Morphological Effects of G-Quadruplex Stabilization Using a Small Molecule in Zebrafish

Zebrafish (Danio rerio) embryos are transparent and advantageous for studying early developmental changes due to ex utero development, making them an appropriate model for studying gene expression changes as a result of molecular targeting. Zebrafish embryos were injected with a previously reported G-quadruplex selective ligand, and the phenotypic changes were recorded. We report marked discrepancies in the development of intersegmental vessels. In silico analysis determined that the putative G-quadruplex motif occur in the upstream promoter region of the Cdh5 (N-cadherin) gene. A real-time polymerase chain reaction-based investigation indicated that in zebrafish, CDH-2 (ZN-cad) was significantly downregulated in the ligand-treated embryos. Biophysical characterization of the interaction of the ligand with the G-quadruplex motif found in this promoter yielded strong binding and stabilization of the G-quadruplex with this ligand. Hence, we report for the first time the phenotypic impact of G-quadruplex targeting with a ligand in a vertebrate organism. This study has unveiled not only G-quadruplex targeting in non-human animal species but also the potential that G-quadruplexes can provide a ready tool for understanding the phenotypic effects of targeting certain important genes involved in differentiation and developmental processes in a living eukaryotic organism.

A Mycobacterial Phosphoribosyltransferase Promotes Bacillary Survival by Inhibiting Oxidative Stress and Autophagy Pathways in Macrophages and Zebrafish

Mycobacterium tuberculosis employs various strategies to modulate host immune responses to facilitate its persistence in macrophages. The M. tuberculosis cell wall contains numerous glycoproteins with unknown roles in pathogenesis. Here, by using Concanavalin A and LC-MS analysis, we identified a novel mannosylated glycoprotein phosphoribosyltransferase, encoded by Rv3242c from M. tuberculosis cell walls. Homology modeling, bioinformatic analyses, and an assay of phosphoribosyltransferase activity in Mycobacterium smegmatis expressing recombinant Rv3242c (MsmRv3242c) confirmed the mass spectrometry data. Using Mycobacterium marinum-zebrafish and the surrogate MsmRv3242c infection models, we proved that phosphoribosyltransferase is involved in mycobacterial virulence. Histological and infection assays showed that the M. marinum mimG mutant, an Rv3242c orthologue in a pathogenic M. marinum strain, was strongly attenuated in adult zebrafish and also survived less in macrophages. In contrast, infection with wild type and the complemented Delta mimG: Rv3242c M. marinum strains showed prominent pathological features, such as severe emaciation, skin lesions, hemorrhaging, and more zebrafish death. Similarly, recombinant Msm Rv3242c bacteria showed increased invasion in non-phagocytic epithelial cells and longer intracellular survival in macrophages as compared with wild type and vector control M. smegmatis strains. Further mechanistic studies revealed that the Rv3242c- and mimG-mediated enhancement of intramacrophagic survival was due to inhibition of autophagy, reactive oxygen species, and reduced activities of superoxide dismutase and catalase enzymes. Infection with MsmRv3242c also activated the MAPK pathway, NF-kappa B, and inflammatory cytokines. In summary, we show that a novel mycobacterial mannosylated phosphoribosyltransferase acts as a virulence and immunomodulatory factor, suggesting that it may constitute a novel target for antimycobacterial drugs.

REPERTOIRE OF PROTEIN KINASES ENCODED IN THE GENOME OF ZEBRAFISH SHOWS REMARKABLY LARGE POPULATION OF PIM KINASES

In recent times, zebrafish has garnered lot of popularity as model organism to study human cancers. Despite high evolutionary divergence from humans, zebrafish develops almost all types of human tumors when induced. However, mechanistic details of tumor formation have remained largely unknown. Present study is aimed at analysis of repertoire of kinases in zebrafish proteome to provide insights into various cellular components. Annotation using highly sensitive remote homology detection methods revealed ``substantial expansion'' of Ser/Thr/Tyr kinase family in zebrafish compared to humans, constituting over 3% of proteome. Subsequent classification of kinases into subfamilies revealed presence of large number of CAMK group of kinases, with massive representation of PIM kinases, important for cell cycle regulation and growth. Extensive sequence comparison between human and zebrafish PIM kinases revealed high conservation of functionally important residues with a few organism specific variations. There are about 300 PIM kinases in zebrafish kinome, while human genome codes for only about 500 kinases altogether. PIM kinases have been implicated in various human cancers and are currently being targeted to explore their therapeutic potentials. Hence, in depth analysis of PIM kinases in zebrafish has opened up new avenues of research to verify the model organism status of zebrafish.

