The Gene for Hands Also Codes for What?

 In this NYT article, "How Did Hands Evolve? The Answer Is Behind You.", scientists had discovered a strange connection between the stretch of DNA called 5DOM that had been found in both mammals and zebrafish. It was found by Dr. Duboule and his colleagues, who were looking at molecular locks that sat along 5DOM. They had snipped 5DOM out of the DNA of a mouse embryo, and it ended up developing legs, but not feet. This led to more questions about when this section of DNA came about in animals, so Christopher Bolt, a graduate student at the time, looked through the zebrafish's genome and found 5DOM there too. This suggests that this set of genes was also present in the primordial ancestor of zebrafish and mammals.

 Dr. Hintermann took over the research and, using CRISPR, removed the 5DOM molecular locks from zebrafish embryos. The deletion didn't have much of an effect on the development of fins, but it did affect the development of the cloaca. When looking back at the same area in mouse embryos, the researchers discovered that the sequence codes for the urogenital sinus in mammals. Scientists are proposing that 5DOM went through evolutionary change, since it is easier to recode than to build a whole new sequence. Both structures that form are extremities that developed towards the far end of the body as well. There is more research needed on exactly why this change in 5DOM came about, but this is a starting point.

 Researchers are slowly finding more pieces of how the different gene codes for mammals came about with the shift onto land. This discovery at least gives a jumping point for how connected animals are and where mutations could have taken place in DNA, or how adapting to environments could have played a role in this.

Genetic Modification caused by Electric Eels.

 Electroporation is a phenomenon where electricity is used to open up small temporary pores within cells.  The purpose of this is to deliver medicine, DNA, bacteria or whatever desired substance into cells in a way that won't destroy the cells.  Since electricity is the basis of this process, scientists in Japan wondered if electric eels could cause the same effect of electroporation in other living organisms.  To test this, zebra fish larvae were put into a tank with an electric eel.  DNA with a gene that would make the fish glow green was put into the tank.  The eel was fed a goldfish, which caused it to emit 185-volt pulses into the water.  A day after, some of the fish larvae started to glow, which lasted for about 3-7 days.  This affected 5% of the larvae, and it suggests that electric eels are able to cause electroporation.  However since this was done in a lab, it's not definitive that this effect occurs out in the wild.

The phenomenon described in this article reminds me of the electrophoresis lab.  In that lab electricity was used to transport genetic material across a medium, using the slight negative charge of DNA to move it towards a more positively charged source.  Electroporation is similar but it involves the process of opening up cells in order to take up a desired substance.  The article suggested that electric eels may cause genetic modification and diversity.  However it concedes that the scientists who conducted the experiment can't conclusively say that because the experiment was done in a lab.  Genetic modification due to electric eels hasn't been observed out in nature to my knowledge.  I personally don't understand electricity too well and how shocks from an electric eel would affect its surrounding area.  But I know that when these eels use electricity, it's usually with the purpose of killing some nearby animal that they're defending themselves from or trying to hunt.  So while the experiment suggests the eels may cause electroporation leading to DNA take up, I doubt it's very common due an organism being killed by the eel by being too close to it.

Article: https://www.smithsonianmag.com/smart-news/eels-can-genetically-modify-nearby-fish-with-their-electrical-pulses-180983422/

Article about electroporation: https://www.technologynetworks.com/cell-science/articles/an-introduction-to-electroporation-a-tool-for-transfection-and-competent-cell-generation-363195

You are Getting Sleepy: Tiredness, Proteins, and DNA Repair

 

Researchers in Israel have been working to unravel the mystery of sleep by examining the mechanisms that cause organisms to get tired. Homeostatic sleep pressure builds up in our body the longer we stay awake and begins to decrease as we fall asleep. But what causes homeostatic pressure to increase to the point of tiredness and how does sleep cause it decrease? The pressure is built during waking hours due to accumulating DNA damage in neurons, caused by things like UV light, neuronal activity, oxidative stress, radiation, and enzymatic errors. And during sleep, sleep recruit repair systems correct DNA breaks that cause excessive DNA damage in our brains. To see if DNA damage was the trigger for homeostatic pressure and sleep state, the researchers examined zebrafish. These fish are particularly easy to study because of their nocturnal sleeping patterns and simple brain that is comparable to a human's. 

