AspSnFR: A genetically encoded biosensor for real-time monitoring of aspartate in live cells.

Aspartate is crucial for nucleotide synthesis, ammonia detoxification, and maintaining redox balance via the malate-aspartate-shuttle (MAS). To disentangle these multiple roles of aspartate metabolism, tools are required that measure aspartate concentrations in real time and in live cells. We introduce AspSnFR, a genetically encoded green fluorescent biosensor for intracellular aspartate, engineered through displaying and screening biosensor libraries on mammalian cells.

Recording physiological history of cells with chemical labeling.

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins that become labeled in the presence of both a specific cellular activity and a fluorescent substrate.

Elucidating the Morphology of the Endoplasmic Reticulum: Puzzles and Perspectives.

Artificial or synthetic organelles are a key challenge for bottom-up synthetic biology. So far, synthetic organelles have typically been based on spherical membrane compartments, used to spatially confine selected chemical reactions. In vivo, these compartments are often far from being spherical and can exhibit rather complex architectures.

A general method for the development of multicolor biosensors with large dynamic ranges.

Fluorescent biosensors enable the study of cell physiology with spatiotemporal resolution; yet, most biosensors suffer from relatively low dynamic ranges. Here, we introduce a family of designed Förster resonance energy transfer (FRET) pairs with near-quantitative FRET efficiencies based on the reversible interaction of fluorescent proteins with a fluorescently labeled HaloTag. These FRET pairs enabled the straightforward design of biosensors for calcium, ATP and NAD with unprecedented dynamic ranges.

Exchangeable HaloTag Ligands for Super-Resolution Fluorescence Microscopy.

The specific and covalent labeling of the protein HaloTag with fluorescent probes in living cells makes it a powerful tool for bioimaging. However, the irreversible attachment of the probe to HaloTag precludes imaging applications that require transient binding of the probe and comes with the risk of irreversible photobleaching. Here, we introduce exchangeable ligands for fluorescence labeling of HaloTag (xHTLs) that reversibly bind to HaloTag and that can be coupled to rhodamines of different colors.

Metal contamination in sediments of dam reservoirs: A multi-facetted generic risk assessment.

The quality of bottom sediments is a key factor for many functions of dam reservoirs, which include water supply, flood control and recreation. The aim of the study was to combine different pollution indices in a critical generic risk assessment of metal contamination of bottom sediments. Both geochemical and ecological indices reflected that sediment contamination was dominated by Zn, Pb and Cd.

Immobilisation of metals from bottom sediments using two additives and thermal treatment.

A major problem associated with the land-based management of bottom sediments is their contamination with metals. The aims of the study were: 1) to use two additives for the immobilisation of metals; and 2) to evaluate the effect of three combustion temperatures on metal content and bottom sediment properties. The mixtures were prepared using contaminated bottom sediment and the following waste materials: cellulosic waste and biomass ash.

Engineered HaloTag variants for fluorescence lifetime multiplexing.

Self-labeling protein tags such as HaloTag are powerful tools that can label fusion proteins with synthetic fluorophores for use in fluorescence microscopy. Here we introduce HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines. Combining these HaloTag variants enabled live-cell fluorescence lifetime multiplexing of three cellular targets in one spectral channel using a single fluorophore and the generation of a fluorescence lifetime-based biosensor.

Integration and Application of Multimodal Measurement Techniques: Relevance of Photogrammetry to Orthodontics.

Multimodal imaging, including 3D modalities, is increasingly being applied in orthodontics, both as a diagnostic tool and especially for the design of intraoral appliances, where geometric accuracy is very important. Laser scanners and other precision 3D-imaging devices are expensive and cumbersome, which limits their use in medical practice. Photogrammetry, using ordinary 2D photographs or video recordings to create 3D imagery, offers a cheaper and more convenient alternative, replacing the specialised equipment with handy consumer cameras.

Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag.

The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates.

Concentration of dioxin and screening level ecotoxicity of pore water from bottom sediments in relation to organic carbon contents.

The information about concentrations of dioxin in pore water, ecotoxicity and DOC and TOC content can be key factor for the prediction of the fate of dioxins in the aquatic environment as well as an ecological risk assessment. The aims of the study were to assess the concentration of PCDDs/PCDFs and ecotoxicity of pore water and to compare above results in relation to the dissolved organic carbon (DOC) and total organic carbon (TOC) content. The concentration of dioxins was assessed using an enzyme-linked immunoassay test, while the ecotoxicity of pore water was determined using a crustacean Daphnia magna and bacteria Aliivibrio fischeri.

Ecotoxicological and chemical properties of the rożnów reservoir bottom sediment amended with various waste materials.

In the study, an attempt was made to create innovative mixtures based on bottom sediment and various types of waste to be tested for use as a substrate in the cultivation of consumer and non-consumer plants. The aim of the study was to assess the chemical and ecotoxicological properties of the growing medium prepared on the basis of bottom sediment (BS) and different carbon rich waste (cellulose waste (CW), biomass ash (BA), coffee hulls (CH), and sludge from water treatment (SW)) with a combination of 75% bottom sediment and 25% waste material. The mixtures had deacidifying properties, significant content of total organic carbon (TOC), the total quantities of macro- and micronutrients, and good sorption properties.

Chemogenetic Control of Nanobodies.

