- Nov 2023
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www.facebook.com www.facebook.com
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法務看英文
這個臉書專頁「法務看英文」,我早已加入favorite書籤,果真是「乾貨」滿滿,含金量高,每篇都有垂手可得的精準雙語詞彙和文脈。
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www.axios.com www.axios.com
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Move over "LOL": Gen Z embraces "IJBOL"
Z世代用語
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www.axios.com www.axios.com
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Gen Z shakes up workplace communication
Z世代用語
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URL
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- Jul 2023
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Glossary of some important musical terms
Tags
- modes
- mode-hemiolic
- mode-ekmelic
- phrase
- dynamics
- texture
- instrumentation
- dissonance-melodic
- modes-tetratonic
- modes-hexatonic
- heterophony
- modal-harmony
- modes-tritonic
- modes-heptatonic
- texture-part-vs-voice
- consonance-melodic
- dissonance
- modes-octatonic
- phrase-cadence
- consonance
- dissonance-harmonic
- rhythm-class
- monody
- harmony
- melody
- multitony
- tempo
- diatony
- mode-rhythmic
- AOEs
- tonal-gravity
- tonality
- texture-polyphony
- mode-khasmatonal
- phrase-climax
- interval-class
- modality
- hypermode
- rhythm
- register
- modes-pentatonic
- motif
- meter
- modes-monotonic
- tone-class
- phrasing
- source:nikolsky-glossary
- modes-ditonic
- double-note
- tonicity
- monophony
- melodic-intonation
- form
- pitch-class
- mode-timbral
- articulation
- mesotony
- texture-voluminousness
- melodic-inclination
Annotators
URL
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- May 2023
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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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.
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vacuolar protease Pep4
Pep4, a vacuolar protease required for function of multiple hydrolases, is required for autophagic cargo degradation
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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
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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
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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.
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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.
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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.
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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
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- Apr 2023
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tanyerilab.net tanyerilab.net
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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
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inflammatory responses
Immune response when tissues react to foreign materials (like silica) and become damaged and swollen
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(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.
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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.
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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.
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reactive oxygen species (ROS)
An unstable molecule containing oxygen that easily reacts to other cell molecules and can be toxic.
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quantum dots
Nanoscopic fluorescent particles used to track and quantify membrane stretching
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Annotators
URL
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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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.
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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’
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docs.google.com docs.google.com
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demure
"Demure" means reserved, modest, and shy.
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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?
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- Mar 2023
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tanyerilab.net tanyerilab.net
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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!
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inspiration
drawing in breath/ breathing in
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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
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barrier integrity
Referring to the ability of the alveolar cell monolayers to selectively accept/retain nutrients and reject/eject wastes in the lungs
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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"
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silica nanoparticles
Small particles of silicon dioxide, which when inhaled can cause pulmonary damage and even lung cancer
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unidirectional mechanical strain
Deformation of a body caused by an outside force in one direction.
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Annotators
URL
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docs.google.com docs.google.com
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"Háblame en español"
This phrase, when translated into English, means "Talk to me in Spanish."
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"Cálmate, cálmate,
In English, this phrase would be translated as "calm down, calm down."
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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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.
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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.
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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.
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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.
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- Feb 2023
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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hormone
A hormone is a chemical produced by organisms to regulate activities such as growth, development and resposes to the environment.
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computed tomography
Computed tomography is a technique that uses X-ray and computational tools to generate images.
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transcription factor
A transcription factor is a protein that facilitates transcription, a process that makes RNA from DNA.
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oseil1
This is a type of rice plant in which EIL1 (EIN3-like 1) gene is not functional.
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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.
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cortical cell
Cortical cell is a layer of cells lying underneath the epidermal cells.
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epidermal cell
Epidermal cells are the cells on the surface of plants.
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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.
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phenocopied
Phenocopy means the plants grown under a certain condition have similar characteristics to the plants grown under a different condition.
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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.
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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.
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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.
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hypoxia
Hypoxia means a condition with not enough oxygen.
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root elongation zone
Root elongation zone is a zone of roots where root cells are expanding.
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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.
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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.
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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.
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wild-type
Wild-type refers to individuals of a species that are in the typical form of that species and occur in nature.
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Arabidopsis
Arabidopsis (Arabidopsis thaliana) is a plant species that is widely used as a model organism in plant research.
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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.
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ethylene
Ethylene is a gaseous plant hormone that regulates many plant activities such as fruit ripening, leaf development, responses to environmental stresses etc.
