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Effective Lysis of Cyanobacterial and Green Algal Single Cells for Whole Genome Amplification in Microfluidics

Single-cell sequencing is becoming popular for analyzing the genome of a single cell within a heterogenous cell population. It often relies on ...

Mayo Clinic

Single-cell sequencing is a powerful technology that provides the capability of analyzing a single cell within a population. This technology is mostly coupled with microfluidic systems for controlled cell manipulation and precise fluid handling to shed light on the genomes of a wide range of cells. So far, single-cell sequencing has been focused mostly on human cells due to the ease of lysing the cells for genome amplification. The major challenges that bacterial species pose to genome amplification from single cells include the rigid bacterial cell walls and the need for an effective lysis protocol compatible with microfluidic platforms. In this work, we present a lysis protocol that can be used to extract genomic DNA from both gram-positive and gram-negative species without interfering with the amplification chemistry.  was chosen as a typical gram-positive model and  sp. as a gram-negative model due to major challenges reported in previous studies. Our protocol is based on thermal and chemical lysis. We consider 80% of single-cell replicates that lead to >5 ng DNA after amplification as successful attempts. The protocol was directly applied to  sp. and the single cells of the eukaryotic  sp. and achieved a 100% success rate.

The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms.

This work presents a heterogeneous immunoassay using the integrated functionalities of a channel and droplets in a digital microfluidic (DMF) platform. Droplet functionality in DMF allows for the programmable manipulation of discrete sample and reagent droplets in the range of nanoliters. Pressure-driven channels become advantageous over droplets when sample must be washed, as the supernatant can be thoroughly removed in a convenient and rapid manner while the sample is immobilized. Herein, we demonstrate a magnetic bead-based, enzyme-linked immunosorbent assay (ELISA) using ~60 nL of human interleukin-6 (IL-6) sample. The wash buffer was introduced in the form of a wall-less virtual electrowetting channel by a syringe pump at the flow rate of 10 μL/min with ~100% bead retention rate. Critical parameters such as sample wash flow rate and bead retention rate were optimized for reliable assay results. A colorimetric readout was analyzed in the International Commission on Illumination (CIE) color space without the need for costly equipment. The concepts presented in this work are potentially applicable in rapid neonatal disease screening using a finger prick blood sample in a DMF platform.

Heterogeneous Immunoassay Using Channels and Droplets in a Digital Microfluidic Platform.

Single cell RNA sequencing is a technology that provides the capability of analyzing the transcriptome of a single cell from a population. So far, single cell RNA sequencing has been focused mostly on human cells due to the larger starting amount of RNA template for subsequent amplification. One of the major challenges of applying single cell RNA sequencing to microbial cells is to amplify the femtograms of the RNA template to obtain sufficient material for downstream sequencing with minimal contamination. To achieve this goal, efforts have been focused on multiround RNA amplification, but would introduce additional contamination and bias. In this work, we for the first time coupled a microfluidic platform with multiple displacement amplification technology to perform single cell whole transcriptome amplification and sequencing of Porphyromonas somerae, a microbe of interest in endometrial cancer, as a proof-of-concept demonstration of using single cell RNA sequencing tool to unveil gene expression heterogeneity in single microbial cells. Our results show that the bacterial single-cell gene expression regulation is distinct across different cells, supporting widespread heterogeneity.

Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity.

Whole genome sequencing is emerging as a promising tool for the untargeted detection of a broad range of microbial species for diagnosis and analysis. However, it is logistically challenging to perform the multistep process from sample preparation to DNA amplification to sequencing and analysis within a short turnaround time. To address this challenge, we developed a digital microfluidic device for rapid whole genome amplification of low-abundance bacterial DNA and compared results with conventional in-tube DNA amplification. In this work, we chose  DNA as a bacterial target for method development and optimization, as it is not a common contaminant. Sequencing was performed in a hand-held Oxford Nanopore Technologies MinION sequencer. Our results show that using an in-tube amplification approach, at least 1 pg starting DNA is needed to reach the amount required for successful sequencing within 2 h. While using a digital microfluidic device, it is possible to amplify as low as 10 fg of  DNA (equivalent to the amount of DNA within a single bacterial cell) within 2 h and to identify the target bacterium within 30 min of MinION sequencing-100× lower than the detection limit of an in-tube amplification approach. We demonstrate the detection of  DNA in a mock community DNA sample and characterize the limit of bacterial detection in the presence of human cells. This approach can be used to identify microbes with minute amounts of genetic material in samples depleted of human cells within 3 h.

Amplification of Femtograms of Bacterial DNA Within 3 h Using a Digital Microfluidics Platform for MinION Sequencing.

The Nostoc sp. strain CCCryo 231-06 is a cyanobacterial strain capable of surviving under extreme conditions and thus is of great interest for the astrobiology community. The knowledge of its complete genome sequence would serve as a guide for further studies. However, a major concern has been placed on the effects of contamination on the quality of sequencing data without a reference genome. Here, we report the use of microfluidic technology combined with single cell sequencing and  assembly to minimize the contamination and recover the complete genome of the Nostoc strain CCCryo 231-06 with high quality. 100% of the whole genome was recovered with all contaminants removed and a strongly supported phylogenetic tree. The data reported can be useful for comparative genomics for phylogenetic and taxonomic studies. The method used in this work can be applied to studies that require high-quality assemblies of genomes of unknown microorganisms.

Yuguang Liu

Department of Surgery,
Division of Surgical Research,
Department of Surgery, Division of Surgical Research

Mayo Clinic

Effective Lysis of Cyanobacterial and Green Algal Single Cells for Whole Genome Amplification in Microfluidics

Yuguang Liu

Department of Surgery,Division of Surgical Research,Department of Surgery, Division of Surgical Research

Mayo Clinic

Effective Lysis of Cyanobacterial and Green Algal Single Cells for Whole Genome Amplification in Microfluidics

Department of Surgery,
Division of Surgical Research,
Department of Surgery, Division of Surgical Research