Biology Online is a Biology blog and dictionary site that provides up to date articles on the latest developments in biological science. The Biology Online Dictionary is a completely free and open dictionary with over 60,000 biology terms. It uses the wiki concept, so that anyone can make a contribution.
Category: Molecular Biology

Biomolecule β-Hydroxybutyrate – key to vascular youth?

One of the hallmarks of old age is vascular aging. Researchers found that a biomolecule, β-Hydroxybutyrate (BHB), can serve as a key to turning the time around. Apparently, BHB has anti-aging effects on the vascular system.

 

 

 

β-Hydroxybutyrate – a biomolecule

 

Beta-hydroxybutyrate biomolecule
Molecular structure of the biomolecule, β-Hydroxybutyrate

 

β-Hydroxybutyrate is a biomolecule with a chemical formula, C4H803. Many regard it as a ketone; however, under a strict definition, it would not technically fit as a ketone. That is because its carbonyl carbon binds to only one instead of two other carbon atoms. Nonetheless, BHB appears to be physiologically related to other ketone bodies (such as acetate and acetoacetate) based on the metabolic aspect. For instance, the tissue level of BHB rises during calorie restrictions, fasting, prolonged intense workout, and when following a ketogenic diet.1 Accordingly, BHB level occurs the highest among the three circulating ketones in the body.

 

 

 

β-Hydroxybutyrate – biological sources

The body naturally produces BHB through the process of ketogenesis. Low-carb diet and fasting lead to the rise of BHB level. Firstly, the body breaks down fatty acids to produce acetyl CoA. This precursor goes through a series of reactions leading to acetoacetate synthesis. In turn, the acetoacetate circulates via the bloodstream, and subsequently reaches the liver. The BHB-dehydrogenase enzyme in the liver reduces the acetoacetate to BHB. 1

 

Another biochemical pathway that leads to the synthesis of this biomolecule uses butyrate. The body metabolizes butyrate and produce D-β-hydroxybutyrate through the aid of the enzyme, hydroxybutyrate-dimer hydrolase.

 

 

 

β-Hydroxybutyrate –  biological action

In humans, D-β-hydroxybutyric acid is one of the major endogenous agonist of hydroxycarboxylic acid receptor 2 (HCA2), a receptor protein encoded by the HCAR2 gene. It binds to and activates HCA2. Upon activation, HCA2 can inhibit the breakdown of fats and mediates niacin-induced flushing. Moreover, it induces the dilation of blood vessels.

 

Based on recent research, BHB might serve as a biomolecule that could help turn time around for the vascular system. Old age faces an increased risk to cancer and cardiovascular diseases since the vasculature ages as well. Dr. Ming-Hui Zou, director at Georgia State University, explains. “When people become older, the vessels that supply different organs are the most sensitive and more subject to aging damage….”2

 

 

β-Hydroxybutyrate –  vascular study

biomolecule for vascular youth
The biomolecule, β-Hydroxybutyrate, apparently has anti-aging effects, particularly keeping the vascular system young

 

Zou et al. 2, 3 conducted a study on vascular aging, exploring the link between calorie restrictions and delayed vascular aging. Accordingly, calorie restrictions averted vascular aging.

 

They found that BHB, the biomolecule naturally produced from the liver, has anti-aging effects, particularly on endothelial cells. The endothelial cells line the interior surface of the vascular system. Based on the results, BHB promoted mitosis of endothelial cells, thus, pre-empting vascular aging.3 Furthermore, they saw that BHB binds to a certain protein, which stimulates a series of reactions that consequently rejuvenate, thus, keep the blood vessels young.2

 

 

 

BHB could eventually become a biomolecular tool that promotes mitosis of endothelial cells. In being able to do so, it could help prevent endothelial cell senescence. Hence, this potential rejuvenating effect on the vascular system may soon become valuable not just in keeping the blood vessels young but also in preventing cardiovascular diseases related to old age.

 

 

— written by Maria Victoria Gonzaga

 

 

 

References:
1 Martins, N. (2018 Sept. 26). Beta-hydroxybutyrate or BHB –All You Need to Know. Retrieved from https://hvmn.com/blog/exogenous-ketones/beta-hydroxybutyrate-or-bhb-all-you-need-to-know
2 Georgia State University. (2018 Sept. 10). Researchers Identify Molecule With Anti-Aging Effects On Vascular System. Retrieved from https://www.technologynetworks.com/neuroscience/news/fasting-molecule-delays-vascular-aging-309380
3 Han, Y. M., Bedarida, T., Ding, Y., Somba, B. K., Lu, Q., Wang, Q., Song, P., & Zou, M.H. (2018). β-Hydroxybutyrate Prevents Vascular Senescence through hnRNP A1-Mediated Upregulation of Oct4. Molecular Cell, 71(6):1064-1078.e5. https://doi.org/10.1016/j.molcel.2018.07.036

