Multiomics identifies tumor-intrinsic SREBP1 driving immune exclusion in hepatocellular carcinoma by Jie Chen, Arjun Singh, Riyue Bao, Jason John Luke, Sarah Newman, Aatur Singhi, Carsten Krieg, Ryan Augustin, Aofei Li, Brian Isett, Rebekah E Dadey, Ruxuan Li, Jake Griner, Joseph A Manning, Satdarshan P Monga, David A A Geller, Ioannis K Zervantonakis

“…Integration of IMC and MALDI images revealed distinct lipid species differentially abundant in tumor regions with low versus high CD8+ T cell infiltration. …”
Get full text

A trans-acting sRNA SaaS targeting hilD, cheA and csgA to inhibit biofilm formation of S. Enteritidis by Chongyang Lyu, Haijing Hu, Linlin Cai, Shuwen He, Xinglian Xu, Guanghong Zhou, Huhu Wang

“…The RNA-protein pull-down and promoter–reporter β-galactosidase activity assays were employed to analyze RNA binding proteins and identify target mRNAs, respectively. …”
Get full text

The N-Terminal Region of the Transcription Factor E2F1 Contains a Novel Transactivation Domain and Recruits General Transcription Factor GTF2H2 by Lin Zhao, Rinka Nakajima, Yaxuan Zhou, Mashiro Shirasawa, Mariana Fikriyanti, Yuki Kamiya, Hiroyuki Toh, Hideyuki Komori, Ritsuko Iwanaga, Andrew P. Bradford, Hideo Nishitani, Kenta Kurayoshi, Keigo Araki, Kiyoshi Ohtani

“…Conversely, the knockdown of GTF2H2 compromised both. E2F1 binding enhanced the binding of GTF2H2 to target promoters depending on the integrity of the N-terminal region. …”
Get full text

C-Coil: A High Performance Computing Approach for Magnetostatic Circular Coil Calculations by Davor Dobrota, Lara Vrabac, Nikola Socec, Filip Vucic, Dario Bojanjac

“…While other approaches strive to reduce the number of integration directions in the six-fold integral to 2 or 4, we propose a five-fold integral with simple-to-evaluate integrands. …”
Get full text

A single donor cassette enables site-specific knock-in at either the αAmy3 or αAmy8 locus in rice cells via CRISPR/Cas9 by Desyanti Saulina Sinaga, Po-Yu Huang, Chun‑Kai Huang, Chung-An Lu, Li-Fen Huang

“…Abstract CRISPR/Cas9 gene editing is widely used to manipulate gene expression and integrate transgenes into specific target sites, making it a powerful tool for recombinant protein expression. …”
Get full text

A proteomic network approach across the ALS‐FTD disease spectrum resolves clinical phenotypes and genetic vulnerability in human brain by Mfon E Umoh, Eric B Dammer, Jingting Dai, Duc M Duong, James J Lah, Allan I Levey, Marla Gearing, Jonathan D Glass, Nicholas T Seyfried

“…Our systems‐level analysis of the brain proteome integrated both differential expression and co‐expression approaches to assess the relationship of these differences to clinical and pathological phenotypes. …”
Get full text

Network pharmacology-driven investigation of luteolin from Annona muricata as a promising multi-target inhibitor for pancreatic cancer by Shalini Mathpal, P. Priyamvada, Gayathri Ashok, Tushar Joshi, Deepanjan Saha, Ankit Mukherjee, Biraj Roy, Sudha Ramaiah, Anand Anbarasu

“…Molecular docking studies identified luteolin and kaempferol as the most effective compounds, exhibiting strong binding affinities across the hub targets, with luteolin demonstrating the lowest binding energies. …”
Get full text

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination. by Xiaomin Dong, Kenian Chen, Raquel Cuevas-Diaz Duran, Yanan You, Steven A Sloan, Ye Zhang, Shan Zong, Qilin Cao, Ben A Barres, Jia Qian Wu

“…We performed motif searches in ENCODE DNase I digital footprint data and Mouse ENCODE promoters to infer transcription factor (TF) occupancy. By integrating TF binding and cell-type specific transcriptomic data, we constructed a novel framework that is useful for systematically identifying lncRNAs that are potentially essential for brain cell fate determination. …”
Get full text

Hydroxyethylamine based analog targets microtubule assembly: an in silico study for anti-cancerous drug development by Pawan Kumar, Rajni Khan, Basant Narain Singh, Anisha Kumari, Ankit Rai, Anil Kumar Singh, Amresh Prakash, Shashikant Ray

Get full text

Decoding the FSHR gene: a multi-tool computational approach to SNPs with potential application in PCOS by Dolly J. Patel, Kinnari N. Mistry

Get full text

Structural mechanisms behind the neutralisation of long-chain α-neurotoxins by broadly neutralising VHHs discovered using a consensus antigen by Anna Damsbo, Nick J. Burlet, Monica L. Fernández-Quintero, Melisa Benard-Valle, Max D. Overath, Alid Guadarrama-Martínez, Anneline Vlamynck, Ida Bisbo, Cesar Villalobos, Tulika Tulika, Alejandro Alagón, Johannes R. Loeffler, Andrew B. Ward, Kim Boddum, Jens Preben Morth, Esperanza Rivera-de-Torre, Andreas H. Laustsen

