Article
Genetics & Heredity
Fabian A. Diaz, Emilio J. Gutierrez-Castillo, Brittany A. Foster, Paige T. Hardin, Kenneth R. Bondioli, Zongliang Jiang
Summary: The study found that heat stress negatively affects oocyte quality, transcriptomic profiles, and DNA methylation. During the transition from spring to summer, fewer high-quality oocytes were obtained in the summer season compared to the spring season. RNA sequencing revealed differential gene expression in GV and MII oocytes due to heat stress, with five common genes significantly affected in both types of oocytes. Pathways related to glucocorticoid biosynthesis, apoptosis signaling, Oct4 pluripotency, and Wnt/beta-catenin signaling were influenced by heat stress. Additionally, there was no significant difference in DNA methylation levels between spring and summer oocytes.
FRONTIERS IN GENETICS
(2021)
Review
Cell Biology
Yesim Bilmez, Gunel Talibova, Saffet Ozturk
Summary: Histone methylation is a crucial epigenetic mechanism for regulating gene expression. KMTs and PRMTs catalyze the methylation of lysine and arginine residues, while HDMs can reversibly remove the added methyl groups.
HISTOCHEMISTRY AND CELL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Amirhossein Davoodvandi, Banafsheh Nikfar, Russel J. Reiter, Zatollah Asemi
Summary: Melatonin plays important roles in mammals, regulating circadian rhythms, enhancing immunity, and inhibiting cancer. Epigenetic drugs have gained attention for their potential in cancer treatment. This report summarizes the effects of melatonin on DNA methylation in cancer cells and discusses the impact of artificial light on melatonin secretion and cancer cell DNA methylation.
CELLULAR & MOLECULAR BIOLOGY LETTERS
(2022)
Article
Oncology
Xiaoqing Yu, Ling Cen, Y. Ann Chen, Joseph Markowitz, Timothy Shaw, Kenneth Y. Tsai, Jose R. Conejo-Garcia, Xuefeng Wang
Summary: DNA methylation signatures can be used as reliable biomarkers to predict patient prognosis and immune status in tumors. This study introduces the concept of tumor-based expression quantitative trait methylation (eQTM) for the identification of predictive biomarkers. eQTM CpGs and genes represent new and efficient candidate targets for prognosis and immune status monitoring.
Article
Endocrinology & Metabolism
Mingru Yin, Weina Yu, Wenzhi Li, Qianqian Zhu, Hui Long, Pengcheng Kong, Qifeng Lyu
Summary: The study found that AOA treatment affects the pre- and post-implantation embryo development in mice, resulting in increased expression of the maternal allele-specific gene Igf2r but significantly lower birth weight in newborn mice. However, no other abnormalities were observed in the offspring born following AOA treatment.
REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Taynan Stonoga Kawamoto, Joao Henrique Moreira Viana, Thais Preisser Pontelo, Mauricio Machaim Franco, Otavio Augusto Costa de Faria, Andrei Antonioni Guedes Fidelis, Luna Nascimento Vargas, Ricardo Alamino Figueiredo
Summary: This study characterized the reproductive physiology, oocyte competence, and chromatin compaction in Nelore calves during the early-prepubertal and intermediate-prepubertal periods. The oocyte competence gradually improved during the prepubertal period, which can help determine whether to collect oocytes from calves.
Article
Biochemical Research Methods
Manqi Cai, Molin Yue, Tianmeng Chen, Jinling Liu, Erick Forno, Xinghua Lu, Timothy Billiar, Juan Celedon, Chris McKennan, Wei Chen, Jiebiao Wang
Summary: This study focuses on using cellular deconvolution methods to extract cell-type-specific signals from tissue-level omics data. However, different methods produce different results under various real data settings. The study proposes EnsDeconv, an ensemble deconvolution method that synthesizes the results from multiple single deconvolution methods to achieve robust and accurate estimation of cellular fractions.
