Vesicles: membrane-bound organelle intermediates

The endomembrane system is perhaps the easiest way to identify a eukaryotic cell. It is composed of the various membranes that surround the organelles including the nuclear envelope, the endoplasmic reticulum (ER),  the Golgi bodies, the lysosomes (in animals), the vacuoles (in plants), endosomes and the plasma membrane.

This GIF, found on the Brooklyn Cuny Website, illustrates the pathways of proteins through the endomembrane system from the nuclear membrane (at the bottom-most part of the ER) to the lysosome or the plasma membrane. Proteins are stored in the lysosome or moved into the extracellular place. Note that transport vesicles link the larger organelles and carry proteins between them. 

Artemisa Garnica, a senior zoology major at CSU, explained that scientists study the endomembrane system to understand how and why proteins go to their respective locations. In this, we might be able to understand secretory diseases in both humans and animals, including some forms of cancer. 

Discovering Sec(retory) Mutants: The Genetics Behind Vesicles

On March 28, Randy Schekman, a 2013 Nobel Prize winner, gave a lecture in CSU's Lory Student Theater on "Genes and proteins that organize secretion and autophagy." Until the last 30 years, the mechanisms of the endomembrane transport system were largely unknown.

 Schekman and his lab were responsible for identifying secretory defects and looking for their genetic basis. One of the genes they related to a defect  became known as yeast cell gene Sec1 (labeled after its secretory mutation), according to Scheckman.  The Sec1 mutation disallowed membrane fusing between the vesicle and the plasma membrane so that the vesicles accumulated just inside the membrane.

His lab went on to identify several genes with secretory mutations, defects in vesicle budding, formation, and fusion.

In the lecture, he also explained that several human diseases occur due to secretory defects, including anemia and a rare condition that leads to incomplete formation of the skull.

The Mechanism
Schekman's lab also headed research on COPII, a coat protein that coats the vesicles.

According to Marinus Pilon, a Cell Biology professor at CSU who worked with Schekman, COP II is catalyzed to bind Sar during vesicle budding.

This image, found on the nature website shows vesicle budding, when a vesicle forms on the surface of the ER. The outer proteins (Sec23) bind to Sar  along with other proteins and form vesicles, which allow the stable transport of protein products through the cytoplasm.

These mechanisms provide possible points of investigation for diseases, especially if they result in the build-up of certain secreted proteins.

The exosome as a transporter of diseases and treatments

This infographic, found on The Scientist website, shows a basic understanding of exosomes, which carry proteins outside of the cell. Click the link to see it larger.

General

Exosomes were once thought to discard waste outside the cell. 7th Space Interactive, however, just published an article saying that according to some studies in the Journal of Neuroinflammation, exosomes also transfer proteins between cells.

This concept is not entirely new, as a 2011 article published on The Scientist called "Exosome Explosion" looks at the exosome as a cell signal transmitter that carries not just proteins, but protein precursors (like mRNA).

Disease Carriers

Exosomes have been found to carry infected material between cells, contributing to the growth of cancer, as explained in this article from PubMed. Additionally, exosomes may export therapeutic drugs, inhibiting their effectiveness.

The article from 7th Space Interactive also says that, in neurological pathways, the build up of neurotoxins may cause cellular damage and may contribute to Alzheimer's, Parkinson's and other neurological diseases. 

Treatments

A study done by the Department of Physiology, Anatomy, and Genetics at the University of Oxford looked at synthetic exosome delivery of drugs as a possible route for treatment of neurodiseases, according to Molecular Therapy.  The exosomes could possibly carry tumor inhibitors, as stated in the article:

Zhuang et al.1 build on previous findings by the same researchers that T-cell-derived exosomes are preferentially taken up by immature myeloid cells such as macrophages and microglial cells.10 Given the selective uptake of exosomes by macrophages, already demonstrated by these authors, and the newly established properties of exosomes as drug delivery vehicles,8 Zhuang and colleagues investigated whether T-cell-derived exosomes could be used to deliver anti-inflammatory agents specifically to microglial cells in the brain. They used a noninvasive intranasal route to bypass the BBB. Unloaded exosomes derived from a variety of mouse cell lines and labeled with a biological dye were first administered intranasally 2 µg at a time over a 10-minute period. Labeled exosomes were detected in the olfactory bulb within 30 minutes and up to 24 hours after administration. Multiorgan imaging demonstrated their selective homing to the brain and, to a lesser extent, the intestine. These initial experiments with unloaded exosomes demonstrated their fast and selective homing to the brain after intranasal administration.

