Uncovering proteome variations and concomitant quality changes of different drying methods Cordyceps sinensis by 4D-DIA structural proteomics by Mengjun Xiao, Chuyu Tang, Tao Wang, Min He, Yuling Li, Xiuzhang Li

“…Notably, there was a significant overlap between ribosome and ribosome biogenesis in eukaryotes pathways. The process of drying Cordyceps sinensis resulted in a significant upregulation of the expression of proteins linked to various metabolic pathways. …”
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Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene by David W Morgens, Leah Gulyas, Xiaowen Mao, Alejandro Rivera-Madera, Annabelle S Souza, Britt A Glaunsinger

“…Abstract Complex transcriptional control is a conserved feature of both eukaryotes and the viruses that infect them. Despite viral genomes being smaller and more gene dense than their hosts, we generally lack a sense of scope for the features governing the transcriptional output of individual viral genes. …”
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Detection of CRISPR cassettes and cas genes in the Arabidopsis thaliana genome by Yu. M. Konstantinov, I. S. Petrushin

“…The discovery of CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins), which implement the adaptive immunity function in prokaryotes, raises the question whether such a mechanism of antiviral protection could be caught up by evolution and used by representatives of eukaryotes (in particular, plants). The purpose of this work was to analyze the complete sequences of nuclear, mitochondrial, and chloroplast genomes of Arabidopsis thaliana in order to search for genetic elements similar to those in CRISPR-Cas systems of bacteria and archaea. …”
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A conserved fungal Knr4/Smi1 protein is crucial for maintaining cell wall stress tolerance and host plant pathogenesis. by Erika Kroll, Carlos Bayon, Jason Rudd, Victoria J Armer, Anjana Magaji-Umashankar, Ryan Ames, Martin Urban, Neil A Brown, Kim Hammond-Kosack

“…Orthologues of the FgKnr4 gene are widespread across the fungal kingdom but are absent in other Eukaryotes, suggesting the protein has potential as a promising intervention target. …”
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Two cellular models for analyzing mitochondrial heteroplasmy by Yaning Hu, Lin Jiang, Wen Liu, Xingbo Zhao

“…Heteroplasmy is commonly observed in eukaryotes due to mitochondrial genome (mtDNA) mutation, paternal leakage, mitochondria transplantation/mitotherapy, and somatic cell nuclear transfer (SCNT). …”
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N6-Methyladenosine in RNA and DNA: An Epitranscriptomic and Epigenetic Player Implicated in Determination of Stem Cell Fate by Pengfei Ji, Xia Wang, Nina Xie, Yujing Li

“…N6-Methyladenosine modification in DNA (m6dA), mRNA (m6A), tRNA, and other noncoding RNAs has been defined as another important epigenetic and epitranscriptomic marker in eukaryotes in recent years. The mRNA m6A modification has been characterized biochemically, molecularly, and phenotypically, including elucidation of its methyltransferase complexes (m6A writer), demethylases (m6A eraser), and direct interaction proteins (readers), while limited information on the DNA m6dA is available. …”
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Diversity of <i>mariner</i>-like elements in Orthoptera by K. Ustyantsev, M. Biryukov, I. Sukhikh, N. V. Shatskaya, V. Fet, A. Blinov, I. Konopatskaia

“…Mariner-like elements (MLEs) are among the most widespread DNA transposable elements in eukaryotes. Insects were the first organisms in which MLEs were identified, however the diversity of MLEs in the insect order Orthoptera has not yet been addressed. …”
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New insights into the N-glycomes of Dictyostelium species by Alba Hykollari, Daniel Malzl, Chunsheng Jin, Carina Eschenbach, Kristína Kianičková, Iain B.H. Wilson, Katharina Paschinger

“…In previous studies on Dictyostelium discoideum, it was demonstrated that their N-glycans, as in most eukaryotes, derive from the Glc3Man9GlcNAc2-PP-Dol precursor; however, unique glyco-epitopes, including intersecting GlcNAc, core α1,3-fucosylation, sulphation and methylphosphorylation, were detected. …”
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Enhanced Tolerance to Antifungals as a General Feature of Rho⁻ Mutants in Yeast Species: Implications to Positive Selection of Respiratory Deficiency by Zachary Johnson, Farhan Nadim, Mikhajlo K. Zubko

“…Although the mitochondrial genome is an attribute of all eukaryotes, some yeast species (called petite-positive) can replicate without mitochondrial DNA (mtDNA). …”
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Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3 by Valentin Hure, Florence Piron-Prunier, Tamara Yehouessi, Clémentine Vitte, Aleksandra E. Kornienko, Gabrielle Adam, Magnus Nordborg, Angélique Déléris

“…It also suggests dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.…”
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Polytene chromosomes reflect functional organization of the Drosophila genome by D. S. Sidorenko, T. Yu. Zykova, V. A. Khoroshko, G. V. Pokholkova, S. A. Demakov, J. Larsson, E. S. Belyaeva, I. F. Zhimulev

