Ghosh S et al. (2017) Worm "Non-neuronal cell outgrowth in C. elegans."

Sternberg PW, Vetrone SA, Ghosh S

[Worm, 2017]

Cell outgrowth is a hallmark of some non-migratory developing cells during morphogenesis. Understanding the mechanisms that control cell outgrowth not only increases our knowledge of tissue and organ development, but can also shed light on disease pathologies that exhibit outgrowth-like behavior. C. elegans is a highly useful model for the analysis of genes and the function of their respective proteins. In addition, C. elegans also has several cells and tissues that undergo outgrowth during development. Here we discuss the outgrowth mechanisms of nine different C. elegans cells and tissues. We specifically focus on how these cells and tissues grow outward and the interactions they make with their environment. Through our own identification, and a meta-analysis, we also identify gene families involved in multiple cell outgrowth processes, which defined potential C. elegans core components of cell outgrowth, as well as identify a potential stepwise cell behavioral cascade used by cells undergoing outgrowth.

Ghosh, Rajarshi et al. (2013) International Worm Meeting "Evolution of avermectin resistance in C. briggsae."

Kruglyak, Leonid, Thomas, Cristel, Wang, Wei, Jovelin, Richard, Cutter, Asher, Ghosh, Rajarshi

[International Worm Meeting, 2013]

Several nematode species have evolved resistance to the widely used anthelmintic avermectins (AVM). AVM is produced naturally by S.avermitilis, a ubiquitous soil bacterium. As many nematodes spend part of their life cycle in contact with soil, they are likely to encounter S.avermitilis. Widespread AVM resistance may be a result of different nematode species' ability to counter a common selective pressure, namely the toxins produced by S. avermitilis. To test this hypothesis we surveyed AVM resistance in diverse nematode species. We found that resistance to AVM and to S. avermitilis was prevalent in this phylum. To identify the genetic basis of natural AVM resistance we focused on C. briggsae. We found that two divergent isolates of C. briggsae differed significantly in their responses to AVM. Using QTL mapping approach with these two strains , we identified a significant locus on Chromosome II underlying responses to AVM. We also surveyed 50 isolates of C. briggsae for responses to AVM and found that they exhibit wide variation. The pattern of variation in responses to AVM correlated significantly with the observed phylogeographic pattern in C. briggsae, with temperate isolates being more likely to be resistant than tropical ones. To gain insights into the evolution AVM resistance in C. briggsae, we obtained whole genome sequences of these isolates. Using this data we confirmed that glc-1, the causative gene for natural AVM resistance in C. elegans, is the result of a duplication of another GluCl subunit in the elegans lineage. Thus glc-1 is absent in C. briggsae suggesting that the genetic mechanisms of natural resistance to AVM in C. briggsae are likely different from C. elegans. The sequence data will help us determine if variation in candidate targets for AVM correlate with the pattern of resistance in C. briggsae and map the genetic basis of differences in responses to AVM in C. briggsae .

Ghosh DD et al. (2017) Curr Opin Neurobiol "Multisensory integration in C. elegans."

Ghosh DD, Harris G, Nitabach MN, Zhang Y

[Curr Opin Neurobiol, 2017]

Multisensory integration is a neural process by which signals from two or more distinct sensory channels are simultaneously processed to form a more coherent representation of the environment. Multisensory integration, especially when combined with a survey of internal states, provides selective advantages for animals navigating complex environments. Despite appreciation of the importance of multisensory integration in behavior, the underlying molecular and cellular mechanisms remain poorly understood. Recent work looking at how Caenorhabditis elegans makes multisensory decisions has yielded mechanistic insights into how a relatively simple and well-defined nervous system employs circuit motifs of defined features, synaptic signals and extrasynaptic neurotransmission, as well as neuromodulators in processing and integrating multiple sensory inputs to generate flexible and adaptive behavioral outputs.

