Bioinformatics Project Final

1. Protein information

Protein information; location in the body as function of time and place; active site; function; functioning; nearest homologous families; is the structure of the protein known, or if not, is there a homolog in the PDB from which the structure could be modelled by homology (full length or domain only); if the structure is known, where are the mutations located on the structure and which effect do you expect from the mutation (protein won't fold, reduced binding to receptor, etc); domain structure of the protein; other functional sites; etc.

Disease: Type 1 diabetes

Protein: Insulin

Location in the body: Insulin is produced by beta cells in the pancreas

Active site of insulin: Insulin attaches and signals to the cells to absorb sugar which is used as energy in the bloodstream.

Function of Insulin: Insulin plays several roles in the body.

The key role of insulin is controlling blood glucose level in the body. When blood glucose level rises, the amount of insulin secreted into the blood increases. Similarly, when blood glucose level falls, the amount of insulin secreted into the blood decreases. Insulin controls blood glucose levels by signalling cells to take in glucose and ensures there is sufficient amount of glucose produced by the liver. When there is low levels of insulin in the body, it signals the liver to produce and release more insulin. When there is high levels of insulin in the body, it signals the liver to take in and store glucose as glycogen to prevent glucose production.

Another role of insulin is to promote synthesis of fatty acids in the liver. As the liver is full of glycogen from high levels of insulin in the body, additional glucose taken in by the liver is released as lipoprotein. Lipoprotein is then ripped apart to produce fatty acids which are used as tissues and adipocytes to form triglycerides. Insulin also helps to accumulate triglyceride in fat cells. Lipoproteins are molecules made up of proteins and lipids. They allow fats to be carried to the bloodstream.

Nearest homologous family of Insulin: Relaxin Peptide Family

Relaxin Family Peptides belong to the human insulin superfamily of polypeptide hormones which consists of seven Relaxin family peptides. The seven Relaxin family peptides have two subfamilies of Relaxin peptides and insulin-like peptides. There are three relaxin peptides - Relaxin-1, Relaxin-2, Relaxin-3 and four insulin-like peptides - insulin-like peptide-3 (INSL3), insulin-like peptide-4 (INSL4), insulin-like peptide-5 (INSL5), insulin-like peptide-6 (INSL6).

Relaxin Family Peptides are structurally similar to insulin and play a wide variety of psychological roles in humans. They are bound to G-protein coupled receptors (GPCRs) and Relaxin family peptide receptors 1-4 (RXFP1-4). GPCRs act as messengers to inform cells about the presence/absence of nutrients in an environment and convey information sent by other cells. RXFP1-4 are for glycoprotein hormones such as follicle-stimulating hormone (TSH) and thyroid-stimulating hormone (TSH).

Relaxin, Relaxin peptides and Insulin-like peptides

Relaxin consists of 53 amino acid peptides containing six cysteine residues to form three disulphide bonds - one intra chain within A-peptide chain and two inter-chain disulphide bonds between A- and B-peptide chains. It plays roles in male and female reproduction, neuropeptide in the central nervous system (CNS). A Relaxin gene produces Relaxin peptides that circulate in the blood during pregnancy. This shows that Relaxin plays a role in early stages and cardiovascular changes of pregnancy. Insulin-like peptides play key roles in metabolism, growth, reproduction and ageing.

Relaxin-1, Relaxin-2 and Relaxin-3

Structure: Relaxin-1, 2 and 3 have three disulphide bonds and a two-chain structure that consist of A- and B- peptide chains. Although relaxin-3 has similar structures as relaxin-1 and 2, it cannot be prepared by combining individual chains together. It uses regioselective disulphide bond strategy. Relaxin-3 is acquired by solid phase synthesis of the separate, selectively S-protected A- and B- peptide chains and their purification and subsequent stepwise formation of each of the three disulphide bonds.

Function: Relaxin 1 and 2 enhances sperm motility, regulates blood pressure, controls heart rate and releases oxytocin and vasopressin. They also play key roles in inflammatory and matrix remodelling processes. Furthermore, relaxin-2 is the only relaxin to circulate in the blood. Relaxin 3 activates and binds to native Relaxin receptors in vitro and stimulates water drinking through central Relaxin receptors in vitro.

INSL3, INSL4, INSL5 and INSL6

Structure: INSL3, 4, 5 and 6 consist of three disulphide bonds and a complex two-chain hormone.

Function: INSL3 plays a key role in testicular descent during pregnancy and is a large gender-specific hormone in bone metabolism. It is a parameter in comparing testosterone and is used to assess Leydig cell functional capacity in testes and to analyse factors affecting hypothalamic pituitary gonadal axis. INSL4 plays key roles in trophoblast development of placenta and uterus and in bone development. INSL5 plays a key role in regulation of insulin secretion and beta cell homeostasis. It is also an orexigenic gastrointestinal hormone released from colonic L-cells that promotes appetite when energy levels are low. INSL6 is produced by the body and it relays growth signals to the body. It plays a key role in male fertility and promotes growth during nutritional deprivation.

What is the active site of a protein?

It consists of both the secondary and tertiary structures, proteins adopt specific shapes. The spot at which two molecules with specific shapes fit together to interact is called the active site. This active site is the basis of the lock and key model. The active site is called active because interaction of the molecules in this way usually results in some chemical change or reaction. Figure 1 is a representation of a small molecule (green helix) interacting with a large molecule (gray globular shape with yellow, orange and red colors) in the active site. The colored regions indicate where the large molecule touches the small one. (Refer to figure 1)

What is the structure of the protein(insulin)?

Normal insulin that is biologically active is monomeric or exists as a single molecule. It has two long amino acid chains or polypeptide chains. The chains are chain A with 21 amino acids and chain B with 30 amino acid. (Refer to figure below)

Where are the mutations located on the structure?

Mutations located at the insulin gene cause disorders of glucose homeostasis through effects of the mutant insulin on beta cell function, insulin receptor affinity, or processing of proinsulin to insulin. The effects of the mutations on glucose homeostasis are variable with associated phenotypes ranging from permanent neonatal diabetes with complete insulin deficiency to near-normal glucose homeostasis. Maturity-onset diabetes of the young (MODY) and type 1b diabetes mellitus are other clinical manifestations of heterozygous insulin gene mutations.

What effects do you expect from the mutation?

As gene mutations can prevent one or more of these proteins from working properly. By changing a gene’s instructions for making a protein, a mutation will result in the protein to malfunction or to be missing entirely. When a mutation alters a protein that plays a critical role in the body, it will disrupt the normal development or cause a medical condition. A condition caused by mutations in one or more genes is called a genetic disorder.

2. Disease symptoms

Disease; symptoms; other diseases caused by the same protein(insulin); are receptors involved and if so what do you know about them; can a diet or other conditions help the patient; what is the life-expectancy; how did the disease get its name; etc.

What is Type 1 diabetes?

Type 1 diabetes is a chronic (lifelong) disease in which there is high blood glucose or hyperglycemia in your blood. It occurs during childhood (most of the cases) but can also occur in adults. It is caused by genetic, autoimmunity or viral infection. It is a more severe form of diabetes in which the pancreas produces little or no insulin due to non-functional beta cells. In type 1 diabetes, the body’s immune system attacks the pancreas as it mistakenly sees insulin-producing beta cells in the pancreas as foreign substances and destroys them.This autoimmune destruction progresses without notice over time until the mass of these cells decreases to the extent that the amount of insulin produced is insufficient for controlling blood glucose levels in the body.

How can insulin damage the body?

Insulin is produced by beta cells in the pancreas to control blood glucose levels in the body. It can damage the body when the body stops making insulin due to type 1 diabetes which causes insulin to not function properly. Insulin serves as a “key” to open your cells and allows glucose to enter to use it as energy for the body. Without insulin, there is no “key.” Hence, glucose does not enter your cells but instead builds up in your blood. The cells starve and die from the lack of glucose.

