The major goal for genomics is that to determining the sequence of molecules that make up the genomic content of an organism. The genes are contained in the chromosomes and it can be further described as containing the fundamental units of heredity. These genes are known as transcriptional unit, those regions of chromosomes that under appropriate circumstances are capable of producing RNA then these RNA is translated into molecules of protein.
Basically human genome variants causes’ difference between individuals include the exchange of genes during meiosis and various mutational events. The usual reasons for genetic variation exists between populations one is all about Natural selection and the other one is Neutrality of most mutations due to the random drift. Studies proved that Human genome variants have both evolutionary significance and medical applications. Evolutionary significance is to understand ancient human population as well as how the different human groups are biologically related to one another, in the case of medicine some disease causing alleles occur more often in people from specific geographical regions.
A specific condition which may cause by the alteration or mutation of a specific gene will lead to particular disorders; these single gene disorders are often heritable so that single gene disorder may be at risk for passing the condition onto their children.
The fact is quite essential to know that how do mutations occur in genome. Gene mutation is a permanent change in DNA sequence that makes up a gene.
The mutations can occur in two ways, one can be through inherited from a parent or acquired during a person’s lifetime.
Mutations passed from parent to child are called hereditary mutations or germ line mutations. This type of mutations is present throughout a person’s life in virtually every cell cycle in the body. Some mutations are called De novo mutations, these kinds of mutations are occur only in egg or sperm cell, or those that occur just after fertilization, so this mutations are also called new mutation. Denovo mutations may specify genetic disorders in which an affect child has a mutation in every cell, but it has no family history of the disorder. But in the case of acquired mutations occur in the DNA of individual cells at some time during a person’s life. Environmental factor such as ultraviolet radiation from the sun or can be the cause of these mutation. Also it can occur if mistake is made as DNA copies itself during cell division (mitosis) so that it cannot be passed in to the next generation, but in the failure in the DNA mechanism then the mutation can be passed to future copies of the altered cell.
Single cell within an early embryo may also occur mutation in single cell .As all the cell divide during growth and development, the individual will have some cells with the mutation and some cells without the genetic change and this situation is called mosaicism.
Some genetic changes are very rare; others are common in the population. Genetic changes that occur in more than 1% of the population are called polymorphisms. These are considered to be as a normal variation in the DNA.
Any way by changing gene’s instruction for making a protein a mutation can cause the protein to malfunction or to be missing entirely. Here we can say that the condition caused by mutation in one or more genes is called a genetic disorder, these genetic disorder causes the disease by making a gene function improperly.
There are number of ways of alteration can be happen in DNA sequence, depends up on their occurring place and alteration in the function of essential proteins gene mutations have varying effects on health. Basically the types of
Missense mutation will make a change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene.
An insertion changes the number of DNA bases in a gene by adding a piece of DNA. As a result, the protein made by the gene may not function
Deletion changes the number of DNA bases by removing a piece of DNA .The deleted DNA may alter the function of the resulting proteins, so the small deletions may remove one or a few base pairs within a gene, while larger deletion can remove an entire gene or several neighbouring genes.
Duplication in DNA sequence will alter the function of the resulting protein a duplication consists of a piece of DNA that is abnormally copied one or more times.
Frame shift mutation is a type of mutation occurs when the addition or loss of DNA bases changes a gene’s reading frame. Basically a reading frame consists of groups of 3 bases that each code for one amino acid. A frame shift mutation shifts the grouping of these bases and challenges the code for amino acids. Then the resulting protein is usually non-functional, so that the frame shift mutation can be Insertions, deletion.
Repeat expansion is a kind of nucleotide repeats which are short DNA sequence that are repeated a number of times in a row. A tri nucleotide repeat is made up of 3-base-pair sequence, and a tetra nucleotide repeat is made up of 4-base-pair sequences. A repeat expansion is a mutation that increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly.
Mutation and Disease
DNA is constantly subject to mutations, accidental changes in its code. Mutations can lead to missing or malformed proteins, and that can lead to disease.
We all start out our lives with some mutations. These mutation inherited from your parents are called germ-line mutations.
Generally some mutations are bad for the human body but some mutations can be beneficial. To keep population healthy genetic mutations create genetic diversity, many mutations have no effect at all and these mutations are called silent mutations. But the common mutations which were most concerned mutations are which causing disease’s mostly those diseases are happening due to the mutation of a single gene. Most inherited genetic diseases are recessive that means a human must inherit two copies of the mutated gene to inherit a disorder. Diseases caused by a one copy of a defective gene are rare.
