Time-resolved assessment of single-cell protein secretion by sequencing.

Secreted proteins play critical roles in cellular communication. Methods enabling concurrent measurement of cellular protein secretion, phenotypes and transcriptomes are still unavailable. Here we describe time-resolved assessment of protein secretion from single cells by sequencing (TRAPS-seq). Released proteins are trapped onto the cell surface and probed by oligonucleotide-barcoded antibodies before being simultaneously sequenced with transcriptomes in single cells. We demonstrate that TRAPS-seq helps unravel the phenotypic and transcriptional determinants of the secretion of pleiotropic TH1 cytokines (IFNγ, IL-2 and TNF) in activated T cells. In addition, we show that TRAPS-seq can be used to track the secretion of multiple cytokines over time, uncovering unique molecular signatures that govern the dynamics of single-cell cytokine secretions. Our results revealed that early central memory T cells with CD45RA expression (TCMRA) are important in both the production and maintenance of polyfunctional cytokines. TRAPS-seq presents a unique tool for seamless integration of secretomics measurements with multi-omics profiling in single cells.

Six-orders-of-magnitude-spanning dispersion measurement via Kalman filtering-aided white-light interferometry.

Dispersion plays a great role in ultrafast laser oscillators, ultrashort pulse amplifiers, and many other nonlinear optical dynamics. Therefore, dispersion measurement is crucial for device characterization, system design and nonlinear dynamics investigation therein. In this work, we demonstrate a versatile approach, i.e., Kalman filtering-aided white-light interferometry, for group delay dispersion (GDD) characterization. Extended Kalman filter is adopted to track the cosine-like interferogram, and to eliminate the unintended bias and the envelope, providing a nearly ideal phase retrieval and GDD estimation. The measurement range could span from tens of fs2 to tens of ps2, with an uncertainty of about 0.1%, enabling precise GDD measurement for diverse optical components, ranging from a millimeter-thick glass slide to highly dispersive chirped fiber Bragg gratings. Benefited by the simplicity, convenient setup, and easy operation as well as relatively low cost, this approach would help photonic device characterization, dispersion management and nonlinear dynamics investigation in the laboratory and work plant.

An integral terminal sliding mode control scheme for speed control system using a double-variable hydraulic transformer.

In recent years, with the aggravation of energy crisis and environmental pollution, the Common Pressure Rail (CPR) system with great energy saving potential has become a research hotspot in the hydraulic research area. However, as the key component of CPR system, hydraulic transformers have the problems of low efficiency and poor control effect, which limit its practical application. The main contribution of the paper is to propose a new type of double-variable hydraulic transformer (DVHT) and address the control issue. As the displacement is adjustable, DVHT can achieve pressure regulation while maintaining the cylinder speed in the high-efficiency area. According to the system characteristics, a new control strategy is designed for the two control variables, and an adaptive integral terminal sliding mode controller is proposed to guarantee the robustness of the system. The simulation results prove the feasibility of the DVHT and show that the control method can achieve multitasking control and effectively improve the control effect.

Antibody-Oligonucleotide Conjugation Using a SPAAC Copper-Free Method Compatible with 10× Genomics' Single-Cell RNA-Seq.

Recent advances in multimodal approaches toward single-cell analyses present valuable data points that can complement standard flow cytometry data. In particular, the overlay of cell-surface proteome data with gene expression analysis presents a necessary advancement, particularly in the field of immunology. Here we describe a copper-free click chemistry method for the generation of antibody-oligonucleotide complexes and present the steps for its employment in the context of the 10× genomics droplet-based single-cell RNA-seq workflow, providing a method for coupling proteomic and transcriptomic analyses in an efficient and cost-effect manner.

Plugging High-Permeability Zones of Oil Reservoirs by Microbially Mediated Calcium Carbonate Precipitation.

Simple plugging of the high-permeability "thief zones" of oil reservoirs is the most plausible and also the most straightforwardly achievable approach to enhance sweep efficiency and oil recovery. Sporosarcina pasteurii is a representative microorganism with the ability to precipitate calcium carbonate (CaCO3) via enzymatic hydrolysis of urea in the presence of calcium ions. Microbially induced calcium carbonate precipitation (MICP) can cement and seal the granular and fractured media and thus can be used as a potential microbial plugging agent for the high-permeability zones of oil reservoirs. The following investigated the microscopic characteristics of MICP plugging and its efficacy in permeability reduction. The columns of near-spherical silica sand and angular silica sand with three separate granularities (40/60, 60/80, and 80/120 mesh) were used as artificial rock cores representing distinct pore sizes and pore characteristics to investigate the efficacy and microprocess of MICP plugging with different biotreatment periods. The results indicated that permeability is reduced significantly after only short periods of biotreatment. After eight cycles of MICP treatments, the permeability for each type of cores dropped by 54-90% of individual initial permeabilities. The measured CaCO3 content indicated that the decreasing rate in permeability with the increasing CaCO3 content experiences three contrasting stages, namely, slow decline, speedy decline, and plateauing. X-ray diffraction indicated that most of the generated CaCO3 crystals occur as vaterite with only a small amount of calcite. Imaging by scanning electron microscopy further revealed the microprocess of MICP plugging. Microorganisms first concentrate on the pore wall to secrete CaCO3, forming a thin and large uniform layer of CaCO3. Then, some nucleation sites of CaCO3 crystals will experience further preferential growth, resulting in large, dominant crystals that act as a plugging agent within the pore space. Compared to extracellular polymeric substances, which are currently the primary microbial plugging agent used to enhance sweep efficiency of oil reservoirs, bio-CaCO3 appears more effective in plugging in terms of its morphology, size, and growth characteristics.

Apolipoprotein ɛ4 is Associated with Dementia and Cognitive Impairment Predominantly Due to Alzheimer's Disease and Not with Vascular Cognitive Impairment: A Singapore-Based Cohort.

BACKGROUND AND OBJECTIVE: While the association for apolipoprotein ɛ4 allele (APOE4) with Alzheimer's disease (AD) has been consistently confirmed, the association with vascular cognitive impairment (VCI) is unclear. We therefore explored the relationship of APOE with both AD and cerebrovascular disease (CeVD) by examining the prevalence of APOE4 in AD, AD with CeVD and vascular dementia (VaD), as well as in cognitive impairment no dementia (CIND) with and without CeVD. METHODS: We performed a case-control study with subjects recruited from memory clinics and the community. All subjects underwent standardized brain neuroimaging, clinical and neuropsychological assessments, following which they were classified using research criteria. RESULTS: A total of 411 subjects; 92 controls with no cognitive impairment (NCI), 77 CIND without CeVD, 87 CIND with CeVD, 55 AD without CeVD, 68 AD with CeVD, and 32 VaD patients were recruited. Compared to NCI (16.3%), the prevalence of APOE4 carriers was significantly higher only in CIND (37.7%) and AD in the absence of CeVD (45.5%), but not in the three subgroups of VCI, namely CIND with CeVD (20.7%), AD with CeVD (27.9%) and VaD (25.0%). Logistic regression analyses also showed that APOE4 carriers were more likely to have CIND without CeVD (Odds Ratio [OR]: 3.34; 95% Confidence Interval [CI]: 1.59-7.03) and AD without CeVD (OR: 7.21; 95% CI: 2.74-18.98), but no such association was observed in the VCI subgroups. CONCLUSION: APOE4 is significantly associated with dementia and CIND due to AD pathology, but not with VCI.