The building of glucose in your blood causes high blood glucose, which can lead to:

Dehydration. When there’s extra sugar in your blood, you pee more. That’s your body’s way of getting rid of it. A large amount of water goes out with that urine, causing your body to dry out.
Weight loss. The glucose that goes out when you pee takes calories with it. That’s why many people with high blood sugar lose weight. Dehydration also plays a part.
Diabetic ketoacidosis (DKA). If your body can't get enough glucose for fuel, it breaks down fat cells instead. This creates chemicals called ketones. Your liver releases the sugar it stores to help out. But your body can’t use it without insulin, so it builds up in your blood, along with the acidic ketones. This combination of extra glucose, dehydration, and acid buildup is known as "ketoacidosis" and can be life-threatening if not treated right away.
Damage to your body. Over time, high glucose levels in your blood can harm the nerves and small blood vessels in your eyes, kidneys, and heart. They can also make you more likely to get hardening of the arteries, or atherosclerosis, which can lead to heart attacks and strokes.

What are the symptoms?

The symptoms of type 1 diabetes are often subtle, however they can also be severe. They consists of:

Heavy thirst
Increased hunger (especially after eating)
Dry mouth
Nausea and vomiting
Pain in your belly
Frequent urination
Unexplained weight loss (even though you’re eating and feel hungry)
Fatigue (weak, tired feeling)
Blurred vision
Heavy, labored breathing (your doctor will call this Kussmaul respiration)
Frequent infections of the skin, urinary tract, or vagina

What are the complications?

Type 1 diabetes can affect major organs in your body, including heart, blood vessels, nerves, eyes and kidneys. Keeping your blood sugar level close to normal most of the time can dramatically reduce the risk of many complications.

Long-term complications of type 1 diabetes develop gradually, over decades. Good blood sugar management can help lower the risk of complications. Eventually, diabetes complications may be disabling or even life-threatening.

Heart and blood vessel disease. Diabetes dramatically increases your risk of various cardiovascular problems, including coronary artery disease with chest pain (angina), heart attack, stroke, narrowing of the arteries (atherosclerosis) and high blood pressure.
Nerve damage (neuropathy). Excess sugar can injure the walls of the tiny blood vessels (capillaries) that nourish your nerves, especially in the legs. This can cause tingling, numbness, burning or pain that usually begins at the tips of the toes or fingers and gradually spreads upward. Poorly controlled blood sugar could cause you to eventually lose all sense of feeling in the affected limbs.
Damage to the nerves that affect the gastrointestinal tract can cause problems with nausea, vomiting, diarrhea or constipation. For men, erectile dysfunction may be an issue.
Kidney damage (nephropathy). The kidneys contain millions of tiny blood vessel clusters that filter waste from your blood. Diabetes can damage this delicate filtering system. Severe damage can lead to kidney failure or irreversible end-stage kidney disease, which requires dialysis or a kidney transplant.
Eye damage. Diabetes can damage the blood vessels of the retina (diabetic retinopathy), potentially leading to blindness. Diabetes also increases the risk of other serious vision conditions, such as cataracts and glaucoma.
Foot damage. Nerve damage in the feet or poor blood flow to the feet increases the risk of various foot complications. Left untreated, cuts and blisters can become serious infections, which often heal poorly and may ultimately require toe, foot or leg amputation.
Skin and mouth conditions. Diabetes may leave you more susceptible to skin problems, including bacterial and fungal infections.
Pregnancy complications. High blood sugar levels can be dangerous for both the mother and the baby. The risk of miscarriage, stillbirth and birth defects are increased when diabetes isn't well-controlled. For the mother, diabetes increases the risk of diabetic ketoacidosis, diabetic eye problems (retinopathy), pregnancy-induced high blood pressure and preeclampsia.

Furthermore, there are also short term Diabetes Complications which is known as Hypoglycemia. Hypoglycemia is low blood glucose (blood sugar). It develops when there’s too much insulin—meaning that you’ve taken (or given your child) too much insulin or that you haven’t properly planned insulin around meals or exercise. Other possible causes of hypoglycemia include certain medications (aspirin, for example, lowers the blood glucose level if you take a dose of more than 81mg) and alcohol (alcohol keeps the liver from releasing glucose).

There are three levels of hypoglycemia, depending on how low the blood glucose level has dropped: mild, moderate, and severe. If you treat hypoglycemia when it’s in the mild or moderate stages, then you can prevent far more serious problems; severe hypoglycemia can cause a coma and even death (although it is very rare).

Can the protein (insulin) cause any other disease besides Type 1 diabetes?

It can also cause type 2 diabetes or known as non-insulin-dependent diabetes mellitus. This begins as a syndrome of insulin resistance. That is, target tissues fail to respond appropriately to insulin. Typically, the onset of this disease is in adulthood. Despite monumental research efforts, the precise nature of the defects leading to type II diabetes have been difficult to ascertain, and the pathogenesis of this condition is plainly multifactorial. On the other hand, Obesity is clearly a major risk factor, but in some cases of extreme obesity in humans and animals, insulin sensitivity is normal. Because there is not, at least initially, an inability to secrete adequate amounts of insulin, insulin injections are not useful for therapy. Rather the disease is controlled through dietary therapy and hypoglycemic agents.

Furthermore, it can also result in Hyperinsulinemia or excessive insulin secretion which are most commonly a consequence of insulin resistance, associated with type 2 diabetes or metabolic syndrome. More rarely, hyperinsulinemia results from an insulin-secreting tumor (insulinoma) in the pancreas. Hyperinsulinemia due to accidental or deliberate injection of excessive insulin is dangerous and can be acutely life-threatening because blood levels of glucose drop rapidly and the brain becomes starved for energy (insulin shock).

Receptors involved in Type 1 diabetes

The receptors involved in type 1 diabetes are NKp46 receptor and Toll-like receptor 3 (TLR3).

NKp46 receptor plays a critical role in the development of the disease. BL-9020 is an antibody treatment to prevent destruction of insulin producing beta cells in the pancreas. It targets the NKp46 receptor which is involved in the innate immune response against the pancreas to destroy beta cells. Research has shown that this could significantly delay the maturation of the disease and potentially prevent the disease. This is not scientifically proven yet and is still under research.

Toll-like receptor 3 also plays a crucial role in the development of the disease. It is

involved in the innate immune response triggered by viral infection for the disease.

Can a diet or other conditions help the patient?

Firstly, create a diabetes management plan to help him or her manage the condition and stay healthy and active at the same time. Furthermore, treatment plans for type 1 diabetes are based on each patient's needs and the suggestions of the diabetes healthcare team. Treatment approaches differ in, among other things, the types of insulin given and the schedules for giving insulin given each day. The advantages and disadvantages of a plan should be considered for each patient. However, the basics of the treatment goals for patients with diabetes are to control the condition in a way that minimizes symptoms, prevents short- and long-term health problems, and helps them to have normal physical, mental, emotional, and social growth and development. To achieve this, all people should aim for the goal of keeping blood sugar levels as close to normal as possible.

Does Type 1 Diabetes affect life expectancy?

According to a study, type 1 diabetes reduces life expectancy for male around 11 years whereas for females it is around 13 years.Diabetes' impact on heart health appeared to be the largest single cause of lost years, according to the study. But, the researchers also found that type 1 diabetics younger than 50 are dying in large numbers from conditions caused by issues in management of the disease -- diabetic coma caused by critically low blood sugar, and ketoacidosis caused by a lack of insulin in the body. Furthermore, these conditions reflect through the day-to-day challenge that people with type 1 diabetes continue to face. For example,how to get the right amount of insulin delivered at the right time to deal with your blood sugar levels.

