In insects, the glutathione S-transferase is initiated in both the detoxification process and the protection of cellular membranes against oxidative damage. In this study, we identified the open reading frame (ORF) sequence of GST-iso1 and 2 from Tenebrio molitor (TmGST-iso1 and 2). To investigate the expression patterrns of TmGST-iso1 and 2 in response to herbicide, 0.06, 0.6, and 6 ㎍/㎕ of butachlor (FarmHannong, Seoul, South Korea) was challenged into T. molitor larvae, resulting that the TmGST-iso1 were highly induced at 3 and 24 h-post injection. Whereas, the highest expression of TmGST-iso2 was detected at 24 h after treatment. This study may contribute to basic information about the detoxifying activities of T. molitor.

The red imported fire ant (Solenopsis invicta) is a species of ant native to South America. The fire ant was inadvertently introduced into USA, Australia, New Zealand, and other Asian countries including China and Taiwan. Since the first report of the fire ant in port city of Busan, Korea in 2017, it was found in many other cities of Korea in following year. To obtain the molecular information of this invasive species, total RNA was extracted from the abdominal segment of the ants collected in Incheon, and subjected to transcriptome sequencing. By using Illumina sequencer platform, 101 base pared-end sequencing generated 2 × 50,064,081 of raw reads to obtain 2 × 45.95 Gbase of quality filtered nucleotide sequences. The in silico cDNA library was constructed by Trinity de novo assembler followed by TransDecoder ORF finder and CD-HIT clustering program to streamline the library. The final version of cDNA library contains 20,442 contigs with protein coding capability. To survey the virome of this ant, these contigs were searched against the viral reference sequences from NCBI RefSeq database with BLASTN program. As a result, contigs which showed high sequence identities with several RNA viruses including previously reported SINV-2 were found from the fire ant. This virome information might give an idea of a shift of virological environment of this newly found ant isolate or population in Korea.

Although the grasshopper Oxya chinensis sinuosa has long been used as a food in Korea, there is little data on itsfunctional effects. Thus we prepared and analyzed total RNA from the whole body of adult Escherichia coli non-immunizedand immunized Oxya chinensis sinuosa strains. Using an Illumina Hiseq sequencer, we generated a total of 66,555 pooledtranscriptome and singletons with and without Escherichia coli immunization, respectively. Then, we performed in silicoanalysis of the Oxya chinensis sinuosa transcriptome, using bioinformatics tools for screening putative antimicrobial peptides(AMPs) and 38 AMPs were finally selected and tested their antimicrobial activity of Gram positive, Gram negative bacteriaand antifungal activity with radial diffusion assay. As a result, 5 out of 38 AMPs showed the highest antimicrobial activityand antifungal activity against microbes and it also evidenced with no hemolytic activity.

Selecting an appropriate antigen with optimal immunogenicity and physicochemical properties is a pivotal factor to develop a protein based subunit vaccine. Despite rapid progress in modern molecular cloning and recombinant protein technology, there remains a huge challenge for purifying and using protein antigens rich in hydrophobic domains, such as membrane associated proteins. To overcome current limitations using hydrophobic proteins as vaccine antigens, we adopted in silico analyses which included bioinformatic prediction and sequence-based protein 3D structure modeling, to develop a novel periodontitis subunit vaccine against the outer membrane protein FomA of Fusobacterium nucleatum. To generate an optimal antigen candidate, we predicted hydrophilicity and B cell epitope parameter by querying to web-based databases, and designed a truncated FomA (tFomA) candidate with better solubility and preserved B cell epitopes. The truncated recombinant protein was engineered to expose epitopes on the surface through simulating amino acid sequence-based 3D folding in aqueous environment. The recombinant tFomA was further expressed and purified, and its immunological properties were evaluated. In the mice intranasal vaccination study, tFomA significantly induced antigen-specific IgG and sIgA responses in both systemic and oral-mucosal compartments, respectively. Our results testify that intelligent in silico designing of antigens provide amenable vaccine epitopes from hard-to-manufacture hydrophobic domain rich microbial antigens.

Varroa destructor is a devastating ectoparasitic mite which attacks Honeybee, Apis mellifera. V. destructor feeds on honeybee hemolymph, and often harbors small RNA viruses such as the deformed wing virus to transmit these viruses in the infested bee hive. To survey the genes of V. destructor, total RNA was subjected to high-throughput transcriptome sequencing to construct in silico cDNA library by using the Illumina HiSeq 2000 platform. Total of 2×107,748,792 paired-end short reads were obtained and quality filtered reads were subjected to Trinity de novo assembler followed by TransDecoder, and CD-HIT program to make a V. destructor reference cDNA library containing 28,023 of clustered contigs with protein coding capacity. These cDNA sequences will help us to understand the molecular biology of V. destructor.