The biology of how the brain forgets

Our brain tends to forget things that we wish we would always remember. And yet, it cannot forget certain things we wish never occurred and existed. How does your brain forget? And, can your brain forget on purpose? By nature, the human brain forgets. Inopportunely, the biological mechanism underlying this brain process is poorly understood. Only few studies shed light on this aspect. In May 2012, scientists attempted to explain the molecular biology of active elimination of memories on their report. In September 2018, another team of researchers identified the parts of the brain associated with forgetting. Based on brain frequencies, they analyzed how the human brain voluntarily forgets.

 

 

 

Molecular biology of forgetting

In 2012, an independent research team from the Scripps Research Department of Neuroscience attempted to understand the molecular biology of active forgetting.1 To do so, they used fruit flies (Drosophila) as key model since this species is often used for studying memory. Accordingly, they found that a small subset of dopamine neurons regulated the acquisition as well as the forgetting of memories. In other words, they saw that the neurons that acquired memory on one hand also eliminated the memory on the other hand. Notably, they identified the two dopamine receptors involved, i.e. dDA1 and DAMB.

 

In this case, dopamine, a neurotransmitter, seemingly performs dual, yet opposing, roles. At first, the dopamine activates the dDA1 receptor of a neuron. In effect, the neuron begins forming memories. However, the same neuron sends out signal via another dopamine receptor, DAMB. As dopamine binds to the DAMB receptor, it activates the receptor. As a result, it triggers events that lead to the forgetting of the recently acquired memory (provided that the memory has not been consolidated yet). A process, called consolidation, protects important memories from being forgotten. In essence, while memory actively forms, a dopamine-based forgetting mechanism works as well. Unless the brain reckoned the memory as important, it erases the forming memory.

 

 

 

Forgetting on purpose

In September 2018, researchers from Ruhr-Universität Bochum and the University Hospital of Gießen and Marburg collaborated with researchers from Bonn, the Netherlands, and the UK.2  In brief, they identified the parts of the brain involved in the process of voluntary forgetting. In particular, these brain areas include the prefrontal cortex and the hippocampus, the brain region associated with memories.

 

In this recent study,  the researchers found that the prefrontal cortex regulates the activity in the hippocampus. One of the leaders of the team, Carina Oehrn, explicated that the prefrontal cortex suppressed hippocampus activity. Further, she noted that the frequency changed. Accordingly, the difference in frequency caused the currently processed information to cease from being encoded. They referred to this frequency as the forgetting frequency.2

 

 

 

Forgetting – crucial to health

biology of forgetting - post-traumatic stress disorder
A Marine attended art therapy to relieve post-traumatic stress disorder painted this mask. Credit: Work by Cpl. Andrew Johnston, and released by the United States Marine Corps.

 

As much as recalling is important, forgetting certain things is pivotal to mental and emotional well being. We inherently forget on purpose. Imagine remembering all – both good and bad. Not only we would have to deal with information overload but we would also be long exposed to feelings associated with those memories.

 

Post-traumatic stress disorder, regarded as a mental disorder, develops when a person has gone through a traumatic event. People with this condition face higher risks of inflicting self-harm, or worse, committing suicide.3 Hyperthymesia, a condition wherein an individual can extraordinarily recall much of one’s life in vivid and perfect detail, can be off-putting and distressing to the affected individual. Based on one such case, the patient recounted how the ability to remember constant, uncontrollable chain of memories could be exhausting and a burden.4

 

 

More research

The metaphorical inability to forget hinders a person to move on and focus on the tasks at hand. Traumatic events seem to be ingrained deeply in mind and soul. For instance, loss of a loved one, warfare, and sexual assaults prove to be difficult to ignore. Thus, we need more insights on the neuro- and molecular biology of forgetting. More studies could help shape up future therapeutic intervention. It may not necessarily lead to the absolute incapacity to recall. But, hopefully, it can help set aside spiteful memories. In that way, affected individuals could be freed from the traps of the past, and help them live life with a sanguine hope for a future.

