Blanchette and Scalera et al., discover new insights into an intercellular communication method in neurons

Fruit fly neuron (magenta) with extracellular vesicle cargoes (green). Cargoes are packaged inside the neuron and, then released outside of the neuron in extracellular vesicles.

Research scientist Cassie Blanchette and Neuroscience Ph.D. student Amy Scalera, working in the Rodal lab, discovered a new mechanism of regulation of extracellular vesicles (EVs). EVs are small, membrane-bound compartments that can transfer cargoes such as DNA and proteins between cells for communication. EVs are important for normal cell-cell signaling, but they are also hijacked in neurodegenerative disease to spread toxic disease proteins to other cells. Therefore, it is crucial to understand how and where EVs are formed. Blanchette and Scalera discovered a novel method of regulation of EVs specifically at the synapses (the region of the neuron that contacts adjacent cells), using the fruit fly nervous system as an experimental model.

EVs are derived from endosomes, a network of intracellular sorting compartments that cells use to separate cargoes into different ‘packages’ with distinct inter and intracellular destinations. Blanchette and Scalera found a surprising function for the proteins that regulate endocytosis, a process in which the cell membrane buds inward, thus forming a compartment to bring cargoes to endosomes. The authors found that mutants lacking endocytic proteins lose the local pool of EV cargoes that are available for release from synapses, and instead send these cargoes for disposal elsewhere in the neuron. They hypothesized that the normal function of endocytosis  is akin to a plane circling in a holding pattern at an airport – while it waits for its time to land, it is better for the passengers to circle (between the cell membrane and endosomes), nearby their destination (release in EVs), rather than being sent to an entirely different city (a different region of the neuron). They also found that disrupting this holding pattern had consequences for the physiological functions of EV cargoes; in endocytic mutants, loss of Synaptotagmin-4, an EV cargo important for neuronal adaptability, was associated with failure of the neuron to grow in response to firing. Endocytic mutants also caused synaptic depletion of the Alzheimer’s disease associated EV cargo Amyloid Precursor Protein (APP), thus suppressing its toxicity and increasing the survival of APP-expressing flies. These discoveries raise the possibility that proteins regulating EV traffic may be targets for neurodegenerative disease therapies.

SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

SARS-CoV-2 is the pathogen causing the COVID-19 pandemic, that as of early February 2022 has caused 5.7 million deaths worldwide.

When a virus infects a cell, it transforms it, so it can become a “virus factory”. To do so, it needs to suspend it from doing the normal functions, but not to a point that the immune system will detect those changes and “decide” to kill the infected cell. Understanding how viruses accomplish that is very important for virology and medicine as, for example, it could be used to help the immune system identify these cells and stop the virus from spreading through the body.

Graphical abstract for Zaffagni post

To tackle this issue, researchers identify genes that get activated or repressed when a virus infects a cell. One way to monitor the genes that are “on” or “off” during the infection is to measure RNAs abundance by RNA sequencing (RNA-seq). Through this approach, recent studies showed that SARS-CoV-2 infection induces big changes on the cells that it infects. Generally, scientists believe changes induced by viral infection are the consequence of the concerned action of the virus proteins acting within the host cell. For example, the SARS-CoV-2 genome encodes 29 proteins. The effect of the virus is so strong that it changes more than 5000 genes in just 48hs, this is almost ¼ of our genes.

How do individual viral proteins contribute to these changes? To answer this question, the Kadener lab in the Department of Biology introduced singular viral SARS-CoV-2 proteins into human cells and monitored gene expression changes through RNA-seq. Between the 26 tested proteins, non-structural protein 14 (Nsp14) was the one inducing the most dramatic effect, altering the expression of ≈4000 genes. Importantly, these changes overlap well with previously published RNA-seq data from human cells infected with SARS-CoV-2. This suggests that transient expression of Nsp14 partially recapitulates the molecular events downstream to SARS-CoV-2 infection. They also showed that a cellular enzyme (IMPDH2) mediates these changes, and that treatment with IMPDH2 inhibitors partially rescues the changes induced by Nsp14.

