User:IamtheStudent/sandbox





Exemplary Example

 * Social Interaction Anxiety Scale
 * CD/DVD based immunoassay
 * Defamation
 * Bind fallout
 * Ginsenoside
 * Bowhead whale
 * Mechanism of action
 * Oyster reef
 * Tuna penning
 * User:rhoffing
 * User:Posner.c

LYSOSOME Comments, proposals for EDITING
A lysosome (derived from the Greek words lysis, meaning "to loosen", and soma, "body") is a membrane-bound cell organelle found in animal cells. They are spherical vesicles containing hydrolytic enzymes capable of breaking down virtually all kinds of biomolecules, including proteins, nucleic acids, carbohydrates, lipids, and cellular debris. They are known to contain more than 50 different enzymes, which are all optimally active at an acidic environment of about pH 4.5 (about the pH of black coffee). Thus lysosomes act as the waste disposal system of the cell by digesting unwanted materials in the cytoplasm, both from outside of the cell and obsolete components inside the cell. Furthermore, Also, lysosomes are responsible for help to maintain homeostasis, due to their roles in secretion, plasma membrane repair, cell signalling and energy metabolism, which are related to health and diseases.[this sentence could use some additional cleaning-up. Depending on their functional[?] activity, their sizes can be very different—the biggest ones can be more than 10 times bigger than the smallest ones. They were discovered and named by Belgian biologist Christian de Duve, who eventually received the Nobel Prize in Physiology or Medicine in 1974.

Enzymes of the lysosomes are synthesised in the rough endoplasmic reticulum. The enzymes are released from Golgi apparatus in small vesicles which ultimately fuse with acidic vesicles called endosomes, thus[not necessarily, this isn't the relationship] becoming full lysosomes. In this process, the enzymes are specifically tagged with the molecule mannose 6-phosphate to differentiate them from other enzymes[other?]. Lysosomes are interlinked with three intracellular processes, namely phagocytosis, endocytosis and autophagy. [(5)Extracellular materials such as microorganisms taken up by phagocytosis, macromolecules by endocytosis, and unwanted cell organelles are fused with lysosomes in which they are broken down to their basic molecules.] [this is a do-nothing sentence, irrelevant source]Thus[the preceding sentence does not lead into this one, thus nullifying the point of "thus"] lysosomes are the recycling units of a cell.

Synthesis of lysosomal enzymes is controlled by nuclear genes.[yes of course] Mutations in the genes for these enzymes are responsible for more than 30 different human genetic diseases, which are collectively known as lysosomal storage diseases. These diseases are due to deficiency in a single lysosomal enzyme, that prevents breakdown of target molecules; consequently the undegraded materials accumulate within the lysosomes and often giving rise to severe clinical symptoms. Further, such genetic defects are related to[related to? play part in, cause directly, exacerbate?] several neurodegenerative disorders, cancer, cardiovascular diseases, and ageing-related diseases.

Changes:

- 1st sentence: -["(they are absent in red blood cells)"]

- 1st sentence -"most"

- 2nd sentence -"Structurally and chemically"

- "In this process" sentence is awk.

- (5) wow this sentence is confusing... gram. incorrect?

TODO: It is similar to an abstract atm for the intro.

- Add a picture of the lysosome above the linking-template, similar format in mitochondria

Discovery
Christian de Duve, then chairman of the Laboratory of Physiological Chemistry at the Catholic University of Louvain in Belgium, had been studying the mechanism of action of a pancreatic hormone insulin in liver cells. By 1949, he and his team had focused on the enzyme called glucose 6-phosphatase, which is the first crucial enzyme in sugar metabolism and the target of insulin. They already suspected that this enzyme played a key role in regulating blood sugar levels. However, even after a series of experiments, they failed to purify and isolate the enzyme from the cellular extracts. Therefore, they tried a more arduous procedure of cell fractionation, by which cellular components are separated based on their sizes using centrifugation.

