Genetics

Chromosome > DNA > gene. Humans have 46 total chromosomes, and 22,258 genes. (The 22,258 genes are found in the total 46 chromosomes, but are not divided equally.). Chromosomes are found inside the nucleus of cells, and range .2 to 20 micrometers in eukaryotic cells. STR techniques (short tandem repeats) are used for paternity testing.

DNA found in mitochondria of cells are called mitochondrial DNA (mtDNA). Animals, plants, and fungi all have mtDNA. Human mtDNA has 37 genes. Half of your nuclear DNA came from your mom, but 100% of mtDNA came from your mom. The genes of mtDNA control cellular metabolism: the processing of energy inside the cell.

Male children receive their 1 and only Y chromosome from their father.

Alleles are different versions or variants of a gene that can exist at a particular genetic locus. In diploid organisms like humans, each individual inherits 1 allele for each gene from each parent. In the context of genetic disorders, specific alleles can be responsible for causing the trait or disorder, and different alleles may have different effects on the phenotype.

A phenotype is a single observable trait. In classical genetics, each phenotype is determined by a combination of 2 alleles contributed by 2 copies of the same (but not necessarily identical) chromosome, where 1 allele is generally dominant (meaning it is expressed), and the other is recessive.

After genomics and transcriptomics, proteomics is the next step in the study of biological systems. It is more complicated than genomics because an organism's genome is more or less constant, whereas proteomes differ from cell to cell and from time to time.

Inheritance patterns.

These terms refer to different inheritance patterns of genetic traits or disorders based on the location of the responsible gene on the chromosomes.

1. Autosomal Dominant: occurs when a mutated (disease-causing) gene is located on 1 of the autosomes (non-sex chromosomes). In this pattern, only 1 copy of the mutated gene, inherited from 1 parent, is sufficient to express the trait or disorder. The presence of the dominant allele will result in the appearance of the trait, even if the other allele (from the other parent) is normal.

Example:
-Huntington's disease (caused by a dominant mutation in the HTT gene, if a person inherits 1 copy of the mutated gene from either parent, they will develop the disease),
-Marfan syndrome (connective tissue disorder caused by mutations in the FBN1 gene, if a person inherits 1 copy of the mutated gene, they will exhibit the features of Marfan syndrome).
-Achondroplasia.

2. Autosomal Recessive: occurs when a mutated gene is located on 1 of the autosomes. In this pattern, 2 copies of the mutated gene (1 from each parent) are necessary for the trait or disorder to be expressed. If an individual inherits only 1 copy of the mutated gene and 1 copy of the normal gene, they are carriers of the trait but do not show symptoms. Both parents of an affected individual are usually carriers.

Example:
-Cystic fibrosis (caused by mutations in the CFTR gene, both copies of the CFTR gene need to be mutated for an individual to develop cystic fibrosis).
-Sickle cell anemia (blood disorder caused by mutations in the HBB gene, both copies of the HBB gene need to be mutated for an individual to have sickle cell anemia).
-Tay-sachs disease, phenylketonuria (PKU).

3. X-linked Dominant: occurs when the mutated gene responsible for the trait or disorder is located on the X chromosome. In this pattern, only 1 copy of the mutated gene on either of the X chromosomes (in males) or 1 of the 2 X chromosomes (in females) is enough to express the trait. Affected individuals can inherit the trait from an affected parent of either gender.

Example:
-Rett syndrome (caused by mutations in the MECP2 gene, a single copy of the mutated gene on the X chromosome is sufficient for the expression of Rett syndrome).
-Hypophosphatemic rickets (caused by mutations in the PHEX gene, females with a single copy of the mutated gene on 1 of their X chromosomes can show symptoms).

4. X-linked Recessive: occurs when the mutated gene is located on the X chromosome. In this pattern, males have only 1 X chromosome, so a single copy of the mutated gene will express the trait. Females have 2 X chromosomes, and they need 2 copies of the mutated gene to express the trait, similar to autosomal recessive inheritance. X-linked recessive disorders are more commonly seen in males since they have only 1 X chromosome, making them more susceptible to the effects of a mutated gene on the X chromosome.