This research contributes to understanding the function of viral proteins on the host cell and on the molecular mechanisms that control the progression of viral infection. The Kadener lab showed that Nsp14 also modulates gene expression of the host cell by activating a cellular enzyme. These events may be conserved in other coronaviruses infections and the discovery of these molecular mechanisms may be important for designing new therapeutic approaches.


SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome. Michela Zaffagni, Jenna M Harris, Ines L Patop, Nagarjuna Reddy Pamudurti, Sinead Nguyen, Sebastian Kadener.  eLife 2022;11:e71945 DOI: 10.7554/eLife.71945.

Schmidt-Rohr examines why plants need two different photosystems

In a recent paper in Life (Basel), Klaus Schmidt-Rohr, Professor of Chemistry, introduces a self-explanatory description of the energetics of photosynthesis in plants, the so-called EZ-scheme. It shows the energies of molecules in kJ/mol instead of the classical Z-scheme’s shifted energy differences that are misleadingly encrypted in volts. Unlike its predecessor, the EZ-scheme includes the Kok cycle in the water-splitting complex, charge separation after photon absorption, and the Calvin cycle with carbohydrate synthesis (in a simplified form). It also shows O2 correctly as a high-energy product, due to its relatively weak double bond, and demonstrates that Photosystem II pumps more of the absorbed photon energy into O2 than into the plant.

This paper provides the first valid explanation of why plants need two different photosystems: PSII mostly extracts hydrogen (as protons plus electrons) from H2O, producing PQH2 (plastoquinol), and generates the energetically expensive product O2, providing little energy directly to the plant. PSI is needed to produce significant chemical energy for the organism, in the form of ATP, and to generate a less reluctant hydrogen donor, NADPH. This work fundamentally revises received notions of the energetics of photosynthesis, by pointing out the classical Z-scheme’s bewildering implication that H2O gives off electrons spontaneously to chlorophyll while releasing energy, and by showing that the concept of energy transport by “high-energy electrons” in photosynthesis is misguided, since energy and electrons flow in opposite directions.

Figure #1 from Schmidt-Rohr paper

Figure 1 Simplified EZ-scheme of the energetics of photosynthesis in plants, converting H2O and CO2 to O2 and carbohydrate, [CH2O]. The direction of energy transfer and release is indicated by straight red arrows at the top, formal hydrogen transfer by blue dashed curved arrows at the bottom of the diagram. Three dots … indicate omitted redox reactions.

Schmidt-Rohr K. O2 and Other High-Energy Molecules in Photosynthesis: Why Plants Need Two Photosystems. Life (Basel). 2021 Nov 5;11(11):1191.

Han paper describes electrochemical switching of arylazopyrazole & heat release

Research image from paperMihael Gerkman and Prof. Grace Han in the Department of Chemistry report the first demonstration of redox-induced energy release from molecular solar thermal (MOST) compounds in condensed phases, in collaboration with a team of Prof. Matthew Fuchter at Imperial College London. MOST compounds that utilize light-induced chemical isomerization for harnessing solar photon energy have emerged as an alternative to photovoltaics and artificial photosynthesis, enabling a closed-system solar photon energy storage and controlled release. Despite the discovery of various photoswitch systems that show improved photon energy storage efficiencies, the efficient and complete energy release from such photoswitches has remained a major challenge.

This work describes electrochemically-induced switching of arylazopyrazole-based photoswitches. The switching itself is electrocatalytic, requiring only a substoichiometric amount of charge, and its efficiency is improved by over an order of magnitude in the condensed phase compared to in solution. Moreover, electrochemically-induced switching affords a significantly higher completeness of switching than what could be achieved photochemically, which addresses the critical limitation of various azoheteroarene-based MOST materials. We envision that this work will promote exploration of the use of an electrical trigger for MOST material applications for a wide variety of photoswitches.

