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Kumar, Himansu,Srikanth, Krishnamoorthy,Park, Woncheol,Lee, Seung-Hoon,Choi, Bong-Hwan,Kim, Hana,Kim, Yong-Min,Cho, Eun-Seok,Kim, Jin Hyoung,Lee, Jang Hee,Jung, Ji Yeon,Go, Gwang-woong,Lee, Kyung-Tai Elsevier 2019 Gene Vol.703 No.-
<P><B>Abstract</B></P> <P>Long non coding RNAs (lncRNA) have been previously found to be involved in important cellular activities like epigenetics, implantation, cell growth etc. in pigs. However, comprehensive analysis of lncRNA in back fat tissues at different developmental stages in pigs is still lacking. In this study we conducted transcriptome analysis in the back fat tissue of a F1 crossbred Korean Native Pig (KNP) × Yorkshire Pig to identify lncRNA. We investigated their role in 16 pigs at two different growth stages; stage 1 (10 weeks, n = 8) and stage 2 (26 weeks, n = 8). After quality assessment of sequencing reads, we got a total of 1,641,165 assembled transcripts out of eight paired end read from each stage. Among them, 6808 lncRNA transcripts were identified by filtering on the basis of multiple parameters like read length ≥ 200 nucleotides, exon numbers ≥2, FPKM ≥0.5, coding potential score < 0 etc. PFAM and RFAM were used to filter out all possible protein coding genes and housekeeping RNAs respectively. A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed (DE) between the two stages (|log2FC| > 2, q < 0.05). We also identified 306 genes located around 100 kb upstream and 234 genes downstream around these DE lncRNA transcripts. The expression of top eleven DE lncRNAs (COL4A6, LY7S, MYH2, OXCT1, SMPDL3A, TMEM182, TTC36, RFOOOO4, RFOOO15, RFOOO45, CADM2) had been validating by qRT-PCR. Pathway and GO terms analysis showed that, positive regulation of biosynthetic process, Wnt signaling pathway, cellular protein modification process, and positive regulation of nitrogen compound were differentially enriched. Our results suggested that, KEGG pathways such as protein digestion and absorption, Arrhythmogenic right ventricular cardiomyopathy (ARVC) to be significantly enriched in both DE lncRNAs as well as DE mRNAs and involved in back fat tissues development. It also suggests that, identified lncRNAs are involved in regulation of important adipose tissues development pathways.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Analysis of lncRNAs in back fat tissues at different developmental stages in the pigs </LI> <LI> A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed. </LI> <LI> KEGG pathway and GO analysis for functional annotation of lncRNAs </LI> <LI> Top DE transcripts were validated by qRTPCR. </LI> <LI> Relation between back fat metabolism and lncRNAs were established. </LI> </UL> </P>
Exploration of OMIA Registered Recessive Mutations in Hanwoo Cattle
Devender Arora,Krishnamoorthy Srikanth,Do-jung Lim,Jong-myeon Park,so-yeong choe,Seung-hwan Lee,Dong-hyun Shin,Won-choul Park 경상대학교 농업생명과학연구원 2021 농업생명과학연구 Vol.55 No.2
Embryonic lethality due to recessive alleles is a major concern in livestock breeding programs. The Online Mendelian Inheritance in Animal (OMIA) is a database of reported recessive mutations in livestock that helps breeders to manage the segregation of these mutations in their population. Recessive alleles are lethal in the offspring of two carrier parents; therefore, identifying and eliminating carrier animals are critical for maintaining the breed. Hanwoo cattle is native to the Korean peninsula and is of great economic importance to Korea. Due to geographical constraints and the controlled breeding program with very few proven bulls, if not monitored periodically, the threat of segregation of recessive lethal alleles in the population remains high. Therefore, identifying potential carriers of lethal recessive alleles is critical in Hanwoo. In this regard, we genotyped 17,325 animals using bovine 50K Illumina SNP chip and also sequenced a further 311 animals which was mapped against the bovine reference genome sequence. We then used the OMIA database to identify reported recessive alleles and calculated the allele frequency of these mutations in the population to determine potential lethal alleles carried by the animals.
