GENOME POLITICS: STRATEGY AND TACTICS by Jonas Rubikas

“…This is clearly seen when the comparison between the information content (the gene number) and the life cycle of small genomes (plasmids, viruses, singlecellular prokaryotic organisms) is made: large space is occupied by information on replication enzymes and the sequence of replication origin. …”
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Development and evaluation of a novel E7 multi-epitopic vaccine for human papillomavirus type 16: design, expression, purification, and immunological characterization by Bahareh Bahmani, Zahra Amini-bayat, Mohammad Mehdi Ranjbar, Masoud Hassanzadeh Makoui, Amir-Hassan Zarnani

“…Methods A HPV16-E7 multi-epitopic vaccine (MEVE7) was designed to comprise potent CD4 + and CD8 + T cell epitopes and optimally expressed in a prokaryotic expression system. Polyclonal antibodies were generated, and their reactivity with immunizing antigen and native protein in E7 expressing cells (TC-1) was assessed by ELISA and immunofluorescent staining, respectively. …”
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Predicting climate-change impacts on the global glacier-fed stream microbiome by Massimo Bourquin, Hannes Peter, Grégoire Michoud, Susheel Bhanu Busi, Tyler J. Kohler, Andrew L. Robison, Mike Styllas, Leïla Ezzat, Aileen U. Geers, Matthias Huss, Stilianos Fodelianakis, The Vanishing Glaciers Field Team, Tom J. Battin

“…However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth’s major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. …”
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Involvement of the TGF-β pathway in epithelialmesenchymal transition promoted by the pulmonary microenvironment in Mycoplasma pneumoniae pneumonia by Fan Lu, Wang Huixia, Xu Nuo, Guo Yun, Li Ling

“…Mycoplasma pneumoniae (MP), one of the smallest prokaryotic microorganisms capable of independent survival, causes respiratory tract infections and various extrapulmonary diseases. …”
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Decoding the trajectory of antibiotic resistance genes in saline and alkaline soils: Insights from different fertilization regimes by Dandan Zhang, Jie Li, Guilong Zhang, Yan Xu

“…The functional gene related to salinity and alkalinity, like cysH, cysK, plsB and plsC showed negative correlations with MDR. Prokaryotic transcription assays validated these relations. …”
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Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis by Cláudia Ferreira, Ilia Burgsdorf, Tzipora Perez, Gustavo Ramírez, Maya Lalzar, Dorothée Huchon, Laura Steindler

“…Results Our analysis uncovered several differences between symbiotic and free-living bacteria, including an increased abundance of genes encoding prokaryotic defense systems (PDSs) and eukaryotic-like proteins (ELPs) in symbionts. …”
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Long-term effect of repeated application of pig slurry digestate on microbial communities in arable soils by Daniela Mora-Salguero, Lionel Ranjard, Thierry Morvan, Samuel Dequiedt, Vincent Jean-Baptiste, Sophie Sadet-Bourgeteau

“…Differential abundance analysis at the phylum level revealed few significant differences between digestate- and mineral fertilizer-treated plots for both prokaryotic and fungal communities. Only plots amended with cattle manure exhibited higher soil organic carbon content. …”
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Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC by William Boulton, Asaf Salamov, Igor V. Grigoriev, Sara Calhoun, Kurt LaButti, Robert Riley, Kerrie Barry, Allison A. Fong, Clara J. M. Hoppe, Katja Metfies, Kersten Oetjen, Sarah Lena Eggers, Oliver Müller, Jessie Gardner, Mats A. Granskog, Anders Torstensson, Marc Oggier, Aud Larsen, Gunnar Bratbak, Andrew Toseland, Richard M. Leggett, Vincent Moulton, Thomas Mock

“…This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. …”
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Expression and delivery of HA1-M2e antigen using an innovative attenuated Salmonella–mediated delivery system confers promising protection against H9N2 avian influenza challenge by Ram Prasad Aganja, In-Shik Kim, Hyun-Jin Tae, John Hwa Lee

“…This study explores a dual expression vector system for delivering prokaryotic and eukaryotic antigens to improve conventional vaccination strategies. …”
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<i>Bacillus cabrialesii</i> subsp. <i>cabrialesii</i> Strain TE5: A Promising Biological Control Bacterium Against the Causal Agent of Spot Blotch in Wheat by Ixchel Campos-Avelar, Michelle Fabiela García Jaime, Pamela Helué Morales Sandoval, Fannie Isela Parra-Cota, Sergio de los Santos Villalobos

“…Genomic annotation using Rapid Annotation Using Subsystems Technology (RAST) and Rapid Prokaryotic Genome Annotation (Prokka) indicated the presence of 4615 coding DNA sequences (CDSs) distributed across 330 subsystems, which included gene families associated with biocontrol, stress response, and iron competition. …”
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Stimulation of DC-CIK with PADI4 Protein Can Significantly Elevate the Therapeutic Efficiency in Esophageal Cancer by Chunyan Liu, Yingying Zheng, Junyi Tang, Dawei Wang, Zhenshen Ma, Shutong Li, Xiaotian Chang

