homeRNA self-blood collection enables high-frequency temporal profiling of presymptomatic host immune kinetics to respiratory viral infection: a prospective cohort studyResearch in... by Fang Yun Lim, Hannah G. Lea, Ashley M. Dostie, Soo-Young Kim, Tammi L. van Neel, Grant W. Hassan, Meg G. Takezawa, Lea M. Starita, Karen N. Adams, Michael Boeckh, Joshua T. Schiffer, Ollivier Hyrien, Alpana Waghmare, Erwin Berthier, Ashleigh B. Theberge

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Sources and Transmission Routes of Carbapenem-Resistant <i>Pseudomonas aeruginosa</i>: Study Design and Methodology of the SAMPAN Study by Anneloes van Veen, Selvi N. Shahab, Amber Rijfkogel, Anne F. Voor in ’t holt, Corné H. W. Klaassen, Margreet C. Vos, Yulia Rosa Saharman, Anis Karuniawati, Silvia Zelli, Desy De Lorenzis, Giulia Menchinelli, Giulia De Angelis, Maurizio Sanguinetti, Merel Kemper, Anniek E. E. de Jong, Sima Mohammadi, Valentine Renaud, Irena Kukavica-Ibrulj, Marianne Potvin, Guillaume Q. Nguyen, Jeff Gauthier, Roger C. Levesque, Heike Schmitt, Juliëtte A. Severin

“…Additionally, samples will be taken twice from wet hospital environments and monthly from the hospitals’ (drinking) water system, hospital and municipal wastewater treatment plants, and receiving rivers. Whole-genome sequencing will be performed to characterize CRPA isolates and determine the genetic relatedness among the isolates from different reservoirs. …”
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Characterization of the Phosphotransferase from <i>Bacillus subtilis</i> 1101 That Is Responsible for the Biotransformation of Zearalenone by Yuzhuo Wu, Qiuyu Zhou, Junqiang Hu, Yunfan Shan, Jinyue Liu, Gang Wang, Yin-Won Lee, Jianrong Shi, Jianhong Xu

“…In this study, a ZEA phosphotransferase, ZPH1101, was identified from <i>Bacillus subtilis</i> 1101 using genome sequencing. The product transformed by ZPH1101 was identified as phosphorylated ZEA (ZEA-P) through LC-TOF-MS/MS analysis. …”
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Détection de différents rétrovirus chez des primates non-humains infectés par STLV-1 ou SFV et pathologie viro-induite by Jocelyn Turpin, Sandrine Alais, Ambroise Marçais, Olivier Hermine, Réjane Rua, Antoine Gessain, Romain Lacoste, Renaud Mahieux

“…Une lymphocytose associée à une charge provirale (PVL ou nombres de copies du génome viral, intégrées dans la cellule hôte) élevée et à une prolifération monoclonale de cellules infectées constituent des marqueurs de la maladie. …”
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Assessment of Antibiotic Resistance Among Isolates of <i>Klebsiella</i> spp. and <i>Raoultella</i> spp. in Wildlife and Their Environment from Portugal: A Positive Epidemiologic Ou... by Carolina Sabença, Rani de la Rivière, Paulo Barros, João Alexandre Cabral, Roberto Sargo, Luís Sousa, Maria de Lurdes Enes Dapkevicius, Filipe Silva, Filipa Lopes, Ana Carolina Abrantes, Madalena Vieira-Pinto, Manuela Caniça, Gilberto Igrejas, Carmen Torres, Patrícia Poeta

“…Extended-spectrum β-lactamase (ESBL) production was tested by the double-disc synergy test, and one ESBL-producing <i>K. pneumoniae</i> isolate was screened by PCR and whole-genome sequencing. Biofilm production was analyzed using the microtiter plate method. …”
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ENO1 promotes PDAC progression by inhibiting CD8+ T cell infiltration through upregulating PD-L1 expression via HIF-1α signaling by Aziguli Tulamaiti, Shu-Yu Xiao, Yan Yang, Musitaba Mutailifu, Xia-Qing Li, Shi-Qi Yin, Hong-Tai Ma, Hong-Fei Yao, Lin-Li Yao, Li-Peng Hu, Jun Li, Shu-Heng Jiang, Zhi-Gang Zhang, Yan-Miao Huo, Dong-Xue Li, Xue-Li Zhang