Example:
-Hemophilia (caused by mutations in the F8 or F9 gene, males with a single copy of the mutated gene on their X chromosome will have hemophilia since they lack a 2nd, normal copy).
-Color blindness (caused by mutations in the OPN1LW or OPN1MW genes, males have a higher likelihood of being color blind since they have only 1 X chromosome).
-Duchenne muscular dystrophy.

Autosomal Dominant: all fathers who have this trail will pass it to all their sons.
Autosomal Recessive: if both parents have the trait, then all of their children do.
X-linked Dominant: all fathers who have this trait will pass it to all their daughters.
X-linked Recessive: all mothers who have this trait will pass it to all their sons. If the mother is just a carrier, then her son has 50% chance.

Blood and gender.

Gender identity in blood can be determined by the presence or absence of the Y chromosome. Red blood cells, for the most part, do not have a nucleus and therefore do not contain DNA. But red blood cells have a nucleus that contain DNA when they are in the bone marrow. When they leave the bone marrow and into circulation, their nucleus are extracted and discarded, but there are some cases where this process fails. This failing process is more common in neo-natal blood, but rare in adult blood, and their presence would prompt a search for a disease that might be responsible for it. However, blood does contain white blood cells, which do contain a nucleus with DNA.

Red hair.

About 1-2% of the human population has red hair. Research shows red hair usually results from a mutation in a gene called MC1R, which codes for the melanocortin-1 receptor. The pigment found in red hair that makes it red is called pheomelanin.

Plants.

The 1st genetically modified blue rose came in 2004. A gene was spliced that contained the naturally occurring delphinidin into a white rose. After 13 years of collaborative research, this was done by an Australian company called Florigene, with a Japanese company called Suntory. This was done via 3 alterations, adding 2 genes, and interfering with a 3rd. While the companies have called it a blue rose, it is more of a lavender in color. Though, there are no naturally-occurring blue roses, but a plant that is particular blue in nature is Eryngium ovinum, commonly known as the blue devil, which is native to Australia.

Cloning breakthrough.

In the Feb. 8, 2018 edition of the journal Cell, Chinese scientists reported the successful creation via cloning of 2 genetically identical macaque monkeys. It was the 1st time and primates (including humans) had been cloned by means of somatic cell nuclear transfer (SCNT). This basically involves placing the DNA-carrying nucleus of a body-tissue cell into an animal cell whose own nucleus has been removed, then applying enzymes to transform the egg into a productive embryonic state, and finally implanting the egg into a surrogate mother. SCNT has already worked with other mammals, the 1st being Dolly the sheel in 1996, and since then, this method has worked with over 20 different species, but always failed with primates, until the 2 macaque monkeys, named Zhong Zhong and Hua Hua, were born in China, on Nov. 27 and Dec. 5, 2017. Dolly was cloned from an adult cell, while these 2 were from a fetal cell.

Bacteria.

Bacteria can do horizontal gene transfer, which is the transfer of genetic material that are not between parents or offspring. This allows bacteria to acquire new genetic material from other bacterial cells in their environment, or from other organisms. The 3 main mechanisms for this are transformatin, transduction, and conjugation.

Natural transformation is where select organisms acquire extracellular donor DNA via recipient-encoded DNA uptake machinery.
Transduction are where bacteriophages (viruses that infect bacteria) transfer bacterial DNA from 1 bacterium to another, during the process of viral replication.
Conjugation is where bacteria use a tube-like sructure called a pilus, to transfer plamids (small, circular DNA molecules) from 1 bacterium to another.

ComEA and ComEC are proteins involved in the process of DNA uptake during transformation, specifically in Gram-positive bacteria such as Bacilus subtilus. ComEA is involved in the recognition and binding of single-stranded DNA, which is then transported across the bacterial cell membrane. ComEC acts as a DNA translocator or channel protein, facilitating the passage of DNA molecules through the bacterial cell membrane. Once DNA is bound to ComEA on the cell surface, ComEC forms a pore or channel through which the DNA can enter the cell, going to the cytoplasm, where it can undergo recombination and integration into the bacterial genome.

Oncology - the study of cancer.

The fundamental cause of cancer is damaged or faulty genes. Genes instruct cells what to do. Genes are encoded within DNA, so anything that damages DNA can increase the risk of cancer. However, a number of genes in the same cell need to be damaged before it can become cancer.