How did Type 1 diabetes get its name?

Type 1 diabetes is a form of diabetes mellitus. The term diabetes is the shortened version of the full name diabetes mellitus. Diabetes mellitus is derived from the Greek word diabetes meaning siphon - to pass through and the Latin word mellitus meaning honeyed or sweet. This is because in diabetes excess sugar is found in blood as well as the urine. It was known in the 17th century as the “pissing evil”.

The term diabetes was probably coined by Apollonius of Memphis around 250 BC. Diabetes is first recorded in English, in the form diabete, in a medical text written around 1425. It was in 1675 that Thomas Willis added the word “'mellitus'” to the word diabetes. This was because of the sweet taste of the urine. This sweet taste had been noticed in urine by the ancient Greeks, Chinese, Egyptians, Indians, and Persians as is evident from their literature.

3. Population

Population; where does disease occur; age of patients; quality of life of patients; is disease a danger to our civilisation; etc.

What is the age group that usually suffers from this disease?

According to a study, Every year in the United States, 13,000 children are diagnosed with type 1 diabetes, and more than 1 million American kids and adults deal with the disease every day. Therefore, it is a disease more commonly found in children. Furthermore, Type 1 diabetes can affect anyone, however it is more common towards people under 30 years and tends to begin in childhood. Other names for type 1 diabetes have included juvenile diabetes and insulin-dependent diabetes mellitus (IDDM).

How does this disease affect the quality life of patients?

It can affect a person emotionally, for example:

As blood-sugar levels can cause significant mood changes, new research suggests that frequent changes in blood-sugar levels (called glycemic variability) also can affect mood and quality of life for those with diabetes.

For example, in a case of an increased risk of depression, diabetes can affect mood even from minute to minute. For example, someone who experiences low blood sugar may suddenly become irritable, even combative, and may act as if they are drunk, slurring their words. Although diabetes and blood-sugar levels can affect emotions, emotions also can affect patients' blood-sugar levels and diabetes control.

Will type 1 diabetes cause a danger to our civilization?

It will not bring a danger to the entire population. However, there might be other autoimmune diseases seen with increased frequency in Type 1 diabetes as the most common form of autoimmune disease in families with Type 1 diabetes will be the thyroid disease.

4. Cure

Cure; can anything be done against the disease or against the symptoms; medicines; including TCM (Traditional Chinese Medicine ).

Treatment for Type 1 diabetes

Type 1 diabetes is incurable but is controllable. It can be treated by administering insulin, either using injection or pump. Not only that, a healthy balanced diet and regular physical exercising can also help.

Against the disease (the purpose of doing all these is to keep your blood sugar as close to normal as possible to delay or prevent more complications.)

Intake of insulin through insulin therapy

blood sugar monitoring
healthy diets- nutritious, low-fat, high fiber foods.
exercise regularly to maintain a healthy weight
refined carbohydrates

Medication

Medication includes injection in which using a needle and syringe to inject insulin under your skin, insulin pumps in which is a device which has a tube that connects a reservoir of insulin to a catheter that's inserted under the skin of your abdomen.

There are other medications such as:

Pramlintide which is an injection before a meal which can slow down the movement of the food through your stomach to slow down the blood sugar level after a meal.
High blood pressure medication known as angiotensin-converting enzyme (ACE) inhibitors or angiotensin II receptor blockers (ARBs), because these medications also can help keep your kidneys healthy.
Aspirin which is used to protect your heart.
Cholesterol lowering drugs used to lower the cholesterol as Cholesterol guidelines tend to be more aggressive for people with diabetes because of the elevated risk of heart disease.

Traditional Chinese Medicine(TCM)

Not really a cure for diabetes, but instead aims to optimize the body’s ability to function normally. TCM such as:

Acupuncture/Moxibustion

Used to reduce blood glucose levels and also normalise the endocrine function. It is a treatment which involves needling 4-12 points. Needles may be stimulated manually or by using a small electrical current. In addition, the practitioner may warm the points with moxibustion.

Qi gong

Qigong is used as a means of promoting health, healing, spiritual growth, and overall well-being. While Qigong is not typically used as a major treatment modality for diabetes, it has been found to be a valuable adjunctive therapy for this condition. There are specific Qigong exercises for diabetes.

Tui na

Tui Na is a traditional form of Chinese massage that uses hand manipulations, such as pulling, kneading, pushing, and grasping to stimulate acupuncture points and other parts of the body to create balance and harmony in the system. It can be used effectively in lieu of acupuncture in patients who have an aversion to needles, particularly pediatric patients.

Diet therapy

TCM defines diabetes as a disease characterized by Yin deficiency and excess internal heat, an example of a dietary prescription would be to consume spinach, which is cooling, “strengthens all the organs, lubricates the intestines, and promotes urination. Meals should be smaller, eaten more frequently, and eaten at regular times each day.

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Herbals

Panax ginseng which is used as a hypoglycemic agent that lowered blood glucose levels and improved mood and psychological performance.Recommended dosage is 100–200 mg/day.
Momordica charantia(balsam pear) which is dried, powdered, and made into pills. A dosage of 18 g/day has been shown to reduce blood glucose.
Lagenaria siceraria(bottle gourd) given as a decoction or pills. The recommended dose is 3 g/day. This, too, has been shown to reduce blood glucose levels.
Psidium guajava, taken in the form of fresh leaves or as an infusion and drunk as a tea. The dosage is 9 g/day. It acts to reduce blood glucose levels.

5. Origin of disease

Origin of disease; if genetic, is it dominant, recessive, autosomal, etc; viral; bacterial; etc.

Genetic- More than 50 well validated genes are associated with type 1 diabetes, which can be dominant, recessive or somewhere in between. The risk of a child developing type 1 diabetes is about 10% if the father has it, about 10% if a sibling has it, about 4% if the mother has type 1 diabetes and was aged 25 or younger when the child was born, and about 1% if the mother was over 25 years old when the child was born.

Environmental- For identical twins, when one has a type 1 diabetes, the other twin would have it about 30-50% of the time. Thus, for 50-70 % of the identical twins, one would have it and the other would not. Other indications of environmental influence include the presence of a 10-fold difference in occurrence among Caucasians living in different areas of Europe, and that people tend to acquire the rate of disease of their particular destination country.

Viral- As type 1 diabetes being a virus-triggered autoimmune response in which the immune system would attack the virus infected cells along with the beta cells in the pancreas.

Chemical and drugs- Pyrinuron (Vacor), a rodenticide introduced in the United States in 1976, selectively destroys pancreatic beta cells, resulting in type 1 diabetes after ingestion. Pyrinuron was withdrawn from the U.S. market in 1979 but is still used in some countries. .Streptozotocin (Zanosar), an antibiotic and antineoplastic agent used in chemotherapy for pancreatic cancer which kills beta cells, resulting in loss of insulin production.

Other pancreatic problems, including trauma, pancreatitis, or tumors (either malignant or benign) can also lead to loss of insulin production.

References

http://consumer.healthday.com/mental-health-information-25/anxiety-news-33/diabetes-can-take-a-toll-on-your-emotions-664847.html - How it affects the quality life of patients

http://www.chemeddl.org/resources/TSTS/Gellman/Gellmanpg5-8/Active%20Sites.html

http://www.endocrineweb.com/conditions/type-1-diabetes/type-1-diabetes-exercise

http://ghr.nlm.nih.gov/handbook/mutationsanddisorders/mutationscausedisease

Links

https://www.youtube.com/watch?v=jxbbBmbvu7I - Type 1 Diabetes

https://www.youtube.com/watch?v=ae_jC4FDOUc - Insulin, Glucose and you

https://www.youtube.com/watch?v=hnUTJxhgiSY - How To Prevent Type 1 Diabetes

https://www.youtube.com/watch?v=lsZFAAVEJkQ - Type 1 Diabetes and Exercise

https://www.youtube.com/watch?v=biYA24-ywA0 - Recommended Food choices for the Type 1 diabetes patients.

https://www.youtube.com/embed/42DJPDb-hRU"

https://www.youtube.com/embed?v=NaNDTr1A_H8

Topic 1

What is bioinformatics?

science of using info to understand biology
subset of the larger field of computational biology, application of quantitative analytical techniques.