Methods involving irradiation, pharmacology, and optogenetics were used to induce DNA damage in the zebrafish. They discovered that after subjecting the zebrafish to light interruption during the dark period when they'd be sleeping, six hours of sleep was enough to reduce DNA damage. But with less than six hours of sleep, DNA damage was not adequately reduced and the zebrafish continued to sleep during daylight hours. The mechanism that tells them (and us) to sleep is the protein PARP1. It's the among the first to rapidly respond to DNA damage sites in cells and recruits relevant systems to clean out the damage. PARP1 increasingly clusters at DNA break sites during wakefulness and decreases during sleep. Inhibition of the protein in zebrafish meant that the fish weren't aware they were tired, didn't sleep, and the DNA didn't get repaired. Understanding the purpose of sleep on a cellular level may help with future research on sleep disturbances, aging, and neurogenerative disorders. 

https://www.sciencedaily.com/releases/2021/11/211118203657.htm

Fish Eyes Help Human Blindness

https://www.sciencedaily.com/releases/2017/04/170405101940.htm

https://www.eurekalert.org/pub_releases/2017-04/oios-fet040517.php

        Researchers have discovered a possible cure for congenital blindness and it is all due to the Zebrafish. One of the most popular and widespread causes of child blindness is Leber Congenital Amaurosis (LCA). This syndrome is genetically transmitted to the child if both parents contain at least one of the improper copies of the gene involved in eye development. 

       It was discovered that Zebrafish have a very similar gene that leads to blindness as well. The Aipl1b gene is important in both visual functions and the the maintenance of core photoreceptors. Without this gene the fish are unable to detect light and during development they eventually lose sight.It is this gene that is being studied and compared to humans. Humans have a single gene, Aipl, that acts in the same manner.  Researchers are very close to understanding this gene and if they are able to prevent blindness in the fish then they should be able to find a way to prevent blindness in humans. This is a valuable discovery that could help so many people in the near future.

I Can See Clearly Now the GABA is Almost Gone! - How Zebrafish Recover From Blindness

A recent study funded by the National Eye Institute found a link between the neurotransmitter GABA, or gamma-aminobutyric acid, and recovery from blindness in zebrafish.  For some time now, scientists were aware of the zebrafish's ability to recover from loss of vision that would normally blind humans permanently.  This is due to the zebrafish having a miraculous ability to regenerate cells in the retina.  Prior studies showed that dying retinal cells produced signals to trigger Muller glia, which revert back to an undifferentiated state and divide.into new cells.  Studies in mice on the brain and pancreas indicated that GABA could play a role in the regeneration process, where low levels signaled stem cells to  divide.  The researchers of the current study, therefore, hypothesized that GABA in zebrafish could be a factor in the regeneration of retinal cells.  To test their theory they injected zebrafish with GABA inhibitors.  They found that these fish responded with retinal cell regeneration.  Fish with retinal damage that were given high levels of GABA, on the other hand, displayed little to no regeneration.  These findings clearly support the hypothesis that GABA plays a very important roll in the regeneration of new cells.

I found this article interesting because I often joke about how I'm going blind because my vision is so poor.  But on a serious note I think the findings in this study could be very significant for finding cures to diseases in humans that affect vision, and it could lead to new treatments to cure blindness.  It is also the first study to report these kind of results, so with more experiments in the future it would be fascinating to see what else researchers find out about the subject.

New gene-editing enzyme, NgAgo, proving to be difficult replicate in lab

There are reports that a new enzyme can edit genes, but no one has been able to replicate the original experiment.

Extraordinary research that shows promise in altering mammalian DNA more efficiently than CRISPR-Cas9, but after multiple attempts, no one can recreate the experiment? What gives? There is a lot of speculation, but mostly complaints as to why researchers failed to replicate it.

