While a number of large consortia collect and profile several different types of microbiome and genomic time series data, very few methods exist for joint modeling of multi-omics data sets. We developed a new computational pipeline, PALM, which uses dynamic Bayesian networks (DBNs) and is designed to integrate multi-omics data from longitudinal microbiome studies.

Conventional manufacturing methods for polydimethylsiloxane (PDMS)-based microdevices require multiple steps and elements that increase cost and production time. Also, these PDMS microdevices are mostly limited to single use, and it is difficult to recover the contents inside the microchannels or perform advanced microscopy visualization due to their irreversible sealing method. Herein, we developed a novel manufacturing method based on polymethylmethacrylate (PMMA) plates adjusted using a mechanical pressure-based system. One conformation of the PMMA plate assembly system allows the reproducible manufacture of PDMS replicas, reducing the cost since a precise amount of PDMS is used, and the PDMS replicas show uniform dimensions. A second form of assembling the PMMA plates permits pressure-based sealing of the PDMS layer with a glass base. By reversibly sealing the microdevice without using plasma for bonding, we achieve chip on/off configurations, which allow the user to open and close the device and reuse it in an easy-to-use way. No deformation was observed on the structures of the PDMS microchannels when a range of 10 to 18 kPa pressure was applied using the technique. Furthermore, the functionality of the proposed system was successfully validated by the generation of microdroplets with reused microdevices via three repetitions.

Over the past few years, image analysis has emerged as a powerful tool for analyzing various cell biology parameters in an unprecedented and highly specific manner. The amount of data that is generated requires automated methods for the processing and analysis of all the resulting information. The software available so far are suitable for the processing of fluorescence and phase contrast images, but often do not provide good results from transmission light microscopy images, due to the intrinsic variation of the acquisition of images technique itself (adjustment of brightness / contrast, for instance) and the variability between image acquisition introduced by operators / equipment. In this contribution, it has been presented an image processing software, Python based image analysis for cell growth (PIACG), that is able to calculate the total area of the well occupied by cells with fusiform and rounded morphology in response to different concentrations of fetal bovine serum in microfluidic chips, from microscopy images in transmission light, in a highly efficient way.

To produce innovative biopharmaceuticals, highly flexible, adaptable, robust, and affordable bioprocess platforms for bioreactors are essential. In this article, we describe the development of a large-area microfluidic bioreactor (LM bioreactor) for mammalian cell culture that works at laminar flow and perfusion conditions. The 184 cm² 32 cisterns LM bioreactor is the largest polydimethylsiloxane (PDMS) microfluidic device fabricated by photopolymer flexographic master mold methodology, reaching a final volume of 2.8 mL. The LM bioreactor was connected to a syringe pump system for culture media perfusion, and the cells’ culture was monitored by photomicrograph imaging. CHO-ahIFN-α2b adherent cell line expressing the anti-hIFN-$a$2b recombinant scFv-Fc monoclonal antibody (mAb) for the treatment of systemic lupus erythematosus were cultured on the LM bioreactor. Cell culture and mAb production in the LM bioreactor could be sustained for 18 days. Moreover, the anti-hIFN-$a$2b produced in the LM bioreactor showed higher affinity and neutralizing antiproliferative activity compared to those mAbs produced in the control condition. We demonstrate for the first-time, a large area microfluidic bioreactor for mammalian cell culture that enables a controlled microenvironment suitable for the development of high-quality biologics with potential for therapeutic use.