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Cityblog Science Club

Cityblog introduces Science club for young and old interested readers. This section is edited by  Riya Naik (CT USA)

Link of the Day

Genetic discovery holds implications for better immunity, longer life

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Laboratory-evolved bacteria switch to consuming carbon dioxide for growth



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Laboratory-evolved bacteria switch to consuming carbon dioxide for growth







Could cytotoxic T-cells be a key to longevity?







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Romania's forests under mounting threat—along with rangers

Sorry, wrong number: Statistical benchmark comes under fire

Flu Season Is Here and Cases Are on the Rise

Flipping a molecular switch can turn warrior ants into foragers

Ancient Egyptians gathered birds from the wild for sacrifice and mummification: DNA study rejects the idea that…

Research reveals new state of matter: a Cooper pair metal





Ancient gas cloud shows that the first stars must have formed very quickly

New printer creates extremely realistic colorful holograms

'Artificial leaf' successfully produces clean gas



Time ticks away at wild bison genetic diversity









By targeting flu-enabling protein, antibody may protect against wide-ranging strains: The findings could lead to a…

Mathematicians prove a theorem that would help calculate the movement of water in porous rock

Engineers develop a new way to remove carbon dioxide from air: The process could work on the gas at any concentrations, from power plant emissions to open air



Bioprinting: Living cells in a 3D printer




Mathematicians report way to facilitate problem solving in queueing theory

Nobel Prize in Chemistry 2019: Lithium-ion batteries

Lifestyle is a threat to gut bacteria: Ötzi proves it, study shows





The violent history of the big galaxy next door

Atlantic Ocean may get a jump-start from the other side of the world



Tiny, biocompatible nanolaser could function inside living tissues: Nanolaser has potential to treat neurological disorders or sense disease biomarkers

Implanted memories teach birds a song: Discovery boosts understanding of how human brain learns speech





Saturn surpasses Jupiter after the discovery of 20 new moons: And you can help name them!







Molecule links weight gain to gut bacteria

Losing genes may have helped whales’ ancestors adapt to life under the sea



Algorithms could stop an 'internet of things' attack from bringing down the power grid

Study sheds new light on how the Earth's crust was formed





Ancient DNA reveals the first glimpse of what a Denisovan may have looked like



Renewable bonds



Atlantic Ocean may get a jump-start from the other side of the world



Gravity surveys using a mobile atom interferometer

People can see beauty in complex mathematics: Discovery may make abstract maths more accessible to children

Chameleon inspires 'smart skin' that changes color in the sun: A new concept in the field of photonic crystals



Breakdown in coral spawning places species at risk of extinction



Riya's Blog

Author/Editor Science club runs blog
http://riyaongentics.blogspot.com


The Potential of CRISPR




Introduction:

Genome editing is a method utilized by the biologists to modify the genetics in order to change the traits of that particular organism. The biologists can also apply the technique of genome editing to delete certain genes which can cause diseases in an organism. This deleted gene can be replaced with another gene. In order to achieve this, the recently developed technology which is known as CRISPR is widely employed. CRISPR has the potential to cure diseases including cancer, cystic fibrosis, blood disorders, blindness, AIDS, Muscular Dystrophy and Huntington’s Disease. While editing the genome through CRISPR, an enzyme called Cas9 is used as a “tool” that cuts the DNA at a specific location for adding or deleting the fragments. Currently, the Cas9 enzyme is widely accepted, the Cas13 enzyme is also exhibiting that some potential benefits. Although CRISPR has promising results of curing certain disease, there are ethical questions which need to be considered. This blog summarizes various researches conducted that address the potential of CRISPR. This blog also includes the various ethical debates around the utilization of CRISPR. 

The History of CRISPR:

 The idea of CRISPR was first discovered in 1987 in E.Coli, by the scientists who were analyzing the role of the genes in phosphate metabolism. In 1993, CRISPR segments were discovered in the archaea, single-celled organisms, Haloferax Mediterranei. In the initial years of the 2000s, the similarity of these fragments to that of the bacteriophages, archaeal viruses and plasmids suggested that the CRISPR can be a part of the immune system of bacteria and archaea. Once this was discovered, scientists were eager to research the mechanism of genetic elements which destroys the other genetic element. The papers published by scientists suggested that the CRISPR/Cas “cut” the invading DNA utilizing the information from the CRISPR spacers. Spacers are inserted into the CRISPR arrays and then utilized as the “guides” to determine and inactivate the invading DNA. Certain RNA fragments, crRNA and tracrRNA, which are produced by the virus-resistant bacteria from different locations are required for cleaving the DNA. These fragments can guide the Cas9 enzyme which later cuts the DNA. The scientists later combined the RNA fragments and tagged them as “guide RNAs”. This proved to be significant research as editing genomes was now available. 
                                                                     Abstract:
The newly developed technique, CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats, is based on the bacterial “immune system”. CRISPR-Cas9 system was discovered in the 1970s in the E.Coli bacteria. This system is naturally found in the bacteria as an anti-infection mechanism. If an analogy is to be drawn, the CRISPR-Cas9 system can be compared to the antibodies in humans. When the bacteria sense a viral invasion, it targets the viral DNA and creates strands of this targeted DNA. These fragments are known as the “CRISPR fragments” and are stored as a memory when there is an invasion by the same virus. If there is an invasion by the same virus, the CRISPR fragments produce RNA which later targets the viral DNA. The Cas9 enzyme functions to destroy the viral DNA. Similarly, in the lab, a biologist can target a specific sequence of the gene and use the CRISPR “scissors” to cut the DNA at a specific site. Scientists aim to apply this technique for cancer cures, disease prevention and as a treatment to the genetic diseases. If applied properly, this technique can be useful for research and disease prevention. However, there are many ethical dilemmas. Although this is a useful technology to treat diseases, the real question is whether or not the biologists are “playing Gods” by editing and modifying the genes. These days it is possible to modify or enhance the genetics of an unborn child through the application of CRISPR. Parents can choose the appropriate genes which will help their unborn child and can also delete the genes with a mutation. This can prove helpful for the unborn child to avoid having the genetic disease. However, choosing genes that can enhance the potential of that particular child can result in the unfair advantages to that child. Genetically modified children can have exceptional abilities which might be uncommon in other children. Also is it ethical to change the genes of a child without his or her consent? This remains a common debate in eugenics which involves the modification of genes of a particular person. But this is definitely a valuable technology that can serve as a solution to the different genetic diseases. 


