Something that generates fluorescence.

Example: The green fluorescent protein (GFP) is a protein that emits bright green fluorescence upon exposure to light in the blue to ultraviolet range. Hence GFP can be said to be fluorogenic.

Large complexes of enzymes in the cytosol of the cell that are involved in various cellular pathways including metabolism, biosynthesis and cell signalling.

The cytosol is the aqueous part of the cytoplasm of a cell where cellular components (e.g., organelles) are suspended.

Distance-time plots that are used in biology to monitor and track the movement of fluorescent or fluorescently-labeled particles (e.g., molecules, organelles etc.) along a predicted path.

Describes a system with two stable equilibrium states and therefore capable of resting in (or reaching) either of the two states. It arises from feedback loops that exhibit mutual activation or mutual repression.

A protein made by combining two or more genes that code for the synthesis of their individual proteins joined together. Synthesis results in the formation of one protein with specific functional properties.

Contains the all the internal contents of the cell

Preparation obtained by crushing the eggs of the African clawed frog (Xenopus laevis) to release its internal contents.

A protein that is popularly used as a tag for the purification of recombinant proteins. It can be fused to either ends of the desired protein, usually the end that does not affect the function of the target protein.

A recombinant protein is produced by cloning a gene into a system that allows the expression of that gene and the translation of its gene product.

Self-renewing biological phenomenon that is capable of long-range transmission/propagation of information.

A series of events that are genetically programmed to result in the death of a cell. It takes place as a normal part of the growth and development of an organism.

Here is an animation video that illustrates apoptosis: https://www.youtube.com/watch?v=-vmtK-bAC5E

Here is an introductory lecture to the process of apoptosis https://www.youtube.com/watch?v=31dmXwBZNWI&ab_channel=iBiology

See transgenic above

A group of undifferentiated cells that eventually form the drosophila wing.

Experiments are carried out within the living organisms as opposed to the experiments in test tubes or Petri dishes. Up until here, all experiments done in this paper are in vitro.

A protein that emits bright green fluorescence upon exposure to light in the blue to ultraviolet range.

Fluorescence occurs when light of a shorter/high-energy wavelength (such as UV light) is directed on a surface allowing a specific component (e.g. green fluorescent protein) on the targeted surface to emit light of a specific wavelength.

An increase in the concentration calcium ions in the cytosol which causes a succession of the same events to take place in a wave-like manner. The generation of calcium waves can therefore be viewed a positive feedback mechanism.

Here is a visualization of the propagation of calcium waves in a fertilized egg: https://www.youtube.com/watch?v=M8GC-zwlF8w

Used here to refer to the cytosolic extract where the mitochondria has been added back.

Remember that the cytosolic extract is devoid of mitochondria.

A fluorescent compound that can re-emit light upon excitation. They are typically used in techniques such as fluorescent imaging.

A form of microscopy where microscopic images are first recorded sequentially and then viewed at a higher speed to provide an accelerated view of the process being visualized.

A short protein sequence that serves as a signal for target proteins to be transported from the cytoplasm to the nucleus. In this chimeric (fusion) protein, the sequence the GST-GFP component to be transported into the nucleus.

One of two or more versions of a gene (found at the same place on the chromosome) that comes about due to changes in the DNA sequence.

A method used to separate cellular components

The ER exit sites are specialized ER zones for the transport of cargo proteins from the ER to the Golgi apparatus.

The degradation of damaged mitochondria in the cell through selective autophagy.

A type of selective autophagy to degrade a specific organelle called peroxisomes in the cell.

Nuclear component that is selectively degraded via autophagy pathway.

Nucleophagy and ER-phagy

Misfolded protein are retained in the ER and subjected for proteosomal degradation which occurs in the cytosol.

Learning from the youtube:

https://www.youtube.com/watch?v=fEEbyYjXNUU

When newly synthesized protein is not properly folded into their correct orientation in the endoplasmic reticulum (ER), the ER now is under the stress to degrade the misfolded protein. To degrade the misfolded proteins and maintain the ER homeostasis, the cellular signaling will turn on the unfolded protein response to help the cell deals with problematic proteins for recycle and degradation.

https://www.youtube.com/watch?v=vy4m-fUOn9o

Genes are commonly generate isoforms from the same locus to produce different mRNA and thus give rise to different length of amino acid with similar protein functions.

Lst1 and SEC24C, are homologous gene in yeast and mammalian respectively. The protein or DNA sequence of these genes, Lst1 and SEC24C, are highly similar and evolutionary share the common ancestor, termed as homolog.

ER is a transportation system of the eukaryotic cell composed of network of tubules and sheet-like area adjacent with the nuclear envelope and stretches out to the cell periphery.

