UNIT -5 DEVELOPMENTAL BIOLOGY (GURKEN PROTEIN )VERY VERY IMPORTANT TOPIC

The gurken gene of Drosophila melanogaster encodes a protein with homology to the transforming growth factor alpha (TGF-a) class of signaling molecules.

During Drosophila oogenesis, the gurken gene is transcribed in the cells of the germline. The gurken messenger RNA accumulates in the oocyte and is translated throughout oogenesis. The Gurken protein is transported to the oocyte membrane, and activates the Drosophila epidermal growth factor receptor (Egfr, tyrosine kinase receptor which is expressed on the adjacent follicle cells that surround the oocyte. The activation of this major transmembrane receptor regulates the expression of a number of genes in the follicle cells, and thus initiates a series of events that lead to the correct patterning of both the anteroposterior and the dorsoventral axis of the egg and embryo.

(1). Gurken acts as a ligand that is specific to oogenesis. The Gurken protein consists of an extracellular domain, which harbors a single epidermal growth factor (EGF)-like domain, a transmembrane domain, and a short cytoplasmic domain

 (2). It is homologous to the gene spitz of Drosophila, which acts as ligand of Egfr in the embryo and in imaginal discs.

Early in oogenesis, gurken mRNA is found in the developing oocyte, and the Gurken protein accumulates in the oocyte membrane. At this stage, the oocyte occupies only a small part of the volume of the egg chamber, and therefore only a limited number of follicle cells at the posterior of the egg chamber are in contact with the oocyte membrane. In this group of follicle cells, the Egfr is activated by Gurken protein, which results in the specification of these follicle cells as posterior cells. 

If  Gurken protein is absent, and the follicle cells at the posterior end of the egg chamber are not induced to assume a posterior cell fate. They consequently develop as anterior follicle cells, which results in the production of an egg with two anterior ends. The posterior follicle cells normally send a signal back to the oocyte, which organizes the cytoskeleton of the oocyte and specifies the posterior end of the oocyte. In the mutant egg chambers, no such signal is sent from the follicle cells, and the cytoskeleton of the oocyte is misorganized. RNAs such as bicoid or oskar, which should normally be localized to one end of the egg RNA localization are mislocalized in these mutant oocytes, and the embryos that develop inside such eggs have an abnormal antero-posterior pattern .

In midoogenesis -The oocyte has grown .The gurken RNA accumulates in the region around the oocyte nucleus, and the Gurken protein is now found in a very restricted part of the oocyte membrane, directly overlying the oocyte nucleus. At this stage, Gurken activates the Egfr in the lateral follicle cells that contact the oocyte on the side where the nucleus is situated. Activation of the Egfr in these lateral follicle cells induces them to become dorsal follicle cells. In the absence of gurken signaling, the lateral follicle cells develop into ventral follicle cells . The ventral follicle cells normally regulate the production of a ventral signal that activates the Toll receptor protein on the ventral side of the egg and is responsible for inducing ventral cell fates in the developing embryo. In the strong gurken mutants, therefore, the ventralization of the follicle cell epithelium leads to an overproduction of the ventral signal, and consequently to a ventralized embryo.

Gurken signaling presumably leads to the formation of a broad field of dorsal cell fates, but secondary patterning mechanisms appear to operate to lead to the final, complex pattern of cell fates of the mature egg. In addition, gurken signaling also interacts with signaling through decapentaplegic (dpp), a molecule with homology to TGF-b. In follicle cells that receive both the gurken signal and the dpp signal, formation of dorsal appendages is repressed, and formation of operculum cell fate is induced . The regulation of the embryonic ventral signal by activation of Egfr seems, however, to be independent of the production of dorsal anterior follicle cell fates. In situations where ectopic activation of Egfr in follicle cells is induced in parts of the follicle cell epithelium, embryos result that show only regional dorsalization, corresponding to the region of the follicle cell epithelium where Egfr was ectopically activated .

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IMPORTANT COMPONENTS OF ECM (EXTRACELLULAR MATRIX)

Elastin -This insoluble fibrous macromolecule provides the resilience (stretch) of the skin, vessels, and ligaments by associating with collagen fibers to limit stretching and preventing tearing. It is highly hydrophobic (proline and glycine), is not glycosylated or "hydroxylized". It has many crosslinks at the lysine residues to stablize the fibers. 