“…Polytene chromosomes of Drosophila melanogaster are a convenient model for studying interphase chromosomes of eukaryotes. They are giant in size in comparison with diploid cell chromosomes and have a pattern of cross stripes resulting from the ordered chromatid arrangement. …”
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Inactivation of the TIM complex components leads to a decrease in the level of DNA import into Arabidopsis mitochondria by T. A. Tarasenko, K. D. Elizova, V. I. Tarasenko, M. V. Koulintchenko, Yu. M. Konstantinov

“…The phenomenon of DNA import into mitochondria has been shown for all major groups of eukaryotes. In plants and animals, DNA import seems to occur in different ways. …”
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The extremely halotolerant black yeast Hortaea werneckii - a model for intraspecific hybridization in clonal fungi by Polona Zalar, Jerneja Zupančič, Cene Gostinčar, Janja Zajc, G. Sybren de Hoog, Filomena De Leo, Armando Azua-Bustos, Nina Gunde-Cimerman

“…Abstract The polymorphic black yeast Hortaea werneckii (Capnodiales, Ascomycota) is extremely halotolerant (growth from 0 to 30% [w/v] NaCl) and has been extensively studied as a model for halotolerance in Eukaryotes for over two decades. Its most frequent sources are hypersaline environments and adjacent sea-water habitats in temperate, subtropical and tropical climates. …”
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Phage WO diversity and evolutionary forces associated with Wolbachia-infected crickets by Qing-Chen Luo, Yue-Yuan Li, Ye-Song Ren, Xiao-Hui Yang, Dao-Hong Zhu

“…This suggests that Wolbachia in crickets may acquire phage WO types through horizontal viral transfer between eukaryotes, independent of Wolbachia involvement. Furthermore, nine putative recombination events were identified across seven cricket species harboring multiple phage types. …”
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Characterization of demethylating DNA glycosylase ROS1 from Nicotiana tabacum L. by D. V. Petrova, N. V. Permyakova, I. R. Grin, D. O. Zharkov

“…One of the main mechanisms of epigenetic regulation in higher eukaryotes is based on the methylation of cytosine at the C5 position with the formation of 5-methylcytosine (mC), which is further recognized by regulatory proteins. …”
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Identifikasi Pertumbuhan Jamur Aspergillus Sp pada Roti Tawar yang Dijual di Kota Padang Berdasarkan Suhu dan Lama Penyimpanan by Dina Khaira Mizana, Netty Suharti, Arni Amir

“…Fungus is the main microorganism which has the main role in the process of loaves production and decomposition. Aspergillusis the eukaryotes microorganism that has the widest spread in the nature. …”
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Importance of benzoyltransferase GcnE and lysine benzoylation of alcohol dehydrogenase AdhB in pathogenesis and aflatoxin production in Aspergillus flavus by Xuan Chen, Lihan Wu, Yuqi Zhang, Sen Wang, Shihua Wang

“…ABSTRACT Lysine benzoylation (Kbz) is a newly identified post-translational modification associated with active transcription and metabolism in eukaryotes. However, whether Kbz exists in pathogenic fungi and its function remains unknown. …”
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Russian Science Foundation grant No. 20-14-00140 supported this study. The authors are thankful to the multi-access Center “Bioinformatics” for the use of computational resources a... by O. V. Vishnevsky, I. V. Chadaeva, E. B. Sharypova, B. M. Khandaev, K. A. Zolotareva, A. V. Kazachek, P. M. Ponomarenko, N. L. Podkolodny, D. A. Rasskazov, E. V. Zemlyanskaya, A. G. Bogomolov, O. A. Podkolodnaya, L. K. Savinkova, M. P. Ponomarenko

“…We focused the search on the TATA­binding protein (TBP)­binding site because it is located within a narrow region (between positions –70 and –20 relative to the corresponding transcription start sites), is the most conserved, necessary for primary transcription initiation, and is the best­studied regulatory genomic signal in eukaryotes. Our previous studies presented our publicly available Web service Plant_SNP_TATA_Z­tester, which makes it possible to estimate the equilibrium dissociation constant (KD) of TBP complexes with plant proximal promoters (as output data) using 90 bp of their DNA sequences (as input data). …”
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EPIGENETICS TODAY AND TOMORROW by B. F. Vanyushin

“…DNA methylation in eukaryotes is species- and tissue (cell) specific. It is regulated by hormones and aging-related changes, being one of the mechanisms controlling cellular and sex differentiation. …”
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Genome-Wide Identification and Expression Analysis of bHLH-MYC Family Genes from Mustard That May Be Important in Trichome Formation by Jianzhong Li, Guoliang Li, Caishuo Zhu, Shaoxing Wang, Shifan Zhang, Fei Li, Hui Zhang, Rifei Sun, Lingyun Yuan, Guohu Chen, Xiaoyan Tang, Chenggang Wang, Shujiang Zhang

“…The bHLH gene family, particularly the Myelocytomatosis (MYC) proteins that possess the structural bHLH domain (termed bHLH-MYC), are crucial to the formation and development of leaf trichomes in plants. bHLH constitutes one of the largest families of transcription factors in eukaryotes, of which MYC is a subfamily member. However, studies on bHLH-MYC transcription factors in mustard have yet to be reported. …”
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