 

 

 

— written by Maria Victoria Gonzaga

 

 

 

References:
1 Sauter, E. (2012, May 14). “Team Identifies Neurotransmitters that Lead to Forgetting”. The Scripps Research Institute. Retrieved from https://www.scripps.edu/newsandviews/e_20120514/davis.html
2 Ruhr-University Bochum. (2018, September 7). This is how the brain forgets on purpose: Two brain regions apparently play a pivotal role in forgetting. ScienceDaily. Retrieved from www.sciencedaily.com/releases/2018/09/180907110501.htm
3 Bisson, JI; Cosgrove, S; Lewis, C; Robert, NP (2015, November 26). “Post-traumatic stress disorder”. BMJ (Clinical research ed.). 351: h6161. doi:10.1136/bmj.h6161. PMC 4663500
4 Parker ES, Cahill L, McGaugh JL (2006, February). “A case of unusual autobiographical remembering”. Neurocase. 12 (1): 35–49. doi:10.1080/13554790500473680.

Porphyromonas gingivalis: Periodontitis bacterium induces memory impairment and neuroinflammation

Porphyromonas gingivalis is a bacterium commonly associated in periodontitis a chronic inflammatory disease in the oral cavity.  Periodontium is composed of periodontal ligament, cementum, alveolar bone and gingiva. Porphyromonas gingivalis is a gram-negative bacterium that contains toxic components. It is characterized by the presence of edema and destruction of tissue supporting the teeth. In which periodontal bacteria enters into circulation that leads to bacteremia and system dissemination of bacterial products. Moreover, Porphyromonas gingivalis can promotes systemic effects through expression of inflammatory mediators like pro-inflammatory cytokines. As a consequence it is confirmed to be associated with systemic diseases such as diabetes, respiratory disease and cardiovascular disease.

Potential effects of Porphyromonas gingivalis

Neurodegenerative diseases have been recognized as the major cause of cognitive and behavioral damage. It is known that peripheral infections could activate microglial cells within the nervous system enhancing development of neurodegeneration. Thus, the inflammatory molecules in the brain could be enhanced by periodontitis that increase inflammatory levels promoting the development of Alzheimer’s disease. In this particular research Porphyromonas gingivalis infection may impair cognition by elevating expression of pro-inflammatory cytokines. It is also shown that the infected mice displayed impaired memory and learning abilities. Elevated levels of pro-inflammatory mediators in the blood can lead to direct or indirect transport to the brain.

 

Periodontal infection caused by Porphyromonas gingivalis promotes neuro-inflammatory response via releasing pro-inflammatory cytokines. In which inflammation induces alterations in neurovascular functions causing increased in blood brain barrier permeability and aggregation of toxins. In brain trauma, infection and presence of endogenic abnormal protein aggregates can activate secretions of TNF-α. That plays a pivotal role in the development and functions of central nervous system. Moreover, aging is also associated to chronic inflammation which exerts additional stress to the brain nerve cells. Additionally, during systemic inflammation the functions of the blood-cerebrospinal fluid barrier were also significantly affected.

 

Therefore, Porphyromonas gingivalis periodontal infection may induce age-dependent brain inflammation. Also periodontitis can cause memory impairment which has a similar effect on the development of Alzheimer’s disease. Furthermore, aging is the major risk factor of Alzheimer’s disease and is correlated with elevated glial responsiveness. And in due course might increase the brain’s susceptibility to injury and disease.

 

Source: Prepared by Joan Tura from BMC Immunity and Aging

Volume 15:6, January 30, 2018

 

Nutrients and bioactive potentials of green and red seaweeds

Seaweeds are macroscopic multicellular algae that have been used as food since ancient time. It was originated in Japan and then China particularly to the people who lived near the coastal areas. In addition to its nutritional value, seaweeds are rich source of structurally diverse bioactive compounds including polysaccharides, phlorotannins and pigments. Because of this, the demand  increases in the global trade wherein Korea is the major producers. In traditional Korean cuisines seaweeds used as soup, snack, pickle, vegetable and salad. Hence, this present research focuses on the edible green and red seaweeds found in Korea.

 

Green and Red Seaweeds Bioactive Compounds

Green seaweeds used to treat stomach disorders and hangovers because it contains 55% polysaccharides, 30% proteins, 13% ash and 1% lipids. It also have micro mineral such as calcium, manganese, iron, selenium, sodium, phosphate and potassium. Additionally, green seaweeds also used to treat wastewater and have significant medicinal value for rheumatism, high blood pressure and diabetes. In recent findings it has potentials bioactive properties to treat cancers and diabetes mellitus. Also it contains essentials oil to inhibit foodborne pathogens, anti-inflammatory, antioxidant and blood lipid reduction. Moreover, it has been used in traditional medicine for sunstroke, urinary diseases and hyperlipidemia. It is also useful to reduce eutrophication in mariculture waters that helps the survival rate productivity of shrimps and prawns.

