Preserving intact genetic material and delivering it to the next generation are the most significant tasks of living organisms. The integrity of DNA sequences is under constant threat from endogenous and exogenous factors. The accumulation of damaged or incompletely-repaired DNA can cause serious problems in cells, including cell death or cancer development. Various DNA damage detection systems and repair mechanisms have evolved at the cellular level. Although the mechanisms of these responses have been extensively studied, the global RNA expression profiles associated with genomic instability are not well-known. To detect global gene expression changes under different DNA damage and hypoxic conditions, we performed RNA-seq after treating human cervical cancer cells with ionizing radiation (IR), hydroxyurea, mitomycin C (MMC), or 1% O2 (hypoxia). Results showed that the expression of 184–1037 genes was altered by each stimulus. We found that the expression of 51 genes changed under IR, MMC, and hypoxia. These findings revealed damage-specific genes that varied differently according to each stimulus and common genes that are universally altered in genetic instability.

The pea aphid, Acyrthosiphon pisum, requires the nutritional endosymbiont, Buchnera, for the production of essential amino acids. However, it is unclear if host plant diet that varies in essential amino acids influences aphid regulation of its nutritional symbioses. We hypothesized that aphid genes respond to host plant diet when aphids feed on their specialized (alfalfa) compared to universal host plant diet (fava), which vary in essential amino acid concentrations. Using RNA-Seq and whole genome bisulfite sequencing, we compared the gene expression profiles and DNA methylation distributions of specialized aphid cells that harbor Buchnera (bacteriocytes) when aphids feed on their specialized compared to their universal host plant diets. Our results show that bacteriocyte transcription and methylation patterns differ between host plant diets. When aphids feed on their specialized host plant, they significantly up-regulate and/or hypo-methylate key aphid genes in bacteriocytes related to the amino acid metabolism, including glutamine synthetase (GS) and the glutamine transporter ApGLNT1. Moreover, regardless of which host plant aphids feed on, we observed significant up-regulation and differential methylation of the key genes in the amino acid metabolism and the glycine/serine metabolism in aphid bacteriocytes. We suggest that the regulatory response of key symbiosis genes in bacteriocytes allows aphids to feed on a specialized host plant diet with suboptimal nitrogen concentrations.

Differential gene regulation is crucial for development. Indianmeal moth is a global pest of stored and processed food products. Here, we determined the whole developmental expression patterns of 13 genes (shsp, hsp70, grp78, and hsp90), ecdysone receptor (EcR), ultraspiracle (USP), hemolin, β-1,3-glucan recognition protein (βgrp), prophenoloxidase (ProPO), superoxide dismutase (SOD) and thioredoxin peroxidase (Tpx), and two hexamerin storage protein genes (SP1 and SP2) related to growth, stress, metabolism, and host defense. We also studies effects of Bracon hebetor envenomation on these gene expressions to explore their role in host regulation. We found unexpected transcriptional peaks especially hsps which were high in egg and adult stages. This study provides comprehensive understanding about development and parasitoid regulation at molecular level.

To determine differential gene expression profiles in the salivary gland of a water stick-insect, Ranatra chinensis Mayrt, a subtractive cDNA library was constructed by suppression subtractive hybridization. The salivary gland was determined among three salivary gland-like tissues by investigating transcription levels of five trypsin genes isolated from R. chinensis. The major transcripts encoding trypsins (64.4% of the total ESTs) were eliminated from the library and then remaining salivary gland-specific genes were searched. A total of 643 expressed sequence tags (ESTs) were clustered and assembled into 148 contigs (49 multiple sequences and 99 singletons), among which 35 contigs had matched BLASTx hits (E ≤ 1.00E-4). Salivary apyrase occupied 5.6% (36 ESTs) of the library. Apyrase is known to be released by female mosquitoes or blood-sucking assassin bugs to prevent blood clots during blood sucking. Therefore, apyrase in the salivary of R. chinensis might allow R. chinensis to facilitate feeding. Several contigs encoding acid phosphatase, hyaluronidase, prophenoloxidase, and dipeptidylpeptidase IV, commonly found in venoms of Hymenoptera, were also identified from the salivary gland-specific library. Discovery of salivary glandspecific genes should promote further studies on biologically active components in the saliva of R. chinensis.

To determine differential gene expression profiles in the salivary gland of a predatory flower bug species, Orius laevigatus Fieber, a subtractive cDNA library was constructed by suppression subtractive hybridization. The major transcripts encoding trypsins (28.6% of the total ESTs) were eliminated from the library and then remaining salivary gland-specific genes were searched. A total of 513 expressed sequence tags (ESTs) were clustered and assembled into 129 contigs (64 multiple sequences and 65 singletons). About 58% were matched with insect genes. In total, 38 genes (179 ESTs) were found from the library by BLASTx search. A hemolysin-like protein occupied ca. 8% (41 ESTs) of the library. Hemolysin is known to destruct cells including blood cells by forming pores on the cell membrane. A hemolysin-like salivary protein of O. laevigatus might be hemolytic against the prey cells, thereby allowing O. laevigatus to facilitate feeding. Several contigs encoding lipase was also identified from the salivary gland-specific library. Discovery of salivary gland-specific genes should promote further studies on biologically active components in the saliva of O. laevigatus.

