Kirby CM et al. (1990) Dev Biol "Mutations in the par genes of Caenorhabditis elegans affect cytoplasmic reorganization during the first cell cycle."

Kirby CM, Kusch M, Kemphues KJ

[Dev Biol, 1990]

A dramatic reorganization of cytoplasm occurs during the first cell cycle in embryos of the nematode, Caenorhabditis elegans. We present here the results of a quantitative study of some of the events during this reorganization in wild-type embryos and in par mutant embryos. The par mutations define a set of genes required for cytoplasmic localization in early embryos. We show that par mutations lead to defects in several events of the reorganization. Mutations in all four of the par genes we studied lead to defects in pseudocleavage and asymmetric redistribution of cortical microfilaments. In addition, some of the par mutations affect streaming of cytoplasm, migration of the pronuclei, and asymmetric shortening of the embryo. We propose that the major function of the par genes might be to orchestrate this initial reorganization of cytoplasm.

Pu S et al. (2010) PLoS One "Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human."

Pu S, Parkinson J, Turinsky AL, Xiong X, Vlasblom J, Wodak SJ, Zhang Z, On T, Emili A, Greenblatt J

[PLoS One, 2010]

Chromatin modification (CM) plays a key role in regulating transcription, DNA replication, repair and recombination. However, our knowledge of these processes in humans remains very limited. Here we use computational approaches to study proteins and functional domains involved in CM in humans. We analyze the abundance and the pair-wise domain-domain co-occurrences of 25 well-documented CM domains in 5 model organisms: yeast, worm, fly, mouse and human. Results show that domains involved in histone methylation, DNA methylation, and histone variants are remarkably expanded in metazoan, reflecting the increased demand for cell type-specific gene regulation. We find that CM domains tend to co-occur with a limited number of partner domains and are hence not promiscuous. This property is exploited to identify 47 potentially novel CM domains, including 24 DNA-binding domains, whose role in CM has received little attention so far. Lastly, we use a consensus Machine Learning approach to predict 379 novel CM genes (coding for 329 proteins) in humans based on domain compositions. Several of these predictions are supported by very recent experimental studies and others are slated for experimental verification. Identification of novel CM genes and domains in humans will aid our understanding of fundamental epigenetic processes that are important for stem cell differentiation and cancer biology. Information on all the candidate CM domains and genes reported here is publicly available.

Rincon S et al. (2019) J Infect Dis "Disrupting Membrane Adaptation Restores In Vivo Efficacy of Antibiotics Against Multidrug-Resistant Enterococci and Potentiates Killing by Human Neutrophils."

Rios R, Dinh AQ, Rincon S, Arias CA, Miller WR, Singh KV, Khan A, Diaz L, Reyes J, Garsin DA, Cruz MR, Tran TT, Panesso D, Shamoo Y

[J Infect Dis, 2019]

Daptomycin resistance in enterococci is often mediated by the LiaFSR system that orchestrates the cell membrane (CM) stress response. Activation of LiaFSR through the response regulator LiaR generates major changes in CM function and architecture (membrane adaptive response), permitting the organism to survive the antibiotic attack. Here, using a laboratory strain of Enterococcus faecalis, we developed a novel Caenorhabditis elegans model of daptomycin therapy and showed that disrupting LiaR-mediated CM adaptation restores the in vivo activity of daptomycin. The LiaR effect was also seen in a clinical strain of DAP-resistant E. faecium using a murine model of peritonitis. Furthermore, alteration of the CM response increased the ability of human-PMNs to readily clear both E. faecalis and MDR-E. faecium. Our results provide proof-of-concept that targeting the CM adaptive response restore the in vivo activity of antibiotics, prevent resistance and enhance the ability of the innate immune system to kill infecting bacteria.

Cheng NN et al. (1995) Genetics "Control of cleavage spindle orientation in Caenorhabditis elegans: the role of the genes par-2 and par-3."

Kirby CM, Cheng NN, Kemphues KJ

[Genetics, 1995]

Polarized asymmetric divisions play important roles in the development of plants and animals. The first two embryonic cleavages of Caenorhabditis elegans provide an opportunity to study the mechanisms controlling polarized asymmetric divisions. The first cleavage is unequal, producing daughters with different sizes and fates. The daughter blastomeres divide with different orientations at the second cleavage; the anterior blastomere divides equally across the long axis of the egg, whereas the posterior blastomere divides unequally along the long axis. We report here the results of our analysis of the genes par-2 and par-3 with respect to their contribution to the polarity of these divisions. Strong loss-of-function mutations in both genes lead to an equal first cleavage and an altered second cleavage. The par-2 mutations lead to transverse spindle orientations in both blastomeres, whereas par-3 mutations lead to longitudinal spindle orientations in both blastomeres. The spindle orientation defects correlate with defects in centrosome movements during both the first and the second cell cycle. Temperature shift experiments with par-2(it5ts) indicate that the par-2(+) activity is not required after the two-cell stage. Analysis of double mutants shows that par-3 is epistatic to par-2. We propose a model wherein par-2(+) and par-3(+) act in concert during the first cell cycle to affect asymmetric modification of the cytoskeleton. This polar modification leads to different behaviors of centrosomes in the anterior and posterior and leads ultimately to blastomere-specific spindle

On T et al. (2010) Proteins "The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses."