 

Red seaweeds are the main source of hydrocolloids and contain vitamins A, B and C. It is also a rich source of carbohydrates particularly galactose and glucose. These red seaweeds are popularly known in agar production. And used as a raw material in bio-ethanol industry due to its high level of ethanol extraction efficiency. Likewise, both red and green seaweeds contain antioxidants properties due to its hydroxyl radical scavenging activity. That is responsible for neuro-protection against oxidative stress. In all, seaweeds have potential properties for anticancer, anti-diabetic, anti-obesity, anti-inflammatory, antimicrobial and anti-coagulant.

 

Therefore, seaweeds are vital source of food and medicine on different applications. The presences of secondary metabolites are potential to develop as functional materials due to its promising bioactive properties. Korea is one of the biggest consumers and producers wherein people mostly incorporate seaweeds on daily diets. This research suggests that increase consumption offers healthy benefits as well as utilization of seaweed materials as functional ingredients.

 

Source: Prepared by Joan Tura from  BMC Fisheries and Aquatic Sciences

Volume 21:19, 6 April 2018

 

A fatal rare disease can now be treated with a historic first FDA-approved gene-silencing drug

Scientists are excited over a gene-silencing drug that recently won an approval from the US Food and Drug Administration (FDA). This approval is historic because it is the first of its kind. The drug works by silencing genes that otherwise lead to the production of damaged proteins associated with certain diseases. The drug is called patisiran and it recently got its approval for use to treat the hereditary transthyretin amyloidosis, a fatal rare hereditary condition associated with damaged nerves.

 

 

 

Gene basis of hereditary transthyretin amyloidosis

The hereditary transthyretin amyloidosis is a rare and fatal hereditary condition that manifests as an autosomal dominant neurodegenerative disease. Because it is dominant, this means that the offspring inheriting the defective autosomal gene will acquire the condition. A defective transthyretin (TTR) gene located on human chromosome 18q12.11 is the genetic cause. The most common type of mutation is the replacement of valine by methionine at position 30.

 

A normal, functional TTR gene codes for transthyretin (TTR) protein that is involved in the transportation of thyroxine (thyroid hormone) and retinol (vitamin A). TTR protein is produced mainly in the liver, and is then secreted into the bloodstream. TTR proteins from a defective TTR gene tend to misfold and stick together, forming amyloids. This building-up of amyloids in tissues is called amyloidosis. In hereditary transthyretin amyloidosis, pathogenic amyloids form especially in the peripheral nervous system, which may eventually lead to a progressive sensory and motor polyneuropathy.

 

 

 

Gene silencing by RNA interference

Normally, the cell performs what is now known as RNA interference (RNAi). It is also known as quelling, co-suppression, and post-transcriptional gene silencing. In this process, the RNA molecules inhibit the translation of a gene. They do so when they neutralize targeted mRNA molecules. RNAi is different from CRISPR, which is a gene-editing tool that makes use of a guide RNA. CRISPR is used to switch off a gene and has a potential therapeutic use to treat cancers. It also had FDA approval in 2016 for use in a clinical trial study. However, recent studies on CRISPR raised issues about its safety since it was found to cause unexpected mutations that involve large deletions and complex genomic rearrangement at target sites.2 To learn more about CRISPR, read: CRISPR caused gene damage? … Unlike CRISPR, the RNAi is presumed not to bring permanent changes to DNA.3

 

 

Patisiran as gene-silencing drug

Patisiran is RNA-based drug that recently received the first FDA approval for use as a gene-silencing tool. People with hereditary transthyretin-mediated amyloidosis can now be treated with it.  The drug interferes with the production of transthyretin. It doses so by preventing the mRNA involved in the translation of the gene that codes for the problematic protein. This is good news to people with such fatal rare condition. FDA has now approved a drug that can be administered to them. The downside, though, is the chillingly high cost. The cost of the therapy is estimated to be about $450,000 in a year.4

 

 

 

 

New therapeutic technologies that delve into the molecular and gene mechanisms hold so much promise especially in conditions that until now lack an efficacious treatment.  RNAi is a precise gene-silencing tool and scientists are excited in its historic FDA approval. This means that it is a glorious start for contemporary therapies involving targeted gene silencing and alterations. The cost of the therapy may be encumbering but it is still a step forward, certainly a scientific feat to reckon.

