Real-space Formalism for the Euler Class and Fragile Topology in Quasicrystals and Amorphous Lattices

We propose a real-space formalism of the topological Euler class, which characterizes the fragile topology of two-dimensional systems with real wave functions. This real-space description is characterized by local Euler markers whose macroscopic average coincides with the Euler number, and it applies equally well to periodic and open boundary conditions for both crystals and noncrystalline systems. We validate this by diagnosing topological phase transitions in clean and disordered crystalline systems with the reality endowed by the space-time inversion symmetry $\mathcal{I}_{ST}$. Furthermore, we demonstrated the topological Euler phases in quasicrystals and even in amorphous lattices lacking any spatial symmetries. Our work not only provides a local characterization of the fragile topology but also significantly extends its territory beyond $\mathcal{I}_{ST}$-symmetric crystalline materials.Comment: 41 pages,8 figure

EVMP: enhancing machine learning models for synthetic promoter strength prediction by Extended Vision Mutant Priority framework

IntroductionIn metabolic engineering and synthetic biology applications, promoters with appropriate strengths are critical. However, it is time-consuming and laborious to annotate promoter strength by experiments. Nowadays, constructing mutation-based synthetic promoter libraries that span multiple orders of magnitude of promoter strength is receiving increasing attention. A number of machine learning (ML) methods are applied to synthetic promoter strength prediction, but existing models are limited by the excessive proximity between synthetic promoters.MethodsIn order to enhance ML models to better predict the synthetic promoter strength, we propose EVMP(Extended Vision Mutant Priority), a universal framework which utilize mutation information more effectively. In EVMP, synthetic promoters are equivalently transformed into base promoter and corresponding k-mer mutations, which are input into BaseEncoder and VarEncoder, respectively. EVMP also provides optional data augmentation, which generates multiple copies of the data by selecting different base promoters for the same synthetic promoter.ResultsIn Trc synthetic promoter library, EVMP was applied to multiple ML models and the model effect was enhanced to varying extents, up to 61.30% (MAE), while the SOTA(state-of-the-art) record was improved by 15.25% (MAE) and 4.03% (R2). Data augmentation based on multiple base promoters further improved the model performance by 17.95% (MAE) and 7.25% (R2) compared with non-EVMP SOTA record.DiscussionIn further study, extended vision (or k-mer) is shown to be essential for EVMP. We also found that EVMP can alleviate the over-smoothing phenomenon, which may contributes to its effectiveness. Our work suggests that EVMP can highlight the mutation information of synthetic promoters and significantly improve the prediction accuracy of strength. The source code is publicly available on GitHub: https://github.com/Tiny-Snow/EVMP

Tracking hantavirus nucleocapsid protein using intracellular antibodies

<p>Abstract</p> <p>Background</p> <p>Hantavirus nucleocapsid (N) protein is a multifunctional viral macromolecule involved in multiple stages of the viral replication cycle. The intracellular trafficking of N protein during virus assembly remains unclear.</p> <p>Methods</p> <p>We used N protein-specific intracellular expressed antibodies to track the localization and distribution of Hantaan virus and Seoul virus N protein. The N protein-specific antibody single-chain variable antibody fragments (scFvs), which bind an N-terminal linear epitope (L13F3) and C-terminal conformational domain (H34), were intracellularly expressed in the endoplasmic reticulum (ER) by fusion of the SEKDEL retention signal peptide at the carboxyl terminus, and in the cytoplasm (Cyto) by deletion of the ER membrane target signal peptide. Stable Vero-E6 cell lines expressing intracellular scFvs were either infected with hantavirus or transfected with an N protein expression plasmid; virus replication and N protein intracellular localization were determined.</p> <p>Result</p> <p>N protein co-localized with scFvs in the ER and cytoplasm with or without viral membrane glycoproteins. Hantavirus replication was inhibited in both the scFvs-ER- and scFvs-Cyto-expressing stable cell lines.</p> <p>Conclusion</p> <p>N protein may be expressed in the ER retention signal peptide of KDEL circulating region (ER/<it>cis</it>-Golgi) without the assistance of G protein, and so expression of N protein in both the cytoplasm and within the ER/<it>cis</it>-Golgi plays an important role in virus replication.</p