Ghosh, Rajarshi et al. (2013) International Worm Meeting "Genetics of praziquantel resistance in C. elegans."

Ghosh, Rajarshi, Levinson, Anya, Tenenbaum, Conrad, Kruglyak, Leonid

[International Worm Meeting, 2013]

The anthelmintic praziquantel (PRZ) is widely used for treating parasitic flatworm infections in human. It is the most-used drug for treating schistosomasis, a debilitating fluke-borne disease. Despite this prevalence, the target of PRZ is still unknown. Dependence on a single drug with unknown target, for a disease affecting 240 million people worldwide, makes the problem of emergence of drug resistance a special concern. The target and mechanism of action of PRZ has been elusive perhaps because it is thought that nematodes are unaffected by this drug. Indeed we found that the laboratory strain N2 is resistant to PRZ relative to other wild isolates of C. elegans. However, we observed that, as in flatworms, PRZ induces spastic paralysis in several nematode species and wild isolates of C. elegans. To identify the genetic targets of PRZ, we mutagenized N2 and Hawaiian (CB4856) strains and selected mutants resistant to high dose of PRZ. We isolated nine and two mutants in the N2 and CB4856 background respectively. Through whole genome sequencing, complementation tests, RNAi and transgenic rescue we identified the first genes contributing to PRZ resistance in C.elegans. Interestingly different genes in the N2 and CB4856 background conferred PRZ resistance. Tissue specific knockdown experiments and epistatsis analysis suggested that PRZ disrupts osmoregulation in C. elegans. We also found that CB4856 animals were significantly more sensitive to PRZ than N2 animals. To identify genetic basis of individual differences in responses to PRZ, we took a quantitative trait loci mapping approach and identified a significant locus on chromosome IV. Currently we are using transgenic rescue to fine map the QTL and testing the interactions between the QTL and the genes identified through mutagenesis. Using classical and quantitative genetic approaches and by studying wild isolates beyond the laboratory strain, we uncovered novel insights into mechanism of action of PRZ .

Ghosh R et al. (2008) J Exp Biol "Episodic swimming behavior in the nematode C. elegans."

Emmons SW, Ghosh R

[J Exp Biol, 2008]

Controlling the choice of behavioral output is a central function of the nervous system. Here we document a novel spontaneous behavioral transition in C. elegans locomotion. Upon transfer of the nematode from a solid surface into a liquid environment, swimming occurs in two phases: an initial, 1-2 h phase of continuous swimming, followed by a second phase during which swimming is episodic. During the second, episodic phase, periods of active swimming alternate in a highly regular fashion with a quiescent state lasting for several minutes. We analyzed the nature of the quiescent state and the basis for spontaneous switching between swimming and quiescence. The transition from swimming to quiescence is promoted by acetylcholine signaling and initially during quiescence body wall muscles are in a state of contraction. After the first minute, quiescent worms respond to prodding and resume swimming normally. The major command interneurons that control the locomotory circuits are not necessary for quiescence since swimming-quiescence cycling occurs after ablation of command interneurons. However, when subsets of neurons including the command interneurons are killed, the switching pattern becomes less regular, suggesting that a timer governing switching may lie within circuitry controlling motor neurons. The results show that the motor circuits have a tendency to switch spontaneously between active and inactive behavioral states. This property might be important to the animal in a uniform environment where sensory input is invariant.

Ghosh, D. D. et al. (2015) International Worm Meeting "Neuroendocrine reinforcement of a dynamic multisensory decision."

Nitabach, M.N., Sanders, T., Cohen, N., Hong, S., Koelle, M.R., Chase, D.L., Ghosh, D. D.

