Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement by Jingye Cheng, Yong Jia, Camilla Hill, Tianhua He, Ke Wang, Ganggang Guo, Sergey Shabala, Meixue Zhou, Yong Han, Chengdao Li

“…Objectives: This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits. …”
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Population genetic analysis of clinical Mycobacterium abscessus complex strains in China by Xiangchen Li, Xiangchen Li, Yelei Zhu, Yewei Lu, Kunyang Wu, Yang Che, Xiaomeng Wang, Weixin Wang, Junli Gao, Junshun Gao, Zhengwei Liu, Zhengwei Liu, Zhuxian Zhou

“…BackgroundTo explore the genetic characteristics of the Mycobacterium abscessus complex (MABC) population in China, given its rising clinical importance among nontuberculous mycobacteria.MethodsWe conducted population genetic analyses on 360 MABC genomes from China, focusing on core genome multilocus sequence typing (cgMLST), pan-genome characterization, population genetics, and antimicrobial resistance gene profiling.ResultsOur analysis identified 273 M. abscessus subsp. abscessus (MabA) and 87 M. abscessus subsp. massiliense (MabM) isolates, uncovering 68 sequence types (STs), with ST5 being the most common. cgMLST classified 33.3% of isolates into six dominant circulating clones (DCCs) and 49.4% into 59 genomic clusters at a threshold of 25 different alleles, including 18 international clusters linking Chinese isolates with seven other countries. …”
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Mutational Landscape of Bone Marrow CD19 and CD138 Cells in Waldenström Macroglobulinemia (WM) and IgM Monoclonal Gammopathy of Undetermined Significance (IgM MGUS) by Alessandra Trojani, Alessandro Beghini, Luca Emanuele Bossi, Marta Rachele Stefanucci, Cassandra Palumbo, Antonino Greco, Annamaria Frustaci, Barbara Di Camillo, Roberto Cairoli

“…Interestingly, we identified new mutated genes, including WNK2 somatic mutations affecting 46% of WM/sWM patients, for which a recurrent allelic variant (V1635Ter) was observed in this cohort. …”
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Diversity in mitotic DNA repair efficiencies between commercial inbred maize lines and native Central American purple landraces by Carlos Víquez-Zamora, Sergio Castro-Pacheco, María Viñas, Pablo Bolaños-Villegas

“…Conclusions Significant differences in DNA repair efficiency exist between inbred lines and landraces of maize and may be linked to allelic diversity in key genes for homologous recombination. …”
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Ductal Carcinoma In Situ (DCIS) Diagnosed by MRI-Guided Biopsy among BRCA1/BRCA2 Mutation Carriers by Renata Faermann, Eitan Friedman, Orit Kaidar-Person, Jonathan Weidenfeld, Malka Brodsky, Anat Shalmon, Osnat Halshtok Neiman, Michael Gotlieb, Yael Yagil, David Samoocha, Dana Madorsky Feldman, Miri Sklair-Levy

“…While BRCA1/BRCA2 pathogenic sequence variants (PSVs) clearly confer an increased risk for invasive breast cancer, the extent to which these mutant alleles increase DCIS risk is less clear. Objective. …”
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Abyssinian pea (Lathyrus schaeferi Kosterin nom. nov. pro Pisum abyssinicum A. Br.) is a problematic taxon by O. E. Kosterin

“…With their karyological variability, the known accessions of the Abyssinian pea are very close to each other genetically, as they diverged just about 4000 years ago. The presence of alleles of molecular markers common with Pisum fulvum Sibth. et Smith on the one hand and P. sativum L. subsp. elatius (Bieb.) …”
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Real-time plasmid transmission detection pipeline by Natalie Scherff, Jörg Rothgänger, Thomas Weniger, Alexander Mellmann, Dag Harmsen

“…Clonal transmissions are detected using core-genome multi-locus sequence typing allelic differences. The tools MOB-suite, NCBI AMRFinderPlus, CGE MobileElementFinder, pyGenomeViz, and MUMmer, integrated in SeqSphere+, are used to characterize plasmids and for visual pairwise plasmid comparisons, respectively. …”
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Impact of inappropriate empirical antibiotic therapy on in-hospital mortality: a retrospective multicentre cohort study of patients with bloodstream infections in Chile, 2018–2022... by Emma Pitchforth, Luis Furuya-Kanamori, Laith Yakob, Anne Peters, Kasim Allel, Maria Spencer-Sandino, Jose M Munita, Eduardo A Undurraga