Fibrilin -Is bound in fibers of microfibril sheaths. The sheaths are composed primarily of this protein.
The elastic fiber is made of two alternating segments of hydrophobicity and alpha-helical segments (alanine/ lysine --> crosslinks)

Integrins-This glycoprotein is a cell receptor that interacts with the surrounding ECM, providing anchor for the cell to the matrix of the collagen + links to peptidoglycans.This transmembrane cell receptor is made of alpha and beta subunits that function in cell signaling (depend on extracell divalent cations) and the regulation of cell cycle, shape, and motility through LINKING the ECM with the actin cytoskeleton.  Integrins can mediate indirect interactions with the cytoplasmic cytoskeleton through intermediary proteins including talin and vinculin.


Selectins-Carbohydrate binding proteins that bind to glycoproteins from other cells, important in WBC extravasation, the movement of them from inside the capillaries into the tissues

Multiadhesive proteins -

Dthrombospondin,tenascin,vitronectn,nidogen/enactin,van willebrand factor ,laminin and fobronectin.

A. Laminin- This is a large adhesive glycoprotein that is a major component of BASAL LAMINA. It has binding domains specific for other actors in the BL, including type IV collagen, heparin sulfate (perlecan), enactin (nidogen), and integrins. It consists of 3 poly peptide chains: alpha, beta, gamma

B.Fibronectin -
This example of an adhesive glycoprotein is found in most ECM and plasma. It binds to collagen and proteoglycans. Type III module contains RGD sequence for binding receptors. Importantly, it exists as a protein dimer, consisting of two nearly identical monomers linked by a pair of disulfide bonds.
Although Fibronectin is produced from one gene, it has highly diverse isoforms due to this mechanism in pre-mRNA.

Examples:
- Soluble plasma fibronectin - component of blood plasma made by liver
- Insoluble cellular fibronectin - component of ECM.

Proteoglycans -

A.Aggrecan -This is a major macromolecule of cartilage (made of several GAGs). Due to extensive hydration, it creates a gel-like matrix. These proteoglycans require a core of Hyaluronan and it binds to TGF-beta to inhibit ECM synthesis.

B.Decorin-Is a ubiquitous proteoglycan wide spread in ECM binds to type 1 collagen fibrils and can limit their size and binds TGF-beta and sequesters it interaction with cells.

C.Perlecan -Type of proteoglycan, found in basal lamina, structural and filtering function in basal lamina, the glycosaminoglycan chains attached to perlecan are responsible for preventing proteins escaping from the serum to the urine during glomerular filtration, is one of the proteins that can be defective in specific form of muscular dystrophy.

Notes on collagen -

http://dnaofbioscience.blogspot.com/2016/10/collagen.html

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DELTA NOTCH SIGNALLING PATHWAY

The Delta-Notch signalling pathway is a highly conserved cellular signaling 

mechanism that is essential for embryonic development .

Notch genes encode for transmembrane protiens, Delta is an example
 of one of the ligands that bind to the extracellular domain of the
 Notch receptor in Drosophila. Delta is a single-pass transmembrane
 protein ligand that is membrane bound. 

Notch signalling determines cell fate of surounding cells by the process of

 lateral inhibition in both vertbrates and invertebrates. 

Different Notch activation results in different biological alterations in

 gene expression. For example in human adult tissue, activation of Notch1 

corresponds to differentiation of T-cells and self-renewal, which path is 

undertaken is dependent on other environmental factors too.

• It involves proteolytic cleavage to release an intracellular fragment (Nicd) that functions to regulate transcription.
• In the nucleus, Nicd displaces a repression complex and, with the DNA-binding CSL (CBF1, Su(H) and LAG-1) protein, recruits . Additional epigenetic cofactors are implicated and recruitment of kinases and ubiquitin ligases probably contribute to rapid turnover of the activator complex.
• Activity of the receptor is also regulated post-translationally. A number of different auxiliary components are implicated, including several ubiquitin ligases and proteins, such as Numb, that have direct links to the endocytic machinery.
• 

  Notch ligands are transmembrane proteins and they require E3 ubiquitin ligases for their activity. The mechanisms whereby the ligands become competent to signal are not yet known, but probably entail endocytosis. Localization and cleavage of ligands might also contribute to their regulation.

