regulation of gene expression



- DNA replication

DNA repair



mRNA processing

- Translation






- DNA cloning 

PCR (Polymerase Chain Reaction)

Gel electrophoresis y DNA fingerprinting

N6-methyladenine: A Newly Discovered Epigenetic Modification 

The majority of cellular functions are carried out by proteins encoded by specific genes present in cellular DNA. Genes are first transcribed to RNA which is then translated to proteins. The regulation of this process is important for maintaining correct cellular function. One of the ways that cells regulate gene expression is by epigenetic modifications to chromatin. The term “epigenetics” refers to reversible chemical modifications of DNA and histone proteins (DNA in the nucleus of eukaryotes is wrapped around histones) that affect the transcriptional status of genes. A number of histone modifications such as methylation and acetylation of lysine residues have already been discovered and characterized. Until recently; however, methylation of the 5 position of cytosine was the only known epigenetic DNA modification (A). Methylation of cytosine by DNA methyltransferases is associated with transcriptional silencing, while the removal of these methyl groups by TET enzymes is associated with transcriptional re-activation (B and C). In addition to controlling gene silencing, cytosine methylation also silences retrotransposons, a class of mobile genetic elements. If left unregulated, transposons can insert themselves into important regions of the genome and lead to mutagenesis.

Recently, N6-methyladenine, a new epigenetic modification, was discovered in mammalian cells. N6-mA had previously been discovered in prokaryotes and simple eukaryotes and was shown to function as a transcriptional activator. By contrast, a recent report published in Nature, has shown that N6-mA functions as a transcriptional silencer in mammalian cells, specifically in mouse embryonic stem cells. N6-mA primarily acts to silence the LINE-1 family of retrotransposons during early embryogenesis, which prevents genomic instability. The authors identified N6-mA by using a modified single molecule DNA sequencing technique. DNA bound to a specific modified histone protein was immunoprecipitated using an antibody against a specific histone modification (H2A.X), sequenced, and analyzed by mass spectrometry (D). This identified and determined the position of N6-mA. The authors then generated knockouts of the enzyme Alkbh1, which they believed may function as a demethylase for N6-mA. When Alkbh1 was absent from cells, they found an increase in the levels of N6-mA, showing that Alkbh1 functions as an N6-mA demethylase in vivo. This is important because epigenetic modifications are reversible. Genes can be turned off by methylation and then turned back on by removing the methyl group, so determining the enzyme responsible for the removal of N6-mA supports its role as an epigenetic modification.

For more information see:

As always, I’m happy to answer any questions or go into more detail.

Black History Month: Why a career in science?

“I have loved insects since I was 8 years old, when I found them in a vacant lot near my house. The discarded appliances, drug paraphernalia, and overgrown weeds provided various microhabitats, in which lived many kinds of insects. This taught me that you can find wondrous things in even the bleakest of places. I continue to study insects because of a simple truth: terrestrial life is one of the most amazing things to happen in the history of the universe. To fully appreciate that truth, you have to study biodiversity, and entomology is the best way to do so.”

– Ralph Washington, Jr., Ph.D. student, Department of Entomology and Nematology, University of California, Davis

“I hail from an urban environment but, as a child I was always fascinated with the wild places I saw through images and videos. I was drawn to science for the adventure, which only becomes more thrilling with each new project and skill I acquire. My research interests include: conservation biology, molecular ecology and genomics. My current research explores the consequences of inbreeding on differential gene expression and gene regulation in abnormal sperm production in carnivores. The mechanisms behind abnormal sperm production in wildlife are largely unexplored and are of key concern in conservation breeding to maintain endangered species.”

– Audra Huffmeyer, Ph.D. student, Ecology and Evolutionary Biology Department, UCLA

Keep reading

[Fic] Tardy Note - General Danvers Teacher AU

“Any questions?” Alex asks, wiping off the diagram she had drawn on the board and turning to address her class. Her students are mostly alert and she isn’t getting any particularly confused stares so she takes it as a sign to move on. “Okay then, everybody turn to page 102 in your textbooks and read the whole chapter on gene expression and regulation and then answer practice questions 1 through—”

The door to her classroom creeks open and the heads of her students collectively turn to glance at the latecomer though it’s pretty much obvious who it is without even having to look. 

