Nitrogen-doped carbon dots as a fluorescent probe for the highly sensitive detection of bilirubin and cell imaging

Nitrogen-doped carbon dots (NCDs) with bright blue fluorescence were constructed by a hydrothermal method using sucrose and l- proline as raw materials. The NCDs were characterized by transmitted electron microscopy, X-ray diffraction, Fourier-transform infrared spectrometry, X-ray photoelectron spectroscopy, and ultraviolet-visible absorption and fluorescence spectroscopy to investigate the morphology, elemental composition, and optical properties. The NCDs had good water solubility, high dispersibility with an average diameter of only 1.7 nm, and satisfactory optical properties with a fluorescence quantum yield of 23.4%. The NCDs were employed for the detection of bilirubin. A good linear response of the NCDs in the range 0.35–9.78 μM was obtained for bilirubin with a detection limit of 33 nM. The NCDs were also applied to the analysis of real samples, serum and urine, with a recovery of 95.34% to 104.66%. The low cytotoxicity and good biocompatibility of the NCDs were indicated by an MTT assay and cell imaging of HeLa cells. Compared with other detection systems, using NCDs for bilirubin detection was a facile and efficient method with good selectivity and sensitivity.     

Synthesis of d-desthiobiotin-AI-2 as a novel chemical probe for autoinducer-2 quorum sensing receptors

In processes regulated by quorum sensing (QS) bacteria respond to the concentration of autoinducers in the environment to engage in group behaviours. Autoinducer-2 (AI-2) is unique as it can foster interspecies communication. Currently, two AI-2 receptors are known, LuxP and LsrB, but bacteria lacking these receptors can also respond to AI-2. In this work, we present an efficient and reproducible synthesis of a novel chemical probe, d-desthiobiotin-AI-2. This probe binds both LuxP and LsrB receptors from different species of bacteria. Thus, this probe is able to bind receptors that recognise the two known biologically active forms of AI-2, presenting the plasticity essential for the identification of novel unknown AI-2 receptors. Moreover, a protocol to pull down receptors bound to d-desthiobiotin-AI-2 with anti-biotin antibodies has also been established. Altogether, this work highlights the potential of conjugating chemical signals to biotinylated derivatives to identify and tag signal receptors involved in quorum sensing or other chemical signalling processes.     

Molecular mechanisms of allosteric probe dependence in μ opioid receptor

Allostery is one of the most important features of proteins. It greatly contributes to the complexity of life, since it enables possibility of precise tuning of protein function, as well as performing more than one function per protein. Probe dependence is one of the unique features of allostery. It allows a protein to respond differently to the same allosteric modulator when different drugs or transmitters are bound. Unfortunately, allosteric mechanisms are difficult to investigate experimentally. Instead, they can be reproduced artificially in simulations. We simulated in silico a native-like cell membrane fragment with an active-state human μ opioid receptor (MOR) in order to investigate diverse effects of a receptor’s positive allosteric modulator on various agonists. Particular emphasis on native-likeness of the environment was put. We managed to reproduce the experimentally observed effects, which allowed us to take deeper insight into their underlying mechanisms. We found an allosteric pathway in the receptor, leading from the ligand binding site to the intracellular, effector site. We observed that the modulator affected the pathway, inducing different resultant responses for full and partial agonists.     

Molecular epidemiology of plasmid mediated resistance to fosfomycin among bacteria isolated from different environments

In this report we present data on the dispersion of a gene responsible for the plasmid-mediated resistance to fosfomycin among bacteria isolated from four hospitals and seven geographically separated domestic sewage treatment plants. Colony hybridization experiments, using a 0.85 kbp DNA fragment which carried the fosfomycin resistance determinant, have shown that the gene was present in isolates from three hospitals and six sewage plants although with different incidence and that it is carried by species of Enterobacteriaceae, Pseudomonas, Acinetobacter, Staphylococcus and Bacillus .     