Genome Projects

project that constructs detailed genetic and physical maps of human genome
use to benefit the public effectively as it uses the advanced means of information to make results available as fast as possible to the scientists and physicians.

Prokaryotic cells

Unicellular cells which lack nuclear membrane and do not develop into multicellular forms.

Eukaryotic cells

Presence of nucleus, a membrane delimited compartment that houses the DNA.
have specialised structures called organelles.

Cell Differentiation

process by which an unspecialised cell becomes specialised into one of the many cells that make up the body such as heart, liver or muscle cell.
During the process, certain genes are turned on while other genes will turn off which results in the development of the specific structures that perform specific functions.

Central Dogma

Genetic information flows from the DNA to RNA and then to the protein which is passed down from generation to generation.
DNA transcription refers to the synthesis of RNA from the DNA template.
mRNA translation to a protein

Translation

DNA codes are being read to make protein.
A dazzling display of choreography.
molecular machine lock together
RNA forms a miniature factory known as ribosome.
Translates genetic information in the RNA to a string of amino acids.
There are different transfer molecules of each of the twenty amino acids.
Each molecule carries a three letter code matched with the RNA.
In the ribosome, RNA is pulled similar to a tape.
Whenever each amino acid is read off, three letters will be matched to three corresponding letters on the transfer molecules.
Amino acid will then be added to the growing protein chain.
After the proteins are assembled, they will emerge from the ribosome and make different kinds of protein.

Transcription

DNA information is copied to messenger RNA for protein production.
Starts off with a bundle of factors assembling at the beginning of gene.
First phase of the process is to read off information that will be needed in making the protein.
Those blue molecules in the DNA will read the gene whereas the yellow chain snaking out of top is a copy of the genetic message after unzipping the double helix.
Building blocks make the RNA enter through an intake hole.
They match to DNA letter by letter to copy letter of the gene. (E.g : As, Cs, Ts, Gs)
Only difference is that in RNA copy, the letter “T” is replaced by “U”.

Gene Finding

Task of finding introns and exons which are the coding parts.
Used to predict the location of genes or even the protein sequence.

Evolutionary biology

New insight of molecular basis of a disease.
Homology refers to facts that two genes share a common evolutionary history.
The potential for uncovering evolutionary relationships and patterns.
With aids of nucleotide and protein sequences.
Possible to find the ancestral ties between different organisms.
Proteins shown a significant sequence conservation to indicate clear evolutionary

are from the same protein family.

Protein folds are able to reconstruct evolutionary relationships between two species and estimated time of divergence between two organisms.

Protein Modeling

process of evolution which results in the production of DNA sequences which encode proteins with specific functions.
Absence of protein structures can be identified using X-ray crystallography or NMR spectroscopy.

Databases and Search Tools

Computational tools and databases are essential to management of identification of subtle patterns.
NCBI( National centre for biotechnology information)
The NCBI are the 2 main life science servers responsible to deal with staggering amounts of data.
NCBI maintains reliable databases and analytical softwares.
Their main tasks is to create automated machines and facilitate usage of databases and analytical software for the scientific community.
Coordinate worldwide efforts to gather biological data.
Conduct research in computerized analysis of structure-function relationships for key biological molecules.
NCBI research will also give results such as analysis of the sequence, gain a better understanding and be able to predict the structures of molecules.
There is another organization known as European Bioinformatics Institute. (EBI)
Similar tasks and goals compared to the NCBI.
Only difference is that EBI research consists of developing more robust comparison algorithms, more elaborate and user-friendly, networked information systems.

Blast

Basic Local Alignment Search Tool
A method of rapid searching of nucleotide and protein databases.

Restriction Enzymes

First restriction enzymes were found in H.Influenza in 1970.
Known as a defense mechanism produced in bacteria.
It can function like scissors such as cutting DNA at a specific cleavage site.
Usually the target is the palindrome.
Many cuts are staggered and tend to leave sticky ends.
Cleavage sites cutted are known as the digestion process.
Fragments are analyzed by gel electrophoresis.
Examples of two types of enzyme, HINDIII and ECORI.

Cloning

Inserting DNA segment into a cloning vector which will replicate the DNA molecule that is not uncontrollable.
Provides high quantities of DNA fragments.
Preserve sequences by keeping cells alive.

Joining DNA

Using the same restriction enzyme to digest both donor DNA and vector RNA.
Sticky ends join donor to vector to create recombinant DNA.
Fragments are sealed permanently by enzyme DNA ligase, which is the DNA glue.
Examples of vector types are such as plasmids, bacterial artificial chromosome and yeast artificial chromosome.

DNA Denaturation & Hybridization

Types of DNA analysis technique.
Separation of double stranded DNA
Re-annealing of single stranded DNA
Denaturation temperature ™( melting temperature)
Common way to detect temperature is to measure the capacity of DNA by absorbing ultraviolet light of wavelength.
Nucleic acid sequence specific properties are the temperature as it varies until critical temperature is arrived at.

Hyperchromic shift

Due to the increase in absorbance of the transition in DNA structure.
The free rotation of the bases in the denatured state is responsible for the observed hyperchromic shift.
This is due to an increase in optical density of a solution which consists of nucleic acid.
The temperature at which the shift occurs is referred to as Tm or melting.

DNA Hybridization

A sheet with attached DNA will be incubated with a tagged denatured DNA population.
If double -stranded DNAs are formed, it will cause the binding of the probe to the sheet.
After excess probe or poorly bound probe molecules and removed by washing, the residue are the formed hybrids with the target DNAs.

Southern Blot

Extraction of DNA from cells, with the help of restriction enzymes.
Run on a gel.
Denature DNA using alkali.
Transfer to nitrocellulose.
block excess DNA.
Hybridize with labeled DNA probes.
Wash off the unbound probe.
Autoradiograph.

Northern Blot

Extraction of RNA from cells.
Denatured with formaldehyde.
Run on a gel.
Transfer to nitrocellulose.
Block with excess RNA.
Hybridize with labeled DNA probes.
Wash off the unbound probe.
Autoradiograph

Western Blot

Extraction of protein from cells
Denatured with SDS
Run on a gel
Transfer to nitrocellulose
Block excess protein
Hybridize with labeled antibody probe
Wash off unbound probe
Autoradiograph or develop with chromogenic substrate.

Gel Electrophoresis

DNA fragments are produced by restriction enzymes.
They are able to be separated by size.
Terminals of electrical power sources are connected to horizontal tubes.
DNA molecules move towards the positive end and depend on the electric field strength.
The movement of charged molecules is known as electrophoresis.
A thin slab of gel (usually agarose or acrylamide)
Consists of small slots called wells.
Rate of movement increases and decreases the size of fragments after electric fields are applied.
This results in electrophoresis of a set of double-stranded DNA molecules in agarose gel.

Molecular biology

They typically utilizes a series of techniques to solve biological questions.
It can also be broken down into multiple smaller sub-problems.
For example, search for a gene in neural degeneration in humans.

TOPIC 2

Bio-Database and Computational Biology

It consists of a biological database,computational biology.
These are required to retrieve the datas, enabling efficient access to various types of data.
There are also Primary and Secondary Data which will have pairwise, sequence of comparison & alignments.