Keep reading

Living and Working Aboard Station

 Join us on Facebook Live for a conversation with astronaut Kate Rubins and the director of the National Institutes for Health on Tuesday, October 18 at 11:15 a.m. ET.

Astronaut Kate Rubins has conducted out of this world research aboard Earth’s only orbiting laboratory. During her time aboard the International Space Station, she became the first person to sequence DNA in space. On Tuesday, she’ll be live on Facebook with National Institute of Health director Francis Collins, who led the effort to map the human genome. You can submit questions for Kate using the hashtag #SpaceChat on Twitter, or during the live event. Here’s a primer on the science this PhD astronaut has been conducting to help inspire your questions: 

Kate has a background in genomics (a branch of molecular genetics that deals with the study of genomes,specifically the identification and sequencing of their constituent genes and the application of this knowledge in medicine, pharmacy,agriculture, and other fields). When she began her tenure on the station, zero base pairs of DNA had been sequenced in space. Within just a few weeks, she and the Biomolecule Sequencer team had sequenced their one billionth base of DNA aboard the orbital platform.

“I [have a] genomics background, [so] I get really excited about that kind of stuff,” Rubins said in a downlink shortly after reaching the one billion base pairs sequenced goal.

Learn more about this achievement:

+First DNA Sequencing in Space a Game Changer

+Science in Short: One Billion Base Pairs Sequenced

Why is DNA Sequencing in Space a Big Deal?

A space-based DNA sequencer could identify microbes, diagnose diseases and understand crew member health, and potentially help detect DNA-based life elsewhere in the solar system.

+Why Sequencing DNA in Space is a Big Deal 

Miss the Reddit AMA on the subject? Here’s a transcript:

+NASA AMA: We just sequenced DNA in space for the first time. Ask us anything! 

NASA and Its Partnerships

We’re not doing this alone. Just like the DNA sequencing was a collaborative project with industry, so is the Eli Lilly Hard to Wet Surfaces investigation, which is a partnership between CASIS and Eli Lilly Co. In this experiment aboard the station, astronauts will study how certain materials used in the pharmaceutical industry dissolve in water while in microgravity. Results from this investigation could help improve the design of tablets that dissolve in the body to deliver drugs, thereby improving drug design for medicines used in space and on Earth. Learn more about what we and our partners are doing:

+Eli Lilly Hard to Wet Surfaces – been happening the last week and a half or so

Researchers to Test How Solids Dissolve in Space to Design Better Tablets and Pills on Earth

With our colleagues at the Stanford University School of Medicine, we’re also investigating the effects of spaceflight on stem cell-derived heart cells, specifically how heart muscle tissue, contracts, grows and changes  in microgravity and how those changes vary between subjects. Understanding how heart muscle cells change in space improves efforts for studying disease, screening drugs and conducting cell replacement therapy for future space missions. Learn more:

+Heart Cells

+Weekly Recap From the Expedition Lead Scientist for Aug. 18, 2016 

It’s Not Just Medicine

Kate and her crew mates have also worked on the combustion experiments.

Kate has also worked on the Bigelow Expandable Activity Module (BEAM), an experimental expandable capsule that docks with the station. As we work on our Journey to Mars, future space habitats  are a necessity. BEAM, designed for Mars or other destinations, is a lightweight and relatively simple to construct solution. Kate has recently examined BEAM, currently attached to the station, to take measurements and install sensors.

Kate recently performed a harvest of the Plant RNA Regulation experiment, by removing seed cassettes and stowing them in cold stowage.

The Plant RNA Regulation investigation studies the first steps of gene expression involved in development of roots and shoots. Scientists expect to find new molecules that play a role in how plants adapt and respond to the microgravity environment of space, which provides new insight into growing plants for food and oxygen supplies on long-duration missions. Read more about the experiment:

+Plant RNA Harvest

NASA Astronaut Kate Rubins is participating in several investigations examining changes in her body as a result of living in space. Some of these changes are similar to issues experienced by our elderly on Earth; for example, bone loss (osteoporosis), cardiovascular deconditioning, immune dysfunction, and muscle atrophy. Understanding these changes and how to prevent them in astronauts off the Earth may help improve health for all of us on the Earth. In additional, the crew aboard station is also working on more generalized studies of aging.

