Golgi apparatus

Golgi apparatus

The Golgi apparatus (Golgi complex) is an organelle found in most eukaryotic cells.[1] It was identified in 1898 by the Italian physician Camillo Golgi, after whom the Golgi apparatus is named.[2]

It processes and packages proteins inside of the cell and before they make their way to their destination; it is particularly important in the processing of proteins for secretion. The Golgi apparatus forms a part of the cellular endomembrane system

Discovery

Due to its fairly large size, the Golgi apparatus was one of the first organelles to be discovered and observed in detail. The apparatus was discovered in 1898 by Italian physician Camillo Golgi during an investigation of the nervous system.[2] After first observing it under his microscope, he termed the structure the internal reticular apparatus. The structure was then renamed after Golgi not long after the announcement of his discovery in 1898. However, some doubted the discovery at first, arguing that the appearance of the structure was merely an optical illusion created by the observation technique used by Golgi. With the development of modern microscopes in the 20th century, the discovery was confirmed.[3]

Structure

Found within the cytoplasm of both plant and animal cells, the Golgi is composed of stacks of membrane-bound structures known as cisternae (singular: cisterna). An individual stack is sometimes called a dictyosome (from Greek dictyon: net + soma: body),[4] especially in plant cells.[5] A mammalian cell typically contains 40 to 100 stacks.[6] Between four and eight cisternae are usually present in a stack; however, in some protists as many as sixty have been observed.[3] Each cisterna comprises a flat, membrane enclosed disc that includes special Golgi enzymes which modify or help to modify cargo proteins that travel through it.[7]

The cisternae stack has four functional regions: the cis-Golgi network, medial-Golgi, endo-Golgi, and trans-Golgi network. Vesicles from the endoplasmic reticulum (via the vesicular-tubular clusters) fuse with the network and subsequently progress through the stack to the trans Golgi network, where they are packaged and sent to the required destination. Each region contains different enzymes which selectively modify the contents depending on where they reside.[8] The cisternae also carry structural proteins important for their maintenance as flattened membranes which stack upon each other.[9]

Diagram of secretory process from endoplasmic reticulum (orange) to Golgi apparatus (pink). 1. Nuclear membrane; 2. Nuclear pore; 3. Rough endoplasmic reticulum (RER); 4. Smooth endoplasmic reticulum (SER); 5. Ribosome attached to RER; 6. Macromolecules; 7. Transport vesicles; 8. Golgi apparatus; 9. Cis face of Golgi apparatus; 10. Trans face of Golgi apparatus; 11. Cisternae of lipids

Function

Cells synthesise a large number of different macromolecules. The Golgi apparatus is integral in modifying, sorting, and packaging these macromolecules for cell secretion[10] (exocytosis) or use within the cell.[11] It primarily modifies proteins delivered from the rough endoplasmic reticulum but is also involved in the transport of lipids around the cell, and the creation of lysosomes.[11] In this respect it can be thought of as similar to a post office; it packages and labels items which it then sends to different parts of the cell.

Enzymes within the cisternae are able to modify the proteins by addition of carbohydrates (glycosylation)[12] and phosphates (phosphorylation). In order to do so, the Golgi imports substances such as nucleotide sugars from the cytosol. These modifications may also form a signal sequence which determines the final destination of the protein. For example, the Golgi apparatus adds a mannose-6-phosphate label to proteins destined for lysosomes.

The Golgi plays an important role in the synthesis of proteoglycans, which are molecules present in the extracellular matrix of animals. It is also a major site of carbohydrate synthesis.[13] This includes the production of glycosaminoglycans (GAGs), long unbranched polysaccharides which the Golgi then attaches to a protein synthesised in the endoplasmic reticulum to form proteoglycans.[14] Enzymes in the Golgi polymerize several of these GAGs via a xylose link onto the core protein. Another task of the Golgi involves the sulfation of certain molecules passing through its lumen via sulfotranferases that gain their sulfur molecule from a donor called PAPs. This process occurs on the GAGs of proteoglycans as well as on the core protein. The level of sulfation is very important to the proteoglycans' signalling abilities as well as giving the proteoglycan its overall negative charge.[13]

The phosphorylation of molecules requires that ATP is imported into the lumen of the Golgi[15] and then utilised by resident kinases such as casein kinase 1 and casein kinase 2. One molecule that is phosphorylated in the Golgi is Apolipoprotein, which forms a molecule known as VLDL that is a constituent of blood serum. It is thought that the phosphorylation of these molecules is important to help aid in their sorting for secretion into the blood serum.[16]

The Golgi has a putative role in apoptosis, with several Bcl-2 family members localised there, as well as to the mitochondria. A newly characterized protein, GAAP (Golgi anti-apoptotic protein), almost exclusively resides in the Golgi and protects cells from apoptosis by an as-yet undefined mechanism.[17]

Vesicular transport

The vesicles that leave the rough endoplasmic reticulum are transported to the cis face of the Golgi apparatus, where they fuse with the Golgi membrane and empty their contents into the lumen. Once inside the lumen, the molecules are modified, then sorted for transport to their next destinations. The Golgi apparatus tends to be larger and more numerous in cells that synthesise and secrete large amounts of substances, for example, the plasma B cells and the antibody-secreting cells of the immune system have prominent Golgi complexes.

Those proteins destined for areas of the cell other than either the endoplasmic reticulum or Golgi apparatus are moved towards the trans face, to a complex network of membranes and associated vesicles known as the trans-Golgi network (TGN).[8] This area of the Golgi is the point at which proteins are sorted and shipped to their intended destinations by their placement into one of at least three different types of vesicles, depending upon the molecular marker they carry:[8]

Transport mechanism

The transport mechanism which proteins use to progress through the Golgi apparatus is not yet clear; however a number of hypotheses currently exist. Until recently, the vesicular transport mechanism was favoured but now more evidence is coming to light to support cisternal maturation. The two proposed models may actually work in conjunction with each other, rather than being mutually exclusive. This is sometimes referred to as the combined model.[13]
Cisternal maturation model: the cisternae of the Golgi apparatus move by being built at the cis face and destroyed at the trans face. Vesicles from the endoplasmic reticulum fuse with each other to form a cisterna at the cis face, consequently this cisterna would appear to move through the Golgi stack when a new cisterna is formed at the cis face. This model is supported by the fact that structures larger than the transport vesicles, such as collagen rods, were observed microscopically to progress through the Golgi apparatus.[13] This was initially a popular hypothesis, but lost favour in the 1980s. Recently it has made a comeback, as laboratories at the University of Chicago and the University of Tokyo have been able to use new technology to directly observe Golgi compartments maturing.[18] Additional evidence comes from the fact that COPI vesicles move in the retrograde direction, transporting endoplasmic reticulum proteins back to where they belong by recognizing a signal peptide.[19]
Vesicular transport model: Vesicular transport views the Golgi as a very stable organelle, divided into compartments in the cis to trans direction. Membrane bound carriers transport material between the endoplasmic reticulum and the different compartments of the Golgi.[20] Experimental evidence includes the abundance of small vesicles (known technically as shuttle vesicles) in proximity to the Golgi apparatus. To direct the vesicles, actin filaments connect packaging proteins to the membrane to ensure that they fuse with the correct compartment
Golgi apparatus during mitosis

In animal cells, the Golgi apparatus will break up and disappear following the onset of mitosis, or cellular division. During the telophase of mitosis, the Golgi apparatus reappears; however, it is still uncertain how this occurs.[21]

Intriguingly, the same is not true of plant or yeast Golgi stacks, which have been observed to remain intact throughout the cell cycle. The reason for this difference is not yet known, but it may, in part, be a consequence of golgin proteins.

Cell Nucleus

CELL NUCLEUS

In cell biology, the nucleus (pl. nuclei; from Latin nucleus or nuculeus, meaning kernel) is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these chromosomes are the cell's nuclear genome. The function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expression — the nucleus is, therefore, the control center of the cell. The main structures making up the nucleus are the nuclear envelope, a triple cell membrane and membrane that encloses the entire organelle and unifies its contents from the cellular cytoplasm, and the nucleoskeleton (which includes nuclear lamina), a meshwork within the nucleus that adds mechanical support, much like the cytoskeleton, which supports the cell as a whole. Because the nuclear membrane is impermeable to most molecules, nuclear pores are required to allow movement of molecules across the envelope. These pores cross both of the membranes, providing a channel that allows free movement of small molecules and ions. The movement of larger molecules such as proteins is carefully controlled, and requires active transport regulated by carrier proteins. Nuclear transport is crucial to cell function, as movement through the pores is required for both gene expression and chromosomal maintenance. The interior of the nucleus does not contain any membrane-bound subcompartments, its contents are not uniform, and a number of subnuclear bodies exist, made up of unique proteins, RNA molecules, and particular parts of the mitochondria. The best-known of these is the nucleolus, which is mainly involved in the assembly of ribosomes. After being produced in the nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA.

History

Oldest known depiction of cells and their nuclei by Antonie van Leeuwenhoek, 1719.

Drawing of a Chironomus salivary gland cell published by Walther Flemming in 1882. The nucleus contains Polytene chromosomes.

