Rational Optimization of Raman-Activated Cell Ejection and Sequencing for Bacteria.

In Raman-activated cell ejection and sequencing (RACE-Seq), success rate and sequence coverage have generally been low for shotgun sequencing of individual post-RACE cells. Here we quantitatively evaluated the influence of cell lysis condition, nucleic acid amplification condition, and parameters of Raman measurement on RACE-Seq performance. Variations in laser energy input during Raman signal acquisition, but not duration of alkaline lysate lysis, temperature, or measurement under dry or aqueous conditions, are vital to the success of multiple displacement amplification (MDA).

Seasonal dynamics of the coastal bacterioplankton at intensive fish-farming areas of the Yellow Sea, China revealed by high-throughput sequencing.

Marine aquaculture areas are facing stressed environmental challenges, especially the degradation of coastal ecosystems. Here a coordinated time-series study was used to investigate the coastal bacterioplankton biodiversity dynamics of the Yellow Sea, China. Bacterial 16S rRNA gene sequencing revealed a temporal pattern of decreasing of diversity in summer.

Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean.

It is of great significance to understand CO fixation in the oceans. Using single cell Raman spectra (SCRS) as biochemical profiles, Raman activated cell ejection (RACE) was able to link phenotypes and genotypes of cells. Here, we show that mini-metagenomic sequences from RACE can be used as a reference to reconstruct nearly complete genomes of key functional bacteria by binning shotgun metagenomic sequencing data.

Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms.

Wider application of single-cell analysis has been limited by the lack of an easy-to-use and low-cost strategy for single-cell isolation that can be directly coupled to single-cell sequencing and single-cell cultivation, especially for small-size microbes. Herein, a facile droplet microfluidic platform was developed to dispense individual microbial cells into conventional standard containers for downstream analysis. Functional parts for cell encapsulation, droplet inspection and sorting, as well as a chip-to-tube capillary interface were integrated on one single chip with simple architecture, and control of the droplet sorting was achieved by a low-cost solenoid microvalve.

Label-free, rapid and quantitative phenotyping of stress response in E. coli via ramanome.

Rapid profiling of stress-response at single-cell resolution yet in a label-free, non-disruptive and mechanism-specific manner can lead to many new applications. We propose a single-cell-level biochemical fingerprinting approach named "ramanome", which is the collection of Single-cell Raman Spectra (SCRS) from a number of cells randomly selected from an isogenic population at a given time and condition, to rapidly and quantitatively detect and characterize stress responses of cellular population. SCRS of Escherichia coli cells are sensitive to both exposure time (eight time points) and dosage (six doses) of ethanol, with detection time as early as 5 min and discrimination rate of either factor over 80%.

Correction: Towards high-throughput microfluidic Raman-activated cell sorting.

Correction for 'Towards high-throughput microfluidic Raman-activated cell sorting' by Qiang Zhang et al., Analyst, 2015, DOI: 10.1039/c5an01074h.

Towards high-throughput microfluidic Raman-activated cell sorting.

Raman-activated cell sorting (RACS) is a promising single-cell analysis technology that is able to identify and isolate individual cells of targeted type, state or environment from an isogenic population or complex consortium of cells, in a label-free and non-invasive manner. However, compared with those widely used yet labeling-required or staining-dependent cell sorting technologies such as FACS and MACS, the weak Raman signal greatly limits the further development of the existing RACS systems to achieve higher throughput. Strategies that can tackle this bottleneck include, first, improvement of Raman-acquisition efficiency and quality based on advanced Raman spectrometers and enhanced Raman techniques; second, development of novel microfluidic devices for cell sorting followed by integration into a complete RACS system.

Effect of fiber length on carbon nanotube-induced fibrogenesis.

Given their extremely small size and light weight, carbon nanotubes (CNTs) can be readily inhaled by human lungs resulting in increased rates of pulmonary disorders, particularly fibrosis. Although the fibrogenic potential of CNTs is well established, there is a lack of consensus regarding the contribution of physicochemical attributes of CNTs on the underlying fibrotic outcome. We designed an experimentally validated in vitro fibroblast culture model aimed at investigating the effect of fiber length on single-walled CNT (SWCNT)-induced pulmonary fibrosis.

A gold@silica core-shell nanoparticle-based surface-enhanced Raman scattering biosensor for label-free glucose detection.

