Molecular Identification, Enzyme Assay, and Metabolic Profiling of Trichoderma spp.

( Soo-jung Bae ),( Young-hwan Park ),( Hyeun-jong Bae ),( Junhyun Jeon ),( Hanhong Bae ) 한국미생물생명공학회(구 한국산업미생물학회) 2017 Journal of microbiology and biotechnology Vol.27 No.6

The goal of this study was to identify and characterize selected Trichoderma isolates by metabolic profiling and enzyme assay for evaluation of their potential as biocontrol agents against plant pathogens. Trichoderma isolates were obtained from the Rural Development Administration Genebank Information Center (Wanju, Republic of Korea). Eleven Trichoderma isolates were re-identified using ribosomal DNA internal transcribed spacer (ITS) regions. ITS sequence results showed new identification of Trichoderma isolates. In addition, metabolic profiling of the ethyl acetate extracts of the liquid cultures of five Trichoderma isolates that showed the best anti-Phytophthora activities was conducted using gas chromatography-mass spectrometry. Metabolic profiling revealed that Trichoderma isolates shared common metabolites with well-known antifungal activities. Enzyme assays indicated strong cell wall-degrading enzyme activities of Trichoderma isolates. Overall, our results indicated that the selected Trichoderma isolates have great potential for use as biocontrol agents against plant pathogens.

'Drawing' a Molecular Portrait of CIN and Cervical Cancer: a Review of Genome-Wide Molecular Profiling Data

Kurmyshkina, Olga V,Kovchur, Pavel I,Volkova, Tatyana O Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.11

In this review we summarize the results of studies employing high-throughput methods of profiling of HPV-associated cervical intraepithelial neoplasia (CIN) and squamous cell cervical cancers at key intracellular regulatory levels to demonstrate the unique identity of the landscape of molecular changes underlying this oncopathology, and to show how these changes are related to the 'natural history' of cervical cancer progression and the formation of clinically significant properties of tumors. A step-wise character of cervical cancer progression is a morphologically well-described fact and, as evidenced by genome-wide screenings, it is indeed the consistent change of the molecular profiles of HPV-infected epithelial cells through which they progressively acquire the phenotypic hallmarks of cancerous cells. In this sense, CIN/cervical cancer is a unique model for studying the driving forces and mechanisms of carcinogenesis. Recent research has allowed definition of the whole-genome spectrum of both random and regular molecular alterations, as well as changes either common to processes of carcinogenesis or specific for cervical cancer. Despite the existence of questions that are still to be investigated, these findings are of great value for the future development of approaches for the diagnostics and treatment of cervical neoplasms.

단백질 발현 양상 기반 생물 특성 이해를 위한 과학영재 대상 분자생물학 실험 프로그램 개발

김진희,김정식 한국과학영재교육학회 2023 과학영재교육 Vol.15 No.3

단백질은 세포 내의 생명활동을 결정하는 주요 생명 분자로 생물의 특성을 이해하는 데 핵심이 되는 분자이며, 이들에 대한 이해는 분자 생명 과학을 이해하는 데 필수적이다. 본 연구에서는 과학영재 대상으로 중등 교육과정에서 단백질 기반 분자생물학적 개념을 효과적으로 학습할 수 있는 실험 교육 프로그램을 제공하고자 한다. 본 실험은 여러 생물계의 대표 단백질을 분석하여 생명체의 특징을 이해하고자 함을 목적으로 한다. 이를 위해 구성한 실험 프로그램은 대장균, 애기장대,사람 혈장/혈구에서 단백질을 추출하고, 농도를 조정하여 단백질 전기영동을 통해 총 단백질을 크기 별로 분리한다. 이후 단백질 겔의 염색/탈색 과정을 통해 단백질의 양 및 크기를 정성적으로 확인하고, 주요 단백질에 대해 생물의 특징과 함께 토론하며 이해하는 과정을 포함한다. 본 실험 프로그램은 6시간이 소요되며, 단백질 분석에 관한 다양하면서도 범용적인 분자 실험 기구 사용법도 이해할 수 있다. 본 수업 프로그램의 효과를 분석하기 위해 본 실험 모듈을 수행한 9명을 대상으로사전, 사후 검사를 진행하였고, 추가로 프로그램 수행 반응을 확인하였다. 본 실험 프로그램을 수행한 결과, 참여 학생들은 높은 프로그램의 만족도를 보였고, 실험 내용을 이해하는 데, 큰 어려움은 발생하지 않았다. 또한 분자생물학에 대한 흥미 및 진로에 대한 관심이 다소 증가하였고, 세포 내 단백질 역할 및 관련된 분자생물학의 지식이 크게 상승하였다. 이에 본 실험 프로그램은 학생들로 하여금 단백질에 관한 분자생물학적 개념을 이해하고, 분자생물학 관련 연구 수행의 기반을 다져, 향후 생명과학과 관련된 진로 선택에 도움을 줄수 있을 것으로 기대된다. Proteins are essential biomolecules that govern cellular activities and play a crucial role in understanding the characteristics of living organisms. A proper understanding of proteins is essential for comprehending the life sciences at the molecular level. In this study, our objective is to provide an experimental educational program for science-gifted middle school students to grasp the concepts of protein-based molecular biology. The experiments we have designed aim to analyze proteins from various organisms, helping students gain insights into their characteristics. To achieve this, we extract proteins from Escherichia coli, yeast, and human plasma/blood cells, and then separate total proteins by size using protein electrophoresis after adjusting their concentrations. Subsequently, we qualitatively determine the quantity and size of proteins through protein staining/de-staining processes. This is followed by discussions and comprehension of the major proteins in relation to biological characteristics. The entire experiment takes approximately 6 hours, allowing participants to learn diverse and universally applicable molecular experimental techniques related to protein analysis. To assess the effectiveness of this program, we conducted both a pre-test and post-test with nine participants who completed the experimental module, and we also gathered additional program feedback. The results of the experimental module showed high satisfaction among the participants, who did not encounter significant difficulties in understanding the experimental content. Furthermore, there was a slight increase in interest and career aspirations in molecular biology, and knowledge of intracellular protein roles and related molecular biology significantly improved. Therefore, This experimental program is expected to facilitate students in comprehending molecular biological concepts based on proteins and establishing a foundation for conducting molecular biology-related research, and ultimately to assist in making their informed career choices in the life sciences.