 

 

— written by Maria Victoria Gonzaga

 

 

 

References:
1 TRANSTHYRETIN; TTR. (n.d.). OMIM.org. Retrieved from https://omim.org/entry/176300
2 Gonzaga, M. V. (17 July 2018). CRISPR caused gene damage? Rise and pitfall of the gene-editor. Biology-Online.org. Retrieved from https://www.biology-online.org/crispr-caused-gene-damage-rise-pitfall-gene-editor/
3 Nield, D. (14 Aug. 2018). A First of Its Kind Gene-Silencing Drug Just Got Historic Approval From The FDA. ScienceAlert. Retrieved from https://www.sciencealert.com/first-drug-silencing-genes-approved-by-fda-for-disease-treatment
4 Lipschultz, B. & Cortez, M. (10 Aug. 2018). Rare-Disease Treatment From Alnylam to Cost $450,000 a Year. Bloomberg. Retrieved from https://www.bloomberg.com/news/articles/2018-08-10/alnylam-wins-first-u-s-drug-approval-in-rare-genetic-disease

Colon cancer : Independent prognostic genes and mechanisms

Colon Cancer is the third most deadly cancer worldwide. There were more than 1.4 million cases each year and 694,000 deaths globally. The treatment of colon cancer includes chemotherapy, surgery and radiation therapy. However, advances in diagnosis and treatment leads to development and improvement in survival. Numerous data point out that genetic changes function as vital role in the development of colon and rectal cancer. In which regulatory molecules mRNA affects various molecular and cellular target including cancer cells. That is why, development in research used mRNA as based diagnostic biomarkers for colon cancer in human. Furthermore, certain kind of mRNA used to predict survival in colon cancer patients. As well as a better knowledge of molecular mechanisms and associated gene is important for early diagnosis and treatment.

 

ULBP2 a novel prognostic biomarker in Colon Cancer

ULBP2 is a potential biomarker in colon cancer survival. Previous study shows that matrix metalloproteinase-9 reveals as an important marker for postoperative prognosis in colorectal cancer patients. Also extracellular matrix plays a vital role in cancer progression in which it provides structural and biochemical support in cells.  Despite from all of these, digestion is also considered to have a major role related to cancer preventive activity. Additionally, an in vitro of peptides gastrointestinal digestion can inhibit colon cancer cells proliferation and inflammation. Moreover, recent study showed that up and down regulated mRNAs are largely amass in extracellular matrix and digestion. As a result, it would entails that abnormality of extracellular matrix and digestion takes part in colon cancer progression.

 

Furthermore, the Wnt signaling pathway gives clinical importance on various diseases including colon cancer. Since alteration of this pathway are mostly observed in colorectal cancer with microsatellite instability. So, inhibiting this pathway might be helpful strategy for targeting chemotherapy-resistance cells. Also drug metabolism determined resistance of colorectal cancer resorcinol-based heat shock protein 90 inhibitors. Therefore, Wnt signaling and drug metabolism are both important pathway enriched by up and down regulated mRNAs.

 

Prognostic biomarkers are very important and have the power to change the course of disease if only knew beyond prognostic factors. In this research ULBP2 gene that encodes cell surface glycoprotein located at chromosome 6 demonstrates prognostic biomarker for colon cancer. High level of ULBP2 is deemed independent indicator for overall survival and identified as the sole outstanding mRNA.

 

Source: Prepared by Joan Tura from BMC Biological Research

Volume 51:10 March 29, 2018

How cell fixes DNA damage

DNA repair strategies – overview

DNA is crucial to life. It carries the fundamental blueprint for the proper functioning of a cell. Thus, a damaged DNA could indicate trouble. A mere structural change could lead to the disruption of the genetic code crucial to the building of proteins. Without an apt and prompt DNA repair, mutation arises. Many of these mutations can lead to genomic instability, and ultimately to metabolic dysfunctions, aging, or diseases, such as cancer. DNA repair strategies are of two major classes: (1) the direct reversal of the chemical process that caused the damage and (2) the replacement of damaged nitrogenous bases.1

 

 

DNA repair by direct reversal

The integrity of DNA structure must be kept up at all times as much as possible. Otherwise, the cell would not be able to function as it normally would. Inopportunely, DNAs are prone to damage when exposed to certain mutagens, such as radiation and chemicals. Exposure to them could lead to the incorporation of an incorrect nucleotide during DNA replication.1 One way to correct this is through a direct reversal DNA repair mechanism. In this DNA repair strategy, a template is not required and the change is superseded as the original nucleotide is restored.

