MANOJ KUMAR (SHELFORD)
Sunday, July 8, 2012
adaptations in insects part 1
Saturday, July 7, 2012
adaptations in insects
Saturday, May 26, 2012
Thursday, April 26, 2012
Thursday, April 5, 2012
An overview of polyadenylation of 3’ end: post transcriptional modification, prior to the nuclear export.
The final RNA processing event, i.e. the polyadenylation of the 3’ end of the mRNA is linked with the termination of the transcription.
The CTD tail of the polymerase is involved in the recruiting of the enzymes necessary for the polyadenylation.
The DNA contains a poly-A signal sequence. Once the polymerase has reached the sequence and transcribed the poly-A signal sequence into the RNA, the poly-A signal sequence (these sequences once transcribed into RNA, triggers transfer of the CPSF and CstF from the CTD tail of the polymerase to the RNA, described in the text later) in the RNA triggers the transfer of polyadenylation enzymes to RNA leading to three events.
1. Cleavage
2. Addition of the “A” residues.
3. Termination of transcription.
The CTD tail of the polymerase carries two protein complexes as it reaches the end of the gene.
1. CPSF (cleavage and polyadenylation specificity factor)
2. CstF (cleavage stimulation factor)
The binding of the CPSF (cleavage and polyadenylation specificity factor) and CstF (cleavage stimulation factor) is followed by the recruitment of other proteins as well. This leads to RNA cleavage and then polyadenylation.
The poly-A polymerase mediates the process of polyadenylation and adds about 200 adenines to the RNA’s 3’ end produced by the cleavage.
The poly-A polymerase uses ATP (adenosine triphosphate) as a precursor and adds the nucleotides using the same chemistry as that of RNA polymerase, but here in the absence of a template. Thus long “A” tail is only present in RNA (and not in the DNA)
After polyadenylation (the final step in post transcriptional modification, prior to the nuclear mRNA transport) the mature mRNA is then transported from the nucleus to the cytosol.
At present, not more is known about the relation of the polyadenylation with the termination of the transcription. Two basic models have been proposed to explain the link between polyadenylation and termination.
· First: the transfer of the enzymes responsible for the polyadenylation from the CTD tail of the polymerase to the RNA triggers a conformational change in the polymerase that reduces the processivity of enzymes leading to spontaneous termination soon afterwards.
· Second: after cleavage of the RNA transcript the polymerase keeps on transcribing the DNA short while, the polymerase senses the absence of the 5’ cap on the second RNA molecule; as a result, the RNA recognizes the transcript as improper and terminates the transcription.
Tuesday, March 27, 2012
Friday, March 23, 2012
hypersensetivity
Thursday, March 15, 2012
PCR: polymerase chain reaction.
Entomology: trap cropping
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- Trap cropping involves planting small areas of crop or other species plants near the protected crop.
- The trap cropping must be done, after closely understanding the seasonal cycle.
- The insects are left to develop in the trap and are killed with pesticides, this process is beneficial, since the pesticides are not spread on the whole of the crop, and thus environment friendly and economically sound too.
- In this practice the trap may be of different species of plant or the same crop but planted in different time.
- For example: an early maturing variety of crop to be protected must be planted on say 8-10 percent of the field. And the main crop is of a late maturing variety. Now the early maturity of the early maturing variety species will attract the pests, they seek food and will lay eggs of the first generation. treatments of insecticides are made in the trap around 7 to 10 days after the emergence of first generation adults, in order to prevent infestations in main planting.
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Thursday, February 23, 2012
Bruce effect
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- The Bruce effect was first noted by HILDA M. BRUCE in 1959.
- The Bruce effect is also known as pregnancy block, it is shown by the rodents, it refers to the tendency of the pregnant female rodents to terminate their pregnancy, when they are exposed to the scent of another male, which is not the father of the embryo carried by the female.
- Still now the Bruce effect has not been confirmed in other non-rodent species.
- In 1959 Bruce kept pregnant female mice with males which were not the father of the carried embryo, it was seen that the female blocked their pregnancy, in the presence of an unfamiliar male. This effect blocking of the pregnancy by the female influenced by the scent of the male mice was termed as BRUCE effect, after the name of HILDA BRUCE.
- The male mouse urine contains MHC CLASS I peptides that binds to the receptor in the females mouse’s vomeronasal organ (it is an organ filled with mucous present in the nasal septum), it stimulates the vomeronasal system to act as a pump and the system draws in the substances actively. These chemical signals which are specific to each male are learned by the females. This chemosensory cue is coupled by the vasopressin, with an appropriate physiological response,
- It is seen that, if the vasopressin 1b gene is knocked out in females, then the presence of an unfamiliar male does not trigger pregnancy disruption.
- Exposure to the male urinal pheromones will activate a neuroendocrine pathway, which leads to the pregnancy failure. However, if these pheromones are pre-memorized by the female mice, then noradrenalin is secreted, which lowers down the receptivity of the olfactory bulb to these pheromones. Thus the pregnancy disruption is averted.
- The hormone oxytocin is also important in Bruce effect, if the males are treated by the oxytocin-antagonist hormone, then the females are unable to recognize the urinary pheromones of the their mate, and terminates pregnancy when exposed any male, known or unknown.
