5,079 Matching Annotations
  1. Feb 2024
    1. inoculation

      The process of introducing a small quantity of bacteria into a growth medium to establish a population of bacteria within a controlled system.

    2. macroscale experiments

      Refers to a large-scale or bulk experiment conducted to study the long-term dynamics of bacterial populations that are undergoing programmed population control in a microchemostat.

    3. intercellular phenotypical variability

      The observable characteristics among individual bacterial cells that contribute to the overall regulation and behavior of the bacterial population.

    4. lysis buffer

      A lysis buffer is a solution used to break open bacterial cells and release their contents, particularly for extracting genetic material for various laboratory analyses.

    5. peristaltic pump

      A peristaltic pump can be used to transfer liquids, such as nutrients, media, or other fluids into the bioreactor vessel without exposing the fluid to the pump components. This approach is essential for preserving a sterile and controlled environment, which is crucial for the biological processes taking place within the bioreactor.

    6. Escherichia coli

      AKA E. Coli. Species of bacteria that is commonly used in research due to its well-studied genetics and ease of cultivation.

    7. progeny

      The offspring or descendants produced by bacterial cells through the process of reproduction.

    8. Microbial biofilms

      A microbial biofilm is a complex and organized community of bacteria that adhere to a surface and are surrounded by a self-produced matrix of extracellular polymeric substances.

    9. quorum sensing

      A process of cell–cell communication that allows bacteria to share information about cell density and adjust gene expression accordingly.

    10. bacto-tryptone

      Bacterial growth medium which provides the necessary nutrients for the cultivation of bacteria in laboratory conditions, facilitating their growth and enabling researchers to conduct experiments.

    11. chemostat

      Chemostats are continuously operated bioreactors where growing cells reach a steady state condition at which specific growth rate, as well as biomass, substrate and the product concentrations remain constant.

    12. microfluidic bioreactor

      A microfluidic bioreactor is a device designed for the cultivation and study of bacteria cells in a controlled and tiny fluidic environment. It allows researchers to studying cellular behavior in conditions that closely mimic the natural environment.

    1. spinal decompression surgeries

      Surgery that is performed on the spine to relieve compressed nerves and reduce pressure on the spine and nerves. More space is created through this surgery to allow better movement of the nerves and help relieve pain.

    2. postoperative acute pain

      Pain that is experienced immediately after surgery and can last up to a week.

    3. local analgesia

      Loss of sensitivity to pain in a specified area.

    4. peripheral nerve

      This refers to any nerve in the peripheral nervous system, which is comprised of the nerves in the body that branch out from the brain and spinal cord.

    5. nonopioid

      Meaning the drug or substance is not an opioid and contains no opioids.

    6. opiate

      Type of opioid that contains natural substances extracted from poppy plants. They are referred to as the natural opioids.

    7. opioids

      These are a class of drugs prescribed to treat severe pain.

    8. invasive

      Relating to medical procedures that involve cutting into the body and doing procedures typically deeper than surface level.

    9. bioresorbable

      The capability of being absorbed or degraded into the body over time after it has been implanted.

    10. Implantable

      Referring to an item that can be surgically put into and function within the body.

    11. transmission

      The action of transferring something or allowing it to pass from one place or object to another.

    12. temporal

      Referring to a current but short period of time.

    13. stimuli

      An object or action that triggers a response or reaction in different components of the body.

    14. analgesics

      A term referring to drugs that are used to relieve pain.

  2. Dec 2023
    1. Glossary of some important musical terms
  3. Nov 2023
  4. May 2023
    1. ubiquitin-like protein Atg8

      Atg8 protein is a marker protein to observe autophagosome formation. When Atg8 protein engineered with the red florescence protein (RFP), RFP-Atg8, RFP-Atg8 protein will be conjugated to the lipids and enable the membrane fusion to localize on the autophagosome.

    2. vacuolar protease Pep4

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

    3. There are two major types of autophagy pathways, bulk and selective

      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.

      Here are two videos for more an explanation: 1) The mechanism of autophagy: https://www.youtube.com/watch?v=Gc9gx33GvF0&t=2s

      2) Self-Eating Cell Research Wins Nobel in Medicine: https://www.youtube.com/watch?v=Ws0mOmfC9EU

    4. ER-associated degradation (ERAD)

      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&t=1s

    5. unfolded protein response (UPR)

      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.

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

    6. isoforms

      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.

    7. mammalian homolog, SEC24C

      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.

    8. endoplasmic reticulum (ER)

      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=Gc9gx33GvF0&t=2s glossary

  5. Apr 2023
    1. extracellular matrix (ECM)

      A series of interconnected protein and carbohydrate networks that surround and support cells in 3 dimensions. The ECM is also a highway of biological signals for cells, often carrying the information needed to begin cell differentiation

    2. inflammatory responses

      Immune response when tissues react to foreign materials (like silica) and become damaged and swollen

    3. (TNF-α),

      Tumor necrosis factor alpha (TNF-alpha), is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and is responsible for a diverse range of signalling events within cells. When a person sustains an injury or experiences bacterial or viral infections, TNF-aplha creates inflammation to protect the area and allow it to heal. TNF alpha does this by triggering the production of several immune system molecules.