Review
Food Science & Technology
Nadir Mustafa Qadir Nanakali, Parisa Maleki Dana, Fatemeh Sadoughi, Zatollah Asemi, Mehran Sharifi, Reza Asemi, Bahman Yousefi
Summary: Natural products such as curcumin, quercetin, and resveratrol have antitumor effects and can affect cancer-related mechanisms, including DNA methylation. These compounds have the potential to be used as cancer treatments by targeting DNA methylation and modifying the expression of tumor suppressor genes.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Environmental Sciences
Thomas Sol Dourdin, Guillaume Riviere, Alexandre Cormier, Carole Di Poi, Killian Guyomard, Manuella Rabiller, Farida Akcha, Thierno Bah Sadialiou, Pauline Le Monier, Rossana Sussarellu
Summary: Early exposure to an environmentally relevant pesticide mixture induces multi-scale latent effects possibly affecting life history traits in the Pacific oyster, Crassostrea gigas. The study found that exposure to a combination of 18 pesticides and metals at environmental concentrations during the embryo-larval stage resulted in disturbed swimming behavior, increased size and weight at specific time points, and altered expression of development-related genes. Additionally, DNA methylation analyses showed significant modifications in exposed larvae, marked by a demethylation trend.
ENVIRONMENTAL POLLUTION
(2023)
Article
Genetics & Heredity
Goncalo Pereira, Joao Pereira, Rita B. Santos, Andreia Figueiredo
Summary: This study reveals the importance of epigenetic regulation in the interaction between grapevine and downy mildew, suggesting that early hypomethylation is associated with resistance to the pathogen.
Review
Pathology
Xin Hub, Yong Wang, Xiaoyu Zhang, Chensheng Li, Xikun Zhang, Dongxia Yang, Yuanyuan Liu, Lianlian Li
Summary: This review focuses on how DNA methylation regulates HOX genes and briefly discusses drug development approaches targeting these mechanisms.
EXPERIMENTAL AND MOLECULAR PATHOLOGY
(2023)
Article
Multidisciplinary Sciences
Xiaojing Chang, Jinguo Ma, Xiaoying Xue, Guohui Wang, Tianfang Yan, Linlin Su, Xuetao Han, Huandi Zhou, Liubing Hou
Summary: The study revealed that in gastric cancer patients, the down-regulation of NDRG1 expression was negatively correlated with DNMT1, DNMT3A, and DNMT3B, while the DNA methylation of NDRG1 was positively correlated with the DNMT family. High expression of NDRG1 may be associated with prolonged overall survival.
Article
Obstetrics & Gynecology
Eric Rhon-Calderon, Cassidy Hemphill, Lisa Vrooman, Casey Rosier, Yemin Lan, Teri Ord, Christos Coutifaris, Monica Mainigi, Richard Schultz, Marisa Bartolomei
Summary: TEBx affects the health of the placenta and embryo during early development, with some changes improving later in development and others worsening, leading to metabolic changes in adult offspring.
HUMAN REPRODUCTION
(2023)
Article
Reproductive Biology
Yuzhen Ma, Chunshen Long, Gang Liu, Hongmei Bai, Lirong Ma, Taji Bai, Yongchun Zuo, Shubin Li
Summary: Understanding the molecular changes in oocyte cryopreservation and thawing processes is crucial for enhancing cryopreservation technologies. The study found differences in global methylation, gene expression, and regulation of specific genes between vitrified and fresh oocytes, shedding light on the impact of vitrification on oocyte quality.
Article
Reproductive Biology
Atieh Hajarizadeh, Akram Eidi, Ehsan Arefian, Eva Tvrda, Abdollah Mohammadi-Sangcheshmeh
Summary: Aflatoxin B1 (AFB1) negatively affects the development of sheep oocytes and embryonic development, leading to decreased meiotic and cytoplasmic maturation, increased intracellular reactive oxygen species (ROS) production, decreased mitochondrial membrane potential, and altered gene expression related to apoptosis and DNA methylation.
Article
Pharmacology & Pharmacy
Mehmet Bulbul, Osman Sinen, V. Nimet Izgut-Uysal, Goekhan Akkoyunlu, Saffet Ozturk, Fatma Uysal
CLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY
(2019)
Review
Biochemistry & Molecular Biology
Saffet Ozturk
MOLECULAR REPRODUCTION AND DEVELOPMENT
(2019)
Article
Geriatrics & Gerontology
Esra Gozde Kosebent, Fatma Uysal, Saffet Ozturk
EXPERIMENTAL GERONTOLOGY
(2020)
Article
Cell Biology
Fatma Uysal, Saffet Ozturk
HISTOCHEMISTRY AND CELL BIOLOGY
(2020)
Article
Genetics & Heredity
Fatma Uysal, Esra Gozde Kosebent, Havva Serap Toru, Saffet Ozturk
Summary: Telomere signal intensities decrease significantly from fetal to postmenopausal groups, with TERT, TRF1, TRF2, and POT1 proteins showing reduced expression levels in oocytes and granulosa cells. These findings suggest that decreased TERT and telomere-binding protein expression may contribute to telomere shortening in aging ovaries, potentially impacting female fertility. Further research is needed to understand the molecular mechanisms involved in this process.