è The activation of vomeronasal neuron receptors by the male pheromones induces a complex neuroendocrine pathway. This works as follows.
i. The pheromonal information is carried by the nerves to the accessory olfactory lobe, and then to the corticomedial amygdala lobe and then to stria.
ii. These areas stimulate the hypothalamus.]
iii. The hypothalamus then secretes the dopamine,
iv. The dopamine prevents the secretion of prolactin from the anterior pituitary (prolactin is necessary for maintaining the corpus luteum, in the absence of the prolactin the corpus luteum undergoes luteolysis)
v. Now in the absence of the corpus luteum the progesterone is not released. Since the progesterone is necessary for maintaining the pregnancy.
vi. Thus in the absence of the progesterone the pregnancy fails.
è Role of oestrogen: oestradiol is a metabolic product of testosterone, the oestrogen (particularly the E2) is a crucial chemo-signal regulating the Bruce effect.
Small steroid molecules such as E2 are able to enter the bloodstream directly via the nasal ingestion, after ingestion the E2 travels to the uterus, which has high level of suitable receptors,
Normally E2 is essential for the preparation of the blastocyst and the uterus for implantation.
However the excessive E2 prevents implantation.
Factors governing the Bruce effect.
1. Timing of exposure: after mating the females experience twice daily surges of prolactin. The incidence of Bruce-phenomena depends on the timing of the exposure to the male pheromones, if the pheromone exposure coincides with the prolactin surges, then only there takes place the Bruce-effect.
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Sunday, February 19, 2012
Innate immunity: elements of innate immune system
1. Innate immunity is present from birth.
2. It provides the first line of defense against pathogens
3. It is not specific to any one pathogen, but rather acts against all foreign molecules.
4. It also does not rely to previous exposure to the pathogens.
5. Its response is functional since birth and has no memory.
Elements of innate immunity:
1. Physical barriers:
Physical barriers are the first line of defence against microorganisms. It includes:
- Mucous membranes
- The acidic pH of sweat and sebaceous glands; fatty acids and hydrolytic enzymes inhibit the growth of microorganisms.
- The respiratory tract is lined by cilia (hair like projection) of epithelial membranes; the synchronous movement of cilia propels mucus entrapped microorganisms from these tracts.
- Conjunctiva is also specialized, the tears contains lysozyme, lactoferin, IgA and thus provide chemical as well as physical protection
In spite of these barriers, some microorganisms are able to penetrate the physical barriers. Then it is up to the adaptive and innate immune system to recognize and destroy them, without harming the host.2. Chemical mediator:
a. Complement: it is a heat labile component of blood plasma that augments phagocytosis. This activity was said to complement the antibacterial activity of the antibody/
It also bridges the innate and adaptive immunity. The complement system is composed of over 30 serum proteins. Activation of complement in response to certain micro-organism results a controlled cascade of enzymatic reactions which targets the membranes of pathogenic organisms and lead to their destruction. A variety of specific and non-specific immunologic mechanisms can convert the inactive form of complement proteins to active forms with the ability to damage the membranes of pathogenic organisms, either destroying the pathogens or facilitating their clearance. Reactions between the complement molecules or fragments of complement molecules and cellular receptor triggers the activation of innate or adaptive immune systems.
b. Cytokines: the term cytokine is a generic term for any low molecular weight soluble protein or glycoprotein released by one cell population which acts as intercellular mediator. Interferon is cytokines made by cell in response to viral infection which essentially induce generalized antiviral state in surrounding cells.
c. Pattern recognition molecule: many molecules involved in innate immunity have the ability to recognize a give class on molecule. I.e. recognize pattern. Pattern recognition molecule that recognizes pattern associated molecular pattern (PAMP) may be soluble circular proteins or cell surface receptors. E.g. Manose-binding lectin (MBL) and C - reactive protein (CRP) are soluble pattern recognition molecules that bind to microbial surface and promote their opsonization.
3. Cellular defence: leukocytes are responsible for both specific and nonspecific immunity. Many specialized cell such as neutrophils, macrophages, monocytes, NK cells, participate in innate host defense mechanism. Once the pathogen invades the physical and chemical barriers, the specialized cells play and important role in protection, phagocytosis is fundamental protective. The phagocytosis is enhanced by the opsonization of pathogens. (opsonization: the process by which particulate antigen are rendered more susceptible to phagocytosis is called opsonization)
After ingestion the foreign particle is trapped in the phagosome (phagocytic vacuole), which fused with lysosome forming phagolysosomes. Now the antimicrobial and cytotoxic substances present within lysosome destroys the phagocytized micro-organism. The destruction of phagocytized micro-organism takes place as follows.
i. Oxygen dependent killing: during this process the phagocytes increase their O2 consumption (such as hydroxyl radicals, superoxide anions, hydrogen peroxide) which acts as antimicrobials.
ii. Oxygen independent killing: activated macrophages also synthesize lysozyme, defensin and various hydrolytic enzymes, who act without oxygen requirement
4. Inflammatory barriers:
- Inflammation is an important non-specific dense reaction to cell injury.