They succeeded in detecting the enzyme activity from the microsomal fraction. This was the crucial step in the serendipitous discovery of lysosomes. To estimate this enzyme activity, they used that of standardised enzyme acid phosphatase, and found that the activity was only 10% of the expected value. One day, the enzyme activity of purified cell fractions which had been refrigerated for five days was measured. Surprisingly, the enzyme activity was increased to normal of that of the fresh sample. The result was the same no matter how many times they repeated the estimation, and led to the conclusion that a membrane-like barrier limited the accessibility of the enzyme to its substrate, and that the enzymes were able to diffuse after a few days (and react with their substrate). They described this membrane-like barrier as a "saclike structure surrounded by a membrane and containing acid phosphatase."

It became clear that this enzyme from the cell fraction came from a membranous fractions, which were definitely cell organelles, and in 1955 De Duve named them "lysosomes" to reflect their digestive properties. The same year, Alex B. Novikoff from the University of Vermont visited de Duve´s laboratory, and successfully obtained the first electron micrographs of the new organelle. Using a staining method for acid phosphatase, de Duve and Novikoff confirmed the location of the hydrolytic enzymes of lysosomes using light and electron microscopic studies. de Duve won the Nobel Prize in Physiology or Medicine in 1974 for this discovery.

Add(moved from intro): "For this function they are popularly[sic] referred to as "suicide bags" or "suicide sacs" of the cell. "

-> This is not a "popular" characterization. Duve said this, and the textbooks quoted him. This sentence does not help illuminate the role of lysosomes.

->link Nature paper as "discrediting proof"

-> find exact quote, and date

TODO: Move this... but where? where are the other organelle-articles shoving their history

Function and structure
Lysosomes are cellular organelles that contain acid hydrolase enzymes that break down waste materials and cellular debris. They can be described as the stomach of the cell. Lysosomes digest excess or worn-out organelles, food particles, and engulfed viruses or bacteria. The membrane around a lysosome allows the digestive enzymes to work at the pH they require. Lysosomes fuse with autophagic vacuoles (phagosomes) and dispense their enzymes into the autophagic vacuoles, digesting their contents. They are frequently nicknamed "suicide bags" or "suicide sacs" by cell biologists due to their autolysis.

The size of supercalifragilisticexpialidocious lysosomes varies from 0.1–1.2 μm. At pH 4.8, the interior of the lysosomes is acidic compared to the slightly basic cytosol (pH 7.2). The lysosome maintains this pH differential by pumping in protons (H+ ions) from the cytosol across the membrane via proton pumps and chloride ion channels. Vacuolar H+-ATPases are responsible for transport of protons, while the counter transport of chloride ions is performed by ClC-7 Cl−/H+ antiporter. In this way a steady acidic environment is maintained. The lysosomal membrane protects the cytosol, and therefore the rest of the cell, from the degradative enzymes within the lysosome. The cell is additionally protected from any lysosomal acid hydrolases that drain into the cytosol, as these enzymes are pH-sensitive and do not function well or at all in the alkaline environment of the cytosol. This ensures that cytosolic molecules and organelles are not destroyed in case there is leakage of the hydrolytic enzymes from the lysosome.



Formation (Endocytosis)
- SNAPIN

- Battenin

- M6RP

- CLCN (drops off sugar-bonders)

- cubulin, LMBRD1

- VPS$a, ESCRT-0, CHMP3

- Nexins

- EEA-1

Maintenance of pH perfect balance
-> Cystinosin & CLCN7

Hydrolytic Activity
General discussion about import process, GOLGI, M6RP

** Sortillin

** ? subsections should be merged into a general seciton

Lipids, phospholipids
- NPC1,2

- MVBs: VPS4A, ESCRT, CHMP3, etc.

- ACP2

Carbohydrates
- GAA**

Proteins
Cystinosin

CTS (Cathepsins-> are they varied, too?)

PQLC2

Regulatory roles
- Apoptosis, autophagy, signalling f/ exo-space

- LAMPs

- SCARBs

- HLA Class II molecules

- TCP, ZincT

- NPC1,2

- TMBIM2

- GLMP, TFEB (? look for a proteomic study on TFEB)

- TICAM

-Battenin, and retrograde transport (though that's more LE, not Ly)

- CTSD, CTSL (apoptosis)

- TM7SF1

* ? ad hoc tissue-specific regulatory roles

Viral Entry
TODO: enumerate some of the most informationally-available viruses, and which proteins they enter from

TODO: exemplify some toxin hijackings by malicious pathogens, such as bacteria w/ cholera toxin and other AB5 toxins.

