Showing posts with label cell biology. Show all posts
Showing posts with label cell biology. Show all posts

Wednesday, June 3, 2009

Apoptosis

Apoptosis (pronounced ă-pŏp-tŏ’sĭs) is a form of programmed cell death in multicellular organisms. It is one of the main types of programmed cell death (PCD) and involves a series of biochemical events leading to a characteristic cell morphology and death, in more specific terms, a series of biochemical events that lead to a variety of morphological changes, including blebbing, changes to the cell membrane such as loss of membrane asymmetry and attachment, cell shrinkage, nuclear fragmentation, chromatin condensation, and chromosomal DNA fragmentation (1-4). Processes of disposal of cellular debris whose results do not damage the organism differentiates apoptosis from necrosis.




In contrast to necrosis, which is a form of traumatic cell death that results from acute cellular injury, apoptosis, in general, confers advantages during an organism's life cycle. For example, the differentiation of fingers and toes in a developing human embryo occurs because cells between the fingers apoptose; the result is that the digits are separate. Between 50 billion and 70 billion cells die each day due to apoptosis in the average human adult. For an average child between the ages of 8 and 14, approximately 20 billion to 30 billion cells die a day. In a year, this amounts to the proliferation and subsequent destruction of a mass of cells equal to an individual's body weight.


Research on apoptosis has increased substantially since the early 1990s. In addition to its importance as a biological phenomenon, defective apoptotic processes have been implicated in an extensive variety of diseases. Excessive apoptosis causes hypotrophy, such as in ischemic damage, whereas an insufficient amount results in uncontrolled cell proliferation, such as cancer.


Process


The process of apoptosis is controlled by a diverse range of cell signals, which may originate either extracellularly (extrinsic inducers) or intracellularly (intrinsic inducers). Extracellular signals may include hormones, growth factors, nitric oxide or cytokines, and therefore must either cross the plasma membrane or transduce to effect a response. These signals may positively or negatively induce apoptosis; in this context the binding and subsequent initiation of apoptosis by a molecule is termed positive, whereas the active repression of apoptosis by a molecule is termed negative.

Intracellular apoptotic signalling is a response initiated by a cell in response to stress, and may ultimately result in cell suicide. The binding of nuclear receptors by glucocorticoids, heat, radiation, nutrient deprivation, viral infection, and hypoxia are all factors that can lead to the release of intracellular apoptotic signals by a damaged cell. A number of cellular components, such as poly ADP ribose polymerase, may also help regulate apoptosis.

Before the actual process of cell death is carried out by enzymes, apoptotic signals must be connected to the actual death pathway by way of regulatory proteins. This step allows apoptotic signals to either culminate in cell death, or be aborted should the cell no longer need to die. Several proteins are involved, however two main methods of achieving regulation have been identified; targeting mitochondria functionality, or directly transducing the signal via adapter proteins to the apoptotic mechanisms. The whole preparation process requires energy and functioning cell machinery.


Mitochondrial regulation




The mitochondria are essential to multicellular life. Without them, a cell ceases to respire aerobically and quickly dies - a fact exploited by some apoptotic pathways. Apoptotic proteins that target mitochondria affect them in different ways; they may cause mitochondrial swelling through the formation of membrane pores, or they may increase the permeability of the mitochondrial membrane and cause apoptotic effectors to leak out.There is also a growing body of evidence that indicates that nitric oxide (NO) is able to induce apoptosis by helping to dissipate the membrane potential of mitochondria and therefore make it more permeable.

Mitochondrial proteins known as SMACs (second mitochondria-derived activator of caspases) are released into the cytosol following an increase in permeability. SMAC binds to inhibitor of apoptosis proteins (IAPs) and deactivates them, preventing the IAPs from arresting the apoptotic process and therefore allowing apoptosis to proceed. IAP also normally suppresses the activity of a group of cysteine proteases called caspases, which carry out the degradation of the cell, therefore the actual degradation enzymes can be seen to be indirectly regulated by mitochondrial permeability.

Cytochrome c is also released from mitochondria due to formation of a channel, MAC, in the outer mitochondrial membrane, and serves a regulatory function as it precedes morphological change associated with apoptosis. Once cytochrome c is released it binds with Apaf-1 and ATP, which then bind to pro-caspase-9 to create a protein complex known as an apoptosome. The apoptosome cleaves the pro-caspase to its active form of caspase-9, which in turn activates the effector caspase-3.

MAC is itself subject to regulation by various proteins, such as those encoded by the mammalian Bcl-2 family of anti-apoptopic genes, the homologs of the ced-9 gene found in C. elegans. Bcl-2 proteins are able to promote or inhibit apoptosis either by direct action on MAC or indirectly through other proteins. It is important to note that the actions of some Bcl-2 proteins are able to halt apoptosis even if cytochrome c has been released by the mitochondria.



