Conformational dynamics of a single protein monitored for 24 hours at video rate

We use plasmon rulers to follow the conformational dynamics of a single protein for up to 24 h at a video rate. The plasmon ruler consists of two gold nanospheres connected by a single protein linker. In our experiment, we follow the dynamics of the molecular chaperone heat shock protein 90, which is known to show open and closed conformations. Our measurements confirm the previously known conformational dynamics with transition times in the second to minute time scale and reveals new dynamics on the time scale of minutes to hours. Plasmon rulers thus extend the observation bandwidth 3/4 orders of magnitude with respect to single-molecule fluorescence resonance energy transfer and enable the study of molecular dynamics with unprecedented precision

OLEDs as models for bird magnetoception: detecting electron spin resonance in geomagnetic fields

Certain species of living creatures are known to orientate themselves in the geomagnetic field. Given the small magnitude of approximately 48 mu T, the underlying quantum mechanical phenomena are expected to exhibit coherence times in the microsecond regime. In this contribution, we show the sensitivity of organic light-emitting diodes (OLEDs) to magnetic fields far below Earth's magnetic field, suggesting that coherence times of the spins of charge-carrier pairs in these devices can be similarly long. By electron paramagnetic resonance (EPR) experiments, a lower bound for the coherence time can be assessed directly. Moreover, this technique offers the possibility to determine the distribution of hyperfine fields within the organic semiconductor layer. We extend this technique to a material system exhibiting both fluorescence and phosphorescence, demonstrating stable anticorrelation between optically detected magnetic resonance (ODMR) spectra in the singlet (fluorescence) and triplet (phosphorescence) channels. The experiments demonstrate the extreme sensitivity of OLEDs to both static as well as dynamic magnetic fields and suggest that coherent spin precession processes of coulombically bound electron-spin pairs may play a crucial role in the magnetoreceptive ability of living creatures

Ecological suicide in microbes

The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment. Examples are the cooperative breakdown of complex nutrients in microbes or the construction of elaborate architectures in social insects, in which the individual profits from the collective actions of her peers. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, for example by resource depletion or the production of toxic byproducts. Here we find an extreme type of negative interactions, in which Paenibacillus sp. bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon that we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely to occur with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances-such as antibiotics-can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We found ecological suicide in a wide variety of microbes, suggesting that it could have an important role in microbial ecology and evolution

Modifying and reacting to the environmental pH can drive bacterial interactions

<div><p>Microbes usually exist in communities consisting of myriad different but interacting species. These interactions are typically mediated through environmental modifications; microbes change the environment by taking up resources and excreting metabolites, which affects the growth of both themselves and also other microbes. We show here that the way microbes modify their environment and react to it sets the interactions within single-species populations and also between different species. A very common environmental modification is a change of the environmental pH. We find experimentally that these pH changes create feedback loops that can determine the fate of bacterial populations; they can either facilitate or inhibit growth, and in extreme cases will cause extinction of the bacterial population. Understanding how single species change the pH and react to these changes allowed us to estimate their pairwise interaction outcomes. Those interactions lead to a set of generic interaction motifs—bistability, successive growth, extended suicide, and stabilization—that may be independent of which environmental parameter is modified and thus may reoccur in different microbial systems.</p></div

Single species can enhance or inhibit their own growth via changing the pH.