Jake L. Greenfield‡, Mihael A. Gerkman‡, Rosina S. L. Gibson, Grace G. D. Han*, and Matthew J. Fuchter* J. Am. Chem. Soc. 2021, 143, 37, 15250–15257. (‡ equal contributions) Publication Date: September 14, 2021.

Grace Han Receives Young Investigator Award

Grace HanGrace Han, Landsman Assistant Professor of Chemistry, has received a Young Investigator Research Program award from the Air Force Office of Scientific Research (AFOSR). The award will support her research on the optically-controlled catalyst recycling for 3 years.

Catalysis is one of the core processes in chemical industry and essential for achieving many products critical to the Department of Defense’s mission – from medicines to counter threats, to radiation-resistant polymeric coatings, and advanced fuels for aircraft. Catalysts are the key components that serve to improve reaction rates and product yields, and these costly compounds are generally disposed after one use. Various concepts for catalyst recycling, particularly using fluorous biphasic systems, have been developed to achieve cost-effective and sustainable synthetic procedures. However, the heating and cooling steps employed in the recycling process are only compatible with a limited scope of reactions and solvents.

To address this challenge, the Han group is developing a new class of biphasic catalysts that are optically activated, or precipitated, at a constant temperature by the incorporation of a photoswitch unit in the catalyst structure. Photoswitches are novel organic molecules that respond to light by changing their shape and physical properties including polarity. The significant shape and polarity change of the photoswitch unit will drastically change the solubility of catalysts in an organic solvent, which regulates the activity and recovery of catalysts. This new method of catalyst recycling is anticipated to reduce the costs as well as environmental impact of the conventional use of catalysts in various industries.

Turrigiano lab uncovers sources of neuronal heterogeneity

High activity neurons have greater instrinsic excitability and response to local inputs, but no difference in total input type or amount

Mammalian cortex has long been one of the most widely studied systems in neuroscience, dating back to the pioneering work of Santiago Ramon y Cajal in the late 19th century. The cortex is much larger in primates than other mammals, and is thought to be responsible for the advanced cognitive abilities of humans. Today, models of cortical connections and computations form the basis for some of the most powerful deep learning paradigms. However, despite this success, there is still much that is unknown about how cortex functions. One feature of cortex that has recently been discovered is that neurons that appear to be similar to each other can have very different baseline activity levels: some neurons are 100x more active than their neighbors. We don’t know how neurons that are otherwise highly similar in shape and genetic makeup can maintain such different activity levels, or if the neurons with high and low activity levels have different functions in the brain. These neurons are otherwise so similar to each other that it is difficult to tell them apart without recording their activity directly, and current techniques for recording the activity of many neurons simultaneously in live animals do not allow us to later re-identify them for further study.

In a paper recently published in Neuron, the Turrigiano lab, led by postdoctoral researcher Nick Trojanowski, reported a new approach for permanently labeling high and low activity neurons in live animals, and then determining what makes them different. To do this they used a fluorescent protein called CaMPARI2 that changes from green to red as activity increases, but only when exposed to UV light. By shining UV light into the brain, they caused neurons with high activity to turn red, while neurons with low activity remained green. This procedure allowed them to run a series of tests on high and low activity neurons to identify differences between them. They found that high activity neurons would intrinsically generate more activity than low activity neurons when presented with the same stimulus. These high activity neurons also receive more excitatory input specifically from nearby neurons of the same type. Surprisingly, however, they found that the total amount of excitatory and inhibitory input that high and low activity neurons received from other neurons was not a major factor in determining their activity levels. Together, these results tell us that the differences in activity between neurons are due to intrinsic differences, as well as their pattern of connectivity to their nearby partners. This has deep implications for how the networks that underlie cortical computations are built and maintained.

With these tools in hand, it is now possible to further explore the differences between high and low activity neurons. Do these neurons serve different functions? Are the baseline activity levels specified from birth? How do these activity levels affect the mechanisms of plasticity that are responsible for learning and memory? The recently published results represent just the tip of the iceberg of information that can be learned with this new technique, in the mammalian cortex as well as other brain regions.

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