We introduce an engineered nanobody whose affinity to green fluorescent protein (GFP) can be switched on and off with small molecules. By controlling the cellular localization of GFP fusion proteins, the engineered nanobody allows interrogation of their roles in basic biological processes, an approach that should be applicable to numerous previously described GFP fusions. We also outline how the binding affinities of other nanobodies can be controlled by small molecules.

Ecotoxicological characteristics and ecological risk assessment of trace elements in the bottom sediments of the Rożnów reservoir (Poland).

The bottom sediments in catchment areas behind dams play a significant role in water ecosystems. On the other hand, the structure of sediments makes them a natural geosorbent, in which pollutants introduced to the aquatic environment accumulate. The use of biotests is recognised as an important approach for the assessment of the quality of bottom sediments, as the chemical analysis of sediment samples alone does not provide evidence of the impact of contaminants on biota.

Content of nutrients, trace elements, and ecotoxicity of sediment cores from Rożnów reservoir (Southern Poland).

The aims of the study were to investigate the concentration of trace elements, nutrients, and ecotoxicity in bottom sediment cores collected from the silted part of the Rożnów reservoir (Southern Poland). Significant differences in the content of nutrients, trace elements, and ecotoxicity between five sediment cores were found. However, in the vertical distribution, there was no high variability of the above parameters, which means that the intensely suspended matter transported by the Dunajec river is and, at various times, has been homogeneous.

The influence of the quantity and quality of sediment organic matter on the potential mobility and toxicity of trace elements in bottom sediment.

Knowledge on the fraction of trace elements in the bottom sediments is a key to understand their mobility and ecotoxicological impact. The purpose of this study was to assess the influence of the content of organic matter fractions on the mobility and ecotoxicity of trace elements in sediments from the Rybnik reservoir. The most refractory fraction of organic matter-Cnh (non-hydrolysing carbon)-dominated in the sediments.

Investigating Cytochrome P450 specificity during glycopeptide antibiotic biosynthesis through a homologue hybridization approach.

Cytochrome P450 enzymes perform an impressive range of oxidation reactions against diverse substrate scaffolds whilst generally maintaining a conserved tertiary structure and active site chemistry. Within secondary metabolism, P450 enzymes play widespread and important roles in performing crucial modifications of precursor molecules, with one example of the importance of such reactions being found in the biosynthesis of the glycopeptide antibiotics (GPAs). In GPA biosynthesis P450s, known as Oxy enzymes, are key players in the cyclization of the linear GPA peptide precursor, which is a process that is both essential for their antibiotic activity and is the source of the synthetic challenge of these important antibiotics.

Impact of delayed umbilical cord clamping on public cord blood donations: can we help future patients and benefit infant donors?

Background: Cord blood (CB) is a widely accepted stem cell source and its clinical utilization depends, to a great extent, on its cell content. Birth-to-clamping (BTC) time of umbilical cord determines placental transfusion to the newborn, and the remaining blood that can be collected and banked. The 2017 Committee Opinion of the American College of Obstetrics and Gynecologists (ACOG) recommends a delay of "at least 30-60 seconds" before clamping the cord for all newborns to ensure adequate iron stores.

Use of Chemical Indicators and Bioassays in Bottom Sediment Ecological Risk Assessment.

This study is was designed to assess the ecological risk associated with chemical pollution caused by heavy metals and PAHs on the basis of their ecotoxicological properties in sediments collected from the Rzeszów dam reservoir (Poland). The sediment samples were collected from three sampling stations: S1-inlet, backwater station, S2-middle of reservoir, S3 outlet, near the dam. The sediments' toxicity was evaluated using a battery of bioassays (Phytotoxkit, Phytotestkit, Ostracodtoxkit F, and Microtox).

Concentration, sources and risk assessment of PAHs in bottom sediments.

The aims of the study were to investigate the concentration, sources and ecological risk of PAHs (polycyclic aromatic hydrocarbons) in bottom sediments collected from nine reservoirs located in south-eastern Poland. The concentration of ∑PAHs in sediments ranged from 150 to 33,900 μg kg. The total PAH concentration in the bottom sediments was arranged in the following order: Rybnik > Rzeszów > Brzóza Królewska > Brzóza Stadnicka > Besko > Chechło > Ożanna > Głuchów > Narożniki.

Cytomegalovirus viral load in cord blood and impact of congenital infection on markers of hematopoietic progenitor cell potency.

Background: The low incidence of cytomegalovirus (CMV) infection in neonates decreases the risk of viral transmission with cord blood transplantation. Cord blood donors are screened by testing the maternal sample for total antibodies to CMV. Some cord blood banks also screen cord blood for CMV-DNA.

Photoactivation Mechanism of a Bacterial Light-Regulated Adenylyl Cyclase.

Light-regulated enzymes enable organisms to quickly respond to changing light conditions. We characterize a photoactivatable adenylyl cyclase (AC) from Beggiatoa sp. (bPAC) that translates a blue light signal into the production of the second messenger cyclic AMP.

LOVTRAP: an optogenetic system for photoinduced protein dissociation.

LOVTRAP is an optogenetic approach for reversible light-induced protein dissociation using protein A fragments that bind to the LOV domain only in the dark, with tunable kinetics and a >150-fold change in the dissociation constant (Kd). By reversibly sequestering proteins at mitochondria, we precisely modulated the proteins' access to the cell edge, demonstrating a naturally occurring 3-mHz cell-edge oscillation driven by interactions of Vav2, Rac1, and PI3K proteins.