Evolutionary age of genes can assist in genome mining

The rate of sequencing microbial genomes is accelerating, with the hope of discovering new antibiotics, cures for various diseases or new industrial enzymes. However, about 25-30% of the genes in the sequenced microbial genomes do not have an assigned function. Predicting the functions of these “unknown” genes could unlock a considerable biological potential for biomedical and biotechnology applications, as well as further our understanding of the molecular tenets of life. Current methods for gene mining rely basically on comparison of primary sequences or 3D-structures to those of already characterized genes. The problem with such approaches is that unknown genes with no homology to the already characterized genes remain completely out of reach. Herein, I argue that evolutionary approaches, such as the genomic phylostratigraphy, can make a substantial contribution to genome mining – especially regarding genes with no homology to the characterized ones. My group has recently used genomic phylostratigraphy to discover new genes involved in sporulation of the bacterial model organism Bacillus subtilis. These new sporulation genes exhibited no sequence homology with the known sporulation genes and were missed by all other genome mining approaches. They have been discovered solely based on their evolutionary age. Along these lines, I argue that phylostratigraphy should be integrated into genome mining pipelines and develop a brief example of how this could be done.</p

Fantastic science and where to find it

No abstract availabl

Learning by teaching efficiently enhances learning outcomes in molecular biology of the cell course

To evaluate the impact of active learning approaches in a basic molecular and cell biology course for undergraduate students, we assessed the effect of learning by teaching and peer review on the learning outcomes. A literature seminar activity with peer review and feedback was organized as a compulsory activity for all students, covering about 25% of the course content. The remaining 75% of the course was delivered as classical lectures. The students collaborated in groups to present the content of a review article complemented with a research article. For each group of students, an opponent group was assigned to challenge the presenting group by questions and contribute to the evaluation of the presentation together with the teacher. Based on the feedback survey, the students reacted positively to this active learning exercise, and they strongly recommended keeping it in the future editions of the course. The students\u27 exam scores strongly indicated that the learning outcomes from the learning by teaching part of the course were consistently higher than from the classical lecture part of the course. Further optimization of the active learning part of the course is outlined based on student feedback

Green synthesis and antibacterial applications of gold and silver nanoparticles from Ligustrum vulgare berries

Increasing demand for green or biological nanoparticles has led to various green technologies and resources, which play a critical role in forming biocompatible or green nanoparticles. So far, numerous medicinal plants have been explored for this purpose, assuming that medicinal components from the plant\u27s material will contribute to corona formation around nanoparticles and enhance their efficacy. Research is also extended to other green and waste resources to be utilized for this purpose. In the current study, we explored Ligustrum vulgare berries, also known as privet berries, to reduce gold and silver salts into nanoparticles. L. vulgare berries showed great potential to form these nanoparticles, as gold nanoparticles (LV-AuNPs) formed within 5\ua0min at room temperature, and silver nanoparticles (LV-AgNPs) formed in 15\ua0min at 90\ua0\ub0C. LV-AuNPs and LV-AgNPs were characterized by various analytical methods, including UV–Vis, SEM, EDX, TEM, DLS, sp-ICP-MS, TGA, FT-IR, and MALDI-TOF. The results demonstrate that the LV-AuNPs are polydisperse in appearance with a size range 50–200\ua0nm. LV-AuNPs exhibit various shapes, including spherical, triangular, hexagonal, rod, cuboid, etc. In contrast, LV-AgNPs are quite monodisperse, 20–70\ua0nm, and most of the population was spherical. The nanoparticles remain stable over long periods and exhibit high negative zeta potential values. The antimicrobial investigation of LV-AgNPs demonstrated that the nanoparticles exhibit antibacterial ability with an MBC value of 150\ua0g/mL against P. aeruginosa and 100\ua0g/mL against E. coli, as determined by plate assay, live and dead staining, and SEM cell morphology analysis

Strong Antimicrobial Activity of Silver Nanoparticles Obtained by the Green Synthesis in Viridibacillus sp. Extracts