The nucleus was the first organelle to be discovered. The probably oldest preserved drawing dates back to the early microscopist Antonie van Leeuwenhoek (1632 – 1723). He observed a "Lumen", the nucleus, in the red blood cells of salmon.[1] Unlike mammalian red blood cells, those of other vertebrates still possess nuclei. The nucleus was also described by Franz Bauer in 1804[2] and in more detail in 1831 by Scottish botanist Robert Brown in a talk at the Linnean Society of London. Brown was studying orchids under microscope when he observed an opaque area, which he called the areola or nucleus, in the cells of the flower's outer layer.[3] He did not suggest a potential function. In 1838, Matthias Schleiden proposed that the nucleus plays a role in generating cells, thus he introduced the name "Cytoblast" (cell builder). He believed that he had observed new cells assembling around "cytoblasts". Franz Meyen was a strong opponent of this view, having already described cells multiplying by division and believing that many cells would have no nuclei. The idea that cells can be generated de novo, by the "cytoblast" or otherwise, contradicted work by Robert Remak (1852) and Rudolf Virchow (1855) who decisively propagated the new paradigm that cells are generated solely by cells ("Omnis cellula e cellula"). The function of the nucleus remained unclear.[4]

Between 1877 and 1878, Oscar Hedwig published several studies on the fertilization of sea urchin eggs, showing that the nucleus of the sperm enters the oocyte and fuses with its nucleus. This was the first time it was suggested that an individual develops from a (single) nucleated cell. This was in contradiction to Ernst Haeckel's theory that the complete phylogeny of a species would be repeated during embryonic development, including generation of the first nucleated cell from a "Monerula", a structureless mass of primordial mucus ("Urschleim"). Therefore, the necessity of the sperm nucleus for fertilization was discussed for quite some time. However, Hertwig confirmed his observation in other animal groups, e.g., amphibians and molluscs. Eduard Strasburger produced the same results for plants (1884). This paved the way to assign the nucleus an important role in heredity. In 1873, August Weismann postulated the equivalence of the maternal and paternal germ cells for heredity. The function of the nucleus as carrier of genetic information became clear only later, after mitosis was discovered and the Mendelian rules were rediscovered at the beginning of the 20th century; the chromosome theory of heredity was developed



Structures

The nucleus is the largest cellular organelle in animals.[5] In mammalian cells, the average diameter of the nucleus is approximately 6 micrometers (μm), which occupies about 10% of the total cell volume.[6] The viscous liquid within it is called nucleoplasm, and is similar in composition to the cytosol found outside the nucleus.[7] It appears as a dense, roughly spherical organelle.


Nuclear envelope and pores




The outer envelope otherwise known as nuclear membrane consists of two cellular membranes, an inner and an outer membrane, arranged parallel to one another and separated by 10 to 50 nanometers (nm). The nuclear envelope completely encloses the nucleus and separates the cell's genetic material from the surrounding cytoplasm, serving as a barrier to prevent macromolecules from diffusing freely between the nucleoplasm and the cytoplasm.[8] The outer nuclear membrane is continuous with the membrane of the rough endoplasmic reticulum (RER), and is similarly studded with ribosomes.[8] The space between the membranes is called the perinuclear space and is continuous with the RER lumen.

Nuclear pores, which provide aqueous channels through the envelope, are composed of multiple proteins, collectively referred to as nucleoporins. The pores are about 125 million daltons in molecular weight and consist of around 50 (in yeast) to 100 proteins (in vertebrates).[5] The pores are 100 nm in total diameter; however, the gap through which molecules freely diffuse is only about 9 nm wide, due to the presence of regulatory systems within the center of the pore. This size allows the not-free passage of small water-soluble molecules while preventing larger molecules, such as nucleic acids and larger proteins, from inappropriately entering or exiting the nucleus. These large molecules must be actively transported into the nucleus instead. The nucleus of a typical mammalian cell will have about 3000 to 4000 pores throughout its envelope,[9] each of which contains a donut-shaped, eightfold-symmetric ring-shaped structure at a position where the inner and outer membranes fuse.[10] Attached to the ring is a structure called the nuclear basket that extends into the nucleoplasm, and a series of filamentous extensions that reach into the cytoplasm. Both structures serve to mediate binding to nuclear transport proteins.[5]

Most proteins, ribosomal subunits, and some DNAs are transported through the pore complexes in a process mediated by a family of transport factors known as karyopherins. Those karyopherins that mediate movement into the nucleus are also called importins, whereas those that mediate movement out of the nucleus are called exportins. Most karyopherins interact directly with their cargo, although some use adaptor proteins.[11] Steroid hormones such as cortisol and aldosterone, as well as other small lipid-soluble molecules involved in intercellular signaling, can diffuse through the cell membrane and into the cytoplasm, where they bind nuclear receptor proteins that are trafficked into the nucleus. There they serve as transcription factors when bound to their ligand; in the absence of ligand, many such receptors function as histone deacetylases that repress gene expression.

The eukaryotic cell nucleus. Visible in this diagram are the ribosome-studded double membranes of the nuclear envelope, the DNA (complexed as chromatin), and the nucleolus. Within the cell nucleus is a viscous liquid called nucleoplasm, similar to the cytoplasm found outside the nucleus.

A cross section of a nuclear pore on the surface of the nuclear envelope (1). Other diagram labels show (2) the outer ring, (3) spokes, (4) basket, and (5) filaments.

Nuclear lamina

In animal cells, two networks of intermediate filaments provide the nucleus with mechanical support: The nuclear lamina forms an organized meshwork on the internal face of the envelope, while less organized support is provided on the cytosolic face of the envelope. Both systems provide structural support for the nuclear envelope and anchoring sites for chromosomes and nuclear pores.[6]

The nuclear lamina is composed mostly of lamin proteins. Like all proteins, lamins are synthesized in the cytoplasm and later transported into the nucleus interior, where they are assembled before being incorporated into the existing network of nuclear lamina.[12][13] Lamins found on the cytosolic face of the membrane, such as emerin and nesprin, bind to the cytoskeleton to provide structural support. Lamins are also found inside the nucleoplasm where they form another regular structure, known as the nucleoplasmic veil,[14] that is visible using fluorescence microscopy. The actual function of the veil is not clear, although it is excluded from the nucleolus and is present during interphase.[15] Lamin structures that make up the veil, such as LEM3, bind chromatin and disrupting their structure inhibits transcription of protein-coding genes.[16]

Like the components of other intermediate filaments, the lamin monomer contains an alpha-helical domain used by two monomers to coil around each other, forming a dimer structure called a coiled coil. Two of these dimer structures then join side by side, in an antiparallel arrangement, to form a tetramer called a protofilament. Eight of these protofilaments form a lateral arrangement that is twisted to form a ropelike filament. These filaments can be assembled or disassembled in a dynamic manner, meaning that changes in the length of the filament depend on the competing rates of filament addition and removal.[6]

Mutations in lamin genes leading to defects in filament assembly are known as laminopathies. The most notable laminopathy is the family of diseases known as progeria, which causes the appearance of premature aging in its sufferers. The exact mechanism by which the associated biochemical changes give rise to the aged phenotype is not well understood.

Chromosomes

The cell nucleus contains the majority of the cell's genetic material in the form of multiple linear DNA molecules organized into structures called chromosomes. Each human cell contains 2m of DNA. During most of the cell cycle these are organized in a DNA-protein complex known as chromatin, and during cell division the chromatin can be seen to form the well-defined chromosomes familiar from a karyotype. A small fraction of the cell's genes are located instead in the mitochondria.

There are two types of chromatin. Euchromatin is the less compact DNA form, and contains genes that are frequently expressed by the cell.[18] The other type, heterochromatin, is the more compact form, and contains DNA that are infrequently transcribed. This structure is further categorized into facultative heterochromatin, consisting of genes that are organized as heterochromatin only in certain cell types or at certain stages of development, and constitutive heterochromatin that consists of chromosome structural components such as telomeres and centromeres.[19] During interphase the chromatin organizes itself into discrete individual patches,[20] called chromosome territories.[21] Active genes, which are generally found in the euchromatic region of the chromosome, tend to be located towards the chromosome's territory boundary.[22]

Antibodies to certain types of chromatin organization, in particular, nucleosomes, have been associated with a number of autoimmune diseases, such as systemic lupus erythematosus.[23] These are known as anti-nuclear antibodies (ANA) and have also been observed in concert with multiple sclerosis as part of general immune system dysfunction.[24] As in the case of progeria, the role played by the antibodies in inducing the symptoms of autoimmune diseases is not obvious.

Nucleolus

An electron micrograph of a cell nucleus, showing the darkly stained nucleolus.