Learning corner with video: https://www.youtube.com/watch?v=an7tpWR16mo

Cells of a type of frogs (Xenopus laevis) native to sub-Saharan Africa. These are used as model organisms for studying cell function such as ion channel which is reported in this paper

A programmed and normal process of cell death. See the YouTube videos here for a little more detail https://www.youtube.com/watch?v=DR80Huxp4y8 https://www.youtube.com/watch?v=F4lUnOY0U5w

Certain sections are located across (intersect) membranes such as cell membrane, lysosome membrane, mitochondria membrane etc.

Reduced body length

Self eating by cells, that is break down of cell components to recycle nutrients for use by the cells

External appearance/morphology of wings

Jumping genes/DNA

Indication of electrical current strength

Electrical current through the channel is proportional to the amount of ions going through the channel.

Electrical properties of cells. These are related to the role of RECS1 as an Ion channel

A web-based computer program for predicting the 3D protein structures. Check it out at the link below. https://www.salilab.org/modeller/

Models based on closely related proteins of known structures.

Structure, shape, size

Fluorescence probe used for measuring lysosomal pH. Find more information about this probe at the following link: https://journals.biologists.com/jcs/article/115/3/599/34970/pH-dependent-regulation-of-lysosomal-calcium-in

Fura-2 is a ratiometric fluorescent dye which binds free intracellular calcium. Find more information about this dye at the following link: https://www.aatbio.com/resources/assaywise/2015-4-1/ratiometric-calcium-indicators

A measure of the readiness/ease by which a protein attaches/bind to calcium

an artificial RNA molecule with a tight hairpin turn that can be used to silence target gene expression via RNA interference. Check out the following page for more information. https://horizondiscovery.com/en/applications/rnai/shrna-applications

To reduce the expression of a specific gene, without completely stopping its function

Short RNA sequences that interfere with the expression of specific genes with sequences similar to the siRNA. The siRNA can be introduced into cells by transformation using plasmids. The siRNAs degrade specific mRNAs of target genes thereby preventing their translation into proteins. Here is a video about siRNA by Nature: https://www.youtube.com/embed/cK-OGB1_ELE?wmode=transparent

RECS1 that naturally exist inside the cells

A technique used in biology to detect proteins bound to DNA based on their rate of movement in a gel. DNA-free protein appear smaller that the same protein bound to DNA.

Proteins whose expression changes during ER stress.

Unfolded protein response characterized by reduced protein production, or increased protein folding or increased protein degradation in response to ER stress.

X-box binding protein is a protein which accumulates in cells experiencing ER stress.

A step in cellular pathway that occurs after another (upstream) step

Lysosomal Membrane Permeabilization - When the lysosomal membrane is forced to take in substances which may otherwise be prevented from entry.

Abnormal changes in the body that result from disease or malfunctioning of the cells/body parts

original/unaltered

Another type of immortal cells used in biomedical research. For a primer on the origin and significancy of HeLa cells, see the following link. https://www.hopkinsmedicine.org/henriettalacks/

Microscopy used to block most of the irrelevant light to produce good quality images. See a glimpse of the operating principle of a confocal microscope: https://en.wikipedia.org/wiki/File:Fluorescent_and_confocal_microscopes.ogv

A technique for determining the location of an antigen (or antibody) in tissues by reaction with an antibody (or antigen) labeled with a fluorescent dye.

Blocks lysosomal pH reduction by V-ATPase protein.

Protein that lowers the pH of vacuoles/lysosomes.

Increased PH

Compounds which induce lysosomal stress such as CQ and HCQ

Change the charge (negative or positive to neutral)

Cells in which both BAX and BAK are non-functional

Proteins that degrade/breakdown other proteins (proteolysis). BAX and BAK are some of these caspases.

Signals from within the cell

Temporary expression of foreign plasmid DNA in cells. The foreign DNA does not get integrated into the cell genome.

A red fluorescent dye that is used to stain DNA and RNA in dead cells. Only cells with a compromised membrane (dead cells) can allow it to enter. So, PI can be used as an indicator of the proportion of cells that are alive or dead.

A small protein (peptide sequence) that is added to the end of the protein. In this case, FLAG was tagged onto RECS1 to enable detection of RECS1 in cells. Tagging is done through transformation

Expressed only in the presence of doxycycline antibiotic

Fibroblast cells (cells that make connective tissue) from mouse embryos. These cells are immortalized (they grow indefinitely when maintained on specific media) and are used for research purposes.

Aspartic acid (D) at position 295 in RECS1 is substituted for Glutamine (Q). This amino acid is necessary for regulation of lysosome membrane properties.

