iBiology Podcast

In her third lecture, Zoghbi explores possible therapies for MECP2 disorders. First, using Deep Brain Stimulation (DBS), Zoghbi’s team together with collaborator Dr. Jianrong Tang were able to rescue learning and memory deficits, enhance neurogenesis, correct abnormal neural network activity, and improve MeCP2-linked gene expression changes in a mouse model of Rett Syndrome. Then, she discusses two approaches to normalize the MeCP2 protein in MECP2 duplication mice: by deleting the duplicated MECP2 gene in the genome, or by decreasing MECP2 mRNA levels using antisense-oligonucleotides. Even though these two approaches seem to rescue developmental issues caused by MECP2 duplication, titrating MeCP2 levels is required in order to avoid Rett-like symptoms caused by lowering the protein too much.

In her second lecture, Zoghbi explains how MeCP2 molecularly modulates neuronal function. Their studies uncovered a critical link between cytosine methylation, MeCP2, and the methylating enzyme Dnmt3a, in Rett Syndrome. They hypothesized that MeCP2 partially causes Rett-Syndrome symptoms by failure of reading methylated DNA marked by Dnmt3 and indeed showed that Dnmt3-dependent mCH plays a central role in Rett pathogenesis.

Dr. Huda Zoghbi’s work has provided insight into Autism Spectrum Disorders (ASD) by focusing on Rett Syndrome, a postnatal progressive neurological disorder. By studying the genetics of Rett Syndrome, her group made the seminal discovery of X-linked Methyl CpG-binding protein 2 (MECP2) as the gene that causes Rett Syndrome. Zoghbi’s group showed that the severity of the disease was highly dependent on the amount of functional MeCP2 protein expressed. Females, who carry one normal and mutant MECP2 allele typically suffer from Rett syndrome, but the amount of functional protein is influenced by X-chromosome inactivation, and girls with more cells expressing normal allele have milder features. Surprisingly, they also showed that duplications spanning MECP2 can cause a Rett-like progressive neurological disease, highlighting the importance of MeCP2 levels for neural functions. Zoghbi describes how these findings have spurred new research into how MeCP2 affects postnatal development and brain function.

As the COVID-19 pandemic escalated in the beginning of 2020, there was a need for the rapid dissemination of scientific information to understand everything from how the virus spreads, to how it affects the human body, to how the disease can be treated and prevented. Jessica Polka, Executive Director of ASAPbio, explains that, for this reason, the pandemic has inspired an increasing number of scientists to post their research papers on preprint servers. Publishing papers in traditional journals with formal peer review can take a lot of time. Posting manuscripts on preprint servers, on the other hand, can happen quite fast. But, considering that preprints do not undergo formal peer review before they are posted, is this prudent? Dr. Polka talks about how preprints experience their own crowd-sourced, informal peer review process through public commentary on social media and other venues by scientists and other experts, and this discourse can actually improve the quality of the paper over time. A major caveat of preprints is the potential for the media and the public, who may not be aware of the provisional nature of preprints, to disseminate erroneous or inaccurate information, and so, this requires proper education and training on what preprints are and how to interpret them.

In the cytoplasm of cells, thousands of tightly packed molecules and structures execute the numerous processes necessary to maintain life. Although there are many ways to study cellular processes, one of the simplest ways to understand the different parts of a cell is to visualize them. Dr. Sven Truckenbrodt sought to better understand the machinery of the neuronal synapse using fluorescence microscopy, yet he was limited by the physical properties of light. To circumvent the 250-nm resolution limit imposed by the photophysics of light waves, Truckenbrodt developed X10 expansion microscopy, based on the original concept of expansion microscopy invented in the Boyden lab. By uniformly expanding the volume of tissue by a thousand-fold using synthetic polymers (the same as those found in baby diapers!), this approach increases the distance between closely packed proteins, allowing them to be visualized with fluorescence microscopy. Truckenbrodt shares the story of the first time he used X10 expansion microscopy to clearly image synaptic vesicles, after studying them for years as a neuroscientist! He describes how he used X10 microscopy to characterize the precise localization of synaptic and cytoskeletal proteins that previously could not be visualized in detail. Truckenbrodt ends his talk by sharing how the X10 approach has been used by other research groups and encourages his viewers to consider applying this method in their own research to make new discoveries.

In his last lecture, Singer continues the story of the life and death of RNA. His lab has developed several more fluorescence microscopy techniques that let them study, in real time, the translation and degradation of mRNA. These techniques allow them to track when and where translation begins, how quickly a ribosome binds to a mRNA once it has reached its destination, how long the ribosome stays bound and how rapidly it adds amino acids to a growing protein chain.  In addition, these techniques can be used to unveil the dynamics of RNA degradation. In an interesting twist, it turns out that for mRNAs that must be degraded during the cell cycle, their fate is decided at the time of their birth.

To understand the relationship between RNA localization and translation, it is necessary to visualize the movement of the RNA in real time. In his second lecture, Singer explains how his lab found an ingenious way to label RNAs in live cells and follow their movement. In the nucleus, RNA moves by diffusion and stochastically finds a nuclear pore to exit. In the cytoplasm, however, it is a different story. RNA, in a translationally repressed state, undergoes directed movement along the cytoskeleton. Once it reaches its destination, translation is activated. Singer’s lab showed that neuronal stimulation leads to ß-actin mRNA localization to dendritic spines, followed by translation, and stabilization of the synapse; events that are crucial for memory and learning.

In this series of lectures, Dr. Robert Singer explains how it is possible to follow a single mRNA molecule from its birth to its death. Singer begins by explaining that cell cultures are heterogeneous and analyzing single cells provides spatial and temporal information not available from bulk analysis. He outlines how his lab developed techniques such as fluorescence in situ hybridization (FISH) that have allowed them to measure gene expression in single cells. Using these techniques, they discovered that some RNAs localize to specific areas in the cell and RNA localization is linked to its regulation and function. For example, ß-actin mRNA localization to the leading edge of fibroblasts aids in cell motility. Singer’s lab identified “zip code” regions in mRNAs that are responsible for regulating mRNA localization.

In his second talk he reviews makeup of the plant cell wall and how hemicellulose, cellulose, and lignin can be broken down for use in aviation biofuel production. He describes the Joint BioEnergy Institute (JBEI) approach to maximize carbon efficiency at every step in the production of biofuels, from developing and feedstocks, deconstructing biomass, and use of microbes and enzymes to generate target intermediates for fuels. A major part of optimizing this process is the development of a one-pot process, in which conversion of biomass to fuel can be achieved in a single chamber.

Biofuels have been around for decades, but interest in them has grown considerably in recent years due to climate change. While they have the potential to provide a sustainable and renewable way to power our transportation systems, Dr. Blake Simmons points out that in order to become a viable replacement for fossil fuels, biofuels must also be efficient and affordable at global scales. In his first talk, he provides an overview of the advantages of using biofuels and walks through the biochemical processes required in order to convert biomass into usable fuels. He also discusses the ideal properties for advanced biofuels, the projected markets for these fuels in the coming years, and some of the key challenges associated with optimization of advanced biofuel production.