The nucleolus is a discrete densely stained structure found in the nucleus. It is not surrounded by a membrane, and is sometimes called a suborganelle. It forms around tandem repeats of rDNA, DNA coding for ribosomal RNA (rRNA). These regions are called nucleolar organizer regions (NOR). The main roles of the nucleolus are to synthesize rRNA and assemble ribosomes. The structural cohesion of the nucleolus depends on its activity, as ribosomal assembly in the nucleolus results in the transient association of nucleolar components, facilitating further ribosomal assembly, and hence further association. This model is supported by observations that inactivation of rDNA results in intermingling of nucleolar structures.[25]

In the first step of ribosome assembly, a protein called RNA polymerase I transcribes rDNA, which forms a large pre-rRNA precursor. This is cleaved into the subunits 5.8S, 18S, and 28S rRNA.[26] The transcription, post-transcriptional processing, and assembly of rRNA occurs in the nucleolus, aided by small nucleolar RNA (snoRNA) molecules, some of which are derived from spliced introns from messenger RNAs encoding genes related to ribosomal function. The assembled ribosomal subunits are the largest structures passed through the nuclear pores.[5]

When observed under the electron microscope, the nucleolus can be seen to consist of three distinguishable regions: the innermost fibrillar centers (FCs), surrounded by the dense fibrillar component (DFC), which in turn is bordered by the granular component (GC). Transcription of the rDNA occurs either in the FC or at the FC-DFC boundary, and, therefore, when rDNA transcription in the cell is increased, more FCs are detected. Most of the cleavage and modification of rRNAs occurs in the DFC, while the latter steps involving protein assembly onto the ribosomal subunits occur in the GC

Function

The main function of the cell nucleus is to control gene expression and mediate the replication of DNA during the cell cycle. The nucleus provides a site for genetic transcription that is segregated from the location of translation in the cytoplasm, allowing levels of gene regulation that are not available to prokaryotes.

Cell compartmentalization

The nuclear envelope allows the nucleus to control its contents, and separate them from the rest of the cytoplasm where necessary. This is important for controlling processes on either side of the nuclear membrane. In some cases where a cytoplasmic process needs to be restricted, a key participant is removed to the nucleus, where it interacts with transcription factors to downregulate the production of certain enzymes in the pathway. This regulatory mechanism occurs in the case of glycolysis, a cellular pathway for breaking down glucose to produce energy. Hexokinase is an enzyme responsible for the first the step of glycolysis, forming glucose-6-phosphate from glucose. At high concentrations of fructose-6-phosphate, a molecule made later from glucose-6-phosphate, a regulator protein removes hexokinase to the nucleus,[44] where it forms a transcriptional repressor complex with nuclear proteins to reduce the expression of genes involved in glycolysis.[45]

In order to control which genes are being transcribed, the cell separates some transcription factor proteins responsible for regulating gene expression from physical access to the DNA until they are activated by other signaling pathways. This prevents even low levels of inappropriate gene expression. For example, in the case of NF-κB-controlled genes, which are involved in most inflammatory responses, transcription is induced in response to a signal pathway such as that initiated by the signaling molecule TNF-α, binds to a cell membrane receptor, resulting in the recruitment of signalling proteins, and eventually activating the transcription factor NF-κB. A nuclear localisation signal on the NF-κB protein allows it to be transported through the nuclear pore and into the nucleus, where it stimulates the transcription of the target genes.[6]

The compartmentalization allows the cell to prevent translation of unspliced mRNA.[46] Eukaryotic mRNA contains introns that must be removed before being translated to produce functional proteins. The splicing is done inside the nucleus before the mRNA can be accessed by ribosomes for translation. Without the nucleus, ribosomes would translate newly transcribed (unprocessed) mRNA, resulting in misformed and nonfunctional proteins.

Gene expression

Gene expression first involves transcription, in which DNA is used as a template to produce RNA. In the case of genes encoding proteins, that RNA produced from this process is messenger RNA (mRNA), which then needs to be translated by ribosomes to form a protein. As ribosomes are located outside the nucleus, mRNA produced needs to be exported.[47]

Since the nucleus is the site of transcription, it also contains a variety of proteins that either directly mediate transcription or are involved in regulating the process. These proteins include helicases, which unwind the double-stranded DNA molecule to facilitate access to it, RNA polymerases, which synthesize the growing RNA molecule, topoisomerases, which change the amount of supercoiling in DNA, helping it wind and unwind, as well as a large variety of transcription factors that regulate expression.[48]
Processing of pre-mRNA


Newly synthesized mRNA molecules are known as primary transcripts or pre-mRNA. They must undergo post-transcriptional modification in the nucleus before being exported to the cytoplasm; mRNA that appears in the cytoplasm without these modifications is degraded rather than used for protein translation. The three main modifications are 5' capping, 3' polyadenylation, and RNA splicing. While in the nucleus, pre-mRNA is associated with a variety of proteins in complexes known as heterogeneous ribonucleoprotein particles (hnRNPs). Addition of the 5' cap occurs co-transcriptionally and is the first step in post-transcriptional modification. The 3' poly-adenine tail is only added after transcription is complete.

RNA splicing, carried out by a complex called the spliceosome, is the process by which introns, or regions of DNA that do not code for protein, are removed from the pre-mRNA and the remaining exons connected to re-form a single continuous molecule. This process normally occurs after 5' capping and 3' polyadenylation but can begin before synthesis is complete in transcripts with many exons.[5] Many pre-mRNAs, including those encoding antibodies, can be spliced in multiple ways to produce different mature mRNAs that encode different protein sequences. This process is known as alternative splicing, and allows production of a large variety of proteins from a limited amount of DNA.

Nuclear transport

Macromolecules, such as RNA and proteins, are actively transported across the nuclear membrane in a process called the Ran-GTP nuclear transport cycle.




The entry and exit of large molecules from the nucleus is tightly controlled by the nuclear pore complexes. Although small molecules can enter the nucleus without regulation,[49] macromolecules such as RNA and proteins require association karyopherins called importins to enter the nucleus and exportins to exit. "Cargo" proteins that must be translocated from the cytoplasm to the nucleus contain short amino acid sequences known as nuclear localization signals, which are bound by importins, while those transported from the nucleus to the cytoplasm carry nuclear export signals bound by exportins. The ability of importins and exportins to transport their cargo is regulated by GTPases, enzymes that hydrolyze the molecule guanosine triphosphate to release energy. The key GTPase in nuclear transport is Ran, which can bind either GTP or GDP (guanosine diphosphate), depending on whether it is located in the nucleus or the cytoplasm. Whereas importins depend on RanGTP to dissociate from their cargo, exportins require RanGTP in order to bind to their cargo.[11]

Nuclear import depends on the importin binding its cargo in the cytoplasm and carrying it through the nuclear pore into the nucleus. Inside the nucleus, RanGTP acts to separate the cargo from the importin, allowing the importin to exit the nucleus and be reused. Nuclear export is similar, as the exportin binds the cargo inside the nucleus in a process facilitated by RanGTP, exits through the nuclear pore, and separates from its cargo in the cytoplasm.

Specialized export proteins exist for translocation of mature mRNA and tRNA to the cytoplasm after post-transcriptional modification is complete. This quality-control mechanism is important due to the these molecules' central role in protein translation; mis-expression of a protein due to incomplete excision of exons or mis-incorporation of amino acids could have negative consequences for the cell; thus, incompletely modified RNA that reaches the cytoplasm is degraded rather than used in translation.Anucleated and polynucleated cells

Human red blood cells, like those of other mammals, lack nuclei. This occurs as a normal part of the cells' development.

Although most cells have a single nucleus, some eukaryotic cell types have no nucleus, and others have many nuclei. This can be a normal process, as in the maturation of mammalian red blood cells, or a result of faulty cell division.

Anucleated cells contain no nucleus and are, therefore, incapable of dividing to produce daughter cells. The best-known anucleated cell is the mammalian red blood cell, or erythrocyte, which also lacks other organelles such as mitochondria, and serves primarily as a transport vessel to ferry oxygen from the lungs to the body's tissues. Erythrocytes mature through erythropoiesis in the bone marrow, where they lose their nuclei, organelles, and ribosomes. The nucleus is expelled during the process of differentiation from an erythroblast to a reticulocyte, which is the immediate precursor of the mature erythrocyte.[53] The presence of mutagens may induce the release of some immature "micronucleated" erythrocytes into the bloodstream.[54][55] Anucleated cells can also arise from flawed cell division in which one daughter lacks a nucleus and the other has two nuclei.

Polynucleated cells contain multiple nuclei. Most Acantharean species of protozoa[56] and some fungi in mycorrhizae[57] have naturally polynucleated cells. Other examples include the intestinal parasites in the genus Giardia, which have two nuclei per cell.[58] In humans, skeletal muscle cells, called myocytes, become polynucleated during development; the resulting arrangement of nuclei near the periphery of the cells allows maximal intracellular space for myofibrils.[5] Multinucleated and Binucleated cells can also be abnormal in humans; for example, cells arising from the fusion of monocytes and macrophages, known as giant multinucleated cells, sometimes accompany inflammation[59] and are also implicated in tumor formation

Evolution
As the major defining characteristic of the eukaryotic cell, the nucleus' evolutionary origin has been the subject of much speculation. Four major theories have been proposed to explain the existence of the nucleus, although none have yet earned widespread support.[61]

The theory known as the "syntrophic model" proposes that a symbiotic relationship between the archaea and bacteria created the nucleus-containing eukaryotic cell. (Organisms of the Archaea domain have no cell nucleus.[62]) It is hypothesized that the symbiosis originated when ancient archaea, similar to modern methanogenic archaea, invaded and lived within bacteria similar to modern myxobacteria, eventually forming the early nucleus. This theory is analogous to the accepted theory for the origin of eukaryotic mitochondria and chloroplasts, which are thought to have developed from a similar endosymbiotic relationship between proto-eukaryotes and aerobic bacteria.[63] The archaeal origin of the nucleus is supported by observations that archaea and eukarya have similar genes for certain proteins, including histones. Observations that myxobacteria are motile, can form multicellular complexes, and possess kinases and G proteins similar to eukarya, support a bacterial origin for the eukaryotic cell.[64]