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G Proteins Signal Via Phospholipids

Many GPCRs exert their effects through G proteins that activate the plasma-membrane-bound enzyme phospholipase C-β (PLCβ). The activated GPCR stimulates the plasma-membrane-bound phospholipase C-β (PLCβ) via a G protein called Gq. The α subunit and βγ complex of Gq are both involved in this activation.

 Two second messengers are produced when PI(4,5)P2 is hydrolyzed by activated PLCβ -

1.Inositol 1,4,5-trisphosphate (IP3) IP3 is a water-soluble diffuses through the cytosol and releases Ca2+ from the ER by binding to and opening IP3-gated Ca2+-release channels (IP3 receptors) in the ER membrane. The large electrochemical gradient for Ca2+ across this membrane causes Ca2+ to escape into the cytosol when the release channels are opened.  

2.Diacylglycerol remains embedded in the plasma membrane and, together with phosphatidylserine  and Ca2+, helps to activate protein kinase C (PKC), which is recruited from the cytosol to the cytosolic face of the plasma membrane. 

 The initial rise in cytosolic Ca2+ induced by IP3 alters the PKC so that it translocates from the cytosol to the cytoplasmic face of the plasma membrane. There it is activated by the combination of Ca2+, diacylglycerol, and the negatively charged membrane phospholipid phosphatidylserine). Once activated, PKC phosphorylates target proteins that vary depending on the cell type. 

Diacylglycerol can be further cleaved to release arachidonic acid, which is used in the synthesis of other small lipid signal molecules called eicosanoids. Most vertebrate cell types make eicosanoids, including prostaglandins, which have many biological activities. They participate in pain and inflammatory responses, for example, and many anti-inflammatory drugs (such as aspirin, ibuprofen, and cortisone) act in part by inhibiting their synthesis.  

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Wnt β-Catenin pathway

Wnt Proteins Bind to Frizzled Receptors and Inhibit the Degradation of β-Catenin They were discovered independently in flies and in mice: in Drosophila, the Wingless (Wg) gene originally came to light because of its role as a morphogen in wing development, while in mice, the Int1 gene was found because it promoted the development of breast tumors when activated by the integration of a virus next to it. Both of these genes encode Wnt proteins.There are 19 Wnts in humans, each having distinct, but often overlapping, functions.
 Wnts can activate at least two types of intracellular signaling pathway

1. Wnt/β-catenin pathway (also known as the canonical Wnt pathway), which is centered on the latent transcription regulator β-catenin.

2. Planar polarity pathway, coordinates the polarization of cells in the plane of a developing epithelium and depends on Rho family GTPases. Both of these pathways begin with the binding of Wnts to Frizzled.

The Wnt/β-catenin signaling pathway-

 (A) In the absence of a Wnt signal-

 β-catenin that is not bound to cell–cell adherens junctions interacts with a degradation complex containing APC, axin, GSK3, and CK1. In this complex, β-catenin is phosphorylated by CK1 and then by GSK3, triggering its ubiquitylation and degradation in proteasomes.

In the absence of Wnt signaling, Wnt-responsive genes are kept silent by an inhibitory complex of transcription regulatory proteins of the LEF1/TCF family bound to a co-repressor protein of the Groucho family . In response to a Wnt signal, β-catenin enters the nucleus and binds to the LEF1/TCF proteins, displacing Groucho. The β-catenin now functions as a coactivator, inducing the transcription of the Wnt target genes.Thus, Wnt/β-catenin signaling triggers a switch from transcriptional repression to transcriptional activation. Among the genes activated by β-catenin is Myc, which encodes a protein (Myc) that is an important regulator of cell growth and proliferation .

 (B) In the presence of wnt signal-

 Wnt proteins regulate β-catenin proteolysis by binding to both a Frizzled protein and a co-receptor that is related to the low-density lipoprotein (LDL) receptor  and is therefore called an LDL-receptor-related protein (LRP).  The activated receptor complex recruits the Dishevelled scaffold and the cytosolic tail of LRP is phosphorylated by  a protein kinase called casein kinase 1 (CK1) phosphorylates the β-catenin on a serine. For further phosphorylation by another protein kinase called glycogen synthase kinase 3 (GSK3); this final phosphorylation marks the protein for ubiquitylation and rapid degradation in proteasomes.

