TALome and phenotypic analysis of Pakistani Xanthomonas oryzae pv. oryzae population revealed novel virulent TALEs contributing to bacterial blight of rice by Syed Mashab Ali Shah, Rafia Ahsan, Linlin Liu, Ying Li, Qi Wang, Yong Wang, Jiali Yan, Moein Khojasteh, Xiameng Xu, Zhengyin Xu, Awais Rasheed, Muhammad Zakria, Gongyou Chen

“…In this study, 101 Xoo strains were screened using specific PCR primers. The genomic DNA from these strains underwent BamHI digestion and hybridized with the internal SphI fragment of PthXo1. …”
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Possible scenarios for the spread of mpox outside the endemic focus in Africa by Eskild Petersen, Ulrik Hvid, Oyewale Tomori, Anders Gorm Pedersen, Jacco Wallinga, Richard Pebody, Orlando Cenciarelli, Preben Aavitsland, David Van Laeken, Viggo Andreasen, Uffe Schneider, Julia Kinane Simonsen, Marlies Jilles Francine Goedknegt, Caroline Klint Johannesen, Jens D. Lundgren, Anders Koch, Bolette Søborg, Anna Mia Ekström, Hannah Nohynek, Frank M. Aarestrup, Tyra G. Krause, Lone Simonsen

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Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus by Gang Wang, Yuanyuan Wang, Lianfu Chen, Hongbo Wang, Lin Guo, Xuan Zhou, Meijie Dou, Baiyu Wang, Jingxian Lin, Lei Liu, Zhengchao Wang, Youjin Deng, Jisen Zhang

“…Together, our study provides insights into the genomic basis of mating compatibility in H. marmoreus.…”
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Quantitative proteomic analysis unveils a critical role of VARS1 in hepatocellular carcinoma aggressiveness through the modulation of MAGI1 expression by Natalia Hermán-Sánchez, Mercedes del Rio-Moreno, Rubén Ciria, Marina E. Sánchez-Frias, Maite G. Fernández-Barrena, Iker Uriarte, Eduardo Chicano-Galvez, Ignacio Ortea, Ángela Peralbo-Molina, Javier Briceño, Matías A. Avila, Manuel Rodríguez-Perálvarez, Raúl M. Luque, Juan L. López-Cánovas, Manuel D. Gahete

“…Patients with ARSs upregulation had genomic/transcriptomic characteristics of the proliferative HCC. …”
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Germline BRCA testing in Denmark following invasive breast cancer: Progress since 2000 by Aleksandar M. Kostov, Maj-Britt Jensen, Bent Ejlertsen, Mads Thomassen, Caroline Maria Rossing, Inge S. Pedersen, Annabeth H. Petersen, Lise Lotte Christensen, Karin A.W. Wadt, Anne-Vibeke Lænkholm

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scCamAge: A context-aware prediction engine for cellular age, aging-associated bioactivities, and morphometrics by Vishakha Gautam, Subhadeep Duari, Saveena Solanki, Mudit Gupta, Aayushi Mittal, Sakshi Arora, Anmol Aggarwal, Anmol Kumar Sharma, Sarthak Tyagi, Rathod Kunal Pankajbhai, Arushi Sharma, Sonam Chauhan, Shiva Satija, Suvendu Kumar, Sanjay Kumar Mohanty, Juhi Tayal, Nilesh Kumar Dixit, Debarka Sengupta, Anurag Mehta, Gaurav Ahuja