There have been many controversial reports as to what the possible role of NgAgo is, but none of them involve editing of genes. One theory was that NgAgo was thought to clamp onto a gene and limit it's expression, noted in the experiment on eye development in zebrafish, but this were correct, the enzyme would not permanently change gene function that's passed down every generation.

Another theory was that temperature could play a key aspect to a successful experiment. The original experiment was carried out in a cool environment, which allows the bacteria, that makes the protein, lives.

Whether this protein's role is entirely different than what the original report says it is, needs to be kept in a cool environment, or just simply doesn't work, the debate surrounding this experiment is insane. Until the NgAgo experiment is published, we will never know whether this enzyme is used for gene editing.

Skinbows leave no pot of gold but they do shine!

        Today I've brought you a look into a topic we've covered in class and in lab. Fluorescence in bacteria is one thing, but the study conducted in Nature magazine shows viewers what happens when you add these fluorescent proteins into zebrafish DNA. Scientists have studied how DNA can be transferred into other organisms and through experimentation have found that when the skin cells regenerate in the fish after sustaining damage they actually made several different bundles of color. When these pigments are allowed to be varied with these colors rather than following the normal genetic make-up, the expression is pretty interesting to see. It doesn't help the fish to be fluorescent in the wild as they can be spotted by predators. But it gives us a way to view what happens when skin cells are doing their designated function, as well as explains a little as to why scarred tissue appears different than the skin around it.

        There is a video of the what the cells look like during the process of regeneration in the link above to the magazine. And I have included a link to the research paper here. Other than these pictures they have plenty of other data that goes into detail about the experiment itself. They talked about barcoding the superficial epithelial cells, (SEC's) those on the outer part of the skin, so that each variation of color is linked to specific strains of cells. They documented the interactions the cells underwent to achieve these interactions.

       Perhaps research like this can lead to advances in skincare. If we know in which concentrations the variations of our own skin cells are affected when we get scarred or burned perhaps we can learn how to improve skincare treatments for lacerated and burn victims. Or at least find safer ways to get the right kind of tan for the summer. There are many possibilities to explore.

CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation

Apparently, Crohn's disease and plasma palmitoleric acid have an association. Using a new technology, CPAG or Cross-Phenotype Analysis of GWAS, scientists were able to perform meta-analyses of genome-wide association studies (GWAS) and search for similarities between over 600 traits. Using GWAS is particularly helpful being that Crohn's disease is associated with a genetic variant. Pleiotropic SNPs (single polynucleotide polymorphisms) are common within the human genome, which means one genetic locus affects multiple phenotypes. The significance of cross-phenotype associations lies in the fact that they may represent pleiotropy, and it has been discovered that the PTPN22 gene is associated with many conditions, such as Crohn's disease, rheumatoid arthritis, type 1 diabetes, and more. It was found that 7% of SNPs are associated with more than one raw trait. In addition, by identifying traits associated with particular genetic variants and clustering the traits in order to visualize associations, clusters of known cholesterol-related traits, such as type 2 diabetes, obesity, and autoimmunity, were easy to see and represented known relationships. 

The results were compared using a Chao-Sorensen model, the first use of a model usually used for ecology research, to study genetics. The model assessed heterogeneity, or the discordance of observed disease groups with already defined disease group. Many traits were had a high correspondence, which can be explained by reasons such as a similar risk factor, consequence of a disease, a similar gene affecting different pathways. Crohn's disease and psoriasis only overlap with two SNPs but were found to have genes in the interleukin (IL)-23 pathway, suggesting that the risk of both conditions could be related to signaling. Researchers went on to test whether increased plasma fatty acid would induce intestinal inflammation in zebrafish to find that plasma fatty acids have an effect on intestinal inflammation. It is known that countries with high fat diets have a stronger correlation with Crohn's disease. Three different fatty acids were injected into zebrafish larvae. Palmitic acid induced a greater increase in inflammation compared to TNBS-exposed and BSA-injected. Linoileic acid was suggestive of having an anti-inflammatory effect. 

