-/-) knockout (KO) mice, a sclerosing cholangitis model. KO mice fed GC-1 diet for 2 and 4 weeks had decreased serum alkaline phosphatase but increased serum transaminases compared with KO alone. KO mice on GC-1 also had higher levels of total liver BA due to alterations in expression of BA detoxification, transport, and synthesis genes, with the net result being retention of BA in the hepatocytes. Interestingly, GC-1 does not induce hepatocyte proliferation or Wnt/β-catenin signaling in KO mice, likely a result of decreased thyroid hormone receptor β expression without Mdr2. Therefore, although GC-1 treatment induces a mild protection against biliary injury in the early stages of treatment, it comes at the expense of hepatocyte injury and is suboptimal because of lower expression of thyroid hormone receptor β. Thus, thyromimetics may have limited therapeutic benefits in treating cholestatic liver disease.

Genome of the webworm Hyphantria cunea unveils genetic adaptations supporting its rapid invasion and spread

BackgroundThe fall webworm Hyphantria cunea is an invasive and polyphagous defoliator pest that feeds on nearly any type of deciduous tree worldwide. The silk web of H. cunea aids its aggregating behavior, provides thermal regulation and is regarded as one of causes for its rapid spread. In addition, both chemosensory and detoxification genes are vital for host adaptation in insects.ResultsHere, a high-quality genome of H. cunea was obtained. Silk-web-related genes were identified from the genome, and successful silencing of the silk protein gene HcunFib-H resulted in a significant decrease in silk web shelter production. The CAFE analysis showed that some chemosensory and detoxification gene families, such as CSPs, CCEs, GSTs and UGTs, were expanded. A transcriptome analysis using the newly sequenced H. cunea genome showed that most chemosensory genes were specifically expressed in the antennae, while most detoxification genes were highly expressed during the feeding peak. Moreover, we found that many nutrient-related genes and one detoxification gene, HcunP450 (CYP306A1), were under significant positive selection, suggesting a crucial role of these genes in host adaptation in H. cunea. At the metagenomic level, several microbial communities in H. cunea gut and their metabolic pathways might be beneficial to H. cunea for nutrient metabolism and detoxification, and might also contribute to its host adaptation.ConclusionsThese findings explain the host and environmental adaptations of H. cunea at the genetic level and provide partial evidence for the cause of its rapid invasion and potential gene targets for innovative pest management strategies.

Neuronal Activity and Its Role in Controlling Antioxidant Genes.

Forebrain neurons have relatively weak intrinsic antioxidant defenses compared to astrocytes, in part due to hypo-expression of Nrf2, an oxidative stress-induced master regulator of antioxidant and detoxification genes. Nevertheless, neurons do possess the capacity to auto-regulate their antioxidant defenses in response to electrical activity. Activity-dependent Ca2+ signals control the expression of several antioxidant genes, boosting redox buffering capacity, thus meeting the elevated antioxidant requirements associated with metabolically expensive electrical activity. These genes include examples which are reported Nrf2 target genes and yet are induced in a Nrf2-independent manner. Here we discuss the implications for Nrf2 hypofunction in neurons and the mechanisms underlying the Nrf2-independent induction of antioxidant genes by electrical activity. A significant proportion of Nrf2 target genes, defined as those genes controlled by Nrf2 in astrocytes, are regulated by activity-dependent Ca2+ signals in human stem cell-derived neurons. We propose that neurons interpret Ca2+ signals in a similar way to other cell types sense redox imbalance, to broadly induce antioxidant and detoxification genes.

Identification and characterization of detoxification genes in two cerambycid beetles, Rhaphuma horsfieldi and Xylotrechus quadripes (Coleoptera: Cerambycidae: Clytini).