Activates or positively regulates cell death

Change in amino acid or DNA sequence, resulting in altered function/structure of a protein

Lysosomal Membrane Permeabilization - Making the lysosome membrane able to take up substance easily.

Chemicals that may be toxic to cells at certain doses

Enhance (gain) or reduce/block (loss) the expression of a gene to study its biological function

Inside the cell

One of the cell organelles

A similar gene in different species of organisms

Thought to be

Regulation by control of the levels of contrasting signals

A passage in the cell membranes through which charged chemical elements (ions) enter or exit the cell or cell compartment

Regulation of Calcium use in cells.

Cyto (from cell) - toxic: Poisonous situation/condition/change in a cell

Related proteins across different organisms

A group of proteins that span membranes and oppose the function of BAX (a positive regulator of apoptosis).

Disease-related

Making a membrane easily take up external substances, where it would normally not

A group of proteins that function together in programmed cell death

Protein associated with the inner membrane of mitochondria and is involved in apoptosis

Protein complex consisting of identical protein subunits.

Activation preceded by a change in protein structure

Positively regulate programmed cell death. Proteins such as BAK and BAX

Zebrafish embryos with abnormal morphology/structure/shape.

An organic dye for cell imaging. Dead cells are stained more by AO.

Two conserved Aspartic acid residues in all proteins in this group. These two residues are involved in sensing lysosomal pH changes.

Proteins inside the lysosomes that degrade other proteins

Toxic to cells at certain doses

Reverse

To remove

Two of the proteins that are well known to be activators of cell death (proapoptotic proteins)

A green fluorescent dye that stains live cells

Chemicals that cause stress to lysosomes

Proteins that possess a characteristic short protein (or peptide) sequence termed the "BH3 domain" (also called the death domain).

Members of this family of proteins are known to trigger key mitochondrial events that kill the cell and hence are associated with apoptosis.

The process of constructing a curve that has the best fit to a series of data points.

An experiment which uses colored of fluorescent substrates (e.g., Z-DEVD-R110) to quantify the activity of an enzyme (e.g., caspase).

As a result, the higher the fluorescence detected, the higher the enzyme activity.

Process where pores are created in the outer membrane of the mitochondria to facilitate the release of cytochrome c which in turn activates caspases necessary for apoptosis to occur.

A protein that blocks apoptosis by keeping caspase-3 and caspase-7 in an inactive state where they are not able to perform their roles in apoptosis.

To break down (a compound) by chemical reaction with water.

A molecule upon which an enzyme (e.g., caspase) acts. Enzymes catalyze chemical reactions involving the substrate(s).

Refers to "interphase cytoplasmic extract" with no cycloheximide treatment and no cytochrome c.

A nucleic acid–protein complex that makes up eukaryotic chromosomes

Refers to the cycloheximide-treated interphase with cytochrome c

Small protein which is loosely associated with the inner membrane of the mitochondria [powerhouse of the cell]. Perturbations to the inner mitochondrial membrane causes the release of cytochrome c which then activates apoptosis.

Dye used to monitor cell division and track the movement of live cells.

A chemical that blocks protein synthesis in eukaryotic organisms. Upon exposure, many cell types rapidly undergo apoptosis.

Provides live feed (real-time) video image directly to a computer for visualization and monitoring.

Defense mechanism used by an organism to remove harmful agents (such as damaged cells and pathogens).

Used here to describe a system of biological molecules that interact to obtain desired outcome such as apoptosis.

A stage in cell division where chromatids [one half of a duplicated chromosome] separate.

The second stage of cell division where the chromosomes prepare to be separated into daughter cells by aligning in the equator of the parent cell.

A form of cellular communication involving the reception, processing and transmission of biological and chemical signals.

Proteases (enzymes that break down proteins) that function as the main effectors of apoptosis

An immature egg

Used here to describe assays or experiments involving the blocking of activity of an enzyme or biological process.

Steady state conditions (no disturbances)

Describes a process or feature that is maintained and takes place across different species (organisms that share common characteristics)

Describes a process where cells destroy themselves when they are no longer needed.

The movement caused within a fluid by the forces acting on the fluid, primarily due to pressure.

Relates to the intermingling of substances by the natural movements of their molecules or particles.

The regular changes in the prototype's structure, where the original size and shape is retained after contact forces have been removed.

an electrical component's effective resistance to alternating current

Aqueous buffer is a solution of weak acid and its conjugate base which provides a degree of stability to prevent the rapid fluctuation in pH when a small amount of strong acid or base is added.

Flows constrained along a single dimension such as those found in the microchannels of microfluidic devices.

Digital Object Identifier (DOI) is a standardized method for uniquely referencing digital documents with the aim of easily leading to the documents location. Almost all published academic journal articles as well as research reports and data sets have an assigned DOI.

