Genome-wide identification and characterization of the NF-Y proteins in Zanthoxylum armatum by Xianzhe Zheng, Yanling Duan, Huifang Zheng, Hao Tang, Liumeng Zheng, Xiaobo Yu

“…Despite its significance, the identification and functional analysis of the NF-Y transcription factor family in Zanthoxylum armatum (Z. armatum) remains unexplored. …”
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Parity influences postpartum adaptations in the maternal gut microbiota by Zharkyn Jarmukhanov, Elizaveta Vinogradova, Nurislam Mukhanbetzhanov, Samat Kozhakhmetov, Deniza Khassenbekova, Almagul Kushugulova

“…We identified parity-specific signatures, with first-time mothers showing enrichment in Dysosmobacter welbionis, Candidatus Saccharibacteria, and Anaerotruncus species. Functional analysis revealed distinct metabolic reprogramming patterns, including increased amino acid biosynthesis and modified fermentation pathways supporting postpartum recovery. …”
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Molecular Genetic Analysis of Human Endometrial Mesenchymal Stem Cells That Survived Sublethal Heat Shock by A. E. Vinogradov, M. A. Shilina, O. V. Anatskaya, L. L. Alekseenko, I. I. Fridlyanskaya, A. Krasnenko, A. Kim, D. Korostin, V. Ilynsky, A. Elmuratov, O. Tsyganov, T. M. Grinchuk, N. N. Nikolsky

“…This study aimed to investigate the fate of eMSC-survived sublethal heat shock (SHS) with special emphasis on their genetic stability and possible malignant transformation using methods of classic and molecular karyotyping, next-generation sequencing, and transcriptome functional analysis. G-banding revealed random chromosome breakages and aneuploidy in the SHS-treated eMSC. …”
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Exploring CAZymes Differences in <i>Pediococcus acidilactici</i> Strain OM681363 and <i>Lacticaseibacillus paracasei</i> Strain ON606241 Based on Whole-Genome Sequencing by Miao Lin, Shakib Mohamed Jama, Zhiqiang Cheng, Yujie Zong, Yanjing Su, Wengboyang Liu, Li Liu

“…Despite their widespread presence in the gastrointestinal tracts of humans and animals, where they play important physiological roles, functional analysis of specific strains from particular sources requires further enrichment. …”
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Genetic background and oncogenic driver determines the genomic evolution and transcriptomics of mammary tumor metastasis by Christina R. Ross, Karol Szczepanek, Jack Sanford, Gabriel Needle, Tinghu Qiu, Larry Pearce, Maxwell P. Lee, Kent W. Hunter

“…Despite the diversity of MSCNV and MSGE, functional analysis revealed that both mechanisms converge on the modulation of key cellular processes, including immune responses, metabolism, and extracellular matrix interactions. …”
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Chemoproteogenomic stratification of the missense variant cysteinome by Heta Desai, Katrina H. Andrews, Kristina V. Bergersen, Samuel Ofori, Fengchao Yu, Flowreen Shikwana, Mark A. Arbing, Lisa M. Boatner, Miranda Villanueva, Nicholas Ung, Elaine F. Reed, Alexey I. Nesvizhskii, Keriann M. Backus

“…However, despite their ubiquity, nearly all acquired cysteines remain unidentified via chemoproteomics; identification is a critical step to enable functional analysis, including assessment of potential druggability and susceptibility to oxidation. …”
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Phenotypic divergences in a subpopulation of Mangalarga Marchador equine: May we improve the breed's definitive register? by Alan Freire, Felipe Amorim Caetano de Souza, Alex de Oliveira Ribeiro, Sarah Laguna Conceição Meirelles, Kleber Villela Araújo, José Camisão de Souza, Raquel Silva de Moura

“…In addition, their weight and 11 indexes used for functional analysis were calculated. Gait and morphology scores were provided by the Associação Brasileira dos Criadores do Cavalo Mangalarga Marchador (ABCCMM). …”
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Lactic Acid Bacteria and Yeast Fermentation to Improve the Nutritional Value of <i>Ulva rigida</i> by Marta Brandão, Diogo J. Marques, Sofia Sousa, Marília Mateus, Helena M. Pinheiro, M. Manuela R. da Fonseca, Carla Pires, Maria Leonor Nunes, António Marques, M. Teresa Cesário

“…Three types of fermentation were tested, namely, with a consortium of four lactic acid bacteria (LAB), with <i>Saccharomyces cerevisiae</i>, and with a co-culture of lactobacilli and yeast. A functional analysis of lyophilized whole-fermentation broths revealed that the yeast-fermented products had stronger antioxidant properties when compared to the LAB-fermented products. …”
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Cultivation of niche crops and prospects of eco-innovative agricultural production in Ukraine by liliia Hebryn-Baidy, Oksana Sakal, Nataliia Tretiak, Andrii Kovalenko, Halyna Shtogryn, Oleksandra Kovalyshyn, Olena Vrublevska

“…Material and methods: At the empirical and theoretical levels sets of general scientific and special methods were used for the paper purpose, in particular: structural and functional analysis, abstraction, synthesis, deduction and induction, comparison, formalization, graphic image (mapping). …”
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Transcriptome analysis of liver and ileum reveals potential regulation of long non-coding RNA in pigs with divergent feed efficiency by Zhenjian Zhao, Shujie Wang, Kai Wang, Xiang Ji, Dong Chen, Qi Shen, Yang Yu, Shendi Cui, Junge Wang, Ziyang Chen, Guoqing Tang