JOURNAL OF ASSISTED REPRODUCTION AND GENETICS
(2021)
Review
Biochemistry & Molecular Biology
Saffet Ozturk
MOLECULAR REPRODUCTION AND DEVELOPMENT
(2020)
Article
Andrology
Esra G. Kosebent, Saffet Ozturk
Summary: Telomeres at the ends of eukaryotic chromosomes consist of repetitive DNA sequences and telomere-associated proteins, including telomerase which elongates them in germ cells. A study on postnatal mouse testes revealed significant differences in the spatial and temporal expression patterns of telomerase and telomere-associated proteins, suggesting their importance in maintaining telomere length and integrity in spermatogenic cells from newborn to adult stages.
Article
Multidisciplinary Sciences
Esra Gozde Kosebent, Saffet Ozturk
Summary: Telomeres cap the ends of eukaryotic chromosomes to maintain genomic stability and integrity throughout an organism's lifespan. During ovarian aging, telomeres progressively shorten, potentially leading to loss of fertility. Reduced expression of telomere-associated genes and TERT protein levels in certain follicles of aged mice may contribute to telomere shortening and infertility in later reproductive years.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Saffet Ozturk
Summary: This review comprehensively evaluates the molecular determinants of developmental and permanent arrests occurring in mammalian oocytes, and discusses potential approaches for inducing permanent arrests to obtain competent oocytes.
Review
Cell Biology
Yesim Bilmez, Gunel Talibova, Saffet Ozturk
Summary: Histone methylation is a crucial epigenetic mechanism for regulating gene expression. KMTs and PRMTs catalyze the methylation of lysine and arginine residues, while HDMs can reversibly remove the added methyl groups.
HISTOCHEMISTRY AND CELL BIOLOGY
(2022)
Article
Cell Biology
Yesim Bilmez, Gunel Talibova, Saffet Ozturk
Summary: The study aimed to determine the expression patterns of Setd1b, Setdb1, Setd2, and Cxxc1 genes in postnatal mouse ovaries. The results showed that the expression levels of these genes changed significantly with ovarian development and age, and these changes may be associated with female fertility loss.
HISTOCHEMISTRY AND CELL BIOLOGY
(2022)
Article
Genetics & Heredity
Saffet Ozturk, Esra Gozde Kosebent, Gunel Talibova, Yesim Bilmez, Betul Tire, Alp Can
Summary: The expression of EPAB is high until embryonic genome activation and then decreases significantly. It plays key roles in translational regulation, stabilization, and protection of maternal mRNAs. It interacts with other cellular proteins and undergoes phosphorylation to carry out these functions.
JOURNAL OF ASSISTED REPRODUCTION AND GENETICS
(2023)
Review
Developmental Biology
Saffet Ozturk
Summary: Developmental arrest in preimplantation embryos is a major cause of assisted reproduction failure. This review comprehensively evaluates the biological impacts of molecular biological defects, including epigenetic disturbances, ART processes, and genetic variants, on embryonic development. The creation of diagnostic gene panels and potential ways of preventing developmental arrests are also discussed.
MOLECULAR HUMAN REPRODUCTION
(2023)
Article
Agriculture, Dairy & Animal Science
Filiz Tepekoy, Gokhan Akkoyunlu
ANIMAL REPRODUCTION
(2020)
Article
Developmental Biology
Fatma Uysal, Gokhan Akkoyunlu, Saffet Ozturk
REPRODUCTION FERTILITY AND DEVELOPMENT
(2019)
Article
Biochemistry & Molecular Biology
Siva Santhiya Arul, Brinda Balakrishnan, Savithri S. Handanahal, Sangita Venkataraman
Summary: Viral nanoparticles are self-assembling delivery systems used for vaccines and therapeutic agents. They have improved biocompatibility and are widely used in various biomedical applications. However, large-scale production of VNPs still faces challenges.