A second model proposes that proto-eukaryotic cells evolved from bacteria without an endosymbiotic stage. This model is based on the existence of modern planctomycetes bacteria that possess a nuclear structure with primitive pores and other compartmentalized membrane structures.[65] A similar proposal states that a eukaryote-like cell, the chronocyte, evolved first and phagocytosed archaea and bacteria to generate the nucleus and the eukaryotic cell.[66]

The most controversial model, known as viral eukaryogenesis, posits that the membrane-bound nucleus, along with other eukaryotic features, originated from the infection of a prokaryote by a virus. The suggestion is based on similarities between eukaryotes and viruses such as linear DNA strands, mRNA capping, and tight binding to proteins (analogizing histones to viral envelopes). One version of the proposal suggests that the nucleus evolved in concert with phagocytosis to form an early cellular "predator".[67] Another variant proposes that eukaryotes originated from early archaea infected by poxviruses, on the basis of observed similarity between the DNA polymerases in modern poxviruses and eukaryotes.[68][69] It has been suggested that the unresolved question of the evolution of sex could be related to the viral eukaryogenesis hypothesis.[70]

A very recent proposal suggests that traditional variants of the endosymbiont theory are insufficiently powerful to explain the origin of the eukaryotic nucleus. This model, termed the exomembrane hypothesis, suggests that the nucleus instead originated from a single ancestral cell that evolved a second exterior cell membrane; the interior membrane enclosing the original cell then became the nuclear membrane and evolved increasingly elaborate pore structures for passage of internally synthesized cellular components such as ribosomal subunits

C. elegans

                                                       C. elegans as a Model System
Several approaches can be used to study how a biological system functions. You will use a type of genetics during the course of this project. You will use a technique called RNAi (which we will discuss later) to reduce (or eliminate) the function of a single gene, and look to see how that reduction affects the development of the worms. It is just like removing (or breaking!) part of a car and seeing if the car will move. If development is disrupted, you have identified a gene that is required for normal development. Thus, you have defined a function of your gene. Next you would want to do additional experiments to find out what the role of the gene is in development, what it actually does to control or participate in the process. This "second step" can be years or a lifetime of work.

Why study C. elegans?
There are several attractive features that make Caenorhabditis elegans (C. elegans) an ideal organism for the study of gene regulation and function:
C. elegans is a eukaryote, which means that it shares cellular and molecular structures (membrane bound organelles; DNA complexed into chromatin and organized into discreet chromosomes, etc.) and control pathways with higher organisms. C. elegans is a multicellular organism, which means that it goes through a complex developmental process, including embryogenesis, morphogenesis, and growth to an adult. Thus, biological information that we learn from C. elegans may be directly applicable to more complex organisms, such as humans, which are somewhat more refractory to laboratory scrutiny. About 35% of C. elegans genes have human homologs. A homolog is a DNA or protein sequence that is similar to another DNA or protein sequence because the sequences have common ancestry. The definition of a homolog includes common ancestry, but, in practice, we often INFER that two sequences are homologs by similarity of sequence. We believe that the only plausible way for two sequences to share extensive similarity is by having a common ancestry. Remarkably, it has been shown repeatedly that human genes replace their C. elegans homologs when introduced into C. elegans. Conversely, many C. elegans genes can function similarly to mammalian genes.
The C. elegans genome size is relatively small (9.7 x 107 base pairs or 97 Megabases), when compared to the human genome which is estimated to consist of 3 billion base pairs (3 X 109 bp or 3000 Megabases). The entire C. elegans genome has been sequenced. Furthermore, several novel molecular biological techniques exist for C. elegans experimentation that are not available to researchers studying higher eukaryotes. For example, manipulation of the genome by adding, removing, or altering specific genes occurs by relatively routine procedures.
C. elegans is easy to maintain in the laboratory (in petri dishes) and has a fast and convenient life cycle. Embryogenesis occurs in about 12 hours, development to the adult stage occurs in 2.5 days, and the life span is 2-3 weeks. The development of C. elegans is known in great detail because this tiny organism (1 mm in length) is transparent and the developmental pattern of all 959 of its somatic cells has been traced.

General Biology of C. elegans
The nematode Caenorhabditis elegans is a multicellular organism that is utilized as a model system to address fundamental questions in developmental biology, neurobiology and behavioral biology. One of the key strengths of the model system is that sophisticated genetic approaches can be applied to address questions of interest.
Features of the animal.
C. elegans is a small (about 1 mm long as an adult), free living (as opposed to parasitic) round worm. The normal habitat of the animal is in soil, where it feeds on bacteria and fungi. In the lab, it is grown by spreading a layer of E. coli onto a plate and letting the animal feed on the bacterial lawn.

Because C. elegans is so small and because its anatomy is invariant from one animal to the next, it has been possible to describe the anatomy in exquisite detail by performing serial section electron microscopy through the entire animal. By stacking together more than 200,000 minute sections, a three-dimensional picture of the entire animal has been reconstructed! For example, all synaptic connections made by each of the 302 neurons of the animal are known. This is the only animal for which the entire "wiring diagram" has been determined and it makes C. elegans an excellent model for study of neurodevelopment.

Basic Hermaphrodite Anatomy:

Sex and the single nematode.
C. elegans exists either as a hermaphrodite or a male. The predominant sexual form of C. elegans is the hermaphrodite — this animal produces both sperm and eggs. Thus, it can self-fertilize. When it does, each animal produces about 300 progeny. The standard lab strain of C. elegans has beem propagated by self-fertilization for many generations. Self-fertilization leads to homozygosity of alleles; therefore, individual worms are considered to be genetically identical (as long as mutations have not occurred).

Note that in C. elegans hermaphrodite development there is a developmental switch — first sperm are produced and stored in the spermatheca and then oocytes are produced. Oocyte nuclei are produced by meiotic cell division at the distal end of the gonad. They mature in a syncytium--without complete plasma membranes that separate them from one another. The nucleus and cytoplasm are completely enclosed in a plasma membrane later, just prior to fertilization. After fertilization, the eggshell is added. Fertilization takes place as maturing oocytes are squeezed through the spermatheca. Eggs develop in the hermaphrodite body briefly and then are laid through the vulva at about the 40-cell stage.

Here is a closer look at the organization of the hermaphrodite gonad:

Hermaphrodites have about 10 eggs inside--the older eggs are laid about as fast as new eggs are made.





Oocytes pass into the spermatheca and are fertilized. Embryos develop in the uterus, and have a few cleavages before the eggs are laid, so the embryos have a few dozen cells when the embryos are laid. The embryos develop into worms over the next 8-18 hours (depending on temperature).  

Chromosomes and males.
There are six chromosomes in C. elegans — five pairs of autosomes (chromosomes I, II, III, IV, V) and the sex chromosome, X (this is the letter X, not the Roman numeral ten). Hermaphrodites have two X chromosomes (designated XX). Males have one X chromosome (designated XO); having only one chromosome instead of a pair is called the hemizygous state. This state can be produced by the loss of one X chromosome or by mating. Males cannot produce progeny on their own. However, they can cross-fertilize hermaphrodites. They are commonly used in C. elegans genetics for making genetic combinations.

Life cycle.
One of the advantages of working with C. elegans is that it has a short life cycle. The life cycle is temperature-dependent. C. elegans goes through a reproductive life cycle (egg to egg-laying parent) in 5.5 days at 15°C, 3.5 days at 20°C, and 2.5 days at 25°C.

C. elegans eggs are fertilized within the adult hermaphrodite and laid a few hours afterward--at about the 40 cell stage. Eggs hatch and animals proceed through 4 larval stages, each of which ends in a molt. When animals reach adulthood, they produce about 300 progeny each. They live a total of about 2 weeks.

Note that C. elegans can adopt an alternative life form, called the dauer larval stage, if plates are too crowded or if food is scarce. Dauer larvae are thin and can move but their mouths are plugged and they cannot eat. Interestingly, dauers can remain viable for three months. They appear to be non-aging: dauer larvae can roam around for months and then reenter the L4 stage when they encounter a food source and live about 15 more days! Think about it--those worms can live nearly 10 times their normal lifespan!

C. elegans development.
C. elegans development is characterized better than any multicellular organism the complete cell lineage of the animal has been recorded. A cell lineage is a description of all the cell divisions that occur to generate a specific group of differentiated cells (in the case of C. elegans, the entire animal!). In other words, the developmental pattern of each somatic cell is known, from the zygote to the adult worm. Thus, a scientist can identify any cell at any point in development, and know the fate of that particular cell.

CSIR

                                                                     

                                  CSIR FAQs,CSIR SYLLABUS and APPLICATION PROCEDURE

CSIR FAQs

How can CSIR help me to begin my research career? 

CSIR provides Junior Research Fellowship in various fields of Science & Technology and Medical Sciences. If you are a bright postgraduate with an intense desire to do good science, the EMR Division, HRD Group, CSIR would be delighted to hear from you.

Keep your eyes open for all-India press advertisements that are published twice a year inviting applications. Just fill in the prescribed application form and send the completed application form to the Controller of Examinations, Examination Unit, CSIR Complex Building, Opp. Institute of Hotel Management, Pusa, New Delhi –110 012. Also visit HRDG for details.