“…Under hypoxic conditions, the “Warburg effect” occurs to meet the nutrient and energy demands of rapid genome replication, remodeling the tumor microenvironment (TME) and influencing tumor immunity. α-Enolase (ENO1) is a multifunctional protein, acting as a glycolytic enzyme that catalyzes the conversion of 2-phosphoglyceric acid to phosphoenolpyruvic acid. …”
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Peptide P2 targeting Vibrio parahaemolyticus PirB toxins blocks the cytotoxic effects to shrimp Litopenaeus vannamei by Xin Zhang, Ting Chen, Chunhua Ren, Yanhong Wang, Xiao Jiang, Jiasheng Huang, Bo Ma, Boxiang Zhu, Jiayue Yin, Chaoqun Hu, Peng Luo

“…The receptor candidates for PirB were genome-wide identified and selected based on gene expression profiles, and the biological function of Lv-APN1 was confirmed through RNAi. …”
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Differentiation of high risk prostate cancer with a facile urinary exosome detection workflow by Shuai Qiu, Yue Li, Zheng Zhang, Chunchang Li, Haoyu Wang, Ao Chen, Zhi Yan, Yang Liu, Zifei Li, Hua Huang, Yi Liu, Yiqi Seow, Ruibing Chen, Jinhong Guo, Simeng Wen, Jing Tian, Hongtuan Zhang, Ranlu Liu, Gang Han, Baolong Wang, Yong Wang, Yuanjie Niu, HaiFang Yin

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Source attribution of human Campylobacter infection: a multi-country model in the European Union by Cecilie Thystrup, Maja Lykke Brinch, Clementine Henri, Lapo Mughini-Gras, Lapo Mughini-Gras, Eelco Franz, Kinga Wieczorek, Montserrat Gutierrez, Deirdre M. Prendergast, Geraldine Duffy, Catherine M. Burgess, Declan Bolton, Julio Alvarez, Julio Alvarez, Vicente Lopez-Chavarrias, Thomas Rosendal, Lurdes Clemente, Ana Amaro, Aldert L. Zomer, Katrine Grimstrup Joensen, Eva Møller Nielsen, Gaia Scavia, Magdalena Skarżyńska, Miguel Pinto, Mónica Oleastro, Wonhee Cha, Amandine Thépault, Katell Rivoal, Martine Denis, Marianne Chemaly, Tine Hald

“…The aim of this study was to predict the sources of human campylobacteriosis cases across multiple countries using available whole-genome sequencing (WGS) data and explore the impact of data availability and sample size distribution in a multi-country source attribution model.MethodsWe constructed a machine-learning model using k-mer frequency patterns as input data to predict human campylobacteriosis cases per source. …”
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Mangrove plants using deoxyribonucleic acid barcodes for enhancing biodiversity and conservation by M. Basyuni, R. Syahbana, A.B. Rangkuti, N.A. Pradisty, A. Susilowati, L.A.M. Siregar, S.S. Al Mustaniroh, A.A. Aznawi, A. Mubaraq, E.R. Ardli, S.H. Larekeng, V. Leopardas, Y. Isowa, T. Kajita

“…METHODS: This study focused on selecting the main regions where mangroves are predominantly distributed in the provinces of North Sumatra and Aceh: Percut Sei Tuan and Deli Serdang mangrove areas, Pulau Sembilan and Lubuk Kertang of Langkat mangrove areas in North Sumatra, and Langsa mangrove areas in Aceh. The genomic deoxyribonucleic acid of mangrove plants was isolated from fresh leaf material using the Geneaid genomic deoxyribonucleic acid mini kit. …”
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N6-methyladenosine RNA modification regulates the transcription of SLC7A11 through KDM6B and GATA3 to modulate ferroptosis by Haisheng Zhang, Cheng Yi, Jianing Li, Yunqing Lu, Haoran Wang, Lijun Tao, Jiawang Zhou, Yonghuang Tan, Jiexin Li, Zhuojia Chen, Gholamreza Asadikaram, Jie Cao, Jianxin Peng, Wanglin Li, Junming He, Hongsheng Wang