Article
Biochemistry & Molecular Biology
Wisely Chua, Carl O. Marsh, Si En Poh, Winston LC. Koh, Melody Li Ying Lee, Li Fang Koh, Xin-Zi Emily Tang, Peter See, Zheng Ser, Shi Mei Wang, Radoslaw M. Sobota, Thomas L. Dawson Jr, Yik Weng Yew, Steven Thng, Anthony J. O'Donoghue, Hazel H. Oon, John E. Common, Hao Li
Summary: In this study, the gene expression of enzymes secreted by Malassezia globosa in the skin was investigated using targeted RNA sequencing. The study found that the expression of these enzymes is regulated by the fungus's environment and differs significantly from healthy skin sites. Additionally, a pseudoprotease MGL_3331 was identified to elicit an immune reaction in patients with atopic dermatitis. This highlights the importance of studying fungal proteins in physiologically relevant environments and their role in host immunity.
Article
Biochemistry & Molecular Biology
Belisa Parmeggiani, Marian Flores Signori, Cristiane Cecatto, Marina Rocha Frusciante, Manuela Bianchin Marcuzzo, Debora Guerini Souza, Rafael Teixeira Ribeiro, Bianca Seminotti, Diogo Onofre Gomes de Souza, Cesar Augusto Joa o Ribeiro, Moacir Wajner, Guilhian Leipnitz
Summary: Non ketotic hyperglycinemia (NKH) is a disorder caused by mutations in the genes encoding glycine cleavage system proteins, leading to severe neurodegeneration and white matter alterations. The study found that glycine affects myelin structure, glutamatergic system, and induces oxidative stress in neonatal rats and MO3.13 oligodendroglial cells.
Review
Biochemistry & Molecular Biology
Marie Rose Ndella Thiaw, Pascal Gantet
Summary: Mini zinc fingers play important roles in plant development, including control of cell division and expansion, meristem state transition, and growth and organ development. They have diverse modes of action, such as direct gene activation, interaction with specific transcription factors, and aggregation of protein complexes for chromatin remodeling. Further research is needed to explore their wider range of biological functions and their involvement in biotic and abiotic stress responses.
Article
Biochemistry & Molecular Biology
Shao-Jui Lai, Takahiro Kameda, Maasa Morita, Yuka Yamagata, Kaoruko Nishizaka, Yuna Horiuchi, Yukihiro Kobayashi, Yoko Usami, Jun-Jen Liu, Takeshi Kasama, Minoru Tozuka, Ryunosuke Ohkawa
Summary: In this study, the co-modification and impact of chymase and MPO on HDL were investigated. Sequential treatment with MPO and chymase generated two novel apoA-I fragments from HDL, one of which has a specific immunological property and can be used to predict patients with normal HDL-C levels and cardiovascular diseases.
Article
Biochemistry & Molecular Biology
Xiao-Mi Sun, Asami Yoshida, Takuya Ishii, Yan-Rong Jiang, Yi-Li Gao, Mikinori Ueno, Katsuya Hirasaka, Kiyoshi Osatomi
Summary: This study found that infection with the causative bacteria of edwardsiellosis, Edwardsiella tarda NUF251, leads to the production of superoxide radicals, causing oxidative stress. The research on the Jfsod1 gene suggests that the transcription factor NF-IL6 plays a significant role in upregulating the transcriptional activity of the gene in response to oxidative stress induced by NUF251 infection.
Article
Biochemistry & Molecular Biology
Shane M. Carey, Sean P. Kearns, Matthew E. Millington, Gregory S. Buechner, Beda E. Alvarez Jr, Leily Daneshian, Brendan Abiskaroon, Maksymilian Chruszcz, Edward L. D'Antonio
Summary: The importance of F337 in TcGlcK was investigated using the hole mutagenesis approach, revealing its key interactions with aromatic tail groups in inhibitor molecules. Mutants retaining activity and structural similarity were obtained, suggesting the possibility of TcHxK existing as a monomer lacking the F337 residue. Similar D-glucosamine inhibitors may bind less strongly to TcHxK due to the absence of van der Waals contacts from residue side chains.
Article
Biochemistry & Molecular Biology
Catia Barria, Diogo Athayde, Guillem Hernandez, Leonor Fonseca, Jorge Casinhas, Tiago N. Cordeiro, Margarida Archer, Cecilia M. Arraiano, Jose A. Brito, Rute G. Matos
Summary: Ribonucleases play a crucial role in RNA regulation by processing, degrading, and quality controlling cellular transcripts. Campylobacter jejuni, the main cause of human gastroenteritis, relies on the exoribonuclease PNPase (CjPNP) for low-temperature survival, virulence factor synthesis, and swimming, cell adhesion/invasion, and chick colonization abilities. The crystallographic structure of CjPNP, along with SAXS analysis, confirms its trimeric arrangement and provides insight into domain arrangement and flexibility. Mutations in highly conserved residues reveal unexpected RNA degradation activity even under conditions favoring polymerization. These findings have significant implications for the development of strategies to combat C. jejuni infections.
