Biofilm formation of a bacterial consortium on linuron at micropollutant concentrations in continuous flow chambers and the impact of dissolved organic matter

Bacterial multispecies biofilms are catalysts for pollutant degradation in aqueous ecosystems. Their activity in systems where xenobiotics occur as micropollutants (μg L(-1) level) and natural dissolved organic matter provides carbon and energy instead remains uncharacterized. Biofilm formation of a bacterial consortium consisting of the linuron-degrading Variovorax sp. WDL1 and metabolite-degrading strains Comamonas sp. WDL7 and Hyphomicrobium sp. WDL6 at micropollutant linuron concentrations and the impact of auxiliary carbon sources on degradation and biofilm composition were investigated. Biofilms formed at concentrations of 1000, 100, and 10 μg L(-1) linuron. The highest biomass, organized in mixed-species mounds, was observed at 1000 μg L(-1) linuron, while at 100 and 10 μg L(-1) , thin layers of cells occurred. Linuron removal efficiencies decreased from c. 85% when fed with 100 and 1000 μg L(-1) linuron to 30% in case of 10 μg L(-1) linuron due to reduced specific activity. Biofilms grown on 10 μg L(-1) linuron were subsequently fed with easily and less degradable carbon sources in addition to 10 μg L(-1) linuron. Although co-feeding with more degradable C-sources increased biofilm biomass, linuron removal remained 30%. Calculations based on biofilm volume measurements pointed toward reduced specific activity, compensated by a higher biomass. Uncertainties about biofilm heterogeneity and cell volume can undo this explanation.

A surface-bound molecule that undergoes optically biased Brownian rotation

Developing molecular systems with functions analogous to those of macroscopic machine components, such as rotors, gyroscopes and valves, is a long-standing goal of nanotechnology. However, macroscopic analogies go only so far in predicting function in nanoscale environments, where friction dominates over inertia. In some instances, ratchet mechanisms have been used to bias the ever-present random, thermally driven (Brownian) motion and drive molecular diffusion in desired directions. Here, we visualize the motions of surface-bound molecular rotors using defocused fluorescence imaging, and observe the transition from hindered to free Brownian rotation by tuning medium viscosity. We show that the otherwise random rotations can be biased by the polarization of the excitation light field, even though the associated optical torque is insufficient to overcome thermal fluctuations. The biased rotation is attributed instead to a fluctuating-friction mechanism in which photoexcitation of the rotor strongly inhibits its diffusion rate.

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).

Cellular localization and dynamics of the Mrr type IV restriction endonuclease of Escherichia coli

In this study, we examined the intracellular whereabouts of Mrr, a cryptic type IV restriction endonuclease of Escherichia coli K12, in response to different conditions. In absence of stimuli triggering its activity, Mrr was found to be strongly associated with the nucleoid as a number of discrete foci, suggesting the presence of Mrr hotspots on the chromosome. Previously established elicitors of Mrr activity, such as exposure to high (hydrostatic) pressure (HP) or expression of the HhaII methyltransferase, both caused nucleoid condensation and an unexpected coalescence of Mrr foci. However, although the resulting Mrr/nucleoid complex was stable when triggered with HhaII, it tended to be only short-lived when elicited with HP. Moreover, HP-mediated activation of Mrr typically led to cellular blebbing, suggesting a link between chromosome and cellular integrity. Interestingly, Mrr variants could be isolated that were specifically compromised in either HhaII- or HP-dependent activation, underscoring a mechanistic difference in the way both triggers activate Mrr. In general, our results reveal that Mrr can take part in complex spatial distributions on the nucleoid and can be engaged in distinct modes of activity.

Photoswitchable fluorescent proteins for superresolution fluorescence microscopy circumventing the diffraction limit of light

In the last two decades, fluorescent proteins became an indispensable tool to noninvasively label a protein in living cells. The discovery of photoswitchable fluorescent proteins expanded the applications of the fluorescent proteins to techniques such as molecular tracking and highlighting on a microscope. Recently, a new microscopic modality to achieve a superresolution circumventing the diffraction limit of light (photoactivated localization microscopy, PALM) has been developed based on the photoswitchable fluorescent proteins. Here we introduce a basic protocol of PALM through the visualization of actin bundles with superresolution.

