The small brown planthopper (SBPH), Laodelphax striatellus Fallén (Hemiptera: Delphacidae) is one of the major insect pest against rice, Oryza sativa L. in Korea. High density of SBPH could cause severe damage on rice plant by directly sucking and indirectly transmitting viral pathogens, Rice stripe virus and Rice streaked dwarf virus. As a preliminary study for de novo whole-genome sequencing of SBPH, we investigated 6 transcriptomes isolated from different developmental stages, sex, and tissue (egg, 1st ~ 3rd nymphs, 4th ~ 5th nymphs, female and male adults, salivary gland). Clean-sequence data of 19.3 Gb were obtained from total 47.8 Gb raw data after adaptor and quality trimming (Q30) and overlapped reads joining. As a suitable assembler, Bridger was selected based on the results of reference mapping (93.45%) and CEGMA completeness (95.97%). Finally, we obtained 158,207 reads (size range: 201 ~ 22,162 bp; Mean size: 1,048.04 bp; N50: 2,417 bp) after clustering the assembly results by CD-HIT-EST (similarity threshold: 99%). Based on these results, we are conducting further studies such as transcript expression pattern among different developmental stages and gene annotation.

Next Generation Sequencing을 이용한 분석 서열을 기반으로 매미나방의 Microsatellite loci 탐색 및 marker 개발을 수행하였다. 매미나방의 Genomic DNA 서열 분석은 MiSeq Sequencer (Illumina)의 1/8 plate를 이용하여 실시하였다. 판독된 유전자 서열의 길이는 총 3,974,358,483 bp로 평균 248.58 bp로 구성된 총 15,988,036 개의 분석 단편이 확보되었으며, 이를 CLC workbench를 이용하여 총 367,397,618 bp로 조합하였다. 조합된 Genomic DNA 서열을 대상으로 반복서열길이 2~4 bp, 반복횟수 4회 이상의 조건으로 총 1,864 개의 Microsatellite loci를 탐색하였다. 이 중 반복횟수 6회 이상의 430 loci에 대한 marker 제작 가능성을 TM 55.5~56.5℃, GC contents 30% 이상, primer length 18~22 bp의 조건으로 Primer3을 이용하여 분석하였으며, 총 207 개의 marker를 제작하였다. 선별된 207개 marker 중 150개 마커에 대해 일반 올리고 primer set를 제작하여 PCR을 통한 유용성 평가를 실하였으며, 그 결과 총 29개의 마커에 대한 유효성이 확인되어 Genotyping 용 형광 dye인 FAM을 부착한 분석용 마커로 제작하였다. FAM을 부착한 마커에 대한 PCR 효율 검사를 통해 최종적으로 10개 마커를 선별하여 한국 4개 지역(Korea 1, Korea 22, Korea 26, Korea 31) 및 러시아(Vladivostok), 몽고(Shagaarnur) 각 1개 지역의 개체군을 대상으로 유전적 구조 분석을 수행하였다. 유전적 유사도를 평가하기 위하여 Fst Pairwise UPGMA tree를 분석한 결과, Korea 1과 러시아 개체군, Korea 22와 Korea 26 개체군의 유전적으로 유사도가 높은 것으로 나타났으며, Korea 31과 몽고 개체군은 유사도의 기부에 위치하는 것을 확인할 수 있었다. 또한, Baysian Algorithm을 기반으로 한 유전적 구조 분석에서도 각 개체 및 개체군의 구조는 UPGMA tree 동일한 양상을 나타내는 것으로 확인되었다. 따라서, 현 연구를 통해 개발된 매미나방의 Microsatellite 마커는 한국을 비롯한 인근 지역의 지역적 개체군 분석을 가능하게 할 수 있을 것으로 판단되며, 결국 식물검역에서 매미나방의 유출 국가 및 지역에 대한 판별 분석에 유용할 수 있을 것이다.