Understanding of organelle changes treatment approach to jellyfish stings

Photo: Wikipedia.

According to The Australian "Higher Education," scientists from James Cook University and Cairns Hospital claim that vinegar should not be used to treat jelly fish stings.

This short video (embedding was disabled) talks about the mechanism for a jellyfish sting. Generally speaking, an electric pulse through the tentacles triggers a reaction in the cnidoblasts, the stinging cell. The nematocyst, an organelle in the cnidoblasts is  harpooned into the prey, and the nematocysts release neurotoxins into the organism.

This diagram, found on the Kennesaw State University website, shows the nematocyst in the cnidoblast before and after discharge.

When scientists initially recommended vinegar for jelly fish sting treatment, they  based their recommendation on the discovery that vinegar reduces the ability of inactive nematocysts to activate. However, according to Higher Education, the research groups involved in this newly published study discovered higher levels of toxicity in patients treated with vinegar because the vinegar made the already discharged nemacysts discharge more venom.

Lysosomal degradation of ferritin found crucial to iron homeostasis

A study published by the Harvard Medical School, Dana-Farber Cancer Institute and Beth Israel Deaconess Medical Center demonstrated a lysosome-dependent mechanism for iron storage and release in cells, according to medicalxpress.com .

Although cells need iron, especially red blood cells that depend on iron (II) to carry oxygen, too much iron free radicals lose in the cells can cause iron overload that transfers to and damages organs. A more complete analysis of iron-related health concerns can be found  in Jane Brody's New York Times health blog article published in 2012, "A Host of Ills When Iron’s Out of Balance."

The basic science behind the maintenance of iron levels can be traced to ferritin, a protein that surrounds unused iron ions and stores them. 

This diagram, retrieved on April 2nd from the Memorial University of Newfoundland Website shows the production of the ferritin, which is regulated by an iron-activated regulator protein. In the picture on the left (a), the active IRE binding protein is blocking the expression of the iron response element. In the picture on the right (b), when iron levels are high, iron binds to the active IRE binding protein, changing it's shape and causing it to detach from the mRNA. The mRNA that follows it, the ferritin encoding sequence, is then expressed in order to bind and store the iron.

However, the new study published in Nature looks at the next stage, after expression of the ferritin protein, when iron levels decrease. After someone has been seriously injured, given blood, or even menstruated, iron levels can become low. The cell then requires a mechanism to retrieve iron from the ferritin protein.

The study suggests that phagocytosis occurs as the lysosome digests the ferritin protein to release the iron contained within its cage-like structure. The scientists also found the cargo carrier that constitutes the ferritin's specific pathway of ferritin to lysosomal degradation.

Read Elizabeth Cooney's medicalxpress article for more information. Additionally, the abstract and images are available from nature.com.
 

Researchers at the Pacific Northwest Research laboratory develop action based probe technique

According to an article published Monday on Phys.org, researchers at the Pacific Northwest Research Laboratory developed a new tool called an action based probe (ABP) that allows scientists to see processes occurring in living cells.

This image is from the primary article available at Wiley.com from the journal Angewandte Chemie (International Edition) and shows the movement of the enzymes within the cell. 

The technique allows fluorescent tags to enter the lysosome and trace only active forms of the cathepsins, a group of cysteine proteases (cysteine-cutting enzymes). Cysteine is an amino acid with a terminal sulfur hydryl (sulfur and hydrogen) group, and proteases digest proteins and their components for recycling in the cell. Thus, if the cathepsins malfunction, a cell cannot digest proteins containing cysteine.

In the particular case of studying cathepsins, this technique can be used to analyze certain types of cancer associated with the malfunction of this family of enzymes.

