A genome-wide approach to the systematic and comprehensive analysis of LIM gene family in sorghum (Sorghum bicolor L.)

Md. Abdur Rauf Sarkar,Salim Sarkar,Md Shohel Ul Islam,Fatema Tuz Zohra,Shaikh Mizanur Rahman Korea Genome Organization 2023 Genomics & informatics Vol.21 No.3

The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.

Identification and characterization of protein coding genes in monsonia (Monsonia burkeana Planch. ex harv) using a combination of approaches

Adugna A. Woldesemayat,Khayalethu Ntushelo,David M. Modise 한국유전학회 2017 Genes & Genomics Vol.39 No.3

The advent of next generation sequencing has made possible massive availability of sequence information for in-depth structural and functional analysis of the genes and their encoded biological state in model and nonmodel organisms. In this study, we demonstrate a combinatorial approach for finding protein coding genes using ab initio and extrinsic evidence-based methods in monsonia (Monsonia burkeana Planch. ex harv). This is an important herbal tea crop, yet little is known about its coding genes. To our knowledge, this is the first description of protein coding genes with detailed functional annotation in M. burkeana. This study demonstrates that (1) regions of transcript assembly potentially encode protein coding genes, (2) homologous evidence with known functions reliably assigns functions to the identified genes (3) conserved domains suggest evolutionary and functional relationship of the crop with other lineage and (4) accuracy of finding coding genes in alignment free models and in RNA-seq alignment based transcript assembly performs well. This study provides a glimpse of functional information of the protein coding region at the transcriptome level and can be used as the basis for further investigation of the underlying genetic composition and molecular functions associated with M. burkeana.

Identification of Egr1 Direct Target Genes in the Uterus by In Silico Analyses with Expression Profiles from mRNA Microarray Data

Seo, Bong-Jong,Son, Ji Won,Kim, Hye-Ryun,Hong, Seok-Ho,Song, Haengseok The Korean Society of Developmental Biology 2014 발생과 생식 Vol.18 No.1

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.

Identification of Egr1 Direct Target Genes in the Uterus by In Silico Analyses with Expression Profiles from mRNA Microarray Data

서봉정,손지원,김혜련,홍석호,송행석 한국발생생물학회 2014 발생과 생식 Vol.18 No.1

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.

Identification of Egr1 Direct Target Genes in the Uterus by In Silico Analyses with Expression Profiles from mRNA Microarray Data

Bong-jong Seo,Ji Won Son,Hye-Ryun Kim,Seok-Ho Hong,Haengseok Song 한국발생생물학회 2014 발생과 생식 Vol.18 No.1

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.