Comparative Characterization of Two cxcl8 Homologs in Oplegnathus fasciatus : Genomic, Transcriptional and Functional Analyses

Navaneethaiyer Umasut,SDNK Bathige,William Shanthakumar Thulasitha,Minyoung Oh,Jehee Lee 제주대학교 해양과학연구소 2020 해양과환경연구소 연구논문집 Vol.44 No.-

CXCL8 (interleukin-8, IL-8) is a CXC family chemokine that recruits specific target cells and mediates inflammation and wound healing. This study reports the identification and characterization of two cxcl8 homologs from rock bream, Oplegnathus fasciatus. Investigation of molecular signature, homology, phylogeny, and gene structure suggested that they belonged to lineages 1 (L1) and 3 (L3), and designated Ofcxcl8-L1 and Ofcxcl8-L3. While Ofcxcl8-L1 and Ofcxcl8-L3 revealed quadripartite and tripartite organization, in place of the mammalian ELR (Glu-Leu-Arg) motif, their peptides harbored EMH (Glu-Met-His) and NSH (Asn-Ser-His) motifs, respectively. Transcripts of Ofcxcl8s were constitutively detected by Quantitative Real-Time PCR (qPCR) in 11 tissues examined, however, at dierent levels. Ofcxcl8-L1 transcript robustly responded to treatments with stimulants, such as flagellin, concanavalin A, lipopolysaccharide, and poly(I:C), and pathogens, including Edwardsiella tarda, Streptococcus iniae, and rock bream iridovirus, when compared with Ofcxcl8-L3 mRNA. The dierences in the putative promoter features may partly explain the dierential transcriptional modulation of Ofcxcl8s. Purified recombinant OfCXCL8 (rOfCXCL8) proteins were used in in vitro chemotaxis and proliferation assays. Despite the lack of ELR motif, both rOfCXCL8s exhibited leukocyte chemotactic and proliferative functions, where the potency of rOfCXCL8-L1 was robust and significant compared to that of rOfCXCL8-L3. The results, taken together, are indicative of the crucial importance of Ofcxcl8s in inflammatory responses and immunoregulatory roles in rock bream immunity.

빅벨리해마(Hippocampus abdominalis) 글루코코르티코이드 수용체의 분자 유전학적 동정과 발현 분석

조은영 ( Eunyoung Jo ),오민영 ( Minyoung Oh ),이숙경 ( Sukkung Lee ),완창 ( Qiang Wan ),이제희 ( Jehee Lee ) 한국수산과학회 2015 한국수산과학회지 Vol.48 No.3

