Ge Y et al. (2021) Food Funct "Naringenin prolongs lifespan and delays aging mediated by IIS and MAPK in Caenorhabditis elegans."

Ge Y, Liu G, Chen H, Wang J, Cui SW, Wang H, Kang J, Jiang Y

[Food Funct, 2021]

Naringenin (NN) is one of the most abundant flavonoids in citrus and grapefruits and has been shown to have antioxidant properties in vitro. The purpose of the study is to examine the antioxidant and anti-aging activities of NN in C. elegans, and to further explore the molecular mechanism. The results showed that NN enhanced the lifespan under normal and oxidative stress induced by H2O2. After treatment with NN, locomotion capability was improved and aging pigment accumulation was suppressed. NN also delayed the paralysis and reversed the defective chemotaxis behavior induced by Abeta protein. Meanwhile, the treatment with NN enhanced the activities of antioxidant enzymes and reduced the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) content. The possible targets and pathways interacting with NN were predicted by network pharmacology. Real-time PCR analysis indicated that NN upregulated the expression levels of daf-16, sek-1 and skn-1, downregulated the expression levels of daf-2, age-1 and akt-1, and further activated sod-3, ctl-1, ctl-2, gst-4 and mtl-1. Moreover, the selected mutant strains were used and molecular docking was conducted to further suggest that IIS and MAPK pathways could be involved in the NN-mediated longevity-promoting effect.

Gotz J et al. (2012) Front Physiol "Alzheimer's disease models and functional genomics-How many needles are there in the haystack?"

Gotz J, Eckert A, Gotz NN, Matamales M, Ittner LM

[Front Physiol, 2012]

Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are complex human brain disorders that affect an increasing number of people worldwide. With the identification first of the proteins that aggregate in AD and FTLD brains and subsequently of pathogenic gene mutations that cause their formation in the familial cases, the foundation was laid for the generation of animal models. These recapitulate essential aspects of the human conditions; expression of mutant forms of the amyloid- protein-encoding APP gene in mice reproduces amyloid- (A) plaque formation in AD, while that of mutant forms of the tau-encoding microtubule-associated protein tau (MAPT) gene reproduces tau-containing neurofibrillary tangle formation, a lesion that is also prevalent in FTLD-Tau. The mouse models have been complemented by those in lower species such as C. elegans or Drosophila, highlighting the crucial role for A and tau in human neurodegenerative disease. In this review, we will introduce selected AD/FTLD models and discuss how they were instrumental, by identifying deregulated mRNAs, miRNAs and proteins, in dissecting pathogenic mechanisms in neurodegenerative disease. We will discuss some recent examples, which includes miRNA species that are specifically deregulated by A, mitochondrial proteins that are targets of both A and tau, and the nuclear splicing factor SFPQ that accumulates in the cytoplasm in a tau-dependent manner. These examples illustrate how a functional genomics approach followed by a careful validation in experimental models and human tissue leads to a deeper understanding of the pathogenesis of AD and FTLD and ultimately, may help in finding a cure.

Wan CC et al. (2015) IEEE/ACM Trans Comput Biol Bioinform "Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods."

Wan CC, Freitas AA, de Magalhaes JP

[IEEE/ACM Trans Comput Biol Bioinform, 2015]

Ageing is a highly complex biological process that is still poorly understood. With the growing amount of ageing-related data available on the web, in particular concerning the genetics of ageing, it is timely to apply data mining methods to that data, in order to try to discover novel patterns that may assist ageing research. In this work, we introduce new hierarchical feature selection methods for the classification task of data mining and apply them to ageing-related data from four model organisms: Caenorhabditis elegans (worm), Saccharomyces cerevisiae (yeast), Drosophila melanogaster (fly), and Mus musculus (mouse). The main novel aspect of the proposed feature selection methods is that they exploit hierarchical relationships in the set of features (Gene Ontology terms) in order to improve the predictive accuracy of the Naive Bayes and 1-Nearest Neighbour (1-NN) classifiers, which are used to classify model organisms' genes into pro-longevity or anti-longevity genes. The results show that our hierarchical feature selection methods, when used together with Naive Bayes and 1-NN classifiers, obtain higher predictive accuracy than the standard (without feature selection) Naive Bayes and 1-NN classifiers, respectively. We also discuss the biological relevance of a number of Gene Ontology terms very frequently selected by our algorithms in our datasets.