+ Study of the effects of aging on C. elegans, a model organism for a range of biological studies.

Epigenome orchestrates embryonic development

The early stages of embryonic development shape our cells and tissues for life. It is during this time that our newly formed cells are transformed into heart, skin, nerve or other cell types. Scientists are finding that this process is largely controlled not by the genome, but by the epigenome, chemical markers on DNA that tell cells when to turn genes on and off.

Now, studying zebrafish embryos, researchers at Washington University School of Medicine in St. Louis have shown that the epigenome plays a significant part in guiding development in the first 24 hours after fertilization.

The research, which appears Feb. 20 in the journal Nature Communications, may deepen understanding of congenital defects and miscarriage.

The epigenome is a bit like software that makes sense of the DNA code hard-wired into each of the body’s cells. While the DNA hardware is the same in each cell, differences in the epigenome — the software — differentiate brain cells from muscle, skin, eye or heart cells.

Using zebrafish as a model of vertebrate development, the new study is the first to map changes in the epigenome of whole embryos and their roles in gene regulation during the earliest hours of development.

“Our study suggests that an underappreciated fraction of the genome is involved in gene regulation,” said senior author Ting Wang, PhD, assistant professor of genetics. “Another surprising finding is that many of the important regions of DNA we identified are pretty far away from the genes they regulate.

“The field long has been focused on identifying genes that manufacture proteins,” Wang added. “We are showing that the epigenome is just as important and is an area that is largely uncharted.”

Wang is a principal investigator on the Roadmap Epigenomics Program, a national initiative to map the human epigenome, supported by the National Institutes of Health (NIH). Researchers leading this program recently published large data sets detailing information about human epigenetics.

“The human genome, like the zebrafish genome, is epigenetically regulated,” Wang said. “But in humans, for ethical reasons, we can only look at tissues in childhood and adulthood and describe differences between cell types. With zebrafish, we can watch the developmental process as it unfolds.”

To do so, Wang and first author Hyung Joo Lee, a graduate student in Wang’s lab, studied zebrafish embryos at five intervals after fertilization, stopping at the 24-hour mark, when the embryos start to develop separate tissues.  

At each of these points in time, the investigators measured several ways the epigenome regulates gene expression, one of the most important of which was with methyl groups. Methyl groups are organic compounds that attach to the DNA in different places. If many methyl groups are concentrated in a given area, the DNA is packaged away and gene expression is shut down. If the DNA is demethylated — with few or no methyl groups — genes are unpackaged and can be expressed.

Most studies of DNA methylation have focused on areas close to genes called promoters, which function like switches, turning gene expression on or off.

“But our data show that only 5 percent of DNA methylation changes happen in conventionally defined promoters,” Wang said.

The scientists were surprised to discover the remaining 95 percent of the methylation changes happened in regions far from genes and their promoters, in parts of the genome considered noncoding because they don’t tell the cell to make a particular protein.

Most of the changes in methylation at these distant sites involved losing methyl groups, which tends to increase gene expression. This gradual loss of methyl groups increased as the stages of development progressed, presumably turning on gene expression somewhere else. Using several techniques, the researchers were able to correlate the loss of methyl groups in one location with the dialing up of gene expression elsewhere.

This allowed them to statistically predict which noncoding regions of the genome were dialing up expression of distant genes. They determined these noncoding regions functioned as developmental enhancers, and they experimentally verified 20 of them in zebrafish. The data showed that these 20 enhancers drove expression of developmental genes in specific tissues, including the eye and parts of the brain and spinal cord.

The investigators pointed out that many developmental problems, whether they result in the loss of the embryo through miscarriage or in later disorders, can’t be pinned to a particular gene.

“This study suggests that many diseases may have an epigenetic origin,” Wang said. “Even if there is nothing wrong with the protein coding genes themselves, there are lots of different regulatory changes that could mess up gene expression and lead to disease.”

Wang noted that this study supports the trend of scientists finding more and more noncoding parts of the genome that play essential roles in gene regulation.

“I’m sure there are parts of the genome for which we may never find a function,” he said. “But when we look deep, we can derive very complex regulatory relationships between noncoding regions and the distant genes they regulate.”