Genetic and Physical Mapping

They serve as a scaffold for orienting sequence information.
Numbers of high-quality genome-wide maps
They are able to assign a gene to a small area of chromosome.
Linkage analysis which is the probability that a recombination occurs between each pair of markers.
It causes gene hunting faster, cheaper and more practically.
Whereas physical mapping is used to examine regions of interest in a close up.
For example, ( it is use to determine the precise location of a gene after using genetic mapping)

Protein structure Modeling

Firstly, they are the fundamental components of all living cells.
Next,in terms of chemical and structural diversity, they are an extraordinarily diverse range of biological functions.
They have critical features such as ability to adopt the right shape for carrying out a particular function.
The importance to identify the shape or structure of a protein is to understand the biological function and the role it plays in terms of health or disease.
X-rays crystallography, Nuclear Magnetic Resonance Spectroscopy or Homology Modeling can be used to determine the structure of a protein.

Single Nucleotide Polymorphism

A small genetic change or variation that occurs within a person's DNA sequence.
Four letters are specific to represent the genetic code, A (adenine) , C (cytosine) , T (thymine) , G (guanine) .
Around 1% in the human population however 3% - 5% in coding sequence.
Due to advances in technology, genetic variations to facilitate gene identification have a recent flurry of Single Nucleotide Polymorphism and detection.

Expressed Sequence Tags

It is used to obtain genomic sequence and identify complete sets of genes.
The aim is to find out how to gain an understanding of when, where and how a gene is turned on.
Under normal circumstances, study about the disease is to understand the gene expression.
These tags can be used to find a gene out from a portion of chromosomal DNA by matching base pairs.

Microarrays

Since every cell of the body consists of a full set of chromosomes and identical genes.
Microarrays are useful for researchers when they want to survey a large number of genes quickly.
As they can be used to assay gene expression within a simple sample or comparing it with gene expression.
They can also be used to examine expression of thousands genes at the same time.
They can provide a systematic way to survey both DNA and RNA variations too.

Topic 3

Human Genome Project

To create genetic and physical Maps.
To sequence all base pairs.
To create information, tools, forum, training.

DNA Sequencing by Sanger method

It is known as the chain-termination method or dideoxy method.
It uses an enzymatic procedure to synthesize DNA chains of varying lengths in four different reactions.
This stops the DNA from replicating at one of the four bases.
These chain terminating nucleotides (initiated by dideoxynucleoside triphosphates, ddNTP) differ from their normal counterparts.
They are missing their 3’ hydroxyl group which the next nucleotide in a growing DNA strand is attached to.
Each of the resulting fragments is then analyzed by electrophoresis and a base sequence can be read from the results.

Automated sequencing Method

Labels 4 different fluorescent labels.
One for each base specific fragmentation.
Run on gel
Scan gel with laser, excite each fluorescent band to emit a different colour.
Sequences will be read off by computer.

Manual sequencing Vs Automated sequencing

Manual method is for sequencing small regions of interest.
Time and cost is prohibitive.
Smallest human genome is 50Mb.
Largest continuous DNA is 35000 bp.
Manual Sequencing can sequence at best of 50000 bases per year for $2 per base.
Approximately 30000 work years and make $3 billion.

Shotgun Sequencing method

It is a shotgun sequencing approach used to sequence a clone larger than the average read length.
It is to pepper the DNA with sequence reads such that they overlap, yield.
When assembled, the complete sequence of the clone is completed.

What is pairwise sequence alignment?

To measure the similarity of two sequences.
To determine the residue-residue correspondences.
To observe patterns of conservation and variability.
To infer evolutionary relationships.

Importance of pairwise sequence alignment

It is useful in determining whether genetic sequences from two species are evolutionarily related.
It is also useful in database searching, since alignment scores provide a measure of similarity between sequences.
Pairwise alignment scores can be used as a distance metric for constructing phylogenetic trees.

How to determine which is the best alignment?

Firstly, examine all possible alignments systematically.
Next, compute a score reflecting the quality of each possible alignment.
Lastly, identify the alignment with optimal score. (Note that minor variation in scoring scheme could change the ranking of alignments.)

Biological Motivation Sequence Alignment

To discover functional, structural and evolutionary information in biological sequences.
It is the most important primitive operation in Bioinformatics.
To find out many sequences of unknown structures and functions and fewer sequences of known structures and functions.
There are similar sequences having the same function for similar DNA molecules and similar sequences having the same biochemical function for proteins.
However, different organisms with similar sequences may have been from a common ancestor.
Such sequences are known as homologous sequences.

Homology

It refers to homologous sequences being identified through sequence alignment.
Therefore, it is possible to predict or infer structures and functions of these sequences from primary sequence analysis.
Homologous sequences can be divided into two groups, Orthologous and Paralogous.
Orthologous refers to similar sequences in two different organisms that have arisen due to a speciation event.
Paralogous refers to similar sequences within a single organism that have arisen due to a gene duplication event.

What are the issues in sequence Alignment?

Sequences might differ in length significantly.
There may be only a relatively small region of matching sequences.
It allows partial matches. (E.g: Some amino acid pairs are more substitutable than others.)
Variable length regions may have been inserted or deleted from the ancestral sequences.

What are Gaps?

They are sequences that may have diverged from common ancestor through mutations:
Substitution (AAG > AAGT)
Insertion ( AAG > AAGT)
Deletion (AAGC > AAG)
Latter two operations result in gaps (-)
- k contiguous spaces = gap of length k
There are basically three types of alignment - Global, Local, Semi-global alignment.

Global Alignment (Needleman-Wunsch algorithm)

It focuses on regions of similarity between two sequences across the full extent of the sequences.
It finds the best match of both sequences by finding the best alignment of all prefixes of the sequences.

Local Alignment (Smith-Waterman algorithm)

It focuses on regions of similarity in parts of the sequences to find the best subsequence match.
It is useful for comparing sequences that share a common motif (conserved pattern) or domain (independently folded unit) but differ elsewhere.
However, it is also more sensitive when comparing highly diverged sequences.

Semi-global Alignment

It refers to finding the best match without charging for gaps on the ends of the alignment. It is also known as the end-space-free alignment.
It is useful when lengths of sequences differ significantly and aligning the shorter sequences in the interior of the other.
An example would be protein structure against genomic DNA sequence.
It is also useful for aligning the suffix of one sequence to the prefix of the other.

Pseudocode

It refers to computing the similarity score of the optimal global alignment with linear gap penalty.

Traceback

It is a process to find alignment itself from the path of choices that led to the score after computing the similarity score. This procedure is known as Traceback.
The traceback idea : each cell saves pointers to parent cells.
In an event of several optimal alignments that exist for a pair of sequences, we can use preference ordering over paths while doing traceback (1 = highest priority) if we only want to output one of the optimal alignments.

Scoring an alignment

It requires a substitution matrix to indicate scores of aligning character x and y.
It also requires a gap penalty function to indicate the cost of a gap of length k.
Therefore, there is a linear gap penalty function which is somewhat different to dynamic programming algorithms.

What is the use of a scoring matrix in sequence alignment?

When we evaluate a sequence alignment, we are interested in knowing whether the alignment is random or meaningful.
If the alignment is meaningful, we would need to know how “aligned’ are the sequences. We know this by using a scoring matrix.

Substitution Matrices - PAM Matrices

- It is also known as Point/Percent Accepted Mutation (PAM) Matrices.

It is commonly used for scoring matrices based on observed substitution rates.
PAM matrices are based on global alignments of closely related proteins.
It is the alignment of common protein sequences, involving 1572 amino acid substitutions and 71 groups of proteins.
The alignment is constructed between similar sequences with very high percentage identity (>85%).
Lastly, similar sequences can also be organized into phylogenetic trees and the number of amino acids that changes are counted.