CRISPR potential as a cancer cure:

With the newly developed technique, CRISPR, there is a possibility of curing cancer without
painful chemotherapy. The possibility of curing CRISPR was tested for the first time in China. The T-cells of the lung cancer patient were obtained. The PD-1 genes
1 were “switched off” with the help of CRISPR. PD1, “Programmed Cell Death Protein” produces signals which turn off the immune response and hence prevent the damage of the healthy tissues by the T-Cells. In cancer cells, this checkpoint is disabled and cancer grows without any check. The scientists in China hoped that knocking PD1 off can help the T-Cells to identify cancer and destroy the cancerous cells. When the patients were monitored for 6 months, the patients were doing fine. The first T-Cell injections were successful. The phase two trials are currently being held. This involves the trials to be tested on esophageal cancer patients. In order to implement CRISPR, further research still needs to be done.

CRISPR potential for genetic diseases cure:

CRISPR can be a technique to cure genetic diseases while the fetus is still in the uterus. Scientists are aiming to prevent the inheritance of genetic mutations through CRISPR. In order to do this, scientists inject an RNA sequence in the nucleolus of a stem cell or a zygote. This RNA sequence guides the Cas9 enzyme which leads to the desired DNA sequence. The Cas9 enzyme then “nicks or cuts” the sequence. Introducing an appropriate sequence to the DNA can result in the deletion of the mutation. This indeed is important research that might prevent genetic diseases in the future. In fact, a Netherland based stem cell research scientist, Hans Clevers, was successful in knocking off the cystic fibrosis gene in human stem cells (Grens, 2013). The target of this team was the Cystic Fibrosis transmembrane conductor receptor. Intestinal cells from two pediatric patients who were homologous for the gene were obtained and extracted. A mutation in this receptor results in Cystic Fibrosis. A mutation in this receptor is also responsible for an accumulation of mucous fluid in the pulmonary and gastrointestinal cavities, thus, causing cystic fibrosis. Introducing a donor plasmid served as a replacement sequence in the mutated allele. The cells which were isolated and cultured were proven to have a non-mutated delta F5082, which is a common mutation causing cystic fibrosis. Along with Cystic Fibrosis, Duchenne Muscular Dystrophy is a genetic disease that affects 1 in 3500 male births (“About Duchenne Muscular Dystrophy,” 2013). This disease is caused by a mutation or alteration of the DMD gene, the largest known human gene, which is responsible for the production of the protein Dystrophin. This protein is important for the strengthening and protection of muscle fiber. Due to the absence of this essential protein, the muscles of the lower limbs start getting weak which eventually progresses to the entire body. Thus causing weakness and loss of function in the muscles. As this is an X-linked recessive disorder3, this disease is found in the males. Various labs have utilized the CRISPR technique to delete the mutations on exon 234 in the mice which causes muscular dystrophy. After deleting the mutation, the scientists reported the production of the dystrophin fibers. They also reported an improvement in grip strength, force generation, and decreased fibrosis. Thus, CRISPR is a promising cure for Muscular Dystrophy. Similarly, the researchers at the Columbia University Medical Center and the University of Iowa have employed CRISPR to repair the gene mutation which causes Retinitis Pigmentosa, a genetic condition that affects 1.5 million cases(“CRISPR Used to Repair Blindness-causing Genetic Defect in Patient-derived Stem Cells,” 2019). The researchers isolated skin cells belonging to the patient, in order to produce stem cells. After creating the stem cells, the researchers implemented CRISPR to delete the faults in the RPGR Gene ORF Region5. Because of the repetitive sequence and length of this gene, this gene remains a challenge to modify. However, the scientists were successful in editing this disease-causing gene. The next task for the scientists was to convert the induced stem cells to the retinal cells. This study suggested the importance of CRISPR to heal other diseases related to photoreceptor degeneration (Bassuk, Zheng, Li, Tsang, & Mahajan, 2016). 
                                        The potential of CRISPR in tissue engineering:
Tissue engineering is a developing field, where scientists develop a polymer scaffold that is implanted in the human body to replace the damaged tissue. For example, the common treatment for coronary heart disease is to take autologous arteries or veins and place it in the damaged site of the coronary disease. There are many advantages of implanting the autologous blood vessel including the

reduction in the risk of an immune response. However, there is an increased risk of infection at the site the vessels were extracted. The most common infection type is the Great Saphenous Vein Harvest Site infection. This kind of infection is diagnosed when the great saphenous vein is used as a coronary artery implant. If the mammary artery is used as an implant, in some cases, it can result in the resistance in the blood flow which can ultimately cause a heart attack. Hence, a solution to these problems is introduced by biomedical engineers. This solution is Tissue Engineering. In tissue engineering, a biodegradable polymer like PGA, PLA can be used as a scaffold to implant as a graft. These scaffolds are covered with autologous stem cells to facilitate the growth at the site of damage. The biggest challenge to this solution is the stem cell differentiation. However, with CRISPR stem cell differentiation can be possible through gene editing. 

The Potential of CRISPR to cure AIDS:

 AIDS is one of the leading diseases worldwide with more than 35 million people affected (Ophinni, Inoue, Kotaki, & Kameoka, 2018). This is caused by the Human Immunodeficiency Virus or HIV which destroys the human immune system. This virus destroys the T helper cells, a type of white blood cell which is a part of the immune system and replicates itself in the destroyed T Helper cells, thus preventing an individual’s immune system to fight off any other infections. In order to cure AIDS, researchers adopted CRISPR which resulted in some promising outcomes. The researchers targeted the Tat and Rev genes, which are HIV regulatory genes, through the use of guide RNAs6. Most importantly, the CRISPR treatments showed no signs of decreased cellular functions or off-target gene knockouts. This in-vivo research demonstrates a potential treatment for AIDS. 