Shen X et al. (2010) Neuronal Development, Synaptic Function and Behavior, Madison, WI "Biomechanical analysis of C. elegans motility"

Arratia P E, Krajacic P, Lamitina T, Purohit P, Shen X

[Neuronal Development, Synaptic Function and Behavior, Madison, WI, 2010]

Previous studies of C. elegans motility have focused mainly on simple quantitative assays, such as the ''thrashing'' assay. More recently, quantitative approaches have been used to study nematode kinematics. Such quantitative approaches could provide a new level of phenotypic resolution to the study of C. elegans motility. We recently developed a simple mathematical model to describe the C. elegans swim gait. This model provides estimates for the biomechanical properties of motility including force, power, tissue viscosity, and Young''s modulus. Here, we used high-speed video as well as image analysis and particle tracking methods to experimentally measure the forces imparted on the surrounding fluid by a swimming C. elegans. Analysis of the local forces (propulsive and lateral) over the wave period is computed by performing a simple force balance and by coupling the fluid velocity field with the nematode body postures. The propulsive force shows a sharp peak as the lateral force approaches zero. The magnitude of the peak propulsive force (i.e. thrust) and the average mechanical power of a swimming nematode in M9 solution are approximately 3.0 nN and 2.0 pW. By comparison, values of force and power estimated using theoretical models are approximately 3.5 nN and 5.0 pW. These data provide experimental validation for our model of motility and demonstrate that biomechanical phenotyping can provide a sensitive and quantitative phenotypic metric for the analysis of C. elegans motility.

Jago A et al. (2014) J Vis Exp "Single wavelength shadow imaging of Caenorhabditis elegans locomotion including force estimates."

Raley-Susman KM, Kpulun T, Jago A, Magnes J

[J Vis Exp, 2014]

This study demonstrates an inexpensive and straightforward technique that allows the measurement of physical properties such as position, velocity, acceleration and forces involved in the locomotory behavior of nematodes suspended in a column of water in response to single wavelengths of light. We demonstrate how to evaluate the locomotion of a microscopic organism using Single Wavelength Shadow Imaging (SWSI) using two different examples. The first example is a systematic and statistically viable study of the average descent of C. elegans in a column of water. For this study, we used living and dead wildtype C. elegans. When we compared the velocity and direction of nematode active movement with the passive descent of dead worms within the gravitational field, this study showed no difference in descent-times. The average descent was 1.5 mm/sec +/- 0.1 mm/sec for both the live and dead worms using 633 nm coherent light. The second example is a case study of select individual C. elegans changing direction during the descent in a vertical water column. Acceleration and force are analyzed in this example. This case study demonstrates the scope of other physical properties that can be evaluated using SWSI while evaluating the behavior using single wavelengths in an environment that is not accessible with traditional microscopes. Using this analysis we estimated an individual nematode is capable of thrusting with a force in excess of 28 nN. Our findings indicate that living nematodes exert 28 nN when turning, or moving against the gravitational field. The findings further suggest that nematodes passively descend in a column of water, but can actively resist the force of gravity primarily by turning direction.

Petzold, Bryan C. et al. (2011) International Worm Meeting "Influence of Body Mechanics on Force Thresholds for Touch Sensation in C. elegans."

Park, Sung-Jin, Pruitt, Beth L., Goodman, Miriam B., Petzold, Bryan C.