Two scaffold proteins called axin and Adenomatous polyposis coli (APC) hold the protein complex together .APC gets its name from the finding that the gene encoding it is often mutated in a type of benign tumor (adenoma) of the colon; the tumor projects into the lumen as a polyp and can eventually become malignant. (This APC should not be confused with the anaphase-promoting complex, or APC/C, that plays a central part in selective protein degradation during the cell cycle.

Axin binds to the phosphorylated LRP and is inactivated and/or degraded, resulting in disassembly of the degradation complex. The phosphorylation of β-catenin is thereby prevented, and unphosphorylated β-catenin accumulates and translocates to the nucleus, where it binds to LEF1/ TCF, displaces the co-repressor Groucho, and acts as a coactivator to stimulate the transcription of Wnt target genes. The scaffold protein Dishevelled is required for the signaling pathway to operate; it binds to Frizzled and becomes phosphorylated .

NOTE -The Wnt/β-catenin pathway acts by regulating the proteolysis of the multifunctional protein β-catenin (or Armadillo in flies).

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Hedgehog signalling pathway

The Hedgehog proteins were discovered in Drosophila .
 At least three genes encode Hedgehog proteins in vertebrates—Sonic, Desert, and Indian hedgehog. The active forms of all Hedgehog proteins are covalently coupled to cholesterol, as well as to a fatty acid chain.

 The effects of Hedgehog are mediated by a latent transcription regulator called Cubitus interruptus (Ci).
1.In the absence of a Hedgehog signal- Most Patched is in intracellular vesicles , where it keeps Smoothened inactive and sequestered. The Ci protein is bound in a cytosolic protein degradation complex, which includes the protein kinase Fused and the scaffold protein Costal2. Costal2 recruits three other protein kinases (PKA, GSK3, and CK1; not shown), which phosphorylate Ci. Phosphorylated Ci is ubiquitylated and then cleaved in proteasomes  to form a transcriptional repressor, which accumulates in the nucleus to help keep Hedgehog target genes inactive.

 2.In the presence of a Hedgehog  signal-  Binding to iHog and Patched removes the inhibition of Smoothened by Patched. Smoothened is phosphorylated by PKA and CK1 and translocates to the plasma membrane, where it recruits the complex containing Fused, Costal2, and Ci. Costal2 releases unprocessed Ci, which accumulates in the nucleus and activates the transcription of Hedgehog target genes. Many details in the pathway are poorly understood, including the role of Fused.

Hedgehog functions by blocking the proteolytic processing of Ci, thereby changing it into a transcriptional activator. It does this by a convoluted signaling process that depends on three transmembrane proteins:
                                       ( Patched, iHog, and Smoothened. )

. Hedgehog signaling can promote cell proliferation, and excessive Hedgehog signaling can lead to cancer. Inactivating mutations in one of the two human Patched genes, for example, which lead to excessive Hedgehog signaling, occur frequently in basal cell carcinoma of the skin, the most common form of cancer in Caucasians. A small molecule called cyclopamine, made by a meadow lily, is being used to treat cancers associated with excessive Hedgehog signaling. It blocks Hedgehog signaling by binding tightly to Smoothened and inhibiting its activity.

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The PI-3-Kinase –Akt Signaling Pathway

Extracellular signals are usually required for animal cells to grow and divide, as well as to survive .

Members of the insulinlike growth factor (IGF) family of signal proteins, for example, RTKs stimulate many types of animal cells to survive and grow. 

1.They bind to specific RTKs which activate PI 3-kinase to produce PI(3,4,5)P3. 
2.The PI(3,4,5)P3 recruits two protein kinases to the plasma membrane via their PH domains—
                 a. Akt (also called protein kinase B, or PKB) 
                 b. Phosphoinositide-dependent protein kinase 1 (PDK1), and this leads to the activation of Akt ).
3. Once activated, Akt phosphorylates various target proteins at the plasma membrane, as well as in the cytosol and nucleus. 
4.Actions of Akt all conspire to enhance cell survival and growth.

