luxA Gene From Enhygromyxa salina Encodes a Functional Homodimeric Luciferase.

Several clades of luminescent bacteria are known currently. They all contain similar lux operons, which include the genes luxA and luxB encoding a heterodimeric luciferase. The aldehyde oxygenation reaction is presumed to be catalyzed primarily by the subunit LuxA, whereas LuxB is required for efficiency and stability of the complex.

Reengineering of a flavin-binding fluorescent protein using ProteinMPNN.

Recent advances in machine learning techniques have led to development of a number of protein design and engineering approaches. One of them, ProteinMPNN, predicts an amino acid sequence that would fold and match user-defined backbone structure. Its performance was previously tested for proteins composed of standard amino acids, as well as for peptide- and protein-binding proteins.

Mesenchymal-epithelial transition and AXL inhibitor TP-0903 sensitise triple-negative breast cancer cells to the antimalarial compound, artesunate.

Triple-negative breast cancer (TNBC) is a difficult-to-treat, aggressive cancer type. TNBC is often associated with the cellular program of epithelial-mesenchymal transition (EMT) that confers drug resistance and metastasis. EMT and reverse mesenchymal-epithelial transition (MET) programs are regulated by several signaling pathways which converge on a group of transcription factors, EMT- TFs.

Two distinct mechanisms of flavoprotein spectral tuning revealed by low-temperature and time-dependent spectroscopy.

Flavins such as flavin mononucleotide or flavin adenine dinucleotide are bound by diverse proteins, yet have very similar spectra when in the oxidized state. Recently, we developed new variants of flavin-binding protein CagFbFP exhibiting notable blue (Q148V) or red (I52V A85Q) shifts of fluorescence emission maxima. Here, we use time-resolved and low-temperature spectroscopy to show that whereas the chromophore environment is static in Q148V, an additional protein-flavin hydrogen bond is formed upon photoexcitation in the I52V A85Q variant.

Fine spectral tuning of a flavin-binding fluorescent protein for multicolor imaging.

Flavin-binding fluorescent proteins are promising genetically encoded tags for microscopy. However, spectral properties of their chromophores (riboflavin, flavin mononucleotide, and flavin adenine dinucleotide) are notoriously similar even between different protein families, which limits applications of flavoproteins in multicolor imaging. Here, we present a palette of 22 finely tuned fluorescent tags based on the thermostable LOV domain from Chloroflexus aggregans.

Development and Characterization of Flavin-Binding Fluorescent Proteins, Part I: Basic Characterization.

Flavin-based fluorescent proteins (FbFPs) are small fluorescent proteins derived from light-oxygen-voltage (LOV) domains. The proteins bind ubiquitous endogenous flavins as chromophores and can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents the methodology to identify LOV domain sequences in genomic databases; design new FbFPs; characterize their biochemical, spectroscopic, photophysical, and photochemical properties; and conduct basic fluorescence microscopy experiments.

Opposing Roles of Wild-type and Mutant p53 in the Process of Epithelial to Mesenchymal Transition.

The central role of an aberrantly activated EMT program in defining the critical features of aggressive carcinomas is well documented and includes cell plasticity, metastatic dissemination, drug resistance, and cancer stem cell-like phenotypes. The p53 tumor suppressor is critical for leashing off all the features mentioned above. On the molecular level, the suppression of these effects is exerted by p53 via regulation of its target genes, whose products are involved in cell cycle, apoptosis, autophagy, DNA repair, and interactions with immune cells.

Machine Learning Estimation of COVID-19 Social Distance using Smartphone Sensor Data.

Airborne infectious diseases such as COVID-19 spread when healthy people are in close proximity to infected people. Technology-assisted methods to detect proximity in order to alert people are needed. In this work we systematically investigating Machine Learning (ML) methods to detect proximity by analyzing data gathered from smartphones' built-in Bluetooth, accelerometer and gyroscope sensors.

Zeb1-mediated autophagy enhances resistance of breast cancer cells to genotoxic drugs.

Autophagy is a highly conserved process of cellular self-digestion that involves the formation of autophagosomes for the delivery of intracellular components and dysfunctional organelles to lysosomes. This process is induced by different signals including starvation, mitochondrial dysfunction, and DNA damage. The molecular link between autophagy and DNA damage is not well understood yet.

Extreme dependence of Chloroflexus aggregans LOV domain thermo- and photostability on the bound flavin species.

Light-oxygen-voltage (LOV) domains are common photosensory modules that found many applications in fluorescence microscopy and optogenetics. Here, we show that the Chloroflexus aggregans LOV domain can bind different flavin species (lumichrome, LC; riboflavin, RF; flavin mononucleotide, FMN; flavin adenine dinucleotide, FAD) during heterologous expression and that its physicochemical properties depend strongly on the nature of the bound flavin. We show that whereas the dissociation constants for different chromophores are similar, the melting temperature of the protein reconstituted with single flavin species varies from ~ 60 °C for LC to ~ 81 °C for FMN, and photobleaching half-times vary almost 100-fold.

High-resolution structure of a naturally red-shifted LOV domain.

LOV domains are widespread photosensory modules that have also found applications in fluorescence microscopy, optogenetics, and light-driven generation of reactive oxygen species. Many of these applications require stable proteins with altered spectra. Here, we report a flavin-based fluorescent protein CisFbFP derived from Chloroflexus islandicus LOV domain-containing protein.