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tanyerilab.net tanyerilab.net
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phagocytosis
The process where a cell engulfs a smaller particle (bacteria, smaller cells, etc) where it is trapped and subsequently defused.
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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.
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nanotoxicology
the study of adverse health effects of nanoscale (with sizes on the order of 10^-9 meters) particles.
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alveolar-capillary interface
where exchange of gasses such as oxygen and carbon dioxide occurs between the tiny air sacs in lung (alveolus) and capillaries.
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microdevice
A very small device, whose dimensions are on the micro scale (under 1mm). Often referenced in the context of biomechanical-electric system (bioMEM)
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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.
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translocation
The movement of something (nanoparticles) from one place (alveolar) to another (capillary).
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pathogens
A "germ", bacterium, virus, or other microorganism that can cause disease.
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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.
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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.
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physiological
Refers to the physical actions of normal bodily processes.
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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.
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alveoli
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vascular conduits
Blood vessels like veins and arteries
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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.
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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.
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- Jan 2023
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tanyerilab.net tanyerilab.net
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microvascular endothelium
The sheet of cells covering the inner lining of the smallest vessels in the vascular system.
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peristalsis
Involuntary contraction or relaxation in a muscular canal (such as intestines) causing wave-like movements.
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parenchymal
Tissue that conducts the function of the organ
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spatiotemporal
Having qualities in both space and time
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cytokines
small molecules secreted by cells in the immune system that also have an effect on other cells
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organ-on-a-chip
Microdevices that mimics a specific organ or tissue
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Annotators
URL
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- Dec 2022
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digitalcredentials.mit.edu digitalcredentials.mit.edu
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Glossary
In particular, the "Trusted Issuer List"
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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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
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vacuolar protease Pep4
Pep4, a vacuolar protease required for function of multiple hydrolases, is required for autophagic cargo degradation
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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reconstituted nuclei
Used here to refer to the sperm chromatin added to the extract
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amplitude
The maximum amount of distance a wave can travel from its rest position
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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.
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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.
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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.
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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.
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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.
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cytoplasmic extract
Contains the all the internal contents of the cell
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cell-free Xenopus laevis egg extracts
Preparation obtained by crushing the eggs of the African clawed frog (Xenopus laevis) to release its internal contents.
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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.
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self-regenerating trigger waves
Self-renewing biological phenomenon that is capable of long-range transmission/propagation of information.
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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
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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transgene
See transgenic above
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imaginary discs
A group of undifferentiated cells that eventually form the drosophila wing.
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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.
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- Nov 2022
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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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.
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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
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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.
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fluorophore
A fluorescent compound that can re-emit light upon excitation. They are typically used in techniques such as fluorescent imaging.
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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.
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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.
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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.
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Fractionation
A method used to separate cellular components
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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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.
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mitophagy
The degradation of damaged mitochondria in the cell through selective autophagy.
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pexophagy
A type of selective autophagy to degrade a specific organelle called peroxisomes in the cell.
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nucleophagy
Nuclear component that is selectively degraded via autophagy pathway.
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nuclear ER degradation
Nucleophagy and ER-phagy
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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:
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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.
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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.
-
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.
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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
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tmrc.mit.edu tmrc.mit.edu
Tags
Annotators
URL
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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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
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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
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transmembrane domains
Certain sections are located across (intersect) membranes such as cell membrane, lysosome membrane, mitochondria membrane etc.
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anterior-posterior shortening
Reduced body length
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autophagy
Self eating by cells, that is break down of cell components to recycle nutrients for use by the cells
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wing phenotype
External appearance/morphology of wings
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transposon
Jumping genes/DNA
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current spikes
Indication of electrical current strength
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single-channel currents in the cell-attached mod
Electrical current through the channel is proportional to the amount of ions going through the channel.
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electrophysiological properties
Electrical properties of cells. These are related to the role of RECS1 as an Ion channel
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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/
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homology models of the three-dimensional (3D)
Models based on closely related proteins of known structures.
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morphology
Structure, shape, size
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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
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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
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calcium-binding affinities
A measure of the readiness/ease by which a protein attaches/bind to calcium
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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
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Silencing
To reduce the expression of a specific gene, without completely stopping its function
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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
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endogenous RECS1
RECS1 that naturally exist inside the cells
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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.
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ip/Grp78 and Chop/Gadd153 (fig. S5H), two sensitive markers of ER stress (13, 15).
Proteins whose expression changes during ER stress.