[PIC: virus hijacking a lysosomal body, w.e. its association with w.e. glycoprotein]

HIGHLIGHTS: This should be expanded, annotated proteins:
(or could provide a link to GO database, uniprot map'd search, etc.)


 * 1) LAMPs (signalling proteins, with specific glycan patterns
 * 2) SCARB (Lyso membrane prot. 2) (basically like LAMPs)
 * 3) SNAPIN (lysosomal expansion? where is directed in pathway)  -> caveat: neuron-specific? probably not
 * 4) *** GAA (digesting enzyme -- macro-sugars)
 * 5) HLA Class II (flesh-out immune system role?) -> may want to exclude as it is not generalized function
 * 6) NPC1,2 (Niel protein... Cholesterol TDD)
 * 7) *** PLEKHF1 (caspase-independent apoptosis) -> Role in apoptosis, communication with mitochondrium
 * 8) *** M6PR (directs contents to lumen, is recycled by RAB29)
 * 9) LRRK2 (autophagy by inc. Ca2+ release)
 * 10) TCP (calcium transporter)
 * 11) Zinc Transporter SZ1 (Zinc cofactors?)
 * 12) *** CLCN7 (H+/Cl- symport) [super important for acidification of lumen]
 * 13) opposite the activity of Cystosin... fine-tune-control for pH @4.8
 * 14) Battenin (CLN3) [directs anterograde (towards inner leaflet) Mt-mediated transport of the lysosomal vesicular compartmnets]
 * 15) Cystinosin (Cys/H+ symport -> Cys-digestion + implicated in LSD accumulative disease)
 * 16) NOT limited to skin in expression, so even if it is important in melanocytes, it is just as important in regular lysosomal functioning
 * 17) over-expressed in testis
 * 18) Cubulin (Intestinal-specific mediator of macropinocytosis (i.e. for absorption of large, undigested molecules)
 * 19) Major interaction: LRP2 (single-pass protein, facilitates via coated pits)
 * 20) It will bind cholesterol & chol-like molecules, along w/ Ca2+, and ensure its endocytosis upon LRP2 organization
 * 21) both mediate HDL endocytosis
 * 22) Cubulin is a peripheral protein
 * 23) EVA1A (autophagy & apoptosis regulator)
 * 24) ****CTS (Cathepsins -> major grouping of all the proteases of the lysosome) -> CTSL & CTSD are involved in apoptosis, being transported across the membrane
 * 25)  TM7SF1 -> signal transduction of LE, Lyso (for what? unknown, probs. not going to include)
 * 26) GLMP (its transcription of activated by TFEB; regulatory network in lysosome...interconnected?)
 * 27) PQLC2 (lysosomal aa exporter -- for cationic aa's)
 * 28) LMBRD1 -- lysosomal coblamin transporter (vitamin B and some others... is it tissue-specific?)
 * 29) TMBIM1 (protein lifeguard, regulatory of the death processes ofc)
 * 30) ACP2 (lysosomal acid phosphatase) **** key for glycolipids ->>> important in being able to digest phospho/lipids, hydrolysing the monoester bond
 * 31) **** Sortillin (SORT1): GOLGI -> Lysosome (M6PR-independent)
 * 32) VPS4A = Creates MVBs, which come from invaginated & scissioned pieces of the limiting membrane. This is essential for outer-leaflet directed proteins, for lipids, and for other membrane-integral proteins. (especially "activated" receptors) [Vacuolar protein sorting-associated 4-A]
 * 33) ESCRT-III; the main actor in MVB formation. Creates ILVs.
 * 34) CHMP3 - Charged Multivesicular Body protein 3: essential for many membrane-fission events, including EGFR-sorting, virus budding, cytokinesis. Selectively binds PtdIns(3,5)P2, versus other phosphatidylinositides.
 * 35) SNX-2, has a BAR domain, ofc, bc it can sense membrane curvature
 * 36) TLR4(->|LPS), TICAM involved
 * 37) EEA1 = Early-Endosome Antigen 1 -> is a phosphatidylinositol-binder, participating in trafficking. SITS ON OUTSIDE OF CELL, PERIPHERALLY-BOUND.