    4. ECM (fibronectin or collagen)

      ECM refers to Extracellular Matrix, connective tissues used for (but not limited to) anchoring cells. Here, the authors used Fibronectin ( that helps connect cells to the ECM) and Collagen (that is the main structural proteins in connective tissue) to help culture cells on both sides of the thin polymeric membrane.

    5. neutrophils

      The most common type of white blood cell in humans (40-70%), whose function varies between animal to animal. In humans they are the first responders to combat the intruder while signaling to other immune cells for more help.

    6. reactive oxygen species (ROS)

      An unstable molecule containing oxygen that easily reacts to other cell molecules and can be toxic.

    7. quantum dots

      Nanoscopic fluorescent particles used to track and quantify membrane stretching

    1. retrotranslocates

      To cause, or to undergo retrotranslocation.

      Retrotranslocation is the reverse process of translocation.

      Translocation is a transfer of a chromosomal segment to a new position, especially on a nonhomologous chromosome; the segment so transferred.

    2. vesicles

      Vesicles are compartments formed by a lipid bilayer separating its contents from the cytoplasm or a fluid-based extracellular environment. They can contain either liquids or gases and have a wide range of functions in cells across the living world from regulating buoyancy to secreting hormones.

      The word ‘vesicle’ derives from the Latin word vesicula meaning ‘small bladder’

    1. demure

      "Demure" means reserved, modest, and shy.

    2. ensnared

      "Ensnared" means trapped. Here, Prose writes that because the concept of "beauty" is so complex and difficult to define, many academics and artists agree not to use the word. I think one could also argue that the word's meaning is so vast and overarching that it has little to no communicative value. What is yall's opinion on the word "beauty"? Do you think it can be adequately defined? If so, how would you define it?

  6. Mar 2023
    1. ICAM-1)

      ICAM-1 is a special glycoprotein found on the surface of endothelial cells. ICAM-1 directly contributes to inflammatory responses within the blood vessel wall by increasing endothelial cell activation. ICAM-1 basically calls the immune cells to the rescue!

    2. inspiration

      drawing in breath/ breathing in

    3. blood-borne immune cells

      White blood cells that help you fight infections when exposed to a sickness. Helper T cells that recognize pathogens and help organize the immune response, neutrophils that chew up bacteria, and monocytes (macrophages) that recycle old cells and engulf pathogens are some examples

    4. barrier integrity

      Referring to the ability of the alveolar cell monolayers to selectively accept/retain nutrients and reject/eject wastes in the lungs

    5. cyclic stretching

      Referring to the mimicked inhaling and exhaling of the lungs over long periods of time. The human lungs experience 672,768,000+ breaths in a lifetime and can regenerate themselves as you age. The lung-on-a-chip must be able to handle the tissue stretching associated with normal breathing if it is to be considered a true "biomimicked lung device"

    6. silica nanoparticles

      Small particles of silicon dioxide, which when inhaled can cause pulmonary damage and even lung cancer

    7. unidirectional mechanical strain

      Deformation of a body caused by an outside force in one direction.

    1. ubiquitin-like protein Atg8

      Atg8 protein is a marker protein to observe autophagosome formation. When Atg8 protein engineered with the red florescence protein (RFP), RFP-Atg8, RFP-Atg8 protein will be conjugated to the lipids and enable the membrane fusion to localize on the autophagosome.

    2. green fluorescent protein (GFP)–autophagy-related protein 8 (Atg8)

      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.

    3. vesicles

      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.

    4. 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.

  7. Feb 2023
    1. hormone

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

    2. computed tomography

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

    3. transcription factor

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

    4. oseil1

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

    5. osein2

      "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.

    6. cortical cell

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

    7. epidermal cell

      Epidermal cells are the cells on the surface of plants.

    8. anatomical analysis

      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.

    9. phenocopied

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

    10. RAP2.12-GFP

      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.

    11. pPCO2:GFP-GUS

      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.

    12. pPCO1:GFP-GUS

      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.

    13. hypoxia

      Hypoxia means a condition with not enough oxygen.

    14. root elongation zone

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

    15. EIN3-GFP (green fluorescent protein)

      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.

    16. bulk density (BD)

      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.

    17. rhizosphere

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

    18. wild-type

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

    19. Arabidopsis

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

    20. mutant

      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.

    21. ethylene

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

    1. phagocytosis

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

    2. intrapleural pressure

      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.

    3. nanotoxicology

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

    4. alveolar-capillary interface

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

    5. microdevice

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

    6. cyclic mechanical strain

      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.

    7. translocation

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

    8. pathogens

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

    9. soft lithography

      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.

    10. endothelium

      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.

    11. physiological

      Refers to the physical actions of normal bodily processes.

    12. epithelium

      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.

    13. alveoli

      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.