“…We present scCamAge, an advanced context-aware multimodal prediction engine that co-leverages image-based cellular spatiotemporal features at single-cell resolution alongside cellular morphometrics and aging-associated bioactivities such as genomic instability, mitochondrial dysfunction, vacuolar dynamics, reactive oxygen species levels, and epigenetic and proteasomal dysfunctions. scCamAge employed heterogeneous datasets comprising ∼1 million single yeast cells and was validated using pro-longevity drugs, genetic mutants, and stress-induced models. scCamAge also predicted a pro-longevity response in yeast cells under iterative thermal stress, confirmed using integrative omics analyses. …”
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Characterization of CO1 and 18S rDNA genes from Indonesian native ornamental shrimp Caridina boehmei cultured in Jakarta by Ekky Ilham Romadhona, Novi Megawati, Handang Widantara, Sutanti Sutanti, Arif Rahman Ardiansyah, Kiki Mariya Dewi, Annisa Fitri Larassagita, Aditia Firman, Moh Risky, Rahmat Rahmat, Ayub Ayub

“…The 654 bp partial coding sequence (cds) of the CO1 and 380 bp partial cds of 18S rDNA have been successfully amplified from genomic DNA. The CO1 sequencing produced fragments consisting of 25.84% adenine, 20.95% cytosine, 19.11% guanine, and 34.10% thymine. …”
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Proteogenomic annotation of T6SS components identified in Bacteroides fragilis secretome by Natalya B. Zakharzhevskaya, Olga Yu Shagaleeva, Daria A. Kashatnikova, Daria A. Kashatnikova, Anton O. Goncharov, Anton O. Goncharov, Daria V. Evsyutina, Dmitry A. Kardonsky, Elizaveta A. Vorobeva, Artemiy S. Silantiev, Viktoria D. Kazakova, Irina V. Kolesnikova, Ivan O. Butenko, Anna A. Vanyushkina, Svetlana V. Smirnova, Andrei V. Chaplin, Andrei V. Chaplin, Boris A. Efimov, Boris A. Efimov

“…Proteogenomic annotation and comparative genomic study of the T6SS loci of the toxigenic Bf BOB25 were carried out by comparison with the reference genomes of the following Bf strains: JIM10, NCTC 9343 and 638R.ResultsAccording to the data obtained, T6SS components were represented in all types of the analysed samples. …”
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Genetic and Molecular Characterization of Avian Influenza A(H9N2) Viruses from Live Bird Markets (LBM) in Senegal by Mamadou Malado Jallow, Moussa Moise Diagne, Marie Henriette Dior Ndione, Mamadou Aliou Barry, Ndiendé Koba Ndiaye, Davy Evrard Kiori, Marie Pedapa Mendy, Déborah Goudiaby, Gamou Fall, Malick Fall, Ndongo Dia

“…Among these, A/H9N2 was the only subtype detected in both markets, with a detection rate of 47.7% (82/172) in Thiaroye and 35.3% (42/119) in Tilene, resulting in an overall positivity rate of 42.6% (124/291). Genome sequencing of 22 A/H9N2 isolates, including 11 poultry drinking water samples, 7 carcass wash water samples, 3 fecal samples, and 1 cloacal swab, yielded 7 complete and 15 partial genomic sequences. …”
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Mechanisms of blaIMP-4 dissemination across diverse carbapenem-resistant clinical isolates by Ying Fu, Faye C. Morris, Stephanie C. Pereira, Xenia Kostoulias, Yan Jiang, Callum Vidor, Galain Williams, Yogi Srikhanta, Nenad Macesic, Yunsong Yu, Dena Lyras, Anton Y. Peleg

“…Sequence homology was observed across all plasmids at the blaIMP-4 location, termed Region I, with IS26 on IncHI2A, and IS5075 and Tn3 resistance gene cassettes present on IncC plasmids. Genomic rearrangements mediated by IS26 or Tn3 and IS5075 were identified in Region I of plasmids from the same Inc type. …”
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<i>ACE</i> I/D Genotype and Risk of Non-Contact Injury in Moroccan Elite Athletes: A Pilot Study by El Mokhtar El Ouali, Jihan Kartibou, Juan Del Coso, Rashmi Supriya, Ismail Laher, Zineb El Kettani, Hassan Ghazal, Najib Al Idrissi, Ayoub Saeidi, Abdelhalem Mesfioui, Hassane Zouhal