Delayed electron–hole pair recombination in iron(iii)-oxo metal–organic frameworks

The photodynamic properties of a series of Fe(iii)-MOFs have been examined via redox reactions with N,N,N′,N′-tetramethyl-p-phenylenediamine as an electron donor and methyl viologen as an electron acceptor. Furthermore, photogeneration of long-lived species in MIL-88B(Fe) has been proven via transient absorption spectroscopy.

Fabrication of silver nanoparticles with limited size distribution on TiO2 containing zeolites

Fabrication of silver nanoparticles with limited size distribution on TiO₂ containing zeolites.

X-ray irradiation-induced formation of luminescent silver clusters in nanoporous matrices

The formation of highly luminescent silver clusters in zeolites using X-ray lithography is reported in this study.

Excited state dynamics of photoswitchable fluorescent protein Padron

The key events in the light-induced switching mechanism of the photochromic green fluorescent protein Padron have been investigated by employing femtosecond fluorescence up-conversion, femtosecond transient absorption, and time-correlated single photon counting techniques. In contrast to Dronpa, excitation of protein's neutral state at 395 nm triggers an efficient and complex photoswitching to a dark state whereas irradiation with 495 nm light reverses the protein to its initial state restoring the bright fluorescence. On the basis of the kinetics observed upon irradiation of the chromophore in the protonated state, we suggest that the switching mechanism consists of a light-initiated excited state process (presumably ESPT) with a time constant of 1 ps producing an unstable intermediate state, tentatively assigned to the excited state of the cis-anionic form, that is followed by a cis- to trans- isomerization (14.5 ps) forming the trans-anionic state in which the dark chromophore resides. In the trans-state, the protonation equilibrium strongly favors the anionic form. Consequently, upon excitation of the formed anionic species a trans-cis isomerization of the chromophore was found to occur with a time constant as fast as 5.2 ps switching the chromophore quantitatively to the bright (anionic) state.

Auto-production of biosurfactants reverses the coffee ring effect in a bacterial system

The deposition of material at the edge of evaporating droplets, known as the ‘coffee ring effect’, is caused by a radially outward capillary flow. This phenomenon is common to a wide array of systems including colloidal and bacterial systems. The role of surfactants in counteracting these coffee ring depositions is related to the occurrence of local vortices known as Marangoni eddies. Here we show that these swirling flows are universal, and not only lead to a uniform deposition of colloids but also occur in living bacterial systems. Experiments on Pseudomonas aeruginosa suggest that the auto-production of biosurfactants has an essential role in creating a homogeneous deposition of the bacteria upon drying. Moreover, at biologically relevant conditions, intricate time-dependent flows are observed in addition to the vortex regime, which are also effective in reversing the coffee ring effect at even lower surfactant concentrations.

The coffee ring effect is commonly observed in drying droplets containing suspended matter leading to a deposition at the droplet edge. Sempels et al. show that self-generated biosurfactants in living bacterial systems reverse the coffee ring effect and result in a homogeneous deposition.

Automatic particle detection in microscopy using temporal correlations

One of the fundamental problems in the analysis of single particle tracking data is the detection of individual particle positions from microscopy images. Distinguishing true particles from noise with a minimum of false positives and false negatives is an important step that will have substantial impact on all further analysis of the data. A common approach is to obtain a plausible set of particles from a larger set of candidate particles by filtering using manually selected threshold values for intensity, size, shape, and other parameters describing a particle. This introduces subjectivity into the analysis and hinders reproducibility. In this paper, we introduce a method for automatic selection of these threshold values based on maximizing temporal correlations in particle count time series. We use Markov Chain Monte Carlo to find the threshold values corresponding to the maximum correlation, and we study several experimental data sets to assess the performance of the method in practice by comparing manually selected threshold values from several independent experts with automatically selected threshold values. We conclude that the method produces useful results, reducing subjectivity and the need for manual intervention, a great benefit being its easy integratability into many already existing particle detection algorithms.

Determination of the bulk scattering parameters of diffusing materials

Diffusors are widely used optical components having numerous applications. They are commonly used to homogenize light beams and to create particular intensity distributions. The angular scattering profile of bulk scattering diffusing materials is determined by three bulk scattering parameters that are, however, not commonly available. This hampers an accurate implementation of bulk diffusors in ray tracing simulations. In this paper, the bulk scattering parameters of a concentration series of milk diluted with water were determined with the inverse adding-doubling method. Using these values as input, the macroscopic angular scattering profile was simulated using ray tracing software. The simulation results were compared to experimental data, and a good agreement between measured and simulated data was found. The method was also proven to be successful when applied to commercial diffusors.