Evaluation of developmental toxicity and apoptotic induction of the aqueous extract of Millettia pachycarpa using zebrafish as model organism

Extensive and indiscriminate use of synthetic compounds and natural compounds obtained from plant sources have resulted in serious threats to the aquatic ecosystem and human health. Aqueous extract of the root of the plant, Milletia pachycarpa Benth, is currently used for killing fish in the state of Manipur, India. Moreover, this plant is also used as traditional medicine in this region. Although it is widely used in traditional medicine, there is limited information available regarding the adverse effects and mechanism underlying its toxicity. This study examined the effects of exposure to aqueous extract of M. pachycarpa (AEMP) on early embryonic development of zebrafish embryos and mechanisms underlying toxicity. Zebrafish embryos treated with different concentrations of the AEMP produced embryonic lethality and developmental defects. The 96-hr-LC50 of AEMP was found to be 4.276 mu g/mL. Further, multiple developmental abnormalities such as pericardial edema, yolk sac edema, spinal curvature, swim bladder deflation, decreased heart rate, and delayed hatching were also observed in a dose-dependent manner. Zebrafish embryo showing moderate-to-severe developmental defects following AEMP exposure cannot swim properly. Further, this study examined oxidative stress and apoptosis in embryos exposed to AEMP. Enhanced production of ROS and apoptosis was found in brain, trunk, and tail of zebrafish embryos treated with AEMP. Data suggest that oxidative stress and apoptosis are associated with AEMP-induced embryonic lethality and developmental toxicity in zebrafish embryos.

Miniature Compliant Grippers With Vision-Based Force Sensing

This paper is concerned with grasping biological cells in aqueous medium with miniature grippers that can also help estimate forces using vision-based displacement measurement and computation. We present the design, fabrication, and testing of three single-piece, compliant miniature grippers with parallel and angular jaw motions. Two grippers were designed using experience and intuition, while the third one was designed using topology optimization with implicit manufacturing constraints. These grippers were fabricated using different manufacturing techniques using spring steel and polydimethylsiloxane ( PDMS). The grippers also serve the purpose of a force sensor. Toward this, we present a vision-based force-sensing technique by solving Cauchy's problem in elasticity using an improved algorithm. We validated this technique at the macroscale, where there was an independent method to estimate the force. In this study, the gripper was used to hold a yeast ball and a zebrafish egg cell of less than 1 mm in diameter. The forces involved were estimated to be about 30 and 10 mN for the yeast ball and the zebrafish egg cell, respectively.

Haptic Feedback for Injecting Biological Cells using Miniature Compliant Mechanisms

We present a real-time haptics-aided injection technique for biological cells using miniature compliant mechanisms. Our system consists of a haptic robot operated by a human hand, an XYZ stage for micro-positioning, a camera for image capture, and a polydimethylsiloxane (PDMS) miniature compliant device that serves the dual purpose of an injecting tool and a force-sensor. In contrast to existing haptics-based micromanipulation techniques where an external force sensor is used, we use visually captured displacements of the compliant mechanism to compute the applied and reaction forces. The human hand can feel the magnified manipulation force through the haptic device in real-time while the motion of the human hand is replicated on the mechanism side. The images are captured using a camera at the rate of 30 frames per second for extracting the displacement data. This is used to compute the forces at the rate of 30 Hz. The force computed in this manner is sent at the rate of 1000 Hz to ensure stable haptic interaction. The haptic cell-manipulation system was tested by injecting into a zebrafish egg cell after validating the technique at a size larger than that of the cell.

Generation of extended light-sheets for single and multi-photon fluorescence microscopy

We theoretically propose and computationally demonstrate the generation of extended light-sheet for fluorescence microscopy. This is made possible by the introduction of a specially designed double-window spatial filter that allows the light to pass through the periphery and center of a cylindrical lens. When illuminated with a plane wave, the proposed filter results in an extended depth-of-focus along with side-lobes which are due to other interferences in the transverse focal plane. Computational studies show a maximum extension of light-sheet by 3.38 times for single photon excitation and 3.68 times for multiphoton excitation as compared to state-of-art single plane illumination microscopy system. This technique may facilitate the study of large biological specimens (such as Zebrafish embryo and tissue) with high spatial resolution and reduced photobleaching. (C) 2013 AIP Publishing LLC.

COMPOSITE AND MULTI-SCALE COMPLIANT MECHANISMS FOR MANIPULATION AND MECHANICAL CHARACTERIZATION

In this paper, we integrate two or more compliant mechanisms to get enhanced functionality for manipulating and mechanically characterizing the grasped objects of varied size (cm to sub-mm), stiffness (1e5 to 10 N/m), and materials (cement to biological cells). The concepts of spring-lever (SL) model, stiffness maps, and non-dimensional kinetoelastostatic maps are used to design composite and multi-scale compliant mechanisms. Composite compliant mechanisms comprise two or more different mechanisms within a single elastic continuum while multi-scale ones possess the additional feature of substantial difference in the sizes of the mechanisms that are combined into one. We present three applications: (i) a composite compliant device to measure the failure load of the cement samples; (ii) a composite multi-scale compliant gripper to measure the bulk stiffness of zebrafish embryos; and (iii) a compliant gripper combined with a negative-stiffness element to reduce the overall stiffness. The prototypes of all three devices are made and tested. The cement sample needed a breaking force of 22.5 N; the zebrafish embryo is found to have bulk stiffness of about 10 N/m; and the stiffness of a compliant gripper was reduced by 99.8 % to 0.2 N/m.