Substitution Matrices - BLOSUM Matrices

It is also known as Blocks Amino Acids Substitution Matrices (BLOSUM).
It is commonly used as a scoring matrix based on observed differences among sequences among the very conserved regions of a protein family.
BLOSUM matrices are based on local alignments of closely related proteins.
Ungapped alignments of related proteins are grouped using statistical clustering techniques and substitution rate between the clusters are calculated.
They can be constructed to compare sequences with different degrees of relatedness.
The significance of the numbering for BLOSUM matrices can be thought of as the inverse of the PAM numbers.
Lower numbered PAM matrices are used for comparing closely related sequences.
Lower numbered BLOSUM matrices are used for comparing more distantly related sequences.
BLOSUM-62 matrix is more appropriate for comparing sequences of approximately 62% sequence similarity, while BLOSUM-80 matrix is more appropriate for sequences of about 80% similarity.

Dot Plot

It is the visual representation of comparison between two sequences.
It is a picture that gives an overview of the similarities between two sequences.
To construct a simple dot plot, the first sequence to be compared is assigned to the horizontal axis of a plot space and the second is assigned to the vertical axis.
Dots are placed in the plot space as each position where both of the sequence elements are identical.
Adjacent regions of identity between the two sequences giving rise to diagonal lines of dots in the plot.

Database Searching Tools - BLAST, FASTA

It displays a list of top scoring sequences from the database.
It contains a series of alignments for scoring sequences from the database.
BLAST is also known as Basic Local Alignment Search Tool.
BLAST is a method of rapid searching of nucleotide and protein databases.
BLAST is the most frequently used program to search for sequence databases.
BLAST and FASTA scans fast to remove unrelated sequences.
BLAST and FAST
A difference in statistical model, heuristics, and tuning.

Topic 4

Multiple Sequence Alignment (MSA)

- It produces pairwise sequence alignment which has more than two sequences.

- The input has more than 2 sequences in a set and is a method for scoring an alignment.

- The output determines the connection between the sequences such that it maximises similarity or minimises divergence distance.

Motivation

- It is a set of sequences in characters.

- It characterized a protein family into two groups:

- What is conserved

- It reveals the precise conserved family characteristics, evolution relations

- What varies

- Evolution and development biology, mutation’s effects

- Substitution rates and tendencies

- Profiles and patterns for searching

- Protein modelling

- Construction of phylogenies

MSA scoring

- The problem: It is assumed that the sum of column scores is the alignment score.

- To get an accurate MSA, the alignment score should be the sum of column scores with a score assigned to each column.

- To score a column, there should be a function with k arguments where k is the number of sequences.

- Hence, we can use the Sum-of-Pairs (SP) function to solve this problem.

- SP scoring is the adding of scores of pairwise alignments in each column.

- SP scoring is widely used due to its simplicity and effectiveness.

Methods for MSA

- Multidimensional Dynamic Programming

- Star alignment

- ClustalW

- Profile Hidden Markov Models (HMMs) with Baum-Welch and Viterbi Algorithms

- Expectation Maximization (EM) Algorithm

Dynamic Programming (DP) Approach

- It is used with 2 Sequences.

-Relatively easy in coding

-100% chance in obtaining optimal alignment

- It can be extended to multiple sequences (E.g Amino acid sequences - VSNS, SNA, AS).

-Put one sequence per axis (x,y,z).

- It requires a 3-dimensional array.

Heuristic Alignment Method

- It is used due to complexity of DP approach which is exponential in the number of sequences.

- Progressive alignment: It is the construction of a succession of pairwise alignments. - Star approach

- ClustalW

- Iterative refinement

-Given a multiple alignment, remove the sequence, realign it to a profile of other sequences then repeat until convergence (E.g SAGA, MSASA).

Star Alignment

- Input: k sequences, scoring scheme

- Choose one sequence as the center known as Sc.

- Si is not equal to Sc, determine an optimal pairwise alignment between Si and Sc.

- Compute all the pairwise alignment and select the maximising sequence.

- Sim (Si, Sj) denotes the score of optimal global alignment score of sequence Si, Sj.

- Aggregate pairwise alignment

- It uses “once a gap, always a gap” technique.

- It shifts the entire column when incorporating gaps

- Output: MSA result from aggregate

Progressive Alignment Method

- Multiple alignments are made using progressive alignment methods.

- The alignments are constructed by adding one sequence at a time to a growing alignment.

- Basic progressive alignment steps:

- 1) It determines the distance between the sequences.

- 2) It uses the distance based method to construct a phylogenetic tree for the sequence.

- 3) It adds sequences to the growing alignment using the order given by the tree.

- Progressive alignments are fast to allow hundreds and thousands of sequences to be aligned ( E.g: ClustalW).

ClustalW

- Pairwise alignment: Calculate distance matrix

- Creation of unrooted Neighbor-Joining (NJ) Tree

- Rooted NJ tree and calculate sequence weights

- Progressive alignment following the guide tree (NJ tree)

Problems with Progressive Alignment

- Not 100% guarantee that a global optimal solution will be found.

- It uses “once a gap, always a gap” technique.

- Any mistakes made in any alignment cannot be changed as new information from other sequences is added.

- When all sequences are highly divergent ( E.g less than 25-30% identity between any pair), the progressive alignment becomes less reliable.

- Once a group of sequences have been aligned, their alignments cannot be changed at later stages.

Integrated Approach

- It aligns similar sequences easily.

- It generates an alignment and a phylogenetic tree at same time.

- It requires many rounds of phylogenetic analysis and sequence alignment.

Integrated Approach - Strategies

Generate a pairwise distance matrix using possible pairwise alignment.
Use a statistically based approach to construct the initial tree.

3) Realign the sequences progressively in order of the relatedness.

4) Construct a new tree from pairwise distances obtained in new multiple alignment.

5) Repeat the process if the new tree is different from the previous one.

Phylogenetic Tree

- It is a diagram of evolutionary lineage of species or genes.

- It is constructed to understand lineage of various species and how the various functions are evolved.

- It informs multiple alignments.

- Examples of Phylogenetic Tree include Tree of life, Kinesin KHC subfamily sequences and Classification of Languages.

- Tree of life is a phylogenetic study of how the evolution of species occurred.

- Kinesin is a mechanochemical protein capable of utilizing chemical energy from ATP hydrolysis to generate mechanical force.

Basics of Phylogenetic Tree

- They are made by arranging nodes and branches.

- Each node represents a distinct taxonomic unit.

- Terminal nodes or leaves correspond to a gene or organism which data have been collected for analysis.

- Internal nodes representing an inferred common ancestor giving rise to two independent lineage in the past are also known as hypothetical ancestral units.

- Leaves represent things such as genes, species being compared.

- Rooted tree with a path from root to a node represents an evolutionary path.

- Unrooted tree specifies relationships among things, but not evolutionary paths.

Data for Building Trees

- Distance-based data measures the distance between species, genes or languages.

- Character-based data consists of morphological features, DNA or protein sequences.

- Gene-order data is the linear order of orthologous genes in given genomes.

Background on Trees

- All trees are binary with edges that branches split into two daughter edges.

- Types of trees :

- Rooted or Unrooted,

- Scaled or Unscaled

- Computer programs conveying basic information about a structure of a phylogenetic tree in a series of nested parentheses are also known as Newick format.

Phylogenetic Tree Approach

- Distance : Find the tree involved in estimated evolutionary distances.

- Parsimony : Find the tree that explains the data with a minimal number of changes.

- Maximum likelihood : Find the tree maximising the likelihood of the data.

UPGMA Method

- It is also known as the Unweighted Pair Group Method using Arithmetic Averages/Means (UPGMA) Method.

- It produces rooted trees.

- The basic Idea includes picking two taxa or clusters and merging them together to create a new node in the tree for the merged cluster.

- It starts with clustering two species with the smallest distance separating them into a single composite group.

