Channels and transporters of the ClC family serve a variety of physiological functions. Understanding of their gating and transport mechanisms remains incomplete, with disagreement over the extent of protein conformational change involved. Using site-directed fluorescence labeling, we probe ClC-ec1, a prokaryotic ClC, for transport-related structural rearrangements. We specifically label cysteines introduced at several positions in the R helix of ClC-ec1 with AlexaFluor 488, an environment-sensitive fluorophore, and demonstrate that the labeled mutants show H+/Cl- transport activity indistinguishable from that of the wild-type protein. At each position that we examined we observe fluorescence changes upon acidification over the same pH range that is known to activate transport. The fluorescence change is also sensitive to Cl- concentration; furthermore, the Cl- and H+ dependencies are coupled as would be expected if the fluorescence change reflected a conformational change required for transport. Together, the results suggest that the changes in fluorescence report protein conformational changes underlying the transport process. Labeled transporters mutated to remove a glutamate critical to proton-coupled chloride transport retain pH-dependent fluorescence changes, suggesting that multiple residues confer pH dependence on the transport mechanism. These results have implications for models of transport and gating in ClC channels and transporters.

Interacting with biological systems via experiments is important for academia, industry, and education, but access barriers exist due to training, costs, safety, logistics, and spatial separation. High-throughput equipment combined with web streaming could enable interactive biology experiments online, but no such platform currently exists. We present a cloud experimentation architecture (paralleling cloud computation), which is optimized for a class of domain-specific equipments (biotic processing units -BPU) to share and execute many experiments in parallel remotely and interactively at all time. We implemented an instance of this architecture that enables chemotactic experiments with a slime mold Physarum Polycephelum. A user study in the blended teaching and research setting of a graduate-level biophysics class demonstrated that this platform lowers the access barrier for non-biologists, enables discovery, and facilitates learning analytics. This architecture is flexible for integration with various biological specimens and equipments to facilitate scalable interactive online education,

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Hypervisors use software switches to steer packets to and from virtual machines (VMs). These switches frequently need upgrading and customization-to support new protocol headers or encapsulations for tunneling and overlays, to improve measurement and debugging features, and even to add middleboxlike functions. Software switches are typically based on a large body of code, including kernel code, and changing the switch is a formidable undertaking requiring domain mastery of network protocol design and developing, testing, and maintaining a large, complex codebase. Changing how a software switch forwards packets should not require intimate knowledge of its implementation. Instead, it should be possible to specify how packets are processed and forwarded in a high-level domainspecific language (DSL) such as P4, and compiled to run on a software switch. We present PISCES, a software switch derived from Open vSwitch (OVS), a hard-wired hypervisor switch, whose behavior is customized using P4. PISCES is not hard-wired to specific protocols; this independence makes it easy to add new features. We also show how the compiler can analyze the high-level specification to optimize forwarding performance. Our evaluation shows that PISCES performs comparably to OVS and that PISCES programs are about 40 times shorter than equivalent changes to OVS source code.