EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES by T. M. Khlebodarova, D. Yu. Oshchepkov, V. G. Levitsky, O. A. Podkolodnaya, E. V. Ignatieva, E. A. Ananko, I. L. Stepanenko, N. A. Kolchanov

“…The development of in vitro methods produced new experimental information on protein binding to DNA, which is accumulated in databases and used in studies of mechanisms regulating gene expression and in the development of computer-assisted methods of binding site recognition in pro- and eukaryotic genomes. However, it is still questionable to what extent sequences selected in vitro reflect the actual structures of natural transcription factor (TF) binding sites. …”
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Synthetic genomics in crop breeding: Evidence, opportunities and challenges by Yuhan Zhou, Ziqi Zhou, Qingyao Shu

“…These advancements open promising avenues for the application of synthetic genomics in multicellular eukaryotic organisms, particularly in the realm of crop improvement. …”
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Mitochondrial DNA Structure in <i>Trypanosoma cruzi</i> by Alfonso Herreros-Cabello, Francisco Callejas-Hernández, Manuel Fresno, Núria Gironès

“…In <i>Trypanosoma cruzi</i>, maxicircles contain typical mitochondrial genes found in other eukaryotes. They consist of coding and divergent/variable regions, complicating their assembly due to repetitive elements. …”
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ATG8 delipidation is not universally critical for autophagy in plants by Yong Zou, Jonas A. Ohlsson, Sanjana Holla, Igor Sabljić, Jia Xuan Leong, Florentine Ballhaus, Melanie Krebs, Karin Schumacher, Panagiotis N. Moschou, Simon Stael, Suayib Üstün, Yasin Dagdas, Peter V. Bozhkov, Elena A. Minina

“…Our findings underscore the evolutionary diversification of the molecular mechanism governing the maturation of autophagosomes in eukaryotic lineages and highlight how this conserved pathway is tailored to diverse organisms.…”
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Anti-microbial cetylpyridinium chloride suppresses mast cell function by targeting tyrosine phosphorylation of Syk kinase by Bright Obeng, Lucas J. Bennett, Bailey E. West, Dylan J. Wagner, Patrick J. Fleming, Morgan N. Tasker, Madeleine K. Lorenger, Dorothy R. Smith, Tetiana Systuk, Sydni M. Plummer, Jeongwon Eom, Marissa D. Paine, Collin T. Frangos, Michael P. Wilczek, Juyoung K. Shim, Melissa S. Maginnis, Julie A. Gosse

“…Yet, there is minimal published data on CPC effects on eukaryotes, immune signaling, and human health. Previously, it was shown that low-micromolar CPC inhibits rat mast cell function by inhibiting antigen (Ag)-stimulated Ca2+ mobilization, microtubule polymerization, and degranulation. …”
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Role of calpain system in meat tenderness: A review by Z.F. Bhat, James D. Morton, Susan L. Mason, Alaa El-Din A. Bekhit

“…Calpains are intracellular calcium-dependent cysteine proteases found in most eukaryotes. At least three calpains (μ- and m-calpains and calpain 3) and calpastatin, their specific endogenous inhibitor, are found in muscle. …”
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Systematic expression analysis of cysteine‐rich secretory proteins, antigen 5, and pathogenesis‐related 1 protein (CAP) superfamily in Arabidopsis by Megumi Matsuzawa, Takumi Nakayama, Masa H. Sato, Tomoko Hirano

“…Abstract The Cysteine‐rich secretory proteins (CRISPS), Antigen 5 (Ag5), and Pathogenesis‐related 1 (PR‐1) protein (CAP) superfamily members are found in multiple eukaryotic organisms, including yeasts, animals, and plants. …”
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RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes by Fortmann-Grote, Carsten, Irmer, Julia von, Bertels, Frederic

“…Compared to eukaryotes, repetitive sequences are rare in bacterial genomes and usually do not persist for long. …”
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Viroids and Retrozymes: Plant Circular RNAs Capable of Autonomous Replication by Alexander A. Lezzhov, Anastasia K. Atabekova, Denis A. Chergintsev, Ekaterina A. Lazareva, Andrey G. Solovyev, Sergey Y. Morozov

“…Among the long non-coding RNAs that are currently recognized as important regulatory molecules influencing a plethora of processes in eukaryotic cells, circular RNAs (circRNAs) represent a distinct class of RNAs that are predominantly produced by back-splicing of pre-mRNA. …”
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Comprehensive Analysis of the Proteome of <i>S. cerevisiae</i> Wild-Type and <i>pdr</i>5Δ Cells in Response to Bisphenol A (BPA) Exposure by Valentina Rossio, Joao A. Paulo