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Study of the association of polymorphisms of the folate cycle enzyme gene with the degree of cognitive and affective disorders in patients in the post-covid period by A.A. Shuprovych, O.V. Zinych, N.M. Kushnareva, O.M. Trofymenko, K.P. Komisarenko

“…Therefore, the use of a molecular genetic approach made it possible to pay attention to the possible predisposition to hyperhomocysteinemia in individuals who have a folic acid deficiency, and different combination of alleles of the MTHGFR gene C677T and A1298C.…”
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Genetic inbreeding load and its individual prediction for milk yield in French dairy sheep by Simona Antonios, Silvia T. Rodríguez-Ramilo, Andres Legarra, Jean-Michel Astruc, Luis Varona, Zulma G. Vitezica

“…However, these ancestors carry different alleles at potentially deleterious loci and therefore there is individual variability of this inbreeding load. …”
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Temporal Changes in Plasmodium Falciparum Genetic Diversity and Multiplicity of Infection Across Three Areas of Varying Malaria Transmission Intensities in Uganda. by Mwesigwa, Alex, Kiwuwa, Steven M., Musinguzi, Benson, Kawalya, Hakiim, Katumba, James Davis, Baguma, Andrew, Mutuku, Irene M., Adebayo, Ismail Abiola, Nsobya, Samuel L., Byakika‐Kibwika, Pauline, Kalyango, Joan N., Karamagi, Charles, Nankabirwa, Joaniter I.

“…Genetic diversity metrics, including the number of alleles and expected heterozygosity, were calculated using GENALEX and ARLEQUIN software. …”
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Systematic identification of pathogenic variants of non-small cell lung cancer in the promoters of DNA-damage repair genesResearch in context by Mingxing An, Congcong Chen, Jun Xiang, Yang Li, Pinyu Qiu, Yiru Tang, Xinyue Liu, Yayun Gu, Na Qin, Yuanlin He, Meng Zhu, Yue Jiang, Juncheng Dai, Guangfu Jin, Hongxia Ma, Cheng Wang, Zhibin Hu, Hongbing Shen

“…Findings: We identified 750 rare functional regulatory variants (frVars) that showed allelic differences in transcriptional activity within the promoter regions of DDR genes. …”
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Epitope identification of SARS-CoV-2 structural proteins using in silico approaches to obtain a conserved rational immunogenic peptide by Leonardo Pereira de Araújo, Maria Eduarda Carvalho Dias, Gislaine Cristina Scodeler, Ana de Souza Santos, Letícia Martins Soares, Patrícia Paiva Corsetti, Ana Carolina Barbosa Padovan, Nelson José de Freitas Silveira, Leonardo Augusto de Almeida

“…Afterward, each selected epitope was evaluated by molecular docking to reference MHC-I or MHC-II allelic protein sequences. Taken together, the results obtained in this study showed a rational search for a putative immunogenic peptide of SARS-CoV-2 structural proteins that can improve vaccine development using in silico approaches. …”
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Single-nucleotide polymorphisms in genes associated with the vitamin D pathway related to clinical and therapeutic outcomes of American tegumentary leishmaniasis by Iara Barreto Neves Oliveira, Ramon Vieira Nunes, Vanessa Rafaela Milhomem Cruz Leite, Camila Freire Araújo, Murilo Barros Silveira, Sebastião Alves Pinto, Lorena Andrade Lamounier, Clayton Luiz Borges, Edésio Martins, Iane de Oliveira Pires Porto, Rodrigo Saar Gomes, Fátima Ribeiro-Dias

