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

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

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

[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.

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

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

[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."

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

[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."

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

[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).

Chris Gabel et al. (2004) East Coast Worm Meeting "Quantification of electrotaxis"

Dmitri Pavlichin, Chris Gabel, Aravi Samuel, Albert Kao

[East Coast Worm Meeting, 2004]

In an electric field, the worm has preferred trajectories for forward crawling movement that depend on the direction and magnitude of the electric field. In weak fields (<5 V/cm), worms tend to crawl towards either the positive or negative pole. In moderate fields, ~5 V/cm, worms crawl straight towards the negative pole. In stronger fields, >5 V/cm, worms crawl towards the negative pole in trajectories at an angle to the direction of the field. The angle of approach towards the negative pole increases with field strength, rising from 0 degrees (parallel to the field lines) towards 90 degrees (perpendicular to the field lines). We have quantified these electrotactic movements by tracking wild-type and mutant worms crawling over agar surfaces containing different types and concentrations of ions while responding to electric fields varied in amplitude, frequency, and direction.

Mendoza, S. et al. (2017) International Worm Meeting "W-TEM: A microscope to study C. elegans behavior under external stimulations."

Lam, B., Mendoza, S., D'Orazio, E., Sherry, T., Madruga, B., Mai, P., Arisaka, K., Jiang, K.

[International Worm Meeting, 2017]

The ability to monitor neural activity in freely behaving animals is important in determining neural mechanisms responsible for behavior. Real time worm tracking with neuronal observation has been used to study worm behavior in freely moving C. elegans. However, few setups have attempted to use worm tracking in conjunction with behavioral stimulations. The difficulty being that most behavioral stimulations used to study C. elegans such as electrotaxis and thermotaxis are difficult to incorporate into existing worm tracking platforms. We present a novel microscope platform, W-TEM ( Worm Tracking Epifluorescence Microscope), to bridge this gap in our understanding of worm behavior. The microscope is a standard wide field epi-fluorescence microscope placed on top of a stable platform to move the microscope as it tracks along the sample plane, accommodating most C. elegans behavioral stimulations. This microscope can incorporate a stimulation system that covers 20 cm x 20 cm of worm area movement, 50 cm x 50 cm of total size, and a height of up to 30 cm, which is larger than most other stimulation systems. It can take data at video rate 30 fps, for cameleon ratiometic imaging, as well as monitor whole worm behavior. In addition, our platform can be moved easily between different experiments, using a system of rails that is attached to the microscope platform. Using this system, we have been able to study both Electrotaxis and Thermotactic behaviors using the same system. In the case of Electrotaxis, we have found that high voltages corresponding to 8V/cm create a dampening effect of worm motion, possibly due to paralyzing the lower half of the worm body. We also conduct investigations into the AFD and AIY neurons during isothermal behavior and find a phase lag of 0.8 seconds between neural activity and head location during isothermal tracking.

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

Kovacs IA, Wytock TP, Harris MR

[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."

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

[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.

Wang Y et al. (2020) Sci Total Environ "Assessing the combined toxicity of carbamate mixtures as well as organophosphorus mixtures to Caenorhabditis elegans using the locomotion behaviors as endpoints."

Wang ZJ, Xu YQ, Wang Y, Liu SS, Huang P

[Sci Total Environ, 2020]

Carbamate pesticides (CMs) and organophosphorus pesticides (OPs) have been widely used in agriculture and toxicologically affect non-target organisms. Although there are many reports about their toxicities, the combined behavioral toxicities of CM/OP mixtures on Caenorhabditis elegans have rarely been studied. In this study, body bend inhibition (BBI), head thrash inhibition (HTI), and swimming speed inhibition (SSI) by CMs and OPs were chosen as the toxicity endpoints. The locomotion behavioral toxicities of individual pesticides (carbofuran (CAR), methomyl (MET), chlorpyrifos (CPF), and triazophos (TAP)) and their binary mixtures on C. elegans were determined systematically and the toxicological interaction profiles of various CM/OP mixture rays constructed using the combination index. It was shown that four pesticides and their binary mixture rays have significant inhibitory effects on the locomotion behavior of C. elegans; that is, they produce locomotion behavioral toxicities and the toxicity of two OPs is higher than those of two CMs. The toxicological interactions in the binary CM and OP mixtures are different from each other. For example, one mixture ray (CAR-MET-R1) in the CM system on the SSI endpoint exhibits synergism at all concentration levels, another ray (CAR-MET-R3) displays low-dose synergism and high-dose additive action on BBI and HTI endpoints, and weak synergism at high-dose on SSI, and other rays perform additive action. Two rays (CPF-TAP-R1 and CPF-TAP-R2) in the OP mixture system display low-dose additive action and high-dose antagonism on the three endpoints. Another ray (CPF-TAP-R3) shows the additive action at all concentration levels. It can be concluded that it is not sufficient to evaluate the combined toxicity of binary CM/OP mixtures using only one concentration ratio ray and that it is necessary to examine multiple concentration ratios.