 

 

DNA repair by excision

Damaged DNA may also be repaired by excision. Unlike the first DNA repair mechanism that does not require a template (as described above) DNA repair by excision requires one. DNA is a double helical structure. Because of this, the undamaged DNA strand could be used as a basis when correcting the damaged strand. It is done so by excising and replacing the damaged DNA with new nucleotides. There are three forms of excision repair: (1) base-excision repair (where a single nucleotide change is recognized and subsequently excised by glycosylases), (2) nucleotide excision repair (where multiple base changes are recognized and then cleaved by endonucleases), and (3) mismatch repair (when mismatched bases are later recognized and eventually corrected by excising the error). All these excision repair mechanisms lead to the definitive restoration of the original sequence.1

DNA repair mechanisms

 

 

Recent study on DNA repair

A recent study by a research team from the University of Southern California reported a DNA repair mechanism in fruit fly cells and mouse cells. They likened the mechanism to an emergency responding team. Accordingly, the DNA repair mechanism of the cell includes a team of paramedics (i.e. myosins) that carry damaged DNA to an emergency room (i.e. nuclear pore) located at the periphery of the nucleus. They found that broken DNA strands prompt a series of threads, called nuclear actin filaments, to assemble and form a transient “road” that links to the edge of the nucleus. The myosin (i.e. a protein conveyed to be “walking” because of the presence of “two legs”) treads the road formed by the nuclear actin filaments while it carries the injured DNA strand towards the nuclear pore. The nuclear pore is viewed by the researchers as the emergency room for damaged DNAs since it is where the cell repairs them.2

An illustration depicting myosins that act as paramedics carrying damaged DNA along nuclear actin filaments, which serve as a transient road towards the nuclear pore. (Illustrator: Vix Maria ©Biology-Online.org)

 

 

The cell with its own scheme for DNA repair is indeed remarkable. DNA carries the code that specifies how proteins are made. Without the cell’s innate ability to correct DNA damage, its integrity would be impaired as well. Two major strategies arise: one that rolls the error back to the original and the other that replaces the damage anew based on a template. The recent findings on DNA repair mechanism on fruit flies and mouse cells revealed how remarkable the process already is and how it can pave the way for more highly anticipating research in humans.

— written by Maria Victoria Gonzaga

References:
1 Farrar , S. (2018). Mechanisms of DNA Repair. Retrieved from https://www.news-medical.net/life-sciences/Mechanisms-of-DNA-Repair.aspx
2 University of Southern California. (2018, June 20). The world’s tiniest first responders: ‘Walking molecules’ haul away damaged DNA to the cell’s emergency room. ScienceDaily. Retrieved from www.sciencedaily.com/releases/2018/06/180620170951.htm

CRISPR caused gene damage? Rise and pitfall of the gene-editor

CRISPR as a gene editing tool made a prodigious leap forward in science. In 2015, it was heralded as Science’s 2015 Breakthrough of the Year.1 It stymied other impressive contenders like Ebola vaccine. It supersedes other gene-editing predecessors, such as TALENs (transcription activator-like effector nucleases) and ZFNs (zinc finger nucleases). Unlike these two, CRISPR does not need a custom protein for every targeted DNA sequence. It does, however, require a guide RNA (gRNA). Even so, the process of designing a gRNA is easier and less time-consuming than creating a custom protein. For that, it is favoured over other gene-editing tools.

 

 

The rise of a revolutionary gene-editing tool — CRISPR

CRISPR-Cas9 – a customizable tool that cuts and inserts small pieces of DNA at specific areas along a DNA strand. (Credit: Ernesto del Aguila III, National Human Genome Research Institute, NIH)

 

The discovery of CRISPR was indeed phenomenal. Short for clustered regularly interspaced short palindromic repeats, CRISPR swiftly opened avenues for biological and medical innovations. Initially identified as a family of viral DNA snippets, it was discovered to inherently protect bacteria against re-invading bacteriophages akin to our immune system’s adaptive immunity. This natural gene-editing system in bacteria has two key players: gRNA and Cas9 (CRISPR-associated enzyme). The gRNA finds and binds to specific DNA target. The Cas9 goes where the gRNA is, and then cuts the DNA target, disabling the latter. Now, scientists exploit it as a way to splice specific DNA targets and then replace them with a DNA that would yield the desired outcome. For instance, CRISPR can be used to correct physiological anomalies caused by gene mutations or defective genes.


CRISPR-Cas9 system. (Credit: marius walter, Wikimedia Commons under CC BY-SA 4.0 Int’l license)

 

 

 

CRISPR – a versatile gene-editing tool

CRISPR has been shown to have the potential to slow down the progression of cancers. It can switch off a gene in immune cells. The altered immune cells can be designed to fight cancer. In 2016, US FDA approved the clinical trial study where CRISPR technology would be used to cure patients with cancers. 2 Not only in biology and medicine, the use of CRISPR has also extended to agriculture and animal husbandry. Through it, the genes of crops and livestock can be improved. They can be made more resistant to certain diseases.

 

 

 

CRISPR causing gene damage?