“…We analyzed the differential expressed lncRNAs, microRNAs (miRNAs), and messenger RNAs through target gene prediction and functional analysis. And we identified key lncRNAs and their potential regulatory genes associated with feed efficiency through the construction of competitive endogenous RNA network. …”
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A rare natural variation in TaFT-D2 underlies QTss.cas-3D associated with increased total spikelet number per spike in wheat by Hong Liu, Zhipeng Shi, Guohao Han, Jinpeng Zhang, Tiantian Gu, Jing Wang, Hanwen Yan, Lixian Xing, Lihui Li, Diaoguo An

“…This study provides a valuable gene resource and functional marker for wheat molecular breeding aimed at improving TSS and establishes a foundation for gene functional analysis of TaFT-D2.…”
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The homeodomain transcription factor VvOCP3 negatively regulates white rot resistance in grape by Zhen Zhang, Cui Chen, Changyue Jiang, Hong Lin, Yuhui Zhao, Yinshan Guo

“…Expression analysis showed that VvOCP3 expression was significantly down-regulated upon inoculation with C. diplodiella. Functional analysis with transient injection in grape berries and stable overexpression in grape calli demonstrated that VvOCP3 negatively regulates grape resistance to C. diplodiella. …”
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Multiomics analysis of Staphylococcus aureus ST239 strains resistant to virulent Herelleviridae phages by M. Kornienko, D. Bespiatykh, N. Abdraimova, R. Gorodnichev, V. Gostev, D. Boldyreva, O. Selezneva, V. Veselovsky, O. Pobeguts, I. Smirnov, G. Arapidi, K. Klimina, E. Shitikov

“…Proteomic analysis identified 184 differentially abundant proteins (41↑ 143↓) at 30 min. Functional analysis highlighted changes in the glycolysis, the tricarboxylic acid cycle, and transport systems; notable, changes were also observed in the transcription of prophage genes. …”
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miRNA-29b-1-5p mediates an antiviral activity by targeting the HBV entry receptor in human hepatocytes by Luc Gailhouste, Yutaka Furutani, Xian-Yang Qin, Shoko Higuchi, Mariko Toguchi, Kaori Yanaka, Koichi Watashi, Takaji Wakita, Soichi Kojima

“…Notably, predictive analysis identified miR-29b-1-5p as interacting with the 3ʹ-untranslated region (3ʹ-UTR) of NTCP, suggesting a post-transcriptional regulatory mechanism. Functional analysis indicated that miR-29b-1-5p directly targeted the NTCP 3ʹ-UTR, leading to significant inhibition of NTCP transcripts. …”
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Deciphering functional landscape and clinical implications of enhancer RNAs in lung adenocarcinoma by Aike Li, Liguang Zhang, Xinsheng Du, Yi Dong, Yan Guo, Jiwei Zhao, Xiuli Fang, Pingping Lin

“…Through integrated bioinformatics and experimental approaches, we identified differentially expressed eRNAs associated with LUAD progression. Functional analysis demonstrated that these eRNAs regulate critical pathways related to cell growth, division, repair, immune response, and tumor development. …”
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Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights by Caixia Liu, Huimin Wang, Zheng Wang, Lingyu Liang, Yaning Li, Duanchong Liu, Quan Lu

“…Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. …”
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Identification of a key amino acid residue in the cofactor-independent oxidase ActVA-ORF3 involved in actinorhodin biosynthesis using AlphaFold2-predicted modeling and mutational a... by Susumu Watari, Makoto Hashimoto, Kazuki Ishikawa, Takuya Kumamoto, Hideaki Kakeya, Koji Ichinose

“…The cofactor-independent oxidase ActVA-ORF3 participates in the dimerization step of ACT biosynthesis and oxidizes both monomeric and dimeric substrates. We conducted functional analysis of ActVA-ORF3 using AlphaFold2-based structural modeling, followed by mutational analysis. …”
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FRET imaging of glycoRNA on small extracellular vesicles enabling sensitive cancer diagnostics by Tingju Ren, Yingzhi Zhang, Yuxiao Tong, Qi Zhang, Tianhao Wang, Yue Wang, Chunguang Yang, Zhangrun Xu

“…The drFRET strategy provides a versatile and sensitive platform for the imaging and functional analysis of sEV glycoRNAs, with promising implications for clinical applications.…”
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Bioinformatics Approaches for Molecular Characterization of CT670 Hypothetical Protein of <em>Chlamydia pneumoniae</em> by Abu Saim Mohammad Saikat, Tazin Afrose, Umme Saoda, Kazi Nur Uddin, Mir Monir Hossain, Md. Lutful Kabir

“…We modeled and assessed the secondary and tertiary structures to understand the nature of the selected protein. Computational functional analysis predicted that the protein would be a chaperone effector. …”
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New insights into radioresistance in breast cancer identify a dual function of miR‐122 as a tumor suppressor and oncomiR by Isidro X. Perez‐Añorve, Claudia H. Gonzalez‐De la Rosa, Ernesto Soto‐Reyes, Fredy O. Beltran‐Anaya, Oscar Del Moral‐Hernandez, Marisol Salgado‐Albarran, Oscar Angeles‐Zaragoza, Juan A. Gonzalez‐Barrios, Daniel A. Landero‐Huerta, Margarita Chavez‐Saldaña, Alejandro Garcia‐Carranca, Nicolas Villegas‐Sepulveda, Elena Arechaga‐Ocampo

“…In the present study, differential expression profiling assays identified 16 deregulated miRNAs in acquired radioresistant breast cancer cells, of which miR‐122 was observed to be up‐regulated. Functional analysis revealed that miR‐122 has a role as a tumor suppressor in parental cells by decreasing survival and promoting radiosensitivity. …”
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