The beginning of a long quest
It was the year 1856 when few limestone excavators working near Düsseldorf, Germany, unveiled bones that resembled to humans and initial analysts inferred them as belonging to a deformed human, citing their oval shaped skull, with a low, receding forehead, distinct brow ridges, and bones that were unusually thick. It was only subsequent studies that revealed that the remains belonged to a previously unknown species of hominid, or early human ancestor, that was similar to our own species, Homo sapiens. In 1864, the specimen was dubbed Homo neanderthalensis, after the Neander Valley where the remains were found.Neanderthals rose to prominance around 200,000 and 250,000 years ago and ruled the hills and grasslands of europe till extiction around 30000 years ago. The exact date of their extinction had been disputed but in 2014, a team led by Thomas Higham of the University of Oxford used an improved radiocarbon dating technique on material from 40 archaeological sites to show that Neanderthals died out in Europe between 41,000 and 39,000 years ago, with the last group disappearing from southern Spain 28,000 years ago.
Similarity of Neanderthals with Rhodesian Man (Homo rhodesiensis) made early investigators infer that they share similar ancestor but comparison of the DNA of Neanderthals and Homo sapiens suggests that they diverged from a common ancestor between 350,000 and 400,000 years ago, which some argue might be Homo rhodesiensis but this argument assumes that H. rhodesiensis goes back to around 600,000 years ago. However one can not rule out convergent evolutionary paths for the two hominids displaying feathres such as distinct brow ridges. Neanderthals settled in Eurasia, but not extending beyond modern day Israel. No neanderthal sites were observed in the African continent and Homo sapiens appears to have been the only human type in the Nile River Valley because of the warmer climate present in that period.
Are Neanderthals really extinct?
Sudden disappearnce of Neanderthals from Europe co-incides with the arrival of H. sapiens and this information prompted many scientists to suspect that the two events are closely linked, and humans contributed to the demise of their close cousins, either by outcompeting them for resources or through open conflict. The hypothesis that early humans violently replaced Neanderthals was first proposed by French palaeontologist Marcellin Boule (the first person to publish an analysis of a Neanderthal) in 1912. However according to a 2014 study by Thomas Higham and colleagues based on organic samples suggest that the two different human populations shared Europe for several thousand years. Therefore outright violent extinction seems less plausible and leads to the formation of two scenarios for Neanderthal extinction.
Possible scenarios for the extinction of the Neanderthals are:
Ancient DNA to the rescue
DNA sequence analysis of the fossils can reveal an entirely new world of information to us, but recovering DNA from samples that are fossilized thousands of years ago, is a daunting task in itself making ancient DNA research far from routine. The samples are prone to degradtion and contamination by DNA from other sources, and retriving data out of the ancient material is costly and painstaking work. At a more fundamental level, it requires determining whether the necessary samples even exist and, if so, how to get access to them.
An international group of Anthropologists from Max Planck Institute for Evolutionary Anthropology, Cold Spring Harbour Laboratories and Cornell University using various different methods of DNA analysis estimated an interbreeding to have happened less than 65,000 years ago, around the time that modern human populations spread across Eurasia from Africa. They reported evidences for a modern human contribution to the Neanderthal genome.
Martin Kuhlwilm, co-first author of the new paper, identified the regions of the Altai Neanderthal genome sharing mutations with modern humans. They found evidences of gene flow from descendants of modern humans into the Neanderthal genome to one specific sample of Neanderthal DNA recovered from a cave in the Altai Mountains in southern Siberia, near the Russia-Mongolia border.
Earlier studies have observed that DNA of modern humans contains 2.5 to 4 percent Neanderthal DNA. However studies conducted by Mendez et. al. revealed that no Neanderthal Y chromosomal DNA was ever observed in any human sample they have tested. Contemplating upon the observations they initially felt that the Neanderthal Y chromosome genes could have drifted out of the human gene pool by chance over the millennia, or there are possibilities that the Neanderthal Y chromosomes include genes that are incompatible with other human genes. Mendez, and his colleagues have found evidence supporting this idea, and they think that the two groups may have been reproductively isolated unlike thought earlier. Their study identified protein-coding differences between Neandertal and modern human Y chromosomes. Changes included potentially damaging mutations to PCDH11Y, TMSB4Y, USP9Y, and KDM5D, and three of these changes are missense mutations in genes producing male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation.