YouTube Videos on Genetics

I went apprehensively to my first genetics lecture this morning; some acquaintances who had taken the course before said they hadn’t gotten much out of this particular professor’s lectures. But then an amazing thing happened! The professor announced that the course was going to be  different this year. 

Apparently, last year he noticed that a particular student was doing very well on the exams, despite never attending lecture. He pulled her aside and asked her where she was getting her information, since she wasn’t coming to class.

The answer? YouTube, of course! 

The professor has thoroughly embraced the idea, and now the syllabus is full of videos for us to watch before lecture. I love studying by watching YouTube videos (preferably at 1.5x or 2x speed) so this made me super happy.

And here, for your enjoyment (and so I’ve got an easily clickable list for my own use), are the videos on my professor’s syllabus for intro to genetics. I’ve listed them in the following format: “Channel Name: Video Subject (video length).”

I. Basic Mendelian Genetics

  1. Useful Genetics: Introduction to genetic analysis (5:58)
  2. Useful Genetics: Genetic nomenclature (19:29)
  3. Useful Genetics: Mendelian genetics (20:57)
  4. Useful Genetics: How to do genetic analysis (30:44)
  5. Bozeman Science: Punnett Squares (12:14)
  6. Bozeman Science: Chi square test (11:52)
  7. Useful Genetics: Chi square test (25:03)
  8. Todd Nickle: Branch diagram Mendelian genetics problem (12:59)
  9. DNAunion: Branch diagram method for trihybrid cross (2:52) [NB: Watch this one on mute. The audio is just really annoying music, unrelated to the video content.]
  10. Non-genetic chi square example (4:00)
  11. Another non-genetic chi square example (3:53)

II. The Physical Basis of Mendelian Principles

  1. Biology / Medicine Animations HD: Mitosis animation (6:20)
  2. Useful Genetics: Mitosis (20:19)
  3. Crash Course Biology: Mitosis (10:47)
  4. MrAac007: Meiosis (2:57)
  5. Biology / Medicine Animations HD: Meiosis and Crossing Over (6:45)
  6. Crash Course Biology: Meiosis (11:42)
  7. Useful Genetics: Sexual Life Cycles (12:03)
  8. Useful Genetics: Sex Chromosomes in Meiosis (11:44)
  9. Useful Genetics: Crossing Over (20:51)
  10. Useful Genetics: Following genotypes through meiosis (16:24)

III. Sex-chromosome linkage

  1. Useful Genetics: Sex linkage (19:47)
  2. Useful Genetics: Sex determination (10:06)
  3. Biology / Medicine Animations HD: X inactivation (1:47)
  4. Useful Genetics: X-linked gene expression in females (15:21)
  5. Useful Genetics: X-linked gene expression in males (12:28)

IV. Pedigree Analysis

  1. Juliana Agostino: Karyotyping (10:17)
  2. Suman Bhattacharjee: Pedigree analysis (15:29)
  3. Biologybyme: How to do pedigree analysis (8:42)
  4. Biologybyme: Autosomal dominant pedigree (6:48)
  5. Biologybyme: X-linked recessive pedigree (7:11)
  6. Biologybyme: Autosomal recessive pedigree (8:00)
  7. Biologybyme: X-linked dominant pedigree (11:16)

V. Extensions of Mendelian Genetics

  1. Bozeman Science: Chromosomal Genetics (14:22)
  2. Useful Genetics: Extensions of Mendelian Analysis and Linkage (23:11)
  3. John Munro: Biochemical Pathways (1:12)
  4. Biology Rangitoto: Types of biochemical pathways (8:14)
  5. Useful Genetics: Gene interaction in biochemical pathways (14:11)

VI. Mutation and Mutational Analysis

  1. Useful Genetics: Central Dogma of Molecular Biology (19:55)
  2. Biology / Medicine Animations HD: Transduction (1:08)
  3. Anirban Basu: Bacterial Conjugation (3:11)
  4. John Munro: Bacterial Transformation (1:15)
  5. The Petersson Lab: Doing bacterial transformation in a molecular biology lab (8:27)
  6. Life Technologies: Invitrogen (6:57)

VII. Control of Gene Expression in Bacteria and Bacteriophage

  1. iBiology: Gene Regulation Part One (31:28)
  2. iBiology: Gene Regulation Part Two (41:20)
Small DNA modifications predict brain's threat response

The tiny addition of a chemical mark atop a gene that is well known for its involvement in clinical depression and posttraumatic stress disorder can affect the way a person’s brain responds to threats, according to a new study by Duke University researchers.

