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Expression of the central circadian oscillator components CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), TIMING OF CAB1 (TOC1), GIGANTEA (GI), and CONSTANS (CO) occurs in Glycine max root cells (syncytia) parasitized by the nematode Heterodera glycines while undergoing resistance, indicating a defense role. GmCCA1-1 relative transcript abundance (RTA) in roots experiencing overexpression (OE) or RNA interference (RNAi) is characterized by rhythmic oscillations, compared to a ribosomal protein gene (GmRPS21) control. A GmCCA1-1 RTA change, advancing by 12 h, exists in H. glycines -infected as compared to uninfected controls in wild-type, H. glycines -resistant, G. max [Peking/PI 548402]. The G. max [Peking/PI 548402] transgenic controls exhibit the RTA change by 4 h post infection (hpi), not consistently occurring in the H. glycines -susceptible G. max [Williams 82/PI 518671] until 56 hpi. GmCCA1-1 expression is observed to be reduced in H. glycines -infected GmCCA1-1 -OE roots as compared to non-infected transgenic roots with no significant change observed among RNAi roots. The GmCCA1-1 expression in transgenic GmCCA1-1 -OE roots remains higher than control and RNAi roots. Decreased GmCCA1-1 mRNA among infected roots shows the altered expression is targeted by H. glycines. Gene expression of proven defense genes including 9 different mitogen activated protein kinases (GmMAPK s), NON-RACE SPECIFIC DISEASE RESISTANCE 1 (GmNDR1-1), RPM1-INTERACTING PROTEIN 4 (GmRIN4-4), and the secreted xyloglucan endotransglycosylase/hydrolase 43 (GmXTH43) in GmCCA1- 1-OE and GmCCA1-1 -RNAi roots, compared to controls, reveal a significant role of GmCCA1-1 expression in roots undergoing defense to H. glycines parasitism. The observation that GmCCA1-1 regulates GmXTH43 expression links the central circadian oscillator to the functionality of the secretion system. • Central circadian oscillator genes are expressed in nematode-parasitized root cells undergoing defense. • The overexpression of the central circadian oscillator genes suppresses parasitism. • The central circadian oscillator gene CCA1-1 regulates the expression of proven defense genes. [ABSTRACT FROM AUTHOR]

Human body is colonized by a complex ecosystem of microbes that play a significant role in determining the fitness of the host. The epigenetic signatures of probiotic microorganisms also define the functional role of microbiota in the intestine and further facilitate exploring their beneficial properties. Development in the areas of molecular biology and genomics has paved way for engineering of microorganisms. The advent of genome editing tools such as CRISPR-Cas, has revolutionized new possibilities for genetic engineering in probiotics for enhanced immune response, antimicrobial properties and applications in biotherapeutics. Here, we discuss the present status of genome editing used in epigenome engineering of the gut microbiota and role of different types of CRISPR-Cas systems. Applications of CRISPR-Cas system can be harnessed to modify probiotic microbes in order to regulate gene expressions and produce desired metabolite. These techniques illuminate novel approaches to metabolic engineering and draw attention towards poorly characterized biosynthetic pathways. In addition, future prospects of these tools can be applied to investigate the interactions between gut microbiome and the host, hence, contributing to the development of novel therapeutics. [ABSTRACT FROM AUTHOR]

Zinc oxide nanoparticles (ZnONPs) are widely used in several commercial products due to their unique physicochemical properties. However, their release into the aquatic environments through various anthropogenic activities will lead to toxic effect in aquatic organisms. Although several investigations have been reported on the effect of ZnONPs in aquatic organisms using traditional end points such as survival, growth, and reproduction, the molecular level end points are faster and sensitive. In this study, the expression of different genes involved in oxidative stress response, detoxification, and cellular defense was studied in an ecotoxicologically important bio-monitoring organism Chironomus riparius in order to understand the subcellular effects of ZnONPs. The fourth instar larvae were exposed to 0, 0.2, 2, 10, and 20 mg/L of ZnONPs and Zn ions (in the form of ZnSO 4 .7H 2 O) for 24 and 48 h period. The expression of CuZn superoxide dismutase, manganese superoxide dismutase, catalase, phospholipid hydroperoxide glutathione peroxidase, thioredoxin reductase 1 and delta-3, sigma-4 and epsilon-1 classes of glutathione S -transferases, cytochrome p4509AT2, and heat shock protein 70 were studied using real-time polymerase chain reaction method. Gene expression results showed that the expression of genes related to oxidative stress response was more pronounced as a result of ZnONPs exposure as compared to Zn ions. The mRNA expression of genes involved in detoxification and cellular protection was also modulated. Significantly higher expression levels of oxidative stress-related genes shows that oxidative stress is an important mechanism of toxicity as a result of ZnONPs exposure in C. riparius . [ABSTRACT FROM AUTHOR]