The Potential to cure Blood Disorders:

Due to a mutation or an alteration in the Beta Thalassemia gene( responsible for producing hemoglobin) deformed shape of the Red Blood Cell is produced. Hemoglobin is crucial for transporting oxygen throughout the blood. A mutation in the Beta Thalassemia gene results in a faulty shape in the blood cells. The “sickle shape” of the RBCs causes clumping in the blood vessels. This can cause a lot of problems including reduced blood circulation and much worse: organ failure. Thus, many researchers are attempting to find a cure to “Sickle Cell Anemia”. A possible solution for curing the sickle cell anemia is turning on the gene that expresses fetal hemoglobin. Normally, the gene that produces fetal hemoglobin is turned off after birth. However, by disrupting the BCL11 gene (which is responsible for turning on the fetal hemoglobin gene), the researchers are hoping to cure sickle cell anemia. CRISPR can be used to disrupt the BCL11 gene. Researchers obtained Human Hematopoietic Stem Cells from patients suffering from Sickle Cell Anemia. The researchers later disrupted the BCL11 gene and transmitted it in the mice. It was reported that the mice had an increased level of fetal hemoglobin production and resistance to sickle cell anemia. More interestingly, Vortex Pharmaceuticals, Sangamo Therapeutics and CRISPR Therapeutics have received FDA approval to conduct human trials to cure sickle cell anemia. 
                                                  The Potential to cure Huntington’s Disease:
Huntington’s Disease is an autosomal dominant disorder, which means that only one copy of the mutated gene can cause the disease. This disease results in the degeneration of the nerve cells in the brain which affects cognitive abilities and also results in involuntary movements. Repetition in the Huntingtin gene causes the development of toxic materials which usually leads to the damage of the neurons. Through CRISPR, Polish researchers were successful in deleting the repetitive sequence and inhibit the production of toxic materials. 


What is Cas13?

CRISPR/Cas9 system is based on the modification of the DNA where the Cas9 enzyme “cuts” the
specific DNA sequence and the cell repair mechanism, Non-Homologous End Joining (NHEJ)
6 or Homology Directed Repair (HDR)7, thus changing the genome. This can lead to the expression of the desired proteins in order to treat a specific disease. However, editing the genome can have undesired effects. What if a wrong sequence is targeted? The proteins expressed can result in undesired effects which might include cancer. That is why the Cas13 enzyme which is functions in knocking out the messenger RNA through the guide RNAs8. As RNA codes for the polypeptides (the protein chain), the protein expression can be altered in order to cure the diseases. A recent research study by Zhang Lab suggests that cancer-related protein expression can be reduced. 

The Ethical Debate around CRISPR:

With the promising technology of genome editing through CRISPR, it is now possible to enhance the genetic traits of an embryo. However, editing the genome of the embryo paves way for many ethical debates. A few questions are considered to question the ethicality of genome editing. Is it ethical to edit the genome of an embryo without its consent? Is it possible that through genome editing, the scientists are encouraging social discrimination? Is the genetically enhanced individual getting an unfavored advantage over the others? These questions certainly need to be considered for the germline genome edition. To discuss these questions, the United States National Academies of Science, Engineering, and Medicine had invited the Chinese Academy of Science and the United
Kingdom’s Royal Society in 2015 to discuss the ethical guidelines for CRISPR
(Brokowski & Adli, 2019). This committee decided that somatic editing is permissible for the cure of genetic
diseases. Nevertheless, the genome editing for the purpose of the enhancement
is not permissible. To date, these guidelines are maintained as embryo research
still remains controversial. 
 

What are your opinions about CRISPR and the ethical debate surrounding it? Please comment below. 




Notes:

1: PD1 genes or programmed cell death protein regulates the human immune system by reducing the immune system attack and promoting tolerance for native cells by minimizing T-Cell inflammatory
activity

2: delta F508 is a gene which is commonly mutated in a cystic fibrosis

3: X-Linked Recessive Disorder: These types of disorders are associated with the sex chromosome: X. As men contain one X gene and one Y gene, the mutation in the X gene is expressed. 

4: Exon 23: An exon is a segment on the RNA or DNA which contains the “instructions” for creating polypeptides or protein sequences. Therefore, a mutation in this exon causes muscular dystrophy

5: RPGR Gene ORF Region: Proteins, encoded by this gene, interact with the outer rod photoreceptors and are responsible for their sustenance. Mutation in this gene is associated with retinitis pigmentosa. 

6: Non-Homologous End Joining (NHEJ): A
DNA Repair mechanism found in many organisms including bacteria and man. There
are a series of proteins that join the broken DNA ends. Example of such a
protein is DNA Ligase

7: Homology Directed Repair: a DNA Repair mechanism by introducing d DNA donor which is similar to the sequence of the broken DNA sequence. 

8: guide RNAs: an RNA sequence which binds
to the desired sequence and thus is necessary for Cas binding




Work Cited:



About Duchenne Muscular
Dystrophy. (2013). Retrieved August 26, 2019, from Genome.gov website:
https://www.genome.gov/Genetic-Disorders/Duchenne-Muscular-Dystrophy

Bassuk, A. G., Zheng,
A., Li, Y., Tsang, S. H., & Mahajan, V. B. (2016). Precision Medicine:
Genetic Repair of Retinitis Pigmentosa in Patient-Derived Stem Cells.
Scientific Reports, 6(1).
https://doi.org/10.1038/srep19969

Begley, S. (2018, July 16). Potential DNA Damage from
CRISPR has been ‘seriously underestimated,’ study finds. Retrieved August 1,
2019, from STAT website:
https://www.statnews.com/2018/07/16/crispr-potential-dna-damage-underestimated/