모색 발현 유전자의 DNA Marker를 이용한 쇠고기 품종 판별

정의룡,정구용,Chung Eui-Ryong,Chung Ku-Young 한국축산식품학회 2004 한국축산식품학회지 Vol.24 No.4

본 연구는 축우의 모색발현에 관여하는 MC1R, MGF 및 TYRP1 3종류의 모색 유전자의 PCR-RFLP marker를 이용하여 쇠고기 품종 판별기술을 개발하고자 수행하였다. MC1R 유전자의 104번째 아미노산을 지정하는 codon에 GGT 염기를 갖고 있는 Holstein 젖소와 Angus 육우는 제한효소 인지부위가 존재하여 537 bp증폭산물이 절단되어 329와 208bp 두개의 band가 검출되었으나 한우에서는 GTG로 G 염기가 T염기로 치환됨으로써 제한효소 인식부위가 소실되어 537 bp의 단일 bind 만이 검출되었다. 따라서, 이처럼 MC1R 모색유전자의 품종 간 특정 염기서열의 차이가 곧 특정 제한효소의 염기 서열상의 인지 부위 차이를 가져와 한우와 Holstein 젖소 및 Angus 육우 품종간의 RFLP 유전자형 출현에 확실한 차이가 인정되어 한우 품종에 특이적인 MC1R 유전자의 RFLP marker를 이용한 한우육 판별이 가능하였다. 또한, MGF 유전자의 RFLP 유전자형 출현빈도에서 한우는 r/r형이 75%로 출현율이 매우 높은 유전자형으로 분석된 반면 Hereford종은 R/R 형이 80%로 출현율이 매우 높았고 Holstein종과 Angus종은 R/r형이 100% 출현함으로써 한우와 Holstein 및 수입육우 품종간의 MGF 유전자형 출현빈도에 뚜렷한 차이가 인정되었다. 한편, TYRP1 유전자의 RFLP유전자형을 분석한 결과 모든 품종에서 동일한 RFLP type이 검출되어 TYRP1 모색 유전자를 이용한 쇠고기 품종 구별은 불가능한 것으로 나타났다. 따라서, 소 모색 관련 MC1R과 MGF 두 유전자의 품종 특이적 PCR-RFLP 유전자형은 한우육과 국내산 Holstein젖소고기 및 Angus 수입육간의 품종을 식별하는데 매우 유용한 DNA marker로 이용될 수 있음이 확인되었다. In Korean beef market, one of the major problems is mislabeling or fraudulent distribution of Holstein dairy meat or imported beef as domestic Hanwoo meat. Therefore, there has been a great need for a development of technology to identify beef breeds in meat and meat products. This study was carried out to develop the accurate and reliable method for the identification of beef breed using PCR-RFLP marker of MC1R, MGF and TYRPl genes affecting coat colors in cattle. A single base substitution (G\longrightarrowT transition) at the codon for amino acid position 104 of MC1R gene was identified between Hanwoo and Holstein and Angus breeds. The change at this position creates Msp I restriction site in Holstein and Angus, but not in Hanwoo. When the DNA amplified products (537 bp) was digested with Msp I, Hanwoo meat showed a single band of 537bp, while two fragments of 329bp and 208 bp were observed in Holstein meat and Angus breed, respectively. Thus, breed-specific RFLP marker in the MC1R gene can be used to distinguish between Hanwoo meat and Holstein and Angus meats. In the RFLP genotype of MGF gene, the frequency of r/r type was 75% in Manwoo, whereas the frequency of R/R was 80% in Hereford breed. Holstein and Angus breeds showed 100% for R/r type. Therefore, Hanwoo meat showed significant difference in the MGF genotype frequencies compared with those of Holstein meat and imported beef cattle breeds. However, TYRP1 gene showed the same genotype in all breeds examined. Thus, this TYRP1 gene can not be used as a molecular marker for breed identification. As a consequence, we suggest that RFLP markers of the MC1R and MGF coat color genes could be used as DNA marker for identification of Hanwoo meat from Holstein and imported meats.

Vibrio 임상 분리주의 균종 동정을 위한 dnaJ 및 16S rDNA의 서열 분석법 비교

최인선,문대수,박건,강성호,김춘미,안영준,김동민,윤나라,임동훈,신성희,국중기,장영효,장숙진 대한진단검사의학회 2018 Laboratory Medicine Online Vol.8 No.1