Next Generation Sequencing을 이용한 분석 서열을 기반으로 매미나방의 Microsatellite loci 탐색 및 marker 개발을 수행하였다. 매미나방의 Genomic DNA 서열 분석은 MiSeq Sequencer (Illumina)의 1/8 plate를 이용하여 실시하였다. 판독 된 유전자 서열의 길이는 총 3,974,358,483 bp로 평균 248.58 bp로 구성된 총 15,988,036 개의 분석단편이 확보되었으며, 이를 CLC workbench를 이용하여 총 367,397,618 bp로 조합하였다. 조합된 Genomic DNA 서열을 대상으로 반복서열 길이 2~4 bp, 반복횟수 4회 이상의 조건으로 총 1,864 개의 Microsatellite loci를 탐 색하였다. 이 중 반복횟수 6회 이상의 430 loci에 대한 marker 제작 가능성을 TM 55.5~56.5℃, GC contents 30% 이상, primer length 18~22 bp의 조건으로 Primer3 을 이용하여 분석하였으며, 총 207 개의 marker를 제작하였다. 선별된 207개 marker 중 150개 마커에 대해 일반 올리고 primer set를 제작하여 PCR을 통한 유용 성 평가를 실하였으며, 그 결과 총 51개의 마커에 대한 유효성이 확인되어 Genotyping 용 형광 dye인 FAM을 부착한 분석용 마커로 제작하였다. 현재는 PCR 을 통한 결과만을 이용하여 유용성 평가를 실시하였다. 추후 분석용 마커를 이용하 여 Genotyping을 통한 유용성 평가를 수행할 예정이다. 주요 검역 해충으로 알려져 있는 매미나방의 Microsatellite 마커의 개발은 한국을 비롯한 인근 지역의 지역적 개체군 분석을 가능하게 할 수 있을 것으로 판단되며, 결국 식물검역에서 매미나방 의 유출 국가 및 지역에 대한 판별 분석에 유용할 수 있을 것이다.

Establishment of rapid resistance level detection system is essential step to adopt the adaptive management for the control of various kinds of resistant pest population. Here, we established acaricides resistance detection methods based on residual contact vial bioassay (RCV) and quantitative sequencing methods (QS), and applied to determine the resistance levels from several populations in two-spotted spider mite, Tetranychus urticae, which has been considered as major notorious pest in rose cultivation area in worldwide. 12 acaricides were applicable to the RCV among 19 representative acaricides by showing the dose-dependent mortality within 8 hr, suggesting the acaricide suitability for the RCV might be varied by toxicity mechanism in each acaricides. The QS regression was established for 10 point mutations associated with five number of acaricides resistance such as organophosphate, pyrethroid, abamectin, bifenazate and etoxazol. The 95% prediction level was ranged from 10.8±5.4∼92.2±3.2%. The resistance levels were determined by above two detection methods from a total 12 strains. The laboratory-reared populations were revealed high susceptibility with low resistance allele frequencies to some acaricides, suggesting the several acaricides would be chosen for the control of those populations. However, the field-collected populations were exhibited a severe cross resistance with low susceptibility and high resistance allele frequency to almost tested acaricides, suggesting the current acaricides resistance levels are serious in rose cultivation area in Korea. The RCV and QS methods would be useful for the rapid and accurate collection of valuable information associated with acaricide resistance.

C/N 비가 낮은 농촌마을 하수의 고도처리를 위하여 0.4 µm의 세공크기를 갖고 있는 평막이 침지된 연속회분식 반응기를 사용하였다. 분말활성탄의 투입, 폭기량 및 유입 유기물 농도가 처리효율과 여과 성능에 미치는 영향을 조사하였다.54일 이내의 조업 초기에서는 C/N 비가 증가할수록 COD, T-N 및 T-P의 제거율과 MLSS 농도는 증가하였다. 조업 89일 후의 COD, T-N 및 T-P의 제거율은 각각 97.1%, 75.0% 및 48.3%이었다. 막여과에 의해 처리수에서 SS는 검출되지 않았으며,T-P의 제거율이 낮게 나온 이유는 과잉의 슬러지를 배출하지 않았기 때문이다. 분말활성탄을 투여한 경우 조업이 진행됨에따라 분말활성탄의 혼합강도와 충돌빈도가 증가하여 슬러지의 입자크기가 감소하였으며, 이로 인해 분말활성탄을 투여하지 않은 경우에 비해 TMP 상승이 크게 나타났다.