“…The dm6ACRISPR system was utilized for the demethylation of specific transcripts. The Cancer Genome Atlas Program (TCGA) database and immunohistochemistry validated the role of the METTL3/SLC7A11 axis in cancer progression. …”
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Global Patterns of Prostate Cancer Incidence, Aggressiveness, and Mortality in Men of African Descent by Timothy R. Rebbeck, Susan S. Devesa, Bao-Li Chang, Clareann H. Bunker, Iona Cheng, Kathleen Cooney, Rosalind Eeles, Pedro Fernandez, Veda N. Giri, Serigne M. Gueye, Christopher A. Haiman, Brian E. Henderson, Chris F. Heyns, Jennifer J. Hu, Sue Ann Ingles, William Isaacs, Mohamed Jalloh, Esther M. John, Adam S. Kibel, LaCreis R. Kidd, Penelope Layne, Robin J. Leach, Christine Neslund-Dudas, Michael N. Okobia, Elaine A. Ostrander, Jong Y. Park, Alan L. Patrick, Catherine M. Phelan, Camille Ragin, Robin A. Roberts, Benjamin A. Rybicki, Janet L. Stanford, Sara Strom, Ian M. Thompson, John Witte, Jianfeng Xu, Edward Yeboah, Ann W. Hsing, Charnita M. Zeigler-Johnson

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Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations] by Petr Danecek, Amy Hough, John Wright, Karen Ho, Nicholas J. Timpson, Sarah J. Lindsay, Davide Bonfanti, Daniel S. Malawsky, Rafaq Azad, Deborah Plowman, Sara Widaa, Gemma Shireby, Emla Fitzsimons, David Bann, Matthew E. Hurles, Hilary C. Martin, Susan M. Ring, Dan Mason, Michael A. Quail, Wei Huang, Vivek Iyer, Mahmoud Koko, Iaroslav Popov, Laurie Fabian, Gennadii Zakharov, Ruth Y. Eberhardt, Emma E. Wade, Qin Qin Huang

“…This rich source of longitudinal data, when combined with genomic data, offers the scientific community valuable insights ranging from population genetics to applications across the social sciences. …”
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Diagnostics of lung cancer by fragmentated blood circulating cell-free DNA based on machine learning methods by Ivan O. Meshkov, Alexander P. Koturgin, Pavel V. Ershov, Liubov A. Safonova, Julia A. Remizova, Valentina V. Maksyutina, Ekaterina D. Maralova, Vasilisa A. Astafieva, Alexey A. Ivashechkin, Boris D. Ignatiev, Antonida V. Makhotenko, Ekaterina A. Snigir, Valentin V. Makarov, Vladimir S. Yudin, Anton A. Keskinov, Sergey M. Yudin, Anna S. Makarova, Veronika I. Skvortsova

“…Twelve variables, describing the abundance and length distribution of cfDNA fragments within each genomic interval, and 40 variables based on the values of position-weight matrices, describing combinations of 5-bp-long terminal motifs of cfDNA fragments, were used to characterize genomic fragmentation. …”
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Clonal hematopoiesis of indeterminate potential and type 2 diabetes mellitus among patients with STEMI: from a prospective cohort study combing bidirectional Mendelian randomizatio... by Xiaoxiao Zhao, Jiannan Li, Shaodi Yan, Yu Tan, Runzhen Chen, Nan Li, Jinying Zhou, Chen Liu, Peng Zhou, Yi Chen, Hongbing Yan, Hanjun Zhao, Li Song

“…Furthermore, a two-sample bidirectional Mendelian randomization study was performed using genetic instruments from the genome-wide association study for TET2 mutation CH from the UK Biobank (UKB) (2041 cases,173,918 controls) to investigate the causal relationship with T2DM from the FinnGen consortium (65,085 cases and 335,112 controls), and vice versa. …”
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Characterisation of pregnancy-induced alterations in apolipoproteins and their associations with maternal metabolic risk factors and offspring birth outcomes: a preconception and l... by Li Chen, Karen Mei-Ling Tan, Melvin Khee-Shing Leow, Kok Hian Tan, Jerry Kok Yen Chan, Shiao-Yng Chan, Yap Seng Chong, Peter D. Gluckman, Johan G. Eriksson, Markus R. Wenk, Sartaj Ahmad Mir