The longhorned beetles, Rhaphuma horsfieldi and Xylotrechus quadripes, are two polyphagous insects with larvae feeding on different host plants. In this study, we identified and characterized three gene superfamilies of cytochrome P450s (CYPs), carboxylesterases (COEs) and glutathione-S-transferases (GSTs) involved in the detoxification of endobiotics (e.g., hormones and steroids) and xenobiotics (e.g., insecticides, sex pheromones and plant allelochemicals) through a combination approach of bioinformatics, phylogenetics, expression profiles and genomics. Transcriptome analyses led to the identification of 281 transcripts encoding 135 P450s, 108 COEs and 38 GSTs from the two beetles, coupled with comparative studies of detoxification genes among coleopteran species, suggesting a correlation between host range and the sizes of P450 or COE gene repertoires. The P450s of two beetles were phylogenetically classified into four clades, representing the majority of genes in the CYP3 clan. The COEs from R. horsfieldi and X. quadripes were separately grouped into 11 and 10 clades, and the GST superfamily was assigned into six clades. Expression profiles revealed that the detoxification genes were broadly expressed in various tissues as an implication of functional diversities. Ultimately and more importantly, five alternative splicing events in the Epsilon GSTs, including RhorGSTe7.1/GSTe7.2 and XquaGSTe3.1/GST3.2, were acquired in Coleoptera, in which these genes and their orthologs shared highly conserved gene structure. Our current study has complemented the resources for the detoxification genes in the family Cerambycidae, and allows for functional experiments to identify candidate molecular targets involved in pest resistance to insecticides like organophosphates, organochlorines and pyrethroids.

The genome of the harpacticoid copepod Tigriopus japonicus: Potential for its use in marine molecular ecotoxicology

The copepod Tigriopus japonicus has been widely used as an experimental species in the field of ecotoxicology. We have sequenced and assembled the whole genome of T. japonicus with comparative analysis of gene families that represent detoxification phases in two additional public genomes of Tigriopus spp., namely, T. californicus and T. kingsejongensis. The total length of the T. japonicus assembled genome was 196.6 Mb with an N50 value of 10.65 Mb and consisted of 339 scaffolds and 25,143 annotated genes. The detoxification gene families encoding cytochrome P450s (CYP450s), glutathione S-transferases (GSTs), and ATP-binding cassette (ABC) proteins in Tigriopus spp. have shown species-dependent diversity in several gene sets, suggesting that these genes have undergone a species-specific expansion to increase their fitness to different marine habitats and environmental pressures. Our study will provide a better understanding of the detoxification system in Tigriopus spp. and will contribute to various areas of research, including ecotoxicology.

Gene family expansion of pinewood nematode to detoxify its host defence chemicals.

Gene gain/loss in the context of gene family dynamics plays an important role in evolutionary processes as organisms, particularly invasive species, adapt to new environments or niches. One notable example of this is the duplication of digestive proteases in some parasitic insects and helminths to meet nutritional requirements during animal parasitism. However, whether gene family expansion participates in the adaptation of a plant parasite nematode to its host remains unknown. Here, we compared the newly sequenced genomes of the pinewood nematode, Bursaphelenchus xylophilus, with the genomes of free-living, animal-parasitic and plant-parasitic nematodes. The results showed gene expansions occurring in 51 gene families in B. xylophilus, especially in xenobiotic detoxification pathways, including flavin monooxygenase (FMO), cytochrome P450 (CYP450), short chain dehydrogenase (SDR), alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), UDP-glucuronosyltransferase (UGT) and glutathione S-transferase (GST). Although a majority of these expansions probably resulted from gene duplications, nine ADH genes were potentially acquired by horizontal gene transfer (HGT) from fungi. From the transcriptomes of B. xylophilus treated with pine saplings and terpenes, candidate xenobiotic detoxification genes were identified. We propose that host defence chemicals led to gene family expansions of xenobiotic detoxification pathways in B. xylophilus facilitating its survival in pine resin ducts. This study contributes to a better understanding of how a parasitic nematode adapts to its host.

