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Patnaik, B.B.,Patnaik, H.H.,Seo, G.W.,Jo, Y.H.,Lee, Y.S.,Lee, B.L.,Han, Y.S. Pergamon Press ; Elsevier Science 2014 DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY Vol.46 No.2
Myeloid differentiation factor 88 (MyD88), an intracellular adaptor protein involved in Toll/Toll-like receptor (TLR) signal processing, triggers activation of nuclear factor-kappaB (NF-κB) transcription factors. In the present study, we analyzed the gene structure and biological function of MyD88 in a coleopteran insect, Tenebrio molitor (TmMyD88). The TmMyD88 gene was 1380bp in length and consisted of five exons and four introns. The 5'-flanking sequence revealed several putative transcription factor binding sites, such as STAT-4, AP-1, cJun, cfos, NF-1 and many heat shock factor binding elements. The cDNA contained a typical death domain, a conservative Toll-like interleukin-1 receptor (TIR) domain, and a C-terminal extension (CTE). The TmMyD88 TIR domain showed three significantly conserved motifs for interacting with the TIR domain of TLRs. TmMyD88 was grouped within the invertebrate cluster of the phylogenetic tree and shared 75% sequence identity with the TIR domain of Tribolium castaneum MyD88. Homology modeling of the TmMyD88 TIR domain revealed five parallel β-strands surrounded by five α-helices that adopted loop conformations to function as an adaptor. TmMyD88 expression was upregulated 7.3- and 4.79-fold after 12 and 6h, respectively, of challenge with Staphylococcus aureus and fungal β-1,3 glucan. Silencing of the TmMyD88 transcript by RNA interference led to reduced resistance of the host to infection by S. aureus. These results indicate that TmMyD88 is required for survival against Staphylococcus infection.
Patnaik, Bharat Bhusan,Kang, Seong Min,Seo, Gi Won,Lee, Hyo Jeong,Patnaik, Hongray Howrelia,Jo, Yong Hun,Tindwa, Hamisi,Lee, Yong Seok,Lee, Bok Luel,Kim, Nam Jung,Bang, In Seok,Han, Yeon Soo Molecular Diversity Preservation International (MD 2013 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.14 No.10
<P>CD63, a member of the tetraspanin membrane protein family, plays a pivotal role in cell growth, motility, signal transduction, host-pathogen interactions and cancer. In this work, the cDNA encoding CD63 homologue (TmCD63) was cloned from larvae of a coleopteran beetle, <I>Tenebrio molitor.</I> The cDNA is comprised of an open reading frame of 705 bp, encoding putative protein of 235 amino acid residues. <I>In silico</I> analysis shows that the protein has four putative transmembrane domains and one large extracellular loop. The characteristic “Cys-Cys-Gly” motif and “Cys188” residues are highly conserved in the large extracellular loop. Phylogenetic analysis of TmCD63 revealed that they belong to the insect cluster with 50%–56% identity. Analysis of spatial expression patterns demonstrated that TmCD63 mRNA is mainly expressed in gut and Malphigian tubules of larvae and the testis of the adult. Developmental expression patterns of CD63 mRNA showed that TmCD63 transcripts are detected in late larval, pupal and adult stages. Interestingly, TmCD63 transcripts are upregulated to the maximum level of 4.5 fold, in response to DAP-type peptidoglycan during the first 6 h, although other immune elicitors also caused significant increase to the transcript level at later time-points. These results suggest that CD63 might contribute to <I>T. molitor</I> immune response against various microbial pathogens.</P>
Bharat Bhusan Patnaik,Hongray Howrelia PATNAIK,박기범,조용훈,이용석,한연수 한국곤충학회 2015 Entomological Research Vol.45 No.2
Insect apolipophorin‐III is an exchangeable protein that is abundantly found in the hemolymph, and serves an important role in lipid transport, development, and innate immunity. In this study, we examined the role of apolipophorin‐III (TmapoLp‐III) during the adult eclosion stages of Tenebrio molitor by RNA interference (RNAi) analysis. After silencing of the mRNA transcripts at both larval and pupal stages, adult phenotypic defects were noticed. Defects included the incomplete shedding of pupal skin, shorter extension of the elytra, and improper folding of the hind wings. Most of the adults were malformed and died possibly due to dehydration. We also showed the involvement of TmapoLp‐III in conferring resistance to T. molitor larvae against Listeria monocytogenes infection. Mortality was found to be lower in non‐silenced intoxicated larvae while the TmapoLp‐III silenced larvae showed a significant susceptibility after 7 days post‐injection with a dose of 106 cfu/larvae.