I found this study to be of great interest, as it supports that environment can have a direct effect on the expression of certain diseases. The consumption of too much unnecessary fat could lead to the expression of Crohn's disease. 

Zebrafish Used to Study Fat Storage Gene

A study involving zebrafish has led to discoveries in understanding certain components of fat storage in relation to humans. The gene, Plexin-D1, plays an important role in controlling the shape of fat cells and their method of storage. Earlier studies hypothesized this gene’s involvement with fat storage, but were unable to determine the exact mechanism behind how it was capable of working.

A team of researchers at Duke University in North Carolina first examined the Plexin-D1 gene in mice, but the project came to a halt when all the mice lacking the gene died. The team was able to continue the experiment using zebrafish, with the added advantage of the zebrafish being partially transparent. This allowed the researchers to visually study fat distribution. Some zebrafish were genetically engineered to lack the Plexin-D1 gene. These genetically modified fish had less overall visceral fat and smaller fat cells than the control group, fish with the Plexin-D1 gene. These fish also did not exhibit insulin resistance, a precursor to diabetes consistent with a diet high in fat.

This research identified a new molecular pathway that affects metabolic health by determining how fat is stored in the body. Researchers believe this gene is responsible for building blood vessels and setting up structures to house fat cells. Now researchers may be able to farther study this pathway to address these concerns in humans as potential targets for the build-up of visceral fat. Though many genes play a role in metabolism and body type, analysis of the Plexin-D1 gene will play an integral part in determining methods of fat accumulation in humans.

Using Zebrafish to Provide Genetic Answers

Susan Brooks, a medical geneticist of the Rutgers Robert Wood Johnson Medical School used zebrafish as a model organism to help identify the cause of a rare genetic disorder affecting a boy and his two uncles.  The boy suffered from seizures, fevers, slow growth, and poor head growth resulting in microcephaly.  Susan Brooks discovered that the peculiar disorder was most likely caused by a recessive mutation on the X-chromosome, as the boy's uncles shared similar symptoms.   These X-linked mutations can be carried by both males and females, but cause symptoms only in males with very few exceptions.

Scientists found a mutation carried by the affected males and their mothers, within a gene known as RPL 10.  It is located on the X-chromosome and encodes part of the ribosome, which is a vital piece of molecular equipment that is responsible for translating genetic code into proteins.  Scientists used zebrafish to test the effect of the mutation.  Duke University researchers led by Erica Davis from the Center for Human Disease Modeling displayed that the diminishing expression of the RPL 10 gene caused organisms to develop notably smaller heads, or the fish version of microcephaly.

The image above displays the effect of the expression of the RPL 10 gene (top), 

versus the suppressed expression of the RPL 10 gene (bottom) in the heads of zebrafish.

Unfortunately, identifying the likely cause of the disorder does not ensure a cure for the boy and his two uncles, but it is the first step for future research in developing treatments.  Erica Davis stated, "This was a one-of-a-kind family affected by a disorder that no one had ever seen before, but they are not alone.  The best way of finding answers for these families is for clinicians and model organism researchers to join forces."  Zebrafish and humans share approximately 70% of protein-coding genes, and 84% when the genes known to be associated with disease are considered.  Zebrafish are a very important model organism in genetics.  They are cheaper to maintain and grow faster than mice.

This article caught my eye immediately, as I conducted research with Dr. Brian Rogerson last semester using zebrafish.  We analyzed AICD (Activation-induced cytidine deaminase) levels in young and old zebrafish, which is an enzyme known to be responsible for the mutation of antibody genes.  Due to being familiar with the use of zebrafish as a model organism, I am very interested in learning about how they are being used in other studies.  I find it fascinating that the diminished expression of the RPL 10 gene had a very similar impact on zebrafish, as it did on humans.  It opens up an unlimited number of possibilities in the future regarding the use of zebrafish in studying human disease.