Glucocorticoids (GCs) are steroid hormones regulated through responses to stress to maintain diverse metabolic and homeostatic functions. GCs act on the glucocorticoid receptor (GR), a member of the nuclear receptor family. This study identified and characterized the GR gene from the big-belly seahorse Hippocampus abdominalis designating it HaGR. The open reading frame of the HaGR cDNA was 2,346 bp in length, encoding a 782-amino-acid polypep-tide with a theoretical isoelectric point of 6.26 and predicted molecular mass of 86.8 kDa. Nuclear receptors share a common structural organization, comprising an N-terminal transactivation domain, DNA-binding domain, and C-terminal ligand-binding domain. The tissue-specific mRNA expression profile of HaGR was analyzed in healthy seahorses using a qPCR technique. HaGR mRNA was expressed ubiquitously in all of the tissues examined, with the highest expression levels in kidney, intestine, stomach, and gill tissues. The mRNA expression in response to im-mune challenge with lipopolysaccharide (LPS), polyinosinic:polycytidylic acid (poly I:C), Edwardsiella tarda, and Streptococcus iniae revealed that it is inducible in response to pathogen infection. These results suggest that HaGR is involved in the immune response of the big-belly seahorse.

Computer Simulation Study of a Porphyrazine Monolayer at a Water-Gas Interface: Structure and Molecular Orientation

Sriprajak Krongsuk 한국물리학회 2008 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.52 No.5

Molecular dynamics simulations were employed to study a porphyrazine (PzH₂) monolayer at a water-gas interface. Five different surface densities, corresponding to a number of PzH₂ molecules of 10, 15, 20, 25 and 30 per an area of 3.77 × 3.77 nm₂, were simulated at a constant volume and temperature (NVT-ensemble). The structure and the molecular orientation of the PzH₂ monolayer were investigated. The results revealed that increasing number of PzH₂ molecules affected not only the monolayer structure but also the layered structure of water. The presence of several PzH₂ orientations indicated that this monolayer was highly inhomogeneous. Molecular dynamics simulations were employed to study a porphyrazine (PzH₂) monolayer at a water-gas interface. Five different surface densities, corresponding to a number of PzH₂ molecules of 10, 15, 20, 25 and 30 per an area of 3.77 × 3.77 nm₂, were simulated at a constant volume and temperature (NVT-ensemble). The structure and the molecular orientation of the PzH₂ monolayer were investigated. The results revealed that increasing number of PzH₂ molecules affected not only the monolayer structure but also the layered structure of water. The presence of several PzH₂ orientations indicated that this monolayer was highly inhomogeneous.

Genomic-based identification of novel potential biomarkers and molecular signaling networks in response to diesel exhaust particles in human middle ear epithelial cells

Kwon, Jee Young,Park, Moo Kyun,Seo, Young Rok,Song, Jae-Jun THE KOREAN SOCIETY OF TOXICOGENOMICS AND TOXICOPRP 2014 MOLECULAR AND CELLULAR TOXICOLOGY Vol.10 No.1

Otitis media (OM) is the most common inflammatory disease of the middle ear cavity. Several factors including viral and bacterial infection, biofilm formation, congenital anomalies, and environmental factors have been recognized as the main causes of OM. Recent epidemiological studies showed that children living in areas with high concentrations of air pollutant including particulate matter and $SO_2$ have significantly higher rates of OM compared with those in the control area. Another study reported that air pollutant exposure results in significant increases in pediatric OM. A large cohort study in Germany suggested that the prevalence of OM is related to air quality. Diesel exhaust particles (DEPs) are among the major toxic air pollutants of motor vehicle emissions. Hence, identifying the biomarkers of a signaling network for air pollutant (particularly DEPs)-mediated inflammatory responses would be meaningful. In this study, we identified novel biomarkers and potential molecular signaling networks induced by DEPs in human middle ear epithelial cells (HMEECs). Genomic expression analysis via microarray was used to discover novel biomarkers. A total of 254 genes were differentially expressed in DEPs-exposed HMEECs; 86 genes and 168 genes were up-and down-regulated, respectively. To verify reliable biomarkers and define meaningful signaling networks in the entire genome profiling, the in silico approach was applied. Based on genomic profiling analysis, we found several novel key molecular biomarkers, including SRC, MUC5AC, MUC2, MMP14, EIF1AK3, KITLG, NOD1, and TP53. Our findings suggested novel biomarkers for DEPs-responsive genes in HMEECs. Furthermore, we provided scientific evidence for the establishment of novel molecular signaling pathway associated with DEPs exposure in HMEECs.

Molecular profiling analysis for colorectal cancer patients with Pi-Xu or Shi-Re syndrome

Xinbing Sui,Yong Guo,Wei Ni,Haiyan Jin,Haoming Lin,Tian Xie 한국한의학연구원 2019 Integrative Medicine Research Vol.8 No.1

Background: Traditional Chinese medicine (TCM) syndromes (ZHENG in Chinese) constitute the basis of understanding the disorders of patients and guiding the use of the Chinese herbs. Colorectal cancer is divided into various subtypes mainly according to the ZHENG identification. Objective: We aimed to determine the molecular basis underlying Pi-Xu (spleen deficiency) and Shi-Re (dampness-heat) ZHENG that are commonly found in colorectal cancer patients. Methods: About 80 colorectal cancer patients, including 47 Pi-Xu ZHENG and 33 Shi-Re ZHENG were enrolled. Blood and tissue samples of these patients were available for protein and mRNA expression. The protein expression was determined by Immunohistochemistry (IHC) staining and mRNA profiling was detected by expression microarray. Furthermore, mRNA fold change was evaluated by qRT-PCR. Results: The colorectal cancer patients with Shi-Re ZHENG had a poor prognosis, compared with Pi-Xu ZHENG (95% CI: 0.05–0.33; p < 0.0001). Moreover, there was a significant difference in protein expression levels (especially for mutant TP53, PCNA, PD-L1 and Ki-67) among Pi-Xu and Shi-Re ZHENG (p < 0.01). Meanwhile, mRNA expression (especially for wild type TP53, KDM6A, PCNA, PD-L1, Ki-67, CCL-2, IL-1a and COX-2) was also remarkably different between Pi-Xu and Shi-Re groups (p < 0.01). Conclusion: Our results suggest that Shi-Re ZHENG conditions may contribute to poor overall survival in patients with colorectal cancer. Compared with Pi-Xu ZHENG, high expression of mutant TP53, PCNA, PD-L1, Ki-67, CCL-2, IL-1a and COX-2 may serve as potential biomarkers for diagnosis and prognosis of colorectal cancer patients displayed Shi-Re ZHENG.

Protein molecular structure, degradation and availability of canola, rapeseed and soybean meals in dairy cattle diets

Yujia Tian,Xuewei Zhang,Rongcai Huang,PeiqiangYu 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.9

Objective: The aims of this study were to reveal the magnitude of the differences in protein structures at a cellular level as well as protein utilization and availability among soybean meal (SBM), canola meal (CM), and rapeseed meal (RSM) as feedstocks in China. Methods: Experiments were designed to compare the three different types of feedstocks in terms of: i) protein chemical profiles; ii) protein fractions partitioned according to Cornell Net Carbohydrate and Protein System; iii) protein molecular structures and protein second structures; iv) special protein compounds-amino acid (AA); v) total digestible protein and energy values; vi) in situ rumen protein degradability and intestinal digestibility. The protein second structures were measured using FT/IR molecular spectroscopy technique. A summary chemical approach in National Research Council (NRC) model was applied to analyze truly digestible protein. Results: The results showed significant differences in both protein nutritional profiles and protein structure parameters in terms of α-helix, β-sheet spectral intensity and their ratio, and amide I, amide II spectral intensity and their ratio among SBM, CM, and RSM. SBM had higher crude protein (CP) and AA content than CM and RSM. For dry matter (DM), SBM, and CM had a higher DM content compared with RSM (p<0.05), whereas no statistical significance was found between SBM and CM (p = 0.28). Effective degradability of CP and DM did not demonstrate significant differences among the three groups (p>0.05). Intestinal digestibility of rumen undegradable protein measured by three-step in vitro method showed that there was significant difference (p = 0.05) among SBM, CM, and RSM, which SBM was the highest and RSM was the lowest with CM in between. NRC modeling results showed that digestible CP content in SBM was significantly higher than that of CM and RSM (p<0.05). Conclusion: This study suggested that SBM and CM contained similar protein value and availability for dairy cattle, while RSM had the lowest protein quality and utilization.

Free-energy Profile along an Isomerization Pathway: Conformational Isomerization in Alanine Dipeptide

이인호 한국물리학회 2013 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.62 No.3

The free-energy profile for the conformational isomerization process in alanine dipeptide is presented in atomistic detail by using an action-derived molecular dynamics (ADMD) method and replica-exchange molecular dynamics (REMD) method. First, by employing ADMD, a dynamic isomerization pathway model of the alanine dipeptide with two available low-energy conformations, C7_<i>ax</i> and C7_<i>eq</i>, is determined. The pathway model is chosen to be the reaction coordinate, so the isomerization process is characterized by the ADMD step index, which is not an <i>a-priori</i> reaction coordinate as found in conventional studies of molecular conformational changes. Second, by employing the REMD method, the free-energy profile is calculated as a function of temperature. This couple of procedures is a quite natural protocol for conformational isomerization process simulations, irrespective of the arbitrary selection of the reaction coordinate. The alliance between the two simulation methods, ADMD and REMD, is demonstrated to have a great synergy effect on understanding the conformational changes in molecules.