 How is the National Eligibility Test structured?

The Selection for award of JRF is made on the basis of a competitive written test called the National Eligibility Test (NET), conducted by CSIR at national level and consisting of two papers. Paper – 1 is objective type consisting of Part (A) general nature and part (B) is subject type. It tests the mental ability and broad awareness of scientific knowledge. You may choose the second paper from amongst (1) Chemical Sciences (2) Earth, Atmosphere, Ocean and Planetary Sciences (3) Life Sciences, (4) Mathematical Sciences and (5) Physical Sciences. For the second paper you will need to give short descriptive answers.

 Usually examinations are held for a day on the third Sunday in June and December, each year.

For more details visit: HRDG

 How will I know if I have cleared the National Eligibility Test?

Don’t worry, all candidates who qualify in the test will be informed individually after the results are finalised. Results are also posted on the Internet. Visit:HRDG

 What are the qualifications needed for NET?

Junior Research Fellowships are awarded each year by CSIR to those holding MSc or equivalent degree, with minimum 55% marks after qualifying the National Eligibility Test. Please visit HRDG for details.

   What are the minimum requirements I must have to join as Scientist or Group IV staff?

The minimum requirement is a First Class M.Sc./B. Tech. And you must not be over 35 years. All reservations that are in force for all entitled categories as per Government of India rules apply.

 What is the expected salary at entry level Scientist post?

The basic salary for Scientist B or Group IV(1) is Rs. 8000-275-13500.

And a senior Scientist i.e., Scientist G or Group IV (6) would be in the basic pay scale of Rs. 18400-500-22400.  

 What are the different every day technologies or items that we use in which CSIR has played a role?

You would be amazed to know about the many items of daily use that CSIR has helped develop. Its contribution extends to almost all fields of human activity, be it agriculture, health, defence, aero- dynamics, genetic engineering and the development of India's first super computer. Eleven of the 14 new drugs developed in independent India are from CSIR.

The entire list would be too long so here is merely a sample. Amul baby food, Nutan stove, Saheli a nonsteroidal once-a-week oral contraceptive pill for women, E-mal for resistant malaria, Asmon, a herbal therapeutic for asthma, SARAS, a multi-role aircraft, Flosolver India's first parallel computer; Swaraj and Sonalika tractors, and the indelible ink that is the mark of a proud Indian voter, are gifts of CSIR to the nation.

No wonder CSIR is recognized as one of the world's largest knowledge enterprises

 What was the second battle of Haldighati in which CSIR was involved?

The “second battle of Haldighati,” is what the media dubbed a pioneering case in a "rule-based" war in the context of what India felt was a wrongly granted US   patent on the use of turmeric for wound healing.

The rule is that the applicant has a right to patent innovations only after demonstrating the novelty, non-obviousness and usefulness of an article. The use of turmeric for wound healing is not novel because it is a part of India’s prior knowledge as recorded in ancient Sanskrit and Pali texts and formal papers in journals such as The Indian Journal of Medical Research, etc. 

CSIR followed the recognized legal procedures and proved to the US Patent Office that such use of turmeric in wound healing was clearly the consequence of prior knowledge. The US Patent Office scrapped the patent. India won that particular battle.

 What is the CSIR Programme on Bioactives? 

The CSIR Programme on Bioactives is a mammoth network programme being coordinated by the R&D Planning Division (RDPD), CSIR. It engages 20 CSIR laboratories, 13 universities and three well-known organizations in the traditional system of medicine. It involves screening of Ayurvedic formulations, plants, fungi, microbes and insects against 14 disease areas including cancer, tuberculosis, filaria, malaria, ulcer, Parkinson’s and Alzheimer diseases, to identify new lead molecules.

Work is being pursued in a well-coordinated manner with different dedicated groups carrying out well-defined tasks. For example, The Indian Institute of Integrative Medicine (previously known as RRL, Jammu) is the Nodal laboratory for investigation of all the Unani drugs. Its activities are to participate in and coordinate plant collection, authentication, and finger printing. It also participates in and coordinates the biological activities such as profiling of the extract to evaluate anticancer activity (in vitro cytotoxicity), and immunomodulatory and hepatoprotective (both in vivo and in vitro) activities of the samples prepared by the participating institutes.  

 The world is turning to herbal medicines. Is CSIR also part of the movement?

Certainly! The Herbal Therapeutics programme of CSIR involves efforts to develop herbal preparations as therapeutics. These herbal preparations are being developed only after conducting all the appropriate studies, viz. standardization, biological activity validation, safety, efficacy and clinical studies.  Products developed would be then introduced as therapeutics in the Indian and the foreign markets.  The CSIR collaboration with the AVS and CCRUM is a major initiative in this direction. 

 Is CSIR also looking at our marine resources as a source for therapeutic products?  

As a leading S&T organization of a nation rich in marine bounty, CSIR is also investigating our oceans. An all India coordinated project ‘Drugs from the Sea’ funded by Department of Ocean Development, Government of India, and coordinated by the Central Drug Research Institute, Lucknow, is being conducted in collaboration with 10 participating laboratories for exploiting marine flora and fauna for development of drugs as well as herbal remedies.  The programme covers all aspects of drug research including isolation of active molecules, their characterization and development.  Several promising samples have been found.  

 Healthcare is one of the primary concerns of the average citizen.  What are the ailments that CSIR is targeting in particular?  

Asthma

A mission mode programme on asthma has been launched for finding a cure for this disease following the realization of CSIR’s role as a nodal player in the field due to the existing expertise in its allergy group and promise shown by its herbal medicine (Asmon) developed by the Indian Institute of Chemical Biology, Kolkata.  Studies carried out by CSIR have already led to significant increase in the understanding of the disease viz., atopic nature of asthma, identification, purification and characterization of allergic proteins, identification of T-cell epitopes of allergens, development of in vitro screening procedure using human endothelial cell adhesion molecules, identification of the human lung surfactant proteins in respiratory disorders, identification of SNPs in few candidate genes for asthma, development and a mouse model of asthma.

The future studies envisaged include an integrated, networked and focused mission aiming at (i) development of therapeutic modalities using SPD and SPA; reversal of TH2 and TH1, response identification of lead molecules by in vitro and in vivo model, (ii) a broad sample collection of affected population, validation of genes involved, studies on gene polymorphism, identification of molecular markers, interactions expressive genes with other genes, determination of the genetic basis of asthma.

Psoriasis

Psoriasis is one of the most common dermatological diseases affecting around 2 per cent of the world population but its cause and pathogenesis are not clearly understood. Most importantly no preventive/curative therapy exists for psoriasis except the symptomatic management.

Based on the traditional knowledge, the development of a single plant based oral herbal formulation was initiated under NMITLI for making it globally acceptable.  The project is being led by Lupin Laboratories as the industry partner.  Extensive studies comprising fingerprinting, activity guided fractionation, efficacy studies, toxicology, safety pharmacology, pharmaco-kinetics and toxico-kinetics enabled the filing of an Investigational New Drug (IND) application for the first time in the country.  The estimated market for psoriasis therapeutics is around 4 billion and the development will enable India to capture a significant part of the market.

Latent Tuberculosis

Worldwide, around two billion people are infected with M. tuberculosis.  Nearly, 8 million new cases are added annually and the biggest burden is in South East Asia. Around 3 million deaths owing to tuberculosis (TB) are reported every year and India accounts for a substantial percentage. With the rampant Human Immunodeficiency Virus (HIV), TB is reaching almost epidemic proportions. It kills one in three people co-infected with HIV/AIDS. Furthermore, TB is a major barrier to economic development, costing India over Rs. 12,000 crore a year. Considering these aspects CSIR through the NMITLI scheme supported a project entitled  “Latent M. tuberculosis:  New targets, drug delivery systems and Bio-enhancers and therapeutics” in the year 2001. Significant success has been achieved in the project.  

An IND for a new pharmacophore for the treatment of tuberculosis has been filed.  This is the first success achieved in developing a new tuberculosis therapeutic in the last 40 years globally.  The molecule, Sudoterb, works through combination therapy (compatible with the present drugs), is less toxic, clears the total infection within two months and no recurrence has been observed. It fits well into the present four-drug therapy by replacing one or two drugs from the present cocktail.  Some new drug targets have also been developed along with a novel drug delivery system.

 What are CSIR’s successes in the field of Bioinformatics?

BioSuite

Eighteen research institutes and three industries, were brought together to develop the comprehensive, portable and versatile software package christened ‘BioSuite’. Led by TCS, the team has developed the software, which will serve as a multipurpose tool for carrying out diverse bioanalyses ranging from gene analysis to comparative genomics, pathway modeling to homology modeling and molecular visualization & manipulation to drug designing.  The software has several unique features, which are not present in similar other packages available in the market.  BioSuite comprises eight modules involving 114 sub modules and 243 algorithms.  

SofComp  

The NMITLI project entitled, "Cost effective Simple Office Computing (SofComp) platform to replace PC" sought to develop platform technology based on Linux.  The Simple Office Computers (SofComp) are thus based on a System-on-Chip architecture with a high degree of integration and several innovative features. 

 The Mashelkar Committee has submitted its report on the National Auto Fuel Policy. What more is CSIR doing?