It is possible that these incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups. Thus Y-chromosomal studies have re-drawn the time-line of divergence of the two species ~4 million years ago, which according to previous estimates based on mitochondrial DNA put the divergence of the human and Neanderthal lineages at between 400,000 and 800,000 years ago.
New data emerging out of GWA studies could shed further light on the evolutionary history of the two hominids. In my opinion the image could resolve better if we look into the pathogen associated and immune response genes that we might have inherited or acquired during our evolutionary journey.
This post is written specially keeping it consistent to the C.B.S.E curriculum for class XII. Nevertheless students from other boards can benefit from it too :)
Sexual reproduction in flowering plants (angiosperms) are carried out with the help of sexual organelles of the plant, i.e Flowers.Angiosperms: Angiosperms (Gr. Angios: Covered, Spermae: seed) are plants that have their seeds enclosed in a ovule inside the ovary of their flowers.
There is a huge diversity among flowers of the angiosperms but all flowers have these structures:
The ovary, which may contain one or multiple ovules, may be placed above other flower parts (referred to as superior); or it may be placed below the other flower parts (referred to as inferior).
Structure of Stamen, Anther, Pollen Sac/Microsporangium and Pollen Grain in Plants!
(a) The Stamen:
Stamen in a flower consists of two parts, the long narrow stalk like filament and upper broader knob-like bi-lobed anther (Fig. 2 A). The proximal end of the filament is attached to the thalamus or petal of the flower. The number and length of stamens vary in different species.
b) Structure of anther:
A typical angiosperm anther is bilobed with each lobe having two theca, i.e they are bithecous or dithecous anther is made up of two anther lobes, which are connected by a strip of sterile part called connective. The anther is a four-sided (tetragonal) structure consisting of four elongated cavities or pollen sacs (microsporangia) the four microsporangia are located at the corners, two in each lobe. The microsporangia develop further and become pollen sacs in which pollen grains are produced.(c) Structure of microsporangium
In a transverse section, a typical microsporangium appears circular in outline, consisting of two parts, microsporangial wall and sporogenous tissue.
i) Microsporangial Wall: Includes the epidermis, endothecium, middle layers and the tapetum. The outer three wall layers perform the function of protection and help in dehiscence of anther to release the pollen. The innermost wall layer is the tapetum, its cells have dense cytoplasm, become large, multinucleate and are specialized in nourishing the developing pollen grains.
Functions of Tapetum
It fills the interior of the microsporangium, all the cells are simmilar and called sporogenous cells. Sporogenous cells devide regularly to from the diploid microspore mother cells. The microspore mother cell devides to form pollen grains.
M icrosporogenesis : As the anther develops, the cells of the sporogenous tissue is capable of giving rise to a microspore tetrad. Each one is a potential pollen or microspore mother cell. The process of formation of microspores from a pollen mother cell (PMC) through meiosis is called microsporogenesis. The microspores, as they are formed, are arranged in a cluster of four cells–the microspore tetradmeiotic divisions to form microspore tetrads.
Types of microspore tetrads
As the anthers mature and dehydrate, the wall of the microspore mother cell degenerates and the microspores dissociate from each other and develop into pollen grains. Inside each microsporangium several thousands of microspores or pollen grains are formed that are released with the dehiscence of anther.
Pollen grains are male reproductive propagule or young male gametophyte which is formed in the anther and is meant for reaching the female reproductive organ through a pollinating agent. Pollen grains are generally spherical measuring about 25-50 micrometers in diameter. The pollen grains are coverd by a two-layered wall called sporoderm. The two layers of sporoderm are inner intine and outer exine.
1. Intine: It is the inner wall of the pollen grain and is a thin and continuous layer made up of cellulose and pectin. Some enzymatic proteins also occour in the intine.
2. Exine: The exine is the hard outer layer made up of sporopollenin which is one of the most resistant organic material known. It can withstand high temperatures and strong acids and alkali. No enzyme that degrades sporopollenin is so far known. Pollen grains where sporopollenin is absent can be easily identified by the presence of prominent apertures called germ pores. The exine surface may be smooth, pitted, reticulate, spiny, warty etc, the exine surface sculpting are specific for each type of pollen grain. Pollen grains are also well preserved as fossils because of the presence of sporopollenin, and thus are helpful in studying the evolutionary history of the plant.