Sunirmal Sheet,Srikanth Krishnamoorthy,Woncheoul Park,Dajeong Lim,Jong-Eun Park,Minjeong Ko,Bong Hwan Choi 한국축산학회 2020 한국축산학회지 Vol.62 No.6
The retinal degenerative disease, progressive retinal atrophy (PRA) is a major reason of vision impairment in canine population. Canine PRA signifies an inherently dissimilar category of retinal dystrophies which has solid resemblances to human retinis pigmentosa. Even though much is known about the biology of PRA, the knowledge about the intricate connection among genetic loci, genes and pathways associated to this disease in dogs are still remain unknown. Therefore, we have performed a genome wide association study (GWAS) to identify susceptibility single nucleotide polymorphisms (SNPs) of PRA. The GWAS was performed using a case–control based association analysis method on PRA dataset of 129 dogs and 135,553 markers. Further, the gene-set and pathway analysis were conducted in this study. A total of 1,114 markers associations with PRA trait at p < 0.01 were extracted and mapped to 640 unique genes, and then selected significant (p < 0.05) enriched 35 gene ontology (GO) terms and 5 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways contain these genes. In particular, apoptosis process, homophilic cell adhesion, calcium ion binding, and endoplasmic reticulum GO terms as well as pathways related to focal adhesion, cyclic guanosine monophosphate)-protein kinase G signaling, and axon guidance were more likely associated to the PRA disease in dogs. These data could provide new insight for further research on identification of potential genes and causative pathways for PRA in dogs.
Confirmation of genotypic effects for the bovine APM1 gene on marbling in Hanwoo cattle
( Anam Kwon ),( Krishnamoorthy Srikanth ),( Eunjin Lee ),( Seonkwan Kim ),( Hoyoung Chung ) 한국동물자원과학회(구 한국축산학회) 2016 한국축산학회지 Vol.58 No.4
Background: Our previous study had identified the SNP (g.81966377T > C) and indel (g.81966364D > I) located in the promoter of APM1 to have a significant effect on marbling in Hanwoo. APM1 encodes an adipocytokine called adiponectin, which plays a significant role in lipogenesis. The aim of this study was to verify and validate the effect of the SNP and indel on marbling and other carcass traits in a large, representative, countrywide population of Hanwoo cattle. The carcass traits measured were marbling (MAR), backfat thickness (BFT), loin eye area (LEA), and carcass weight (CAW). Results: Primers were designed to amplify 346 bp of the genomic segment that contained the targeted SNP (g.81966377) and the indel (g.81966364). After data curation, the genotypes of 8,378 individuals identified using direct sequencing analysis estimated frequencies for C (0.686) and T (0.314) respectively showing genotype frequencies for CC (0.470), CT (0.430) and TT (0.098). The genotypes were significantly associated with MAR, BFT and LEA. The indel had significant effect on marbling (P < .0001) with strong additive genetic effects. The allele frequencies was estimated at (DEL, 0.864) and insertion (INS, 0.136) presenting genotypes of D/D (75.63 %), D/I (21.44 %), and I/I (2.92 %). Significant departure from Hardy-Weinberg equilibrium was not detected for both the SNP and the indel. Conclusion: The SNP genotypes showed significant association with MAR, BFT and LEA with strong additive genetic effects, while the indel was significantly associated with MAR. The results confirmed that the variants can be used as a genetic marker for improving marbling in Hanwoo.
Duraisamy Kalpana,이양수,Krishnamoorthy Srikanth,PB Tirupathi Pichiah,차연수 한국고분자학회 2014 Macromolecular Research Vol.22 No.5
The cultural filtrates of Klebsiella pneumoniae cultured under normal gravity and low shear modeledmicrogravity were potentially used to biosynthesize gold nanoparticles using the precursor gold III chloride trihydrate. The gold nanoparticles produced were spherical, of size between 16-36 and 24-50 nm with the cultural filtratesof normal and low shear modeled microgravity respectively. The characteristic plasmon resonance of gold nanoparticlesoccurred between 535-550 nm in the spectral analysis. XRD reflections (1 1 1), (2 0 0), (2 2 0), (3 1 1) indicatethe face centered cubic and crystalline nature of the biosynthesized gold nanoparticles. The FTIR study proposesthat proteins excreted into the cultural filtrate were involved in the synthesis and stabilization of gold nanoparticles. The in vitro cytotoxicity on 3T3L1, H9c2 and HepG2 cell lines showed the nontoxic and biocompatible nature ofbiosynthesized gold nanoparticles.
