Design and development of a field-deployable single-molecule detector (SMD) for the analysis of molecular markers

Single-molecule detection (SMD) has demonstrated some attractive benefits for many types of biomolecular analyses including enhanced processing speed by eliminating processing steps, elimination of ensemble averaging and single-molecule sensitivity. However, it's wide spread use has been hampered by the complex instrumentation required for its implementation when using fluorescence as the readout modality. We report herein a simple and compact fluorescence single-molecule instrument that is straightforward to operate and consisted of fiber optics directly coupled to a microfluidic device. The integrated fiber optics served as waveguides to deliver the laser excitation light to the sample and collecting the resulting emission, simplifying the optical requirements associated with traditional SMD instruments by eliminating the need for optical alignment and simplification of the optical train. Additionally, the use of a vertical cavity surface emitting laser and a single photon avalanche diode serving as the excitation source and photon transducer, respectively, as well as a field programmable gate array (FPGA) integrated into the processing electronics assisted in reducing the instrument footprint. This small footprint SMD platform was tested using fluorescent microspheres and single AlexaFluor 660 molecules to determine the optimal operating parameters and system performance. As a demonstration of the utility of this instrument for biomolecular analyses, molecular beacons (MBs) were designed to probe bacterial cells for the gene encoding Gram-positive species. The ability to monitor biomarkers using this simple and portable instrument will have a number of important applications, such as strain-specific detection of pathogenic bacteria or the molecular diagnosis of diseases requiring rapid turn-around-times directly at the point-of-use.     

Semipinacol rearrangement of cis-fused β-lactam diols into keto-bridged bicyclic lactams

The 6-azabicyclo[3.2.1]octane ring system, prevalent in a range of biologically active molecules, is prepared through a novel semipinacol rearrangement utilizing a cyclic phosphorane or sulfite intermediate. The rearrangement proceeds with exclusive N-acyl group migration of a β-lactam ring and results in carbonyl functionality at the 7- and bridging 8-position of the bicycle. Precursor ring-fused β-lactam diols are prepared through a sequence of 4-exo trig carbamoyl radical cyclization, regioselective dithiocarbamate group elimination, and dihydroxylation.     

Controlled production of subradiant states of a diatomic molecule in an optical lattice

We report the successful production of subradiant states of a two-atom system in a three-dimensional optical lattice starting from doubly occupied sites in a Mott insulator phase of a quantum gas of atomic ytterbium. We can selectively produce either a subradiant 1(g) state or a superradiant 0(u) state by choosing the excitation laser frequency. The inherent weak excitation rate for the subradiant 1(g) state is overcome by the increased atomic density due to the tight confinement in a three-dimensional optical lattice. Our experimental measurements of binding energies, linewidth, and Zeeman shift confirm the observation of subradiant levels of the 1(g) state of the Yb(2) molecule.     

Neutral Nickel(II) and Copper(II) Tetraazamacrocyclic Complexes as Molecular Rods Attached to Gold Electrodes

New dithiolated derivatives of neutral Cu^II and Ni^II tetraazamacrocyclic complexes have been synthesized and characterized by spectroscopic and diffractional methods. These rod‐shaped molecules were assembled in monocomponent and mixed monolayers on gold electrodes. In the mixed monolayers, the active molecules were embedded in a hexanethiol matrix. The dithiolated complexes are oriented perpendicularly to the electrode, and reveal faster kinetics of electron transfer than those assembled in a single‐component monolayer. They appear as protrusions, which are easily addressed by using the STM method. In the presence of a suitable electron acceptor in the solution, the donor properties of the anchored Cu complex were weakened, which revealed donor–acceptor interactions with the monolayer. The peak position in the voltammogram indicates a stronger interaction of the solution‐based acceptor with the reduced Cu^II form than with the Cu^III complex. This suggests the possibility of switching the association on or off by applying an appropriate potential.     

Intrinsic Ultracontractivity for Stable Semigroups on Unbounded Open Sets

We study the intrinsic ultracontractivity of the semigroup of the isotropic stable process on an unbounded open set. A two-sided estimate of the first eigenfunction of the semigroup is derived. We obtain general geometric conditions for intrinsic ultracontractivity which yield a necessary and sufficient condition for non-degenerate horn-shaped sets. The research was supported by KBN grant 1 P03A 020 28.     

A new method for the synthesis of mixed orthoesters from O-allyl acetals

Two new methods for the synthesis of orthoesters and compounds containing an orthoester moiety (dihydroisoxazoles) are presented. Mixed orthoesters of general formulas RC(OR¹)(OR²)₂ and RC(OR¹)(OR²)(OR³) were prepared via addition of ROH (R = Bu or m-methylphenyl) to O-allyl acetals (acrolein acetals: diethyl or cyclic, i.e., 2-vinyl-1,3-dioxanes or dioxolanes). The catalytic systems for these reactions were generated from [RuCl₂(PPh₃)₃] and Na₂CO₃; {[RuCl₂(COD)]_x} or {[OsCl₂(1,5-COD)]_x}, PPh₃, and Na₂CO₃. Compounds containing an orthoester moiety (dihydroisoxazoles) were prepared via tandem isomerization of O-allyl acetals (to O-vinyl acetals) catalyzed by ruthenium complexes followed by cycloaddition to in situ-generated 2,6-dichlorophenylnitrile oxide.     