But the high impact of natural selection make these dominant genetic diseases tend to get weeded out of populations over time, because afflicted carriers are more likely to die before reproducing.
CFTR are one of the mutated genes this will provide instruction for making a protein called the cystic fibrosis transmembrane conductance, regulator. This protein will produce mucus, sweat, saliva, tears and digestive enzymes. CFTR regulates the channels which transport negatively charged particles and positively charged particles. These channels are necessary for the normal function of organs such as the lungs and pancreas. The most common gene changes involves a single base mismatch a misspelling.. Placing the wrong base in the DNA. At other times, a single base may be dropped or added. And sometimes large pieces of DNA are mistakenly repeated or deleted.
Single Gene Disorder:
The condition caused by the alteration or mutation of a specific gene, these single gene disorders are often heritable, so single gene disorder may be at risk for passing the condition onto their children.
Examples for single gene disorders are: – Cystic fibrosis, Sickle cell anaemia, Tay-sachs disease etc.
In this work the influence of bioinformatics and computational biology is very high, because this work can be go forth only with help of Data bases, tools and programming.
The Data base like OMIM plays a key role because OMIM stands for online mendelian inheritance in man. It is a catalogues of all the known disease with the genetic component and link the disease to the relevant genes in the human genome for further research and tools for genomic analysis of catalogued gene. Basically omim is hosted in the US national centre for biotechnology information (NCBI) .Omim is an abstract of human genes and genetic phenotypes that is freely available and updated daily. Information on all known genetic mandalian disorders and over 12,000genes.
So with the help of Natural Language Processing we can extract key words from this data base and compare with symptoms in any case sheet and identify which disease are belongs to mutations.
Natural language processing is a field of computer science which will concerned with interactions between computers and human natural languages. That is the computers should understand human natural language which enables computers to derive meaning from human or natural language input. Computers use, analyze, understand, generate natural language. It’s originates aprox five decades ago with machine translation systems. Currently NLP includes a wide variety of linguistic theories, cognitive models, and emerging approaches.
The interactive application may be classified along the Speech recognition understanding and synthesis, generation, Natural Language Interfaces, Discourse Management, story Understanding and text generation, Interactive machine translation, Intelligent writing assistants. NLP provides mechanisms for incorporating natural language knowledge and modalities into user interfaces.
By the application of NLP we could easily recognize the language that we required, through this way we can extract the keywords from the Omim database and based on the semantic equivalence compare with the case sheet data and find out the disorders. The semantic equivalence can be find out when we integrate the context distance means finding closeness of word meanings model with morphological analysis.
Then using the tool Alchemyapi which is based on the natural language processing, here API will employ complex linguistic, statistical and natural network algorithms, alchemyapi is able to read and understand text at massive rates of speed. This tool offers a suite of text analysis functions that can add understanding and semantic data to your text content. These functions are all accessed via a REST API and the data is returned as an easy to pores structure that can be integrated in to our application.
So using this application we do keyword extraction – which extract the important terms. Basically keyword are the important topics in our content and can be used to index data, generate tag clouds or for searching. Alchemyapi is capable for finding keywords in text and ranking them. Alchemyapi automatically detects the language of the content and then performs the appropriate analysis. Api puts statistical algorithms and natural LP technology to analyze our content and identify the relevant keywords, and this tool will ranked based on the relevance here the relevance score is calculated for each keyword based on the statistical analysis, and the result are returned sorted by relevancy.
Ultimately through this work will make doctors to easily recognize the diseases related to the symptoms.
Also we could recognize which mutation causes certain disorders.
If we under stood what makes these diseases may be what kind of mutation leads to certain disorders , hopefully we could look forward for the treatments and medicine .
Experimental Design and the Importance of Controls
Were the conclusions you drew from your submitted manuscript valid? Explain your reasoning.
The conclusions are invalid as there is little supporting evidence and controls are absent. There are no controls within either experiment and so the variables have not been investigated. For example, in the first experiment, without controls, it is difficult to distinguish between the effects of the inhibitor and ricin on protein synthesis. Furthermore, in the second experiment, without a galactose control, it is impossible to determine whether yeast cells grow successfully on this carbon source.
Even when controls are implemented, research has shown that ricin is “a poor substrate for proteasomal degradation” (Pietroni, et al., 2013) and that an increase in ricin sensitivity “simply reflects toxicity of the inhibitors themselves” (Pietroni, et al., 2013).