“…<i>ACE</i> I/D polymorphism genotyping was performed by polymerase chain reaction (PCR) using genomic DNA from blood samples. <i>Results:</i> There were four cyclists (21.05%) and eight field hockey players (33.33%) with a non-contact injury during the season. …”
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Molecular Phylogenetics and Estimation of Evolutionary Divergence and Biogeography of the Family Cordycipitaceae (Ascomycota, Hypocreales) by Huili Pu, Jiao Yang, Nemat O. Keyhani, Lixia Yang, Minhai Zheng, Chenghao Qiu, Yuchen Mao, Junya Shang, Yongsheng Lin, Chengjie Xiong, Longbing Lin, Pengyu Lai, Yanbin Huang, Xin Yuan, Huiling Liang, Longfei Fan, Xiaoli Ma, Chunjin Qiu, Junzhi Qiu

“…Based on Bayesian evolutionary analysis of five genomic loci(the small subunit of ribosomal RNA (SSU) gene, the large subunit of ribosomal RNA (LSU) gene, the translation elongation factor 1-α (<i>tef1-α</i>) gene, the largest subunit of RNA polymerase II (<i>rpb1</i>), and the second largest subunit of RNA polymerase II (<i>rpb2</i>), we inferred the divergence times for members of the Cordycipitaceae, improving the internal phylogeny of this fungal family. …”
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Preparedness, prevention and control related to zoonotic avian influenza by EFSA Panel on Animal Health and Animal Welfare (AHAW), ECDC, Julio Alvarez, Anette Boklund, Sabine Dippel, Fernanda Dórea, Jordi Figuerola, Mette S. Herskin, Virginie Michel, Miguel Ángel Miranda Chueca, Eleonora Nannoni, Søren Saxmose Nielsen, Romolo Nonno, Anja B. Riber, Jan Arend Stegeman, Karl Ståhl, Hans‐Hermann Thulke, Frank Tuyttens, Christoph Winckler, Claire Brugerolles, Thorsten Wolff, Anna Parys, Erika Lindh, Neus Latorre‐Margalef, Marie‐Anne Rameix Welti, Ralf Dürrwald, Ramona Trebbien, Sylvie Van der Werf, Magnus Gisslén, Isabella Monne, Alice Fusaro, Claire Guinat, Alessio Bortolami, Leonidas Alexakis, Theresa Enkirch, Olov Svartstrom, Katriina Willgert, Francesca Baldinelli, Ludovica Preite, Malin Grant, Alessandro Broglia, Angeliki Melidou

“…Comprehensive surveillance of AIVs targeting adaptive mutations with whole genome sequencing in animals and humans is essential for early detection of zoonotic AIVs and efficient implementation of control measures. …”
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Co-Infection of <i>Culex tarsalis</i> Mosquitoes with Rift Valley Fever Phlebovirus Strains Results in Efficient Viral Reassortment by Emma K. Harris, Velmurugan Balaraman, Cassidy C. Keating, Chester McDowell, J. Brian Kimble, Alina De La Mota-Peynado, Erin M. Borland, Barbara Graham, William C. Wilson, Juergen A. Richt, Rebekah C. Kading, Natasha N. Gaudreault

“…Furthermore, we observed preferential inclusion of genomic segments from the three parental strains among the reassorted viruses. …”
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Prophylactic phage administration provides a time window for delayed treatment of vancomycin-resistant Enterococcus faecalis in a murine bacteremia model by Wei-Xiao Wang, Jiao-Yang Yu, Xiu-Zhen Chen, Xiu-Zhen Chen, Shi-Yong Fu, Hui Li, Peng-Cheng Yi, Yun-Yao Ren, Shuang-Lin Gu, Jing-Han Gao, Jing Fan, Yan-Mei Sun, Jie Feng, Shi-Wei Wang, Wei Chen, Wei Chen

