Controlling the food search behavior in Caenorhabditis elegans

Animals locate and track chemoattractive gradients in the environment to find food. With its small nervous system, Caenorhabditis elegans is a good model system in which to understand how the dynamics of neural activity control this search behaviour. Extensive work on the nematode has identified the neurons that are necessary for the different locomotory behaviours underlying chemotaxis through the use of laser ablation, activity recording in immobilized animals and the study of mutants. However, we do not know theneural activity patterns inC. elegans that are sufficient to control its complex chemotactic behaviour. To understand how the activity inits interneurons coordinate different motor programs to lead the animal to food, here we used optogenetics and new optical tools to manipulate neural activity directly in freely moving animals to evoke chemotactic behaviour. By deducing the classes of activity patterns triggered during chemotaxis and exciting individual neurons with these patterns, we identified interneurons that control the essential locomotory programs for this behaviour. Notably, we discovered that controlling the dynamics of activity in just one interneuron pair (AIY) was sufficient to force the animal to locate, turn towards and track virtual light gradients. Two distinct activity patterns triggered in AIY as the animal moved through the gradient controlled reversals and gradual turns to drive chemotactic behaviour. Because AIY neurons are post-synaptic to most chemosensory and thermosensory neurons8, it is probable that these activity patterns in AIY have an important role in controlling and coordinating different taxis behaviours of the animal.

Germ Layer Fate Choice of Embryonic Stem Cells

How do pluripotent progenitor cells of the embryo decide what they want to become? We asked how the complex network of proteins within the cell are employed by the cell to decide its fate. By studying the temporal changes in the levels of different proteins in the network as cells differentiate, we found that two key components that are crucial to keeping the cell in the progenitor state, Oct4 and Sox2, also helps the cell decide on its new fate. By employing the same factors to both keep a cell pluripotent and to help it choose a future fate, the cell gains the ability to make decisions in the face of conflicting environmental signals.  

All Optical Interrogation of Neural Circuits

We have developed optical methods whereby, we can stimulate the neuron of choice using channel or halo rhodopsin. This could be one specific neuron among several that express the light activated channels. We can also simultaneously measure calcium activity in other neurons. This allows us to measure functional connections between neurons in live animals using light. The movie shows the excitation (calcium sensor GCaMP signal) of a specific neuron using light in the nematode C. elegans. This neuron first lights up, and two downstream neuron then follow suit. 

Signal processing by the HOG MAP kinase pathway:

For a signaling pathway to carry accurate information about its environment, the output of the pathway must closely follow the input. Pathways measuring stimuli that change more rapidly with time need to carry more information. The information capacity of a pathway, i.e., how much information can be transmitted through the pathway per unit time, is proportional to the bandwidth of the pathway. The larger the bandwidth of a signaling pathway, the shorter its response time and the more accurately it can follow a rapidly varying signal. Bandwidth measurements are routinely used to characterize communications systems. We developed an experimental technique combined with a microfluidic device that allows measurement of signaling-pathway bandwidth. We use this technique to measure the in vivo bandwidth of the hyperosmolar signaling pathway (HOG) in the yeast Saccharomyces cerevisiae.

This prototypical pathway, the HOG pathway, is shown to act as a low-pass filter, integrating the signal when it changes rapidly and following it faithfully when it changes more slowly. We studied the dependence of the pathway’s bandwidth on its architecture. We measured previously unknown bounds on all of the in vivo reaction rates acting in this pathway. We found that the two-component Ssk1 branch of this pathway is capable of fast signal integration, whereas the kinase Ste11 branch is not. Our experimental techniques can be applied to other signaling pathways, allowing the measurement of their in vivo kinetics and the quantification of their information capacity.

Genetic drift at expanding frontiers promotes gene segregation:

 A principal tenet of modern evolutionary biology is that Darwinian selection and random genetic drift compete in driving evolutionary change. It is widely accepted that genetic drift can have significant effects on small populations that may even lead to speciation. In large populations, however, randomsampling effects are generally considered weak compared with selection (law of large numbers). A major departure from this paradigmatic behavior occurs when large populations undergo range expansions. The descendents of individuals first settling in a new territory are most likely to dominate the gene pool as the expansion progresses. Random sampling effects among these pioneers results in genetic drift that can have profound consequences on the diversity of the expanding population. Indeed, spatially varying levels of genetic diversity and colonization patterns appear to be correlated in many species. For example, the often observed south–north gradient in neutral genetic diversity on the northern hemisphere is thought to reflect past range expansions induced by glacial cycles. Although these trends indicate that genetic drift during range expansions has shaped the gene pool of many species, the underlying spatial mechanism remains obscure: Diversity gradients are often difficult to interpret and potentially interfere with the signal of spreading beneficial mutations. In fact, a major challenge of present-day population genetics is to decide whether natural selection or a past demographic process is responsible for the prevalence of common mutations.