The problem of constrained sequencing of a set of jobs on a conveyor system with the objective of minimizing setup cost is investigated in this paper. A setup cost is associated with extra material, labor, or energy required due to the change of attributes in consecutive jobs at processing stations. A finite set of attributes is considered in this research. Sequencing is constrained by the availability of conveyor junctions. The problem is motivated by the paint purge reduction problem at a major U.S. automotive manufacturer. We first model a diverging junction with a sequence-independent setup cost and predefined attributes as an assignment problem and this model is then extended for a more general situation by relaxing the initial assumptions in various ways.

The physiology of parasitic wasp control of their lepidopteran hosts' not only includes injecting their egg but also various factors such as symbiotic virus. This study was focused on the investigation of sophisticated interaction between parasitoid (Diadegma fenestrale) and their host (Plutella xylostella) in P. xylostella larva at transcriptome level, to check whether it is parasitized or not. Short-read deep sequencing method (Hiseq2000) was used for the transcriptome analysis. De novo assembly of cDNA sequence data generated 196,081 contigs between 201bp and 15,853bp in length. Some detoxification enzymes such as cytochrome P450 and Immune-related genes such as antimicrobial peptides were up-regulated after parasitism. Expression of symbiotic ichnovirus genes was detected in parasitized larvae with 55 contigs identified from five ichnovirus gene families including vankyrin, viral innexin, repeat elements, a cysteine-rich motif, and polar residue rich protein. This investigation provides a detailed information on differential expression of P. xylostella larval genes and symbiotic ichnovirus genes following parasitization.

The rapid advances in next generation sequencing (NGS) technologies have brought about huge improvement in sequencing throughput for affordable prices and revolutionized genomics researches. Nowadays, whole genome draft sequence for mid-sized genomes such as insects' can be obtained in a couple of months. And the gene space in action can be easily determined by whole transcriptome sequencing, even when the reference genome sequence is not available. In this workshop, experiences at Macrogen with NGS technology for whole genome sequencing and whole transcriptome sequencing will be presented focusing on insect researches, employing Illumina Hiseq2000 and/or Roche 454 platforms.

스펀지 형태의 담체가 첨가된 침지형 막결합 연속회분식 생물반응기에서 담체가 제거효율과 여과성능에 미치는 영향을 조사하였다. 담체는 반응기 부피 기준으로 각각 5%, 10% 및 20% 첨가하였고, 담체를 첨가하지 않은 반응기를 대조군으로 하였다. COD, T-N 및 T-P에 대한 제거효율은 담체 첨가 유무에 관계없이 큰 차이가 없었다. 그러나 담체를 첨가한 경우, 첨가하지 않은 경우에 비해 조업시간에 따른 막간차압(TMP)은 매우 서서히 증가하였다. 이러한 결과는 폭기에 의해 상승하는 담체가 막 표면과 충돌하게 되고, 이때 막 표면에 형성된 케이크 층을 제거시키기 때문이다. 결론적으로 담체가 첨가된 막결합형 연속회분식 생물반응기는 담체가 없는 반응기에 비해 여과성능이 크게 개선되어, 폐수처리에 효과적으로 활용될 수 있을 것이다.

Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used in aquatic ecotoxicological studies for assessing acute and sub-lethal toxicities of contaminated sediments and for water monitoring due to their widespread occurrence, short life-cycle, easy to be reared in the laboratory, physiological tolerance to various environmental conditions. To date, the endpoints used for monitoring such effects in C. riparius are based on a small number of specific biomarkers and measurements of organism level effects, such as survival and reproduction. Genomic-based techniques based on expression analysis of genes are important tools for investigating molecular level effects caused by exposure to environmental pollutants, which will provide the ability to detect mechanisms of action and subsequent adverse cellular level effects and associated with different types of toxicity. As a pre-requisite for genomic based ecotoxicological studies knowledge on the C. riparius transcriptome is important but despite its ecotoxicological importance, no large scale transcriptome analysis of C. riparius has been done so far. Therefore, to gain a better understanding of C. riparius transcriptome, we recently developed Expressed Sequence Tags (ESTs) sequencing project on C. riparius larvae using 454 pyrosequencing. Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value ≤1-5) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest. The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, C. riparius. Various C. riparius ecotoxicity studies using stress response genes developed from 454 sequencing will be presented in the conference.