“…However, critical gaps remain regarding optimal dosing, therapeutic design, and treatment timing for phage therapy targeting VRE-induced bacteremia.MethodsThe biological and genomic characteristics of a novel lytic phage specific to VRE were investigated. …”
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Tumor mutational burden and survival on immune checkpoint inhibition in >8000 patients across 24 cancer types by Vivek Subbiah, Samuel J Klempner, Neeraj Agarwal, David P Carbone, Amit Mahipal, Shilpa Gupta, David Fabrizio, Jeffrey S Ross, Gerald Li, David R Gandara, Miles C Andrews, Jonathan W Riess, Ramez N Eskander, Ryon P Graf, Geoffrey R Oxnard, Sarah Sammons, Jeremy Snider, Lilia Bouzit, Cheryl Cho-Phan, Megan Price, Julia C F Quintanilha, Richard Sheng Poe Huang

“…Deidentified data from electronic health records from approximately 280 cancer treatment facilities were captured into a clinico-genomic database. This study used the TMB algorithm from the FDA-approved test supporting solid tumor CDx and composite mortality variable validated against the national death index: real-world overall survival (rwOS). …”
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The First Large Identification of 3ANX and NX Producing Isolates of <i>Fusarium graminearum</i> in Manitoba, Western Canada by Maria Antonia Henriquez, Srinivas Sura, Sean Walkowiak, David Kaminski, Anne Kirk, Mark W. Sumarah, Parthasarathy Santhanam, Nina Kepeshchuk, Jules Carlson, E. RoTimi Ojo, Pam de Rocquigny, Holly Derksen

“…Using the same rice culture, genomic DNA was isolated, and the <i>Tri1</i> coding sequence along with its flanking regions (upstream and downstream of the <i>Tri1</i> gene) was amplified and sequenced. …”
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LRRK2 Mutations and Asian Disease-Associated Variants in the First Parkinson’s Disease Cohort from Kazakhstan by Rauan Kaiyrzhanov, Akbota Aitkulova, Chingiz Shashkin, Nazira Zharkinbekova, Mie Rizig, Elena Zholdybayeva, Zharkyn Jarmukhanov, Vadim Akhmetzhanov, Gulnaz Kaishibayeva, Talgat Khaibullin, Altynay Karimova, Serik Akshulakov, Askhat Bralov, Nurlan Kissamedenov, Zhanar Seidinova, Anjela Taskinbayeva, Aliya Muratbaikyzy, Henry Houlden

“…Methods. 246 PD patients were consecutively recruited by movement disorder specialists from four medical centers in Kazakhstan, and clinicodemographic data and genomic DNA from blood were systematically obtained and shipped to the Institute of Neurology University College London together with DNAs from 200 healthy controls. …”
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Identification of strengths and weaknesses of the healthcare system for persons living with rare diseases in Catalonia (Spain), and recommendations to improve its comprehensive att... by José Hernández-Rodríguez, Fernando Martínez-Valle, Xènia Acebes, Carmen Alerany, Jordi Antón, Gonzalo Calvo, Marian Corral, Jordi Cruz, M. Antònia Mangues-Bafalluy, José Mateo, Josefa Rivera, Albert Salazar, Roser Francisco, Cristina Mallol, Rita Reig-Viader, Ariadna Tigri-Santiña, Assumpta Ricart, Francesc Palau

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Dissection of the genetic loci for grain hardness and variation of the key genes in common wheat (Triticum aestivum L.) by Jinna Hou, Pengge Sun, Pei Yan, Shenghui Geng, Wenxu Li, Maomao Qin, Ziju Dai, Baoming Tian, Zhengqing Wu, Zhengfu Zhou, Changwen Li, Zhensheng Lei

“…The genetic loci associated with GHI were dissected based on a high-throughput SNPs map through genome-wide association study (GWAS). Finally, eight QTL, which explained 8.29 % – 14.59 % of the phenotypic variation, were revealed on chromosomes 1 A, 1B, 3 A, 3B, 5 A, 5B and 5D (2). …”
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