Article [1]: http://medicalxpress.com/news/2014-10-family-zebrafish-genetic.html 
Related Article: http://www.genetics-gsa.org/news/templates/?a=210&z=1

Transgenic Salmon and the use of genes from the Zebrafish to better protect these cultured fish from diseases and pathogens.

The article, "Isolation of the Atlantic salmon β-actin promoter and its use to drive expression in salmon cells in culture and in transgenic zebrafish," portrays how genetic roles with salmon aquaculture are continuously growing. Researchers are working towards successful genetic improvement of the fish. Many scientists study which genes are in control of disease protection or which genes can be enhanced to enlarge the size of the fish. Transgenic salmon have recently been introduced to the world of aquaculture. Those genes that control the growth hormones in the salmon are altered to be more receptive and therefore pump more of this hormone into the fish. This will increase the size, as stated before, and furthermore increase the production of the salmon crop. To salmon famers this sounds like a dream come true. However, the general consensus of the human population is not as confident with consuming transgenic salmon. This feeling of doubt is not uncommon since there is still minimal evidence of the effects, if any, on human life after they eat these salmon.

I personally feel that introducing genes from another organism into the salmon populations, controlled in cultures, is a smart idea, but with multiple outcomes. I agree with the general consensus of the public,  and demand more answers before this becomes an everyday occurrence in salmon aquaculture. There are so many "what if" questions that come from mixing genetics of different species. Therefore research must be conducted to test not only how the new genes will effect the fish, but also how ingesting the fish will affect the humans who eat them. 



Source: http://fx5ly8ju5l.search.serialssolutions.com

Below is a link to another article which provides more information about the Zebrafish:
http://www.academia.edu/528432/Zebrafish_as_a_model_organism_for_nutrition_and_growth_towards_comparative_studies_of_nutritional_genomics_applied_to_aquacultured_fishes

Zebrafish Important Model For Understanding How Genes Work In Health And Disease

An article found on Medical News Today along with another article talks about how the Zebra Fish can be used to understand how genes work in health and disease. The zebra fish shares 70% of its protein coding genes with humans, and 84% of its overall genome. Due to this astonishing fact, the zebra fish's genome is one of three that has been sequenced in great depth. The other two are the human and the mouse. This genome will be crucial to studying diseases in humans in ways that cannot be studied. Zebra fish research has already been used to understand cancer, heart disease and muscular dystrophy. Scientists are hoping to use the genome to undertand the function of specific genes and develop medicines.

The zebra fish is unlike most other vertebrates. They have the highest repeat content in their genome sequences as well as genes that code for sex determination. The zebrafish also has very few pseudogenes,  or genes that have lost function through evolution, compared to the human genome.

"Armed with the zebrafish genome, we can now better understand how changes to our genomes result in disease," said Professor Christiane Nüsslein-Volhard, author and Nobel laureate from the Max Planck Institute for Developmental Biology.

Nicotine response genetics in the zebrafish

 



Tobacco use is predicted to result in over 1 billion deaths worldwide by the end of the 21^st century. How genetic variation contributes to the observed differential predisposition in the human population to drug dependence is unknown.Tobacco is a carrier for the highly addictive drug nicotine. Once your body gets a taste for nicotine, it can quickly become a life-long addiction, with extremely fatal consequences. Nicotine is the main drug in all forms of tobacco. Nicotine acts as both a stimulant and a sedative. It is one of the most heavily used addictive drugs in the U.S. The zebrafish is an emerging vertebrate model system for understanding the genetics of behavior. They developed a nicotine behavioral assay in zebrafish and applied it in a forward genetic screen using gene-breaking transposon mutagenesis. We show this insertional method generates mutant alleles that are reversible through Cre-mediated recombination, representing a conditional mutation system for the zebrafish. The combination of this reporter-tagged insertional mutagen approach and zebrafish provides a powerful platform for a rich array of questions amenable to genetic-based scientific inquiry, including the basis of behavior, epigenetics, plasticity, stress, memory, and learning. Looking at the figures below, the zebra fish were quite changed by the nicotine.