Turinsky A, Emili A, Pu S, On T, Zhang Z, Greenblatt J, Gong Y, Wodak SJ, Xiong X, Parkinson J

[Proteins, 2010]

Model organisms such as yeast, fly, and worm have played a defining role in the study of many biological systems. A significant challenge remains in translating this information to humans. Of critical importance is the ability to differentiate those components where knowledge of function and interactions may be reliably inferred from those that represent lineage-specific innovations. To address this challenge, we use chromatin modification (CM) as a model system for exploring the evolutionary properties of their components in the context of their known functions and interactions. Collating previously identified components of CM from yeast, worm, fly, and human, we identified a "core" set of 50 CM genes displaying consistent orthologous relationships that likely retain their interactions and functions across taxa. In addition, we catalog many components that demonstrate lineage specific expansions and losses, highlighting much duplication within vertebrates that may reflect an expanded repertoire of regulatory mechanisms. Placed in the context of a high-quality protein-protein interaction network, we find, contrary to existing views of evolutionary modularity, that CM complex components display a mosaic of evolutionary histories: a core set of highly conserved genes, together with sets displaying lineage specific innovations. Although focused on CM, this study provides a template for differentiating those genes which are likely to retain their functions and interactions across species. As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems.

Khan A et al. (2019) Proc Natl Acad Sci U S A "Antimicrobial sensing coupled with cell membrane remodeling mediates antibiotic resistance and virulence in Enterococcus faecalis."

Singh KV, Ton-That H, Rincon S, Rios R, Miller WR, Cruz MR, Nguyen AH, Davlieva M, Narechania A, Siegel SD, Khan A, Panesso D, Reyes J, Garsin DA, Arias CA, Shamoo Y, Diaz L, Tran TT, Planet PJ, Latorre M, Pemberton O

[Proc Natl Acad Sci U S A, 2019]

Bacteria have developed several evolutionary strategies to protect their cell membranes (CMs) from the attack of antibiotics and antimicrobial peptides (AMPs) produced by the innate immune system, including remodeling of phospholipid content and localization. Multidrug-resistant <i>Enterococcus faecalis,</i> an opportunistic human pathogen, evolves resistance to the lipopeptide daptomycin and AMPs by diverting the antibiotic away from critical septal targets using CM anionic phospholipid redistribution. The LiaFSR stress response system regulates this CM remodeling via the LiaR response regulator by a previously unknown mechanism. Here, we characterize a LiaR-regulated protein, LiaX, that senses daptomycin or AMPs and triggers protective CM remodeling. LiaX is surface exposed, and in daptomycin-resistant clinical strains, both LiaX and the N-terminal domain alone are released into the extracellular milieu. The N-terminal domain of LiaX binds daptomycin and AMPs (such as human LL-37) and functions as an extracellular sentinel that activates the cell envelope stress response. The C-terminal domain of LiaX plays a role in inhibiting the LiaFSR system, and when this domain is absent, it leads to activation of anionic phospholipid redistribution. Strains that exhibit LiaX-mediated CM remodeling and AMP resistance show enhanced virulence in the <i>Caenorhabditis elegans</i> model, an effect that is abolished in animals lacking an innate immune pathway crucial for producing AMPs. In conclusion, we report a mechanism of antibiotic and AMP resistance that couples bacterial stress sensing to major changes in CM architecture, ultimately also affecting host-pathogen interactions.

Pang S et al. (2010) Lab Chip "Implementation of a color-capable optofluidic microscope on a RGB CMOS color sensor chip substrate."

DeModena J, Pang S, Yang C, Wang YM, Cui X, Sternberg P

[Lab Chip, 2010]

We report the implementation of a color-capable on-chip lensless microscope system, termed color optofluidic microscope (color OFM), and demonstrate imaging of double stained Caenorhabditis elegans with lacZ gene expression at a light intensity about 10 mW/cm(2).

Harris MR et al. (2022) Adv Sci (Weinh) "Computational Inference of Synaptic Polarities in Neuronal Networks."