The cytoplasm of a mature pollen grain is surrounded by a plasma membrane and contains two cells, the vegetative cell and generative cell. The vegetative cell is bigger, has abundant food reserve and a large irregularly shaped nucleus. The generative cell is small and floats in the cytoplasm of the vegetative cell. It is spindle shaped with dense cytoplasm and a nucleus. In over 60 per cent of angiosperms, pollen grains of a microsporeare shed at this 2-celled stage. In the remaining species, the pollen grain generative cell divides mitotically to give rise to the two male gametes before pollen grains are shed (3-celled stage).
Pollen grains of many species cause severe allergies and bronchial afflictions in some people often leading to chronic respiratory disorders – asthma, bronchitis, etc. However they are rich in neutrients and thus often consumed as food suppliment.
The Pistil, Megasporangium (ovule) and Embryo sac
The female reproductive parts of the flower are knwon as carpels, and are collectively called as gynoecium. Gynoecium may consist of a single pistil (monocarpellary) or may have more than one pistil (multicarpellary). When there are more than one carpel the pistils may be fused together (syncarpous) or may be free (apocarpous).
Each pistil has three parts, the stigma, style and ovary. The stigma serves as a landing platform for pollen grains. The style is the elongated slender part beneath the stigma. The basal bulged part of the pistil is the ovary. Inside the ovary is the ovarian cavity (locule). The placenta is located inside the ovarian cavity.
Structure of a Megasporangium (Ovule)
The ovule is a small structure attached to the placenta by means of a stalk called funicle. The body of the ovule fuses with funicle in the region called hilum. Thus, hilum represents the junction between ovule and funicle. Each ovule has one or two protective envelopes called integuments. Integuments encircle the nucellus except at the tip where a small opening called the micropyle is organised. Opposite the micropylar end, is the chalaza, representing the basal part of the ovule. The main body of the ovule is composed of parenchymatous mass called nucellus. Cells of the nucellus has abundant reserve of food. Located in the nucellus is the embryo sac or female gametophyte. An ovule generally has a single embryo sac formed from a megaspore.
It is the process of formation of haploid megaspore from the diploid megaspore mother cell (MMC). Usually a single MMC differentiates in the micropylar region. It is a large cell containing dense cytoplasm and a prominent nucleus. The MMC undergoes meiotic division. which results in the production of four haploid megaspores, arranged generally in the form of a linear tetrad.
Female gametophyte or Embryo sac: Only one of the megaspores is functional while the other three degenerate. The functional megaspore develops into the female gametophyte (embryo sac).
Pollination is the process of transferring pollen from the stamens to the stigmatic surface in angiosperms or the micropyle region of the ovule in gymnosperms. Depending on the source of pollen, pollination can be divided into three types.
Pollen transfer can be facilitated by the aid of abiotic (wind, water), abiotic (insects, birds, mammals).In some cases, pollen is transferred simply by gravity and the proximity of the anthers to the stigma.
Both wind and water pollinated flowers are not very colourful and do not produce nectar.
3. Zoophily It is a mode of pollination in which the biotic agents bring about pollination in flowering plants. Zoophily has several subtypes eg. Entomophily (by insects) malacophily (by snails ) chiropterophily (by Bats), ornithophilly (by birds eg. Humming bird), myrmecophily (by ants), anthrophily (by Humans).
Flower traits associated with different pollination agents
Advantages and Disadvantages of Cross Pollination
1. A number of plants are self-sterile, that is, the pollen grains cannot complete growth on the stigma of the same flower due to mutual inhibition or incompatibility, e.g., many crucifers, solanaceous plants. Several plants are pre-potent, that is, pollen grains of another flower germinate more readily and rapidly over the stigma than the pollen grains of the same flower, e.g., Grape, Apple. Such plants of economic interest give higher yield only if their biotic pollinators like bees are available along-with plants of different varieties or descent
2. Cross pollination introduces genetic re-combinations and hence variations in the progeny.
3. Cross pollination increases the adaptability of the offspring towards changes in the environment.
4. It makes the organisms better fitted in the struggle for existence.
5. The plants produced through cross pollination are more resistant to diseases.
6. The seeds produced are usually larger and the offspring have characters better than the parents due to the phenomenon of hybrid vigour.