The physiological and molecular level changes of silver nanoparticles (AgNPs) exposure were investigated in rice (Oryza sativa L.) seedlings. The seedlings were exposed to different concentrations of (0, 0.2, 0.5 and 1mgL−1) AgNPs for one week. Significant reduction in root elongation, shoot and root fresh weights, total chlorophyll and carotenoids contents were observed. Exposure to 0.5 and 1mgL−1 of AgNPs caused significant increase in hydrogen peroxide formation and lipid peroxidation in shoots and roots, increased foliar proline accumulation and decreased sugar contents. AgNPs exposure resulted in a dose dependant increase in reactive oxygen species generation and also caused cytotoxicity as evidenced by increased dihydroethidium, 3′-(p-hydroxyphenyl) fluorescein and propidium iodide fluorescence. Tetramethylrhodamine methyl ester assay showed decreased mitochondrial membrane potential with increasing concentrations of AgNPs exposure in roots. Real Time PCR analysis showed differential transcription of genes related to oxidative stress tolerance viz. FSD1, MSD1, CSD1, CSD2, CATa, CATb, CATc, APXa and APXb in shoots and roots of rice seedlings. The overall results suggest that exposure to AgNPs caused significant physiological and molecular level changes, oxidative stress and also resulted in the induction oxidative stress tolerance mechanisms in rice seedlings. [ABSTRACT FROM AUTHOR]

Highlights: [•] Chironomus riparius cytochrome p450 (CrCYP9AT2) cDNA was characterized. [•] Studied the transcriptional modulation of CrCYP9AT2 gene. [•] CrCYP9AT2 expression varied upon exposure to environmental xenobiotics. [•] CrCYP9AT2 could be potentially used as a molecular biomarker. [ABSTRACT FROM AUTHOR]

Highlights: [•] Glutathione biosynthesis genes from Chironomus riparius were characterized. [•] Transcriptional regulation of GSH biosynthesis genes was studied after exposure to Cd and NP. [•] Modulation in the expression of GSH biosynthesis genes was observed after exposure to Cd and NP. [•] Potentially used as biomarkers of Cd and NP stress in aquatic environment. [ABSTRACT FROM AUTHOR]

Highlights: [•] Toxicogenomic response of AgNPs and Ag+ ions is studied in Chironomus riparius. [•] AgNPs and Ag+ ions showed different toxicogenomic patterns. [•] AgNPs promoted pronounced induction of antioxidant genes. [Copyright &y& Elsevier]

Abstract: Superoxide dismutase (SOD, EC 1.15.1.1) is an enzyme involved in the scavenging of reactive oxygen species (ROS) into molecular oxygen and hydrogen peroxide. In this study, a copper–zinc superoxide dismutase (Cu–ZnSOD) gene and a manganese superoxide dismutase (MnSOD) gene in aquatic midge, Chironomus riparius (CrSODs) was identified using an Expressed Sequence Tag (EST) database generated by 454 pyrosequencing. A multiple sequence alignment of C. riparius sequences revealed high homology with other insect sequences in terms of the amino acid level. Phylogenetic analysis of the CrSODs revealed that they were grouped with SODs of other organisms, such as Polypedilum vanderplanki, Drosophila melanogaster, Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus and Bombyx mori. Expression of the corresponding CrSODs was analyzed during different developmental stages and following exposure to various environmental contaminants with different mode of actions i.e., paraquat, cadmium, benzo[a]pyrene, and chloropyrifos. CrSOD gene expression was significantly up or down regulated in response to exposure to the chemicals tested. The overall results suggested that SOD gene expression provided a platform for the understanding of oxidative stress responses caused by exposure to various environmental contaminants, and the SOD genes could be used as biomarkers for environmental disturbances such as oxidative stress initiated by xenobiotics. [Copyright &y& Elsevier]