Bharat Bhusan Patnaik,Seong Min Kang,Gi Won Seo,Hyo Jeong Lee,Hongray Howrelia Patnaik,Yong Hun Jo,Hamisi Tindwa,Yong Seok Lee,Bok Luel Lee,Nam Jung Kim,In Seok Bang,Yeon Soo Han 한국응용곤충학회 2013 한국응용곤충학회 학술대회논문집 Vol.2013 No.10
CD63, a member of tetraspanin membrane protein family, plays pivotal role in cell growth, motility, signal transduction, host-pathogen interactions and cancer. In this work, the cDNA encoding CD63 homologue (TmCD63) was cloned from larvae of coleopteran beetle, Tenebrio molitor. The cDNA is comprised of an open reading frame of 705 bp, encoding putative protein of 235 amino acid residues. In silico analysis shows that the protein has four putative transmembrane domains and one large extracellular loop. The characteristic ‘Cys-Cys-Gly’ motif and ‘Cys188’ residues are highly conserved in the large extracellular loop. Phylogenetic analysis of TmCD63 revealed that they belong to the insect cluster with 50-56% identity. Analysis of spatial expression patterns demonstrated that TmCD63 mRNA is mainly expressed in gut and Malphigian tubules of larvae and the testis of the adult. Developmental expression patterns of CD63 mRNA showed that TmCD63 transcripts are detected in late larval, pupal and adult stages. Interestingly, TmCD63 transcript was upregulated the maximum 4.5 fold in response to DAP-type peptidoglycan during the first 6 h, although other immune elicitors also made significant increase in the transcript level at later time-points. These results suggest that CD63 might contribute to T. molitor immune response against various microbial pathogens.
Ju Young Noh,Bharat Bhusan Patnaik,Hamisi Tindwa,Gi Won Seo,Dong Hyun Kim,Hongray Howrelia Patnaik,Yong Hun Jo,Yong Seok Lee,Bok Ruel Lee,Nam Jung Kim,In Seok Bang,Yeon Soo Han 한국응용곤충학회 2013 한국응용곤충학회 학술대회논문집 Vol.2013 No.10
Apolipophorin III (apoLp-III) is a well-known hemolymph protein having a functional role in lipid transport and immune response of insects. We cloned full-length cDNA encoding putative apoLp-III from larvae of the coleopteran beetle, Tenebrio molitor (TmapoLp-III), by identification of clones corresponding to the partial sequence of TmapoLp-III, subsequently followed with full length sequencing by a clone-by-clone primer walking method. The complete cDNA consists of 890 nucleotides, including an ORF encoding 196 amino acid residues. Excluding a putative signal peptide of the first 20 amino acid residues, the 176-residue mature apoLp-III has a calculated molecular mass of 19,146 Da. Genomic sequence analysis with respect to its cDNA showed that TmapoLp-III was organized into four exons interrupted by three introns. Several immune-related transcription factor binding sites were discovered in the putative 5’-flanking region. BLAST and phylogenetic analysis reveals that TmapoLp-III has high sequence identity (88%) with Tribolium castaneum apoLp-III but shares little sequence homologies (<26%) with other apoLp-IIIs. Homology modeling of Tm apoLp-III shows a bundle of five amphipathic helices, including a short helix 3’. The ‘helix-short helix-helix’ motif was predicted to be implicated in lipid binding interactions, through reversible conformational changes and accommodating the hydrophobic residues to the exterior for stability. Highest level of TmapoLp-III mRNA was detected at late pupal stages, albeit it is expressed in the larval and adult stages at lower levels. The tissue specific expression of the transcripts showed significantly higher numbers in larval fat body and adult integument. In addition, TmapoLp-III mRNA was found to be highly up-regulated in late stages of L. monocytogenes or E. coli challenge. These results indicate that TmapoLp-III may play an important role in innate immune responses against bacterial pathogens in T. molitor.
Patnaik, Bharat Bhusan,Hwang, Hee-Ju,Kang, Se Won,Park, So Young,Wang, Tae Hun,Park, Eun Bi,Chung, Jong Min,Song, Dae Kwon,Kim, Changmu,Kim, Soonok,Lee, Jae Bong,Jeong, Heon Cheon,Park, Hong Seog,Han, MDPI 2015 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.16 No.12
<P>The Lycaenidae butterflies, <I>Protantigius superans</I> and <I>Spindasis takanosis</I>, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the <I>P. superans</I> and <I>S. takanosis</I> transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The <I>P. superans</I> and <I>S. takanosis</I> transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (<I>E</I>-value of 1.0 × 10<SUP>−5</SUP>) against the known protein databases annotated a total of 46,754 and 51,908 transcripts for <I>P. superans</I> and <I>S. takanosis</I>. Approximately 41.25% and 38.68% of the unigenes for <I>P. superans</I> and <I>S. takanosis</I> found homologous sequences in Protostome DB (PANM-DB). BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO) terms and a total of 5259 unigenes assigned to 116 pathways for <I>P. superans</I>. For <I>S. takanosis</I>, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs) were compiled from the unigenes of <I>P. superans</I> and <I>S. takanosis</I>, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species.</P>
Patnaik, Bharat Bhusan,Park, So Young,Kang, Se Won,Hwang, Hee-Ju,Wang, Tae Hun,Park, Eun Bi,Chung, Jong Min,Song, Dae Kwon,Kim, Changmu,Kim, Soonok,Lee, Jae Bong,Jeong, Heon Cheon,Park, Hong Seog,Han, Hindawi Publishing Corporation 2016 International journal of genomics Vol.2016 No.-
