ALE reveals a surprising link between [Fe-S] cluster formation, tryptophan biosynthesis and the potential regulatory protein TrpP in Corynebacterium glutamicum by Rico Zuchowski, Simone Schito, Christina Mack, Astrid Wirtz, Michael Bott, Tino Polen, Stephan Noack, Meike Baumgart

“…With external supplementation of the required metabolite, most auxotrophic strains reach wild-type level growth. …”
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Structural and regulatory determinants of flagellar motility in Rhodobacterales—the archetypal flagellum of Phaeobacter inhibens DSM 17395 by Jürgen Tomasch, Pascal Bartling, John Vollmers, Lars Wöhlbrand, Michael Jarek, Manfred Rohde, Henner Brinkmann, Heike M. Freese, Ralf Rabus, Jörn Petersen

“…Using comparative transcriptomics of ΔcckA, ΔchpT, and ΔctrA mutants of the distantly related model organisms P. inhibens and Dinoroseobacter shibae DSM 16493, we identified genes for the flagellum and cyclic di-GMP turnover as core targets of the CtrA phosphorelay and a conserved connection with quorum sensing across members of the Rhodobacterales.IMPORTANCEThe bacterial flagellum is a sophisticated nanomachine for swimming motility and rapid chemotactic response to gradients of attractants or repellents in the environment. …”
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CRISPR/dCas-mediated counter-silencing: reprogramming dCas proteins into antagonists of xenogeneic silencers by Johanna Wiechert, Biel Badia Roigé, Doris Dohmen-Olma, Hindra, Xiafei Zhang, Roberto G. Stella, Marie A. Elliot, Julia Frunzke

“…The most prominent CRISPRcosi effect was observed when targeting the CgpS nucleation site, an effect that was also seen in S. venezuelae when targeting a known Lsr2 nucleation site within the chloramphenicol biosynthesis gene cluster. …”
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A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins by Sodbo Sharapov, Anna Timoshchuk, Olga Zaytseva, Denis E. Maslov, Anna Soplenkova, Elizaveta E. Elgaeva, Evgeny S. Tiys, Massimo Mangino, Clemens Wittenbecher, Lennart Karssen, Maria Timofeeva, Arina Nostaeva, Frano Vuckovic, Irena Trbojević-Akmačić, Tamara Štambuk, Sofya Feoktistova, Nadezhda A. Potapova, Viktoria Voroshilova, Frances Williams, Dragan Primorac, Jan Van Zundert, Michel Georges, Karsten Suhre, Massimo Allegri, Nishi Chaturvedi, Malcolm Dunlop, Matthias B. Schulze, Tim Spector, Yakov A. Tsepilov, Gordan Lauc, Yurii S. Aulchenko

“…These genes are predominantly expressed in the liver and show a previously unknown genetic link between plasma protein N-glycosylation, metabolic and liver diseases, and inflammatory response. By integrating glycomics, proteomics, transcriptomics, and genomics, we provide a resource that facilitates deeper exploration of disease pathogenesis and supports the discovery of glycan-based biomarkers.…”
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Some molecular aspects of larval development in Paralithodes camtschaticus. by Alexey V Boyko, Igor Yu Dolmatov, Alexander S Girich, Sergey I Maslennikov

“…Based on our RNA-seq data and paired-end reads from 112 libraries obtained by other researchers earlier, the transcriptome assembly for P. camtschaticus that we obtained has proven to be the most complete of those reported to date. …”
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Genome‐wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy by Avinash Das Sahu, Joo S Lee, Zhiyong Wang, Gao Zhang, Ramiro Iglesias‐Bartolome, Tian Tian, Zhi Wei, Benchun Miao, Nishanth Ulhas Nair, Olga Ponomarova, Adam A Friedman, Arnaud Amzallag, Tabea Moll, Gyulnara Kasumova, Patricia Greninger, Regina K Egan, Leah J Damon, Dennie T Frederick, Livnat Jerby‐Arnon, Allon Wagner, Kuoyuan Cheng, Seung Gu Park, Welles Robinson, Kevin Gardner, Genevieve Boland, Sridhar Hannenhalli, Meenhard Herlyn, Cyril Benes, Keith Flaherty, Ji Luo, J Silvio Gutkind, Eytan Ruppin