    14. vascular conduits

      Blood vessels like veins and arteries

    15. confluence

      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.

    16. poly(dimethylsiloxane) (PDMS)

      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.

  8. Jan 2023
    1. microvascular endothelium

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

    2. peristalsis

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

    3. parenchymal

      Tissue that conducts the function of the organ

    4. spatiotemporal

      Having qualities in both space and time

    5. cytokines

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

    6. organ-on-a-chip

      Microdevices that mimics a specific organ or tissue

  9. Dec 2022
    1. There are two major types of autophagy pathways, bulk and selective

      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

    2. vacuolar protease Pep4

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

    1. reconstituted nuclei

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

    2. amplitude

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

    3. fluorogenic

      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.

    4. cytosolic proteins

      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.

    5. kymograph

      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.

    6. bistable biochemical reactions

      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.

    7. chimeric protein

      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.

    8. cytoplasmic extract

      Contains the all the internal contents of the cell

    9. cell-free Xenopus laevis egg extracts

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

    10. glutathione S-transferase

      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.

    11. self-regenerating trigger waves

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

    12. Apoptosis

      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

    1. transgene

      See transgenic above

    2. imaginary discs

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

    3. in vivo

      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.

  10. Nov 2022
    1. green fluorescent protein

      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.

    2. calcium waves

      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

    3. reconstituted extract

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

      Remember that the cytosolic extract is devoid of mitochondria.

    4. fluorophore

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

    5. time-lapse fluorescence microscopy

      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.

    6. nuclear localization sequence

      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.

    7. allele

      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.

    8. Fractionation

      A method used to separate cellular components

    1. ER exit sites (ERES)

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

    2. mitophagy

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

    3. pexophagy

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

    4. nucleophagy

      Nuclear component that is selectively degraded via autophagy pathway.

    5. nuclear ER degradation

      Nucleophagy and ER-phagy

    6. ER-associated degradation (ERAD)

      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

    7. unfolded protein response (UPR)

      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

    8. isoforms

      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.

    9. mammalian homolog, SEC24C,

      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.

    10. endoplasmic reticulum (ER)

      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

    1. Xenopus laevis oocytes

      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

    2. Apoptosis

      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

    3. transmembrane domains

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

    4. anterior-posterior shortening

      Reduced body length

    5. autophagy

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

    6. wing phenotype

      External appearance/morphology of wings

    7. transposon

      Jumping genes/DNA

    8. current spikes

      Indication of electrical current strength

    9. single-channel currents in the cell-attached mod

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

    10. electrophysiological properties

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

    11. MODELLER platform

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

    12. homology models of the three-dimensional (3D)

      Models based on closely related proteins of known structures.

    13. morphology

      Structure, shape, size

    14. pH (OGDx)

      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

    15. atiometric calcium (Fura-2Dx)

      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

    16. calcium-binding affinities

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

    17. short hairpin RNA (shRNA)

      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

    18. Silencing

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

    19. siRNAs

      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

    20. endogenous RECS1

      RECS1 that naturally exist inside the cells

    21. mobility shift

      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.

    22. ip/Grp78 and Chop/Gadd153 (fig. S5H), two sensitive markers of ER stress (13, 15).

      Proteins whose expression changes during ER stress.

    23. UPR

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

    24. XBP1s

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

    25. downstream

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

    26. LMP

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

    27. pathophysiological processes

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

    28. endogenous

      original/unaltered

    29. HeLa

      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/

    30. confocal microscopy

      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

    31. immunofluorescence

      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.

    32. bafilomycin A1

      Blocks lysosomal pH reduction by V-ATPase protein.

    33. V-ATPase (vacuolar H+-ATPase)

      Protein that lowers the pH of vacuoles/lysosomes.

    34. pH alkalization

      Increased PH

    35. lysosomotropic agents

      Compounds which induce lysosomal stress such as CQ and HCQ

    36. depolarize

      Change the charge (negative or positive to neutral)

    37. BAX and BAK double-knockout (DKO) background (Fig. 1F)

      Cells in which both BAX and BAK are non-functional

    38. caspases

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

    39. intracellular signals

      Signals from within the cell

    40. transient transfection

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

    41. propidium iodide (PI)

      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.

    42. FLAG

      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

    43. doxycycline-inducible

      Expressed only in the presence of doxycycline antibiotic

    44. embryonic fibroblast (MEF)

      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.

    45. (D295Q)

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

    46. proapoptotic

      Activates or positively regulates cell death

    47. mutation

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

    48. LMP,

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

    49. cytotoxic agents

      Chemicals that may be toxic to cells at certain doses

    50. gain- and loss-of-function approaches

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

    51. intracellular

      Inside the cell

    52. Golgi apparatus

      One of the cell organelles

    53. ortholog

      A similar gene in different species of organisms

    54. putative

      Thought to be

    55. rheostat

      Regulation by control of the levels of contrasting signals

    56. ion channe

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

    57. calcium homeostasis

      Regulation of Calcium use in cells.

    58. cytotoxic stimuli

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