Recently, green silver nanoparticles (G-AgNPs) have gained much attention in medical science due to their extraordinary effects against multidrug-resistant microorganisms. The strong antimicrobial nature of G-AgNPs corresponds to their unique physicochemical properties such as size, shape, surface charge, and active surface groups available to interact with the pathogens. The current study demonstrates a simple, environmentally friendly, and economical method to produce G-AgNPs from an environmental isolate of Viridibacillus sp. The produced G-AgNPs were characterized by various analytical methods, including UV-Vis spectroscopy, single-particle inductively coupled plasma-mass spectrometry (sp-ICP-MS), scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDX), elemental mapping, transmission electron microscopy (TEM), dynamic light scattering (DLS), Fourier-transform infrared spectroscopy (FTIR), and Thermogravimetric analysis (TGA). The reduction of Ag+ to Ag\ub0 was observed by UV-Vis spectroscopy, which demonstrated the formation of stable G-AgNPs with a Surface Plasmon Resonance (SPR) band at the maximum of 430 nm. TEM analysis demonstrated that the G-AgNPs were spherical with a 5–30 nm size range. The produced G-AgNPs were stable for more than 1 year in an aqueous solution at 4\ub0C. Importantly, G-AgNPs showed remarkable antimicrobial activity against Gram-negative pathogens- E. coli and P. aeruginosa with MIC values of 0.1 and 4 μg/mL and MBC values of 1 and 8 μg/mL, respectively. This level of antimicrobial activity is superior to other AgNPs reported in the literature

Rowan Berries: A Potential Source for Green Synthesis of Extremely Monodisperse Gold and Silver Nanoparticles and Their Antimicrobial Property

Rowanberries (Sorbus aucuparia) are omnipresent in Europe. The medicinal importance of rowanberries is widely known and corresponds to the active ingredients present in the fruits, mainly polyphenols, carotenoids, and organic acids. In the current study, we explored rowanberries for the reduction of gold and silver salts into nanoparticles. Rowanberries-mediated gold nanoparticles (RB-AuNPs) formed within 5 s at room temperature, and silver nanoparticles (RB-AgNPs) formed in 20 min at 90◦ C. The produced nanoparticles were thoroughly characterized by UV-Vis spec-troscopy, scanning electron microscopy (SEM), energy dispersive X-ray (EDX), transmission electron microscopy (TEM), dynamic light scattering (DLS), single-particle inductively coupled plasma– mass spectrometry (sp-ICP-MS), thermogravimetric analysis (TGA), Fourier transform-infrared spectroscopy (FT-IR) and matrix-assisted laser desorption/ionization time of flight mass spectrome-try (MALDI-TOF). The characterization confirmed that the nanoparticles are highly monodisperse, spherical, stable over long periods, and exhibit a high negative zeta potential values. The produced RB-AuNPs and RB-AgNPs were 90–100 nm and 20–30 nm in size with a thick biological corona layer surrounding them, providing extreme stability but lowering the antimicrobial activity. The antimicrobials study of RB-AgNPs revealed that the nanoparticles have antimicrobial potential with an MBC value of 100 \ub5g/mL against P. aeruginosa and 200 \ub5g/mL against E. coli

Exploring the diversity of protein modifications: special bacterial phosphorylation systems

Protein modifications not only affect protein homeostasis but can also establish new cellular protein functions and are important components of complex cellular signal sensing and transduction networks. Among these post-translational modifications, protein phosphorylation represents the one that has been most thoroughly investigated. Unlike in eukarya, a large diversity of enzyme families has been shown to phosphorylate and dephosphorylate proteins on various amino acids with different chemical properties in bacteria. In this review, after a brief overview of the known bacterial phosphorylation systems, we focus on more recently discovered and less widely known kinases and phosphatases. Namely, we describe in detail tyrosine -and arginine-phosphorylation together with some examples of unusual serine-phosphorylation systems and discuss their potential role and function in bacterial physiology, and regulatory networks. Investigating these unusual bacterial kinase and phosphatases is not only important to understand their role in bacterial physiology but will help to generally understand the full potential and evolution of protein phosphorylation for signal transduction, protein modification and homeostasis in all cellular life