With the advent of the genomics era powered by DNA sequencing technologies, life science is being transformed significantly and biological research and development have been accelerated. Environmental biology concerns the relationships among living organisms and their natural environment, which constitute the global biogeochemical cycle. As sustainability of the ecosystems depends on biodiversity, examining the structure and dynamics of the biotic constituents and fully grasping their genetic and metabolic capabilities are pivotal. The high-speed highthroughput next-generation sequencing can be applied to barcoding organisms either thriving or endangered and to decoding the whole genome information. Furthermore, diversity and the full gene complement of a microbial community can be elucidated and monitored through metagenomic approaches. With regard to human welfare, microbiomes of various human habitats such as gut, skin, mouth, stomach, and vagina, have been and are being scrutinized. To keep pace with the rapid increase of the sequencing capacity, various bioinformatic algorithms and software tools that even utilize supercomputers and cloud computing are being developed for processing and storage of massive data sets. Environmental genomics will be the major force in understanding the structure and function of ecosystems in nature as well as preserving, remediating, and bioprospecting them.

This paper focuses on scheduling problems arising in the military. In planned artillery attack operations, a large number of threatening enemy targets should be destroyed to minimize fatal loss to the friendly forces. We consider a situation in which the

The resistance levels to carbamate (CB) and organophosphate (OP) insecticides were determined by topical application in 14 field strains of Nilaparvata lugens. The resistance levels to CB and OP were 1.3~47.5-fold and 1.4~14.4-fold higher than a susceptible strain, respectively. A quantitative sequencing (QS) protocol was established to determine the allele frequencies of four acetylcholinesterase point mutations putatively associated with CB and OP resistance. The allele frequencies of the four mutations (G119A, F/Y330S, F331H and I332L) in field strains ranged from ca. 0.0~51.7%, 0.0~88.9%, 2.5~47.7%, 5.1~56.0% and 6.7~57.3%, respectively. The F331H and I332L were tightly linked each other, suggesting these mutations may occur simultaneously. In the correlation analysis, G119A was not well correlated with actual resistance levels (r2= < 0.232), whereas F331H and I332L showed a better correlation with the resistance levels of benzofuranyl methylcarbamates (r2= 0.595). This finding indicates that F331H and I332L mutation frequencies may be used as molecular markers for detecting carbamate resistance in N. lugens. A QS protocol detecting the F331H and I332L mutation frequencies would be employed as a supportive tool for rapid monitoring of CB insecticide resistance levels in N. lugens

This dissertation focuses on scheduling problems arising in the military. In planned artillery attack operations, a large number of threatening enemy targets should be destroyed to minimize fatal loss to the friendly forces. We consider a situation in which the number of available weapons is smaller than the number of targets. Therefore it is required to develop a new sequencing algorithm for the unplanned artillery attack operation. The objective is to minimize the total loss of the targets, which is expressed as a function of the fire power potential, after artillery attack operations are finished. We develop a algorithm considering the fire power potential and the time required to destroy the targets. The algorithms suggested in this dissertation can be used in real artillery attack operations if they are modified slightly to cope with the practical situations.