배경: Vibrio 종에는 치명적인 패혈증을 일으키는 균종들도 포함되어 있어서 정확한 균종 동정이 매우 중요하다. 일부 비전형적인표현형을 보이는 균종이 있어 정확한 동정을 위해 적절한 분자 진단법의 도입이 필요하다. 방법: 본 연구에서는 Vibrio 임상 분리주 53주와 표준균주 8주가이용되었다. 분자 진단법으로는 dnaJ 유전자 서열 분석, 16S rDNA 서열 분석, gyrB V. vulnificus–특이적 PCR 서열 분석, gyrB V. navarrensis– 특이적 PCR 서열 분석, V. vulnificus hemolysin 유전자(vvh) PCR (V. vulnificus-특이적 PCR)를 시행하였다. 또한 16S rDNA 와 dnaJ 유전자, gyrB 유전자의 서열분석 결과를 토대로 계통수분석을 실시하였으며 상기 검사 결과를 종합하여 균의 최종 동정명이 결정되었다. 16S rDNA 서열 분석과 dnaJ 유전자 서열 분석 간의 일치율 분석은 카이 제곱 검정을 이용하였다. 결과: 61주의 Vibrio 균주의 최종 균종명 분포를 내림차순으로 배열하면 다음과 같다: V. vulnificus (78.69%), V. parahaemolyticus (6.56%), V. navarrensis (4.92%), V. mimicus (1.64%), V. cholera (1.64%), V. furnissii (1.64%), V. alginolyticus (1.64%), Grimontia hollisae (1.64%). dnaJ 유전자 서열 분석의 정확도는 91.80%였고16S rDNA 서열 분석의 정확도는 86.89%였다. dnaJ 유전자 서열 분석법과 16S rDNA 서열 분석법 간의 일치도는 0.45로서, 중등도의일치도였다. 결론: 본 연구는 dnaJ 유전자 서열 분석법이 서로 밀접히 관련된Vibrio 종 간의 정확한 균 종정에 유용한 방법이라는 것을 보여주었다. Background: Among the many Vibrio species that can cause infections in humans, several species can cause a fatal outcome. Therefore, accurate identification of Vibrio species is very important. Since some species show atypical phenotypic features, selecting an appropriate molecular method is necessary to avoid misdiagnosis. Methods: Vibrio clinical isolates (N=53) and reference strains (N=8) were used in this study. We analyzed the following sequences for identification: dnaJ gene, 16S rDNA, gyrase B (gyrB) V. vulnificus–specific sequence, gyrB V. navarrensis–specific sequence, and V. vulnificus hemolysin gene PCR (Vvh PCR). We performed phylogenetic analysis of the 16S rDNA, dnaJ, and gyrB sequences. Final identification was based on the combined results of all tests described above. Concordance of the 16S rDNA and dnaJ sequence analysis was measured using the Chi-square test. Results: The 61 Vibrio strains were identified as follows, in descending order: V. vulnificus (78.69%), V. parahaemolyticus (6.56%), V. navarrensis (4.92%), V. mimicus (1.64%), V. cholera (1.64%), V. furnissii (1.64%), V. alginolyticus (1.64%), and Grimontia hollisae (1.64%). The accuracy rates of the dnaJ gene and 16S rDNA sequence for identification were 91.80% and 86.89%, respectively. The 16S rDNA and dnaJ sequences showed a concordance rate of 0.45, which indicates moderate agreement. Conclusions: Our results suggest that analysis of the dnaJ sequence may be a useful method for the identification of clinical isolates of Vibrio species, especially for distinguishing between closely related Vibrio species.

Molecular identification of a forensically relevant blowfly species (Diptera: Calliphoridae) from the Nagpur region of Maharashtra, India

Apurva M. SHINDE 한국곤충학회 2021 Entomological Research Vol.51 No.6

Blowflies (Diptera: Calliphoridae) are widely distributed in many parts of the world. These flies have forensic importance, as they infest carrion soon after death; this helps not only to estimate the post-mortem interval, but also other forensic interpretations. However, the forensic value of most entomofauna found at crime scenes is dependent on accurate species identification. Traditional identification of blowflies is based on morphology, but this has limitations when it comes to identifying degraded or damaged samples, or immature stages of the flies. To increase the accuracy of species identification, DNA-based technologies have been applied. Molecular identification, using the mitochondrial cytochrome C oxidase I gene coupled with its phylogenetic analysis, has demonstrated the potential for rapid and accurate identification of Calliphoridae species. The present study used this process of molecular identification to identify blowflies collected from the Nagpur region (Maharashtra, India). Five flies belonging to two species (Chrysoma megacephala and Chrysomya rufifacies)have been identified by mitochondrial cytochrome C oxidase I gene sequences, and have been added to GenBank [Accession nos: - (MT502110, MT502109 Chrysomya megacephala) (MT502108, MT502111 – Chrysomya rufifacies) to aid researchers in the correct identification of blowfly species for future research or forensic applications.

