In short, GFP-ATG8. GFP is a protein in the jellyfish Aequorea Victori that exhibits bright green fluorescence when excited at a wavelength of 488nm and has an emission peak at about 507nm ( blue to ultraviolet range).

GFP is served as biological marker for monitoring physiological processes, visualizing protein localization, and detecting transgenic expression.

GFP consists of 238 amino acid with 27 kilo Dalton of the protein size. When ATG8 fused to GFP (GFP-ATG8), the ATG8 here as a protein of interest (ATG8 is a ubiquitin-like protein required for the formation of autophagosomal membranes) to carry the GFP which used as a reporter and exhibit green signal.

GFP-ATG8 will serve as a protein visualized marker gene which localized on the double membrane vesicle, the autophosome.

Bubble-shape like membrane bound transport vesicles that are made from the reticulum endoplasmic (ER) membrane, functions to carry the proteins (wanted or unwanted) and move from ER to Golgi apparatus before going to their destination, which is lysosome, peroxisomes or vacuole for degradation or recycle.

Here, refer to bubble-shaped membrane-bound transport vesicle that buddling from the endoplasmic reticulum (ER) membrane, functions to transport proteins from ER and fuse to golgi apparatus.

A hormone is a chemical produced by organisms to regulate activities such as growth, development and resposes to the environment.

Computed tomography is a technique that uses X-ray and computational tools to generate images.

A transcription factor is a protein that facilitates transcription, a process that makes RNA from DNA.

This is a type of rice plant in which EIL1 (EIN3-like 1) gene is not functional.

"Os" represents Oryza sativa, which is the name for rice in a scientific naming system.

This is a type of rice plant in which EIN2 (ETHYLENE INSENSITIVE2) gene is not functional.

Cortical cell is a layer of cells lying underneath the epidermal cells.

Epidermal cells are the cells on the surface of plants.

Anatomy is a branch of biology focusing on the structure of organisms or a certain part of organisms.

Anatomical analysis is the analysis in such field. Here, the authors focus on the stucture of root cells.

Phenocopy means the plants grown under a certain condition have similar characteristics to the plants grown under a different condition.

RAP2.12 (RELATED TO AP2 12) is a protein, of which the level increases when plants are under hypoxia condition. RAP2.12-GFP is a protein made by fusing RAP2.12 protein with GFP and is used to indicate whether hypoxia response is triggered in plants.

This is a GFP-based reporter indicating whether hypoxia response is activated in plants. The presence of green signals in roots means hypoxia response is activated.

pPCO1 means the promoter region of the gene PCO1 (PLANT CYSTEINE OXIDASE 1), which is required to turn PCO1 on. PCO1 gene is turned on under hypoxia condition, which is a indicator of hypoxia response in plants.

Here, pPCO1 is fused with DNA sequences encodes GFP and GUS. Under hypoxia condition, pPCO1 turns on the production of GFP so scientists can determine if hypoxia response is activated in plants by visualizing GFP.

Hypoxia means a condition with not enough oxygen.

Root elongation zone is a zone of roots where root cells are expanding.

Green fluorescent protein is a protein that emits green light after absorbing light at a different wavelength. EIN3 (Ethylene-insensitive 3) is a protein, of which the level increases when plants' response to ethylene is triggered. EIN3-GFP is a protein made by fusing EIN3 protein with GFP and is used to indicate whether ethylene response is triggered in plants.

Bulk density indicates the degree of soil compaction. it is calculated as the dry weight of soil per unit soil volume. The soil volume includes the volume of soil particles and the volume of soil pore space among particles.

Rhizosphere is defined as the section of of soil surrounding plant roots, which contains chemicals released from plant roots and a population of microorganisms.

Wild-type refers to individuals of a species that are in the typical form of that species and occur in nature.

Arabidopsis (Arabidopsis thaliana) is a plant species that is widely used as a model organism in plant research.

Mutants refer to individual organisms of a certain species that are considered "abnormal" when compared to normal individuals of the same species that occur in nature. Usually, in a mutant, at least one gene is artificially disrupted and does not function normally. Mutants are powerful tools to study the function of a gene.

Ethylene is a gaseous plant hormone that regulates many plant activities such as fruit ripening, leaf development, responses to environmental stresses etc.

The process where a cell engulfs a smaller particle (bacteria, smaller cells, etc) where it is trapped and subsequently defused.

Pressure associated within the pleural cavity, the space enclosed by the pleura, which is a thin layer of tissue that covers the lungs and lines the interior wall of the chest cavity.

the study of adverse health effects of nanoscale (with sizes on the order of 10^-9 meters) particles.

where exchange of gasses such as oxygen and carbon dioxide occurs between the tiny air sacs in lung (alveolus) and capillaries.

A very small device, whose dimensions are on the micro scale (under 1mm). Often referenced in the context of biomechanical-electric system (bioMEM)

The human body has lots of moving internal parts. Repeated and regular contractions caused by the movement of food through the intestines puts pressure on surrounding tissues. Another example is the human lungs expanding and contracting during breathing.

The movement of something (nanoparticles) from one place (alveolar) to another (capillary).

A "germ", bacterium, virus, or other microorganism that can cause disease.

A molding technique that involves casting materials like PDMS into channels or chambers. This technique is used in microdevice fabrication because it is cost-effective and relatively simple to perform.

Your endothelium consists of a single layer of cells, called endothelial cells, which line all your blood vessels and lymphatic vessels. These include your: Arteries, Veins, Capillaries, and Lymph capillaries. Your endothelium provides a space for your blood and tissues to interact.

Refers to the physical actions of normal bodily processes.

The epithelium is a type of body tissue that forms the covering on all internal and external surfaces of your body, lines body cavities and hollow organs and is the major tissue in glands. Epithelial tissue has a variety of functions depending on where it's located in your body, including protection, secretion and absorption.

Tiny sacs where the lungs and the blood exchange oxygen and carbon dioxide during the process of breathing in and out. Each sac is lined with cells that allow gases to diffuse in and out of the lung.

Blood vessels like veins and arteries

Having enough cells grown on a surface to cover the entire area. Here, air is introduced to the lung microchip once there is enough cells to cover the entire membrane surface area.

Polydimethylsiloxane, called PDMS or dimethicone, is a polymer widely used for the fabrication and prototyping of microfluidic chips. PDMS is the most widely used silicon-based organic polymer, as its versatility and properties lead to many applications.

The sheet of cells covering the inner lining of the smallest vessels in the vascular system.

Involuntary contraction or relaxation in a muscular canal (such as intestines) causing wave-like movements.

Tissue that conducts the function of the organ

Having qualities in both space and time

small molecules secreted by cells in the immune system that also have an effect on other cells

Microdevices that mimics a specific organ or tissue

In particular, the "Trusted Issuer List"

Bulk autophagy also called non-selective macroautophagy. During bulk autophagy, autophagosomes fuse with lysosomes or vacuoles resulting in the degradation of the cargo.

While during selective autophagy, the cargo is distinguished (mitochondria, ER, ribosomes, peroxisomes and etc.) and recognized by specific cargo receptors, or selective autophagy receptors, to connect with the autophagosome for degradation.

https://www.youtube.com/watch?v=Gc9gx33GvF0&t=2s https://www.youtube.com/watch?v=Ws0mOmfC9EU

Pep4, a vacuolar protease required for function of multiple hydrolases, is required for autophagic cargo degradation

Used here to refer to the sperm chromatin added to the extract

The maximum amount of distance a wave can travel from its rest position

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.