Modulation of Keap1/Nrf2/ARE Signaling Pathway by Curcuma- and Garlic-Derived Hybrids.

Nrf2 is a basic leucine zipper transcription factor that binds to the promoter region of the antioxidant response element (ARE), inducing the coordinated up-regulation of antioxidant and detoxification genes. We recently synthesized a set of new molecules by combining the functional moieties of curcumin and diallyl sulfide, both known to induce the expression of antioxidant phase II enzymes by activating Nrf2 pathway. The aim of the study is to investigate the ability of such compounds to activate Keap1/Nrf2/ARE cytoprotective pathway, in comparison with two reference Nrf2-activators: curcumin and dimethyl fumarate, a drug approved for the treatment of relapsing-remitting multiple sclerosis. Furthermore, since Nrf2 pathway is known to be regulated also by epigenetic modifications, including key modifications in microRNA (miRNA) expression, the effects of the hybrids on the expression levels of selected miRNAs, associated with Nrf2 signaling pathway have also been investigated. The results show that compounds exert antioxidant effect by activating Nrf2 signaling pathway and inducing the ARE-regulated expression of its downstream target genes, such as HO-1 and NQO1, with two hybrids to a higher extent than curcumin. In addition, some molecules induce changes in the expression levels of miR-125b-5p, even if to a lesser extent than curcumin. However, no changes have been observed in the expression levels of mRNA coding for glutathione synthetase, suggesting that the modulation of this mRNA is not strictly under the control of miR-125b-5p, which could be influenced by other miRNAs.

Evaluation of polymorphisms in repair and detoxification genes in alcohol drinkers and non-drinkers using capillary electrophoresis.

Alcohol use disorder (AUD) causes about 3.3 million deaths around the world each year. It is the primary risk factor for the global burden of diseases in American countries. Long-term abuse of alcohol induces numerous molecular and biochemical changes in tissues exposed to alcohol. The toxic effects of alcohol are mediated by DNA damage through various mechanisms, such as induction of oxidative damage, DNA adducts, crosslinks, and DNA strand breaks. The main aim of the current study was to compare the frequency of SNP polymorphisms in XRCC1 (rs7997782) and GSTP1 (rs1695) genes involved in DNA repair of single strand breaks (SSB) and xenobiotic detoxification between alcohol addicts and a control group comprised of non-drinkers. Genetic polymorphisms were identified following allelic specific PCR designed to generate the amplicons containing the variants. Then amplicons were sequenced, and sequences were aligned against the human genome reference deposited in GenBank using the CLC Sequence Viewer software (version 7.6.1). The GG homozygotes in rs1695 (GSTP1) were significantly (p = 0.023) 3.8x more frequent among those with AUD when compared to the control group. No SNP variation was observed in rs7997782 (XRCC1). rs1695 variant has been associated with susceptibility to various diseases, including those related to alcohol consumption.

Identification and expression analysis of cytochrome P450 genes in Plecoptera oculata (Lepidoptera: Noctuidae)

AbstractCytochrome P450 monooxygenases (CYPs) play an important role in the decomposition of insecticides. Plecoptera oculata Moore is a lepidopteran forestry pest that severely affects Dalbergia odorifera T. Chen. In this study, 27 putative CYP genes were identified in the transcriptome of larval P. oculata. Phylogenetic analysis showed that these genes are grouped into four clans, 15 families, and 22 subfamilies. The tissue‐specific expression profile for each gene was determined using real‐time reverse transcription‐quantitative PCR (RT‐qPCR), and the 27 genes were found to be ubiquitously expressed, mainly in the midgut, Malpighian tubules, and fat body. The expression profiles of all 27 PoCYP genes exposed to half the lethal concentration (LC50) of sendebao and lambda‐cyhalothrin were determined using RT‐qPCR. The results showed that six and twelve PoCYP genes were significantly down‐ and up‐regulated, respectively, by exposure to sendebao, and three and twelve PoCYP genes were significantly down‐ and up‐regulated, respectively, by exposure to lambda‐cyhalothrin. To the best of our knowledge, this study is the first to show the expression of CYP genes in P. oculata. Our results provide a basis for further investigation of the roles of PoCYP genes in insecticide detoxification and as potential targets for novel pesticides.