The gold nanostar@silica core-shell nanoparticles conjugated with glucose oxidase (GOx) enzyme molecules have been developed as the surface-enhanced Raman scattering (SERS) biosensor for label-free detection of glucose. The surface-immobilized GOx enzyme catalyzes the oxidation of glucose, producing hydrogen peroxide. Under laser excitation, the produced H2O2 molecules near the Au nanostar@silica nanoparticles generate a strong SERS signal, which is used to measure the glucose concentration.

Detection of the ovarian cancer biomarker CA-125 using chemiluminescence resonance energy transfer to graphene quantum dots.

An immunoassay has been developed for the detection of the ovarian cancer biomarker CA-125 by utilizing the chemiluminescence resonance energy transfer to graphene quantum dots. This biosensor shows a wide linear range from 0.1 U mL(-1) to 600 U mL(-1) with a limit of detection of 0.

Dual detection of cancer biomarker CA125 using absorbance and electrochemical methods.

An enzyme-linked immunoassay based on dual signal transduction mechanisms has been developed for detection of ovarian cancer biomarker CA125. The immunoassay uses a nanoelectrode array (NEA) chip and absorbance methods for the dual detection. The NEA is used to confirm the optical detection of CA125 that is carried out in a high-binding 96-well plate.

Label-free electrical discrimination of cells at normal, apoptotic and necrotic status with a microfluidic device.

As a label-free alternative of conventional flow cytometry, chip-based impedance measurement for single cell analysis has attracted increasing attentions in recent years. In this paper, we designed a T-shape microchannel and fabricated a pair of gold electrodes located horizontally on each side of the microchannel using a transfer printing method. Instant electric signals of flowing-through single cells were then detected by connecting the electrodes to a Keithley resistance and capacitance measurement system.

Air plasma assisting microcontact deprinting and printing for gold thin film and PDMS patterns.

In this paper, we present a simple method to fabricate gold film patterns and PDMS patterns by air plasma assisting microcontact deprinting and printing transfer approaches. Chemical gold plating is employed instead of conventional metal evaporation or sputtering to obtain perfect gold film both on flat and topographic PDMS chips, and complicated SAM precoating is replaced by simple air plasma treatment to activate both the surface of gold film and PDMS. In this way, large area patterns of conductive gold film and PDMS patterns could be easily obtained on the elastomeric PDMS substrate.

Molding a silver nanoparticle template on polydimethylsiloxane to efficiently capture mammalian cells.

Herein, a functional template made up of in situ synthesized silver nanoparticles (AgNPs) is prepared on polydimethylsiloxane (PDMS) for the spatial control of cell capture, where the residual Si-H groups in the PDMS matrix are used as reductants to reduce AgNO(3) for forming AgNPs. In virtue of microfluidic system, a one-dimensional array pattern of AgNPs is obtained easily. Further combining with plasma treatment, a two-dimensional array pattern of AgNPs could be achieved.

Cytosensing and evaluation of cell surface glycoprotein based on a biocompatible poly(diallydimethylammonium) doped poly(dimethylsiloxane) film.

In this paper, we constructed an interface that not only retains viability of immobilized BGC823 human gastric carcinoma cells (BGC823 cells) but also efficiently resists nonspecific adsorption of the P-glycoprotein antibody and its secondary antibody, which enabled us to sensitively detect the number of cells and P-glycoproteins on the BGC823 cell surface by the immunoassay method. Preparation of the film was quite simple and inexpensive just by spin-coating poly(dimethylsiloxane) (PDMS) doped with poly(diallydimethylammonium) (PDDA) on the surface of gold electrodes. The composite film's biocompatibility, antinonspecific adsorption ability, and the conductivity for electrochemical probe ([Fe(CN)6]3-/4-) were proved by cell culture experiments, blocking experiments, and electrochemical experiments.

Patterned Au/poly(dimethylsiloxane) substrate fabricated by chemical plating coupled with electrochemical etching for cell patterning.

In this paper, we present a novel approach for preparing patterned Au/poly(dimethylsiloxane) (PDMS) substrate. Chemical gold plating instead of conventional metal evaporation or sputtering was introduced to achieve a homogeneous gold layer on native PDMS for the first time, which possesses low-cost and simple operation. An electrochemical oxidation reaction accompanied by the coordination of gold and chloride anion was then exploited to etch gold across the region covered by electrolyte.