It has been established throughout many theoretical and experimental studies that guanine is the most easily damaged DNA base by ionizing UV radiation and that the guanine holes created during photoionization are the targets for carcinogenesis. Electron donation by nucleotides are the key initial steps than can lead to direct DNA damage and mutation.

DNA bases can be methylated. Methylation of DNA bases is an epigenetic mechanism that occurs by the covalent addition of a methyl group to a base and this has been found to influence a variety of processes including DNA integrity and function. Methylation might also play a role in the onset or course of cancer. Guanine in double- or singled-stranded DNA can be methylated by carcinogenic agents.

Case-study: Dimethyl sulfate (DMS) can be found in the environment in its gas phase and in airborne particulate matter that primarily originates from coal combustion. DMS is a monofunctional strong alkylating agent and reacts rapidly with DNA at room temperature and penetrates intact cells. DMS methylates predominately nitrogen sites, such as the N7 of guanine at the major groove and N3 of adenine at the minor groove in double-stranded DNA. In single-stranded DNA, DMS methylates the N7 site of guanine; the N1, N3 and N7 sites of adenine; and the N3 site of cytosine.

The most frequently mutated oncogene across various cancers is KRAS (Kirsten rat sarcoma viral oncogene homolog). Mutations in the KRAS gene are particularly common in a variety of cancer types, including colorectal cancer, pancreatic cancer, and non-small cell lung cancer. Phosphatidylinositol 3-kinase (alpha) (PIK3CA) is the second-most-frequently mutated oncogene across all cancers. Downstream of PIK3CA in the growth factor pathway lies the mechanistic target of rapamycin (mTOR) kinase, which integrates nutrient and growth hormone availability. The natural product rapamycin inhibits mTOR by acting as a molecular glue, recruiting the chaperone protein FKBP12 to mTOR’s FRB domain to block substrate binding to mTOR.

Trivial research:

1. What is the probability that 2 siblings will have the same DNA?

If take into account crossovers, virtually infinity. If ignoring crossovers, 1 in 70.37 trillion.

Independent assortment: each of our 23 chromosomes independently assorts to make gametes. A human embryo is composed of 46 chromosomes (23 from each parent). For each chromosome, there is a 50% chance that the 2 embryos will inherit a copy of the same chromosome. 2⁴⁶ = 70,368,744,177,664.

Which is also 4²³.

However, if you want to consider the possibility of inbreeding, 1 of the parents could have 2 copies of the same chromosome. Or the 2 parents could have inherited the same chromosome. Each such chromosome would double the chance of producing the same embryo. So if the parents are brother and sister, mother/son or father/daughter, the chances of producing the same embryo is 1 in 8,388,608.

While you are 50/50 of each of your parents, you are not necessarily 25/25/25/25 of your 4 grandparents. For each of your chromosome, there is a 50% chance that your mom got it from 1 of her parent, and therefore none of it from the other grandparent.

Note: mitochondrial DNA only make up a little less than .0003% of you total DNA, and is only passed from the mother.

2. How do you make seedless fruit, from non-seedless fruit? Watermelon, grapes, oranges.

Depending on the fruit, some are via grafting, some are via without fertilization, without pollination, or via cloning.

For making seedless watermelons, you take a diploid (2 sets of chromosomes) plant and force it to double its chromosomes (such as by applying colchicine, a mutagenic chemical). This results in a tetraploid (4 sets of chromosomes) plant, which is still fertile and seed-producing.

Then, you cross the diploid plant with the tetraploid plant and get a triploid (3 sets of chromosomes) plant. Because 3 isn't an even number, the plant can't divide its chromosomes in the way necessary for sexual reproduction, rendering it sterile and also seedless.

In order to produce more seedless plants, 1 has to maintain 2 separate gene pools of diploid and tetraploid plants to hybridize into triploid plants. A tetraploid female flower is fertilized with diploid pollen, and the resulting seeds grow triploid plants that are sterile (and thus don't produce seeds).

The above process described is not cloning. However, if it's possible to propagate the infertile/seedless plant vegetatively (meaning by taking a piece of vegetative growth like a root or a stem and growing a whole new plant from it), then the new plants would be clones of the original.

