Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.

Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. We hypothesized that an obligate and mutual exchange of metabolites, as is very common among bacterial cells, could stabilize different genotypes within microbial communities. To test this, we developed a cellular automaton to model interactions among six empirically characterized genotypes that differ in their ability and propensity to produce amino acids. By systematically varying intrinsic (i.e. benefit-to-cost ratio) and extrinsic parameters (i.e. metabolite diffusion level, environmental amino acid availability), we show that obligate cross-feeding of essential metabolites is selected for under a broad range of conditions. In spatially structured environments, positive assortment among cross-feeders resulted in the formation of cooperative clusters, which limited exploitation by non-producing auxotrophs, yet allowed them to persist at the clusters' periphery. Strikingly, cross-feeding helped to maintain genotypic diversity within populations, while amino acid supplementation to the environment decoupled obligate interactions and favored auxotrophic cells that saved amino acid production costs over metabolically autonomous prototrophs. Together, our results suggest that spatially structured environments and limited nutrient availabilities should facilitate the evolution of metabolic interactions, which can help to maintain genotypic diversity within natural microbial populations.

Photothermal laser fabrication of micro- and nanostructured chemical templates for directed protein immobilization.

Photothermal patterning of poly(ethylene glycol) terminated organic monolayers on surface-oxidized silicon substrates is carried out using a microfocused beam of a CW laser operated at a wavelength of 532 nm. Trichlorosilane and trimethoxysilane precursors are used for coating. Monolayers from trimethoxysilane precursors show negligible unspecific protein adsorption in the background, i.e., provide platforms of superior protein repellency. Laser patterning results in decomposition of the monolayers and yields chemical templates for directed immobilization of proteins at predefined positions. Characterization is carried out via complementary analytical methods including fluorescence microscopy, atomic force microscopy, and scanning electron microscopy. Appropriate labeling techniques (fluorescent markers and gold clusters) and substrates (native and thermally oxidized silicon substrates) are chosen in order to facilitate identification of protein adsorption and ensure high sensitivity and selectivity. Variation of the laser parameters at a 1/e(2) spot diameter of 2.8 µm allows for fabrication of protein binding domains with diameters on the micrometer and nanometer length scale. Minimum domain sizes are about 300 nm. In addition to unspecific protein adsorption on as-patterned monolayers, biotin-streptavidin coupling chemistry is exploited for specific protein binding. This approach represents a novel facile laser-based means for fabrication of protein micro- and nanopatterns. The routine is readily applicable to femtosecond laser processing of glass substrates for the fabrication of transparent templates.

'Phytochip': on-chip detection of phytopathogenic RNA viruses by a new surface plasmon resonance platform.

The surface plasmon resonance (SPR) based 'Phytochip' was developed to distinguish virus-infected plants from non-infected plants. The system detects DNA-RNA hybridization to show the presence of phytopathogenic viruses such as the RNA virus barley stripe mosaic virus (BSMV) in wheat leaves. To achieve this BSMV and wheat specific oligonucleotides, and a negative control yeast oligonucleotide, were immobilized on a SPR gold surface chip. After optimization of the hybridization parameters with purified wheat samples, wheat infected with BSMV resulted in detectable signals with both the BSMV and the wheat probes. In contrast, a hybridization reaction was not be detected with the negative probe. The method is fast and sensitive with a detection time of 3000s (50min), a detection limit of 14.7pgµl(-1) BSMV RNA and a measuring range of 14.7-84pgµl(-1) BSMV RNA (1.323-7.56ng BSMV RNA per 90µl sample). These characteristics, combined with the high throughput design, make it suitable for application in plant breeding and virus control.

Substrate-mediated effects in photothermal patterning of alkanethiol self-assembled monolayers with microfocused continuous-wave lasers.

In recent years, self-assembled monolayers (SAMs) have been demonstrated to provide promising new approaches to nonlinear laser processing. Most notably, because of their ultrathin nature, indirect excitation mechanisms can be exploited in order to fabricate subwavelength structures. In photothermal processing, for example, microfocused lasers are used to locally heat the substrate surface and initiate desorption or decomposition of the coating. Because of the strongly temperature-dependent desorption kinetics, the overall process is highly nonlinear in the applied laser power. For this reason, subwavelength patterning is feasible employing ordinary continuous-wave lasers. The lateral resolution, generally, depends on both the type of the organic monolayer and the nature of the substrate. In previous studies we reported on photothermal patterning of distinct types of SAMs on Si supports. In this contribution, a systematic study on the impact of the substrate is presented. Alkanethiol SAMs on Au-coated glass and silicon substrates were patterned by using a microfocused laser beam at a wavelength of 532 nm. Temperature calculations and thermokinetic simulations were carried out in order to clarify the processes that determine the performance of the patterning technique. Because of the strongly temperature-dependent thermal conductivity of Si, surface-temperature profiles on Au/Si substrates are very narrow ensuring a particularly high lateral resolution. At a 1/e spot diameter of 2 µm, fabrication of subwavelength structures with diameters of 300-400 nm is feasible. Rapid heat dissipation, though, requires high laser powers. In contrast, patterning of SAMs on Au/glass substrates is strongly affected by the largely distinct heat conduction within the Au film and in the glass support. This results in broad surface temperature profiles. Hence, minimum structure sizes are larger when compared with respective values on Au/Si substrates. The required laser powers, though, are more than one order of magnitude lower. Also, the laser power needed for patterning decreases with decreasing Au layer thickness. These results demonstrate the impact of the substrate on the overall patterning process and provide new perspectives in photothermal laser patterning of ultrathin organic coatings.

Characterization and expression analysis of a gene cluster for nitrate assimilation from the yeast Arxula adeninivorans.

In Arxula adeninivorans nitrate assimilation is mediated by the combined actions of a nitrate transporter, a nitrate reductase and a nitrite reductase. Single-copy genes for these activities (AYNT1, AYNR1, AYNI1, respectively) form a 9103 bp gene cluster localized on chromosome 2. The 3210 bp AYNI1 ORF codes for a protein of 1070 amino acids, which exhibits a high degree of identity to nitrite reductases from the yeasts Pichia anomala (58%), Hansenula polymorpha (58%) and Dekkera bruxellensis (54%). The second ORF (AYNR1, 2535 bp) encodes a nitrate reductase of 845 residues that shows significant (51%) identity to nitrate reductases of P. anomala and H. polymorpha. The third ORF in the cluster (AYNT1, 1518 bp) specifies a nitrate transporter with 506 amino acids, which is 46% identical to that of H. polymorpha. The three genes are independently expressed upon induction with NaNO(3). We quantitatively analysed the promoter activities by qRT-PCR and after fusing individual promoter fragments to the phytase (phyK) gene from Klebsiella sp. ASR1. The AYNI1 promoter was found to exhibit the highest activity, followed by the AYNT1 and AYNR1 elements. Direct measurements of nitrate and nitrite reductase activities performed after induction with NaNO(3) are compatible with these results. Both enzymes show optimal activity at around 42 degrees C and near-neutral pH, and require FAD as a co-factor and NADPH as electron donor.