[International Worm Meeting, 2011]

We assessed the interplay between body mechanics and touch sensitivity by modulating muscle tone with Channelrhodopsin-2 and measuring force thresholds with a novel force-clamp metrology. Touch sensation is poorly understood despite the prevalence of disrupted touch and associated pain in pervasive diseases like diabetes. C. elegans is an ideal model for touch with its six touch receptor neurons (TRNs) and behavioral response to gentle touch. Force applied to the body results in stress/strain of nearby TRNs, triggering opening of force-gated ion channels, cellular depolarization, and an avoidance response for sufficiently large forces. Previously, we developed a behavioral force-clamp metrology capable of applying nN-mN forces to moving L4/young adult animals (Park et al, Rev Sci Instr, in press). Using this metrology, we showed that wild-type (N2) animals respond to forces ³ 100 nN, revealing unprecedented mechanical sensitivity. Previously, we showed that the three-layered outer shell (cuticle, hypodermis, and body wall muscle) plays a crucial role in filtering and transmitting applied forces (Park et al, PNAS 104:17376, 2007) and that body wall muscle tone regulates body mechanics (Petzold et al, Biophys J, in press). Now, we are testing the hypothesis that changes in body mechanics modulate touch sensitivity. To do this, we compare force-response curves in un-stimulated and hyper-contracted animals. Preliminary results show that larger forces are needed to evoke avoidance responses in hyper-contracted animals. We used light to manipulate body wall muscle contraction in transgenic animals expressing ChR2 under the control of a body wall muscle-specific promoter. This study provides a way to study the interplay between body mechanics and touch sensitivity in C. elegans and will further our understanding of the role of the outer shell in filtering and transmitting loads to the TRNs.

How, J.J. et al. (2019) International Worm Meeting "Graph-theoretic analysis of whole-brain imaging reveals stimulus-specific changes in patterns of neural activity."

How, J.J., Navlakha, S., Chalasani, S.H.

[International Worm Meeting, 2019]

Patterned neural activity has been shown to underlie the perception of olfactory stimuli. However, most work to date has focused on early stages of sensory processing, and thus it is unclear how the rest of the nervous system interprets information transduced at the sensory periphery. Here, we used whole-brain calcium imaging of thirty immobilized Caenorhabditis elegans to study how different chemical stimuli induce unique patterns of neural activity. We exposed groups of three worms to one of ten conditions: benzaldehyde (BZ), diacetyl (DA), isoamyl alcohol (IAA), 2-nonanone (NN), or NaCl, at either high or low concentrations. We generated networks that describe the functional interactions between neurons using mutual information, and extracted 22 graph-theoretic properties that characterize the network's functional integration, segregation, and resilience. We identified a few properties that can distinguish between low and high stimulus concentrations, one between attractants (BZ, DA, IAA, and a low concentration of NaCl) and repellents (NN and a high concentration of NaCl), and a third set of properties that can accurately classify the attractants. High concentrations of chemical stimuli tend to induce a network that is more functionally segregated, while repellents induce a network with a shorter path between any two neurons. Furthermore, attractants can be grouped by three different properties - the centrality of an average neuron, how often a strongly connected neuron is connected to weakly connected neurons, and the distance between the furthest apart pair of neurons. Importantly, all of these properties have values that are different from those obtained by analyzing the structural connectivity between neurons in the head of the worm. Thus, we conclude that the structural connectome provides a rich substrate that is employed in very distinct ways to support perception and, ultimately, behavior. Many of these graph-theoretic features deal with how efficiently information is transmitted throughout the C. elegans nervous system, and may reflect the saliency of the stimulus in question.

Balasubramaniam M et al. (2024) iScience "Alzheimer's-specific brain amyloid interactome: Neural-network analysis of intra-aggregate crosslinking identifies novel drug targets."