“…Findings: The concentrations of ApoC-III, ApoB and ApoL1 substantially increased in pregnancy compared to preconception and postpartum. Genome-wide association studies (GWAS) identified multiple single-nucleotide polymorphisms (SNPs) associated with plasma apolipoproteins (P < 5.00E-08), including APOE-rs7412 for ApoE, LPA-rs56393506 for Apo(a), APOM-rs707921 for ApoM, ABCC4-rs117797426 for ApoJ, THSD7B-rs575613 for ApoA-II, and LOC102724443-rs140433245 for ApoA-IV. …”
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Linking obesity-associated genotype to child language development: the role of early-life neurology-related proteomics and brain myelinationResearch in context by Jian Huang, Jinyi Che, Michelle Z.L. Kee, Ai Peng Tan, Evelyn C. Law, Patricia Pelufo Silveira, Irina Pokhvisneva, Sachin Patel, Keith M. Godfrey, Lourdes Mary Daniel, Kok Hian Tan, Yap Seng Chong, Shiao-Yng Chan, Johan G. Eriksson, Dennis Wang, Jonathan Yinhao Huang

“…Interpretation: This study demonstrates the potential of examining early-life proteomics in conjunction with deep genotyping and phenotyping and provides biological insights into the shared genomic links between obesity and language development. …”
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Expression‐based machine learning models for predicting plant tissue identity by Sourabh Palande, Jeremy Arsenault, Patricia Basurto‐Lozada, Andrew Bleich, Brianna N. I. Brown, Sophia F. Buysse, Noelle A. Connors, Sikta Das Adhikari, Kara C. Dobson, Francisco Xavier Guerra‐Castillo, Maria F. Guerrero‐Carrillo, Sophia Harlow, Héctor Herrera‐Orozco, Asia T. Hightower, Paulo Izquierdo, MacKenzie Jacobs, Nicholas A. Johnson, Wendy Leuenberger, Alessandro Lopez‐Hernandez, Alicia Luckie‐Duque, Camila Martínez‐Avila, Eddy J. Mendoza‐Galindo, David Cruz Plancarte, Jenny M. Schuster, Harry Shomer, Sidney C. Sitar, Anne K. Steensma, Joanne Elise Thomson, Damián Villaseñor‐Amador, Robin Waterman, Brandon M. Webster, Madison Whyte, Sofía Zorilla‐Azcué, Beronda L. Montgomery, Aman Y. Husbands, Arjun Krishnan, Sarah Percival, Elizabeth Munch, Robert VanBuren, Daniel H. Chitwood, Alejandra Rougon‐Cardoso

“…Abstract Premise The selection of Arabidopsis as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural‐ or ecological‐based model species were rejected, in favor of building knowledge in a species that would facilitate genome‐enabled research. …”
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Stromal architecture and fibroblast subpopulations with opposing effects on outcomes in hepatocellular carcinoma by Yifei Cheng, Xiaofang Chen, Li Feng, Zhicheng Yang, Liyun Xiao, Bin Xiang, Xiaodong Wang, Dongbin Liu, Penghui Lin, Jieyi Shi, Guohe Song, Wulei Qian, Boan Zhang, Yanan Xu, Zheng Gao, Lv Chen, Yingcheng Wu, Jiaqiang Ma, Youpei Lin, Haichao Zhao, Lihua Peng, Xuebin Mao, Yang Liu, Hao Hou, Mingyu Yang, Yuan Ji, Xiaoying Wang, Jian Zhou, Xun Xu, Xiyang Liu, Wu Wei, Xiaoming Zhang, Qiang Gao, Hu Zhou, Yidi Sun, Kui Wu, Jia Fan

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Duckweed: a starch-hyperaccumulating plant under cultivation with a combination of nutrient limitation and elevated CO2 by Ling Guo, Ling Guo, Yang Fang, Songhu Wang, Yao Xiao, Yanqiang Ding, Yanling Jin, Xueping Tian, Anping Du, Zhihua Liao, Kaize He, Shuang Chen, Yonggui Zhao, Li Tan, Zhuolin Yi, Yuqing Che, Lanchai Chen, Jinmeng Li, Leyi Zhao, Peng Zhang, Zhengbiao Gu, Fangyuan Zhang, Yan Hong, Qing Zhang, Hai Zhao

“…In this study, we integrated whole-genome sequencing, epigenomics, transcriptomics, enzyme activity, and composition variation to elucidate the mechanisms of efficient starch accumulation in duckweed in terms of starch accumulation and carbon partitioning, regulation of the expression of genes in the starch metabolic pathway, and sucrose biosynthesis and transportation.Results and discussionAlthough Landoltia punctata exhibits dramatic gene family contraction, its starch content and productivity reached 72.2% (dry basis) and 10.4 g m-2 d-1, respectively, in 10 days, equivalent to a yield of 38.0 t ha-1 y-1, under nutrient limitation treatment with elevated CO2 levels. …”
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