LEDGINs inhibit late stage HIV-1 replication by modulating integrase multimerization in the virions

BACKGROUND

LEDGINs are novel allosteric HIV integrase (IN) inhibitors that target the lens epithelium-derived growth factor (LEDGF)/p75 binding pocket of IN. They block HIV-1 integration by abrogating the interaction between LEDGF/p75 and IN as well as by allosterically inhibiting the catalytic activity of IN.

RESULTS

Here we demonstrate that LEDGINs reduce the replication capacity of HIV particles produced in their presence. We systematically studied the molecular basis of this late effect of LEDGINs and demonstrate that HIV virions produced in their presence display a severe replication defect. Both the late effect and the previously described, early effect on integration contribute to LEDGIN antiviral activity as shown by time-of-addition, qPCR and infectivity assays. The late effect phenotype requires binding of LEDGINs to integrase without influencing proteolytic cleavage or production of viral particles. LEDGINs augment IN multimerization during virion assembly or in the released viral particles and severely hamper the infectivity of progeny virions. About 70% of the particles produced in LEDGIN-treated cells do not form a core or display aberrant empty cores with a mislocalized electron-dense ribonucleoprotein. The LEDGIN-treated virus displays defective reverse transcription and nuclear import steps in the target cells. The LEDGIN effect is possibly exerted at the level of the Pol precursor polyprotein.

CONCLUSION

Our results suggest that LEDGINs modulate IN multimerization in progeny virions and impair the formation of regular cores during the maturation step, resulting in a decreased infectivity of the viral particles in the target cells. LEDGINs thus profile as unique antivirals with combined early (integration) and late (IN assembly) effects on the HIV replication cycle.

Self-assembled organic microfibers for nonlinear optics

While highly desired in integrated optical circuits, multiresponsive and tunable nonlinear optical (NLO) active 1D (sub)wavelength scale superstructures from organic materials are rarely reported due to the strong tendency of organic molecules to self-assembly in centrosymmetric modes. Here a solution-processed assembly approach is reported to generate non-centrosymmetric single-crystalline organic microfibers with a cumulative dipole moment for anisotropic combined second- and third-order NLO.

Bacterial Obg proteins: GTPases at the nexus of protein and DNA synthesis

Obg proteins (also known as ObgE, YhbZ and CgtA) are conserved P-loop GTPases, essential for growth in bacteria. Like other GTPases, Obg proteins cycle between a GTP-bound ON and a GDP-bound OFF state, thereby controlling cellular processes. Interestingly, the in vitro biochemical properties of Obg proteins suggest that they act as sensors for the cellular GDP/GTP pools and adjust their activity according to the cellular energy status. Obg proteins have been attributed a host of cellular functions, including roles in essential cellular processes (DNA replication, ribosome maturation) and roles in different stress adaptation pathways (stringent response, sporulation, general stress response). This review summarizes the current knowledge on Obg activity and function. Furthermore, we present a model that integrates the different functions of Obg by assigning it a fundamental role in cellular physiology, at the hub of protein and DNA synthesis. In particular, we believe that Obg proteins might provide a connection between different global pathways in order to fine-tune cellular processes in response to a given energy status.

Revealing the excited-state dynamics of the fluorescent protein Dendra2

Green-to-red photoconversion is a reaction that occurs in a limited number of fluorescent proteins and that is currently mechanistically debated. In this contribution, we report on our investigation of the photoconvertible fluorescent protein Dendra2 by employing a combination of pump-probe, up-conversion and single photon timing spectroscopic techniques. Our findings indicate that upon excitation of the neutral green state an excited state proton transfer proceeds with a time constant of 3.4 ps between the neutral green and the anionic green states. In concentrated solution we detected resonance energy transfer (25 ps time constant) between green and red monomers. The time-resolved emission spectra suggest also the formation of a super-red species, first observed for DsRed (a red fluorescent protein from the corallimorph species Discosoma) and consistent with peculiar structural details present in both proteins.