[International Worm Meeting, 2015]

To navigate complex natural environments containing both dangerous and valuable items, animals must make economic decisions on the basis of information transduced by multiple senses. However, detailed underlying neural mechanisms of multisensory decision making remain poorly understood. Here we confronted worms with a multisensory decision in which the reward of food must be balanced with the threat of desiccation imposed by a hyperosmotic barrier intervening between the worm and a source of food odor. We find that this decision is modulated by food deprivation. To identify neural substrates underlying this decision, we focused on the RIM interneuron, which is advantageously positioned to transduce integrated multisensory information into locomotor outputs. Consistent with this hypothesis, we find that the activation of a neuropeptide receptor in RIM sets the balance of threat and reward in this decision, with greater receptor activation biasing the worm against crossing the dangerous barrier. Unexpectedly, however, RIM controls the decision not by synaptic signaling to the downstream premotor command circuit, but rather by extrasynaptic aminergic signaling directly onto the primary osmosensory neuron to tune its sensitivity. Additionally, our results suggest that this neuromodulator relay is suppressed in food deprived states, thereby providing a link between internal state, neural network activity, and decision making. Finally, to characterize the complex and dynamic interplay between neuromodulator activity, neuron state, and behavior in the decision making arena, we reproduced the paradigm in silico [1]. Computational modeling revealed how non-linear sensory integration in RIM modulates neuromodulator circuit activity to implement the decision. Taken together, these studies reveal a cellular and molecular mechanism for a dynamic multisensory decision. Intriguingly, our results identified organizational circuit principles conserved between mammalian and C. elegans multisensory decision making. Therefore our studies have broad implications for understanding principles underlying multisensory decision making in Metazoans.1Sanders, T., Ghosh, D.D., Nitabach, M.N., and Cohen, N. "Nonlinear sensory integration in C. elegans: a computational model." International C. elegans meeting.

Ghosh DD et al. (2021) Science "C. elegans discriminates colors to guide foraging."

Lee D, Ghosh DD, Nitabach MN, Jin X, Horvitz HR

[Science, 2021]

Color detection is used by animals of diverse phyla to navigate colorful natural environments and is thought to require evolutionarily conserved opsin photoreceptor genes. We report that <i>Caenorhabditis elegans</i> roundworms can discriminate between colors despite the fact that they lack eyes and opsins. Specifically, we found that white light guides <i>C. elegans</i> foraging decisions away from a blue-pigment toxin secreted by harmful bacteria. These foraging decisions are guided by specific blue-to-amber ratios of light. The color specificity of color-dependent foraging varies notably among wild <i>C. elegans</i> strains, which indicates that color discrimination is ecologically important. We identified two evolutionarily conserved cellular stress response genes required for opsin-independent, color-dependent foraging by <i>C. elegans</i>, and we speculate that cellular stress response pathways can mediate spectral discrimination by photosensitive cells and organisms-even by those lacking opsins.

Ghosh, Rajarshi et al. (2011) International Worm Meeting "Quantitative genetic dissection of a behavioral sequence in C. elegans."

Kruglyak, Leonid, Ryu, William S., Ghosh, Rajarshi

[International Worm Meeting, 2011]

Individuals within species exhibit heritable variation in sub-steps of a behavioral sequence. How are different parts of a behavioral sequence parsed at the genetic level? What genetic changes and architecture allow for natural variation in substeps of a behavioral sequence? To address these questions we transiently raised the local temperature around a worm and recorded several aspects of the resulting escape response. Upon sensation of a thermal impulse worms exhibit a behavioral sequence in which they enter a pause state followed by reversals, omega turn and resumption of forward movement. We characterized several aspects of the escape response for the laboratory strain (N2) and a wild isolate (CB4856) of C. elegans for stimuli resulting in 0.3, 0.8, 3 or 7.5degC rise in temperature. We found that various aspects of the response to 0.3degC increase in temperature exhibited the greatest difference between these strains. We employed a quantitative trait loci (QTL) mapping approach and measured several traits including but not limited to speeds at every 0.18 seconds during the assay, probability of transition between various states, duration and number of reversals in recombinant inbred lines (RIAIL) made from N2 and CB4856. We identified several QTL suggesting different aspects of the escape response are under distinct genetic control e.g. different phases of speed-profile during the assay were genetically separable. npr-1, shown to be responsible for variation in speed between N2 and CB4856, contributes to variation in pre-stimulus speed and deceleration. QTL on chromosome(chr) IV contributes to variation in acceleration to maximum speed after the thermal impulse. Probability of responding by reversal is regulated by additive QTL on chr V and X. For this trait, F1 worms resulting from reciprocal crosses between N2 and CB4856, responded like CB4856 suggesting molecular loss of function allele(s) in N2. Using introgression lines we narrowed down the QTL interval on chr X to ~90 genes. To determine if the pattern of genetic correlation between different aspects of escape behavior in the RIAILs reflect the broader population of C.elegans we quantified responses of 70 wild isolates of distinct haplotypes. Preliminary analysis suggests abundant phenotypic variation and a pattern of genetic correlation among the different sub-behaviors similar to RIAILs.