Elucidating Host-Pathogen Interactions Based on Post-Translational Modifications Using Proteomics Approaches

Microbes with the capability to survive in the host tissue and efficiently subvert its innate immune responses can cause various health hazards. There is an inherent need to understand microbial infection patterns and mechanisms in order to develop efficient therapeutics. Microbial pathogens display host specificity through a complex network of molecular interactions that aid their survival and propagation. Co-infection states further lead to complications by increasing the microbial burden and risk factors. Quantitative proteomics based approaches and post-translational modification analysis can be efficiently applied to gain an insight into the molecular mechanisms involved. The measurement of the proteome and post-translationally modified proteome dynamics using mass spectrometry, results in a wide array of information, such as significant changes in protein expression, protein abundance, the modification status, the site occupancy level, interactors, functional significance of key players, potential drug targets, etc. This mini review discusses the potential of proteomics to investigate the involvement of post-translational modifications in bacterial pathogenesis and host pathogen interactions

Technologies for biological removal and recovery of nitrogen from wastewater

Water contamination is a growing environmental issue. Several harmful effects on human health and the environment are attributed to nitrogen contamination of water sources. Consequently, many countries have strict regulations on nitrogen compound concentrations in wastewater effluents. Wastewater treatment is carried out using energy- and cost-intensive biological processes, which convert nitrogen compounds into innocuous dinitrogen gas. On the other hand, nitrogen is also an essential nutrient. Artificial fertilizers are produced by fixing dinitrogen gas from the atmosphere, in an energy-intensive chemical process. Ideally, we should be able to spend less energy and chemicals to remove nitrogen from wastewater and instead recover a fraction of it for use in fertilizers and similar applications. In this review, we present an overview of various technologies of biological nitrogen removal including nitrification, denitrification, anaerobic ammonium oxidation (anammox), as well as bioelectrochemical systems and microalgal growth for nitrogen recovery. We highlighted the nitrogen removal efficiency of these systems at different temperatures and operating conditions. The advantages, practical challenges, and potential for nitrogen recovery of different treatment methods are discussed

Antimicrobial Activity of Graphene Oxide Contributes to Alteration of Key Stress-Related and Membrane Bound Proteins

Introduction: Antibacterial activity of graphene oxide (GO) has been extensively studied, wherein penetration of the bacterial cell membrane and oxidative stress are considered to play a major role in the bactericidal activity of GO. However, the specific mechanism responsible for the antibacterial activity of GO remains largely unknown. Hence, the goal of this study was to explore the mode of action of GO, via an in-depth proteomic analysis of the targeted bacteria. Methods: Staphylococcus aureus was grown in the presence of GO and samples were collected at different growth phases to examine the cell viability and to analyze the changes in protein expression. Antimicrobial efficiency of GO was tested by assessing bacterial viability, live/dead staining and scanning electron microscopy. The intracellular reactive oxygen species (ROS) induced by GO treatment were examined by fluorescence microscopy. Label-free quantitative proteomics analysis was performed to examine the differentially regulated proteins in S. aureus after GO treatment. Results: GO treatment was observed to reduce S. aureus viability, from 50 \ub1 17% after 4 h, to 93 \ub1 2% after 24 h. The live/dead staining confirmed this progressive antimicrobial effect of GO. SEM images revealed the wrapping of bacterial cells and their morphological disruption by means of pore formation due to GO insertion. GO treatment was observed to generate intracellular ROS, correlating to the loss of cell viability. The proteomics analysis revealed alteration in the expression of cell membrane, oxidative stress response, general stress response, and virulence-associated proteins in GO-treated bacterial cells. The time-dependent bactericidal activity of GO correlated with a higher number of differentially regulated proteins involved in the above.-mentioned processes. Conclusion: The obtained results suggest that the time-dependent bactericidal effect of GO is attributed to its wrapping/trapping ability, ROS production and due to physical disruption of the cell membrane