7. New and more useful varieties can be produced through cross pollination.
8. The defective characters of the race are eliminated and replaced by better characters.
9. Yield never falls below an average minimum.
1. It is highly wasteful because plants have to produce a larger number of pollen grains and other accessory structures in order to suit the various pollinating agencies.
2. A factor of chance is always involved in cross .pollination.
3. It is less economical.
4. Some undesirable characters may creep in the race.
5. The very good characters of the race are likely to be spoiled.
As continued self-pollination result in inbreeding depression, flowering plants have developed many devices to discourage self- pollination and to encourage cross-pollination.
Artificial hybridisation is one of the major approaches of crop improvement programme. Here only the desired pollen grains are used for pollination and the stigma is protected from contamination (unwanted pollen). This is achieved by emasculation and bagging techniques. Anthers from the flower bud before the anther dehisces using a pair of forceps is necessary. This step is referred to as emasculation.
Ref: NCERT Biology for Class 12
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It was Charls Darwin in 1859 who first sketched the evolutionary tree in his book The Origin of Species, and since then trees have remained a central metaphor in evolutionary biology even the present day. Today, phylogenetics (Greek: phylé, phylon = tribe, clan, race +genetikós = origin, source, birth)– is the study of the evolutionary history and relationships among individuals or groups of organisms therefore evolutionary trees—have permeated within and increasingly outside evolutionary biology and fostering skills in reading and interpreting trees are therefore a critical component of biological education. Conversely, misconceptions and erroneous understanding of the evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life.
This article is aimed as an aide to students and enthusiasts to read and interpret a phylogenetic tree, however it does not intend to teach how to create one. We can discus that in a separate article later.
So what is an Evolutionary Tree anyway?
In the most simplistic terms, an evolutionary tree—also known as a phylogenetic tree/ cladogram is a 2D graph or diagram depicting biological entities (sequences or species) that are connected through common descent (i.e. their evolutionary relationship). Thus evolutionary trees provide us some basic information regarding: historical pattern of ancestry, divergence, and descent, by depicting a series of branches that merge at points representing common ancestors, which themselves are connected through more distant ancestors. Consider the tree shown below, here you and your siblings share a common ancestor (your parents) and your parents and aunt with their parents, however you and your cousins share the same ancestry but have divergent origins.
Components of a tree
A typical phylogenetic tree as shown above consists of the following components
What's the difference between a dendogram, a phylogenetic tree, and a cladogram?
For general purposes, not much, and many biologists, often use these terms interchangeably. However in the most general terms, tree diagrams are known as “dendrograms” (after the Greek for tree), cladogram only represent a branching pattern; i.e., its branch spans do not represent time or relative amount of character change. While in contrast,trees known as phylograms or phylogenetic trees present branch lengths as being proportional to some measure of divergence between species and typically include a scale bar to indicate the degree of divergence represented by a given length of branch.
Homology Vs Similarity
Now you may say that since closely related species share a common ancestor and often resemble each other, it might seem that the best way to uncover the evolutionary relationships would be with overall similarity? Surprisingly the answer would be No, and to understand why is it so? we will have to look deeper into the difference between similarity and homology.
Similarity may be misleading as because when unrelated species adopt a similar way of life, their body parts may take on similar functions and end up resembling one another due to convergent evolution and result in the formation of analogous features. One classical example is the wings of birds and bats. However when two species have a similar characteristic because it was inherited by both from a common ancestor, it is called a homologous feature (or homology). For example, the even-toed foot of the deer, camels, cattle, pigs, and hippopotamus is a homologous similarity because all inherited the feature from their common paleodont ancestor.
How to read a Phylogenetic tree?
Phylogenetic trees contain a lot of information which can be both qualitative and quantitative, and decoding them is not always straightforward and requires understanding of the above basic facts. Consider the hypothetical tree of different viruses shown below:
Qualitatively here the length of the branches in horizontal dimension gives the amount of genetic change, thus the longer the branch is, larger is the amount of change. While the quantitative information regarding the amount of genetic change is given by the bar at the bottom of the figure which acts as a scale for this. In this case the line segment with the number '0.07' shows the length of branch that represents an amount genetic change of 0.07. The units of branch length are nucleotide substitutions per site – that is the number of changes or 'substitutions' divided by the length of the sequence. The scale may also sometimes represent the % change, i.e., the number of changes per 100 nucleotide sites.