“…The aim of this study was to evaluate single-nucleotide polymorphisms (SNPs) in the components of the vitamin D pathway and associated cytokine genes that could be related to resistance or susceptibility to American tegumentary leishmaniasis (ATL).MethodsThe expressions of IFNG, IL15, IL32, CYP27B1, VDR, and other pro-inflammatory cytokines TNF, IL6, and IL17 genes were evaluated using real-time polymerase chain reaction (qPCR) in lesions of patients with localized cutaneous leishmaniasis (LCL) or mucosal leishmaniasis (ML). SNP genotypes/alleles (in IL15, IL32, CYP27B1, and VDR) were evaluated by TaqMan PCR assays using DNA from the blood of patients and healthy individuals. …”
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Bread wheat cultivar Popo harbors QTLs for seedling and adult plant resistance to leaf rust in South African and Argentine environments by Sandiswa Figlan, Tsepiso Hlongoane, Carlos Bainotti, Pablo Campos, Leonardo Vanzetti, Gabriela Edith Tranquilli, Toi John Tsilo

“…Interestingly, both Popo and Kariega contributed with alleles for resistance. Significant loci for reducing leaf rust infection at seedling stage were designated QLr.arc-1A, QLr.arc-2B, QLr.arc-5B, QLr.arc-6A and QLr.arc-6D. …”
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Late blight resistant potato hybrid clones in the VIR collection of plant genetic resources by E. V. Rogozina, N. A. Chalaya, M. A. Kuznetsova, V. N. Demidova, A. N. Rogozin, T. I. Smetanina, M. P. Beketova, O. A. Fadina, E. Е. Khavkin

“…Selection of hybrid potato clones with high and long-term resistance to LB and identification of genotypes that can serve as the most promising sources of new LB resistance genes or new alleles of the already known resistance genes.Materials and methods. …”
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Durable benefit from immunotherapy and accompanied lupus erythematosus in pancreatic adenocarcinoma with DNA repair deficiency by Lei Zhang, Lin Lin, Hua Jin, Henghui Zhang, Juanjuan Qian, Yuli Wang, Xionghao Pang, Yi Lei, Zeqiang Zhou, Meixiang Li

“…Additionally, humanleukocyte antigen (HLA) typing assay identified two previously reported systemic lupus erythematosus risk alleles HLA-DRB1*15:01 and HLA-DQB1*06:02 in this patient.Conclusions The deleterious mutations of PALB2 closely related to homologous recombination deficiency or alterations of DNA damage response and repair genes might be promising biomarkers for predicting efficacy of immune checkpoint inhibitors in pancreatic adenocarcinoma. …”
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NanoCore: core-genome-based bacterial genomic surveillance and outbreak detection in healthcare facilities from Nanopore and Illumina data by Sebastian A. Fuchs, Lisanna Hülse, Teresa Tamayo, Susanne Kolbe-Busch, Klaus Pfeffer, Alexander T. Dilthey

“…In the Nanopore-only mode, NanoCore-based pairwise distances between closely related isolates were near-identical to Illumina-based SeqSphere+ distances, a gold standard commercial method (average differences of 0.75 and 0.81 alleles for MRSA and VRE; sd = 0.98 and 1.00), and gave an identical clustering into closely related and non-closely related isolates. …”
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The gene Sr38 for bread wheat breeding in Western Siberia by E. S. Skolotneva, V. N. Kelbin, V. P. Shamanin, N. I. Boyko, V. A. Aparina, E. A. Salina

“…The presence of the gene was postulated by genotyping with specific primers (VENTRIUP-LN2) and phytopathological tests with avirulent clones of the fungus. Dominant Sr38 alleles were identified in Lutescens 12-18, Lutescens 81-17, Lutescens 66-16, Erythrospermum 79/07, 9-31, and 8-26. …”
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Analysis on Mapping of Rice Grain Thickness QTLs under Multiple Environments by Haifeng XU, Qiang PENG, Zhongyuan CHEN, Xian WU, Chaoxin WU, Dashuang ZHANFG, Xue JIANG, Susong ZHU

“…Five grain thickness QTLs (qGT3-1, qGT5-1, qGT5-2, qGT8-1, and qGT10-1) were detected on chromosomes 3, 5, 8, and 10 in rice under the three different ecological environments. The beneficial alleles of these five QTLs were all from the parent V20B, with LOD values ranging from 3.431 to 14.081 and a range of phenotypic contribution rates from 5.479% to 26.483%. …”
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