- After that, a new distance matrix is computed with the distance between the new composite group and the remaining species calculated.

- Species that are separated by the smallest distance are clustered together to make a new composite species.

- The process is repeated until all the species are grouped.

- Scaled branch lengths are used on the tree to show the evolutionary distance between species.

- Branch points are at halfway distance between each of the species being grouped.

UPGMA

- It assumes a constant mutation rate for all branches.

- Hence, this satisfies a molecular clock with constant rate.

- The correct tree is constructed if the tree does not satisfy a molecule clock and the distance data is ultrametric.

- Ultrametric test condition: It is tested when any triplet I,j,k are either all equal or both are equal and the remaining is smaller.

- The fit of the realized tree is assessed to the data by adding squares of differences between the measured distances and those from the tree.

Fitch Margoliash Method

- It constructs a tree by iteratively joining subtrees.

- It does not make molecular clock assumptions.

- It produces unrooted trees.

- It has higher accuracy calculation of branch lengths.

Parsimony

- Find the tree that explains the data with a minimal number of changes.

- The tree requiring the least inferred mutations is the correct tree.

- Input: Character-based data

- It does not provide a method in constructing the tree topology, but a principle for deciding the best topology.

MSA and Phylogenetic Trees

- It is an integrated or unified approach to generate an alignment and a phylogeny.

- It has difficulty in aligning multiple sequences that is computational.

- The order in which the sequences are added to a multiple alignment can significantly affect the end result.

- The branching order of the sequences being studied should be taken into consideration for the alignment of multiple sequences due to higher accuracy and easier alignment of similar sequences.

- When the phylogeny of sequences being aligned is known before the alignment is made, sequences will be added one at a time to the growing multiple alignment with the most related sequence added first and the least related sequence added last.

- Phylogenetic relationships are determined by analysing the sequences.

MSA and Phylogenetic Trees - Strategies

1) Generate a pairwise distance matrix using possible pairwise alignment.

2) Use UPGMA or Fitch-Margoliash to construct the initial tree.

3) Realign the sequences progressively in order of the relatedness.

4) Construct a new tree from pairwise distances obtained in new multiple alignment.

5) Repeat the process if the new tree is different from the previous one. This requires many rounds of phylogenetic analysis and sequence alignment.

Additional information :

Part 1 of 3: What is type 2 diabetes?

Diabetes mellitus type 2 (formerly non insulin-dependent diabetes mellitus (NIDDM) or adult-onset diabetes) is a metabolic disorder that is characterized by hyperglycemia (high blood sugar) in the context of insulin resistance and relative lack of insulin.

Symptoms of Type 2 Diabetes

Type 2 diabetes is a chronic disease that can cause blood sugar (glucose) to be higher than normal. In addition, many people do not feel symptoms with type 2 diabetes. However, there are some common symptoms that it is important to be aware of. These are examples of symptoms for type 2 diabetes when blood sugar levels are abnormally high.

The most common symptoms of type 2 diabetes include:

excessive thirst
frequent or increased urination, especially at night
excessive hunger
fatigue
blurry vision
sores or cuts that won’t heal

Part 2 of 3: Common Symptoms

Common Symptoms of Type 2 Diabetes

If you have diabetes, it can help to understand how your blood sugar levels affect the way you feel. Most common symptoms of diabetes are caused by elevated glucose levels.

Frequent or Increased Urination

Elevated glucose levels force fluids from your cells. This increases the amount of fluid delivered to the kidneys. This results in urinating frequently which eventually causes one to become dehydrated.

Thirst

As your tissues become dehydrated, you will become thirsty. Increased thirst is another common diabetes symptom. As, the more you urinate, the more you need to drink, and vice versa.

Fatigue

Feeling worn down is another common symptom of diabetes. Glucose is normally one of the body’s main sources of energy. When cells cannot absorb sugar, you can become fatigued or feel exhausted.

Blurred Vision

Due to high glucose levels can cause a swelling of the lens in the eye. This leads to blurry vision. Getting your blood sugar under control can help correct vision problems. If blood sugar levels remain high for a long time, other eye problems can occur.

Recurring Infections and Sores

Elevated glucose levels may make it harder for your body to heal. Therefore, injuries like cuts and sores stay open longer. Which results in making them more susceptible to infection.

Others:

Very often, people don’t notice that they have high blood sugar levels because they don’t feel any symptoms. High blood sugars can lead to long term problems, such as a higher risk for heart disease, foot problems, nerve damage, eye diseases, and kidney disease. People with diabetes are also at risk for serious bladder infections. In people without diabetes, bladder infections are usually painful. However, diabetics may not have that sensation of pain with urination. The infection may not be detected until it has spread to the kidneys.

Part 3 of 3: Emergency Symptoms

Emergency Symptoms of Type 2 Diabetes

As stated, high blood sugar causes long-term damage to the body. However, low blood sugar, called hypoglycemia, can be a medical emergency. Hypoglycemia occurs when there are dangerously low levels of blood sugar. For people with type 2 diabetes, only those people who are on medications that increase the body’s insulin levels are at risk for low blood sugar.

Symptoms of hypoglycemia include:

shaking
dizziness
hunger
headache
sweating
trouble thinking
irritability or moodiness
rapid heartbeat

If you are on medicines that increase the amount of insulin in your body, be sure you know how to treat low blood sugar.

Causes of type 2 diabetes

Type 2 diabetes occurs when the pancreas doesn't produce enough insulin to maintain a normal blood glucose level, or the body is unable to use the insulin that is produced – known as insulin resistance.

The pancreas (a large gland behind the stomach) produces the hormone insulin, which moves glucose from your blood into your cells, where it's converted into energy.

In type 2 diabetes, there are several reasons why the pancreas doesn't produce enough insulin.

Risk factors for type 2 diabetes

Four of the main risk factors for developing type 2 diabetes are:

age – being over the age of 40 (over 25 for south Asian people)
genetics – having a close relative with the condition (parent, brother or sister)
weight – being overweight or obese
ethnicity – being of south Asian, Chinese, African-Caribbean or black African origin (even if you were born in the UK)

Age

Your risk of developing type 2 diabetes increases with age. Especially being over the age above 40. This may be because people tend to gain weight and exercise less as they get older.

Maintaining a healthy weight by eating a healthy, balanced diet and exercising regularly are ways of preventing and managing diabetes.

White people over the age of 40 have an increased risk of developing type 2 diabetes. People of south Asian, Chinese, African-Caribbean and black African descent have an increased risk of developing type 2 diabetes at a much earlier age.

However, despite increasing age being a risk factor for type 2 diabetes, over recent years younger people from all ethnic groups have been developing the condition.

It's also becoming more common for children, in some cases as young as seven, to develop type 2 diabetes.

Genetics

Genetics is one of the main risk factors for type 2 diabetes.

Your risk of developing the condition is increased if you have a close relative – such as a parent, brother or sister – who has the condition. The closer the relative, the greater the risk.

A child who has a parent with type 2 diabetes has about a one in three chance of also developing it (see below).

Being overweight or obese

You're more likely to develop type 2 diabetes if you're overweight or obese (with a body mass index (BMI) of 30 or more).

In particular, fat around your tummy (abdomen) increases your risk. This is because it releases chemicals that can upset the body's cardiovascular and metabolic systems.

This increases your risk of developing a number of serious conditions, including coronary heart disease, stroke and some types of cancer.

Measuring your waist is a quick way of assessing your diabetes risk. This is a measure of abdominal obesity, which is a particularly high-risk form of obesity.

Women have a higher risk of developing type 2 diabetes if their waist measures 80cm (31.5 inches) or more. Asian men with a waist size of 89cm (35 inches) or over have a higher risk, as do white or black men with a waist size of 94cm (37 inches) or over.

Use the BMI calculator to find out if you're a healthy weight for your height.

