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Real-time precise microfluidic droplets label-sequencing combined in a velocity detection sensor.

ABSTRACT: Droplets microfluidics is broadening the range of Lab on a Chip solutions that, however, still suffer from the lack of an adequate level of integration of optical detection and sensors. In fact, droplets are currently monitored by imaging techniques, mostly limited by a time-consuming data post-processing and big data storage. This work aims to overcome this weakness, presenting a fully integrated opto-microfluidic platform able to detect, label and characterize droplets without the need for imaging techniques. It consists of optical waveguides arranged in a Mach Zehnder's configuration and a microfluidic circuit both coupled in the same substrate. As a proof of concept, the work demonstrates the performances of this opto-microfluidic platform in performing a complete and simultaneous sequence labelling and identification of each single droplet, in terms of its optical properties, as well as velocity and lengths. Since the sensor is realized in lithium niobate crystals, which is also highly resistant to chemical attack and biocompatible, the future addition of multifunctional stages into the same substrate can be easily envisioned, extending the range of applicability of the final device.

SUBMITTER: Zamboni R

PROVIDER: S-EPMC8429775 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Real-time precise microfluidic droplets label-sequencing combined in a velocity detection sensor.

Zamboni R R Zaltron A A Chauvet M M Sada C C

Scientific reports 20210909 1

Droplets microfluidics is broadening the range of Lab on a Chip solutions that, however, still suffer from the lack of an adequate level of integration of optical detection and sensors. In fact, droplets are currently monitored by imaging techniques, mostly limited by a time-consuming data post-processing and big data storage. This work aims to overcome this weakness, presenting a fully integrated opto-microfluidic platform able to detect, label and characterize droplets without the need for ima ...[more]

PMID: 34504237

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Project description:UnlabelledNext-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio-generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism's biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes.ImportanceStudying whole-genome sequences has become an important aspect of biological research. The advent of next-generation sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBio-generated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome analyses to facilitate functional studies into an organism's biology.

Dataset Information

Real-time precise microfluidic droplets label-sequencing combined in a velocity detection sensor.

Publications

Real-time precise microfluidic droplets label-sequencing combined in a velocity detection sensor.

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