REVOLVER: a low-cost automated protein purifier based on parallel preparative gravity column workflows

Protein purification is a ubiquitous operation in biochemistry and life sciences and represents a key step to producing purified proteins for research (understanding how proteins work) and various applications. The need for scalable and parallel protein purification systems keeps growing due to the increase in throughput in the production of recombinant proteins and in the ever-growing scale of biochemistry research. Therefore, automating the process to handle multiple samples in parallel with minimal human intervention is highly desirable; yet only a handful of such tools have been developed, all of which are closed source and expensive. To address this challenge, we present REVOLVER, a 3D-printed programmable and automatic protein purification system based on gravity-column workflows and controlled by Arduino boards that can be built for under $130 USD. REVOLVER completes a full protein purification process with almost no human intervention and yields results equivalent to those obtained by an experienced biochemist when purifying a real-world protein sample. We further present and describe MULTI-VOLVER, a scalable version of the REVOLVER that allows for parallel purification of up to six samples and can be built for under $250 USD. Both systems will be useful to accelerate protein purification and ultimately link them to bio-foundries for protein characterization and engineering.

On the Applicability of Electrophoresis for Protein Quantification

Polyacrylamide gel electrophoresis is widely used for studying proteins and protein-containing objects. However, it is employed most frequently as a qualitative method rather than a quantitative one. This paper shows the feasibility of routine digital image acquisition and mathematical processing of electropherograms for protein quantification when using vertical gel electrophoresis and Chrom & Spec software. Both the well-studied model protein molecules (bovine serum albumin) and more complex real-world protein-based products (casein-containing isolate for sports nutrition), which were subjected to mechanical activation in a planetary ball mill to obtain samples characterized by different protein denaturation degrees, were used as study objects. Protein quantification in the mechanically activated samples was carried out. The degree of destruction of individual protein was shown to be higher compared to that of the protein-containing mixture after mechanical treatment for an identical amount of time. The methodological approach used in this study can serve as guidance for other researchers who would like to use electrophoresis for protein quantification both in individual form and in protein mixtures. The findings prove that photographic imaging of gels followed by mathematical data processing can be applied for analyzing the electrophoretic data as an affordable, convenient and quick tool.

On the Applicability of Electrophoresis for Protein Quantification

Polyacrylamide gel electrophoresis (PAGE) is widely used for studying proteins and protein-containing objects. However, it is employed most frequently as a qualitative method rather than a quantitative one. In this paper, we show the feasibility of routine digital image acquisition and mathematical processing of electrophoregrams for protein quantification. Both the well-studied model protein molecules (bovine serum albumin) and more complex real-world protein-based products (casein-containing isolate for sports nutrition), which were subjected to mechanical activation in a planetary ball mill to obtain samples characterized by different protein denaturation degrees, were used as study objects. Protein quantification in the mechanically activated samples was carried out. The degree of destruction of individual protein was shown to be higher compared to that of protein-containing mixture after mechanical treatment for an identical amount of time. The methodological approach used in this study can serve as guidance for other researchers who would like to use electrophoresis for protein quantification both in individual form and in protein mixtures. The findings prove that photographic imaging of gels followed by mathematical data processing can be applied for analyzing the electrophoretic data.

Comparative Computational Analysis of SARSCoV-2 Nucleocapsid Epitope with Taxonomically Related Corona Viruses

Several research lines are currently ongoing to address the multitude of facets of the pandemic COVID-19. In line with the One-Health concept, extending the target of the studies to the animals which humans are continuously interacting with may favor a better understanding of the SARS-CoV-2 Biology and pathogenetic mechanisms; thus, helping to adopt the most suitable containment measures. The last two decades have already faced severe manifestations of the coronavirus infection in both humans and animals, thus, circulating epitopes from previous outbreaks might confer partial protection from SARS-CoV-2 infections. In the present study, we provide computational analysis of the major nucleocapsid protein epitopes and compare them with the homologues of taxonomically-related coronaviruses with tropism for animal species that are closely inter-related with the human being population all over the world. Protein sequence alignment provides evidence of high sequence homology for some of the investigated proteins. Moreover, the way the receptor binding domains of the nucleocapsid epitopes interact with their specific proteins is different from the closely related viruses. These evidences provide a molecular structural rationale for a potential role in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic- oriented strategies.

Simulasi Docking Senyawa Aktif Daun Binahong Sebagai Inhibitor Enzyme Aldose Reductase

The metabolic syndrome is the cause of death around the world caused by diabetic mellitus. Binahong leaf is a kind of plant that is widely used to treat various diseases. This study aims to investigate the inhibitory activity of binahong leaves compound in inhibiting the aldose reductase which has role of converting glucose into sorbitol by docking simulation. The compound of binahong leaves consists of ursolic acid, vitexin, and oleonolic acid (ligand testing). These compound were taken from PubChem site, while aldose reductase enzyme (receptor) was obtained from the world protein bank with PDB 2HV5 code. This study incorporated in silica technique by using Auto dock vina software, Discovery Studio and Ligplot as visualization. The result of grid box optimization by redocking comparative ligand was 0.7Å RMSD. The docking result showed that the free Gibbs energy (∆G) of aldose reductase was (-11.7), Vitexin (-8.3), Ursolic acid (-7.7) and Oleonolic acid (-8.6). These value suggested that there was a stable inhibition reaction from the binahong leaves compound and the comparative ligand. Based on the Lipinski Rule, the composition of binahong leaves compound meets the Lipinski Rule criteria which means this medicine can be used orally except for vitexin and comparative ligands of zopolrestate which exceed the number of the atom.

A modelling study of world protein supply and nitrogen fertilizer demand in the 21st century

The implications of world population growth for future fertilizer use and impact on the environment have scarcely been predicted. We investigated world protein production using a global nitrogen balance model. The model assumes that world population continues to grow and crop yield per unit area is closely related to nitrogen fertilizer use. About five times more cereal protein is needed to produce meat protein through farming. Advanced countries consume more meat than people in developing countries. Assuming the world's arable land remains constant in area in the next century, and if the meat consumption in advanced countries is matched by the rest of the world, the demand for fertilizer will increase and reach 220 Tg y-1 by the middle of the next century. This is approximately three times more fertilizer than is currently used, and would accelerate environmental deterioration. The world would be suffering from conflict between supplying sufficient protein and greater nitrogen pollution of the environment.