This new technique has several other applications, especially if active enzyme-specific tags can be developed for a series of enzymes that cause other diseases and symptoms. It will allow scientists to see not just when enzymes are present and working, but also detect when they are lacking or malfunctioning.

According to Phys.org, researchers at Harvard's Wyss Institute have built self-assembling nanocages comprised of DNA. 

This image, found with the article on Phys.org, shows the DNA 3-D figures the scientists have made and imaged with the PAINT DNA technique. Each structure is composed of DNA tripods that attach end-to-end, forming polygons.

The researchers hope to use this for several medical applications, such as highly localized drug administration with metal coating, but currently are working to ensure the stability of the structures and the DNA. Although DNA is a fairly stable molecule in itself, common enzymes and components of the extra-cellular matrix easily disassemble the DNA.

The rightmost cage shown above, the biggest created to date, is about 1-tenth the size of a bacteria cell.

The Abstract for the research, published in Science Magazine, can be found here.

Researchers at MIT work to create nanobiotic plants inserting modified nanotubes into chloroplasts

According to Business Standard, a research team led by Michael Strano at MIT is working to produce plants that can sense pollution, explosives, and chemical weapons. The team might also try to incorporate electronics into plants.

The mechanisms the teams are using, such as those used to sense pollutants like nitric oxide, requires inserting modified nanotubes into functional parts of the plant, such as the chloroplast.

This image, found on Guardian Liberty Voice, illustrates how fluorescence can be seen in plants. This particular part of the experiment showed a 30% increase in the plants' ability to harvest energy from sunlight.

The first step with each new detection ability is to synthesize nanotubules with sensory ability. These tubes have a fluorescent pigment in them that changes when the target molecule (such as a pollutant) binds to the receptors.

The original article about the photonic chemical sensors in vivo and ex vivo, authored by Giraldo, was published in Nature Materials earlier this month.

This study suggests that plants may be a more reliable detector for small levels of pollutants than man-made detectors. 

The Golgi Apparatus during cell division: new 3-D images

Researchers for the National Institute of Health recently produced 3-D images of the Golgi Apparatus during cell division, according to Photonics.

Cell division is the process by which cells reproduce and make two daughter cells that are identical to themselves. The elementary study of cell division includes a detailed explanation of the chromosomes' behavior, but the rest of the cells content must be copied and transferred to the daughter cells as well. 

This image found on Scitable by Nature shows just a few of the organelles that have to be duplicated in cell division. Additionally, the interactions between the Golgi and the ER help uphold their finding.

The researchers found, according to the photonics article, that the Golgi breaks up during during cell division, gets absorbed by the endoplasmic reticulum, and the Golgi reconstitutes in the daughter cells. 

The mechanism for reconstitution would be helpful in understanding the endomembrane system and how it functions, interacts, and forms, as well as in understanding evolutionary implications.

Kinase cascading and circuit analysis, a new way to look at organelles

Researchers at the UNC School of Medicine have developed a circuit analysis method of studying the cascading effects of kinases, enzymes that are involved in cell movement, cell death (apoptosis), metabolism, enzyme secretion, and various other cell activities, according to Phys.org.

This diagram shows an example of "cascading" kinase events. Each of the different molecules are kinases that undergo activation, such as substrate-level phosphorylation in MEK and MAPk. Each activation leads to another activation until the signal reaches the response site, in this case, in the nucleus.

The researchers' methods involved deactivating one of the enzymes, then reactivating it and observing where the signal went. In this way, they can control the signal's activation time and trace its next interaction. This means real time in-cell analysis of kinase cascade triggered reactions.

Given the prevalence of kinases and their association with many cell activities and organelles, this disruption and tracing technique may lead to further discoveries in organelle activity.

Readers' choice: things you didn't know about your favorite organelles

Biologists and biology lovers alike have their own favorite chemical reactions, factoids, and even organelles. I asked some readers what their favorite organelles were, and set out to find some interesting or new factoids about each of them. 