To determine differential gene expression profiles in the venom gland and sac (gland/sac) of a solitary hunting wasp species, Eumenes pomiformis Fabricius (1781), a subtractive cDNA library was constructed by suppression subtractive hybridization. A total of 541 expressed sequence tags (EST) were clustered and assembled into 102 contigs. In total, 37 genes were found from the library by BLASTx search and manual analysis. A eumenitin-like venom peptide, EpVP1, occupied ca. 26% of the library. A novel venom peptide, EpDTX, shared sequence similarity with trypsin inhibitors and dendrotoxin-like venom peptides known as K+ channel blockers, implying it could be responsible for the paralysis of prey. As well as phospholipase A2 and hyaluronidase known to be main components of wasp venoms, several contigs encoding enzymes, including metalloendopeptidases and a decarboxylase likely involved in the processing and activation of venomous proteins, peptides, and neurotransmitters, were also isolated from the library. The presence of a gene encoding insulin-like growth factor binding protein suggests that solitary hunting wasps might control the prey to stay in larval stage by their venom. The abundance of these venom components in the venom gland/sac and alimentary canal was confirmed by quantitative real-time PCR.

To determine differential gene expression profiles in a cypermethrin-resistant strain (CR) of diamondback moth, Plutella xylostella Linnaeus (1758), a subtractive cDNA library was constructed by suppression subtractive hybridization. A total of 1196 expressed sequence tags (EST) were clustered and assembled into 579 contigs (100 multiplets and 479 singletons). About 46% (267) of 579 contigs had the matched BLASTx hits (E ≤ 10-5). Among these, 143 contigs had similarity to proteins with assigned molecular function in the Functional Catalogue database, and most of them (86%) were homologous to the genes from insects, particularly to Lepidoptera (56%). The contigs encoding carboxylesterase and cytochrome P450 known to be involved in the insecticide resistance were found in the library. They were identified as pxest3, pxest4, and CYP9G2 gene by 5' and 3' RACE. Among these, pxest4 was determined to be 2-fold over-transcribed in the CR strain by qrtPCR. Several contigs encoding enzymes including cytochrome oxidase subunit I that are likely involved in the insecticide resistance were also identified from the library. Discovery of the genes specific to cypermethrin resistance should promote further studies on the molecular mechanisms of insecticide resistance in P. xylostella.

Abiotic stresses such as extreme temperatures frequently limit the plant growth and productivity of major crop species. Two Chinese cabbage DH lines that have different geographic origins, in that Chiifu is from temperate regions, while Kenshin is from subtropical and tropical regions have been expected to show the specific response to high or low temperature. To find the temperature response genes between Chiifu and Kenshin, we analyzed transcriptomic profiling from light-chilling (6h at 4°C) and high temperature (6h at 38°C) treated plants using the KBGP-24K chip. Distribution of genes classified by PI (probe intensity) values showed remarkable difference between Chiifu and Kenshin. The number of genes up- and down-regulated gens by both temperatures were 135 and 79 genes, respectively. These genes may be temperature stress-related genes. Genes involved in the response to stress were changed by light-chilling stress. Chiifu specifically up-regulated genes upon light chilling-stress belong to cold acclimation proteins, calcium binding proteins, cell wall biogenesis proteins and lipoxygenase. On the other hand, Kenshin specifically up-regulated genes by heat-shock treatment include heat-shock proteins, phosphatases, protein folding and phosphorylation-associated ones. Further study on these specific genes function may provide insight to adaptation of Chinese cabbage and clue to develop molecular markers.

Ionizing radiation is known to cause chromosomal alterations such as inversions and deletions and affects gene expression within the plant genome. To monitor the genome-wide transcriptome changes by ionizing radiation, we used rice Affimetrix GeneChip microarray to identify genes that are up- or down regulated by gamma-ray (200 Gy, 60Co source), cosmic-ray and ion beam (40 Gy, 220 MeV carbon ion). The overall expression patterns between gamma-ray and ion beam were similar but cosmic-ray was regulated differently. Combined results from all 3 radiations identified 27 up-regulated genes and 188 down regulated genes. These results mean the induction of similar mechanism changes in treatments of gamma ray and ion beam. However the different expression in treatment of cosmic-ray might be due to the other environmental conditions. Among the commonly up- or down- regulated genes, we chose highly up- or down- regulated several genes and confirmed its regulation in response to ionizing radiation exposure by RT-PCR analysis. Moreover, we showed that specific co-expression networks of candidate radio marker genes by ARACNE algorithm. Our results present profiles of gene expression related to different ionizing radiation and marker gene to predict sensitivity to ionizing radiation, such as GS (glutelin subunit) and FBX322.