Chen Zhang

Event-driven acquisition for content-enriched microscopy

Juliette Griffie, Dora Mahecic, Suliana Manley, Willi Leopold Stepp, Martin Weigert, Chen Zhang

Event-driven acquisition uses neural-network-based recognition of specific biological events to trigger switching between slow and fast super-resolution imaging, enriching the capture of interesting events with high spatiotemporal resolution. A common goal of fluorescence microscopy is to collect data on specific biological events. Yet, the event-specific content that can be collected from a sample is limited, especially for rare or stochastic processes. This is due in part to photobleaching and phototoxicity, which constrain imaging speed and duration. We developed an event-driven acquisition framework, in which neural-network-based recognition of specific biological events triggers real-time control in an instant structured illumination microscope. Our setup adapts acquisitions on-the-fly by switching between a slow imaging rate while detecting the onset of events, and a fast imaging rate during their progression. Thus, we capture mitochondrial and bacterial divisions at imaging rates that match their dynamic timescales, while extending overall imaging durations. Because event-driven acquisition allows the microscope to respond specifically to complex biological events, it acquires data enriched in relevant content.

NATURE PORTFOLIO2022

Fluorescent D-Amino Acids for Super-resolution Microscopy of the Bacterial Cell Wall

Juliette Griffie, Suliana Manley, Jiangtao Qiao, Luc Reymond, Ophélie Rutschmann, Faustine Ambroisine Charline Ryckebusch, Willi Leopold Stepp, Chen Zhang

Fluorescent D-amino acids (FDAAs) have previ-ously been developed to enable in situ highlighting of locations of bacterial cell wall growth. Most bacterial cells lie at the edge of the diffraction limit of visible light; thus, resolving the precise details of peptidoglycan (PG) biosynthesis requires super-resolution micros-copy after probe incorporation. Single molecule localization microscopy (SMLM) has stringent requirements on the fluorophore photophysical properties and therefore has remained challenging in this context. Here, we report the synthesis and characterization of new FDAAs compatible with one-step labeling and SMLM imaging. We demonstrate the incorporation of our probes and their utility for visualizing PG at the nanoscale in Gram-negative, Gram-positive, and mycobacteria species. This improved FDAA toolkit will endow researchers with a nanoscale perspective on the spatial distribution of PG biosynthesis for a broad range of bacterial species.

AMER CHEMICAL SOC2022

Probing the growth and mechanical properties of Bacillus subtilis biofilms through genetic mutation strategies

Lei Wang, Chen Zhang

Bacterial communities form biofilms on various surfaces by synthesizing a cohesive and protective extracellular matrix, and these biofilms protect microorganisms against harsh environmental conditions. Bacillus subtilis is a widely used experimental species, and its biofilms are used as representative models of beneficial biofilms. Specifically, B. subtilis biofilms are known to be rich in extracellular polymeric substances (EPS) and other biopolymers such as DNA and proteins like the amyloid protein TasA and the hydrophobic protein BslA. These materials, which form an interconnected, cohesive, three-dimensional polymer network, provide the mechanical stability of biofilms and mediate their adherence to surfaces among other functional contributions. Here, we explored how genetically-encoded components specifically contribute to regulate the growth status, mechanical properties, and antibiotic resistance of B. subtilis biofilms, thereby establishing a solid empirical basis for understanding how various genetic engineering efforts are likely to affect the structure and function of biofilms. We noted discrete contributions to biofilm morphology, mechanical properties, and survival from major biofilm components such as EPS, TasA and BslA. For example, EPS plays an important role in maintaining the stability of the mechanical properties and the antibiotic resistance of biofilms, whereas BslA has a significant impact on the resolution that can be obtained for printing applications. This work provides a deeper understanding of the internal interactions of biofilm components through systematic genetic manipulations. It thus not only broadens the application prospects of beneficial biofilms, but also serves as the basis of future strategies for targeting and effectively removing harmful biofilms.

KEAI PUBLISHING LTD2022

RFID seeking: Finding a lost tag rather than only detecting its missing

Qiang Wang, Lei Xie, Jian Xu, Chen Zhang

This paper proposes a novel type of RFID application, i.e., RFID seeking. Several existing types of RFID applications such as monitoring, searching, locating/navigating, are similar with RFID seeking. However, they are either inapplicable or vulnerable for RFID seeking scenarios, in which a user is to find a lost tagged item in a blind spot, or to find a wanted item among a mass of similar ones. In this paper, detailed requirements for RFID seeking are suggested. The first secure RFID seeking protocol is proposed, meeting all the given requirements. Its security is formally verified by using the AVISPA tool. The proposed protocol is server-less, lightweight, privacy-friendly to both RFID readers and tags, and is secure against common attacks such as eavesdropping, manipulating, replaying, tracing, Denial of Service (DoS), etc.

Elsevier2014

TOA: a tag-owner-assisting RFID authentication protocol toward access control and ownership transfer

Chao Wang, Qiang Wang, Lei Xie, Chen Zhang

This paper addresses radio frequency identification (RFID) authentication and ownership transfer in offline scenarios. Four typical related works are reviewed in detail. A series of shortcomings and vulnerabilities of them are pointed out. A new RFID authentication protocol based on a novel tag-owner-assisting architecture is proposed, making a tag's owner an essential participant of the RFID authentication process. The proposed protocol is distinguished from existing works in providing ownership transfer, access control, and mutual authentication without any centralized database neither on a backend server nor in a reader. The security of the proposed protocol is verified by using automated validation of Internet security protocols and applications tool. The proposed protocol is server-less, simple, scalable, untraceable, and device-independent. These features are simultaneously achieved in a single RFID authentication protocol for the first time. Copyright (c) 2014 John Wiley & Sons, Ltd.

Wiley-Blackwell2014