Ghosh I et al. (1998) Mol Biochem Parasitol "Thioredoxin peroxidases from Brugia malayi."

Scott AL, Raghavan N, Ghosh I, Eisinger SW

[Mol Biochem Parasitol, 1998]

Parasite-derived antioxidant proteins have been implicated in playing an important role in protection against the oxygen radicals that are generated during aerobic metabolism and in defense against host immune cell attack. Here we report that filarial nematodes include the thioredoxin peroxidase/thiol-specific antioxidant (TPx/TSA) family of antioxidant proteins as part of their complex defense against radical-mediated damage. At the protein level, the TPx/TSA from Brugia malayi (Bm-TPx-1) was approximately 50% identical and approximately 60% similar to TPx/TSAs from mammals, amphibians and yeast. Bm-TPx-1 was also approximately 60% identical to putative TPx proteins from a related filarial nematode, Onchocerca volvulus, and from the free-living nematode Caenorhabditis elegans. That B. malayi may express multiple forms of molecules with TPx/TSA activity was indicated by the identification of a B. malayi gene encoding a second, distinct member of the TPx/TSA family (Bm-tpx-2). Bm-tpx-1 was found to be transcribed in all stages of the parasite present in the mammalian host and the 25 kDa translation product was present in all of the developmental stages studied. The results of immunohistochemical, immunofluorescent and immunoprecipitation studies showed Bm-TPx-1 to be localized in the cells of the hypodermis/lateral chord in adult parasites and not to be present at the surface or in excretory/secretory products. The distribution in the parasite suggests that Bm-TPx-1 may play its major role in countering radicals produced within cells. A recombinant form of Bm-TPx-1 was biologically active and capable of protecting DNA from oxygen radical-mediated damage. Thioredoxin peroxidases may prove to be a critical component in the parasite's defense against injury caused by oxygen radicals derived from endogenous and exogenous sources.

Ghosh K et al. (2010) Biophys J "Cellular proteomes have broad distributions of protein stability."

Ghosh K, Dill K

[Biophys J, 2010]

Biological cells are extremely sensitive to temperature. What is the mechanism? We compute the thermal stabilities of the whole proteomes of Escherichia coli, yeast, and Caenorhabditis elegans using an analytical model and an extensive database of stabilities of individual proteins. Our results support the hypothesis that a cell's thermal sensitivities arise from the collective instability of its proteins. This model shows a denaturation catastrophe at temperatures of 49-55C, roughly the thermal death point of mesophiles. Cells live on the edge of a proteostasis catastrophe. According to the model, it is not that the average protein is problematic; it is the tail of the distribution. About 650 of E. coli's 4300 proteins are less than 4 kcal mol(-1) stable to denaturation. And upshifting by only 4 from 37 to 41C is estimated to destabilize an average protein by nearly 20%. This model also treats effects of denaturants, osmolytes, and other physical stressors. In addition, it predicts the dependence of cellular growth rates on temperature. This approach may be useful for studying physical forces in biological evolution and the role of climate change on biology.