Rapid identification of unknown carboxyl esterase activity in <i>Corynebacterium glutamicum</i> using RNA-guided CRISPR interference

Lee, Seung Soo,Shin, Hyojung,Jo, Suah,Lee, Sun-Mi,Um, Youngsoon,Woo, Han Min Elsevier 2018 Enzyme and microbial technology Vol.114 No.-

<P><B>Abstract</B></P> <P>RNA-guided genome engineering technologies have been developed for the advanced metabolic engineering of microbial cells to enhance production of value-added chemicals in <I>Corynebacterium glutamicum</I> as an industrial host. In this study, the RNA-guided CRISPR interference (CRISPRi) was applied to rapidly identify of unknown genes for native esterase activity in <I>C. glutamicum</I>. Combining with the carboxyl esterase (MekB) protein sequence alignment, two target genes (the <I>cg0961</I> and <I>cg0754</I>) were selected for the CRISPRi application to investigate the possible native esterase in <I>C. glutamicum</I>. The recombinant strain with repressed expression of the <I>cg0961</I> gene exhibited almost no capability on degradation of methyl acetate as a substrate of carboxyl esterase. This result was also confirmed in the <I>cg0961</I> gene deletion mutant. Thus, we concluded that Cg0961 plays a major role of the native carboxyl esterase activity in <I>C. glutamicum</I>. In addition, CRISPRi demonstrated an application for gene identification and its function as another genetic tool for metabolic engineering in <I>C. glutamicum.</I> </P> <P><B>Highlights</B></P> <P> <UL> <LI> RNA-guided genome engineering technology was applied for the gene identification. </LI> <LI> Cg0961 plays a major role of the native esterase activity in <I>C. glutamicum</I>. </LI> <LI> CRISPR interference saved time for the laborious work to delete the target gene. </LI> <LI> CRISPR interference has potentials used for genome-wide gene identifications. </LI> </UL> </P>

Sex Identification of the First Incubated Chicks of the Crested Ibis Nipponia nippon in Korea

Kyung A Kim(김경아),Jae Seok Cha(차재석),Tae Jwa Kim(김태좌),Kyung Min Kim(김경민),Hee Cheon Park(박희천) 한국생명과학회 2011 생명과학회지 Vol.21 No.5

세계적 멸종위기종인 따오기(Nipponia nippon)는 2008년 10월에 중국에서 1쌍이 도입된 후 한국최초로 인공번식에 성공하였다. 본 연구는 따오기의 sex-related gene과 Chromodomain Helicase DNA Binding Protein gene(CHD gene)을 가지고 polymerase chain reaction (PCR)을 수행하여 새로 태어난 따오기 유조의 성별을 확인하고자 하였다. 본 연구에서는 따오기의 성별 확인을 위해 PCR후 제한효소의 처리 방법과 P2과 P8를 이용한 PCR 방법을 실시하였을 때 더 정확한 결과가 나타남을 알 수 있었다. 그리고 CHD gene의 염기서열을 선행연구와 비교해 본 결과, 암컷의 염기서열에서 1~2 base pairs 차이가 나타남을 알 수 있었다. In October 2008, a pair of Crested ibis Nipponia nippon, an endangered avian species in the world, was donated to Korea from China. They have since been the subject of a successful program to incubate chicks for the first time in South Korea. This study was carried out to determine the sex of chicks from the Crested ibis through polymerase chain reaction (PCR) using the sex-related gene and the chromodomain helicase DNA binding protein (CHD) gene. The result of the CHD gene, which was used with a single set of primers and a restriction enzyme treatment after the PCR process, was more accurate in identifying the gender of the Crested ibis. In addition, we compared the CHD gene sequences with the previously reported sequences and found 1~2 different bases between females (CI2, CI4, CI5, and CI6) than in studies previously reporting female sequences.