- The signs of inflammation are pain redness (erythema) swelling (edema) and heat.
- Pain is caused due to increased vascular diameter which leads to increased blood flow, thus causing heat and redness in the area.
- These blood vessels become permeable to fluid and proteins, leading to local swelling and an accumulation of blood proteins that aid in defence.
- The inflammatory responses are mediated by a variety of signaling molecules. Activated macrophages produce chemo attractants (known as chemokine).
- Some chemokine attract neutrophils, (which are the first cells, which are recruited in large numbers to the site of infection).
- Other chemokine attract the monocytes and dendritic cells. The dendritic cells pick up antigens from the invading pathogens and carry them to nearby lymph nodes, where they present antigens to lymphocytes to marshal the forces of adaptive immune system.
- Two principal mediators of inflammatory response are histamine (released by a variety of cells in response to injury of tissues), kinines (present in blood plasma in active form)
Tuesday, February 14, 2012
Basic structure of antibodies
1. The antibodies reside in the serum.
2. The early experiments of kabat and Tiselius resolved serum proteins into three major non-albumin peaks i.e. α, β, ϒ
3. Antibodies are heterodimers. They have common structure of four peptide chains.
4. The structure consists of two identical light (L) chains and two identical heavy (H) chains.
5. Molecular weight of heavy chain (H) is about 50,000.
6. The molecular weight of the light chain (L) is about 25,000.
7. H and L chains are also called immunoglobulin.
8. Each light chain is bounded to heavy chain by disulphide bonds, and other non-covalent interactions such as salt linkage, hydrogen bond etc….
9. It is sometimes called as the dimers of dimer.
10. Around first 110 (or so) AA of amino-terminal region of light or heavy chain varies greatly among antibodies of different specificity, these segments of highly variable regions are called V-regions. i.e. VL in light chain and VH in heavy chain.
11. The V-region has an area called complementary-determining region called as CDRs. It is this CDR (on both light and heavy chain) that constitute the antigen binding site of antigen molecule.
12. The region of relatively constant region beyond the variable region have been dubbed C regions. I.e. CL in light chain and CH on heavy chains, the site for attatchment of the carbohydrates are restricted to the constant region.
Heavy chain sequencing revealed five basic varieties of heavy chain
a. The sequencing of revealed that the sequence of the heavy chain are very similar to the light chain.
b. The amino terminal part constitute of 100 to 110 amino acid shows great variation among myeloma heavy chains, so were named as V- chains.
c. The remaining part of chains revealed 5 basic sequence patterns corresponding to 5 diferent heavy chain constant regions (i.e. µ, δ, γ, ε, α)
d. Each of these five different heavy chains are called an isotype.
e. The length of constant region is , approximately 330 AA in δ, ϒ, α. And approximately 440 AA in µ, ε.
f. The class of antibody is determined by the type of heavy chain present.
ANTIBODY CLASS | AA length | TYPE OF HEAVY CHAIN |
IgM | 440 | µ |
IgE | 440 | ε |
IgG | 330 | Ï’ |
IgA | 330 | α |
IgD | 330 | δ |
g. A single antibody molecule may have any one type of light chain, i.e. either kappa (Κ) or lambda(λ) light chain.
h. A single antibody molecule has identical pairs of heavy and light chain respectively. i.e. H2L2
i. The isotypes were further classified as subisotypes (similarly were the antibodies classified).
j. In humans there are following subisotypes.
1. α à α1, α2 (IgA1, IgA2)
2. Ï’Ã Ï’1, Ï’2, Ï’3, Ï’4 (IgG1, IgG2, IgG3, IgG4)
3. The δ, ε, µ has no subisotypes.
CLASS | H-CHAIN | SUBCLASS | LIGHT CHAIN |
IgM | µ | none | K or λ |
IgE | ε | none | K or λ |
IgG | ϒ | ϒ1, ϒ2, ϒ3, ϒ4 | K or λ |
IgA | α | α1, α2 | K or λ |
IgD | δ | none | K or λ |
Sunday, February 12, 2012
tips for preparing and scoring for the summative assessment ii, class x examination 2012
2. go through the lessons line by line from the N.C.E.R.T text book, all the questions are directly from the book.
3. try to write as concise as possible, don't put useless information in your answers, since science has nothing to do with useless essays and facts, try to write only what you know, and don't just guess answers, it will surely harm you.
4. if possible try to include diagrams/figures wherever possible, whether it is asked in the question or not.
5. for the objective questions, you should have a good concept of all the practicals included in your syllabus, coz the objective questions are all practical oriented conceptual questions, they cant be just guessed and answered.
Saturday, February 11, 2012
summative assessment ii guess paper (science) for class x -2012
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1. MATERIALS REQUIRED A. Milk sample B. Beaker (50 ml, 100 ml, 250 ml) C. 0.5 N H 2 SO 4 D. Sodium ...
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Aim of the experiment : to determine species area curve for sampling of population by quadrate method. Requirements : quadrate of definite...
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by MANOJ KUMAR 1. POTABLE WATER: Water which has been filtered cleaned or treated to meet the standards of drinking water ...