Re-curated: (probably excluded)

-> would need to find its homologue, though what is the trigger factor for lumen-contributing endocytosis? -> immune-system-specific
 * 1) BLOC
 * 2) KCNQ1 (potassium [voltage-gated] ion channel (probably just neurons, found by regulating-internalization
 * 3) ImpB (implicated in macropinocytosis, starting the feeder pathway)
 * 1) Anitgen-presenting glycoprotein, of glycolipids to macrophages (CD1D)
 * 1) Macrosialin (CD68 -> selectin-affinity, perhaps macrophage crawling)
 * 2) CCZ1 --- unknown... found from high-throughput proteasomal analysis

Areas of discussion:

*** some proteins pick-up a lysosome-signature due to regulatory-intending internalization [caveat]

- Trafficking

- Endosomal entry receptors (viral targets for retrograde-hijacking)

-> choleraT is a fine example, but how to create a usable figure???? can do by self and contribute to commons? what software is used?

- Farnesylation, prenylation, and localization

- Multi-vesicular nature, and the limiting bilayer

- Vesicular fusion (SNARE, SNAPIN)

- LSD's, grouped with significant analysis

- digestive enzymes

- protease-mediated signal peptide cleaving

- cathepsins, and other major metabolic enzymes

- the network of imbued regulation

- Definitive, terminological, technical descriptions & distinctions of: Early E., Late E., Recycling E., Lysosome, Golgi-bound vesicle, macropino, CODI-coated/clathrin

- gel zymography

-> diagram of LE/LS with enriched M6PR's?

-> "payload" delivery of hydrolytic enzymes into engulfed particles, forming phagosome

-> sorting mediated by vacuolar proteins (VPS33B)

-> endosomal membrane fusion hot-spots:

- RAB5

- PLEKHF2

- EEA1 (phosphatidyl-inositol-> endosomal contents associate with the other end -> adaptors, labeling as Endosomes with RAB5 + PLEKHF2)

- retromer complexes which set-fate from the Endosome to the trans-Golgi Network. (versus the lysosome, or recycling endosome/extracellular). Especially important for rescuing, recycling cargo proteins, which ship from TGN-> cell membrane.

_ cargo molecules: sortillin, M6PR, wntless(wnt ->frizzled->disheveled)

_ retromer components: SNXs (nexins) VSP (vacuolar-sorting proteins)

Formation
Many components of animal cells are recycled by transferring them inside or embedded in sections of membrane. For instance, in endocytosis (more specifically, macropinocytosis), a portion of the cell’s plasma membrane pinches off to form a vesicle that will eventually fuse with an organelle within the cell. Without active replenishment, the plasma membrane would continuously decrease in size. It is thought that lysosomes participate in this dynamic membrane exchange system and are formed by a gradual maturation process from endosomes.

The production of lysosomal proteins suggests one method of lysosome sustainment. Lysosomal protein genes are transcribed in the nucleus. mRNA transcripts exit the nucleus into the cytosol, where they are translated by ribosomes. The nascent peptide chains are translocated into the rough endoplasmic reticulum, where they are modified. Upon exiting the endoplasmic reticulum and entering the Golgi apparatus via vesicular transport, a specific lysosomal tag, mannose 6-phosphate, is added to the peptides. The presence of these tags allow for binding to mannose 6-phosphate receptors in the Golgi apparatus, a phenomenon that is crucial for proper packaging into vesicles destined for the lysosomal system.

Upon leaving the Golgi apparatus, the lysosomal enzyme-filled vesicle fuses with a late endosome, a relatively acidic organelle with an approximate pH of 5.5. This acidic environment causes dissociation of the lysosomal enzymes from the mannose 6-phosphate receptors. The enzymes are packed into vesicles for further transport to established lysosomes. The late endosome itself can eventually grow into a mature lysosome, as evidenced by the transport of endosomal membrane components from the lysosomes back to the endosomes.