“…PADI4 gene was also inserted into a prokaryotic expression vector to produce recombinant protein. …”
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Tat-fimbriae (“tafi”): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway by Anna V. Galeva, Dahe Zhao, Alexey S. Syutkin, Marina Yu Topilina, Sergei Yu Shchyogolev, Elena Yu Pavlova, Olga M. Selivanova, Igor I. Kireev, Alexey K. Surin, Gennady L. Burygin, Jingfang Liu, Hua Xiang, Mikhail G. Pyatibratov

“…To our knowledge, this is the first case that the Tat-pathway has been linked to the secretion of protein subunits forming prokaryotic filamentous structures.…”
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Metagenomic insights into the development of microbial communities of straw and leaf composts by Anastasiia K. Kimeklis, Anastasiia K. Kimeklis, Grigory V. Gladkov, Olga V. Orlova, Tatiana O. Lisina, Alexey M. Afonin, Alexey M. Afonin, Tatiana S. Aksenova, Arina A. Kichko, Alla L. Lapidus, Evgeny V. Abakumov, Evgeny V. Abakumov, Evgeny E. Andronov

“…We identified nine metagenome-assembled genomes (MAGs) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of substrate degradation. …”
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Analogs of Precambrian microbial communities formed de novo in Caucasian mineral water aquifers by Daria G. Zavarzina, Alexey A. Maslov, Alexander Y. Merkel, Nataliya A. Kharitonova, Alexandra A. Klyukina, Ekaterina I. Baranovskaya, Elena A. Baydariko, Evgeniy G. Potapov, Kseniya S. Zayulina, Andrey Y. Bychkov, Nikolay A. Chernyh, Elizaveta A. Bonch-Osmolovskaya, Sergey N. Gavrilov

“…Their structure and the metabolic traits of their prokaryotic populations were similar to those presumed to have dominated the Earth’s biosphere during several critical periods of its evolutionary history, that is, the Early Archean, the period of banded iron formations accumulation, and the Great Oxidation Event. …”
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Evaluation of twin-arginine translocation substrate proteins as potential antigen candidates for serodiagnosis of brucellosis by Yao Wu, Yao Wu, Xin Yan, Mingjun Sun, Xiaohan Guo, Jiaqi Li, Xiangxiang Sun, Xiangxiang Sun, Mengda Liu, Mengda Liu, Haobo Zhang, Haobo Zhang, Wenlong Nan, Weixing Shao, Fangkun Wang, Xiaoxu Fan, Xiaoxu Fan, Shufang Sun

“…However, the roles of these Tat substrate proteins in diagnosing brucellosis remain unclear.MethodsIn this study, ErfK, YxeI, and EntF were expressed in prokaryotic cells and utilized as diagnostic antigens. …”
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Cultivating crayfish (Procambarus clarkii) significantly enhances the quantity and diversity of soil microorganisms: evidence from the comparison of rice-wheat and rice-crayfish ro... by Hui Xu, Hui Xu, Dan Wang, Dan Wang, Dan Wang, Xuguang Li, Xuguang Li, Jiajia Li, Jiajia Li, Yu Xu, Yu Xu, Zhiqiang Xu, Zhiqiang Xu

“…Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis revealed that the dominant bacterial functions in the rice-wheat rotation model were aerobic chemoheterotrophy and chemoheterotrophy. …”
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Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys by Yanwei Wang, Yanwei Wang, Yanwei Wang, Tong Hu, Tong Hu, Kaixuan Liang, Kaixuan Liang, Shinuo Li, Shinuo Li, Qiyue Zhang, Qiyue Zhang, Qiyue Zhang, Wenqiang Li, Honglei Qu, Honglei Qu, Boying Dong, Haihua Zhang, Qiugang Ma, Qiugang Ma, Ru Jia, Shimeng Huang, Shimeng Huang

“…A PICRUSt2 functional prediction analysis indicated that carbohydrate metabolism, prokaryotic cellular communities, antimicrobial drug resistance, immune diseases, membrane transport, signal transduction, and transcription exhibited significant differences among the different intestinal segments. …”
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New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia by Luisa Caroline Ferraz Helene, Milena Serenato Klepa, Mariangela Hungria

“…Since early studies, the history of prokaryotes taxonomy has dealt with many changes driven by the development of new and more robust technologies. …”
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Bacterial diversity determination using culture-dependent and culture-independent methods by M. Ghiasian, A. Akhavan Sepahy, M.A. Amoozegar, S. Saadatmand, M. Shavandi

“…Accordingly, it seems necessary to study this phenomenon from the perspective of microbiology in order to identify prokaryotes living in this area. Prokaryotes diversity in Mud volcano has been studied by cultivation techniques, fluorescence in situ hybridization, and denaturing gradient gel electrophoresis of PCR-amplified fragments of 16S rRNA genes. …”
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Eukaryotic DNAJ/K Database: A Comprehensive Phylogenomic Analysis Platform for the DNAJ/K Family by Kyeongchae Cheong, Jaehyuk Choi, Jaeyoung Choi, Jongsun Park, Suwang Jang, Yong-Hwan Lee

“…Proteins in DNAJ/K families are ubiquitous, from prokaryotes to eukaryotes, and function as molecular chaperones. …”
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