Burik, A. (2018,
February 28). Could A More Precise CRISPR/Cas9 System Treat Huntington’s...
Retrieved August 27, 2019, from Labiotech.eu website:
https://labiotech.eu/medical/crispr-cas9-huntingtons-disease/

CRISPR Part 1: A Brief
History of CRISPR | Twist Bioscience. (2017, December 12).Retrieved August 29,
2019, from Twistbioscience.com website:
https://twistbioscience.com/company/blog/crispr-part-1-a-brief-history-of-crispr

Clara Rodríguez
Fernández. (2019, July 23). 7 Diseases CRISPR Technology Could... Retrieved
August 26, 2019, from Labiotech.eu website:
https://labiotech.eu/tops/crispr-technology-cure-disease/

CRISPR Timeline. (2018,
December 7). Retrieved August 29, 2019, from Broad Institute website:
https://www.broadinstitute.org/what-broad/areas-focus/project-spotlight/crispr-timeline

CRISPR/Cas9 Treatment
for Duchenne Muscular Dystrophy. (2018, June 29). Retrieved August 26, 2019,
from Muscular Dystrophy News website:
https://musculardystrophynews.com/crispr-cas9-treatment-dmd/

CRISPR Used to Repair
Blindness-causing Genetic Defect in Patient-derived Stem Cells. (2019, July
10). Retrieved August 26, 2019, from Columbia University Irving Medical Center
website:
https://www.cuimc.columbia.edu/news/crispr-used-repair-blindness-causing-genetic-defect-patient-derived-stem-cells

Dr. Francis Collins. “A
CRISPR Approach to Treating Sickle Cell.”
NIH Director’s Blog, 4
Apr. 2019,

directorsblog.nih.gov/2019/04/02/a-crispr-approach-to-treating-sickle-cell/. 

Accessed 27 Aug. 2019.

Facts About Retinitis
Pigmentosa | National Eye Institute. (2012). Retrieved August 26, 2019, from
Nih.gov website:
https://nei.nih.gov/health/pigmentosa/pigmentosa_facts

Gearing, M. (2017).
CRISPR 101: RNA Editing with Cas13 and REPAIR. Retrieved August 27, 2019, from
Addgene.org website:
https://blog.addgene.org/crispr-101-rna-editing-with-cas13-and-repair

Gebski, B. L., Mann, C.
J., Fletcher, S., & Wilton, S. D. (2003). Morpholino antisense
oligonucleotide induced dystrophin exon 23 skipping in mdx mouse muscle.
Human Molecular Genetics, 12(15), 1801–1811.
https://doi.org/10.1093/hmg/ddg196

Genetics Home Reference.
(2014). DMD gene. Retrieved August 26, 2019, from Genetics Home Reference
website:
https://ghr.nlm.nih.gov/gene/DMD

Homology-directed repair
(HDR) - Innovative Genomics Institute (IGI). (2018). Retrieved August 27, 2019,
from Innovative Genomics Institute (IGI) website:
https://innovativegenomics.org/resources/educational-materials/glossary/hdr/

Improved Genetic
Diagnostics of RPGR ORF15 - associated Retinal Dystrophy. (2018). Retrieved
August 26, 2019, from Blueprint Genetics website:
https://blueprintgenetics.com/resources/improved-genetic-diagnostics-of-rpgr-orf15-associated-retinal-dystrophy/

Ishino, Y., Krupovic,
M., & Forterre, P. (2018). History of CRISPR-Cas from Encounter with a
Mysterious Repeated Sequence to Genome Editing Technology.
Journal of Bacteriology, 200(7).
https://doi.org/10.1128/jb.00580-17

‌News-Medical. (2019, April 30). Manipulating RNA sequences
using CRISPR-Cas13. Retrieved August 27, 2019, from News-Medical.net website:
https://www.news-medical.net/life-sciences/Manipulating-RNA-sequences-using-CRISPR-Cas13.aspx



News-Medical. (2019,
April 30). Manipulating RNA sequences using CRISPR-Cas13. Retrieved August 27,
2019, from News-Medical.net website:
https://www.news-medical.net/life-sciences/Manipulating-RNA-sequences-using-CRISPR-Cas13.aspx

Ophinni, Y., Inoue, M.,
Kotaki, T., & Kameoka, M. (2018). CRISPR/Cas9 system targeting regulatory
genes of HIV-1 inhibits viral replication in infected T-cell cultures.
Scientific Reports, 8(1).
https://doi.org/10.1038/s41598-018-26190-1

Questions and Answers
about CRISPR. (2018, August 4). Retrieved August 26, 2019, from Broad Institute
website:
https://www.broadinstitute.org/what-broad/areas-focus/project-spotlight/questions-and-answers-about-crispr

Regalado, Antonio.
“CRISPR Is Being Used to Treat a Patient with a Dangerous Blood Disease.”
MIT Technology Review, MIT Technology Review, 25 Feb. 2019,
www.technologyreview.com/f/613013/crispr-is-being-used-to-treat-a-patient-with-a-dangerous-blood-disease/.
Accessed 27 Aug. 2019.

(2019). Retrieved August
27, 2019, from Gizmodo.com website:
https://gizmodo.com/new-study-finds-unintended-consequences-of-crispr-gene-1827692218

(2019). Retrieved August
27, 2019, from Ebi.ac.uk website:
https://www.ebi.ac.uk/interpro/potm/2004_7/Page2.htm

RPGR retinitis
pigmentosa GTPase regulator [Homo sapiens (human)] - Gene - NCBI. (2019).
Retrieved August 26, 2019, from Nih.gov website:
https://www.ncbi.nlm.nih.gov/gene/6103

Shmakov, S. A., Sitnik,
V., Makarova, K. S., Wolf, Y. I., Severinov, K. V., & Koonin, E. V. (2017).
The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific
Mobilomes.
MBio, 8(5).
https://doi.org/10.1128/mbio.01397-17

            What are HIV and AIDS? (2019, April 4). Retrieved
August 26, 2019, from AVERT 




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Riya's Blog


http://riyaongenetics.blogspot.com


The Benefits of Tissue Engineering and Regenerative Medicine


With the increasing number of patients enlisted in the transplant list, the supply of healthy organs is quite limited. This is demonstrated in the graph below:






The graph signifies that the number of patients enlisted on the transplant waitlist far surpasses the donors. This is alarming as there are so many patients whose life depends upon a new and healthy organ but organs are not available to them. 