Article
Biochemistry & Molecular Biology
Elvira R. Shaykhutdinova, Maria S. Severyukhina, Inna V. Kholoshenko, Elena A. Gondarenko, Irina V. Shelukhina, Elena V. Kryukova, Alina M. Ismailova, Elena S. Sadovnikova, Igor A. Dyachenko, Arkady N. Murashev, Victor I. Tsetlin, Yuri N. Utkin
Summary: Evidence suggests that activating nicotinic acetylcholine receptors (nAChRs) can reduce cardiac injury caused by ischemia and reperfusion. In this study, the expression of a4, a6, and a132 nAChR subunits in the rat heart's left ventricle was demonstrated. The nAChR agonists cytisine and varenicline, commonly used for nicotine addiction treatment, were found to significantly reduce myocardial ischemia-reperfusion injury, with varenicline showing greater protection. The presence of a4132, a7, and/or a6132-containing receptors suggests that the protective effect of varenicline may be mediated by these subunits. These findings indicate a potential new use for cytisine and varenicline as cardioprotective agents.
Article
Biochemistry & Molecular Biology
Xinhai Xiong, Wenjie Chen, Cheng Chen, Qi Wu, Chaopeng He
Summary: This article summarizes the important roles of Cx43 in disease development from the perspective of subcellular localization and provides new ideas for Cx43 as a therapeutic target and the search for related pathological mechanisms.
Article
Biochemistry & Molecular Biology
Veronica Bastos, Simone Pascoal, Kamila Lopes, Marcia Mortari, Helena Oliveira
Summary: Cancer, especially melanoma, is a major global health problem due to its metastatic capacity, treatment resistance, and high mortality rates. The Chartergellus-CP1 peptide isolated from Chartergellus communis wasp venom showed selective cytotoxicity towards melanoma cell lines, inducing apoptosis, cell cycle impairment, and intracellular ROS increase.
Article
Biochemistry & Molecular Biology
Charlotte Claeyssen, Nathan Bulangalire, Bruno Bastide, Onnik Agbulut, Caroline Cieniewski-Bernard
Summary: Maintenance of striated muscle tissue relies on a dynamic network of protein-protein interactions. Desmin intermediate filaments play a crucial role in heart and skeletal muscle by maintaining cell structure and contributing to various cellular processes. The assembly of desmin intermediate filaments requires aB-crystallin, which is involved in multiple cellular functions.
Article
Biochemistry & Molecular Biology
Dhritiman Dey, Adhiraj Dasgupta, Dipanjan Ghosh, Oindrila Bhattacharjee, Abhrajyoti Ghosh, Ayae Honda, Dhrubajyoti Chattopadhyay
Summary: This study successfully identified host factors that interact with Chandipura Virus (CHPV) and play a critical role in infection, including A2M, LRP1, and GRP78. Knocking out A2M has a severe effect on viral infection, indicating the potential role of these host proteins in viral entry into host cells.
Article
Biochemistry & Molecular Biology
Anna Dotsenko, Igor Sinelnikov, Aleksandra Rozhkova, Ivan Zorov, Arkady Sinitsyn
Summary: Xylanases play important roles in various industrial applications, such as feed additives, pulp and paper bleaching, and the production of bread, food, and drinks. Xylanases from the GH10 family show high thermostability and resistance to protein inhibitors, making them promising candidates for these processes. This study successfully improved the thermostability and enzymatic activity of GH10 xylanase, which could enhance its effectiveness as a feed additive and during pulp and paper bleaching.
Article
Biochemistry & Molecular Biology
M. Jaquet, M. Bengue, K. Lambert, G. Carnac, D. Misse, C. Bisbal
Summary: Changes to our environment have led to the emergence of human pathogens such as chikungunya virus, which is now a major public health concern. In this study, the interconnection between skeletal muscle cells metabolism, their differentiation stage, and the infectivity of chikungunya virus was investigated. The results showed that chikungunya virus infectivity is dependent on cell differentiation and metabolism and that the virus interferes with cellular metabolism.