The RNA-binding protein HuR is a novel target of Pirh2 E3 ubiquitin ligase.

The RING-finger protein Pirh2 is a p53 family-specific E3 ubiquitin ligase. Pirh2 also ubiquitinates several other important cellular factors and is involved in carcinogenesis. However, its functional role in other cellular processes is poorly understood.

Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity.

Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from .

Rational Design of a Split Flavin-Based Fluorescent Reporter.

Protein-fragment complementation assays are used ubiquitously for probing protein-protein interactions. Most commonly, the reporter protein is split in two parts, which are then fused to the proteins of interest and can reassemble and provide a readout if the proteins of interest interact with each other. The currently known split fluorescent proteins either can be used only in aerobic conditions and assemble irreversibly, or require addition of exogenous chromophores, which complicates the design of experiments.

[Analysis of allelic content of genes responsible for baking properties in allocytoplasmic wheat hybrids].

A collection comprised of allocytoplasmic hybrids of mild wheat (ACPH) was screened for the allelic state of genes responsible for baking properties (high-molecular glutenins, puroindolines, and Waxy). The possibility of the introgression of the Waxy gene of T. timopheevii into the mild wheat genome was demonstrated in several ACPH samples using the set of molecular markers.

First-passage properties of molecular spiders.

Molecular spiders are synthetic catalytic DNA-based nanoscale walkers. We study the mean first-passage time for abstract models of spiders moving on a finite two-dimensional lattice with various boundary conditions and compare it with the mean first-passage time of spiders moving on a one-dimensional track. We evaluate by how much the slowdown on newly visited sites, owing to catalysis, can improve the mean first-passage time of spiders and show that in one dimension, when both ends of the track are an absorbing boundary, the performance gain is lower than in two dimensions, when the absorbing boundary is a circle; this persists even when the absorbing boundary is a single site.

pH-controlled recovery of placenta-derived mesenchymal stem cell sheets.

Widely used in different biomedical applications, polyelectrolyte multilayers provide inter alia an attractive way for manufacturing of bio-functionalized, stimuli responsive surface coatings to control cellular behavior. In this study a novel polyelectrolyte-based platform for the engineering and controllable detachment of human mesenchymal stem cell (MSC) sheets is presented. Thin films obtained by layer-by-layer deposition of cationic poly(allylamine hydrochloride) (PAH) and anionic poly(styrene sulfonate) (PSS) polyelectrolytes on conductive indium tin oxide (ITO) electrodes allowed for the fast formation of viable sheets from human placenta-derived mesenchymal stem cells (PD-MSCs).

Mechanism of diffusive transport in molecular spider models.

Recent advances in single-molecule chemistry have led to designs for artificial multipedal walkers that follow tracks of chemicals. We investigate the motion of a class of walkers, called molecular spiders, which consist of a rigid chemically inert body and several flexible enzymatic legs. The legs can reversibly bind to chemical substrates on a surface and through their enzymatic action convert them to products.

Engineering the extracellular environment: Strategies for building 2D and 3D cellular structures.

Cell fate is regulated by extracellular environmental signals. Receptor specific interaction of the cell with proteins, glycans, soluble factors as well as neighboring cells can steer cells towards proliferation, differentiation, apoptosis or migration. In this review, approaches to build cellular structures by engineering aspects of the extracellular environment are described.

Multipotent mesenchymal stem cells from human placenta: critical parameters for isolation and maintenance of stemness after isolation.

Objective: This study was undertaken to isolate and characterize multipotent mesenchymal stem cells from term human placenta (placenta-derived mesenchymal stem cells, PD-MSCs).

Study Design: Sequential enzymatic digestion was used to isolate PD-MSCs in which trypsin removes the trophoblast layer, followed by collagenase treatment of remaining placental tissue. Karyotype, phenotype, growth kinetics, and differentiability of PD-MSC isolates from collagenase digests were analyzed.

Engineered polyelectrolyte multilayer substrates for adhesion, proliferation, and differentiation of human mesenchymal stem cells.

Polyelectrolyte multilayer coatings have emerged as substrates to control cellular behavior, but interactions with human multipotent mesenchymal stromal cells (MSCs) have not been studied. We looked at layer-by-layer coatings of cationic poly-L-lysine (PLL) and anionic hyaluronic acid (HA) as substrates for MSCs of placenta and adipose tissue. This system allows for modulation of thickness (number of deposition cycles), stiffness (chemical cross-linking of bulk layer), and adhesiveness (fibronectin (FN) interface).

[Specific features of source-sink relations in alloplasmic hybrid of winter wheat with alien cytoplasm of goatgrass with emphasis on resistance to low temperature stress].

We studied the influence of alien cytoplasm of spring goatgrass Aegilops ovata L. on some physiological parameters in winter wheat (Triticum aestivum L.), Mironovskaya 808, under normal conditions and in the case of modified source-sink relations.

[Effect of alien cytoplasm of goatgrass on biological and physiological properties of alloplasmic wheats].

Long-term studies of the cytoplasm-nucleus interactions in alloplasmic hybrids with the nucleus of Triticum aestivum functioning in the alien cytoplasm of Aegilops ovata are reviewed. The interaction of heterologous genome and cytoplasm affects the balanced mechanisms of developmental control of the parental forms. The changes are observed at all levels of both physiological and morphological processes.