            However, a new and growing branch of science which is known as tissue engineering is developing to propose a solution to this problem. With the help of various techniques implemented in tissue engineering, patients can receive temporary grafts until a healthy organ is available to them. 

            The various techniques and material implemented in tissue engineering to synthesize new grafts include:

·         Stem cells or regenerative medicine

·         Polymer scaffolds

·         Reprogramming or regeneration of the iPS cells

·         Amniotic fluid or the placental stem cells

·         Adult stem cells

·         Xenogenic cells



            All these methods or materials are currently being applied or being researched for implementing in the development of the graft. The importance of these materials have been discussed below:

Stem cells or regenerative medicine:

            I just cannot stop emphasizing on the importance and the greatness of the stem cells. Stem Cells are the type of cells that have the potential to develop into another tissue type. For example, the embryonic stem cells which are pluripotent, in nature, can differentiate into liver cells. Whereas the adult stem cells are the type of stem cells which are multipotent, this means their ability to divide into a germline is limited. The types of stem cells are summarized in the table below:























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Riya's Blog










Have you ever been in a situation where you had enough ice cream but still crave for more? I have been in this situation while on a beach. Beach is a nice place to relax and welcome the summer vacation. Going to a beach with friends is already very exciting and packing for the beach is more exciting. We had packed a lot of food to enjoy on the beach. There were a lot of delicious chocolate chip cookies, marshmallows, pancakes, waffles, and etc. You name it, we had it. After eating all of the food we had packed, one of my friends saw an ice cream shop. Many people were full and their “sugar cravings” was satisfied. However, half of my friends wanted to eat ice cream, including myself. This provoked a thought that why some people crave for sugar more than others? Do the genes have something to do with it?  Do we inherit the cravings we feel to eat sugar?
To investigate whether there are genes involved in the sugar cravings, an international team studied the genes of more than 6,500 Danish people where they found that the people who craved for the sugar had two variants of  FGF21. FGF21 is a gene that provides instruction for a hormone that is linked with the food regulation in rodents and the non-human primates. Additionally, the new study suggests that this hormone, secreted by the liver, modulates appetite in hormones.
  FGF21 is a short form of “Fibroblast Growth Factor 21” which is a hormone responsible for cellular metabolism and regulation. This protein inspires or motivates the body to indulge in glucose, aka, “sugar” which is then stored in the adipose, aka “fat tissue”. People with metabolic diseases are observed with high levels of FGF21. To test the hypothesis that the FGF21 hormone induces a significant amount of sugar consumption, the researchers conducted an experiment with the mice where there were mice with no FGF21 and mice with FGF21. When given a choice between a standard diet and a high sucrose diet, the mice with no FGF21 preferred a standard diet. Whereas mice with FGF21 opted for a high sucrose diet. Therefore they concluded that “the loss of FGF21 increases macronutrient-specific intake of mono-disaccharide sugars”(“FGF21 Mediates”). 
  However, this hormone has positive functions, too. This hormone in the liver tells the brain when the body does not need sugar. If we want this hormone to not misbehave with us, we need to ensure that it works right for us. That means this hormone is ought to stay happy to achieve summer weight loss goals. Here are some tips to make the FGF21 work right for you:
1.     Eat right sugars
1.     Eating right sugars
like fruit can help control the sugar cravings
2.     Eat a protein filled breakfast
1.     Protein helps you stay
satiated for a long time
3.     Detox your liver
1.   Detoxifying the liver


can be helpful 


2.   Here is a link to a




Following these tips can be helpful in keeping this hormone happy!
Good luck and have a great summer!
References:
“FGF21 Fibroblast Growth
Factor 21 [Homo Sapiens (Human)] - Gene - NCBI.”
National Center for Biotechnology Information, U.S. National Library of Medicine,
www.ncbi.nlm.nih.gov/gene/26291.
Maron, Dina Fine. “Crave
Sugar? Maybe It's in Your Genes.”
Scientific
American
, 2 May 2017,
www.scientificamerican.com/article/crave-sugar-maybe-its-in-your-genes/.
Maron, Dina Fine. “Crave
Sugar? Maybe It's in Your Genes.”
Scientific
American
, 2 May 2017,
www.scientificamerican.com/article/crave-sugar-maybe-its-in-your-genes/.
Von Holstein-Rathlou,
Stephanie, et al. “FGF21 Mediates Endocrine Control of Simple Sugar Intake and
Sweet Taste Preference by the Liver.”
Cell
Metabolism
, U.S. National Library
of Medicine, 9 Feb. 2016,

www.ncbi.nlm.nih.gov/pmc/articles/PMC4756759/
.

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Dream Genes
                                    Author runs blog http://riyaongenetics.blogspot.com




Last night, I was dreaming about a chocolate river and peppermint grass surrounding me. I was having the time of my life consuming these wonderful flavors. I was in the middle of this chocolate dream and alas the alarm went off. Then, I realized it was all because of the movie I watched the previous night, Charlie and the Chocolate Factory Dreams. Now for those who are not aware of this movie, it is an adaptation of Roald Dahl’s novel, Charlie and the Chocolate Factory, where a poor boy Charlie Bucket gets an opportunity to visit Willie Wonka’s famous chocolate factory and all these wonders relating to chocolate. Dreams are an interesting component of anyone’s sleep because they seem so unreal. It is common for people to wake up suddenly after encountering a nightmare or it is possible that many people wish to stay in their perfect dreams. There are instances where people have reported that they have seen dreams which are not closely related to their real-life. How and why do we see dreams?