The selected organelles:

• mitochondria, the powerhouse of the cell
• lysosomes, the destroyer
• ribosomes, protein builders

Mitochondria

 [My favorite organelles are] "mitochondria because they have their own genome," LauraAnn Schmidberger, a senior in high school, said.

Three Parent Controversy- The mitochondria do indeed have their own genome, which is what puts them at the center of the recent 3-Parent controversy discussed on Feb. 26.  However, the controversy is actually international, and the UK may approve it and produce 3-parent babies by 2014, according to The Telegraph.



Mitoflashes and Lifespan- Activity in the mitochondria of worms may be able to predict the worms' lifespan, according to the article "Lifespans predictable at early age: worm study suggests that activity in mitochondria determines ageing" published in February by Nature.com. The article explains the results of a study that found that the frequency of mitoflashes, or quick bursts of mitochondrial activity, is inversely related to longevity; the more mitoflashes, the shorter the lifespan. 

Lysosomes

I like lysosomes because they destroy stuff and I like the name "lysosome," Kylie Baker, a sophomore Molecular Biology Major at Colorado University, Boulder, said. 

Autophagy- Autophagy, or "self-eating" is how eukaryotic organisms survive starvation, digesting their own molecules and organelles for use as energy. Lysosomes, in addition to breaking down macromolecules entering the cell to be used in energy synthesis during normal satiated conditions, can "eat" parts of its own cell through endocytosis and digest its own macromolecules for energy, according to Scitable.

Missing Enzymes and Empty Lysosomes-When one of the ~60 enzymes is missing from the lysosome, a lysosomal deficiency or disease occurs, Biosciencetechnology explains. In extremely rare cases of (Type III) in which none of the enzymes work, the lysosomes remain empty and the children die by age ten. 

Ribosomes

 [My favorite organelle is the] "ribosome... definitely the ribosome. Conserved in all cells and absolutely essential for life!" Amanda Evans, a freshman Biomedical Science Major at Colorado State University said.

Self Assembly- One of the requirements for a molecule that assembles RNA is that it must assemble its own 50-part structure, with the help of some proteins. Phys.org published an article in February, "Advanced techniques yield new insights into ribosome self-assembly" that explains how some of the auxiliary proteins, rather than locking the ribosome into its structure, bind the ribosome's components in other conformations (shapes not found in the ribosomes themselves) to allow other parts to come together. "The team was most interested in a central region of the 16s RNA because it contains signature sequences that differentiate the three cellular 'domains,' or superkingdoms, of life," the article explains.

Energy dependent translational throttle A (EttA)- A collaborative effort between researchers at Lethridge University (Canada) and Columbia University led to the suggestion that a protein, now EttA, binds to ribosomes to slow down protein production once a cell is fully grown, according to Caroline Zentner for the Lethbridge Herald. "Just like a laptop computer that will go into power-save mode when its battery is running low, YjjK [EttA] senses when the cell’s energy is low and then acts like a throttle to put it into energy-saving mode." Zentner writes.

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Leave a comment if you would like me to look into any other organelles! 

Read more at: http://phys.org/news/2014-02-advanced-techniques-yield-insights-ribosome.html#jC

Prostate cancer survival related to organelle function, or malfunction

Researchers at A&M University recently discovered a new biomarker associated with Prostate Cancer prognosis, according to this BioNews Texas article.

The background for the article provided for the paper on Wiley.com, explains that cells' autophagy contributes to tumor production while the protein LRPPRC inhibits autophagy and maintains mitochondrial activity. Autophagy is the highly regulated and controlled recycling of wastes within the cell.

This image, borrowed from Yale Image Finder (and PubMed) shows the LRPPRC supressor protein (near the center), as well as other proteins, suppressing the expression of genes that trigger autophagy and regulate mitochondria activities.

The study, headed by Leyuan Liu found that higher levels of LRPPRC had a positive correlation with more severe prostate cancer.

Essentially, elevated levels of the protein prevent the cells from discarding cellular waste, and the resulting imbalance inhibits mitochondrial function.

This does not mean that elevated LRPPRC causes prostate cancer, but it does mean that generally, someone with a lower LRPPRC will survive longer than someone with elevated levels.