<p>The curves show bacterial density over time, and the color shows the pH. (a) <i>C</i>. <i>ammoniagenes</i> increases the pH and also prefers these higher pH values, leading to a minimal viable cell density required for survival. Increasing the buffer concentration from 10 mM (−buffer) to 100 mM (+buffer) phosphate makes it more difficult for <i>C</i>. <i>ammoniagenes</i> to alkalize the environment and therefore increases the minimal viable cell density. (b) <i>P</i>. <i>veronii</i> also increases the pH yet prefers low pH values. Indeed, <i>P</i>. <i>veronii</i> populations can change the environment so drastically that it causes the population to go extinct. Adding buffer tempers the pH change and thus allows for the survival of <i>P</i>. <i>veronii</i>. An Allee effect can also be found in <i>L</i>. <i>plantarum</i> and ecological suicide in <i>S</i>. <i>marcescens</i> (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#pbio.2004248.s008" target="_blank">S8 Fig</a>). Note that buffering often just slightly affects the final pH values (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#pbio.2004248.s002" target="_blank">S2 Fig</a>) but saves the population by delaying the pH change (as shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#pbio.2004248.s004" target="_blank">S4 Fig</a> and discussed in more detail in [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#pbio.2004248.ref035" target="_blank">35</a>]). Linlog scale is used for the y-axis. The data for this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#pbio.2004248.s022" target="_blank">S1 Data</a>. Ca, <i>Corynebacterium ammoniagenes</i>; CFU, colony-forming unit; Pv, <i>Pseudomonas veronii</i>.</p

Transient invaders can induce shifts between alternative stable states of microbial communities

Microbial dispersal often leads to the arrival of outsider organisms into ecosystems. When their arrival gives rise to successful invasions, outsider species establish within the resident community, which can markedly alter the ecosystem. Seemingly less influential, the potential impact of unsuccessful invaders that interact only transiently with the community has remained largely ignored. Here, we experimentally demonstrate that these transient invasions can induce a lasting transition to an alternative stable state, even when the invader species itself does not survive the transition. First, we develop a mechanistic understanding of how environmental changes caused by these transient invaders can drive a community shift in a simple, bistable model system. Beyond this, we show that transient invaders can also induce switches between stable states in more complex communities isolated from natural soil samples. Our results demonstrate that short-term interactions with an invader species can induce lasting shifts in community composition and function.National Institutes of Health (U.S.) (Grant R01-GM102311

Bacteria modify the environment and react to it.

<p>(a) A collection of soil bacteria grown in a medium that contains urea and glucose can lower or increase the pH (initially set to pH 7, dashed line). The soil the microbes were isolated from has a buffer capacity similar to the experimental medium (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#pbio.2004248.s002" target="_blank">S2 Fig</a>). Also, growing the soil bacteria in Luria-Bertani medium causes pH changes (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#pbio.2004248.s002" target="_blank">S2 Fig</a>). (b) By changing the environment, bacteria influence themselves but also other microbes in the community. (c) <i>Lactobacillus plantarum</i> and <i>Pseudomonas veronii</i> prefer acidic, <i>Corynebacterium ammoniagenes</i> prefers alkaline, and <i>Serratia marcescens</i> has a slight preference towards alkaline environments. Fold growth in 24 h is shown. The bacteria were grown on buffered medium with low nutrients to minimize pH change during growth (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#sec004" target="_blank">Materials and methods</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#pbio.2004248.s002" target="_blank">S2 Fig</a>). (d) Starting at pH 7, <i>L</i>. <i>plantarum</i> and <i>S</i>. <i>marcescens</i> decrease and <i>C</i>. <i>ammoniagenes</i> and <i>P</i>. <i>veronii</i> increase the pH. Only little buffering, 10 g/L glucose and 8 g/L urea as substrates were used in (d). (e) Microbes can increase or decrease the pH (blue environment is alkaline, and red environment is acidic) and thus produce a more or less suitable environment for themselves. Blue bacteria prefer and/or tolerate alkaline and red acidic conditions. The soil bacteria in (a) were isolated from local soil, whereas the 4 species in (c) to (e) were obtained from a strain library (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#sec004" target="_blank">Materials and methods</a> for details). The data for this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2004248#pbio.2004248.s022" target="_blank">S1 Data</a>. Ca, <i>Corynebacterium ammoniagenes</i>; Lp, <i>Lactobacillus plantarum</i>; Pv, <i>Pseudomonas veronii</i>; Sm, <i>Serratia marcescens</i>.</p