The Auto Fuel Policy drafted under the Chairmanship of Dr R. A. Mashelkar, has paved the way for laying Indian standards for auto emissions and thus moving towards meeting the global settings in the domain.  The standards ‘Bharat II, III & IV’ will come into force in phases as per the road map evolved. Improvement in fuel quality is the prime need in addition to changes required in auto engines, use of catalytic converters, etc. 

Under a NMITLI supported programme, effort has been initiated to help improve fuel quality and a novel catalyst has been developed.  The catalyst has remarkable efficiency for desulfurizing diesel, obtained from the first stage of an HDS unit with sulphur (S) content of about 2500 ppm to less than 50 ppm. It performs at the typical refinery process conditions, i.e., < 340º C and 40-bar pressure. The catalyst developed is even active at 30-bar pressure.  The development would be of immense help in providing quality diesel as per Bharat III to IV emission standards.  Efforts are on to identify a refinery to test the catalyst in plant environment.

 What is TKDL? 

The Traditional Knowledge Digital Library (TKDL) is a collaborative project with the Department of AYUSH, Ministry of Health and Family Welfare, Government of India.  The main objective of this network project is to prevent misappropriation of India’s rich heritage of traditional knowledge.  India has had unsavoury experience of noting the grant of wrong patents on turmeric by USPTO and neem by EPO.  These patents were successfully challenged by India and revoked in an expensive and time-consuming process.

The TKDL database provides an easily accessible and retrievable source for patent examiners to verify claims relating to traditional knowledge. The First phase of TKDL-Ayurveda presents information and images gleaned from 14 Ayurvedic texts and transcribed in five international languages -- English, German, French, Spanish and Japanese, using an innovative IT software. Over 36,000 formulations have been transcribed in patent application format. Currently work is in progress on the second phase, which will cover Unani, Siddha, and the residual work on Ayurveda. TKDL-Unani will cover 77,000 formulations.

TKDL has been able to set international specifications and standards for setting up of TK databases and registries based on TKDL specifications. This was presented at the fourth session of Intergovernmental Committee (IGC) of WIPO on Intellectual Property and Genetic Resources, Traditional Knowledge and Expression of Folklore. The Technical Standards presented by India were adopted by the Committee in the fifth session of the IGC.

TKDL has been heralded as a model for other countries for protecting their Traditional Knowledge from misappropriation, and many countries are seeking collaboration with CSIR in this area.  

 What are Saras’s specifications?

Saras is a 14-seater twin-engined turboprop aircraft fully pressurized for passenger comfort. It has a maximum speed of over 600 km/h and a maximum range of 1200 km. Its state-of-the-art avionics, electrical, environmental control and other systems make it a contemporary aircraft of the 21st century

 What role did CSIR play in the Tsunami crisis?

The CSIR efforts at Tsunami relief have been timely, multi-faceted and large. A number of CSIR laboratories rose above the occasion to offer their scientific and technical skills and resources to mitigate the sufferings of the survivors. The offers and initiatives include shelter, food, drinking water, and ongoing studies that in future would improve our knowledge and skills to deal with such disasters.

CFTRI, Mysore, took upon itself the mission of providing food to the survivors. It undertook the largest production of instant food in its history. More than two tonnes of food was sent daily to the affected areas for about seven days to cater to about 50,000 to one lakh meals. Food items even took into account culinary preferences of the local people and the special nutritional requirements of children.

CSMCRI, Bhavnagar, provided drinking water supply in the affected areas by reverse osmosis process.

CBRI, Roorkee, rushed a team of scientists to the affected areas.  It is poised to provide backup support in rehabilitating devastated areas by providing pragmatic solutions to the repair and retrofit of existing infrastructure.

SERC, Chennai, has proposed to help the survivors in structural assessment of damaged buildings and would suggest repairs/remedial measures.

NIO scientists are working on a system to detect earthquakes below the ocean floor.

NGRI’s Seismological Observatory recorded the earthquake and its after-shocks. It continues to monitor the area and provides information so that appropriate action may be taken and loss to life and property minimised.