Analysis of an Intrinsic Mycovirus Associated With Reduced Virulence of the Human Pathogenic Fungus Aspergillus fumigatus.

Aspergillus fumigatus is an airborne fungal pathogen that causes severe infections with invasive growth in immunocompromised patients. Several mycoviruses have recently been isolated from A. fumigatus strains, but there are presently no reports of mycoviral-mediated reduction or elimination of fungal pathogenicity in vertebrate models. Here, we report the biological features of a novel mycovirus, A. fumigatus chrysovirus 41362 (AfuCV41362), isolated from the hypovirulent A. fumigatus strain IFM 41362. The AfuCV41362 genome is comprised of four dsRNAs, each of which contains a single ORF (ORF1-4). ORF1 encodes a protein with sequence similarity to RNA-dependent RNA polymerases of viruses in the family Chrysoviridae, while ORF3 encodes a putative capsid protein. Viral RNAs are expressed primarily during the germination stage, and RNA-seq analysis of virus-infected A. fumigatus at the germination stage suggested that the virus suppressed expression of several pathogenicity-associated host genes, including hypoxia adaptation and nitric oxide detoxification genes. In vitro functional analysis revealed that the virus-infected strain had reduced tolerance to environmental stressors. Virus-infected A. fumigatus strain IFM 41362 had reduced virulence in vivo compared to the virus-free strain in a mouse infection model. Furthermore, introduction of the mycovirus to a natively virus-free KU A. fumigatus strain induced virus-infected phenotypes. To identify mycovirus genes responsible for the reduced virulence of A. fumigatus, each viral ORF was ectopically expressed in the virus-free KU strain. Ectopic expression of the individual ORFs only nominally reduced virulence of the host fungus in a mouse infection model. However, we found that ORF3 and ORF4 reduced tolerance to environmental stresses in in vitro analysis. Based on these results, we suggest that the AfuCV41362 mycovirus ORF3 and ORF4 reduce fungal virulence by suppressing stress tolerance together with other viral genes, rather than alone.

Epigenetic effects of (nano)materials in environmental species – Cu case study in Enchytraeus crypticus

Chemical stressors can induce epigenomic changes, i.e., changes that are transferred to the next generation, even when the stressor is removed. Literature on chemical induced epigenetic effects in environmental species is scarce. We here provide the first results on epigenetic effects caused by nanomaterials with an environmental OECD standard soil model species Enchytraeus crypticus species. We assessed the epigenetic potential in terms of global DNA methylation, gene-specific methylation via bisulfite sequencing and MS-HRM (Methylation Sensitive - High Resolution Melting), and gene expression qPCR for genes involved in DNA methylation, histone modifications, non-coding RNA and stress response mechanisms).We have exposed E. crypticus in a multigenerational (MG) test design to Cu (copper oxide nanomaterials (CuO NMs) and copper salt (CuCl2)). To link possible epigenetic effects to population changes, we used exposure concentrations (ECx) that caused a 10% and 50% reduction in the reproductive output (10% and 50% are the standards for regulatory Risk Assessment), the organisms were exposed for five consecutive generations (F1–F5) plus two generations after transferring to clean media (F5–F7), 7 generations in a total of 224 days. Results showed that MG exposure to Cu increased global DNA methylation and corresponded with phenotypic effects (reproduction). Gene expression analyses showed changes in the epigenetic, stress and detoxification gene targets, depending on the generation and Cu form, also occurring in post-exposure generations, hence indicative of transgenerational effects. There were in general clear differences between organisms exposed to different Cu-forms, hence indicate nanoparticulate-specific effects.

Transcriptome changes for Nile tilapia (Oreochromis niloticus) in response to alkalinity stress

Nile tilapia is an important economic fish in the world because of its fast growth, high meat yield and strong adaptability. It is more adaptable to high alkalinity than common freshwater fish and provides valuable material for developing alkaline-tolerant strains and understanding the adaptation mechanism of fish to extreme environmental stress. In this study, we employed high throughput RNA sequencing to reveal the tissues (gill, kidney and liver) transcriptome differences of O. niloticus at different carbonate alkalinities (FW, AW40 and AW60). A total of 1,369,381,790 raw reads were obtained, including 496,441,232 reads in FW group, 437,907,696 reads in AW40 and 435,032,862 reads in AW60. In addition, 484,555,626 reads in gill, 451,618,224 reads in kidney and 433,207,940 reads in liver. A large number of stress-regulated changes were detected comprehensively. We focused on 3 significantly change pathways (steroid biosynthesis, drug metabolism and protein digestion/absorption) and 17 DEGs (HMG-CoA reductase, UDP-glucuronosyltransferase, and carbonic anhydrase etc.) which were shared among compared groups (AW40 vs FW, AW60 vs FW, AW40 vs 60 AW60) in gill, kidney and liver, respectively. These pathways/genes are sensitive to alkalinity stress and crucial to the alkalinity adaptation of tilapia. Overall, we found a large number of candidate genes, which encode important regulators of stress tolerance and ultimately contribute to future alkaline-tolerant fish breeding. Among these genes, lipid metabolism (involving signal transduction), detoxification and immune related genes are more prominent to the response and adaptability of fish to alkalinity stress.

Whole-transcriptome Analysis of Fully Viable Energy Efficient Glycolytic-null Cancer Cells Established by Double Genetic Knockout of Lactate Dehydrogenase A/B or Glucose-6-Phosphate Isomerase.

Nearly all mammalian tumors of diverse tissues are believed to be dependent on fermentative glycolysis, marked by elevated production of lactic acid and expression of glycolytic enzymes, most notably lactic acid dehydrogenase (LDH). Therefore, there has been significant interest in developing chemotherapy drugs that selectively target various isoforms of the LDH enzyme. However, considerable questions remain as to the consequences of biological ablation of LDH or upstream targeting of the glycolytic pathway. In this study, we explore the biochemical and whole transcriptomic effects of CRISPR-Cas9 gene knockout (KO) of lactate dehydrogenases A and B [LDHA/B double KO (DKO)] and glucose-6-phosphate isomerase (GPI KO) in the human colon cancer cell line LS174T, using Affymetrix 2.1 ST arrays. The metabolic biochemical profiles corroborate that relative to wild type (WT), LDHA/B DKO produced no lactic acid, (GPI KO) produced minimal lactic acid and both KOs displayed higher mitochondrial respiration, and minimal use of glucose with no loss of cell viability. These findings show a high biochemical energy efficiency as measured by ATP in glycolysis-null cells. Next, transcriptomic analysis conducted on 48,226 mRNA transcripts reflect 273 differentially expressed genes (DEGS) in the GPI KO clone set, 193 DEGS in the LDHA/B DKO clone set with 47 DEGs common to both KO clones. Glycolytic-null cells reflect up-regulation in gene transcripts typically associated with nutrient deprivation / fasting and possible use of fats for energy: thioredoxin interacting protein (TXNIP), mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), PPARγ coactivator 1α (PGC-1α), and acetyl-CoA acyltransferase 2 (ACAA2). Other changes in non-ergometric transcripts in both KOs show losses in "stemness", WNT signaling pathway, chemo/radiation resistance, retinoic acid synthesis, drug detoxification, androgen/estrogen activation, and extracellular matrix reprogramming genes. These findings demonstrate that: 1) The "Warburg effect" is dispensable, 2) loss of the LDHAB gene is not only inconsequential to viability but fosters greater mitochondrial energy, and 3) drugs that target LDHA/B are likely to be ineffective without a plausible combination second drug target.

Models of Gen-gene Interaction in Determining the Severity of Bronchial Asthma in Children

Bronchial asthma (BA) has a polygenic nature, and the onset of its manifestation and features course is realized due to the influence of genetic factors. This study aimed to investigate the effect of polymorphisms of the genes of the phase II detoxification system and genes of the cardiovascular tone on the severity of asthma in children. The study included 163 children aged 5–18 years: 38 with severe asthma, 69 with moderate asthma, and 56 with mild asthma. A molecular genetic study was conducted to determine the frequency of gene propagation and gen-gene interaction by GSTT1, GSTM1, GSTP1, ACE, eNOS, AT2R1, NAT2 genes at different severity of bronchial asthma. Found that in the prediction of the severity of asthma special place belongs to the analysis of the combination of genotypes. Independent effects were found for AT2R1 and ACE gene polymorphisms. The ACE (I / D) / AT2R1 (A1166C) / eNOS (T786C) / eNOS (4b / 4a) four-locus model was developed to predict the severe BA course and the need for additional analysis of the interaction of AT2R1 (A1166C) and eNOS (T786C), eNOS (T786C) genes was demonstrated (4b4a) and GSTT1. The risk of developing severe BA has been demonstrated for the combination of 1166SS + 786TT, 1166CC + 786TC genotypes by AT2R1 (A1166C) and eNOS (T786C) genes, and the reduction of this risk for combinations of eNOS (4b4a) 4b4b + GSTT1 genotypes. In moderate asthma, combinations of ACE genotypes DD + AT2R1 1166SS and AT2R1 313AA + GSTP1 1166SS were reliable risk markers for severe asthma. AT2R1 gene polymorphism was the leading marker in more severe asthma. A marker of severe BA was also found for the heterozygous 857GA polymorphism of the NAT2 gene (G857A). Conclusions. The influence of ACE (I / D), AT2R1 (A1166C), eNOS (T-786C), NAT2 (G857A), GSTT1, and GSTP1 gene polymorphisms on the severity of asthma in children has been established.

Trichoderma asperellum reduces phoxim residue in roots by promoting plant detoxification potential in Solanum lycopersicum L.

Phoxim, a broad-spectrum organophosphate pesticide, is widely used in agriculture to control insect pests in vegetable crops as well as in farm mammals. However, the indiscriminate use of phoxim has increased its release into the environment, leading to the contamination of plant-based foods such as vegetables. In this study, we investigated the effect of Trichoderma asperellum (TM, an opportunistic fungus) on phoxim residue in tomato roots and explored the mechanisms of phoxim metabolism through analysis of detoxification enzymes and gene expression. Degradation kinetics of phoxim showed that TM inoculation rapidly and significantly reduced phoxim residues in tomato roots. Phoxim concentrations at 5d, 10d and 15d post treatment were 75.12, 65.71 and 77.45% lower in TM + phoxim than only phoxim treatment, respectively. The TM inoculation significantly increased the glutathione (GSH) content, the activity of glutathione S-transferase (GST) and the transcript levels of GSH, GST1, GST2 and GST3 in phoxim-treated roots. In addition, the activity of peroxidase and polyphenol peroxidase involved in the xenobiotic conversion also increased in TM + phoxim treatment. The expression of detoxification genes, such as CYP724B2, GR, ABC2 and GPX increased by 3.82, 3.08, 7.89 and 2.46 fold, respectively in TM + phoxim compared with only phoxim. Similarly, the content of ascorbate (AsA) and the ratio of AsA to dehydroascorbate increased by 45.16% and 57.34%, respectively in TM + phoxim-treated roots. Our results suggest that TM stimulates plant detoxification potential in all three phases (conversion, conjugation and sequestration) of xenobiotc metabolism, leading to a reduced phoxim residue in tomato roots.