Effect of Ellagic Acid on Seizure Threshold in Two Acute Seizure Tests in Mice

Ellagic acid (EA) is a natural dietary polyphenol that has many beneficial properties, including anti-inflammatory, antioxidant, antiviral, antibacterial, and neuroprotective effects. Studies have revealed that EA may modulate seizure activity in chemically induced animal models of seizures. Therefore, the aim of the present study was to investigate the effect of EA on the seizure threshold in two acute seizure tests in male mice, i.e., in the intravenous (i.v.) pentylenetetrazole (PTZ) seizure test and in the maximal electroshock seizure threshold (MEST) test. The obtained results showed that EA (100 mg/kg) significantly elevated the threshold for both the first myoclonic twitch and generalized clonic seizure in the i.v. PTZ seizure test. At the highest dose tested (200 mg/kg), EA increased the threshold for tonic hindlimb extension in the MEST test. EA did not produce any significant changes in motor coordination (assessed in the chimney test) or muscular strength (investigated in the grip-strength test). The plasma and total brain concentration-time profiles of EA after intraperitoneal and oral administration were also determined. Although further studies are necessary to confirm the anticonvulsant activity of EA, our findings suggest that it may modulate seizure susceptibility in animal models.     

Effects of surface functionalization of hydrophilic NaYF<Subscript>4</Subscript> nanocrystals doped with Eu<Superscript>3+</Superscript> on glutamate and GABA transport in brain synaptosomes

Specific rare earth doped nanocrystals (NCs), a recent class of nanoparticles with fluorescent features, have great bioanalytical potential. Neuroactive properties of NaYF₄ nanocrystals doped with Eu³⁺ were assessed based on the analysis of their effects on glutamate- and γ-aminobutyric acid (GABA) transport process in nerve terminals isolated from rat brain (synaptosomes). Two types of hydrophilic NCs were examined in this work: (i) coated by polyethylene glycol (PEG) and (ii) with OH groups at the surface. It was found that NaYF₄:Eu³⁺-PEG and NaYF₄:Eu³⁺-OH within the concentration range of 0.5–3.5 and 0.5–1.5 mg/ml, respectively, did not influence Na⁺-dependent transporter-dependent l-[¹⁴C]glutamate and [³H]GABA uptake and the ambient level of the neurotransmitters in the synaptosomes. An increase in NaYF₄:Eu³⁺-PEG and NaYF₄:Eu³⁺-OH concentrations up to 7.5 and 3.5 mg/ml, respectively, led to the (1) attenuation of the initial velocity of uptake of l-[¹⁴C]glutamate and [³H]GABA and (2) elevation of ambient neurotransmitters in the suspension of nerve terminals. In the mentioned concentrations, nanocrystals did not influence acidification of synaptic vesicles that was shown with pH-sensitive fluorescent dye acridine orange, however, decreased the potential of the plasma membrane of synaptosomes. In comparison with other nanoparticles studied with similar methodological approach, NCs start to exhibit their effects on neurotransmitter transport at concentrations several times higher than those shown for carbon dots, detonation nanodiamonds and an iron storage protein ferritin, whose activity can be registered at 0.08, 0.5 and 0.08 mg/ml, respectively. Therefore, NCs can be considered lesser neurotoxic as compared to above nanoparticles.     

The effect of core and lanthanide ion dopants in sodium fluoride-based nanocrystals on phagocytic activity of human blood leukocytes

Sodium fluoride-based β-NaLnF4 nanoparticles (NPs) doped with lanthanide ions are promising materials for application as luminescent markers in bio-imaging. In this work, the effect of NPs doped with yttrium (Y), gadolinium (Gd), europium (Eu), thulium (Tm), ytterbium (Yb) and terbium (Tb) ions on phagocytic activity of monocytes and granulocytes and the respiratory burst was examined. The surface functionalization of <10-nm NPs was performed according to our variation of patent pending ligand exchange method that resulted in meso-2,3-dimercaptosuccinic acid (DMSA) molecules on their surface. Y-core-based NCs were doped with Eu ions, which enabled them to be excited with UV light wavelengths. Cultures of human peripheral blood (n = 8) were in vitro treated with five different concentrations of eight NPs for 24 h. In summary, neither type of nanoparticles is found toxic with respect to conducted test; however, some cause toxic effects (they have statistically significant deviations compared to reference) in some selected doses tested. Both core types of NPs (Y-core and Gd-core) impaired the phagocytic activity of monocytes the strongest, having minimal or none whatsoever influence on granulocytes and respiratory burst of phagocytic cells. The lowest toxicity was observed in Gd-core, Yb, Tm dopants and near-infrared nanoparticles. Clear dose-dependent effect of NPs on phagocytic activity of leukocytes and respiratory burst of cells was observed for limited number of samples.     

The Overexpression of YALI0B07117g Results in Enhanced Erythritol Synthesis from Glycerol by the Yeast Yarrowia lipolytica

The unconventional yeast Yarrowia lipolytica is used to produce erythritol from glycerol. In this study, the role of the erythrose reductase (ER) homolog YALI0B07117g in erythritol synthesis was analyzed. The deletion of the gene resulted in an increased production of mannitol (308%) and arabitol (204%) before the utilization of these polyols began. The strain overexpressing the YALI0B07117g gene was used to increase the erythritol yield from glycerol as a sole carbon source in batch cultures, resulting in a yield of 0.4 g/g. The specific consumption rate (qs) increased from 5.83 g/g/L for the WT strain to 8.49 g/g/L for the modified strain and the productivity of erythritol increased from 0.28 g/(L h) for the A101 strain to 0.41 g/(L h) for the modified strain. The application of the research may prove positive for shortening the cultivation time due to the increased rate of consumption of the substrate combined with the increased parameters of erythritol synthesis.