The conclusion that proteasome up-regulation could be a potential therapeutic is invalid as this would be more likely to inflict toxic effects on the cell (by disrupting cell homeostasis). Also, applying the same therapy for Shiga and ricin poisoning would be ineffective. Although both Shiga and ricin toxins utilise endocytosis as a mechanism for entering the cell, the downstream proteins that they bind to are significantly diverse.
What controls should have been performed to support (or negate) your conclusions?
Within the first experiment, a dimethyl sulphoxide (DMSO) control should have been included. DMSO may have possible interactions with clasto Lactacystin β-lactone (cLβ-1) and may enhance its potency as an inhibitor. Therefore, this could result within the IC50 of cLβ-1 being lower than would normally be expected. Also, it could be that DMSO itself may be interfering with protein synthesis.
Another control that was required was the independent testing of cLβ-1. It could be that cLβ-1 is itself exerting toxic effects on the cell (such as through its indirect effects of targeting other proteases and consequently deregulating cell homeostasis) and is therefore responsible for the increased reduction in protein synthesis. A different protease inhibitor such as pepstatin should be included. As this does not target the proteasome, then a wild-type response would be observed. A positive control of protein inhibition is also required (such as neomycin). Figure 1 illustrates a potential new plate layout.
In the yeast expression study, the choice of carbon source rather than the toxic effects of the A chain (RTA) may have affected the growth of the yeast. Research “discovered that glucose withdrawal from the growth medium led to a rapid inhibition of protein synthesis” (Ashe, et al., 1999). The control could have included yeast cells that were transformed with a plasmid containing a galactose-inducible protein that was not toxic. The yeast could have been subsequently grown on a galactose medium. If there was little growth of yeast then this would suggest that galactose was a mediocre carbon source.
How can the experimental design be improved?
The experiment on HeLa cells could be improved by completing a serial dilution of the cLβ-1 in DMSO. This would determine the effects of different concentrations of inhibitor on protein synthesis and would provide a more accurate IC50. The investigator could also conduct a cell count to ascertain if too high a concentration of inhibitor exerts toxic effects on the cell. From this, the investigator could identify the optimal concentration of inhibitor to be used within the assay in the presence of ricin. If this was to be undertaken, a serial dilution of DMSO in growth medium should also be performed. This would ensure that there was a DMSO control for each concentration of inhibitor.
The investigators only studied one time point within their experiment (ricin was incubated with HeLa cells for 6 hours). The investigators could perform a time series alongside a serial dilution to ascertain the time point and concentration in which ricin exerts the greatest toxic effect.
The experiment could also be repeated several times to ensure that the results collected are not simply down to chance. Statistical analysis, such as a two-tailed t-test could be conducted to ascertain whether there is a significant difference between the effects of ricin alone and treatment with ricin and cLβ-1 on protein synthesis. Error bars should be included within the new figure generated.
In the yeast expression study, the yeast could be grown within liquid culture so that a cell count could be conducted using a haemocytometer. The gene CUP1 (confers copper resistance and is specifically found within yeast) could be incorporated into the plasmid under the same galactose-inducible promoter that controls RTA (Koller, et al., 2000). This would ensure that both the RTA gene had been inserted into the plasmid and that transformation of yeast was successful. Little or no growth of yeast cells in the presence of copper would imply that yeast had not been transformed successfully.
Design a new experiment or experiments to test a proposition related to the content already presented.
One experiment could investigate how some of the cytosolic RTA is able to avoid degradation by the proteasome. Research has suggested that several toxins, including ricin have a low number of lysine residues (Deeks, et al., 2002). Ubiquitination may possibly occur at these residues and therefore, if few lysine residues are present, this may decrease the probability of polyubiquitination. As a consequence, the toxin will not be targeted to the proteasome. The number of lysine residues could be increased (however without affecting RTA’s function and stability) to create a polyubiquitination tag and whether this subsequently targets the RTA to the proteasome. Both wild –type and mutant forms of RTA could be run on an SDS-PAGE; if the mutant RTA band is absent from the gel then this suggests that it is possibly degraded by the proteasome.
Recent research has suggested that “Hsc70 cochaperone activity determines the fate of dislocated RTA” (Spooner, et al., 2008). One experiment could include reducing expression of specific chaperones and their cochaperones to identify those that are either required for ricin refolding or its targeting to the proteasome.
A pulse chase experiment could be conducted within yeast, with RTA being radiolabelled to track its location and pathway throughout the cell. This can ascertain whether it interacts with the proteasome. Also, this enables the percentage of RTA that avoids the proteasome to be calculated. Mutagenesis of E3 ligase and the proteasome can be created to see if this affects the movement and location of RTA.
Ashe, M., Long, S.