The control of cell growth by the PI-3-kinase–Akt pathway depends in part on a large protein kinase called TOR (named as the target of rapamycin, a bacterial toxin that inactivates the kinase and is used clinically as both an immunosuppressant and anticancer drug). 

TOR was originally identified in yeasts in genetic screens for rapamycin resistance; in mammalian cells, it is called mTOR, which exists in cells in two functionally distinct multiprotein complexes. 

1.  mTOR complex 1- Contains the protein raptor; this complex is sensitive to rapamycin, and it stimulates cell growth—both by promoting ribosome production and protein synthesis and by inhibiting protein degradation. 

Complex 1 also promotes both cell growth and cell survival by stimulating nutrient uptake and metabolism. The mTOR in complex 1 integrates inputs from various sources, including extracellular signal proteins referred to as growth factors and nutrients such as amino acids, both of which help activate mTOR and promote cell growth. The growth factors activate mTOR mainly via the PI-3-kinase–Akt pathway. Akt activates mTOR in complex 1 indirectly by phosphorylating, and thereby inhibiting, a GAP called Tsc2. Tsc2 acts on a monomeric Ras-related GTPase called Rheb . Rheb in its active form (Rheb-GTP) activates mTOR in complex 1. The net result is that Akt activates mTOR and thereby promotes cell growth 

2.mTOR complex 2 -Contains the protein rictor and is insensitive to rapamycin; it helps to activate Akt , and it regulates the actin cytoskeleton via Rho family GTPases. 

The Akt is phosphorylated on a serine by a third kinase (usually mTOR in complex 2), which alters the conformation of the Akt so that it can be phosphorylated on a threonine by PDK1, which activates the Akt. The activated Akt now dissociates from the plasma membrane and phosphorylates various target proteins, including the Bad protein. When unphosphorylated, Bad holds one or more apoptosis-inhibitory proteins (of the Bcl2 family—) in an inactive state. Once phosphorylated, Bad releases the inhibitory proteins, which now can block apoptosis and thereby promote cell survival. 

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UNIT 1 BIOCHEMISTRY CSIR NET ANFINSEN'S EXPERIMENT

 The classic work of Christian Anfinsen in the 1950s on the enzyme ribonuclease revealed the relation between the amino acid sequence of a protein and its conformation. Ribonuclease is a single polypeptide chain consisting of 124 amino acid residues cross-linked by four disulfide bonds 

 Anfinsen's plan was to destroy the three-dimensional structure of the enzyme and to then determine what conditions were required to restore the structure.

AGENTS -

1. Urea or guanidinium chloride-   Effectively disrupt the noncovalent bonds.
2.β-mercaptoethanol   -The disulfide bonds can be cleaved reversibly by reducing them with a reagent such as β-mercaptoethanol . In the presence of a large excess of β-mercaptoethanol, a protein is produced in which the disulfides (cystines) are fully converted into sulfhydryls (cysteines).

EXPERIMENT-

A. When ribonuclease was treated with β-mercaptoethanol in 8 M urea, the product was a fully reduced, randomly coiled polypeptide chain devoid of enzymatic activity. In other words, ribonuclease was denatured by this treatment.

B. Anfinsen then made the critical observation that the denatured ribonuclease, freed of urea and β-mercaptoethanol by dialysis, slowly regained enzymatic activity . The sulfhydryl groups of the denatured enzyme became oxidized by air, and the enzyme spontaneously refolded into a catalytically active form. Detailed studies then showed that nearly all the original enzymatic activity was regained if the sulfhydryl groups were oxidized under suitable conditions. 

C. A quite different result was obtained when reduced ribonuclease was reoxidized while it was still in 8 M urea and the preparation was then dialyzed to remove the urea. Ribonuclease reoxidized in this way had only 1% of the enzymatic activity of the native protein. 

 The reason is that the wrong disulfides formed pairs in urea. There are 105 different ways of pairing eight cysteine molecules to form four disulfides; only one of these combinations is enzymatically active. The 104 wrong pairings have been picturesquely termed "scrambled" ribonuclease. 