Peptide probes containing a non-hydrolyzable phosphotyrosine-mimetic residue for enrichment of protein tyrosine phosphatases

We developed peptide probes containing a non-hydrolyzable phosphotyrosine mimetic, 4-[difluoro(phosphono)methyl]-L-phenylalanine (F₂Pmp) for the enrichment of protein tyrosine phosphatases (PTPs). We found that different F₂Pmp probes can enrich different PTPs, depending on the probe sequence. Furthermore, proteins containing a Src homology 2 (SH2) domain were enriched together. Importantly, probes containing phosphotyrosine instead of F₂Pmp failed to enrich PTPs due to dephosphorylation during the pulldown step. This enrichment approach using peptides containing F₂Pmp could be a generic tool for tyrosine phosphatome analysis without the use of antibodies.     

X-ray microanalysis of etoposide-induced apoptosis in the PC-3 prostatic cancer cell line.

Apoptosis comprises a critical intracellular defense mechanism against tumourigenic growth. We have been interested in the relationship between morphological changes and intracellular concentration of several cations after etoposide-induced apoptosis in androgen-independent prostate cancer cells. SEM and X-ray microanalysis were performed on freeze-dried PC3 cells after etoposide treatment, and correlated with the morphological features observed after examination by light and fluorescence microscopy. Cell viability assays were also performed. A significant decrease in intracellular Cl(-) and K(+)and a progressive increase in Mg(2+) and Na(+) were observed, with parallel changes in cellular volume as cells passed through three morphological stages of apoptosis. The use of EPXRMA made it possible to evaluate alterations in element composition in prostate cancer cell apoptosis and may be a helpful tool for further studies on apoptosis in prostate cancer.     

The essentials of direct xylem pressure measurement

This paper discusses the essentials of the oil‐filled pressure probe technique in the measurement of negative xylem pressures, focusing in particular on the technique and physics underlying our recent, successful experiment which has rekindled the debate on the validity of the Cohesion–Tension theory. We illustrate a number of general problems associated with the cell pressure probe and xylem pressure probe techniques, and propose appropriate criteria for micropipette construction. We enumerate factors dealing with the cavitation problem and suggest methods for eliminating air seeds in the system. We introduce reliable criteria for the successful measurement of xylem pressure, and emphasize the importance of the probe pressure relaxation test. Several problems regarding the controversy over the Cohesion–Tension theory are also discussed. We discuss the correlation between xylem pressure and the transpiration rate, the existence of absolute negative xylem pressure in intact plants, the most negative values of xylem pressure measured by the pressure probe, the agreement between the pressure probe and pressure bomb techniques, and the vulnerability to cavitation (tensile strength) of pressure probes.     

Environmental factors influencing the distribution of rRNA from Verrucomicrobia in soil

The Verrucomicrobia constitute a newly discovered division of the Bacteria identified as a numerically abundant component of soil microbial communities in numerous sites around the world. The relative abundance of rRNA from Verrucomicrobia was investigated in the soil to examine the influence of specific environmental factors on the distribution of Verrucomicrobia and to better understand the distribution of this group in terrestrial ecosystems. The abundance of the verrucomicrobial rRNA was determined by using a novel oligonucleotide probe that is specific for verrucomicrobial 16S rRNA. The abundance of verrucomicrobial 16S rRNA in soil microbial communities was determined in relation to plant community composition and soil management history over a period of 2 years. Additional samples were analyzed to determine if verrucomicrobial rRNA relative abundance changes in relation to either soil depth or soil moisture content. The Verrucomicrobia composed 1.9+/-0.2% of the microbial community rRNA present in the 85 soil samples examined. The distribution of verrucomicrobial rRNA in the soil reveals that Verrucomicrobia are significantly affected by environmental characteristics that change in relation to time, soil history, and soil depth, and reveals that a statistically significant amount of the variation in verrucomicrobial rRNA abundance can be explained by changes in soil moisture content.