            Let us talk about why we see dreams? Dreams are seen when we are in the REM stage of sleep. REM or Rapid Eye Movement is the stage of sleep where the body is resting, however, the brain is still active. Now, what happens when the brain is active? The brain thinks, rather it can be said the emotional center of the brain stimulates those weird things we perceive in the dreams. But believe it or not, our brains are recollecting the daily-scenarios we encounter and plays it to us. It is like watching the same movie again but with a different perspective. Isn’t it interesting? So those completely unrelated things we see are actually connected to our real-life. That is why many artists rely on dreams to get a different perspective on their idea. Hence, sometimes considering to sleep is a good idea to get brilliant ideas! Because our brain does a lot of work for us when it is actually resting. Many theories have been developed to explain why we dream. One of the theory is that sometimes the brain presents us dreams to escape reality through making connections of emotions and narrating a completely different story. Sometimes, we see nightmares because of excessive stress and anxiety. Perhaps the brain is trying to indicate through a nightmare that we need to go a little easy in the matters of stress.

            Now let us talk about how we see dreams. One recent study discovered the role of the Chrm1 and Chrm2 genes in making our transition from the non-REM sleep to REM sleep mode.  In simple words, non-REM sleep is a “dreamless stage of sleep” contrasting the REM stage of sleep where we normally perceive a dream. The Chrm1 and Chrm2 genes help us to transition from the non-REM stage to the REM stage. This research is important as physiatric disorders and sleep-disorders are linked. So further research in the topic matter can help us in treating the sleep disorders to help psychological disorders.

            Next time when you dream about good things, thank your Chrm1 and Chrm2 genes which facilitated the transfer from the non-dreamy state to the dream state where you can actually escape the reality. But, if you happen to encounter a nightmare, do not be mad at these genes, just thank them to alert you that your stress levels are high.




Works Cited:

            Pappas, Stephanie. “Your Dreams May Come from These Two Genes”. LiveScience. Com. August 29, 2018. Date Accessed: 11 April 2019. https://www.livescience.com/63459-dream-genes-rem-sleep.html

Nierenberg, Cari. “REM vs. Non-REM Sleep: The Stages of Sleep”. LiveScience. Com. July 19, 2017. Date Accessed: 11 April 2019. https://www.livescience.com/59872-stages-of-sleep.html

            Roland, James. “Why Do We Dream?” Healthline. Com. Date Accessed: 11 April 2019. https://www.healthline.com/health/why-do-we-dream



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The importance of FOX1 Genes in the brain development 
Labeled diagram of neuron cells

We execute numerous numbers of functions every day. Some are voluntary like reading, exercising, writing or learning and involuntary like breathing, digesting or maintaining homeostasis or in other words maintaining the normal balance of the body.

            Long story short: we need our brains to breathe, eat, study, exercise and even dream! Our brains are comprised of trillion cells. The two types of brain cells-neurons and glial cells- are crucial for brain functioning. Neurons basically transmit the electrical signals throughout the body. The glial cells just provide insulation to these neurons to prevent damage to these precious brain cells which basically guide us to do everything we do every day. That is why glial cells are extremely important. But, still how does the body determine what cells become neurons and what becomes glial cells? Probably, this question motivated the scientists at SISSA to research about these brain cells and their origins.

            During research, scientists have discovered the importance of FOXg1 gene in the origins of the glial and neuron cell. As the prior knowledge tells us that when the FOX1 gene is mutated, there are abnormalities in the development of the structure of the brain giving rise to FOXG1 syndrome.  Previously it was suggested that the stem cells gave rise to the neurons and which in turn produce the glial cells through astrocytes. Astrocytes provide nutrients to the neurons and modulation of the neuron activity. However, what causes this process of transition was unknown. The SISSA researchers have now discovered the importance of FOXg1gene in the developmental processes.

            During the research, the scientists discovered that the level of FOXg1 gene expression reduces when the astrocyte production begins. Not only that, the FOXg1 “controls” the master genes and implies the choice between that of astrocytes and neurons.

            Now, why is this research important? This research is important because we now can better understand the role of FOXg1 genes in neurological disorders including the FOXg1 syndrome causes abnormal brain structure leading to intellectual disability. The FOXg1 gene plays an important role in brain development and perhaps if this function is compromised it is likely to create a cascade of problems.

However, with this research, the possibility of gene therapy is perceived to overcome the problem of the shortening time of the generation of the astroglial cells which is common in the abnormal brain development syndrome. Also, researching the importance of stem cells in developmental pathways can be useful to research more about the gene therapies to cure such abnormal brain developmental syndromes.


Works Cited:

“Discovery of the genetic “conductor” of brain stem cells. Science Magazine. https://www.sciencedaily.com/releases/2019/03/190304100038.htm. Date published: March 4, 2019. Date Accessed: March 24, 2019

FOXG1 syndrome - Genetics Home Reference - NIH”. U.S. National Library of Medicine. https://ghr.nlm.nih.gov/condition/foxg1-syndrome#genes. Date Accessed: March 24, 2019
















Promising Molecule Drug aimed to treat cancer



The common aim for the majority of the biological scientists is to tackle Cancer. Cancer is a growing complication due to lifestyle changes like long exposure to the UV light, disrupted sleep cycles, stress, and pollution. Many people experience stress caused by their workload. For personal or professional reasons it is a common tendency to compromise sleep which results in a disrupted circadian rhythm. In simple words, circadian rhythm means the normal sleep cycle of human beings. In research named”Circadian Rhythm Disruption in Cancer Biology” conducted by Christos Savvudis and Micheal Koutsilieris, it is cited from the International Agency for Research on (IARC) 2007 that, “shiftwork that involves circadian disruption [as] probably carcinogenic to humans”. Therefore, the disruption in circadian rhythm is linked to the development of cancer in humans.

            Nevertheless, the scientists at the University of Southern California have used the disrupted circadian rhythm as a tool to treat cancer. A disrupted body clock negatively affects the functioning of the normal cells. The same concept applies to the cancer cells. The researchers hypothesized that if the circadian clock of the cancer cells is disrupted it is possible to kill or at least hurt the cancer cells (“University”).