Get full text

Exploring shared therapeutic targets for Alzheimer’s disease and glioblastoma using network pharmacology and protein-protein interaction approach by Sushma Pradeep, Sushma Pradeep, M. R. Sai Chakith, S. R. Sindhushree, Pruthvish Reddy, Esther Sushmitha, Madhusudan N. Purohit, Divya Suresh, Nanjunda Swamy Shivananju, Ekaterina Silina, Natalia Manturova, Victor Stupin, Shiva Prasad Kollur, Chandan Shivamallu, Raghu Ram Achar

“…Luteolin exhibited the highest binding affinity to IL6 (−7.8 kcal/mol), forming stable hydrogen bonds and hydrophobic interactions. …”
Get full text

Modeling SMAD2 Mutations in Induced Pluripotent Stem Cells Provides Insights Into Cardiovascular Disease Pathogenesis by Tarsha Ward, Sarah U. Morton, Gabriela Venturini, Warren Tai, Min Young Jang, Joshua Gorham, Dan Delaughter, Lauren K. Wasson, Zahra Khazal, Jason Homsy, Bruce D. Gelb, Wendy K. Chung, Benoit G. Bruneau, Martina Brueckner, Martin Tristani‐Firouzi, Steven R. DePalma, Christine Seidman, J. G. Seidman

“…Background SMAD2 is a coregulator that binds a variety of transcription factors in human development. …”
Get full text

Mechanistic Role of the Mdm2/MdmX Lid Domain in Regulating Their Interactions with p53 by Qiuyin Wei, Chenqi Li, Yibing Tang, Jinping Bai, Wang Li, Jidong Liu, Zhengding Su, Xiyao Cheng

“…p53 functions as a critical guardian of the genome, orchestrating tumor suppression pathways and ensuring the integrity of chromosomal stability. Mdm2 and MdmX, homologous proteins, serve as negative feedback regulators of p53. …”
Get full text

Shared mechanisms of enhanced plasmid maintenance and antibiotic tolerance mediated by the VapBC toxin:antitoxin system by Sarah Hollingshead, Gareth McVicker, Maria R. Nielsen, YuGeng Zhang, Giulia Pilla, Rebekah A. Jones, Jonathan C. Thomas, Sarah E. H. Johansen, Rachel M. Exley, Ditlev E. Brodersen, Christoph M. Tang

“…Of note, mutations that confer tolerance to antibiotics in Escherichia coli also map to the DNA-binding domain of VapBC encoded by the chromosomally integrated F plasmid. …”
Get full text

Non-targeted metabolomics and network pharmacology of Taohong Siwu Decoction in hepatic fibrosis mouse model using high resolution mass spectrometry by Shengsheng Li, Shengsheng Li, Shenglan Qi, Rongsheng Li, Fangming Yang, Zhenyi Niu, Wei Liu, Suping Ma, Zhun Xiao

“…Molecular docking and molecular dynamics simulations revealed that 3-hydroxy-4-methoxycinnamic acid binds stably to the core target PPARG, exhibiting a binding free energy of −93.68 kJ/mol. …”
Get full text

Axonal RNA localization is essential for long-term memory by Bruna R. de Queiroz, Hiba Laghrissi, Seetha Rajeev, Lauren Blot, Fabienne De Graeve, Marine Dehecq, Martina Hallegger, Ugur Dag, Marion Dunoyer de Segonzac, Mirana Ramialison, Chantal Cazevieille, Krystyna Keleman, Jernej Ule, Arnaud Hubstenberger, Florence Besse

“…Here, we combined synaptosome RNA profiling with whole brain high-resolution imaging to uncover mRNAs with different localization patterns in the axons of Drosophila Mushroom Body memory neurons, some exhibiting regionalized, input-dependent, recruitment along axons. By integrating transcriptome-wide binding approaches and functional assays, we show that the conserved Imp RNA binding protein controls the transport of mRNAs to Mushroom Body axons and characterize a mutant in which this transport is selectively impaired. …”
Get full text

Identification of nanomolar adenosine A2A receptor ligands using reinforcement learning and structure-based drug design by Morgan Thomas, Pierre G. Matricon, Robert J. Gillespie, Maja Napiórkowska, Hannah Neale, Jonathan S. Mason, Jason Brown, Kaan Harwood, Charlotte Fieldhouse, Nigel A. Swain, Tian Geng, Noel M. O’Boyle, Francesca Deflorian, Andreas Bender, Chris de Graaf

“…Experimental validation demonstrates a binding hit rate of 88%, with 50% having confirmed functional activity, including three nanomolar ligands and two novel chemotypes. …”
Get full text

Anti-obesity functions of fucoidan conducted by bioinformatics and validation findings targeting of autophagy by Jinkai Li, Xiaowei Wan, Yonghang Li, Ping Wang, Jian Chen, Weihua Jin, Jiaqi Liu

Get full text

CRISPR/Cas13 sgRNA‐Mediated RNA–RNA Interaction Mapping in Live Cells with APOBEC RNA Editing by Li‐Ting Diao, Shu‐Juan Xie, Wan‐Yi Xu, Hai‐Hui Zhang, Ya‐Rui Hou, Yan‐Xia Hu, Xin‐Xiang Liang, Jun‐Bin Liang, Qi Zhang, Zhen‐Dong Xiao

“…Abstract Current research on long non‐coding RNA (lncRNA) has predominantly focused on identifying their protein partners and genomic binding sites, leaving their RNA partners largely unknown. …”
Get full text