The resistance levels against carbamates (CB) and organophosphates (OP) were determined through bioassay and quantitative sequencing (QS) methods in 16 field populations of Nilaparvata lugens. The resistance levels to CB and OP by bioassay were 1.3~47.5-fold and 1.4~14.4-fold higher than a susceptible strain, respectively. The QS protocol was established to determine the allele frequencies of eight point mutations on acetylcholinesterase putatively associated CB and OP resistance. The allele frequencies of four mutations in local populations (G119A, F/S330Y, F331H and I332L) ranged from ca. 0.0~51.7%, 1.0~44.3%, 8.5~57.3% and 7.12~56.6%, respectively. The average prediction limits were –9.6±5.1~7.7±2.9%. The F330Y, F331H and I332L were tightly linked each other, suggesting these mutations may occur simultaneously. In the correlation analysis, G119A was not well correlated with both insecticides (r2= less 0.25), whereas F/S330Y, F331H and I332L showed better correlation with the resistance levels of carbamate (r2=0.590) than organophosphate (r2=0.235). This finding indicates that F/S330Y, F331H and I332L mutation frequencies are suitable for detecting carbamate resistance in N. lugens. QS will be applicable for the rapid monitoring of resistance levels to CB insecticides in N. lugens.

침지식 막결합형 연속회분식 생물반응기에서 폐수의 도입단계가 제거효율과 여과성능에 미치는 영향을 조사하였다. 호기성 단계의 초기에 공급할 경우(Mode-1)와 무산소 단계의 초기에 공급할 경우(Mode-2)에 대하여 89일 동안 동시에 운전하였다. COD 제거효율과 여과성능은 2가지 운전방식 간에 큰 차이가 없었다. 그러나 영양염류(총질소와 총인)의 제거효율에 있어서 Mode-2가 Mode-1에 비해 보다 효과적이었다. Mode-2의 경우 COD, 총질소 및 총인의 제거율은 각각 99.1, 73.3 및 77.7%이었다.

The differences in the immune response between body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, were regarded as primary factors determining their differential vector competence. To find any differences in genetic components in immune system between body and head lice, whole genome sequences of head lice were determined by both SBS [sequencing by synthesis, Illumina Genome Analyzer (Illumina-GA)] and pyrosequencing (Roche GS FLX), and compared with the reference genome sequences of body lice. The short DNA reads from Illumina-GA (an average mapping depth of 50-fold) were aligned first to the body louse reference genome, to which Roche GS FLX DNA reads (an average depth of 2.5-fold) were subsequently assembled to make up gaps between mapped consensus. Total consensus showed a size of 114 Mb and a coverage of 96% of the published body louse genome sequences. From this head louse genome sequences, a total of 12,651 genes were predicted and used for comparing with the 10,775 genes previously reported from the body louse genome. The homolog analysis identified 873 head louse-specific genes and 422 body lice-specific genes. Comparison of immune response genes between both louse species showed head lice have more number of immune-related genes than body lice. Head lice were determined to possess all of the 107 immune-related genes reported in the previous study (Kim et al., 2011), suggesting that there is no difference in genetic make-up in terms of the 107 immune-related genes between body and head lice.

The genetic diversity of 16 Ganoderma strains was investigated by rDNA-ITS sequencing. Alignment analysis showed that whole length of internal transcribed spacer(ITS1+ITS2) was 500bp and with 139 variation sites (accounting for 23.3％, ITS1 was 66 and ITS2 was 73), 337 conserved sites (accounting for 72.2％), 59 informative sites (accounting for 9.88％), 86 conversion sites (G-A, C-T), 13 transversion site(C-G, T-A). The ratio of transition and transversion in ITS1 was higher than that in ITS2, and the variable sites of ITS2 were more than those of ITS1. The genetic distance among 16 Ganoderma strains is from 0 to 0.121. The genetic distance between G. lipsiense and F-1 was 0, and the genetic distance between Heizhi 02 and Huizhou, Jingda, G. capense was 0.121, 0.117 and 0.120, respectively. The 16 Ganoderma strains were classed into 4 groups. The biggest group is comprised of 12 strains, including Xinzhou, Huizhou, Jingda, 902, F-1, Xianzhi, Meiluo, Taishan, G. applanatum, 05, G. luteomarginatum. The G. atrum and G. sinense were clustered into one group. The G. capense and Zhongzhi was independent group, respectively. These results showed that there were some genetic difference among groups, and there was lower genetic diversity among strains in same groups.

Particle Swarm Optimization (PSO) which has been well known to solve continuous problems can be applied to discrete combinatorial problems. Several DPSO (Discrete Particle Swarm Optimization) algorithms have been proposed to solve discrete problems such a