To make uniform or similar.

What is deferring payment ?

IMF bailout for SriLanka

Piezoelectric materials undergo a shape change when voltage is applied across them. A piezoelectric unimorph is a thin and long microstructure that flexes when voltage is applied to it. In this paper, the properties of the piezoelectric material are used to create forward movement of the robot.

Fraction of time spent in each phase of one cycle of the motion.

Military term for gathering information about an enemy for combat intelligence.

The ability to continue operating despite the failure of one or more components

Revert to a safe state in the event of failure

Mite species native to Southern California. Discovered to be worlds fastest terrestrial animal and passed the Australian Tiger Beetle as the previous record holder.

A pattern of limb movement, where the gallop, commonly seen in horses, is the one of the fastest gait that can be performed.

The force that acts in the direction parallel to ground, with varying magnitudes in different directions.

The lowest frequency at which a system oscillates (displays distinct periodic patterns of motion).

The point within an object at which the whole mass may be considered as concentrated. Here, the authors tracked the center of mass (COM) motion to represent the motion of the entire robot.

Perpendicular to the direction of the flow along the channel

The measurement of a fluid's internal resistance to flow

The process of printing a design onto a flat surface using chemical reactions.

A form of fluid motion dominated by viscous forces. This occurs at low fluid velocities, high fluid viscosities, or very small length-scales of flow.

Lithography techniques rely on fabricating one layer at a time to construct device features at the microscale.

A dimensionless number that represents the ratio of the rate of transport by bulk motion of a fluid to the rate of transport by diffusion.

A magnet obtained by embedding magnetic particles (made of NdFeB) into an elastomer (PDMS).

Sunspots are darker, cooler areas of the sun's surface. The umbra is the darkest part of a sunspot, at its center. It is surrounded by the lighter penumbra.

• idea for glossary

a spring that absorbs up and down movement

a spring that absorbs rotational movement

At resonant frequency, the circuit exhibits a maximum oscillatory, or regularly varying, response at a specific frequency (the number of times the AC switches between positive and negative in 1 second).

This idealized model allows for the characterization of motion animals use, like bouncing. Specifically, it is assumed that the movement behaves like a mass bouncing on a spring.

The ability of the PVDF to generate an electric charge in response to the applied voltage, resulting in expansion (or stretching) and contraction (or shrinking).

A connection between two rigid bodies that allows only relative rotation about a single direction.

SEM is an instrument that produces a largely magnified image by using electrons instead of light to form an image.

A programming language that is primarily used for numerical computation as well as computational modeling, simulation, and prototyping.

The force that opposes gravity because it is exerted by the ground onto a body that is in contact with the ground.

Both the front- and back-legs making contact with the ground

A soft, highly stretchable plastic, which most plastic bottles are made of.

A pressure sensitive substance that can change shape in order to seal gaps in materials.

A polymeric material that has high piezoelectric coefficient, good stability and flexibility. This material is commonly used in soft actuators.

Polymers are materials made of long, repeating chains of subunits called monomers. Examples include plastics, proteins and DNA.

Structures of an object, organism, or material with a typical feature length scale of 1-100 micrometers

Inner layer of the skin tissue containing blood capillaries, nerve endings, sweat glands, and hair follicles.

Receptors typically located on cell membrane that relay external mechanical stimuli such as pressure, touch, or motion.

Synthetic materials/methods that mimic biological materials/mechanisms.

the measurement of the total magnetic field which passes through a specified area

A therapy that uses low-voltage electrical current for pain relief, also known as TENS.

Nerve signals that occur when a neuron sends information away from the cell body. The action potential itself is a burst of electrical energy.

A circuit containing both an inductor (L) and capacitor (C) that oscillates by shifting the energy between the electric and magnetic fields.

An external magnetic field causing a large variation in the electrical impedance of the material.

signal or input that evokes a specific functional reaction in an organ or tissue.

Images obtained by confocal microscopy, a fluorescence imaging technique that uses lasers to create a three-dimensional image of a sample

An arrangement or design consisting of columns of short parallel lines, with all lines from one column slopping in an opposite direction from the next column.

At a right angle, perpendicular

Re is an abbreviation for Reynolds number.

Ridge like structures used to disrupt laminar flow patterns

Fluid flow that is subject to chaotic changes in velocity and pressure. The opposite of laminar flow.

Natural and artificial arrangements of physical features of an area.

The spreading out of a solute in a stream of fluid.

The process of fabricating a structure on a micrometer or smaller scale.

A device that uses small amounts of liquid on a microscopic scale

Steady viscous (thick) fluid flow driven by an effective pressure gradient established between the two ends of a long straight pipe of uniform circular cross-section