<P><I>Vespa mandarinia</I> found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures have been implemented. Here, we performed<I> de novo</I> assembly of the<I> V. mandarinia</I> transcriptome by Illumina HiSeq 4000 sequencing. Over 60 million raw reads and 59,184,811 clean reads were obtained. After assembly, a total of 66,837 unigenes were clustered, 40,887, 44,455, and 22,390 of which showed homologous matches against the PANM, Unigene, and KOG databases, respectively. A total of 15,675 unigenes were assigned to Gene Ontology terms, and 5,132 unigenes were mapped to 115 KEGG pathways. The zinc finger domain (C2H2-like), serine/threonine/dual specificity protein kinase domain, and RNA recognition motif domain were among the top InterProScan domains predicted for<I> V. mandarinia</I> sequences. Among the unigenes, we identified 534,922 cDNA simple sequence repeats as potential markers. This is the first transcriptomic analysis of the wasp<I> V. mandarinia</I> using Illumina HiSeq 4000. The obtained datasets should promote the search for new genes to understand the physiological attributes of this wasp.</P>
A review of the endangered mollusks transcriptome under the threatened species initiative of Korea
Patnaik Hongray Howrelia,Sang Min Kyu,Park Jie Eun,Song Dae Kwon,Jeong Jun Yang,Hong Chan Eui,Kim Yong Tae,Shin Hyeon Jun,Ziwei Liu,Hwang Hee Ju,Park So Young,Kang Se Won,Ko Jung Ho,Lee Jun Sang,Park 한국유전학회 2023 Genes & Genomics Vol.45 No.8
Transcriptome studies for conservation of endangered mollusks is a proactive approach towards managing threats and uncertainties facing these species in natural environments. The population of these species is declining due to habitat destruction, illicit wildlife trade, and global climate change. These activities risk the free movement of species across the wild landscape, loss of breeding grounds, and restrictions in displaying the physiological attributes so crucial for faunal welfare. Gastropods face the most negative ecological effects and have been enlisted under Korea’s protective species consortium based on their population dynamics in the last few years. Moreover, with the genetic resources restricted for such species, conservation by informed planning is not possible. This review provides insights into the activities under the threatened species initiative of Korea with special reference to the transcriptome assemblies of endangered mollusks. The gastropods such as Ellobium chinense, Aegista chejuensis, Aegista quelpartensis, Incilaria fruhstorferi, Koreanohadra kurodana, Satsuma myomphala, and Clithon retropictus have been represented. Moreover, the transcriptome summary of bivalve Cristaria plicata and Caenogastropoda Charonia lampas sauliae is also discussed. Sequencing, de novo assembly, and annotation identified transcripts or homologs for the species and, based on an understanding of the biochemical and molecular pathways, were ascribed to predictive gene function. Mining for simple sequence repeats from the transcriptome have successfully assisted genetic polymorphism studies. A comparison of the transcriptome scheme of Korean endangered mollusks with the genomic resources of other endangered mollusks have been discussed with homologies and analogies for dictating future research.
Omkar Patnaik,Preeti Shahane,Mrudula Chandrupatla,Punnapa Raviteja 대한해부학회 2023 Anatomy & Cell Biology Vol.56 No.4
Anterior cerebral arteries are paired and supply the major portion of the medial surface of the brain. They arebranches of the intracranial part of the internal carotid artery and form the anterior portion of the circle of Willis (CW)which is situated in the interpeduncular fossa. During routine dissection in the department of anatomy, All India Instituteof Medical Sciences, Bibinagar, Hyderabad, a rare variation had been observed in the CW, azygos anterior cerebral arteryassociated with hypoplastic A1 fragment of the right anterior cerebral artery in a 63-year-old female cadaver. It is importantto identify and study this kind of rare variation for surgeons, anatomists, and radiologists during dissection, surgical,radiological, and diagnostic interventions.
Suryakanta Patnaik,Sarveshwaran Saravanabhupathy,Sangeeta Singh,Achlesh Daverey,Kasturi Dutta 대한환경공학회 2022 Environmental Engineering Research Vol.27 No.3
In this study, pretreated organic wastes such as waste paper cups, cardboard waste, and vegetable waste were screened for the growth and lipid production of oleaginous bacteria DS-7 (isolated from the dairy effluent scum). The pretreated vegetable waste was found to be the best feedstock for biomass and lipid production by the DS-7. Further, process parameters such as inoculation time, substrate concentration (w/v) (amount of pretreated vegetable waste), pH, and inoculum size were optimized using a multi-objective optimization technique to enhance the biomass and lipid productions. The optimization study successfully enhanced the biomass concentration (g/L) and lipid content (%) by 47.9% and 15.84%, respectively in comparison with the unoptimized state. The biomass and lipid productivities were 42% (1.449 g/L/d) and 51% (1.267 g/L/d) greater than unoptimized conditions. The characteristics of the biodiesel obtained from the valorization of vegetable waste were comparable to the standard. Thus, the vegetable waste can be utilized as a potential feedstock for microbial biodiesel production.