“…Abstract Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. …”
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The miR-302 cluster-IRFs-IRF1AS axis regulates influenza A virus replication in a species-specific manner by Lingcai Zhao, Chenglin Hou, Xifeng Hu, Chenfeng Jiang, Shengmin Li, Jun Xia, Jihui Ping

“…Our findings indicate that the miR-302 cluster-IRFs axis facilitates the transcription of key hub genes and hub lncRNAs, most of which significantly inhibit influenza virus replication. …”
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Impact of aging on gene expression in human oocytes: a comparative analysis of young and older patients by Raoul Orvieto, Omri Nayshool, Louisa Cohen, Yuval Yung, Adva Aizer, Efrat Glick Saar, Dan Dominissini

“…Moreover, among these genes, LINC02087 was the most downregulated (log2FC = -7.66), while CITED2 showed the strongest upregulation (log2FC = 3.43) in young versus old oocytes. …”
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Genome-Wide Identification of the <i>DOG1</i> Gene Family in Pepper (<i>Capsicum annuum</i>) and Its Expression Profiles During Seed Germination by Zhichao Zhao, Jingbo Sun, Feng Zhang, Chunjuan Dong

“…Moreover, upon abscisic acid treatment, six <i>CaDOG1</i> genes exhibited upregulation, while in response to ethylene, four <i>CaDOG1</i> genes exhibited downregulation. …”
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Machine Learning and Experimental Validation Reveal MYH11 as a Novel Prognostic Biomarker and Therapeutic Target in Bladder Cancer by Tan Z, Chen X, Fu S, Huang Y, Li H, Gong C, Lv D, Yang C, Wang J, Ding M, Wang H

“…Interestingly, high-risk patients showed a significantly lower response to PD-L1 treatment, with higher TIDE scores. …”
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Molecular mechanisms underlying age-dependent effects of rearing system on the goose testicular development and semen quality by Shenqiang Hu, Xiaopeng Li, Enhua Qing, Junqi Wang, Qingliang Chen, Yang Song, Jiasen Chen, Jiwei Hu, Liang Li, Jiwen Wang

“…In the present study, the testicular morphological, histological, and transcriptomic responses of three goose breeds to the two dryland rearing systems (i.e., cage rearing system, CRS and net-floor mixed rearing system, MRS) were systematically analyzed and compared. …”
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Machine learning and multi-omics analysis reveal key regulators of proneural–mesenchymal transition in glioblastoma by Can Xu, Jin Yang, Huan Xiong, Xiaoteng Cui, Yuhao Zhang, Mingjun Gao, Lei He, Qiuyue Fang, Changxi Han, Wei Liu, Yangyang Wang, Jin Zhang, Ying Yuan, Zhaomu Zeng, Ruxiang Xu

“…Abstract Glioblastoma (GBM) is classified into subtypes according to the molecular expression profile; the proneural subtype has a relatively good prognosis, and the mesenchymal type is the most aggressive form with the worst prognosis. GBM undergoes proneural–mesenchymal transition (PMT) during its evolution or in response to changes in the microenvironment or therapeutic interventions. …”
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CYP1B1 knockout enhanced IFN-γ production is required but not sufficient for protection of cigarette smoke-exposed mice against lethal influenza virus infection by Wenxin Wu, Jeremy S. Alexander, J. Leland Booth, Magdalena Chlebicz, Craig A. Miller, Chao Xu, Susan Kovats, Susan Kovats, Jordan P. Metcalf, Jordan P. Metcalf, Jordan P. Metcalf

“…We used an in-vivo mouse model to assess the hypothesis that CYP1B1 modifies innate immune responses to CS and alters survival during IAV infection.MethodsWe measured CYP1B1 induction in bronchial epithelial cells in smokers and nonsmokers obtained by bronchoscopy by whole transcriptome analysis. …”
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Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley by Yi Hong, Hui Zhou, Mengna Zhang, Yuhang Zhang, Juan Zhu, Chao Lv, Baojian Guo, Feifei Wang, Qingliang Li, Jie Sun, Rugen Xu