Kovacs IA, Harris MR, Wytock TP

[Adv Sci (Weinh), 2022]

Synaptic polarity, that is, whether synapses are inhibitory (-) or excitatory (+), is challenging to map, despite being a key to understand brain function. Here, synaptic polarity is inferred computationally considering three experimental scenarios, depending on the nature of available input data, using the Caenorhabditis elegans connectome as an example. First, the inputs consist of detailed neurotransmitter (NT) and receptor (R) gene expression, integrated through the connectome model (CM). The CM formulates the problem through a wiring rule network that summarizes how NT-R pairs govern synaptic polarity, and resolves 356 synaptic polarities in addition to the 1752 known polarities. Second, known synaptic polarities are considered as an input, in addition to the NT and R gene expression data, but without wiring rules. These data train the spatial connectome model, which infers the polarity of 81% of the CM-resolved connections at >95% precision, while also inferring 147 of the remaining unknown polarities. Last, without known expression or wiring rules, polarities are inferred through a network sign prediction problem. As an illustration of high performance in this case, the generalized CM is introduced. These results address imminent challenges in unveiling large-scale synaptic polarities, an essential step toward more realistic brain models.

Reina A et al. (2013) PLoS One "Shifts in the distribution of mass densities is a signature of caloric restriction in Caenorhabditis elegans."

Samuel AD, Whitesides GM, Laromaine A, Reina A, Subramaniam AB

[PLoS One, 2013]

Although the starvation response of the model multicellular organism Caenorhabditis elegans is a subject of much research, there is no convenient phenotypic readout of caloric restriction that can be applicable to large numbers of worms. This paper describes the distribution of mass densities of populations of C. elegans, from larval stages up to day one of adulthood, using isopycnic centrifugation, and finds that density is a convenient, if complex, phenotypic readout in C. elegans. The density of worms in synchronized populations of wildtype N2 C. elegans grown under standard solid-phase culture conditions was normally distributed, with distributions peaked sharply at a mean of 1.091 g/cm(3) for L1, L2 and L3 larvae, 1.087 g/cm(3) for L4 larvae, 1.081 g/cm(3) for newly molted adults, and 1.074 g/cm(3) at 24 hours of adulthood. The density of adult worms under starvation stress fell well outside this range, falling to a mean value of 1.054 g/cm(3) after eight hours of starvation. This decrease in density correlated with the consumption of stored glycogen in the food-deprived worms. The density of the worms increased when deprived of food for longer durations, corresponding to a shift in the response of the worms: worms sacrifice their bodies by retaining larvae, which consume the adults from within. Density-based screens with the drug Ivermectin on worms cultured on single plates resulted in a clear bimodal (double-peaked) distribution of densities corresponding to drug exposed and non-exposed worms. Thus, measurements of changes in density could be used to conduct screens on the effects of drugs on several populations of worms cultured on single plates.

Niebur E et al. (1993) Math Biosci "Theory of the locomotion of nematodes: control of the somatic motor neurons by interneurons."

Niebur E, Erdos P

[Math Biosci, 1993]

The only animal of which the complete neural circuitry is known at the submicroscopical level is the nematode Caenorhabditis elegans. This anatomical knowledge is complemented by functional insight from electrophysiological experiments in the related nematode Ascaris lumbricoides, which show that Ascaris motor neurons transmit signals electrotonically and not with unattenuated spikes. We developed a mathematical model for electrotonic neural networks and applied it to the motor nervous system of nematodes. This enabled us to reproduce experimental results in Ascaris quantitatively. In particular, our computed result of the velocity v approximately equal to 6 cm/s of neural excitations in the Ascaris interneurons supports the simple hypothesis that the so-called rapidly moving muscular wave is produced by a neural excitation traveling at the same speed in the interneuron as the muscular wave. In C. elegans, the computed velocity v approximately equal to 8-30 cm/s of signals in the interneurons is much larger than the observed velocity v approximately equal to 0.2 cm/s of the body wave. Therefore, the hypothesis that the muscular wave is produced by a synchronous neural excitation wave cannot hold for C. elegans. We argue that stretch receptor control is the most likely mechanism for the generation of body waves used in the locomotion of C. elegans. Extending the simulation to larger groups of neurons, we found that the neural system of C. elegans can operate purely electrotonically. We demonstrate that the same conclusion cannot be drawn for the nervous system of Ascaris, because in the long (l approximately equal to 30 cm) interneurons the electrotonic signals would be too strongly attenuated. This conclusion is not in contradiction with the experimental findings of electrotonic signal propagation in the motor neurons of Ascaris because the latter are shorter (l approximately equal to 5 cm) than the interneurons.