One of the issues raised against CRISPR is ethical concerns. Similar to what was ethically raised against other gene-editing technologies, the concern is chiefly about the notion of bias and “playing God”. What are the standards that will define and permit judgment over a gene to be construed as either “good” or “bad”? But taking aside this issue, there is another issue being hurled against CRISPR. Marked of recent as “breaking news”, a study published in Nature warned about the possible pathogenic consequences of CRISPR when the researchers identified on-target mutagenesis in the form of large deletions and complex genomic rearrangements at target sites in mitotically active cells of mice and humans.3 This is not the first time that a study questioned the safety of CRISPR technology. In 2017, researchers from Columbia University reported that it led to hundreds of unexpected mutations. Nevertheless, this claim was retracted when they failed to replicate their results.4

 

 

CRISPR as a gene-editing tool wields so much potential beyond one can imagine. It is easy to use, feasible, and far-reaching. One can expect that issues would come along the way, and thus slow down its fast-paced utilization in different fields. It is a no-nonsense stumbling block for we belong in a community that moves forward through social discourse fueled by scientific nosiness and reasoning. Probing the dangers of CRISPR should be as extensive as exploring its benefits. We must be not too quick to adulate without first bringing out in the open its risks — especially ones that are as crucial as mutations and gene damage.

 

 

— written by Maria Victoria Gonzaga

 

 

References:

1 Science News Staff. (2015). And Science’s 2015 Breakthrough of the Year is…

ScienceMag.org. Retrieved from http://www.sciencemag.org/news/2015/12/and-science-s-2015-breakthrough-year

2 Reardon, S. (2016). First CRISPR clinical trial gets green light from US panel. Retrieved from

https://www.nature.com/news/first-crispr-clinical-trial-gets-green-light-from-us-panel-1.20137

3 Kosicki, M., Tomberg, K. & Bradley, A. (2018 July 16). Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nature Biotechnology. https://doi.org/10.1038/nbt.4192

4 Dockrill, P. (2018 July 16). BREAKING: CRISPR Could Be Causing Extensive Mutations And Genetic Damage After All. ScienceAlert.com. Retrieved from https://www.sciencealert.com/crispr-editing-causes-frequent-extensive-mutations-genetic-damage-target-deletion-site

A Protein Being Born – a live cell imaging of RNA translation

You probably already heard the concepts of translation in the central dogma of molecular biology. The dogma is an elucidation as to how a protein is born based on what the DNA holds. Based on it, the scheme begins at the DNA molecule being transcribed into RNA in a process called transcription, which is then followed by the RNA making a protein in a process called translation.

 

 

 

Crick’s central dogma: from transcription to translation

Francis Crick, the molecular biologist who was recognized together with James Watson as the first to formally reveal the helical structure of the DNA molecule in 1953, was also noted for his use of the term “central dogma”. He described the unidirectional flow of genetic information, i.e. from the transcription process to the translation process, and that the scheme does not entail reversion. Meaning, the scheme does not flow back from protein to DNA.

“The Central Dogma. This states that once ‘information’ has passed into protein it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but the transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein.”1

— Francis Crick, 1958

The dogma is now succinctly known as this: DNA makes RNA, which in turn makes protein.

 

 

 

Real-time imaging of translation in vivo

In vivo transcription was the first to be quantified in real time whereas translation took a while before scientists were able to observe the process within a living cell. 2 It took them about 60 years from the time Francis Crick first described it. Translation is a process occurring in the cytoplasm of a cell by which the genetic code carried by the mRNA is decoded to produce the specific sequence of amino acids in a polypeptide chain. It consists of basically four stages: bioactivation, initiation, elongation, and termination. These translation processes had been more difficult to observe in living systems. Due to the limitations of laboratory tools and techniques it had eluded scientists for quite some time. Then, a team of researchers from the Colorado State University came up with state-of-the-art microscopic techniques, which helped them view for the first time the RNA translation in vivo. Fondly referred to as “Fixie”, the custom-built microscope helped the research team to create a real-time imaging of RNA translation within a living cell in a nanoscale precision.2 The research team was able to capture it firstly by using a tagging process by protein engineering and then using the “Fixie” microscope, which has two highly sensitive cameras enabling the imaging of RNA and proteins as two identifiable colors during the translation process.


In this video, it shows how a protein is being born. The red dots are RNA while the blue or green dots are the proteins. The large green spherical structure in the background is the cell nucleus. It can be seen that the mature proteins gather at the nucleus post-translation.

 

 

 

Real-time imaging of the translation of proteins by the RNA molecules can be regarded as a breakthrough. It can be likened to a key that opens the door to various research fields to explore. Proteins are crucial to the biomechanics of living things. They are the definitive goal of translation. Thus, research findings as fundamental as this is going to be irrefutably monumental.