“…HORVU.MOREX.r3.7HG0650990, a member of the disease resistance protein family (NBS‐LRR class), is the most likely candidate gene for QRym.ZN1‐7H. Enrichment analysis indicated that QRym.ZN1‐7H may be involved in signal transduction in plant innate immune response. …”
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Genome-wide identification and expression of the HB gene family during overwintering in Korla pear (Pyrus sinkiangensis) by LIU Xiaoyan, WANG Lijuan, YANG Shenghui, LUO Guanghong, ZHU Jianbo

“…Additionally, 41.94% and 54.84% of the PsHB genes contained low-temperature responsive elements (LTR) and drought-responsive elements (MBS), respectively. …”
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The transcriptional landscape of Rhizoctonia solani AG1-IA during infection of soybean as defined by RNA-seq. by Tanya R Copley, Raj Duggavathi, Suha Jabaji

“…Overall, this study provides the first insights into R. solani AG1-IA transcriptome responses to soybean invasion providing beneficial information for future targeted control methods of this successful pathogen.…”
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Menisoxoisoaporphine A, a novel oxoisoaporphine alkaloid from Menispermi Rhizoma, inhibits inflammation by targeting PDE4B by Xin Qiao, Xin Qiao, Xin Qiao, Xiaojuan Cao, Xiaojuan Cao, Xiaojuan Cao, Shuang Xu, Shuang Xu, Shuang Xu, Cunlin Wang, Cunlin Wang, Cunlin Wang, Rui Guo, Rui Guo, Rui Guo, Xiaojuan Yao, Xiaojuan Yao, Xiaojuan Yao, Qiong Zhang, Qiong Zhang, Qiong Zhang

“…BackgroundDysregulated and excessive inflammatory reactions can lead to tissue damage, which is the underlying cause of most human diseases. Menisoxoisoaporphine A (MA), a novel oxoisoaporphine alkaloid, was obtained from Menispermi Rhizoma, a traditional Chinese medicinal herb used in the treatment of inflammatory conditions in clinical practice. …”
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Identification and characterization of the tumor necrosis factor receptor superfamily in the Chinese tree shrew (Tupaia belangeri chinensis) by Zongjian Huang, Nan Shi, Zhenqiu Luo, Fangfang Chen, Xunwei Feng, Yongjing Lai, Jian Li, Xiang Yi, Wei Xia, Anzhou Tang

“…The tissue distribution and co-expression were confirmed via RT-qPCR and immunofluorescence. Evaluation of transcriptome data from 70 samples infected with six types of viruses showed that most TNFRSF genes were upregulated in tree shrew post-viral infection. …”
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Contribution of hypoxia-inducible factor 1alpha to pathogenesis of sarcomeric hypertrophic cardiomyopathy by Sarala Raj Murthi, Andreas Petry, Bachuki Shashikadze, Jan B. Stöckl, Manuel Schmid, Gianluca Santamaria, Karin Klingel, Damir Kračun, Xinpei Chen, Sabine Bauer, Joachim P. Schmitt, Florian Flenkenthaler, Josh Gorham, Christopher N. Toepfer, David Potěšil, Pavel Hruška, Zbyněk Zdráhal, Zsuzsanna Mayer, Mathieu Klop, Luisa Lehmann, Yishi Qin, Laura Papanakli, Nadine Spielmann, Alessandra Moretti, Thomas Fröhlich, Peter Ewert, Stefan Holdenrieder, Jonathan G. Seidman, Christine E. Seidman, Agnes Görlach, Cordula M. Wolf

“…Abstract Hypertrophic cardiomyopathy (HCM) caused by autosomal-dominant mutations in genes coding for structural sarcomeric proteins, is the most common inherited heart disease. HCM is associated with myocardial hypertrophy, fibrosis and ventricular dysfunction. …”
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Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia. by Niklaus Zemp, Raquel Tavares, Alex Widmer

“…Such expression differences may also underlie sex-specific responses of hosts to pathogen infections, most notably when pathogens induce partial sex reversal in infected hosts. …”
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