However the vertical lines joining the nodes has no meaning and is used simply to lay out the tree for better visual understanding.
Different presentation schemes of evolutionary trees
Unless indicated otherwise, a phylogenetic tree only depicts the branching history of common ancestry. The pattern of branching (i.e., the topology) is what matters here. Branch lengths are irrelevant. Thus, the three trees shown in here all contain the same information.
This might seem confusing to you at first, but however do remember that that the lines of a tree represent evolutionary lineages--and evolutionary lineages do not have any true position or shape. Therefore it doesn't matter whether branches are drawn as straight diagonal lines, or are kinked to make a rectangular tree, or are curved to make a circular tree.
To further simplify the concept, consider them as flexible pipes rather than rigid rods; similarly, nodes as swivel joints rather than fixed welds. The basic rule is that if you can change one tree into another tree simply by twisting, rotating, or bending branches, without having to cut and reattach branches, then the two trees have the same topology and therefore depict the same evolutionary history.
The battle of our immune system with that of pathogens has been going on for millennia (longer than battle of Avengers and all their their nemesis combined!). The bugle of battle was blown with the occurrence of first multicellular organism 3.5 million years ago and with the rise of first parasite, who knows that it might be our own mitochondria? Its a speculation though, but lack of explanation for its origin and its astounding similarity with prokaryotes, makes it open to any body's guess.
However, in these millions of years both our immune system and pathogens evolved playing the game of hide and seek and developed several weapons in their armory to outsmart each other. Genomic analysis of plants and animals provides evidence that a sophisticated mechanism of host defense was in existence by the time the ancestors of plants and animals diverged. This system, is being shared by plants and animals, and the Toll pathway of NFκB activation is an example, demonstrated conclusively in fruit flies such as Drosophila and in vertebrates such as mice and humans and also believed to occur in plants in the form of Leucin Rich Repeats (LRRs). Now let us introduce ourselves with the three super hero of our immune system.
Granulocyte-Monocyte progenitor cells in the bone marrow differentiate into pro-monocytes, which upon entering blood, further differentiates into mature monocytes. Monocytes circulate in the bloodstream for about 8 h, during which they migrate into the tissues and differentiate into specific tissue macrophages. Enlarge five- to ten fold; its intracellular organelles increase in both number and complexity; and it acquires increased phagocytic ability, produces higher levels of hydrolytic enzymes, and begins to secrete a variety of soluble factors.(Remember Hulk!).
Whenever I think of macrophage it sounds to me like Hulk, and I have reasons to backup the claim, first it is one of the biggest cell observable under microscope with size approx 21 μm (micrometres). Hulk likes to smash, and our macrophage likes to phagocytose its oponents. Macrophages are capable of ingesting and digesting exogenous antigens, such as whole microorganisms and insoluble particles, and endogenous matter, such as injured or dead host cells, cellular debris, and activated clotting factors. Moreover years of selection pressure has made macrophage a more leathal enemy as it equipped itself with many more weapons, such as Opsonization, production of reactive oxygen intermediates (ROIs) and reactive nitrogen intermediates that have potent antimicrobial properties (consider WMDs), along with a group of antimicrobial and cytotoxic peptides, commonly known as defensins. Defensin peptides have been shown to form ion-permeable channels (pores!) in bacterial cell membranes, and can kill a variety of bacteria, including Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli,Pseudomonas aeruginosa, and Haemophilus influenzae. Consider Hulk with a gun huh!
Dendritic Cells (DCs)
Dendritic cells are derived from hematopoietic bone marrow progenitor cells, these progenitor cells initially transform into immature dendritic cells. Dcs acquired its name because it is covered with long membrane extensions that resemble the dendrites of nerve cells. DCs constitutively express high levels of both class II MHC molecules and members of the co-stimulatory B7 family. For this reason, they are more potent antigen-presenting cells than macrophages and B cells, both of which need to be activated before they can function as antigen-presenting cells (APCs). The dendritic cells are constantly in communication with other cells in the body. This communication can take the form of direct cell–cell contact based on the interaction of cell-surface proteins. An example of this includes the interaction of the membrane proteins of the B7 family of the dendritic cell with CD28 present on the lymphocyte. However, the cell–cell interaction can also take place at a distance via cytokines. Following microbial invasion or during inflammation, mature and immature forms of Langerhans cells and interstitial dendritic cells migrate into draining lymph nodes, where they make the critical presentation of antigen to TH cells that is required for the initiation of responses by those key cells. Looks like Captain America isn't it? Flexible, resourceful, communicating crucial intel to raise deffence, planning, integrating and keeps the team going.