 

 

— written by Maria Victoria Gonzaga

 

 

 

References:
1 Crick, F.H.C. (1958). “On Protein Synthesis”. In F.K. Sanders. Symposia of the Society for Experimental Biology, Number XII: The Biological Replication of Macromolecules. Cambridge University Press. pp. 138–163.

2 Manning, A. (2016). No longer lost in translation: CSU biochemists watch gene expression in real time. Colorado State University. Retrieved from https://source.colostate.edu/no-longer-lost-in-translation-csu-biochemists-watch-gene-expression-in-real-time/

Not Junk: ‘Jumping Gene’ Is Critical For Early Embryo

Jumping genes, also known as transposons, are gaining momentum. They are considered either as slacking junks or maleficent parasites in our genome. As such, they are largely taken for granted. However, it seems the tables have turned. There seem to be certain jumping genes that without them we would not move past our embryonic state.  Researchers from the University of California – San Francisco presented proof that certain jumping genes do perform a crucial role during the development of an embryo.  Without them, the embryo would not progress as it should.1

 

 

 

Jumping genes — junk DNAs

Transposons are small segments of DNA  with a special capability. They create copies of the genetic material and then insert at random sites in the genome.2 For that, they are dubbed as “jumping genes” based on the “jumping” activities that they do. Some consider jumping genes as junk DNA because they tend to replicate needlessly multiple copies of DNAs that already exist. Some of these genetic copies could be noncoding (junk) DNAs. Our genome is comprised mostly of junk — about 98-99%! Only 1 or 2 % of it codes for the building blocks of proteins. Scientists presumed that these noncoding regions are unnecessary and therefore viewed as an evolutionary mess in our genome. Apparently, half of our genome is comprised of jumping genes, and the most common is the long interspersed nuclear element-1 (LINE1).1

 

 

Jumping genes — parasitic stowaways

While some people view jumping genes as slackers that add up to the pile of junk littering our genome, others see them as parasitic stowaways. Because they can “jump” at seemingly random sites in the genome, they could insert themselves where they might cause gene disruptions, deleterious mutations, and chromosomal rearrangements resulting in diseases, including cancer.3

 

 

LINE1 — a paradoxical jumping gene

LINE1 (a jumping gene) is crucial during embryonic development

 

Researchers from the University of California – San Francisco recently reported that LINE1 (a jumping gene) is crucial during embryonic development. LINE1 accounts for 20% or more of the human genome. It is a retrotransposon, meaning it is amplified by first transcribing a segment of DNA into RNA, and then reverse-transcribed into DNA. The extra DNA copy will then be inserted at a different site in the genome.2 This jumping gene apparently acts as a critical regulator during the early embryonic development. It appears indispensable for an embryo to develop past the two-cell stage.1 This finding seems paradoxical since LINE1 has been implicated in various diseases, particularly cancers.4 Nevertheless, the important role of LINE1 was revealed when it was eliminated from the fertilized eggs, and consequently, they all remained at the two-cell phase. Accordingly, the role of the jumping gene in embryonic development is associated with the LINE1 RNA forming a complex with Nucleolin and Kap1 (gene regulatory proteins). The complex is believed to regulate embryonic development by turning off the dominant genes orchestrating the embryo’s two-cell state as well as by turning on the genes that promote further cell divisions and development.1

 

 

 

Jumping genes are mostly underappreciated largely because they are believed to be contributors to a pile of genetic junk or as parasitic stowaways. Despite being regarded as such, recent findings poised them as crucial genes.   While most studies focus on the 1-2% of the genome performing a blatantly important role, i.e. to code for amino acids whereby a protein could be spectacularly built from, the recent study implicates that the jumping genes, too, deserve a spot in the research field.

 

 

 

— written by Maria Victoria Gonzaga

 

 

 

References:
1 University of California – San Francisco. (2018, June 21). Not junk: ‘Jumping gene’ is critical for early embryo: Gene that makes up a fifth of the human genome is not a parasite, but key to the first stages of embryonic development. ScienceDaily. Retrieved from www.sciencedaily.com/releases/2018/06/180621141038.htm
2 Transposon. (n.d.). Biology-Online Dictionary. Retrieved from https://biology-online.org/dictionary/Transposon
3 Chénais, B. (2013). Transposable elements and human cancer: A causal relationship? Biochimica et Biophysica Acta (BBA) – Reviews on Cancer, 1835 (1), 28-35. https://doi.org/10.1016/j.bbcan.2012.09.001
4 Burns, K. H. (2017). Transposable elements in cancer. Nature Reviews Cancer, 17, 415–424. https://www.nature.com/articles/nrc.2017.35