The results, which appear online August 3 in Nature Neuroscience, go beyond genetics to help explain why some individuals may be more vulnerable than others to stress and stress-related psychiatric disorders.

The study focused on the serotonin transporter, a molecule that regulates the amount of serotonin signaling between brain cells and is a major target for treatment of depression and mood disorders. In the 1990s, scientists discovered that differences in the DNA sequence of the serotonin transporter gene seemed to give some individuals exaggerated responses to stress, including the development of depression.

(Image caption: An artist’s conception shows how molecules called methyl groups attach to a specific stretch of DNA, changing expression of the serotonin transporter gene in a way that ultimately shapes individual differences in the brain’s reactivity to threat. The methyl groups in this diagram are overlaid on the amygdala of the brain, where threat perception occurs. Credit: Annchen Knodt, Duke University)

Sitting on top of the serotonin transporter’s DNA (and studding the entire genome), are chemical marks called methyl groups that help regulate where and when a gene is active, or expressed. DNA methylation is one form of epigenetic modification being studied by scientists trying to understand how the same genetic code can produce so many different cells and tissues as well as differences between individuals as closely related as twins.

In looking for methylation differences, “we decided to start with the serotonin transporter because we know a lot about it biologically, pharmacologically, behaviorally, and it’s one of the best characterized genes in neuroscience,” said senior author Ahmad Hariri, a professor of psychology and neuroscience and member of the Duke Institute for Brain Sciences.

“If we’re going to make claims about the importance of epigenetics in the human brain, we wanted to start with a gene that we have a fairly good understanding of,” Hariri said.

This work is part of the ongoing Duke Neurogenetics Study (DNS), a comprehensive study linking genes, brain activity and other biological markers to risk for mental illness in young adults.

The group performed non-invasive brain imaging in the first 80 college-aged participants of the DNS, showing them pictures of angry or fearful faces and watching the responses of a deep brain region called the amygdala, which helps shape our behavioral and biological responses to threat and stress.

The team also measured the amount of methylation on serotonin transporter DNA isolated from the participants’ saliva, in collaboration with Karestan Koenen at Columbia University’s Mailman School of Public Health in New York.

The greater the methylation of an individual’s serotonin transporter gene, the greater the reactivity of the amygdala, the study found. Increased amygdala reactivity may in turn contribute to an exaggerated stress response and vulnerability to stress-related disorders.

To the group’s surprise, even small methylation variations between individuals were sufficient to create differences between individuals’ amygdala reactivity, said lead author Yuliya Nikolova, a graduate student in Hariri’s group. The amount of methylation was a better predictor of amygdala activity than DNA sequence variation, which had previously been associated with risk for depression and anxiety.

The team was excited about the discovery but also cautious, Hariri said, because there have been many findings in genetics that were never replicated.

That’s why they jumped at the chance to look for the same pattern in a different set of participants, this time in the Teen Alcohol Outcomes Study (TAOS) at the University of Texas Health Science Center at San Antonio.

Working with TAOS director, Douglas Williamson, the group again measured amygdala reactivity to angry and fearful faces as well as methylation of the serotonin transporter gene isolated from blood in 96 adolescents between 11 and 15 years old. The analyses revealed an even stronger link between methylation and amygdala reactivity.

“Now over 10 percent of the differences in amygdala function mapped onto these small differences in methylation,” Hariri said. The DNS study had found just under 7 percent.

Taking the study one step further, the group also analyzed patterns of methylation in the brains of dead people in collaboration with Etienne Sibille at the University of Pittsburgh, now at the Centre for Addiction and Mental Health in Toronto.

Once again, they saw that methylation of a single spot in the serotonin transporter gene was associated with lower levels of serotonin transporter expression in the amygdala.

“That’s when we thought, ‘Alright, this is pretty awesome,’” Hariri said.

Hariri said the work reveals a compelling mechanistic link: Higher methylation is generally associated with less reading of the gene, and that’s what they saw. He said methylation dampens expression of the gene, which then affects amygdala reactivity, presumably by altering serotonin signaling.