Natural Killer Cell (NK cell)
Natural Killer Cell (NK cell)consists of a small population of large, granular lymphocytes that display cytotoxic activity and are analogous to that of cytotoxic T cells. Cytotoxic activity is displayed against a wide range of cells, both viral infected and transformed. If nature could issue a license to kill NK cells would be the best candidate for it because unlike cytotoxic T cells, NK cell can directly induce the death of tumor cells and virus-infected cells in the absence of specific immunization. Armed with an array of receptors that can either stimulate NK cell reactivity (activating receptors eg. NKG2) or dampen NK cell reactivity (inhibitory receptors e.g. KIRs), NK cells are smart like Tony Stark and lethal like Iron Man! However do not think that all this fire power is uncontrolled, it has a very smart control system like JARVIS, which avoids auto-reactivity, by initiating an education system where NK cells acquire self-tolerance. Unlike T-cells however the potentially autoreactive NK cells are not generally clonally deleted but instead a maintained in a state of hyporesponsiveness or anergy. Several findings suggest that the responsiveness of mature NK cells is not fixed but may adapt to a changing environment in vivo. It is observed that persistent stimulation without inhibition results in NK cell hyporesponsiveness, whereas persistent stimulation coupled with commensurate inhibition results in NK cell responsiveness. These results suggest that NK cell tuning might occur throughout the lifetime of the NK cell under steady-state conditions. In infected animals, however, hyporesponsive NK cells are converted to a higher state of responsiveness.
Most of us grow up listening, reading and learning the fact that we "Human" beings can boast of being the most evolved and a higher organism. Earlier than 1960, the image below would have been correct and sensible. However our idea of supremacy in terms of genome size and number of genes takes a flak when we first started looking at the complexity of genome size, it was soon realized that the large genomes were often composed of huge chunks of repetitive DNA, while only a few percent of the genome in these organisms were unique.
Now lets have a look at the past and try to figure out the origin of this concept.
Classically biologists recognize that the living world comprises two types of organisms. Prokaryotes and Eukaryotes. Assuming that you already know what prokaryotes and eukaryotes are, I am not going to dive into the difference between the two.
So what is C-value?
'C-value ', of an organism is defined as the total amount of DNA contained within its haploid chromosome set. Prokaryotic cells typically have genomes smaller than 10 megabases (Mb), while the genome of single cell eukaryote is typically less than 50Mb. Therefore for simplicity's sake here we are not comparing the genomes from two classes of organisms together.
However eukaryotes alone show immense diversity among their genome sizes, from the smallest eukaryote being less than 10 Mb in length, and the largest over 100 000 Mb, and all these observation seems coinciding to a certain extent with the complexity of the organism, the simplest eukaryotes such as fungi having the smallest genomes, and higher eukaryotes such as vertebrates and flowering plants having the largest ones.
So it seems fair to think that, complexity of an organism is related to the number of genes in its genome - higher eukaryotes need larger genomes to accommodate the extra genes. However, in fact this correlation is far from being precise: if it were, then the nuclear genome of the yeast S. cerevisiae, which at 12 Mb is 0.004 times the size of the human nuclear genome, would be expected to contain 0.004 × 35 000 genes, which is just 140. In fact the S. cerevisiae genome contains about 5800 genes! Therefore for many years this lack of precise correlation between the complexity of an organism and the size of its genome was looked on as a bit of a puzzle, and called as C-value paradox/C-value enigma.
Questions raised by C-value paradox
The C-value paradox not only represents one question, but it rather raises three of them, as suggested by T. R. Gregory(2007), 1) the generation of large-scale variation in genome size, which may occur by continuous or quantum processes, (2) the non-random distributions of genome size variation, whereby some groups vary greatly and others appear constrained, and (3) the strong positive relationship between C-value and nuclear and cell sizes and the negative correlation with cell division rates. Therefore any proposed solution must try to solve these three problems as well.
