Online Schema Evolution is (Almost) Free for Snapshot Databases

Modern database applications often change their schemas to keep up with the changing requirements. However, support for online and transactional schema evolution remains challenging in existing database systems. Specifically, prior work often takes ad hoc approaches to schema evolution with 'patches' applied to existing systems, leading to many corner cases and often incomplete functionality. Applications therefore often have to carefully schedule downtimes for schema changes, sacrificing availability. This paper presents Tesseract, a new approach to online and transactional schema evolution without the aforementioned drawbacks. We design Tesseract based on a key observation: in widely used multi-versioned database systems, schema evolution can be modeled as data modification operations that change the entire table, i.e., data-definition-as-modification (DDaM). This allows us to support schema almost 'for free' by leveraging the concurrency control protocol. By simple tweaks to existing snapshot isolation protocols, on a 40-core server we show that under a variety of workloads, Tesseract is able to provide online, transactional schema evolution without service downtime, and retain high application performance when schema evolution is in progress.Comment: To appear at Proceedings of the 2023 International Conference on Very Large Data Bases (VLDB 2023

Progress in the development of techniques based on light scattering for single nanoparticle detection

Nanoparticles have recently attracted extensive attention in view of their great potential in biomedicine and bioanalytical applications. Single particle detection via light scattering offers a simple and efficient approach for the size, size distribution, and concentration analysis of nanoparticles. In particular, intrinsic heterogeneity or rare events masked by ensemble averaging can be revealed. However, the sixth power dependence of Rayleigh scattering on particle size makes it very challenging to detect individual nanoparticles of small sizes. This article is intended to provide an overview of recent progress in the development of techniques based on light scattering for the detection of single nanoparticles.National Natural Science Foundation of China[20675070, 20975087, 90913015, 21027010]; Program for New Century Excellent Talents in University[NCET-07-0729]; Research Fund for the Doctoral Program of Higher Education of China[20090121120008, 20090121110009]; National Fund for Fostering Talents of Basic Science[J1030415

Analytical techniques for single-liposome characterization

National Natural Science Foundation of China [21225523, 20975087, 90913015, 21027010]; Program for New Century Excellent Talents in University [NCET-07-0729]; NFFTBS [J1210014]Liposomes or phospholipid vesicles are one of the most versatile nanoparticles used to convey drugs, vaccines, genes, enzymes, or other substances to target cells and as a model to mimic biological membranes. To fulfil their roles in drug delivery and biotechnology, the physical and chemical properties of liposomes, such as size, shape, chemical composition, lamellarity, encapsulation efficiency of cargo molecules, and the density of proteins reconstituted in the membrane, need to be characterized to ensure reproducible preparation of the vesicles. Compared to bulk analysis, techniques focusing on the individual analysis of liposomes can reveal heterogeneity that is otherwise masked by ensemble averaging. Herein, we review the recent advances in techniques for single-liposome characterization

Trace Detection of Specific Viable Bacteria Using Tetracysteine-Tagged Bacteriophages

National Key Basic Research Program of China [2013CB933703]; National Natural Science Foundation of China [20975087, 90913015, 21027010, 21105082, 21225523, 91313302]; Research Funds for the Doctoral Program of Higher Education of China [20090121120008, 20090121110009]; NFFTBS [J1310024]Advanced methods are urgently needed to determine the identity and viability of trace amounts of pathogenic bacteria in a short time. Existing approaches either fall short in the accurate assessment of microbial viability or lack specificity in bacterial identification. Bacteriophages (or phages for short) are viruses that exclusively infect bacterial host cells with high specificity. As phages infect and replicate only in living bacterial hosts, here we exploit the strategy of using tetracysteine (TC)-tagged phage in combination with biarsenical dye to the discriminative detection of viable target bacteria from dead target cells and other viable but nontarget bacterial cells. Using recombinant M13KE-TC phage and Escherichia colt ER2738 as a model system, distinct differentiation between individual viable target cells from dead target cells was demonstrated by flow cytometry and fluorescence microscopy. As few as 1% viable E. colt ER2738 can be accurately quantified in a mix With dead E. coil ER2738 by flow cytometry. With fluorescence microscopic measurement, specific detection of as rare as 1 cfu/mL original viable target bacteria was achieved in the presence of a large excess of dead target cells and other viable but nontarget bacterial cells in 40 mL artificially contaminated drinking water sample in less than 3 h. This TC-phage-FlAsH approach is sensitive, specific, rapid, and simple, and thus shows great potential in water safety monitoring, health surveillance, and clinical diagnosis of which trace detection and identification of viable bacterial pathogens is highly demanded

High-throughput single-cell analysis of low copy number β-galactosidase by a laboratory-built high-sensitivity flow cytometer

Single-cell analysis is vital in providing insights into the heterogeneity in molecular content and phenotypic characteristics of complex or clonal cell populations. As many essential proteins and most transcription factors are produced at a low copy number, analytical tools with superior sensitivity to enable the analysis of low abundance proteins in single cells are in high demand. β-galactosidase (β-gal) has been the standard cellular reporter for gene expression in both prokaryotic and eukaryotic cells. Here we report the development of a high-throughput method for the single-cell analysis of low copy number β-gal proteins using a laboratory-built high-sensitivity flow cytometer (HSFCM). Upon fluorescence staining with a fluorogenic substrate, quantitative measurements of the basal and near-basal expression of β-gal in single Escherichia coli BL21(DE3) cells were demonstrated. Statistical distribution can be determined quickly by analyzing thousands of individual cells in 1-2. min, which reveals the heterogeneous expression pattern that is otherwise masked by the ensemble analysis. Combined with the quantitative fluorometric assay and the rapid bacterial enumeration by HSFCM, the β-gal expression distribution profile could be converted from arbitrary fluorescence units to protein copy numbers per cell. The sensitivity and speed of the HSFCM offers great capability in quantitative analysis of low abundance proteins in single cells, which would help gaining a deeper insight into the heterogeneity and fundamental biological processes in microbial populations. ? 2013 Elsevier B.V