Direct signal transduction



Two important examples of the direct initiation of apoptotic mechanisms in mammals include the TNF-induced (tumour necrosis factor) model and the Fas-Fas ligand-mediated model, both involving receptors of the TNF receptor (TNFR) family coupled to extrinsic signals.

TNF is a cytokine produced mainly by activated macrophages, and is the major extrinsic mediator of apoptosis. Most cells in the human body have two receptors for TNF: TNF-R1 and TNF-R2. The binding of TNF to TNF-R1 has been shown to initiate the pathway that leads to caspase activation via the intermediate membrane proteins TNF receptor-associated death domain (TRADD) and Fas-associated death domain protein (FADD). Binding of this receptor can also indirectly lead to the activation of transcription factors involved in cell survival and inflammatory responses.The link between TNF and apoptosis shows why an abnormal production of TNF plays a fundamental role in several human diseases, especially in autoimmune diseases.

The Fas receptor (also known as Apo-1 or CD95) binds the Fas ligand (FasL), a transmembrane protein part of the TNF family.The interaction between Fas and FasL results in the formation of the death-inducing signaling complex (DISC), which contains the FADD, caspase-8 and caspase-10. In some types of cells (type I), processed caspase-8 directly activates other members of the caspase family, and triggers the execution of apoptosis. In other types of cells (type II), the Fas-DISC starts a feedback loop that spirals into increasing release of pro-apoptotic factors from mitochondria and the amplified activation of caspase-8.

Following TNF-R1 and Fas activation in mammalian cells a balance between pro-apoptotic (BAX,BID, BAK, or BAD) and anti-apoptotic (Bcl-Xl and Bcl-2) members of the Bcl-2 family is established. This balance is the proportion of pro-apoptotic homodimers that form in the outer-membrane of the mitochondrion. The pro-apoptotic homodimers are required to make the mitochondrial membrane permeable for the release of caspase activators such as cytochrome c and SMAC. Control of pro-apoptotic proteins under normal cell conditions of non-apoptotic cells is incompletely understood, but it has been found that a mitochondrial outer-membrane protein, VDAC2, interacts with BAK to keep this potentially-lethal apoptotic effector under control.When the death signal is received, products of the activation cascade displace VDAC2 and BAK is able to be activated.



Execution



Although many pathways and signals lead to apoptosis, there is only one mechanism that actually causes the death of the cell in this process; after the appropriate stimulus has been received by the cell and the necessary controls exerted, a cell will undergo the organised degradation of cellular organelles by activated proteolytic caspases. A cell undergoing apoptosis shows a characteristic morphology that can be observed with a microscope:

1. Cell shrinkage and rounding due to the breakdown of the proteinaceous cytoskeleton by caspases.
2. The cytoplasm appears dense, and the organelles appear tightly packed.
3. Chromatin undergoes condensation into compact patches against the nuclear envelope in a process known as pyknosis, a hallmark of apoptosis.
4. The nuclear envelope becomes discontinuous and the DNA inside it is fragmented in a process referred to as karyorrhexis. The nucleus breaks into several discrete chromatin bodies or nucleosomal units due to the degradation of DNA.
5. The cell membrane shows irregular buds known as blebs.
6. The cell breaks apart into several vesicles called apoptotic bodies, which are then phagocytosed.


Apoptosis progresses quickly and its products are quickly removed, making it difficult to detect or visualize. During karyorrhexis, endonuclease activation leaves short DNA fragments, regularly spaced in size. These give a characteristic "laddered" appearance on agar gel after electrophoresis. Tests for DNA laddering differentiate apoptosis from ischemic or toxic cell death.



Removal of dead cells



Dying cells that undergo the final stages of apoptosis display phagocytotic molecules, such as phosphatidylserine, on their cell surface.Phosphatidylserine is normally found on the cytosolic surface of the plasma membrane, but is redistributed during apoptosis to the extracellular surface by a hypothetical protein known as scramblase. These molecules mark the cell for phagocytosis by cells possessing the appropriate receptors, such as macrophages.Upon recognition, the phagocyte reorganizes its cytoskeleton for engulfment of the cell. The removal of dying cells by phagocytes occurs in an orderly manner without eliciting an inflammatory response.

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Wednesday, December 17, 2008

Cloning

Clones are organisms that have identical genetic material. In other words, the sequence of bases n their DNA is exactly same. Long before the birth of Dolly the sheep, clones had bee observed in both nature and in the laboratory.When a couple has an identical twin or identical triplets, the children are clones of one another.A plant cutting can also be used to generate a clone.

Prior to 199, it was thought that cloning an entire animal could only be done with embryonic cells-cells present in the early stages of an organism’s development. In the 1950's, scientists generated entire frogs from embryonic frog cells.