Now we biologists are pretty good at dividing ourselves among different school of thoughts (remember the RNA and DNA world!) and the C-value paradox wasn't an exception either. Nonetheless two school of thoughts emerged here too, one proposing Mutation pressure theories and the other proposing Optimal DNA theories.
The table shown below summarizes the theories proposed along with their proposed mechanism. Each theory can be classified according to its explanation for the accumulation or maintenance of DNA (MP,mutation pressure theory ; OD, optimal DNA theory) and according to its explanation for the observed cellular correlations (CN, coincidental, CE, coevolutionary, CA, causative). Note that these theories are not necessarily mutually exclusive in all respects, since the optimal DNA theories do not specify the mechanism(s) of DNA content change and can include those presented by both mutation pressure theories. (ref: GREGORY, T. R. (2001),page # 69)
So what is the most plausible explanation of C-value paradox?
In 1980s, two landmark papers, by Orgel and Crick and by Doolittle and Sapienza, established a strong case against 'selfish DNA elements' which we better know as transposons. They proposed that ‘selfish DNA’ elements, such as transposons, essentially act as molecular parasites, replicating and increasing their numbers at the (usually slight) expense of a host genome, i.e these elements functions for themselves while providing little or no selective advantage to the host. Computational genomic studies have shown that transposable elements invade in waves over evolutionary time, sweeping into a genome in large numbers, then dying and decaying away leaving the 'Junk DNA' in its trail. 45% of the human genome is detectably derived from these transposable elements. Therefore we can say that C-value paradox is mostly (though not entirely) explained by different loads of leftovers from transposable elements and larger the genomes longer is the trail leftover by transposons.
So, if the C-value paradox is explained and rested for good, why dig it up again?
Recent publications discussing the outcome of ENCODE (Encyclopedia Of DNA Elements) project suggest that 80% of the human genome is reproducibly transcribed, bound to proteins, or has its chromatin specifically modified. Moreover the previously considered junk DNA is found to be biochemically active disapproving the 'Junk DNA' theory.
Now in the light of ENCODE data it is pertinent that scientists need to come up with a alternative hypothesis capable of explaining C-value paradox, for mutational load, and for how a large fraction of eukaryotic genomes is composed of neutrally drifting transposon-derived sequences.
The Toll family of receptors
Toll Like Receptors or TLRs are type I transmembrane proteins of the Interleukin-1 receptor (IL-1R) family that possess an N-terminal leucine-rich repeat (LRR) domain for ligand binding, a single transmembrane domain, and a C-terminal intracellular signaling domain. The TLR C terminus is homologous to the intracellular domain of the IL-1R and is thus referred to as the Toll/IL-1 receptor (TIR) domain. TLRs are expressed at the cell membrane and in sub cellular compartments such as the endosomes and are widely expressed in many cell types, including non hematopoietic epithelial, endothelial cells. Although most cell types express only a select subset of these receptors. However hematopoietically derived sentinel cells, such as macrophages, neutrophils, and dendritic cells (DCs), express most of the TLRs, with some variation in different subsets, e.g., between conventional DCs and plasmacytoid DCs. Thus far, 13 mammalian TLRs, 10 in humans and 13 in mice, have been identified (Beutler 2004). TLRs 1– 9 are conserved among humans and mice, yet TLR10 is present only in humans and TLR11 is functional only in mice. Although much is known about the ligands and signaling pathways of TLRs 1–9 and 11, the biological roles of TLRs 10, 12, and 13 remain unclear, as their expression patterns, ligands, and modes of signaling have yet to be defined.
TLRs mediate initial responses in innate immunity and are required for the development of the adaptive immune response. Toll-like receptors (TLRs) enable innate immune recognition of endogenous and exogenous prototypic ligands. They also orchestrate innate and adaptive immune response to infection, inflammation, and tissue injury. Given their significance in the immune response, it is not surprising that genetic variations of TLRs can affect their function and by extension affect the response of the organism to environmental stimuli. The genetics of TLRs provides important insights in gene-environment interactions in health and disease, and it may enable scientists to assess patients’ susceptibility to diseases or predict their response to treatments.