Following these findings, drug development will ensue to control levels of LRPPRC in prostate cancer patients to increase the timescale and chances of survival, according to Liu. Additionally, other cancers and their progression may be linked to similar mechanisms.  

Plants without chloroplasts or their genomes?

Perhaps the introductory biology class concept of plant cells as eukaryotes with chloroplasts is being defied, as Rappler writer KD Suarez points out in this article posted on rappler.com, a new social media that focuses on news.

This image, borrowed from a BBC KS3 Bitesize Science article, shows the most basic understanding of the animal versus plant cell comparison. Note the little green organelles in the Plant cell, chloroplasts.

In his article, KD Suarez draws attention to two plant population studies published in 2014 in which researchers have found neither chloroplasts nor their genomes. 

Although some plants do not have chloroplasts, it has been generally accepted that plants have chloroplast genomes, perhaps because they are similar to the mitochondria in providing energy to the cell.

The first study examined a parasitic flower species native to the Phillipines that gets its food from its plant host, and the researchers did not find the chloroplast genome, according to Suarez.

The second study looked at an algae and found that although it had neither chloroplasts nor its genomes, it did have proteins associated with the chloroplast and its function. 

The Scientist also pointed out the two studies in its article: "Plants Without Plastid Genomes:Two independent teams point to different plants that may have lost their plastid genomes."

Certainly this communicates a long history of parasitism and environmental dependency for these species, assuming that their ancestors had functioning chloroplasts. It may be more material as well as energy efficient for these plants that do not depend on photosynthesis for energy to not have the genome associated with the "useless organelle."

Nonetheless, these studies challenge how scientists classify plants. Perhaps parasites, like genetic mutants, are key to understanding what functions, what does not, and how some organisms have changed over time.

Mitochondrial Politics: "3 Parent Baby" issue before FDA

This week the FDA examines the "3 Parent Baby" methods, which insert mitochondrial DNA from a third individual into the mother's egg, according to Dina Fine Maron for Scientific American.

The idea arose as a method to increase fertility in mothers with high risk factors for certain mitochondrial diseases and allow their children to be unaffected.  

When most people think of genes, they think of DNA packed within the nucleus that gives rise to proteins that help cells, and in turn, organisms, function. But the cell's genome also contains DNA that associates with other organelles and are passed from generation to generation by cytoplasmic inheritance, particularly in the mitochondria.

In nature, the offspring inherit 100% of their mitochondrial DNA from their mother's egg, since the fertilized egg contains the mother's cytoplasm and organelles.

This image, borrowed from the Nature Education website shows the transmission of mitochondrial DNA from mother to zygote (offspring). The chloroplasts and mitochondria are crossed out in the father's gamete because they are not transmitted. Only the father's nucleus fertilizes the egg.

These mitochondrial diseases, which can include loss of vision, seizures, or premature death "occur in about one in every 5,000 live births and are incurable," according to the Scientific American.

The FDA's approval would permit clinical trials to be run.

Some find that these "3 Parent Babies" may be a cure for infertility, or an increase in the quality of life for offspring, but others see it as a landmark for genetic engineering, and a bad one at that, according to CNN's article "FDA considering '3-parent babies'." 

Magnetosomes transformed, giving organisms and research new directions

Researchers at Albert Ludwigs University of Freiburg transformed a non-magnetic bacteria line with genes for magnetosomes, organelles that sense and respond to the earth's magnetic field, according to Phys.org.

This image, taken from boundless.com, shows a magnetosome in a bacterial cell. Each of the black dots is a magnetic crystal structure. 

Crystal structures inside the magnetosomes act like a compass needle together, thereby navigating the cell along with Earth's magneticism, a process called magnetotaxis.

The paper, Biosynthesis of magnetic nanostructures in a foreign organism by transfer of bacterial magnetosome gene clusters, published by nature.com, explains that the researchers were able to transcribe the  30 gene section of the bacterial genome that encodes for the magnetosensitivity. 

The scientists would like to analyze the set of genes to come up with minimal sets of genes with normal functionality to look at the necessity and evolution of the complex magnetosome. 