After a small number of cell divisions, embryonic cells start to change into the different types of cells that form muscle, blood, liver, etc. This process is called differntiation. Although each of these cells has the same genetic material, each cell can only access the genes needed for its particular function.

Before the experiment at the roslin institute, it was thought that once cells differentiated, they could not be used to generate an entire organism, for instance, in sheep udder cells could generate other udder cells, but not an entire sheep.

The scientist of roslin institute solved this problem by growing sheep udder cells under starvation conditions, this put the cells in a state similar to embryonic cells. This is called the G0 state.

An egg cell was taken from another sheep. The nucleus (which contains the genetic material) was removed from the egg cell using fine needle. They then used electric shock to fuse one starved udder cell with one nucleus free egg cell. They made 277 of these fused cells.

Although the egg cell came from a black-faced sheep, notice that the nucleus with the genetic material came from the white-faced sheep.


The fused egg cell was then inserted into several different sheep. These surrogate mothers also black-faced.

Of the 277 fused cells, only one progressed to form a developed lamb. Dolly was born on July 5, 1996.Scientist found that dolly had same DNA as the udder cells she came from. She is a clone of these udder cells.Dolly has given birth to a lamb named Bonnie, produced the natural way.Other lambs have been born at the roslin institute through their cloning process, some carry genes that will produce usable human drugs.

A laboratory in Hawaii run by Dr.Ryuzo Yanagimachi was the second group to successfully clone an animal from an adult cell. They cloned mice using cumulus cells, a cell type found in the ovaries.

The cloning method used by the lab in Hawaii was different in two ways from the method used to clone Dolly. First, the cells used to clone the mice were not grown in culture, but instead were used immediately.

Second the nucleus was removed from the cumulus cell and then directly injected into the egg cell. This egg cell's nucleus had already been removed.

The yabagimachi lab used coat color to track genetic heritage. The cumulus cell comes from an agouti (brown) mouse, and the cell comes from a black mouse.

The egg cell now had the same genetic information as the nucleus donor mouse. The egg cell was then activated and implanted into a white host mother. On October 3, 1997 the host mouse gave birth to cumulina, named after the cumulus cells she was cloned from.


Cumulina is the same color as the mouse that donated the nucleus. The DNA fingerprinting confirmed that cumulina had the same DNA as the nucleus donor.

The scientist has taken cells from cumulina to make more clones. They have successfully made several generations of clones and all mice seem normal.Dolly the sheep died at the age of 6. Since the world said hello to Dolly, Several other animals have also been cloned.

Both Dolly and cumulina were cloned from cells in the female reproductive system; cows have also been cloned using ovary and cumulus cells with the same method that was used to clone Dolly.Pigs have been added to the cloned animal menagerie. Scientist hopes to use cloned pigs to grow organs that can be transplanted into humans.













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Monday, December 15, 2008

Proteins-How Things Get Done in the Cell lecture

Prof.Stephen Nowicki professor of Biology in Duke University tells about How Things Get Done in the Cell especially about protein studies,Proteomics is one of the important part in biotechnolgical studies,hope this lecture is useful


Proteins-How Things Get Done in the Cell


How Things Get Done in the Cell.




Proteins-How Things Get Done in the Cell 3

Sunday, December 14, 2008

Stem Cells

Stem cells are primal cells common to all multi-cellular organisms that retain the ability to renew themselves through cell division and can differentiate into a wide range of specialized cell types. Research in the human stem cell field grew out of findings by Canadian scientists Ernest A. McCulloch and James E. Till in the 1960s

The three broad categories of mammalian stem cells are: embryonic stem cells, derived from blastocysts, adult stem cells, which are found in adult tissues, and cord blood stem cells, which are found in the umbilical cord. In a developing embryo, stem cells are able to differentiate into all of the specialized embryonic tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body, replenishing specialized cells.




Pluripotent Stem cells




As stem cells can be readily grown and transformed into specialised cells with characteristics consistent with cells of various tissues such as muscles or nerves through cell culture, their use in medical therapies has been proposed. In particular, embryonic cell lines, autologous embryonic stem cells generated through therapeutic cloning, and highly plastic adult stem cells from the umbilical cord blood or bone marrow are touted as promising candidates.





Defining properties



The rigorous definition of a stem cell requires that it possesses two properties:
Self-renewal - the ability to go through numerous cycles of cell division while maintaining the undifferentiated state.
Unlimited potency - the capacity to differentiate into any mature cell type. In a strict sense, this makes stem cells either totipotent or pluripotent, although some multipotent and/or unipotent progenitor cells are sometimes referred to as stem cells.

These properties can be illustrated in vitro, using methods such as clonogenic assays, where the progeny of single cell is characterized. However, in vitro culture conditions can alter the behavior of cells, making it unclear whether the cells will behave in a similar manner in vivo. Considerable debate exists whether some proposed adult cell populations are truly stem cells.