Evolutionary genetics of TLRs
In the domain of the evolutionary genetics of infectious diseases, the aim is to identify the evolutionary footprints of natural selection exerted by past infections in the genome of present day healthy human populations. Given the tremendous selective pressure that pathogens have exerted in the past, and continue to exert, it is hardly surprising that some of the strongest evidence for selection, of various types and intensities, in the human genome has actually been obtained for genes involved in immunity or host defense as immunity related functions seem to be a privileged target of natural selection in the human species as a whole (with respect to other primates) and in different human populations from diverse geographic regions.
Phylogenetic studies have indicated an ancient origin for TLR genes, some 700 million years ago, suggesting that TLR-mediated immune responses originated in the common ancestor of bilaterian animals. However, several recent, independent lines of evidence genomic, phylogenetic, and functional data have suggested that the similarities and differences between TLR-mediated innate immunity functions in insects and vertebrates may instead have resulted from convergent evolution. Convergent evolution refers the phenomenon where organisms that are not closely related independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. Another study showed that vertebrate TLRs can be divided into six major families, with all the TLRs within a given family recognizing the same general or speciﬁc class of microbial compound. The patterns of interspecies divergence and levels of polymorphism in various primates, including humans, have recently been investigated. Signatures of accelerated evolution (species-wide positive selection) was found across primate species for most TLRs, with the strongest evidence of this obtained for TLR1 and TLR4, which have been independently targeted by positive selection. However, within each primate species, the patterns of nucleotide variation were generally constrained.
TLRs and Diseases
TLRs In Pulmonary Diseases
Current data suggest that TLR signaling can modify both allergic asthma and chronic obstructive pulmonary disease (COPD). Activation of TLRs can be either beneﬁcial or detrimental depending on many host factors, as well as dose, duration, and intensity of expo-sure to TLR ligands. Multiple epidemiologic studies have associated childhood exposure to TLR ligands with protection against develop-ing allergic asthma later in life (the “hygiene hypothesis”); for example, individuals living on farms have a reduced risk of developing hay fever or asthma. The most extensively studied TLR is TLR4. A study of asthma speciﬁcally associated with LPS in house dust showed that people with the TLR4 polymorphism Asp299Gly had a de-creased risk of bronchoreactivity. These observations are consistent with the hypothesis that LPS can exacerbate existing airway inﬂammation and that individuals with the Asp299Gly polymorphism have diminished pulmonary responses to LPS.
TLRs In CardioVascular Disease
Atherosclerosis is an inﬂammatory process, and innate immunity has been shown to par-ticipate in the development and rupture of atherosclerotic plaques. TLR4 polymorphisms that render the receptor less responsive to its ligands would therefore be expected to hinder the development and progression of atherosclerosis. Indeed, the Asp299Gly poly-morphism has been associated with decreased atherosclerosis, decreased risk for acute coronary events , and an improved re-sponse to statin treatment. The exact mechanism of this beneﬁcial effect is un-known; however, TLRs are expressed on several cells that participate in the atherosclerotic plaque, such as macrophages, dendritic cells, endothelia, smooth muscle cells, and lymphocytes. As the involvement of innate immunity in atherosclerosis is better understood, more genetic factors are likely to be discovered to inﬂuence both the suscep-tibility to cardiovascular disease and the response to treatment.
TLRs In Cancer
In Cancer inﬂammation acts as a double-edged sword. On one hand, chronic inﬂammation is associated with carcinogenesis, and cancer is a complication of chronic inﬂammatory conditions such as Crohn’s disease, chronic cystitis, and hepatitis. TLR activation leads to production of NF-κ B, which is associated with carcinogenesis and chemoresistance On the other hand, the immune system is necessary for the elimination of malignant cells, and immunosuppressed patients are a risk for the development of cancer. Immunotherapy (i.e., use of the patient’s own immune system to combat cancer, with the aid of vaccination or adjuvants) has been gaining attention as a potential treatment option in cancer. Indeed, we are only now beginning to understand how cancer cells evade elimination by modifying the innate and adaptive immune responses of the host. Activation of the immune system may therefore be a viable approach to cancer therapy.
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Hello! My name is Arunabha Banerjee, and I am the mind behind Biologiks. Leaning new things and teaching biology are my hobbies and passion, it is a continuous journey, and I welcome you all to join with me