An Organelle as Part of a System: Chromatin

Researchers in Edinburgh have presented a quantitative, statistics-based approach to organelle proteonomics, the study of proteins, according to Genome Web. 

The paper, "Proteomics of a fuzzy organelle: interphase chromatin," published on the 17, discusses methods for looking at chromatin, in context, without separating the parts.

Chromatin is the organelle comprised of DNA, histone proteins, and  cofactors present in the nucleus of a cell.

This image from the Molecular Expressions Cell Biology and Microscopy site shows chromatin in its tangled form within the nucleus and stretched out and isolated.

The paper discusses methods to look at not just the DNA, which is often isolated for sequencing studies, but to examine the complex itself and how the components interact with one another. 

This may be another step to understanding the complex functionality of chromatin, and may set an example for other studies, looking at DNA in context, as a 3-D structure with a function dependent on interactions, rather than as a one dimensional piece of isolated information. 

Penn State researchers operate nanomotors in HeLa cells

A team of chemists and engineers at Penn State have been able to insert and control nanomotors within human cells, according to  Krista Weidner for PennStateSCIENCE.

The gold nanoparticles were successfully inserted into live HeLa cells, cervical cancer cells derived from those taken from Henrietta Lacks in 1951.

The chemists were able to use ultrasound pulses to control the nanomotors, according to Weidner's report. These pulses help move and rotate the motors around cell structures.

This video was taken of the nanomotors, also called nanorods, inside the HeLa cells.

 

These molecular motors may have implications not just for diagnosing cellular diseases, but possibly for helping repair cell problems from within. 

Like the HeLa cells they were first used in, scientists can only speculate what contributions the nanomotors will make in biochemistry.

An Organelle's Help in Dinosaur Puzzle

Forms of the melanosome organelle suggest colored, iridescent feathers, were present in dinosaur-era birds, according to an article by Thomas Carannant on the Science World Report website.

The birds of the dinosaur era were previously thought to have little color variation, according to an older (2011) National Geographic article. 

Melanosomes produce and transport melanin, a pigment that gives animal cells color and protects them from the sun.

Carannant explains that the shapes of the melanosomes recently analyzed from fossils resemble those that are known to produce brown, black and gray pigments in modern bird lineages and also cause iridescence. This suggests that the feathered Amniota emerged around the same evolutionary era, during the age of Dinosaurs.  

Photo credit: Li, et al (original article from Nature Magazine), "Melanosome diversity across Amniota." The tree diagram at the bottom shows the proposed evolutionary relationships while the scatter plots show the observed patterns in size (diameters and lengths).

  
The tree of life is revised again, thanks to an organelle. The question remains whether this fits in with most of the accepted taxonomy or changes it completely. 

The Tea Lover's Organelle: Tannosome

A team of French and Hungarian scientists identified an organelle responsible for producing the chemical that gives tea, wine, and unripe fruit a bitter flavor according to Scientific American's blogger Jennifer Frazer.

The tannosome produces tannins, the bitter chemicals that enhances flavor but deter many herbivores. Tannin denatures proteins in the herbivore, making it difficult for the animal to process its food and produce energy at a regular rate. For more information on tannins specifically, see this explanation of the biotoxins from Cornell.

Previously, scientists assumed that the rough endoplasmic reticulum produced the tannins, which were then stored in the vacuoles. Instead, the team found that they are produced within the chloroplasts, and stored in special vesicles  called tonoplasts that prevent the chemicals from disintegrating their own cell's proteins.

Photo credit: Jean-Marc Brillouet, et al. (from the original research paper in the Annals of Botany).
The new process, proposed by the researchers, suggests that tannosomes are found within the inner membrane of the vascular plants' chloroplasts. The tannosomes make the tannins, which are then shuttled by a vesicle into the vacuole where they are stored inside a tonoplast, which separates them from the other contents of the vacuole.

Since organelles are useful in separating biological processes, it is not entirely surprising that tannins require their own production centers. It is worth noting that even the collection of organelles may still increase as scientists turn their attention to new processes and chemicals.