This is, for example, how commercial bananas are propagated, and why the banana industry is particularly susceptible to disease – since all the plants are clones, there's little to no genetic variation in how resistant the plants are to any given disease. bananas have been selectively bred to have no seeds/unnoticeably small seeds, and they're continually propagated from parent plants by pups or tissue culture.

Nearly every perennial fruit variety that has a name is a clone/ramet of the original ortet. Cloning of fruiting plants has been around for hundreds of years.

Grafting is taking a part of 1 plant and attaching it to another. Propagation is a general term for creating new plants, though it's often used to mean vegetative propagation.

Citrus and grapes are both grafted. Cuttings work fine, but there are disease problems if you grow them on their own roots, so they are more or less universally grafted. Some fruits like seedless oranges are the result of a genetic mutation. The tree would have died and being sterile the whole line would have died. But some found the tree and propagated it. All seedless oranges are clones of that tree.

It is also possible to do this without chromosome doubling like in strawberries, where there are many native species with varying chromosome numbers. You cannot however produce seedless fruit on plant that depend on the maturing of seeds to develop the fruit, such as for strawberries. Strawberries require the hormones produced by maturing seeds to stimulate the swelling and growing of the accessory fruit. Which is why seedless strawberries will never exist.

About colchicine: Colchicine is startlingly deadly, lowest reported lethal dose is 7 mg. However, it is applied to the seed during germination, and doesn’t remain in the plant, once you’ve grown out the plant there is no danger, especially since it has likely gone through several “generations” of vegetative propagation since then.

The plants that are cloned would be a genetic dead end without human intervention, since they don't produce seeds, but at some point far enough back the original plant that the clones came from did grow from a seed, and just had the desirable trait of not having seeds of their own. The female flower typically has the fruiting structure even before pollination. This is particularly noticeable on squashes and melons, you can see a small fruit at the base of the female flower, and if they don't get pollinated that structure just falls off the plant eventually. Pollination likely still triggers the fruit to grow, even if the plant is unable to produce seeds. In cases where the fruit is not truly seedless but just has been bred for very tiny seeds, the traits of the seeds are determined by the parent female flower regardless of the male pollinator.

There is no harmful effect from eating seedless fruit. The fleshy part of the fruit is no different from a fruit with seeds as far as nutritional value, and we usually do not derive any nutrition from seeds when they are eaten. Seedless or not, any fruit that is cultivated for sale has been selectively bred for hundreds of years. No fruit you find in a grocery store looks anything like its wild ancestors, as they've all been selectively bred for desirable traits long before genetic modification existed.

As a general rule, in seedy citrus varieties, pollination is required at anthesis for a successful ovule fertilization as a previous step to the development of seeds. Normally, cell division and, consequently, ovary growth slow down during the anthesis, until the pollination and fertilization occurs. Afterwards, the development of the ovary reactivates to form the fruit and seeds. In these varieties, the lack of pollination causes the fruit set to fail, leading to the fall or premature abscission of the ovary.

On the contrary, many varieties of Citrus genus can naturally set fruits without seeds. This phenomenon, called parthenocarpy, is defined as the ability to produce fruits without fertilization of the ovules and, therefore, without seeds development. Parthenocarpy depends on a genetic factor that favors the maintenance of a relatively high hormone level in the ovary during the anthesis and immediately after it, regardless of pollination and fertilization. The hormonal nature of the stimulus that induces fruit set is confirmed by the fact that parthenocarpy can be artificially induced by the application of certain phytohormones.

The most frequent cases of parthenocarpy in citrus fruits are found in:

-Self-incompatible varieties that are unable to produce seeds by self-pollination and which, in the absence of cross pollination, can develop fruits without seeds (facultative parthenocarpy). This is the case, for example, of some hybrid varieties of mandarin, such as Nova, Fortune, Nadorcott, Moncada, etc., or some highly parthenocarpic Clementines, such as Marisol. However, some other self-incompatible varieties with low parthenocarpic ability show low productivity, unless they are pollinated with compatible pollen, setting and developing a large proportion of seedy fruits. This is the case of some Clementine cultivars originated by bud mutations. Varieties with female gametic sterility, which are unable to produce seeds. This kind of sterility appears absolutely in the triploid varieties.