D.Anfinsen found that scrambled ribonuclease spontaneously converted into fully active, native ribonuclease when trace amounts of β-mercaptoethanol were added to an aqueous solution of the protein  The added β-mercaptoethanol catalyzed the rearrangement of disulfide pairings until the native structure was regained in about 10 hours. This process was driven by the decrease in free energy as the scrambled conformations were converted into the stable, native conformation of the enzyme. The native disulfide pairings of ribonuclease thus contribute to the stabilization of the thermodynamically preferred structure.

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QTL ANALYSIS (GENETICS -UNIT 8 CSIR NET LIFE SCIENCES)

 LOCATION OF QUANTITATIVE GENES ON CHROMOSOME-QTL

Quantitative trait locus (QTL) analysis is a statistical method that links two types of information—phenotypic data (trait measurements) and genotypic data (usually molecular markers)—in an attempt to explain the genetic basis of variation in complex traits

 Molecular markers are preferred for genotyping, because these markers are unlikely to affect the trait of interest. Several types of markers are used, including single nucleotide polymorphisms (SNPs), simple sequence repeats(SSRs, or microsatellites), restriction fragment length polymorphisms (RFLPs), and transposable element positions.

 In  QTL analysis, the parental strains are crossed, resulting in heterozygous (F1) individuals, and these individuals are then crossed using either selfing/backcross/testcross.
The phenotypes and genotypes of the derived (F2) population are scored.

Markers that are genetically linked to a QTL influencing the trait of interest will segregate more frequently with trait values (large or small egg size in our example), whereas unlinked markers will not show significant association with phenotype.

 Small sample sizes may fail to detect QTL of small effect and result in an overestimation of effect size of those QTLthat are identified. This is known at the "Beavis effect.

QTL studies require very large sample sizes, and they can only map those differences that are captured between the initial parental strains.
Because these strains are unlikely to contain segregating alleles of large effect at every locus contributing to variation in natural populations, some loci will remain undetected.

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Types of endocytosis

Types of Endocytosis: Pinocytosis, Receptor-Mediated Endocytosis and Phagocytosis

1.Pinocytosis is occurs in   leukocytes, kidney cells, intestinal epithelium, liver macrophages, and plant root cells. Actin filaments are associated with the margins of pinocytic vesicles and are believed to play some role in the vesicle’s in­vagination

2. Receptor-Mediated Endocytosis: 

Here , binding of molecules (hormones, antibodies ,proteins, and lipids to specific receptors in the plasma membrane  which are then internalized by the cell. The receptors that mediate the endocytosis are integral proteins that span the membrane. Substances bound by these receptors, called ligands. Ligand-receptor complexes move laterally in the membrane toward coated pits in which the complexes are then concentrated. Because lateral movement through the membrane by the ligand-receptor complex is quite rapid, a coated pit is encountered within a few seconds.Coated vesicles that have just detached from the plasma membrane move deeper into the cytoplasm, progressively shed their clathrin coats, and fuse with one another to form larger, smooth-surfaced vesicles called endosomes (sometimes receptosomes) As endosomes move even deeper into the cytoplasm, there is a progressive release of ligands from their receptors into the lumen of the vesicle. The endosome develops a tubular portion in which the membrane-bound but ligand-free receptors are concentrated and a vesicular portion containing free ligand. At this stage the endosome . The tubular por­tion of the endosome is subsequently dispatched to the plasma membrane, thereby recycling its ligand recep­tors, and the vesicular portion continues its journey deeper into the cell.If the endosome contains pro­teins, other macromolecules, or particles, it may fuse with a lysosome so that enzymatic digestion of the en­trained material can ensue. 

3. Phagocytosis:It involves the endocytosis of much larger quantities of material than either pinocytosis or receptor-mediated endocytosis. For example, entire ciliates, rotifers, or other micro­scopic organisms may be phagocytosed by an amoeba and enclosed within one or more vacuoles called phagosomes, food vacuoles, or food cups .White blood cells phagocytose hundreds of bacteria. The removal and destruction of old red blood cells in the liver, spleen, and bone marrow by reticuloendothelial cells in these organs also occurs by phagocytosis. Following phagocytosis, the phago­somes fuse with primary lysosomes in the cell. The hydrolytic enzymes from these lysosomes digest the en­gulfed material, converting it to a form that may be transported across the vacuolar membranes and into the cytosol.