CSIR-UGC National Eligibility Test (NET) for Junior Research
Fellowship and Lecturer-ship
SYLLABUS FOR
LIFE SCIENCES
PAPER I AND PAPER II
1. MOLECULES AND THEIR INTERACTION RELAVENT TO BIOLOGY
A. Structure of atoms, molecules and chemical bonds.
B. Composition, structure and function of biomolecules (carbohydrates, lipids,
proteins, nucleic acids and vitamins).
C. Stablizing interactions (Van der Waals, electrostatic, hydrogen bonding,
hydrophobic interaction, etc.).
D. Principles of biophysical chemistry (pH, buffer, reaction kinetics,
thermodynamics, colligative properties).
E. Bioenergetics, glycolysis, oxidative phosphorylation, coupled reaction, group
transfer, biological energy transducers.
F. Principles of catalysis, enzymes and enzyme kinetics, enzyme regulation,
mechanism of enzyme catalysis, isozymes.
G. Conformation of proteins (Ramachandran plot, secondary, tertiary and quaternary
structure; domains; motif and folds).
H. Conformation of nucleic acids (A-, B-, Z-,DNA), t-RNA, micro-RNA).
I. Stability of protein and nucleic acid structures.
J. Metabolism of carbohydrates, lipids, amino acids, nucleotides and vitamins.
2. CELLULAR ORGANIZATION
A. Membrane structure and function: Structure of model membrane, lipid bilayer
and membrane protein diffusion, osmosis, ion channels, active transport, ion pumps,
mechanism of sorting and regulation of intracellular transport, electrical properties of
membranes.
B. Structural organization and function of intracellular organelles: Cell wall, nucleus,
mitochondria, Golgi bodies, lysosomes, endoplasmic reticulum, peroxisomes, plastids,
vacuoles, chloroplast, structure & function of cytoskeleton and its role in motility.
C. Organization of genes and chromosomes: Operon, interrupted genes, gene families,
structure of chromatin and chromosomes, unique and repetitive DNA, heterochromatin,
euchromatin, transposons.
D. Cell division and cell cycle: Mitosis and meiosis, their regulation, steps in cell cycle, and
control of cell cycle.
E. Microbial Physiology: Growth, yield and characteristics, strategies of cell division,
stress response.
3. FUNDAMENTAL PROCESSES
A. DNA replication, repair and recombination: Unit of replication, enzymes involved,
replication origin and replication fork, fidelity of replication, extrachromosomal
replicons, DNA damage and repair mechanisms.
B. RNA synthesis and processing: Transcription factors and machinery, formation of
initiation complex, transcription activators and repressors, RNA polymerases, capping,
elongation and termination, RNA processing, RNA editing, splicing, polyadenylation,
structure and function of different types of RNA, RNA transport.
C. Protein synthesis and processing: Ribosome, formation of initiation complex, initiation
factors and their regulation, elongation and elongation factors, termination, genetic code,
aminoacylation of tRNA, tRNA-identity, aminoacyl tRNA synthetase, translational
proof-reading, translational inhibitors, post- translational modification of proteins.
D. Control of gene expression at transcription and translation level: Regulation of
phages, viruses, prokaryotic and eukaryotic gene expression, role of chromatin in
regulating gene expression and gene silencing.
4. CELL COMMUNICATION AND CELL SIGNALING
A. Host parasite interaction: Recognition and entry processes of different
pathogens like bacteria, viruses into animal and plant host cells, alteration of host
cell behavior by pathogens, virus-induced cell transformation, pathogen-induced
diseases in animals and plants, cell-cell fusion in both normal and abnormal cells.
B. Cell signaling: Hormones and their receptors, cell surface receptor, signaling
through G-protein coupled receptors, signal transduction pathways, second
messengers, regulation of signaling pathways, bacterial and plant two-component
signaling systems, bacterial chemotaxis and quorum sensing.
C. Cellular communication: Regulation of hematopoiesis, general principles of cell
communication, cell adhesion and roles of different adhesion molecules, gap
junctions, extracellular matrix, integrins, neurotransmission and its regulation.
D. Cancer: Genetic rearrangements in progenitor cells, oncogenes, tumor suppressor
genes, cancer and the cell cycle, virus-induced cancer, metastasis, interaction of
cancer cells with normal cells, apoptosis, therapeutic interventions of uncontrolled
cell growth.
E. Innate and adaptive immune system: Cells and molecules involved in innate
and adaptive immunity, antigens, antigenicity and immunogenicity. B and T cell
epitopes, structure and function of antibody molecules, generation of antibody
diversity, monoclonal antibodies, antibody engineering, antigen-antibody
interactions, MHC molecules, antigen processing and presentation, activation and
differentiation of B and T cells, B and T cell receptors, humoral and cellmediated
immune responses, primary and secondary immune modulation, the
complement system, Toll-like receptors, cell-mediated effector functions,
inflammation, hypersensitivity and autoimmunity, immune response during
bacterial (tuberculosis), parasitic (malaria) and viral (HIV) infections, congenital
and acquired immunodeficiencies, vaccines.
5. DEVELOPMENTAL BIOLOGY
A. Basic concepts of development: Potency, commitment, specification, induction,
competence, determination and differentiation; morphogenetic gradients; cell fate
and cell lineages; stem cells; genomic equivalence and the cytoplasmic
determinants; imprinting; mutants and transgenics in analysis of development.
B. Gametogenesis, fertilization and early development: Production of gametes,
cell surface molecules in sperm-egg recognition in animals; embryo sac
development and double fertilization in plants; zygote formation, cleavage,
blastula formation, embryonic fields, gastrulation and formation of germ layers in
animals; embryogenesis, establishment of symmetry in plants; seed formation
and germination.
C. Morphogenesis and organogenesis in animals: Cell aggregation and
differentiation in Dictyostelium; axes and pattern formation in Drosophila,
amphibia and chick; organogenesis – vulva formation in Caenorhabditis elegans;
eye lens induction, limb development and regeneration in vertebrates;
differentiation of neurons, post embryonic development-larval formation,
metamorphosis; environmental regulation of normal development; sex
determination.
D. Morphogenesis and organogenesis in plants: Organization of shoot and root
apical meristem; shoot and root development; leaf development and phyllotaxy;
transition to flowering, floral meristems and floral development in Arabidopsis
and Antirrhinum.
E. Programmed cell death, aging and senescence.
6. SYSTEM PHYSIOLOGY - PLANT
A. Photosynthesis: Light harvesting complexes; mechanisms of electron transport;
photoprotective mechanisms; CO2 fixation-C3, C4 and CAM pathways.
B. Respiration and photorespiration: Citric acid cycle; plant mitochondrial
electron transport and ATP synthesis; alternate oxidase; photorespiratory
pathway.
C. Nitrogen metabolism: Nitrate and ammonium assimilation; amino acid
biosynthesis.
D. Plant hormones: Biosynthesis, storage, breakdown and transport; physiological
effects and mechanisms of action.
E. Sensory photobiology: Structure, function and mechanisms of action of
phytochromes, cryptochromes and phototropins; stomatal movement;
photoperiodism and biological clocks.
F. Solute transport and photoassimilate translocation: Uptake, transport and
translocation of water, ions, solutes and macromolecules from soil, through cells,
across membranes, through xylem and phloem; transpiration; mechanisms of
loading and unloading of photoassimilates.
G. Secondary metabolites - Biosynthesis of terpenes, phenols and nitrogenous
compounds and their roles.
H. Stress physiology: Responses of plants to biotic (pathogen and insects) and
abiotic (water, temperature and salt) stresses; mechanisms of resistance to biotic
stress and tolerance to abiotic stress
7. SYSTEM PHYSIOLOGY - ANIMAL
A. Blood and circulation: Blood corpuscles, haemopoiesis and formed elements,
plasma function, blood volume, blood volume regulation, blood groups,
haemoglobin, immunity, haemostasis.
B. Cardiovascular System: Comparative anatomy of heart structure, myogenic
heart, specialized tissue, ECG – its principle and significance, cardiac cycle, heart
as a pump, blood pressure, neural and chemical regulation of all above.
C. Respiratory system: Comparison of respiration in different species, anatomical
considerations, transport of gases, exchange of gases, waste elimination, neural
and chemical regulation of respiration.
D. Nervous system: Neurons, action potential, gross neuroanatomy of the brain and
spinal cord, central and peripheral nervous system, neural control of muscle tone
and posture.
E. Sense organs: Vision, hearing and tactile response.
F. Excretory system: Comparative physiology of excretion, kidney, urine
formation, urine concentration, waste elimination, micturition, regulation of
water balance, blood volume, blood pressure, electrolyte balance, acid-base
balance.
G. Thermoregulation: Comfort zone, body temperature – physical, chemical, neural
regulation, acclimatization.
H. Stress and adaptation
I. Digestive system: Digestion, absorption, energy balance, BMR.
J. Endocrinology and reproduction: Endocrine glands, basic mechanism of
hormone action, hormones and diseases; reproductive processes, neuroendocrine
regulation.
8. INHERITANCE BIOLOGY
A. Mendelian principles: Dominance, segregation, independent assortment, deviation
from Mendelian inheritance.
B. Concept of gene: Allele, multiple alleles, pseudoallele, complementation tests.
C. Extensions of Mendelian principles: Codominance, incomplete dominance, gene
interactions, pleiotropy, genomic imprinting, penetrance and expressivity, phenocopy,
linkage and crossing over, sex linkage, sex limited and sex influenced characters.
D. Gene mapping methods: Linkage maps, tetrad analysis, mapping with molecular
markers, mapping by using somatic cell hybrids, development of mapping population
in plants.
E. Extra chromosomal inheritance: Inheritance of mitochondrial and chloroplast genes,
maternal inheritance.
F. Microbial genetics: Methods of genetic transfers – transformation, conjugation,
transduction and sex-duction, mapping genes by interrupted mating, fine structure
analysis of genes.
G. Human genetics: Pedigree analysis, lod score for linkage testing, karyotypes, genetic
disorders.
H. Quantitative genetics: Polygenic inheritance, heritability and its measurements, QTL
mapping.
I. Mutation: Types, causes and detection, mutant types – lethal, conditional,
biochemical, loss of function, gain of function, germinal verses somatic mutants,
insertional mutagenesis.
J. Structural and numerical alterations of chromosomes: Deletion, duplication,
inversion, translocation, ploidy and their genetic implications.
K. Recombination: Homologous and non-homologous recombination, including
transposition, site-specific recombination.
9. DIVERSITY OF LIFE FORMS
A. Principles and methods of taxonomy:Concepts of species and hierarchical taxa,
biological nomenclature, classical and quantititative methods of taxonomy of
plants, animals and microorganisms.
B. Levels of structural organization: Unicellular, colonial and multicellular
forms; levels of organization of tissues, organs and systems; comparative
anatomy.
C. Outline classification of plants, animals and microorganisms:Important
criteria used for classification in each taxon; classification of plants, animals and
microorganisms; evolutionary relationships among taxa.
D. Natural history of Indian subcontinent: Major habitat types of the
subcontinent, geographic origins and migrations of species; common Indian
mammals, birds; seasonality and phenology of the subcontinent.
E. Organisms of health and agricultural importance: Common parasites and
pathogens of humans, domestic animals and crops.
10. ECOLOGICAL PRINCIPLES
A. The Environment: Physical environment; biotic environment; biotic and abiotic
interactions.
B. Habitat and niche: Concept of habitat and niche; niche width and overlap;
fundamental and realized niche; resource partitioning; character displacement.
C. Population ecology: Characteristics of a population; population growth curves;
population regulation; life history strategies (r and K selection); concept of
metapopulation – demes and dispersal, interdemic extinctions, age structured
populations.
D. Species interactions: Types of interactions, interspecific competition, herbivory,
carnivory, pollination, symbiosis.
E. Community ecology: Nature of communities; community structure and attributes;
levels of species diversity and its measurement; edges and ecotones.
F. Ecological succession: Types; mechanisms; changes involved in succession;
concept of climax.
G. Ecosystem: Structure and function; energy flow and mineral cycling (CNP); primary
production and decomposition; structure and function of some Indian ecosystems:
terrestrial (forest, grassland) and aquatic (fresh water, marine, eustarine).
H. Biogeography: Major terrestrial biomes; theory of island biogeography;
biogeographical zones of India.
I. Applied ecology: Environmental pollution; global environmental change;
biodiversity-status, monitoring and documentation; major drivers of biodiversity
change; biodiversity management approaches.
J. Conservation biology: Principles of conservation, major approaches to
management, Indian case studies on conservation/management strategy (Project
Tiger, Biosphere reserves).
11. EVOLUTION AND BEHAVIOUR
A. Emergence of evolutionary thoughts: Lamarck; Darwin–concepts of variation,
adaptation, struggle, fitness and natural selection; Mendelism; spontaneity of
mutations; the evolutionary synthesis.
B. Origin of cells and unicellular evolution: Origin of basic biological molecules;
abiotic synthesis of organic monomers and polymers; concept of Oparin and
Haldane; experiment of Miller (1953); the first cell; evolution of prokaryotes;
origin of eukaryotic cells; evolution of unicellular eukaryotes; anaerobic
metabolism, photosynthesis and aerobic metabolism.
C. Paleontology and evolutionary history: The evolutionary time scale; eras,
periods and epoch; major events in the evolutionary time scale; origins of
unicellular and multicellular organisms; major groups of plants and animals;
stages in primate evolution including Homo.
D. Molecular Evolution: Concepts of neutral evolution, molecular divergence and
molecular clocks; molecular tools in phylogeny, classification and identification;
protein and nucleotide sequence analysis; origin of new genes and proteins; gene
duplication and divergence.
E. The Mechanisms: Population genetics – populations, gene pool, gene
frequency; Hardy-Weinberg law; concepts and rate of change in gene frequency
through natural selection, migration and random genetic drift; adaptive radiation
and modifications; isolating mechanisms; speciation; allopatricity and
sympatricity; convergent evolution; sexual selection; co-evolution.
F. Brain, Behavior and Evolution: Approaches and methods in study of
behavior; proximate and ultimate causation; altruism and evolution-group
selection, kin selection, reciprocal altruism; neural basis of learning, memory,
cognition, sleep and arousal; biological clocks; development of behavior; social
communication; social dominance; use of space and territoriality; mating
systems, parental investment and reproductive success; parental care; aggressive
behavior; habitat selection and optimality in foraging; migration, orientation and
navigation; domestication and behavioral changes.
12. APPLIED BIOLOGY:
A. Microbial fermentation and production of small and macro molecules.
B. Application of immunological principles (vaccines, diagnostics). tissue
and cell culture methods for plants and animals.
C. Transgenic animals and plants, molecular approaches to diagnosis and
strain identification.
D. Genomics and its application to health and agriculture, including gene
therapy.
E. Bioresource and uses of biodiversity.
F. Breeding in plants and animals, including marker – assisted selection.
G. Bioremediation and phytoremediation.
H. Biosensors.
13. METHODS IN BIOLOGY
A. Molecular biology and recombinant DNA methods: Isolation and purification
of RNA , DNA (genomic and plasmid) and proteins, different separation
methods; analysis of RNA, DNA and proteins by one and two dimensional gel
electrophoresis, isoelectric focusing gels; molecular cloning of DNA or RNA
fragments in bacterial and eukaryotic systems; expression of recombinant
proteins using bacterial, animal and plant vectors; isolation of specific nucleic
acid sequences; generation of genomic and cDNA libraries in plasmid, phage,
cosmid, BAC and YAC vectors; in vitro mutagenesis and deletion techniques,
gene knock out in bacterial and eukaryotic organisms; protein sequencing
methods, detection of post-translation modification of proteins; DNA sequencing
methods, strategies for genome sequencing; methods for analysis of gene
expression at RNA and protein level, large scale expression analysis, such as
micro array based techniques; isolation, separation and analysis of carbohydrate
and lipid molecules; RFLP, RAPD and AFLP techniques
B. Histochemical and immunotechniques: Antibody generation, detection of
molecules using ELISA, RIA, western blot, immunoprecipitation, floweytometry
and immunofluorescence microscopy, detection of molecules in living cells,
in situ localization by techniques such as FISH and GISH.
C. Biophysical methods: Analysis of biomolecules using UV/visible, fluorescence,
circular dichroism, NMR and ESR spectroscopy, structure determination using
X-ray diffraction and NMR; analysis using light scattering, different types
of mass spectrometry and surface plasma resonance methods.
D. Statistical Methods: Measures of central tendency and dispersal; probability
distributions (Binomial, Poisson and normal); sampling distribution; difference
between parametric and non-parametric statistics; confidence interval; errors;
levels of significance; regression and correlation; t-test; analysis of variance; X2
test;; basic introduction to Muetrovariate statistics, etc.
E. Radiolabeling techniques: Properties of different types of radioisotopes
normally used in biology, their detection and measurement; incorporation of
radioisotopes in biological tissues and cells, molecular imaging of radioactive
material, safety guidelines.
F. Microscopic techniques: Visulization of cells and subcellular components by
light microscopy, resolving powers of different microscopes, microscopy of
living cells, scanning and transmission microscopes, different fixation and
staining techniques for EM, freeze-etch and freeze-fracture methods for EM,
image processing methods in microscopy.
G. Electrophysiological methods: Single neuron recording, patch-clamp recording,
ECG, Brain activity recording, lesion and stimulation of brain,
pharmacological testing, PET, MRI, fMRI, CAT .
H. Methods in field biology: Methods of estimating population density of animals
and plants, ranging patterns through direct, indirect and remote observations,
sampling methods in the study of behavior, habitat characterization-ground
and remote sensing methods.
I. Computational methods: Nucleic acid and protein sequence databases; data
mining methods for sequence analysis, web-based tools for sequence searches,
motif analysis and presentation.