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UPR
Unfolded protein response characterized by reduced protein production, or increased protein folding or increased protein degradation in response to ER stress.
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XBP1s
X-box binding protein is a protein which accumulates in cells experiencing ER stress.
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downstream
A step in cellular pathway that occurs after another (upstream) step
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LMP
Lysosomal Membrane Permeabilization - When the lysosomal membrane is forced to take in substances which may otherwise be prevented from entry.
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pathophysiological processes
Abnormal changes in the body that result from disease or malfunctioning of the cells/body parts
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endogenous
original/unaltered
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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/
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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
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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.
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bafilomycin A1
Blocks lysosomal pH reduction by V-ATPase protein.
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V-ATPase (vacuolar H+-ATPase)
Protein that lowers the pH of vacuoles/lysosomes.
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pH alkalization
Increased PH
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lysosomotropic agents
Compounds which induce lysosomal stress such as CQ and HCQ
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depolarize
Change the charge (negative or positive to neutral)
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BAX and BAK double-knockout (DKO) background (Fig. 1F)
Cells in which both BAX and BAK are non-functional
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caspases
Proteins that degrade/breakdown other proteins (proteolysis). BAX and BAK are some of these caspases.
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intracellular signals
Signals from within the cell
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transient transfection
Temporary expression of foreign plasmid DNA in cells. The foreign DNA does not get integrated into the cell genome.
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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.
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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
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doxycycline-inducible
Expressed only in the presence of doxycycline antibiotic
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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.
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(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.
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proapoptotic
Activates or positively regulates cell death
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mutation
Change in amino acid or DNA sequence, resulting in altered function/structure of a protein
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LMP,
Lysosomal Membrane Permeabilization - Making the lysosome membrane able to take up substance easily.
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cytotoxic agents
Chemicals that may be toxic to cells at certain doses
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gain- and loss-of-function approaches
Enhance (gain) or reduce/block (loss) the expression of a gene to study its biological function
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intracellular
Inside the cell
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Golgi apparatus
One of the cell organelles
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ortholog
A similar gene in different species of organisms
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putative
Thought to be
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rheostat
Regulation by control of the levels of contrasting signals
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ion channe
A passage in the cell membranes through which charged chemical elements (ions) enter or exit the cell or cell compartment
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calcium homeostasis
Regulation of Calcium use in cells.
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cytotoxic stimuli
Cyto (from cell) - toxic: Poisonous situation/condition/change in a cell
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homologs
Related proteins across different organisms
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transmembrane BAX inhibitor motif containing (TMBIM) superfamily
A group of proteins that span membranes and oppose the function of BAX (a positive regulator of apoptosis).
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pathophysiological
Disease-related
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lysosomal membrane permeabilization (LMP)
Making a membrane easily take up external substances, where it would normally not
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caspase cascade
A group of proteins that function together in programmed cell death
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cytochrome c
Protein associated with the inner membrane of mitochondria and is involved in apoptosis
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homo-oligomerization
Protein complex consisting of identical protein subunits.
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conformational activation
Activation preceded by a change in protein structure
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proapoptotic proteins
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Dysmorphic embryos
Zebrafish embryos with abnormal morphology/structure/shape.
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cridine orange (
An organic dye for cell imaging. Dead cells are stained more by AO.
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The di-aspartyl sensor is conserved in all six TMBIM proteins, while the arginine latch is only present in the LFG subfamily (LFG1 to LFG4) but not in BI-1, where it has been replaced by His78 (Fig. 7A) (11).
Two conserved Aspartic acid residues in all proteins in this group. These two residues are involved in sensing lysosomal pH changes.
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intraluminal cathepsins
Proteins inside the lysosomes that degrade other proteins
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cytotoxic
Toxic to cells at certain doses
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abrogate
Reverse
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Ablation
To remove
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BAX and BAK
Two of the proteins that are well known to be activators of cell death (proapoptotic proteins)
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SYTO16 staining
A green fluorescent dye that stains live cells
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lysosomotropic agents
Chemicals that cause stress to lysosomes
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- Oct 2022
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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BH3 protein
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.
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curve fitting
The process of constructing a curve that has the best fit to a series of data points.
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chromogenic caspase assay
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.
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mitochondrial outer membrane permeabilization (MOMP)
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.
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XIAP
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.
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hydrolyzed
To break down (a compound) by chemical reaction with water.
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substrate
A molecule upon which an enzyme (e.g., caspase) acts. Enzymes catalyze chemical reactions involving the substrate(s).
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