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NEUTRAL THEORY OF MOLECULAR EVOLUTION PART B CSIR NET DEC 2017

The neutral theory of molecular evolution (proposed by MOTTO KIMURA) 1968 holds that at the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by genetic drift of mutant alleles that are neutral.

SOME IMPORTANT POINTS -

• Except for advantageous mutations most alleles are under neutral condition.
• The rate of evolution for most genes will be equal to the neutral mutation rate .
• At the level of Dna sequences,genetic drift dominates evolution i,e genetic drift is the main force changing allele frequency .
• The rate of replacement in evolution resulting from the random genetic drift of effectively neutral mutations is equal to the mutation rate to such alleles, μ.
•  Explained the unexpectedly high rate of evolutionary change and very large amount of intraspecific variability at the molecular level that had been uncovered by new techniques in molecular biology. 
• A neutral mutation is one that does not affect an organism's ability to survive and reproduce. 
• The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly purged by natural selection, they do not make significant contributions to variation within and between species at the molecular level. 
• Mutations that are not deleterious are assumed to be mostly neutral rather than beneficial. 

CSIR NET  DEC 2017 PART B 

Which one of the following statements is NOT TRUE about the Neutral Theory as proposed by Motoo Kimura?

1.Except for advantageous mutations, most alleles are under neutral selection

2. The rate of evolution for most genes will be equal to the neutral mutation

rate

3. Advantageous mutations are exceedingly rare

4. At the level of DNA sequences, genetic drift dominates evolution

Answer-  3

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ECOTONE AND EDGE EFFECT

Ecotone-An ecotone is a zone of junction or a transitional area between two biomes [diverse ecosystems]. It is the boundry line where two communities meet and integrate.

 e.g. 1.The mangrove forests represent an ecotone between marine and terrestrial ecosystem

       2. grassland (between forest and desert), estuary (between fresh water and salt water) and river bank or marsh land (between dry and wet).

Characteristics of Ecotone

It may be narrow (between grassland and forest) or wide (between forest and desert). It may be local (zone between field and forest ) or regional (zone between forest and grassland ecosystems ).As it is a zone of transition, it has conditions intermediate to the adjacent ecosystems. It may also include a number of highly adaptable species that tend to colonize .Hence it is a zone of tension.Usually, the number and the population density of the species of an outgoing community decreases as we move away from community or ecosystem.

• Edge Effect –( Edge Species) It is the tendency for increased variety and density at community junctions .It was coined by Aldo Leopold(1933). OR Sometimes the number of species and the population density of some of the species in the ecotone is much greater than either community. This is called edge effect.
• The organisms which occur primarily or most abundantly in this zone are known as edge species.
• In the terrestrial ecosystems edge effect is especially applicable to birds. For example the density of birds is greater in the mixed habitat of the ecotone between the forest and the desert.

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TYPIFICATION TYPES -

The ICBN recognizes seven kinds of types (Article 9)

1.HOLOTYPE- A single specimen (single herbarium )or illustration used or designated by the author and the name is based as the nomenclatural type at the time of publication of the name of the taxon. (PART B -2017 DEC CSIR NET )

2.ISOTYPE -It is the duplicate of holotype specimen collected at the same time ,by the same person and from the same population.

3.LECTOTYPE -When no holotype was indicated or holotype is missing ,lost or damaged  then lectotype is the specimen used as a nomenclatural type which was taken from the orginal material.

4.SYNTYPE-Any one of two or more specimens that is listed in a species description where no holotype was designated. 

5.PARATYPE- These are not name bearing types. When the original description designated a holotype, there may still be additional specimens listed in the type series and those are termed paratypes.

6.NEOTYPE- Belonging to non original collection .A neotype is a specimen later selected to serve as the single type specimen when an original holotype has been lost or destroyed or where the original author never cited a specimen.

7.EPITYPE -Epitype can not be a part of original material. An additional, clarifying type(specimen or illustration) of a species or lower-order taxon , provided when the holotype  and paratypes from the original classification are demonstrably ambiguous or insufficient. 

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