Ayyadevara S, Pahal S, Shmookler Reis RJ, Mainali N, Balasubramaniam M, Ganne A

[iScience, 2024]

Alzheimer's disease (AD) is characterized by peri-neuronal amyloid plaque and intra-neuronal neurofibrillary tangles. These aggregates are identified by the immunodetection of "seed" proteins (A&#x3b2;_1-42 and hyperphosphorylated tau, respectively), but include many other proteins incorporated nonrandomly. Using click-chemistry intra-aggregate crosslinking, we previously modeled amyloid "contactomes" in SY5Y-APP_Sw neuroblastoma cells, revealing that aspirin impedes aggregate growth and complexity. By an analogous strategy, we now construct amyloid-specific aggregate interactomes of AD and age-matched-control&#xa0;hippocampi. Comparing these interactomes reveals AD-specific interactions, from which neural-network (NN) analyses predict proteins with the highest impact on pathogenic aggregate formation and/or stability. RNAi knockdowns of implicated proteins, in <i>C.&#xa0;elegans</i> and human-cell-culture models of AD, validated those predictions. Gene-Ontology meta-analysis of AD-enriched influential proteins highlighted the involvement of mitochondrial and cytoplasmic compartments in AD-specific aggregation. This approach derives dynamic consensus models of aggregate growth and architecture, implicating highly influential proteins as new targets to disrupt amyloid accrual in the AD brain.

Budel RG et al. (2019) Colloids Surf B Biointerfaces "Toxicological evaluation of naringin-loaded nanocapsules in vitro and in vivo."

Boeck CR, da Silva RS, Lopes LQS, Budel RG, Nazario LR, Majolo JH, Santos RCV, da Silva DA, Gomes P, Moreira MP, Dalcin AJF, Antunes Soares FA, da Silva AF

[Colloids Surf B Biointerfaces, 2019]

Naringin is a flavonoid widely known for its pharmacological properties, such as: anti-inflammatory and antioxidant ones, being an ally to avoid oxidative damage. Although naringin is an active easily found in citrus fruits, it has low bioavailability, biodistribution and also undergoes biotransformation in naringenin, limiting the described effects. The use of nanocapsules as drug carriers may increase solubility, improve biodistribution, impede the biotransformation thereof, and thus could improve the performance of naringin for use in treating neurological diseases. Therefore, the objective of this work is to produce a nanocapsule containing naringin, validate an analytical method by RP-HPLC to determination of the drug in nanoparticle and evaluate the toxicity. To that end, the blank nanocapsules (NB, without the drug) or naringin-loaded nanocapsules (NN) at the concentration of 2mg/mL were prepared by interfacial deposition of the preformed polymer and the quantification of naringin by HPLC. Toxicity of the formulations was evaluated in vitro in rat hippocampal slices and in vivo models with C. elegans and Danio rerio (zebrafish). The analytical parameters evaluated (linearity, limit of detection and quantification, specificity, precision, accuracy and robustness) indicated adequate method to assay of naringin in nanocapsules by HPLC. There was no indication of toxicity by the nanocapsules in the evaluated biological assays.

Park SJ et al. (2011) Rev Sci Instrum "Piezoresistive cantilever force-clamp system."

Petzold BC, Pruitt BL, Goodman MB, Park SJ

[Rev Sci Instrum, 2011]

We present a microelectromechanical device-based tool, namely, a force-clamp system that sets or "clamps" the scaled force and can apply designed loading profiles (e.g., constant, sinusoidal) of a desired magnitude. The system implements a piezoresistive cantilever as a force sensor and the built-in capacitive sensor of a piezoelectric actuator as a displacement sensor, such that sample indentation depth can be directly calculated from the force and displacement signals. A programmable real-time controller operating at 100 kHz feedback calculates the driving voltage of the actuator. The system has two distinct modes: a force-clamp mode that controls the force applied to a sample and a displacement-clamp mode that controls the moving distance of the actuator. We demonstrate that the system has a large dynamic range (sub-nN up to tens of N force and nm up to tens of m displacement) in both air and water, and excellent dynamic response (fast response time, &lt;2 ms and large bandwidth, 1 Hz up to 1 kHz). In addition, the system has been specifically designed to be integrated with other instruments such as a microscope with patch-clamp electronics. We demonstrate the capabilities of the system by using it to calibrate the stiffness and sensitivity of an electrostatic actuator and to measure the mechanics of a living, freely moving Caenorhabditis elegans nematode.