TODO: present & explain aetiological agents involved, i.e. which proteins

TODO: figure-enhanced description of process

Late Endosomes: enriched in M6PR, as it is the "check-point" before lysosome for fine-regulation of shuttling

Disease
Lysosomes are responsible for a group of genetically inherited disorders called lysosomal storage diseases (LSD). They are a type of inborn errors of metabolism caused by malfunction of one of the enzymes. The rate of incidence is estimated to be 1 in 5,000 live births, and the true figure expected to be higher as many cases are likely to be undiagnosed or misdiagnosed. The primary cause is deficiency of an acidic hydrolase (a hydrolase which functions best in acidic environments). Other conditions are due to defects in lysosomal membrane proteins that fail to transport the enzyme, non-enzymatic soluble lysosomal proteins. The initial effect of such disorders is accumulation of specific macromolecules or monomeric compounds inside the endosomal–autophagic–lysosomal system. This results in abnormal signaling pathways, calcium homeostasis, lipid biosynthesis and degradation and intracellular trafficking, ultimately leading to pathogenetic disorders. The organs most affected are brain, viscera, bone and cartilage.

There is no direct medical treatment to cure LSDs. The most common LSD is Gaucher's disease, which is due to deficiency of the enzyme glucocerebrosidase. Consequently, the enzyme substrate, the fatty acid glucosylceramide accumulates, particularly in white blood cells, which in turn affects spleen, liver, kidneys, lungs, brain and bone marrow. The disease is characterized by bruises, fatigue, anaemia, low blood platelets, osteoporosis, and enlargement of the liver and spleen.

Metachromatic leukodystrophy is another lysosomal storage disease that also affects sphingolipid metabolism.

TODO: present information is less scrawly-manner

Lysosomotropism
Weak bases with lipophilic properties accumulate in acidic intracellular compartments like lysosomes. While the plasma and lysosomal membranes are permeable for neutral and uncharged species of weak bases, the charged protonated species of weak bases do not permeate biomembranes and accumulate within lysosomes. The concentration within lysosomes may reach levels 100 to 1000 fold higher than extracellular concentrations. This phenomenon is called "lysosomotropism" or "acid trapping". The amount of accumulation of lysosomotropic compounds may be estimated using a cell-based mathematical model.

A significant part of the clinically approved drugs are lipophilic weak bases with lysosomotropic properties. This explains a number of pharmacological properties of these drugs, such as high tissue-to-blood concentration gradients or long tissue elimination half-lifes; these properties have been found for drugs such as haloperidol, levomepromazine, and amantadine. However, high tissue concentrations and long elimination half-lives are explained also by lipophilicity and absorption of drugs to fatty tissue structures. Important lysosomal enzymes, such as acid sphingomyelinase, may be inhibited by lysosomally accumulated drugs. Such compounds are termed FIASMAs (functional inhibitor of acid sphingomyelinase) and include for example fluoxetine, sertraline, or amitriptyline.

Ambroxol is a lysosomotropic drug of clinical use to treat conditions of productive cough for its mucolytic action. Ambroxol triggers the exocytosis of lysosomes via neutralization of lysosomal pH and calcium release from acidic calcium stores. Presumably for this reason, Ambroxol was also found to improve cellular function in some disease of lysosomal origin such as Parkinson's or lysosomal storage disease.

TODO: refine? probs. leave alone

Controversy in botany
By scientific convention, the term lysosome is applied to those vesicular organelles only in animals, and vacuoles to plants, fungi and algae. Discoveries in plant cells since the 1970s started to challenge this definition. Plant vacuoles are found to be much more diverse in structure and function than previously thought. Some vacuoles contain their own hydrolytic enzymes and perform the classic lysosomal activity, which is autophagy. These vacuoles are therefore seen as fulfilling the role of the animal lysosome. Based on de Duve's description that “only when considered as part of a system involved directly or indirectly in intracellular digestion does the term lysosome describe a physiological unit”, some botanists strongly argued that these vacuoles are lysosomes. However, this is not universally accepted as the vacuoles are strictly not similar to lysosomes, such as in their specific enzymes and lack of phagocytic functions. Vacuoles do not have catabolic activity and do not undergo exocytosis as lysosomes do.