            The scientists at the University of Southern California discovered a molecule named GO289 which interacts with a protein which regulates the circadian rhythm of the cells. This interaction also disrupts the four other proteins that are essential for cell growth and survival. These proteins are used by the cancer cells to develop; however, disrupting this cycle can potentially cease the metastasis or spread of cancer. “The GO289 can jam the cogs of the cell’s circadian clock, slowing its cycles. And it can do so with little impact to healthy cells” (“University”).

            To test the efficiency of this new drug, “Go289” the researchers tested it on the human bone cells cancers. It was observed that the drug slowed the tumors; circadian clock. Additionally, it was tested on the human kidney cancer cells and the mice with acute myeloid leukemia. GO289 affected cancer cell metabolism and other circadian cycles that contributed to the growth of cancer.





The above photograph demonstrates the disrupted circadian rhythm of the human bone cancer cells caused by the drug molecule, GO289.

Works Cited:


The University of Southern California. (2019, January 23). Cancer has a biological clock and this drug may keep it from ticking: A promising drug slows cancer's circadian clock, halts its spread. ScienceDaily. Retrieved January 27, 2019, from www.sciencedaily.com/releases/2019/01/190123144524.htm






2018 Genetics Review

As we enter into the year 2019, we expect more scientific questions to be answered; we expect the humankind to progress by discovering unusual scientific phenomena and we expect to provide solutions to the problems through science. However, we all can gather new knowledge by developing from our previous knowledge. 2018 has been a year where new knowledge was available in the field of genetics. This blog is all about 2018 at a glance for genetics.
One such landmark event is the discovery of a human RNA which activates innate immunity when attacked by a virus. Research published in the Journal of Biological Chemistry reveals an RNA molecule which plays an important role in the defense against the virus. This RNA is known as the nc886. “Nc” means noncoding, therefore, this RNA never codes proteins. Nevertheless, it activates the chain of events that destroys viruses. This research can be important to study the human immune system.
Along with the research in the human immune system, a study issued in the journal Cell reported the role of viruses in shaping human evolution. Prior to this research, many believed that the ancestors of the human beings, Neanderthals, moved out of Africa to Eurasia and they adapted to the geographic area. However, this new study delineates a new possibility where the Neanderthals adapted mutations which were beneficial against the pathogens and these mutations were inherited by the humans. This research provides us with an insight that the genes inherit adaptations that are advantageous to us.
Moreover, the researchers at the Okinawa Institute of Science and Technology Graduate University have reported a specific transcription factor which changes gene expression, thus, playing a significant role in maintaining the immune system in the mice. The researchers discovered a factor also known as the JunB which stimulates the cells to activate the immunosuppressive function. This can provide us with an understanding of the development of autoimmune disease and cancer immunosuppression. Researcher, Koizumi, declared that this perception of these immune responses in various tissues can help in the treatment of a range of cancers and autoimmune-related diseases like rheumatoid arthritis.
With these researches in the year 2018, the researchers also discovered why Dunkin Donuts and Starbucks is in a profitable business. Because they studied a gene which is a reason behind why we like coffee so much. They found out that some people have inherited bitter taste genes. These genes stimulate a positive response from the brain causing them to drink more coffee. The scientists want to determine the health implications of this bitter taste genes.
Moreover, the biggest breakthrough news in genetics was the world’s first genetically edited babies in China. However, this is a controversial question. But it is significant as many people realized the importance of CRISPR technology. CRISPR/CAS9 is a gene found in the bacteria which is known for cutting the default gene. When bacterias are infected with a virus, they use this gene to “cut” the DNA of a harmful virus. This gene is used to delete the mutated1gene and add the donor gene. The mutated gene is cut by the “scissors” or CAS9 and the donor gene fills the void in the DNA.
The other research is my personal favorite as it is regarding the mitochondria: the energy bank of our body! In my biology class, I was taught that the mitochondria were inherited exclusively from our mothers. After this research done by the mitochondrial disease researcher at the Mayo Clinic at Jacksonville, FLA, it is revealed that the mitochondria are also passed by the fathers. Nevertheless, this claim is still being researched and we will soon understand the details. Isn’t it exciting???!!!
This year has been impressive as many kinds of research have presented us with new information. And it will be interesting to see how this research provides us with a new understanding of genes.   

1= Mutation
Works Cited:




The world’s first genetically edited baby or in fact babies are born! Isn’t that surprising! But first, we need to know if this is true or fake. This blog summarizes the new controversy about the Chinese Professor, He Jiunki, who claims that he has successfully edited faulty genes in twins.
This all started on the 28th of November 2018 when Professor He at the Genome Summit in Hong Kong announced that he was successful in editing the genes of twin girls. The father of the twins was HIV positive whereas the mother was HIV negative. The twins were at the risk of inheriting HIV. However, Professor He with the use of the CRISPR/ CAS9 technology was able to reduce the twin’s risk of inheriting HIV. CRISPR/CAS9 is a gene found in the bacteria which is known for cutting the default gene. When bacteria are infected with a virus, they use this gene to “cut” the DNA of a harmful virus. This gene is used to delete the mutated1 gene and add the donor gene. The mutated gene is cut by the “scissors” or CAS9 and the donor gene fills the void in the DNA. This way the mutated gene is replaced by the donor gene. Nevertheless, all this is done while there exists a single human cell in other words, this is all performed on an embryo. As it is impossible to alter the DNAs in trillions of cells.  A pretty exciting and interesting technology right?
Many professors believe his research untrue because the University he worked did not fund the research, therefore, denying the validity of this claim. Also, many other scientists believe the information untrue as there is no scientific paper backing up his claims. Professor He asserts that he privately funded the research which involved the deleting of the gene of the twins, Lulu and Nana.
Moreover, the whole ethical questions come into the play. Are the genetic engineers playing Gods by going against nature?
Professor He played God and many ethicists believe that this action is unethical as Professor He has deliberately made one twin as a control which can make her susceptible to HIV whereas the other twin is not. CCR5 is a coreceptor protein which provides a way to infect other cells with the HIV virus. Professor He turned the CCR5 gene off in one twin and kept one gene on in the other twin. This action favors one twin over the other.
In conclusion, many ethicists and scientists reject this claim to be untrue. Please let me know your thoughts on the issue in the comment section below.