The researchers would now like to see how methylation of this specific bit of DNA affects the brain. In particular, this region of the gene might serve as a landing place for cellular machinery that binds to the DNA and reads it, Nikolova said.

The group also plans to look at methylation patterns of other genes in the serotonin system that may contribute to the brain’s response to threatening stimuli.

The fact that serotonin transporter methylation patterns were similar in saliva, blood and brain also suggests that these patterns may be passed down through generations rather than acquired by individuals based on their own experiences.

Hariri said he hopes that other researchers looking for biomarkers of mental illness will begin to consider methylation above and beyond DNA sequence-based variation and across different tissues.

Scientists slow brain tumor growth in mice

Much like using dimmer switches to brighten or darken rooms, biochemists have identified a protein that can be used to slow down or speed up the growth of brain tumors in mice.

Brain and other nervous system cancers are expected to claim 14,320 lives in the United States this year.

The results of the preclinical study led by Eric J. Wagner, Ph.D., and Ann-Bin Shyu, Ph.D., of The University of Texas Health Science Center at Houston (UTHealth) and Wei Li, Ph.D., of Baylor College of Medicine appear in the Advance Online Publication of the journal Nature.

“Our work could lead to the development of a novel therapeutic target that might slow down tumor progression,” said Wagner, assistant professor in the Department of Biochemistry and Molecular Biology at the UTHealth Medical School.

Shyu, professor and holder of the Jesse H. Jones Chair in Molecular Biology at the UTHealth Medical School, added, “This link to brain tumors wasn’t previously known.”

“Its role in brain tumor progression was first found through big data computational analysis, then followed by animal-based testing. This is an unusual model for biomedical research, but is certainly more powerful, and may lead to the discovery of more drug targets,” said Li, an associate professor in the Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology at Baylor. 

Wagner, Shyu, Li and their colleagues discovered a way to slow tumor growth in a mouse model of brain cancer by altering the process by which genes are converted into proteins.

Appropriately called messenger RNA for short, these molecules take the information inside genes and use it to make body tissues. While it was known that the messenger RNA molecules associated with the cancerous cells were shorter than those with healthy cells, the mechanism by which this occurred was not understood.

The research team discovered that a protein called CFIm25 is critical to keeping messenger RNA long in healthy cells and that its reduction promotes tumor growth. The key research finding in this study was that restoring CFIm25 levels in brain tumors dramatically reduced their growth.

“Understanding how messenger RNA length is regulated will allow researchers to begin to develop new strategies aimed at interfering with the process that causes unusual messenger RNA shortening during the formation of tumors,” Wagner said.

Additional preclinical tests are needed before the strategy can be evaluated in humans.

“The work described in the Nature paper by Drs. Wagner and Shyu stems from a high-risk/high-impact Cancer Prevention & Research Institute of Texas (CPRIT) proposal they submitted together and received several years ago,” said Rod Kellems, Ph.D., professor and chairman of the Department of Biochemistry and Molecular Biology at the UTHealth Medical School.

“Their research is of fundamental biological importance in that it seeks to understand the role of messenger RNA length regulation in gene expression,” Kellems said.  “Using a sophisticated combination of biochemistry, genetics and bioinformatics, their research uncovered an important role for a specific protein that is linked to glioblastoma tumor suppression.”

Could boosting brain cells' appetites fight disease? New research shows promise

Deep inside the brains of people with dementia and Lou Gehrig’s disease, globs of abnormal protein gum up the inner workings of brain cells – dooming them to an early death.

But boosting those cells’ natural ability to clean up those clogs might hold the key to better treatment for such conditions.

That’s the key finding of new research from a University of Michigan Medical School physician scientist and his colleagues in California and the United Kingdom. They reported their latest findings this week in the journal Nature Chemical Biology.

Though the team showed the effect worked in animals and human neurons from stem cells, not patients, their discoveries point the way to find new medicines that boost the protein-clearing cleanup process.

The work also shows how an innovative microscope technique can help researchers see what’s going on inside brain cells, as they labor to clear out the protein buildup.