Abstract: We identified and characterized a partial cDNA of StAR-related lipid transfer domain containing protein gene from Chironomus riparius (CrSTART1) having homology with human MLN64 and Drosophila melanogaster START1 (DmSTART1) and evaluated the effects of cadmium chloride (Cd) and nonylphenol (NP) on its expression. Pfam analysis identified the presence of two StAR-related lipid transfer (START) domains in CrSTART1 having several conserved amino acid residues, characteristic of the MLN64 and DmSTART1. The mRNA expression of CrSTART1 was observed in all developmental stages. The modulation in the mRNA expression of CrSTART1 was investigated after exposure to different concentrations Cd (0, 2, 10, and 20mg/L) and NP (0, 10, 50, and 100μg/L) for different time intervals in fourth instar larvae of C. riparius. Significant downregulation of CrSTART1 mRNA was observed after exposure to 2, 10 and 20mg/L of Cd for 24, 48 and 72h. Significant upregulation of CrSTART1 was observed after exposure to 10 and 50μg/L of NP for 24, and 48h period. At 100μg/L of NP significant upregulation of CrSTART1 was observed after 12h and downregulated after 24, 48 and 72h. [Copyright &y& Elsevier]

Abstract: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, although little is known about its genome sequences. Ecdysteroids are steroid hormones that play an important role in development, growth, moulting of larva, and reproduction in Chironomus spp. The effect of ecdysteroids is mediated by their binding to the ecdysteroid receptor (EcR). To study the effect of environmental stressors, nonylphenol and silver nanoparticles (AgNPs), on the modulation of EcR mRNA, in this study, full length cDNA of C. riparius ecdysone receptor (CrEcR) was identified from the Expressed Sequence Tags (ESTs) database and expression of the corresponding mRNA was analyzed following exposure to nonylphenol and AgNPs. The CrEcR cDNA was 2548 base pairs (bp) in length, with a 5′ untranslated region (UTR) of 242bp and a 3′ UTR of 684bp. The open reading frame contains 1617 nucleotides, encoding 539 amino acids with a predicted molecular weight of 61kDa and pI of 5.89, and revealed the presence of several domains associated with DNA binding, dimerization, ligand binding and transcriptional activation characteristic of steroid receptor family members. It was found that the expression level of CrEcR was significantly up-regulated on exposure to nonylphenol and significant up or down regulation was observed on exposure to AgNPs. These finding shows that nonylphenol as well as AgNPs could modulate the ecdysone nuclear receptor and may have significant implications in different developmental stages in C. riparius. [Copyright &y& Elsevier]

Abstract: A full-length ribosomal protein L15 cDNA from Chironomus riparius (CrRPL15) was identified from the Expressed Sequence Tag (EST) database developed vt 454 pyrosequencing, and expression of the corresponding mRNA was analyzed during different developmental stages and following exposure to Cadmium chloride (Cd) and Silver nanoparticles (AgNPs). The CrRPL15 cDNA contains an open reading frame (ORF) of 615 base pairs (bp) encoding a putative protein of 204 amino acids, with a high level of sequence similarity to RPL15 proteins from other species. The consensus sequence, GXXXXGKS, which is present in other RPL15 proteins, was also present in the putative CrRPL15 protein. The CrRPL15 transcript was present at all life stages, but was most abundant in the eggs. Expression of the CrRPL15 gene was significantly down-regulated in response to exposure to both Cd and AgNPs. In contrast, expression of the heat shock protein 70 (HSP70) gene, a general stress indicator, was significantly up-regulated. [Copyright &y& Elsevier]