“…To investigate the impact of BPA on eukaryotic cells, we analyzed the proteome changes of wild-type and <i>PDR5</i>-deleted <i>S. cerevisiae</i> strains exposed to different doses of BPA using sample multiplexing-based proteomics. …”
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CysQ of , a Protozoa, May Have Been Acquired from Bacteria by Horizontal Gene Transfer by Ji Young Lee, Sangsoo Kim

“…According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including C. parvum, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. …”
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Multi-tissue characterization of the constitutive heterochromatin proteome in Drosophila identifies a link between satellite DNA organization and transposon repression. by Ankita Chavan, Lena Skrutl, Federico Uliana, Melanie Pfister, Franziska Brändle, Laszlo Tirian, Delora Baptista, Dominik Handler, David Burke, Anna Sintsova, Pedro Beltrao, Julius Brennecke, Madhav Jagannathan

“…Noncoding satellite DNA repeats are abundant at the pericentromeric heterochromatin of eukaryotic chromosomes. During interphase, sequence-specific DNA-binding proteins cluster these repeats from multiple chromosomes into nuclear foci known as chromocenters. …”
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Protein multiplicity: exemplifying an overwhelmingly likely pattern of molecular evolution? by Les Hatton, Greg Warr

“…We show that the predictions of the CoHSI theory are borne out to a high degree of statistical robustness for the multiplicious proteins of eukaryotes, bacteria, archaea, and viruses whether considered separately or in totality. …”
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Unidirectional MCM translocation away from ORC drives origin licensing by Agata Butryn, Julia F. Greiwe, Alessandro Costa

“…Abstract The MCM motor of the eukaryotic replicative helicase is loaded as a double hexamer onto DNA by the Origin Recognition Complex (ORC), Cdc6, and Cdt1. …”
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Hsp90 and cochaperones have two genetically distinct roles in regulating eEF2 function. by Melody D Fulton, Danielle J Yama, Ella Dahl, Jill L Johnson

“…Protein homeostasis relies on the accurate translation and folding of newly synthesized proteins. Eukaryotic elongation factor 2 (eEF2) promotes GTP-dependent translocation of the ribosome during translation. eEF2 folding was recently shown to be dependent on Hsp90 as well as the cochaperones Hgh1, Cns1, and Cpr7. …”
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The systemic evolutionary theory of the origin of cancer (SETOC): an update by Antonio Mazzocca, Giovanni Ferraro, Giovanni Misciagna

“…Abstract The Systemic Evolutionary Theory of the Origin of Cancer (SETOC) is a recently proposed theory founded on two primary principles: the cooperative and endosymbiotic process of cell evolution as described by Lynn Margulis, and the integration of complex systems operating in eukaryotic cells, which is a core concept in systems biology. …”
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METTL3 regulates autophagy of hypoxia-induced cardiomyocytes by targeting ATG7 by Linnan Li, Hao Cheng, Yufei Zhou, Di Zhao, Xiaoxue Zhang, Yajun Wang, Jianying Ma, Junbo Ge

“…Abstract N6-methyladenosine (m6A) mRNA modification is the most common mRNA internal modification in eukaryotes, which participates in a variety of biological processes. …”
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Structural basis of Spliced Leader RNA recognition by the Trypanosoma brucei cap-binding complex by Harald Bernhard, Hana Petržílková, Barbora Popelářová, Kamil Ziemkiewicz, Karolina Bartosik, Marcin Warmiński, Laura Tengo, Henri Gröger, Luciano G. Dolce, Cameron D. Mackereth, Ronald Micura, Jacek Jemielity, Eva Kowalinski

“…Abstract Kinetoplastids are a clade of eukaryotic protozoans that include human parasitic pathogens like trypanosomes and Leishmania species. …”
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N7-methylguanosine modification in cancers: from mechanisms to therapeutic potential by Qihui Wu, Xiaodan Fu, Guoqian Liu, Xiaoyun He, Yimin Li, Chunlin Ou

“…Abstract N7-methylguanosine (m7G) is an important RNA modification involved in epigenetic regulation that is commonly observed in both prokaryotic and eukaryotic organisms. Their influence on the synthesis and processing of messenger RNA, ribosomal RNA, and transfer RNA allows m7G modifications to affect diverse cellular, physiological, and pathological processes. m7G modifications are pivotal in human diseases, particularly cancer progression. …”
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Lack of Outer Membrane Protein A Enhances the Release of Outer Membrane Vesicles and Survival of Vibrio cholerae and Suppresses Viability of Acanthamoeba castellanii by Soni Priya Valeru, Salah Shanan, Haifa Alossimi, Amir Saeed, Gunnar Sandström, Hadi Abd

“…In conclusion, the results might highlight a regulating rule for OmpA in survival of V. cholerae and OMVs as a potent virulence factor for this bacterium towards eukaryotes in the environment.…”
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