-Other cultivars, such as Navel sweet orange, Satsuma mandarins, and Marsh seedless grapefruit, where a generalized degeneration of the embryo sacs occurs. In a few cases, some of them may develop seeds in a very small number.

Parthenocarpy is of great importance in cultivated varieties of citrus cultivars for fresh consumption, since the market requires seedless fruits.

Can the breeding technique of seedless watermelon be done on other plants?

Hypothetically, yes, though it depends on the ploidy of the original plants. Some species naturally have more than 2 pairs of chromosomes to begin with, meaning you may not necessarily be able to simply double the chromosomes and then breed the mutated plant with the original. (For example, if the original plant had 4 pairs of chromosomes and you doubled it to 8, the offspring of that pairing might have 6 pairs of chromosomes which would likely still be fertile.).

3. When was the 1st DNA paternity test done?

The first DNA-based paternity test was conducted in 1988 in the United Kingdom. It was the result of a collaboration between Professor Sir Alec Jeffreys, a geneticist at the University of Leicester, and his team. (Sir Alec Jeffreys developed DNA fingerprinting in 1984, which allowed for highly accurate paternity tests.). The DNA test was able to conclusively identify biological relationships by comparing DNA sequences between the mother, child, and alleged father. This method was much more accurate and reliable than earlier blood typing tests or HLA (Human Leukocyte Antigen) tests.

For the U.S., the 1st was in 1989, in a California lab (DNA Labs International, now DNA Diagnostics Center). Both these tests did not use PCR, they used Restriction Fragment Length Polymorphism (RFLP). The DNA was cut into fragments by specific enzymes, and the length of these fragments was compared to identify unique patterns that could distinguish between the child and the father.

News.

12/8/2023 - sickle cell disease.

Regulators on Friday approved 2 gene therapies for sickle cell disease that doctors hope can cure the painful, inherited blood disorder that afflicts mostly Black people in the U.S. The Food and Drug Administration said the one-time treatments can be used for patients 12 and older with severe forms of the disease. One, made by Vertex Pharmaceuticals and CRISPR Therapeutics, is the 1st approved therapy based on CRISPR, the gene editing tool that won its inventors the Nobel Prize in 2020. The other is made by Bluebird Bio and works differently.

The 2 gene therapies are the 1st approved in the U.S. for sickle cell disease. The FDA has previously OK'd 15 gene therapies for other conditions.

Current treatments include medications and blood transfusions. The only permanent solution is a bone marrow transplant, which must come from a closely matched donor without the disease and brings a risk of rejection. No donor is required for the gene therapies, which permanently change DNA in the patient’s blood cells. The goal of the Vertex therapy, called Casgevy, is to help the body go back to producing a fetal form of hemoglobin that’s present at birth — it’s the adult form that’s defective in people with sickle cell disease. CRISPR is used to knock out a gene in stem cells collected from the patient.

Bluebird’s treatment, called Lyfgenia, aims to add copies of a modified gene, which helps red blood cells produce "anti-sickling" hemoglobin that prevents or reverses misshapen cells. When patients get the treatments, stem cells are removed from their blood and sent to a lab. Before getting the altered cells back, they must undergo chemotherapy. The process requires at least 2 hospitalizations, 1 lasting 4 to 6 weeks.

The FDA’s approval is the 1st for Bluebird’s treatment; Vertex has been previously authorized in Britain and Bahrain.

5/5/2025.

Researchers have found that a rare genetic condition may allow some people to thrive on as little as 3 hours of sleep, according to a study published in Proceedings of National Academy of Sciences in March 2025. A mutation in salt-induced kinase 3 (hSIK3-N783Y) is identified in a human subject exhibiting the natural short sleep duration trait.

Ying-Hui Fu, the latest study’s co-author and a neuroscientist and geneticist at the University of California, San Francisco, and her team found a rare genetic mutation in a mother and daughter. In previous studies, the Sik3 gene was previously linked to sleepiness, but this newest gene variation appears to combat that.

Researchers genetically modified mice to carry the specified mutation that was believed to be linked to needing less sleep. The mice needed about 31 minutes less sleep a day than the mice that didn’t carry the mutation. "This suggests that the mutation might shorten sleep by supporting brain homeostasis — a theory that sleep helps to reset the brain," Fu told Nature.