Abstract: In this study, we report the identification and characterization of 13 cytosolic GST genes in Chironomus riparius from Expressed Sequence Tags (ESTs) database generated using pyrosequencing. Comparative and phylogenetic analyses were undertaken with Drosophila melanogaster and Anopheles gambiae GSTs and 3 Delta, 4 Sigma, 1 each in Omega, Epsilon, Theta, Zeta and 2 unclassified classes of GSTs were identified and characterized. The relative mRNA expression levels of all of the C. riparius GSTs (CrGSTs) genes under different developmental stages were varied with low expression in the larval stage. The antioxidant role of CrGSTs was studied by exposing fourth instar larvae to a known oxidative stress inducer Paraquat and the relative mRNA expression to different concentrations of cadmium (Cd) and silver nanoparticles (AgNPs) for various time intervals were also studied. All the CrGSTs showed up- or down regulation to varying levels based upon the concentration, and duration of exposure. The highest mRNA expression was noticed in Delta3, Sigma4 and Epsilon1 GST class in all treatments. These results show the role of CrGST genes in defense against oxidative stress and its potential as a biomarker to Cd and AgNPs exposure. [Copyright &y& Elsevier]

Abstract: The eco- and genotoxicity of silver nanoparticles (AgNPs) was investigated in the fourth instar larvae of the aquatic midge, Chironomus riparius. AgNPs did not have acute toxicity in C. riparius, but did exhibited chronic toxicity on development (pupation and emergence failure) and reproduction. Genotoxicity also occurred in AgNPs exposed C. riparius. Differential Display PCR (DD-PCR), based on the Annealing Control Primer (ACP) technique, was conducted to investigate the underlying toxic mechanism, which identified altered gene expression in C. riparius after treatment with AgNPs. The possible toxicity mechanism of AgNPs in C. riparius involves the down regulation of the ribosomal protein gene (CrL15) affecting the ribosomal assembly and consequently, protein synthesis. Up regulation of the gonadotrophin releasing hormone gene (CrGnRH1) might lead to the activation of gonadotrophin releasing hormone mediated signal transduction pathways and reproductive failure. Up regulation of the Balbiani ring protein gene (CrBR2.2) may be an indication of the organism''s protection mechanism against the AgNPs. The overall results suggest that the toxicity of AgNPs towards aquatic organisms should be thoroughly investigated to allow for their safe use, as they seem to exhibit important toxicity towards C. riparius. [Copyright &y& Elsevier]

Summary: SpaI is a small lipoprotein that provides Bacillus subtilis with autoimmunity against the lantibiotic subtilin. We have investigated the maturation of SpaI through the lipoprotein biosynthesis pathway, and analyzed the consequences of maturations in the acylation of the target lipobox in subtilin immunity. Further specificity of lipid acylation of the cysteine within the conserved sequence of the candidate lipobox (LSAC) was studied by site-directed mutagenesis. The mutants LSAA and LSCA blocked lipid attachment to the SpaI protein. Cell-wall stress-sensing B. subtilis BSF 2470 was exploited to study the function of each mutant upon heterologous expression. This system allowed the monitoring of β-galactosidase activity to the added subtilin at a sublethal dose. Mutants exhibited 2-fold reduction in β-Gal activity, suggesting their contribution in subtilin autoimmunity. [Copyright &y& Elsevier]

Transgenic tomato plants accumulating high amounts (70-100 fold) of anthocyanin in the fruit were developed by the fruit specific expression of two transcription factors, Delila and Rosea1 isolated from Antirrhinum majus. The transgenic tomato plants were identical to the control plants, except for the accumulation of high levels of anthocyanin pigments throughout the fruit during maturity, thus giving the fruit a purplish colour. The total carotenoids, including lycopene levels were unaffected in the anthocyanin-rich fruits, while its antioxidant capacity was elevated. The gene expression analysis confirmed the elevated expression of the downstream genes of the anthocyanin pathway due to the expression of the transcription factors and the expression levels coincided with the fruit ripening stages, highest expression occurring during the breaker stage. Anthocyanin-rich tomato fruit is important in view of the protective function of these compounds on consumption against a number of lifestyle-related diseases. [ABSTRACT FROM AUTHOR]