박원철(Woncheoul Park),크리스나무티 스리칸스(Krishnamoorthy Srikanth),박종은(Jong-Eun Park),신동현(Donghyun Shin),고해수(Haesu Ko),임다정(Dajeong Lim),조인철(In-Cheol Cho) 한국생명과학회 2019 생명과학회지 Vol.29 No.1
한우(한국 재래 소)에서 반수체형 페이징을 위한 고밀도 시퀀싱을 이용한 비교 분석 논문은 많지가 않다. 이런 고밀도 시퀀싱 플랫폼 중에서, 일루미나에서 서비스 하는 Truseq Synthetic Long-Read Haplotyping 시퀀싱 플랫폼(TSLRH)과 10X Genomics에서 서비스하는 The Chromium Genome 시퀀싱 플랫폼을 특별히 비교 분석하는 논문은 없다. 우리는 한우 연구소의 한우 종모우(아이디: TN1505D2184 or 27214)의 정액에서 DNA를 추출하였으며, 이 DNA로부터 각각의 시퀀싱 플랫폼을 이용하여 시퀀싱 데이터를 생산하였다. 그 후, 우리는 각각의 시퀀싱 플랫폼에 맞는 분석 방법을 이용하여 단일염기서열변이들은 찾아냈다. 그 결과, TSLRH과 10XG의 전체 리드 수는 각각 355,208,304, 1,632,772,004, 맵핑 리드의 개수는 351,992,768(99.09%), 1,526,641,824(93.50%), Q30(%)은 89.04%, 88.60%, 평균 밀도는 13.04X, 74.3X, 가장 긴 페이즈 블락은 1,982,706bp, 1,480,081 bp, N50 페이즈 블락은 57,637bp, 114,394 bp, 전체 단일염기서열변이는 4,534,989, 8,496,813, 전체 페이징 비율은 72.29%, 87.67%였다. 더욱이, 우리는 각각의 시퀀싱 플랫폼을 비교해서 각각의 시퀀싱 플랫폼의 고유한 단일염기서열변이와 두 시퀀싱 플랫폼에서 공통적으로 존재하는 단일염기서열변이를 각 염색체 별로 확인하였으며, 단일염기서열변이의 개수는 염색체 길이에 정비례한다는 결과를 확인하였다. 결론적으로, 본 연구에서 추천하는 바는 연구비가 충분하지 않을 시에는 TSLRH 보다 10XG을 사용하는 것을 추천한다. 왜냐하면 전체 리드 및 단일염기서열변이 개수, N50 페이즈 블락, 가장 긴 페이즈 블락, 페이즈 비율 그리고 평균 밀도 등이 TSLRH 보다 10XG가 더 높거나 좋기 때문이다. In Hanwoo cattle (Korean native cattle), there is a scarcity of comparative analysis papers using highdepth sequencing and haplotype phasing, particularly a comparative analysis of the Truseq Synthetic Long-Read Haplotyping sequencing platform serviced by Illumina (TSLRH) versus the Chromium Genome Sequencing platform serviced by 10X Genomics (10XG). DNA was extracted from the sperm of a Hanwoo breeding bull (ID: TN1505D2184/27214) provided by Hanwoo research canter and used for the generation of sequence data from both the sequencing platforms. We then identified SNVs using an appropriate analysis pipeline tailored for each platform. The TSLRH and 10XG platforms generated a total of 355,208,304 and 1,632,772,004 reads, respectively, corresponding to a Q30 (%) of 89.04% and 88.60%, respectively, of which 351,992,768(99.09%) and 1,526,641,824(93.50%) were successfully mapped. For the TSLRH and 10XG platforms, the mean depth of the sequencing was 13.04X and 74.3X, the longest phase block was 1,982,706 bp and 1,480,081 bp, the N50 phase block was 57,637 bp and 114,394 bp, the total number of SNVs identified was 4,534,989 and 8,496,813, and the total phased rate was 72.29% and 87.67%, respectively. Moreover, for each chromosome, we identified unique and common SNVs using both sequencing platforms. The number of SNVs was directly proportional to the length of the chromosome. Based on our results, we recommend the use of the 10XG platform for haplotype phasing and SNV identification, as it generated a longer N50 phase block, in addition to a higher mean depth, total number of reads, total number of SNVs, and phase rate, than the TSLRH platform.
Kumar, Himansu,Park, Woncheoul,Lim, Dajeong,Srikanth, Krishnamoorthy,Kim, Jun-Mo,Jia, Xin-Zheng,Han, Jian-Lin,Hanotte, Olivier,Park, Jong-Eun,Oyola, Samuel O. Elsevier 2020 Genomics Vol.112 No.2
<P><B>Abstract</B></P> <P>We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by <I>Bacteroidetes</I> and <I>Firmicutes.</I> We identified 2210 common genes in the two groups. LEfSe showed that the distribution of <I>Coprobacter, Geobacter, Cronobacter, Alloprevotella,</I> and <I>Dysgonomonas</I> were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Microbial comparison of scavenging chicken's cecum content between high land and low land region of Ethiopia. </LI> <LI> Differential functional annotations of identified microbiota from both regions. </LI> <LI> Antibiotic resistant genes identification and their differential abundance. </LI> </UL> </P>