Early growth response 1 (Egr1) is a zinc-finger transcription factor to direct second-wave gene expression leading to cell growth, differentiation and/or apoptosis. While it is well-known that Egr1 controls transcription of an array of targets in various cell types, downstream target gene(s) whose transcription is regulated by Egr1 in the uterus has not been identified yet. Thus, we have tried to identify a list of potential target genes of Egr1 in the uterus by performing multi-step in silico promoter analyses. Analyses of mRNA microarray data provided a cohort of genes (102 genes) which were differentially expressed (DEGs) in the uterus between Egr1(+/+) and Egr1(–/–) mice. In mice, the frequency of putative EGR1 binding sites (EBS) in the promoter of DEGs is significantly higher than that of randomly selected non-DEGs, although it is not correlated with expression levels of DEGs. Furthermore, EBS are considerably enriched within –500 bp of DEG’s promoters. Comparative analyses for EBS of DEGs with the promoters of other species provided power to distinguish DEGs with higher probability as EGR1 direct target genes. Eleven EBS in the promoters of 9 genes among analyzed DEGs are conserved between various species including human. In conclusion, this study provides evidence that analyses of mRNA expression profiles followed by two-step in silico analyses could provide a list of putative Egr1 direct target genes in the uterus where any known direct target genes are yet reported for further functional studies.

Early growth response 1 (Egr1) is an immediate early response gene which is induced by various external stimuli and acts as transcription factor to direct second-wave gene expression leading to cell growth, differentiation and/or apoptosis. It is well known that Egr1 regulates transcription of a cluster of genes in cancers and luteinizing hormone (LH) beta subunit in the pituitary. In addition to function of Egr1 in cancers and pituitary, we recently showed that Egr1 acts as a local master regulator to mediate estrogenic actions in the uterus. However, regulatory mechanism by which Egr1 directs transcription of its downstream target genes in the uterus remains to be yet explored. Thus, we have tried to identify direct target genes of Egr1 in the uterus by analyzing mRNA microarray data sets followed by in silico promoter analyses with chromatin immunoprecipitation (CHIP). mRNA expression profiles of Egr1(－/－) uteri and Egr1(－/－) ovaries were compared to those of wildtype mice to provide a potential list of direct target genes of Egr1 in the uterus. Whereas Egr1 is rapidly and transiently induced in the ovary and the uterus by external stimuli, LH and estrogen, respectively with a similar manner, a list of differentially expressed genes between Egr1(+/+) and Egr1(－/－) mice were barely overlapped between these two datasets. This result suggests that the transcriptional network of Egr1 in the uterus is quite different from that in the ovary. The list of differentially expressed genes in Egr1(－/－) uterus was enriched by RT-PCR. In silico analyses with MatInspector provided evidence that Egr1 binding sites are relatively enriched in －500 bp promoter regions of genes in the list. CHIP assays for Egr1 antibody with uterine tissues 2 h after estrogen treatment reinforced the possibility that genes identified in this study such as Gadd45g and Lbh could be directly regulated by Egr1 in uterine context. Collectively, we show that bioinformatic analyses of expression profiles with in silico analyses could be a useful tool to enrich potential candidates of direct target genes of transcription factors.

Most gene functions of biochemical pathways were still unexplored, especially interactions of constituent genes. We attempted to uncover interaction network of biochemical pathways via a survey of co-expression clusters, which we have constructed from the NCBI GEO database, and then to define key genes of networks with expression correlations between members. Top 20 pathways with high numbers of individual genes were retrieved from 178 pathways. One pathway, ‘removal of superoxide radicals’ was excluded for further study, evidencing somewhat low degree (16%, 13 out of 79 genes) of mapped probes. We employed expression correlations of random pairs of 1,000 randomly selected genes for determining a cut off r-value for gene networks. Numbers of interactions with a significant expression correlation values between members might evidence that “hub genes” play key roles among a given pathway genes. For example most interactive pathway, ‘tRNA charging pathway’, that is composed of 60 probes corresponding to genes showed 264 positive significant interactions between members of 47 genes while 5 negative interactions between members of 7 genes., evidencing ‘Os10g26050’ (methionyl-tRNA synthetase) gene with highest interactions is suggestive of a hub gene. These findings might provide some clues on evolutionary fate of co-expression genes including each of biochemical pathways, e.g. convergent evolution

In order to uncover gene regulatory networks clustering of co-expressing genes was performed using a rice micorarray dataset of 155 gene expression omnibus sample (GSM) plates in NCBI, generating a total of 1660 clusters. One cluster with 85 co-expressing genes was measured with the correlation coefficient between pairs, resulting in an average r value of 0.66 with a range of -0.08 to 0.98. This result might support the notion that genes included in each cluster play common functional role(s). We also retrieved 23 Affymetrix GeneChip spots IDs corresponding to each of candidate genes related to abiotic stresses obtained from the P1antQTL-GE database and subsequently detected 23 clusters including co-expressing genes with each of the genes. Expression profiles of co-expressing genes revealed some degree of tissue-specific expression patterns, probably reflecting the existence of, at least partial, parallel versions of stress-related networks with evolutionary process, such as subfuntionalization. The finding that several cis-elements related to abiotic stresses was detected by differences in frequency between co-expressing genes and randomly selected genes. Clustering, expression profiles, and putative cis-acting regulatory elements of co-expressing genes related to abiotic stresses may provide clues to shed further light on the gene regulatory network of stress-responsive pathway.