Potency definitions



Potency specifies the differentiation potential of the stem cell.



Pluripotent
, embryonic stem cells originate as inner mass cells with in a blastocyst. The stem cells can become any tissue in the body, excluding a placenta. Only the morula's cells are totipotent, able to become all tissues and a placenta.







Totipotent stem cells are produced from the fusion of an egg and sperm cell. Cells produced by the first few divisions of the fertilized egg are also totipotent. These cells can differentiate into embryonic and extraembryonic cell types.



Multipotent stem cells can produce only cells of a closely related family of cells (e.g. hematopoietic stem cells differentiate into red blood cells, white blood cells, platelets, etc.).



Unipotent cells can produce only one cell type, but have the property of self-renewal which distinguishes them from non-stem cells.




Embryonic stem cells



Embryonic stem cell lines (ES cell lines) are cultures of cells derived from the epiblast tissue of the inner cell mass (ICM) of a blastocyst. A blastocyst is an early stage embryo - approximately 4 to 5 days old in humans and consisting of 50-150 cells. ES cells are pluripotent, and give rise during development to all derivatives of the three primary germ layers: ectoderm, endoderm and mesoderm. In other words, they can develop into each of the more than 200 cell types of the adult body when given sufficient and necessary stimulation for a specific cell type. They do not contribute to the extra-embryonic membranes or the placenta.




Embryonic stem cell



When given no stimuli for differentiation, ES cells will continue to divide in vitro and each daughter cell will remain pluripotent. The pluripotency of ES cells has been rigorously demonstrated in vitro and in vivo, thus they can be indeed classified as stem cells.

Because of their unique combined abilities of unlimited expansion and pluripotency, embryonic stem cells are a potential source for regenerative medicine and tissue replacement after injury or disease. To date, no approved medical treatments have been derived from embryonic stem cell research. This is not surprising considering that many nations currently have moratoria on either ES cell research or the production of new ES cell lines.




Adult stem cells




Adult stem cells are undifferentiated cells found throughout the body that divide to replenish dying cells and regenerate damaged tissues. Also known as somatic (from Greek Σωματικóς, of the body) stem cells, they can be found in children, as well as adults.



Adult stem cells





A great deal of adult stem cell research has focused on clarifying their capacity to divide or self-renew indefinitely and their differentiation potential.Many adult stem cells may be better classified as progenitor cells, due to their limited capacity for cellular differentiation.

Nevertheless, specific multipotent or even unipotent adult progenitors may have potential utility in regenerative medicine. The use of adult stem cells in research and therapy is not as controversial as embryonic stem cells, because the production of adult stem cells does not require the destruction of an embryo. In contrast with the embryonic stem cell research, more US government funding has been provided for adult stem cell research. Adult stem cells can be isolated from a tissue sample obtained from an adult. They have mainly been studied in humans and model organisms such as mice and rats.

Embryonic stem cells without an egg or embryo

Researchers at Whitehead Institute for Biomedical Research in Cambridge, Mass., have manipulated mouse fibroblasts and turned them into cells with such developmental elasticity that they appear identical to embryonic stem cells.





Excerpts from the video



Embryonic stem cells have potential to provide people with donor cells which can be used transplantation medicine, one of the problems of embryonic stem cells are they are derived from the embryo and it will not be compatible with immune system of the donor, so the real goal is to generate customized embryonic stem cells, A way that it thought to be accomplished was by nuclear transfer, for example If u take skin cell from a patient and introduce nucleus from the cells into a egg for whose nucleus is removed. The egg is able to reprogram the somatic cell into an embryonic state, from this people are able to isolate customized embryonic cells and those could be new for customized transplantation therapy, there will be no immune rejection.






The problem with this approach is many, it is very complex and inefficient procedure and it only so far in animals (mice only) and secondly there lot of ethical objection in using human embryo and human egg cells for therapy or research, so goal of field is to understand how the egg accomplishes reprogramming the somatic nucleus into embryonic stage once we know the reprogramming rules we could do without the egg.

What we have done in our laboratory was to use the knowledge coming from investigating and finding of molecular circulatory of embryonic stem cells and comparing it with the somatic cells and taking some key regulators or Key switches and express those into the somatic cells .In long process (few weeks) we found that these skin cells become embryonic cells,. Signatures of the reprogrammed cells these cells were indistingusble with normal embryonic stem cells, Molecular expression pattern of the genes is identical, epigenetic stage of these cells are indistinguisable from embryonic stem cells the most important is these reprogrammed cells can do anything biologically as embryonic stem cells with same developmental potency and we tested this by introducing these cells back to embryos of form prim Eric mice and even can contribute to germline, so that it can generate fibroblast after the reprogramming process being introduced we can generate mice, from all,the test we have done ,it appears that these cells have same potential for forming all lineages of the animal but also for therapy has Embryonic stem cell have.