 APPLICATION PROCEDURE

4. EXAMINATION CENTRES


The test will be held at 26 Centres spread all over India, as specified below:
Bangalore, Bhavnagar, Bhopal, Bhubaneshwar, Chandigarh, Chennai, Cochin, Delhi, Guntur, Guwahati, Hyderabad,
Imphal, Jammu, Jamshedpur, Karaikudi, Kolkata, Lucknow, Nagpur, Pilani, Pune, Raipur Roorkee, Srinagar, Thiruvananthapuram, Udaipur and Varanasi.
A candidate may opt for any of the above centres. No request for change of centre would ordinarily be granted. However, a request in writing for change of Centre may be entertained on merits, if received in this unit latest by 03.10.2011. If sufficient number of candidates do not opt for any of the above Centres, that particular Centre may stand deleted from the above list OR otherwise also, the concerned candidates may be allotted another Centre nearest to their place of residence, at the discretion of CSIR. No TA/DA will be admissible to any candidate for attending the test, in any circumstances.

5. HOW TO APPLY:

5.1. OPTION-I : APPLY THROUGH „INFORMATION BULLETIN‟:

5.1.1. BY HAND:
Candidates applying for the Test may obtain the Information Bulletin and Application forms (inclusive of fee payable) through
the branches of the Bank notified below in para 5.4 (within the prescribed dates) by paying the following fee in cash:
Sr.No. CATEGORY FEES
1. General Rs. 400/-
2. Other Backward Classes(OBC) (Non Creamy Layer) Rs. 200/-
3. SC/ST/Physically Handicapped (PH) or Visually Handicapped (VH ) Rs. 100/-

5.1.2. BY POST:
The information Bulletin and Application form may also be obtained through Value Payable Post(V.P.P.) from the Indian Bank,
3/1, West Patel Nagar, New Delhi - 110 008, by sending a crossed Demand draft for Rs. 400/-, Rs. 200/- or Rs.100/-(as the
case may be) drawn in favour of “Indian Bank, West Patel Nagar, New Delhi” payable at New Delhi. For this purpose, the
candidate should send a request to the Bank with TWO self-addressed slips clearly mentioning the address at which he/she desires the Information Bulletin & Application Form to be sent by Value Payable Post (V.P.P.) As above mentioned Bank
will entertain the request for forms through post from Tuesday, the 16th August, 2011 to Tuesday, the 30th August, 2011 only, hence, candidates are advised to send well in advance so as to reach their request within the above said period. The candidate should write his/her name, Date Of Birth, address, date of Examination (18.12.2011) and subject code on the back of the Demand Draft. However, before attaching the draft with letter of request, the candidates should check that it bears the code number of the issuing bank and drawee bank and also amount and signatures of issuing authority.

5.2. OPTION-II : APPLY THROUGH ONLINE APPLICATION:
Interested & eligible candidates may apply for this test Online through a link available at CSIR, HRDG website: www.csirhrdg.res.in. In order to apply Online the candidates are required to download Bank challan Performa from the above website and then deposit the requisite examination fee in any of the Indian Bank branches throughout the country. The examination fee for the Online application is same as mentioned in Para-5.1.1 above. Candidates after successfully submitting application online are required to take print out of the Application Form, paste his/her recent black & white photograph, put mhis/her signature at the required space, attach requisite certificates and send alongwith CSIR marked copy of fee deposited Bank Challan in an envelope to Sr. Controller of Examinations, Human Resource Development Group, Examination Unit, CSIR Complex, Library Avenue, Pusa, New Delhi-110012 so as to reach on or before 09.09.2011 (16.09.2011 for remote areas).
Online applications without hard copy or bank challan receipt or incomplete in any respect will be summarily rejected. Before applying Online, candidates are advised to go through detailed notification available at CSIR, HRDG website. Examination fee paid along with the Information Bulletin or through Bank Challan for a particular examination will neither be adjusted for any subsequent examination nor refunded under any circumstances.Candidates should also check all the columns of Bank Challan, online application, which are to be filled in properly to avoid
cancellation of application, Please note that Fee submitted by any other mode like money order, demand draft, IPO etc. will be summarily rejected.

5.3. CANDIDATE SEEKING FEE CONCESSION
The candidate should attach an attested copy of his/her category certificate as a proof of his/her claim. An application form (either through Bank or online), claiming any concession in fee & education qualification but without an attested copy of a valid SC/ST/OBC(Non Creamy Layer)/PH/VHcertificate from a competent authority and in prescribed format, will be summarily rejected.
Candidate must note that CSIR follows only Central Govt. lists and not state Govt. lists. Similarly, candidate applying under physically handicapped (PH)/ visually handicapped (VH) category may note that Govt. of India rules will be applicable in this regard.
IMPORTANT POINTS:


1. While applying for this test, please ensure that you fulfill all the eligibility conditions and follow all the laid down procedures/guidelines for this test.
2. Purchase the Information Bulletin from the designated Bank branches early enough to avoid any last minute rush.
3. While applying Online, apply early enough to avoid any last minute rush
4. Ensure that completed application Hard Copy (in case of Online application) must reach to this office within stipulated last date for receipt.
5. List of candidates registered for this will be made available on our website tentatively on 1st November, 2011. The candidates must refer to our website for checking their registration in time & for having update from time to time.
6. Admission Certificates to all the registered candidates will be dispatched three weeks before the test, if any candidate does not receive the same by 12th December, 2011; he/she must download duplicate Admission Certificate from our website. CSIR will not be responsible for any delay/non-receipt of the Admission certificate.
7. The Test Booklet for this test will be printed in Hindi & English Version separately. The candidate opting for Hindi medium in Column No. 5 of Application Form, will be supplied Question Booklet/Test Booklet printed in bilingual and Candidate opting for English medium, will be supplied Question Booklet/Test Booklet printed in English Version only. The candidate will be required to answer as per option exercised in Column No.5 of application Form.
8. For applying under “RA” category, the candidate should either has appeared or is appearing in Final year (Last Semester, where semester is there) of M.Sc. or equivalent Degree Examination during the Session 2011-1012.
For more information Download Notification CLICK HERE