We use simple microbial systems to study the nature of random genetic drift in range expansions of large populations. We observe chance effects that segregate the gene pool into well defined, sector-like regions of reduced genetic diversity. The genetic segregation on the population level is the consequence of number fluctuations on a much smaller scale, within a thin region of reproducing pioneers at the expanding frontier. We expect these patterns to be a general signature of continuous range expansions in populations exhibiting moderate rates of turnover and migration.

Timing variability in an environmentally regulated development decision:

In a population of genetically identical single cells, variability in the timing of a developmental switch in response to extreme external conditions might be advantageous when dealing with a fluctuating environment. Such variability might allow a genetically identical population of cells to hedge their bets: in response to an unfavorable environment, some cells could undergo the switch while others waited for a while, in case the situation improved .

We chose to study yeast sporulation as an environmentally regulated developmental switch. Sporulation of diploid cells of S. cerevisiae is induced by extreme nutritional deprivation and produces four haploid spores through meiosis. There is a cell-to-cell variability of up to fifteen hours in the timing of sporulation. This timescale is several times the lifetimes of any of the proteins involved in the process.

The process of sporulation roughly involves the following steps: activation of signaling pathways associated with starvation, the transcription of a master transcription factor (Ime1) and its regulation through phosphorylation, a transcriptional cascade three distinct waves of gene expression, spindle pole body separation (at which point the cell is committed to sporulate), meiosis I, meiosis II and spore wall formation.

We followed various sporulation-induced genes in single yeast cells using time-lapse fluorescence microscopy. We showed that the process of sporulation could be split into several uncorrelated time intervals that are marked by the onset of the expression of different sets of genes. We found that among these intervals, the time for entry into meiosis (measured from the activation of the promoter of Ime1 to the onset of the first wave of gene expression) was the most variable. External variables such as cell size, cell cycle phase or nutrient signaling had little effect on the entry time variability. Through the modeling, we predicted that the timing variability should be determined by the internal dynamics of Ime1 and its positive feedback on its own promoter. We confirmed the existence of such a feedback experimentally. Our models showed that tuning the strength of this feedback could change the cell-to-cell variability in the timing of meiosis. We hence predicted quantitatively, the dependence of the timing variability on the dosages of various genes, and confirmed them experimentally.

Specificity in the osmolar and pheromone MAP kinase pathways:

We studied the Osmolar and Pheromone sensing MAP kinase pathways in S. cerevisiae to  find the mechanism by which they achieved specificity. These two pathways have homologous MAPK proteins Hog1 and Fus3, respectively and share the upstream activating kinase Ste11. We showed that individual cells respond to only one of two stimuli even when exposed to both simultaneously suggesting that mutual inhibition may play an important role in achieving specificity of response between these two pathways.

In the near future, we would like to investigate if the other pathways with homologous genes also behave like switches, and show signs of inhibiting each other. Our models predict that the MAP kinase pathways involved pheromone and filamentous growth do indeed have the potential of showing such an either/or response.

Designing Deformable Wireless Networks:

Ad hoc wireless networks can be set up between wireless devices, such as between wireless mobile stations. Such networks can be used to set up communications in areas where no prior infrastructure exists, or where such infrastructure has been destroyed. 

Motivated primarily by thinking about biological problems, we developed algorithms for decentralized wireless ad hoc networks, which would reconfigure themselves based on both current and upcoming demands. The reconfiguration of these networks could be achieved either through power control or through moving the nodes of the network. The task of the network is to get data across from the source to the destination with minimum delay and packet loss.

We invented a decentralized routing algorithm, such that packets would automatically be routed around areas of high congestion. We could also show that such routing was TCP-IP compatible. We then built on this algorithm, and showed that network break-down happens continuously (the length of queues at nodes diverge continuously as a function of the traffic load), and that we can compute the longest relaxation timescale of this network semi-analytically using just the time averaged values of queue heights, and this timescale correlated very well with the mean transit time of packets from source to destination. The correlations approached unity as the traffic loads increased.

We devised another algorithm that would allow such wireless networks to change their topology in a decentralized way, such that network performance improved dramatically. Our algorithms together result in such decentralized networks both routing traffic and deforming their topology in real time, in response to changing demands on them. We are currently implementing another algorithm that we developed to anticipate future needs by designing appropriate filters. The algorithms and the detailed implementations of it have been patented, and might be implemented in upcoming devices.