The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large collections of phylogenetic trees. Here, we present the third version of PhylomeDB ( http://phylomeDB.org ), a public database for genome-wide collections of gene phylogenies (phylomes). Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416 093 trees and 165 840 alignments. It is also a major source for phylogeny-based orthology and paralogy predictions, covering about 5 million proteins in 717 fully-sequenced genomes. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. The new version of phylomeDB has been extended with novel data access and visualization features, including the possibility of programmatic access. Available seed species include model organisms such as human, yeast, Escherichia coli or Arabidopsis thaliana , but also alternative model species such as the human pathogen Candida albicans , or the pea aphid Acyrtosiphon pisum . Finally, PhylomeDB is currently being used by several genome sequencing projects that couple the genome annotation process with the reconstruction of the corresponding phylome, a strategy that provides relevant evolutionary insights.

Enzymatic luminescent systems are a promising tool for rapid detection of heavy metals ions for water quality assessment. Nevertheless, their widespread use is limited by the lack of test procedure automation and available sensitive handheld luminometers. Herein we describe integration of disposable microfluidic chips for bioluminescent enzyme-inhibition based assay with a handheld luminometer, which detection system is based on a thermally stabilized silicon photomultiplier (SiPM). Microfluidic chips were made of poly(methyl methacrylate) by micro-milling method and sealed using a solvent bonding technique. The composition of the bioluminescent system in microfluidic chip was optimized to achieve higher luminescence intensity and storage time. Results indicate that developed device provided comparable sensitivity with bench-scale PMT-based commercial luminometers. Limit of detection for copper (II) sulfate reached 2.5 mg/L for developed biosensor. Hereby we proved the concept of handheld enzymatic optical biosensors with disposable chips for bioassay. The proposed biosensor can be used as an early warning field-deployable system for rapid detection of heavy metals salts and other toxic chemicals, which affect bioluminescent signal of enzymatic reaction.

The essential advantages of microfluidic studies are the excellent visualization of the processes of oil displacement from the porous medium model, simple cleaning, and the possibility of the repeated use of the microfluidic chip. The present article deals with the process of oil displacement by suspension flooding using a microfluidic chip, simulating a porous medium, and the suspensions of silicon dioxide nanoparticles (22 nm). The mass concentration of nanoparticles in suspensions ranged from 0.1 to 2 wt%. Five mass concentrations (0.125 wt%, 0.25 wt%, 0.5 wt%, 1 wt% and 2 wt%) were considered. The article presents the experimental photographs of the oil displacement process by water and SiO₂ suspension. It is shown that, with the increasing concentration of nanoparticles, the oil recovery factor increases. A significant effect is observed at 0.5 wt% concentration of nanoparticles. It is shown that the increase in oil recovery during flooding by SiO₂ suspension with the maximum concentration was 16%.

Microfluidics is a rapidly growing area that provides innovations in biotechnology, medical diagnostics, and life science. Along with the commercial solutions, there are open-source projects aimed to make such technologies more affordable and flexible for end users. In this article, we developed an open-source, low-cost, and easy-to-use microfluidic pressure controller with a modular design based on electropneumatic regulators to introduce liquids into microfluidic devices under constant pressures. For implementation of complex experimental protocols, the controller contains a vacuum pump, relay outputs, analog inputs, and digital inputs/outputs to connect external equipment. It can be operated using five displays and an encoder or from a personal computer in a manual or automatic regime through the custom open-source software. In this study, we applied this pressure controller for the generation of water-in-oil droplets in microfluidic flow-focusing droplet generators. Droplets’ diameters linearly depended on the dispersed and continuous phases’ ratio in the range 5– $65 \mu \text{m}$ . In all the cases, the generation regimes were stable for at least 4 h. Direct comparison of the droplet generation obtained with the developed pressure controller and precise syringe pumps showed that it will suit the needs of the microfluidic community for different flow-based lab-on-a-chip applications, as a more affordable and flexible solution for introducing liquids and controlling flow sensors, heaters, valves, light sources, and so on during experiments.

A number of approaches have been proposed and tested to transfer enzymatic reactions into the functional elements of microfluidic chips on the example of the bienzyme bioluminescent reaction...