Work cited:



Mutations that caused evolution in the humans



The human body has evolved over the course of million years to perform highly complex mechanisms which are essential for its normal functioning in addition to complex mechanisms like thinking logically and the development of the language. These mechanisms include the development of the signaling in the nervous system which helps in responding to the stimuli, metabolism to provide energy for carrying out other functions in the body, understanding, and thinking, being able to communicate and even a simple task as holding something which is possible because of the development of the thumb. Ever thought how these developed?
It all starts with our good old friends- Primates.  Evidence for this theory can be the mitochondrial difference of 99% between the chimpanzee and the humans. The mitochondrion is the organelle in the cell which is responsible for the cellular respiration. It produces energy in the form of ATP (Adenosine Triphosphate). As the mitochondria contain their own DNA, they are used to identify how distantly or closely related the species are. Primates were basically arboreal which indicates that they lived on the trees.  The most significant evolution was Bipedalism. Bipedalism is a unique characteristic in the humans which allows them to walk on their two limbs. There have been many speculations about how the ancestors of humans developed bipedalism. This connects to the idea of Natural Selection that Charles Darwin presented in his famous work, Origin of Species. Darwin proposed that an offspring inherits the mutation from the parents. And as this mutation, becomes beneficial in a particular species it stays in the gene pool.  Maybe, a mutation was inherited and was beneficial; thus, remained in the gene pool.
Perhaps, the size of the human brain is a noteworthy evolution which gives us the ability to think and to communicate. We need to appreciate the human ability to do so many things many species cannot. Like the development of more than 100 languages and being able to reason and logically applying knowledge in our everyday lives. Extensive research indicates that genetic changes in the human genome were the main causality behind the brain size enlargement. Gene family which is suspected to be responsible for the brain enlargement is called the DUF1220 (Vallender). This is considered a novel gene. Novel genes are hypothesized to be the reason for the evolution in the human phenotype. The function of the DUF1220 is unknown; however, the researchers have discovered that it is expressed in the brain and the neurons. Another significant finding is that the amount of the gene being expressed increases in primates if they are closer to the human phenotype. Therefore, with larger brains, humans are capable of doing many things yet we sometimes find ourselves using it for the wrong means like cheating on a test! Just learn to appreciate the genes as they do so much for us, for example, they express many proteins so that we think and do good for our society!


Everything you need to know about stem cells

Recently, there have been a lot of speculations about stem cells and their ethicality. The main question is: “Is it ethical to kill an embryo in order to procure stem cells where that embryo has a potential to grow into a human being?” To answer this question we first need to understand what are stem cells? What benefits do they provide us with? What are some disadvantages associated? Can they be used to treat a person who has been diagnosed with a terminal illness like cancer or an organ failure?  
So let us begin with some basics. Stem cells are pluripotent cells, that is, they have an ability to develop into an organism. A zygote, product of a sperm and an ovum fusion, is a classic example of an undifferentiated stem cell. A zygote is a single undifferentiated cell which divides itself to form an embryo. The undifferentiated cells found in an embryo are called the Embryonic stem cells. As the embryo enters its eighth week it is called as a fetus. Here, the stem cells begin to form differentiated cells. These stem cells are called the fetal stem cells. Other types of stem cells are the Adult Stem Cells. These are a rare type of stem cells. Because as the human beings grow and mature, the cells in the body become specialized and lose their pluripotency. However, there are few stem cells found in the bone marrow of an adult. Blood stem cells are an example of adult stem cells.
Being said that, let us talk about how the stem cells are used as the regenerative medicine which is a breakthrough research to help cure terminal illnesses like leukemia, organ failure or are used for a joint replacement. Of the four types of stem cells, embryonic stem cells can be regarded as the most effective in developing into an organ or a tissue. The way it is done is by  “pre specializing”(“What”) the stem cells and inject it into the tissue or the organ where a transplant is needed. When the pre-specialized stem cells meet the growth chemicals they grow into a healthy organ or a tissue. It is an effective method which replaces a transplant. However, the risks of graft rejection still remain, as the developing organ is foreign to the body. Yet there are many advantages of stem cell therapy. They have an ability to cure the irreversible Alzheimer's disease, Parkinson’s disease, liver and kidney diseases. Not only transplants, stem cell research can also help the scientists to understand the patterns of human growth.
Nevertheless, with so many advantages there are many disadvantages of using the stem cells which question the ethicality of the stem cell research. Embryonic stem cells are used to study or to use for the most number of transplants. However, to do so the blastocyst is destroyed. Which means it kills an unborn life which could have grown into a human being. That is why many people believe that stem cells are unethical. Another disadvantage with stem cells is that adult stem cells are pre specialized that is they can just develop into specific organs. For example, brain stem cells can develop into brain cells they cannot develop into blood cells. And if the immune system cells are replaced by the stem cells they can identify the indigenous organs as “foreign” and can attack the organs leading to organ failure. Therefore, there are many risks involved in stem cells therapy.
Many people oppose stem cells and label the research “ unethical”. But, the technology is promising. With proper research, stem cells may have more advantages than disadvantages. Yet, the issue of ethicality remains. It is very unethical to kill an embryo for the research. However, I am very positive that the researchers will overcome this hurdle and ensure a breakthrough research which is ethical and helpful. But, as this happens we all need to be open-minded and form opinions after understanding the basics. I hope this blog helps you to understand what the stem cells are and their advantages or disadvantages and allows you to form opinions about this topic.
Please do not forget to check my page to read interesting research analysis or topics happening currently in Genetics.




Works Cited:


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