Exercising regularly and reducing your body weight by about 5% could reduce your risk of getting diabetes by more than 50%.

Ethnicity

People of south Asian, Chinese, African-Caribbean and black African are more likely to develop type 2 diabetes.

Type 2 diabetes is up to six times more common in south Asian communities than in the general UK population, and it's three times more common among people of African and African-Caribbean origin.

People of south Asian and African-Caribbean origin also have an increased risk of developing complications of diabetes, such as heart disease, at a younger age than the rest of the population.

Other risks

Your risk of developing type 2 diabetes is also increased if your blood glucose level is higher than normal, but not yet high enough to be diagnosed with diabetes.

This is sometimes called "pre-diabetes" – doctors sometimes call it impaired fasting glycaemia (IFG) or impaired glucose tolerance (IGT).

Pre-diabetes can progress to type 2 diabetes if you don't take preventative steps, such as making lifestyle changes. These include eating healthily, losing weight (if you're overweight) and taking plenty of regular exercise.

Women who have had gestational diabetes during pregnancy also have a greater risk of developing diabetes in later life.

What kind of diabetes do you have?

The three main types of diabetes are type 1, type 2, and gestational diabetes. People can develop diabetes at any age. Both women and men can develop diabetes.

Type 1 Diabetes

Type 1 diabetes, which used to be called juvenile diabetes, develops most often in young people; however, type 1 diabetes can also develop in adults. In type 1 diabetes, your body no longer makes insulin or enough insulin because the body's immune system, which normally protects you from infection by getting rid of bacteria, viruses, and other harmful substances, has attacked and destroyed the cells that make insulin.

Type 2 Diabetes

Type 2 diabetes, which used to be called adult-onset diabetes, can affect people at any age, even children. However, type 2 diabetes develops most often in middle-aged and older people. People who are overweight and inactive are also more likely to develop type 2 diabetes.

Type 2 diabetes usually begins with insulin resistance—a condition that occurs when fat, muscle, and liver cells do not use insulin to carry glucose into the body’s cells to use for energy. As a result, the body needs more insulin to help glucose enter cells. At first, the pancreas keeps up with the added demand by making more insulin. Over time, the pancreas doesn’t make enough insulin when blood sugar levels increase, such as after meals. If your pancreas can no longer make enough insulin, you will need to treat your type 2 diabetes.

Treatment for type 2 diabetes includes

using diabetes medicines
making healthy food choices
being physically active
controlling your blood pressure levels
controlling your cholesterol levels

Gestational Diabetes (Towards pregnant woman)

Gestational diabetes can develop when a woman is pregnant. Pregnant women make hormones that can lead to insulin resistance. All women have insulin resistance late in their pregnancy. If the pancreas doesn’t make enough insulin during pregnancy, a woman develops gestational diabetes.

Overweight or obese women have a higher chance of gestational diabetes. Also, gaining too much weight during pregnancy may increase your likelihood of developing gestational diabetes.

Gestational diabetes most often goes away after the baby is born. However, a woman who has had gestational diabetes is more likely to develop type 2 diabetes later in life. Babies born to mothers who had gestational diabetes are also more likely to develop obesity and type 2 diabetes.

Genes that have been associated with type 2 diabetes risk include:

TCF7L2, which affects insulin secretion and glucose production
the sulfonylurea urea receptor (ABCC8), which helps regulate insulin
calpain 10, which is associated with type 2 diabetes risk in Mexican Americans
glucose transporter 2 (GLUT2), which helps move glucose into the pancreas
the glucagon receptor (GCGR), a glucagon hormone involved in glucose regulation.

TCF7L2 :

TCF7L2 (Transcription Factor 7-Like 2 (T-Cell Specific, HMG-Box)) is a Protein Coding gene. Diseases associated with TCF7L2 include pitt-hopkins syndrome and tropical calcific pancreatitis. Among its related pathways are Signaling by GPCR and Pathways in cancer.

CF7L2 was discovered as a type 2 diabetes susceptibility gene after a strong linkage signal was mapped to chromosome 10q in a Mexican-American population. This region was later fine-mapped in the Icelandic population and confirmed in United States and Danish cohorts, where the risk locus was found to be located in intron 3 of the TCF7L2 gene. There are indications that this gene may play a role in cancer as well as in diabetes.[9]

TCF7L2 is a transcription factor and key component of the Wnt signaling pathway, and it is involved in the development of a wide variety of cell lineages and organs.[10] Potential mechanisms through which TCF7L2 variants influence type 2 diabetes include its role in adipogenesis, myogenesis, and pancreatic islet development, as well as in beta-cell survival and insulin secretory granule function.[11, 12] It is also involved in the transcriptional regulation of the genes for proglucagon and the glucagon-like peptides GLP-1 and GLP-2; these peptides play a role in postprandial insulin secretion.[13]

Finally, TCF7L2 polymorphisms have been associated with impaired insulin secretion, glucose production, and glucose tolerance via direct effects on pancreatic islet beta cells.[14, 15] Indeed, dysregulation of glucose metabolism, decreased processing of proinsulin, and elevated levels of gastric inhibitory peptide and glycated hemoglobin (HbA1c) can be observed in normoglycemic individuals with TCF7L2 polymorphisms before the onset of type 2 diabetes.[16, 17]

Relevant genes towards TCF7L2 :

Acts as repressor in the absence of CTNNB1, and as an activator in its presence. Activates transcription from promoters with several copies of the Tcf motif 5'-CCTTTGATC-3' in the presence of CTNNB1. TLE1, TLE2, TLE3 and TLE4 repress transactivation mediated by TCF7L2/TCF4 and CTNNB1. Expression of dominant-negative mutants results in cell-cycle arrest in G1. Necessary for the maintenance of the epithelial stem-cell compartment of the small intestine.

What is ABCC8?

The gene is known as “ATP binding cassette subfamily C member 8.”

Pancreatic β-cell ATP-sensitive K(+) (K(ATP)) channels are composed of Kir6.2 and SUR1 subunits encoded by the KCNJ11 and ABCC8 genes, respectively. Although rare monogenic activating mutations in these genes cause overt neonatal diabetes, the common variants E23K (KCNJ11) and S1369A (ABCC8) form a tightly heritable haplotype that is associated with an increased susceptibility to type 2 diabetes (T2D) risk.

Furthermore, Sulfonylureas are a class of drugs used to lower blood glucose in the treatment of type 2 diabetes. These drugs interact with the sulfonylurea receptor of pancreatic beta cells and stimulate insulin release. The sulfonylurea receptor is encoded by the ABCC8 gene, and genetic variation of ABCC8 may impair the release of insulin.

What is GLUT2?

Glucose transporter 2 (GLUT2) also known as solute carrier family 2 (facilitated glucose transporter), member 2 (SLC2A2) is a transmembrane carrier protein that enables protein facilitated glucose movement across cell membranes.

What is GCGR?

GCGR (Glucagon Receptor) is a Protein Coding gene. Diseases associated with GCGR include diabetes mellitus, non insulin-dependent and hyperglycemia. Among its related pathways are Signaling by GPCR and Activation of cAMP-Dependent PKA.

Glucagon is the main secretory product of the pancreatic alpha-cells. The main function of this peptide hormone is to provide sustained glucose supply to the brain and other vital organs during fasting conditions. This is exerted by stimulation of hepatic glucose production via specific G protein-coupled receptors in the hepatocytes. Type 2 diabetic patients are characterized by elevated glucagon levels contributing decisively to hyperglycemia in these patients. Accumulating evidence demonstrates that targeting the pancreatic alpha-cell and its main secretory product glucagon is a possible treatment for type 2 diabetes. Several lines of preclinical evidence have paved the way for the development of drugs, which suppress glucagon secretion or antagonize the glucagon receptor.

References: