Article
Genetics & Heredity
Jiwon Lee, Jong Eun Park, Chung Lee, Ah Reum Kim, Byung Joon Kim, Woong-Yang Park, Chang-Seok Ki, Jeehun Lee
Summary: Microcephaly is a common phenotype in patients with neurodevelopmental problems, often with genetic causes. A study conducted in Korean patients with microcephaly found a different genetic spectrum compared to other ethnicities. Whole exome sequencing (WES) along with copy number variation (CNV) analysis proved to be an effective approach for diagnosing the underlying causes of microcephaly, with a diagnostic yield of 47.5%.
FRONTIERS IN GENETICS
(2021)
Article
Infectious Diseases
Belen Fernandez-Caso, Ana Miqueleiz, Teresa Alarcon
Summary: Antibiotic resistance (AMR) is a worldwide concern, and Helicobacter pylori is no exception. Increasing resistance to antibiotics leads to higher treatment failure rates. Next-generation sequencing-based molecular tools, such as whole genome sequencing (WGS), can be valuable for understanding the genomic mechanisms of resistance and optimizing treatment guidelines based on local epidemiology. Various pipelines and platforms are continuously being developed for analyzing WGS data. This study provides a detailed view of the use and progression of WGS for studying H. pylori's AMR.
Article
Oncology
Chao Zhang, Xiaoyu Zhou, Xiang Huang, Xinghua Ding, Yang Wang, Rong Zhang
Summary: This study provides a comprehensive analysis of the genetic characteristics of intracranial teratomas, which may be valuable for guiding future targeted therapies.
FRONTIERS IN ONCOLOGY
(2022)
Article
Microbiology
Judith Guitart-Matas, Narjol Gonzalez-Escalona, Meghan Maguire, Anna Vilaro, Jaime Martinez-Urtaza, Lorenzo Fraile, Lourdes Migura-Garcia
Summary: This study provides a comprehensive analysis of the genetic variability within Actinobacillus pleuropneumoniae (APP) serotypes and enhances the understanding of transmission and epidemiological patterns. The correlation between resistance and toxin profiles with the presence of specific genetic elements and serotypes is also determined.
MICROBIOLOGY SPECTRUM
(2022)
Article
Plant Sciences
J. Lucas Boatwright, Sirjan Sapkota, Hongyu Jin, James C. Schnable, Zachary Brenton, Richard Boyles, Stephen Kresovich
Summary: Association mapping panels are important resources for understanding the genetic basis of phenotypic diversity and advancing plant breeding. In this study, the whole-genome sequencing of 400 sorghum accessions enabled the development of a high-density genomic marker set and the identification of novel genomic associations for plant height and tannin content. The use of whole-genome sequencing markers improved the predictive ability of genomic models, and the population served as a significant public resource for sorghum research.
Article
Microbiology
Fadi G. Alnaji, William K. Reiser, Joel Rivera-Cardona, Aartjan J. W. te Velthuis, Christopher B. Brooke
Summary: Deletion-containing viral genomes (DelVGs) are commonly produced during influenza A virus infection, influenced by specific molecular mechanisms such as direct sequence repeats and base enrichment. DelVGs face a significant bottleneck during genome packaging, with larger DelVGs showing signs of enrichment in packaged virions, suggesting size as an important determinant of packaging efficiency.
Article
Multidisciplinary Sciences
Jason L. Anders, Mohamed Abdallah Mohamed Moustafa, Wessam Mohamed Ahmed Mohamed, Takashi Hayakawa, Ryo Nakao, Itsuro Koizumi
Summary: Host-microbe interactions in the gastrointestinal tract play a crucial role in shaping host physiology and ecology, with microbial communities varying across gut regions due to physical environment and host immune system. Each animal species may harbor their unique microbial community influenced by ecological traits and physiological characteristics. Interspecific differences in microbiome were found within all gut regions, with the small intestine showing unique microbiome compared to lower GIT in all three host species.
SCIENTIFIC REPORTS
(2021)
Article
Immunology
Mark Itsko, Nadav Topaz, Sani Ousmane, Micheal Popoola, Rasmata Ouedraogo, Kadidja Gamougam, Adodo Yao Sadji, Abass Abdul-Karim, Christine Lascols, Xin Wang
Summary: Genomic surveillance for meningococcal meningitis can be significantly improved using culture-free methods to increase data representativeness and monitor changes in epidemiological landscape, especially for countries with low culture rate.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Biology
Hak-Min Kim, Sungwon Jeon, Oksung Chung, Je Hoon Jun, Hui-Su Kim, Asta Blazyte, Hwang-Yeol Lee, Youngseok Yu, Yun Sung Cho, Dan M. Bolser, Jong Bhak
Summary: The study compared 7 sequencing platforms using the same KOREF sample, and found that MGI platforms showed higher concordance rates for SNP genotyping compared to HiSeq2000 and HiSeq4000. The MGI platforms were also found to have the most similar characteristics to the HiSeq2500 platform according to a similarity matrix of variant calls. Overall, MGI and Illumina sequencing platforms showed comparable levels of sequencing quality, coverage uniformity, percent GC coverage, and variant accuracy, with MGI platforms being cost-effective for a wide range of genomics research fields.
Article
Genetics & Heredity
Ulykbek Kairov, Askhat Molkenov, Aigul Sharip, Saule Rakhimova, Madina Seidualy, Arang Rhie, Ulan Kozhamkulov, Maxat Zhabagin, Jong-Il Kim, Joseph H. Lee, Joseph D. Terwilliger, Jeong-Sun Seo, Zhaxybay Zhumadilov, Ainur Akilzhanova
Summary: Kazakhstan, located along the Great Silk Road, has a rich history and a multiethnic population. By sequencing and analyzing the genomes of five ethnic Kazakhs, this study identified genetic variants associated with higher risks of diseases and demonstrated the importance of genotype-phenotype relations at the population level.
FRONTIERS IN GENETICS
(2022)
Article
Microbiology
Tal Domanovich-Asor, Yair Motro, Boris Khalfin, Hillary A. Craddock, Avi Peretz, Jacob Moran-Gilad
Summary: This study utilized whole genome sequencing to analyze the resistome and phylogeny of Helicobacter pylori in Israel, revealing high resistance rates and novel resistance mutations. Despite inconsistent genotype-to-phenotype correlation, inferring resistance phenotypes from WGS in H. pylori remains challenging.
Editorial Material
Microbiology
Kartika Afrida Fauzia, Ricky Indra Alfaray, Yoshio Yamaoka
Summary: Helicobacter pylori antimicrobial resistance is a significant public health issue. Whole genome sequencing can provide a comprehensive understanding of resistance mechanisms and improve treatment efficacy to prevent gastric cancer.
Article
Plant Sciences
Mark E. Samuels, Cassandra Lapointe, Sara Halwas, Anne C. Worley
Summary: Chenopodium berlandieri is a native North American plant that was cultivated by indigenous peoples and has potential use in breeding for improved quinoa production in North America. The plant is closely related to quinoa and its genome sequence provides valuable information for quinoa adaptation and breeding. The genome assembly of a C. berlandieri accession collected in Canada shows similarities to both C. quinoa and domesticated Mexican C. berlandieri genomes.
Article
Clinical Neurology
Seungbok Lee, Sesong Jang, Jong-Il Kim, Jong Hee Chae, Ki Joong Kim, Byung Chan Lim
Summary: A study using whole-genome sequencing for genetic diagnosis of infantile spasms identified potential pathogenic variants and emphasized the necessity of further research using whole genomic approaches for patients with infantile spasms, despite existing challenges.
FRONTIERS IN NEUROLOGY
(2022)
Article
Microbiology
Xiaosen Jiang, Zheng Xu, Tongda Zhang, Yuan Li, Wei Li, Hongdong Tan
Summary: This study utilized whole genome sequencing to analyze the genetic epidemiology of H. pylori, developing the HpTT typing tool. Asia was found to be the largest source of isolates, with Switzerland and Australia as main sources of widespread isolates in their continents. The development of a user-friendly website allows researchers to easily compare and analyze their data against the global database.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Hsian-Jean Chin, Michael S. Dobbie, Xiang Gao, James E. Hennessy, Ki-Hoan Nam, Je Kyung Seong, Toshihiko Shiroishi, Toru Takeo, Atsushi Yoshiki, Jing Zao, Chi-Kuang Leo Wang
Summary: The Asian Mouse Mutagenesis Resource Association (AMMRA) is a non-profit organization dedicated to supporting biomedical research and fostering international collaboration. By working closely with consortiums like the International Mouse Phenotyping Consortium and the International Mouse Strain Resource, AMMRA aims to strengthen global connections and enhance the quality of life science research worldwide.
Article
Endocrinology & Metabolism
Hye-Sook Han, Sang Gyune Kim, Young Seok Kim, Si-Hyong Jang, Yongmin Kwon, Dahee Choi, Tom Huh, Eunyoung Moon, Eunyong Ahn, Je Kyung Seong, Hee-Seok Kweon, Geum-Sook Hwang, Dae Ho Lee, Kae Won Cho, Seung-Hoi Koo
Summary: The study showed that hepatic depletion of Crtc2 improved HFD-induced fatty liver disease phenotypes by inhibiting the mTORC1 pathway, indicating a potential therapeutic approach for combating NAFLD.
MOLECULAR METABOLISM
(2022)
Article
Neurosciences
Hye Jin Kim, Youn Ju Kim, Je Kyung Seong
Summary: Aerobic exercise activates uncoupling protein 1 (UCP1), leading to thermogenesis and reduction in body weight and fat content. The role of exerkines in modulating UCP1 expression and brown adipose tissue (BAT) activation is not well understood. Four weeks of voluntary wheel-running exercise decreases body weight and fat content. Exercise induces an increase in AMP-activated protein kinase (AMPK) and slow-type muscle fiber marker genes in skeletal muscles, and promotes UCP1 expression in both white and brown adipose tissues. Incubation of brown adipocytes with serum from exercise-trained mice significantly increases UCP1 gene and protein levels, and conditioned media from AMPK-activator-treated C2C12 myotubes induces increased UCP1 expression in brown adipocytes. These findings suggest that aerobic exercise-induced skeletal muscle AMPK plays a significant role in UCP1 expression in BAT.
JOURNAL OF PHYSIOLOGY-LONDON
(2022)
Article
Biochemistry & Molecular Biology
Seok-Hoon Jang, Se Hyun Paek, Jong-Kyu Kim, Je Kyung Seong, Woosung Lim
Summary: Hormone receptor-positive breast cancer cells rely on estrogen and its receptor, but resistance to endocrine therapy is common. By testing different culture conditions, researchers discovered that T47D cells respond well to estrogen under low cell density and medium replacement, which reduces the effectiveness of endocrine therapy. These findings provide new insights into endocrine therapy resistance and offer a new experimental model for future studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Se Hyo Jeong, Hun Hwan Kim, Min Young Park, Pritam Bhagwan Bhosale, Abuyaseer Abusaliya, Chung Kil Won, Kwang Il Park, Eunhye Kim, Jeong Doo Heo, Hyun Wook Kim, Meejung Ahn, Je Kyung Seong, Gon Sup Kim
Summary: Cancer, the second leading cause of death globally, is a widespread and dangerous disease that can affect anyone. Among its various types, prostate cancer is particularly prevalent among men, and extensive research is being conducted to develop effective treatments. Natural products are emerging as a promising alternative to chemical drugs, which often have side effects. This review focuses on three flavones - apigenin, acacetin, and tangeretin - and their potential as natural anticancer agents for prostate cancer treatment, exploring their effects on prostate cancer cells through apoptosis both in vitro and in vivo.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Genetics & Heredity
Hong Thi Lam Phan, Kyoungmi Kim, Ho Lee, Je Kyung Seong
Summary: Programmable nucleases, such as ZFNs, TALENs, and CRISPR/Cas, have diverse applications and enormous potential for targeted genomic modifications. Advances in genome editing tools have accelerated the development of genetically modified animal models for studying human diseases. This review summarizes the progress in developing mouse models of human diseases based on programmable nucleases and discusses their therapeutic applications.
Article
Infectious Diseases
Soomin Lee, Jae-Uk An, Woo-Hyun Kim, Saehah Yi, JunBum Lee, Seongbeom Cho
Summary: This study analyzed the genetic backgrounds and characteristics of mcr-1.1 and mcr-3.1 variants in colistin-resistant E. coli. The results showed that mcr-1.1 had high horizontal transferability and consistent genetic backgrounds, while mcr-3.1 had lower conjugation frequency and unstable genetic backgrounds. mcr-1.1 may play a major role in the spread of colistin resistance, while mcr-3.1 can proliferate stably through vertical transmission.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2023)
Article
Nutrition & Dietetics
Abuyaseer Abusaliya, Se Hyo Jeong, Pritam Bhagwan Bhosale, Hun Hwan Kim, Min Yeong Park, Eunhye Kim, Chung Kil Won, Kwang Il Park, Jeong Doo Heo, Hyun Wook Kim, Meejung Ahn, Je Kyung Seong, Gon Sup Kim
Summary: Previous research has established that plant-based compounds, particularly flavonoids, have significant anti-inflammatory and anti-cancer properties. Prunetrin, a glycosyloxyisoflavone derived from Prunus sp., has shown promising results in an anti-cancer study with liver cancer cells. It decreases cell viability, arrests the cell cycle, induces apoptosis through the mitochondrial pathway, and inhibits the mTOR/AKT signaling pathways.
Article
Cell Biology
Minjin Kang, Jung Ah Kim, Mee Hyun Song, Sun Young Joo, Se Jin Kim, Seung Hyun Jang, Ho Lee, Je Kyung Seong, Jae Young Choi, Heon Yung Gee, Jinsei Jung
Summary: In this study, a novel nonsense homozygous variant in CEP250 was identified among family members with progressive moderate sensorineural hearing loss. This variant resulted in centrosome localization deficit and hair cell degeneration in the cochlea, leading to the progression of hearing loss in humans and mice.
Article
Biochemistry & Molecular Biology
Pritam Bhagwan Bhosale, Hun Hwan Kim, Abuyaseer Abusaliya, Se Hyo Jeong, Min Yeong Park, Hyun-Wook Kim, Je Kyung Seong, Meejung Ahn, Kwang Il Park, Jeong Doo Heo, Young Sil Kim, Gon Sup Kim
Summary: Epidemiologic research suggests that flavonoids in the diet are beneficial for overall health. Apigetrin, a phytonutrient found in fruits and vegetables, has antioxidant and anti-inflammatory properties. This study investigated the effects of apigetrin on HepG2 cells and found that it reduced cell proliferation and induced cell death through the extrinsic apoptotic pathway.
Article
Biochemistry & Molecular Biology
Hye Jin Kim, Youn Ju Kim, Yong Jae Kim, Ji Hyeon Baek, Hak Su Kim, Il Yong Kim, Je Kyung Seong
Summary: Gut microbes play a crucial role in enhancing exercise performance and regulating metabolism in mice. Germ-free mice had reduced aerobic exercise capacity, lower body weight gain, and lower fat mass compared to mice with a healthy microbiome. The absence of gut microbes impaired glucose utilization and led to decreased exercise performance. Identifying key microbial species could be the focus of future research.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
Article
Nutrition & Dietetics
Hun Hwan Kim, Sang Eun Ha, Min Yeong Park, Se Hyo Jeong, Pritam Bhagwan Bhosale, Abuyaseer Abusaliya, Chung Kil Won, Jeong Doo Heo, Meejung Ahn, Je Kyung Seong, Hyun Wook Kim, Gon Sup Kim
Summary: Using RNA sequencing, this study identified KYNA as a potential therapeutic target for gastric cancer. KYNA treatment inhibited cancer cell growth and proliferation, while inducing cell death. This research can provide valuable insights for the development of drugs targeting gastric cancer.
Article
Medicine, Research & Experimental
Hye Jin Kim, Youn Ju Kim, Il Yong Kim, Je Kyung Seong
Summary: Resistance exercise training can improve obesity and glucose tolerance induced by HFD, and the benefits persist even after training cessation. Grip strength is significantly inversely correlated with body weight, fat mass, and glucose tolerance, while hanging time is significantly inversely correlated with body weight only.
LABORATORY ANIMAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Do Hyun Kim, Hye Jin Kim, Je Kyung Seong
Summary: The study suggests that Ucp2 deficiency may prevent high-fat diet-induced obesity by reducing adipocyte apoptosis. However, Ucp2 deficiency does not affect the browning capacity of iWAT.
Article
Biochemistry & Molecular Biology
Jin Kyung Kim, Hye Sun Go, Sol Pin Kim, Il Yong Kim, Yun Hee Lee, Seung Hyun Oh, Ho Lee, Je Kyung Seong
Summary: Obesity is caused by an energy imbalance, and exercise as well as beta-adrenergic receptor agonists can induce "beige adipogenesis" in white adipose tissue.