The researchers focused on a crucial cell-cleaning process called autophagy – a hot topic in basic medical research these days, as scientists discover its important role in many conditions. In autophagy, cells bundle unwanted materials up, break them down and push the waste products out.

In the newly published research, the team showed how the self-cleaning capacity of some brain cells gets overwhelmed if the cells make too much of an abnormal protein called TDP43. They found that cells vary greatly in how quickly their autophagy capacity gets swamped.

In brain cells that were made from stem cells derived from ALS patients, treatment with two drugs that stimulate autophagy led to longer cell survival (middle two lines).

But they also showed how three drugs that boost autophagy – speeding up the clean-out process – could keep the brain cells alive longer.

Longer-living, TDP43-clearing brain cells are theoretically what people with Lou Gehrig’s disease (amyotrophic lateral sclerosis or ALS) and certain forms of dementia (called frontotemporal) need. But only further research will show for sure.

Sami Barmada, M.D., Ph.D., the U-M neurologist and scientist who is first author of the new study, says the new findings are encouraging – and so is the success of a microscope technique used in the research. His new lab, in the U-M Department of Neurology, is continuing to refine ways to view the inner workings of nerve cells.

“Using this new visualization technique, we could truly see how the protein was being cleared, and therefore which compounds could enhance the pace of clearance and shorten the half-life of TDP43 inside cells,” he says. “This allowed us to see that increased autophagy was directly related to improved cell survival.”

Barmada worked on the team at the Gladstone Institutes and the University of California San Francisco headed by Steven Finkbeiner, M.D., Ph.D., that published the new findings. The team used stem cells derived from the cells of people who have ALS to grow neurons and astrocytes – the two types of brain cell most crucial to normal brain function.

Because he both sees patients in clinic and studies neurological disease in the laboratory, Barmada brings a special perspective to the research.

At U-M, he specializes in treating patients who have neurological diseases that affect both thinking and muscle control. About a third of ALS patients develop signs of frontotemporal dementia, also called FTD – and about 10 percent of people with FTD also have a motor neuron disease that affects their brain’s ability to control muscle movement. 

One of the drugs tested in the study, an antipsychotic drug developed in the 1960s to treat people with schizophrenia, had actually shown some anti-dementia promise in human ALS patients, but comes with many side effects. Barmada notes that Finkbeiner’s team at the Gladstone Institute is already working to identify other compounds that could produce the effect with fewer side effects.

Interestingly, small studies have suggested that people with schizophrenia who take antipsychotic drugs are much less likely to develop ALS.

Barmada’s work at U-M now focuses on the connection between brain cells’ ability to clear abnormal proteins. He also studies the cells’ regulation of RNA molecules created as part of expressing protein-encoding genes. Looking further upstream in the protein-producing process could yield further clues to why disease develops and what can be done about it, he says.

Regulation of Gene Expression and Wallets

Before diving into this topic, make sure you understand:

  • Transcription=process of turning DNA into mRNA
  • Transcription requires Initiation step, which is when the RNA polymerase binds to a promoter which allows the DNA strand to unfold and begin to be trasncribed
  • Basically, the RNA polymerase is like your wallet: it gives you an okay on whether or not you can purchase something or not. If the moneys there, you’re probably going to spend it. If it’s not, there’s no possible way you can.

Operons are a set of genes that control expression of genes (discovered by Jacob and Monod).

  • Lac/Inducible operon: switched off until turned on; can be distracted by allolactose, which prevents RNA polymerase from binding to a promoter (instead the allolactose is) 
  • Tryptophan/repressible operon: always on until repressed; when binded with prevents RNA polymerase from binding to a promoter
  • Basically, lac operon is an empty wallet that can have fake money in it. Tryptophan operon is a full wallet of a prudent person
  • Allosteric proteins play a part in both operons by acting as regulatory genes

Noncoding RNAs also control gene expression

  • microRNA (miRNA) blocks translation and degrades mRNA
  • RNA interference (RNAi) turns off genes with matching sequences
  • RNA=those pesky little things you have to pay for that add up

Onco-genes lead to cancer

  • Proto onco-genes are proteins that stimulate cell growth and division; too much leads to too much
  • tumor-suppressor genes lead to uncontrolled cell growth; too much leads to too much
  • Think of when you eat too much food, you just keep on going and going…