{"id":53298,"date":"2022-11-16T12:00:00","date_gmt":"2022-11-16T11:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=53298"},"modified":"2025-03-24T11:18:29","modified_gmt":"2025-03-24T10:18:29","slug":"molecular-solar-panels-can-help-scientists-control-brain-cells","status":"publish","type":"embletc","link":"https:\/\/www.embl.org\/news\/embletc\/issue-99\/molecular-solar-panels-can-help-scientists-control-brain-cells\/","title":{"rendered":"Molecular solar panels can help scientists control brain cells"},"content":{"rendered":"\n

Sunlight delivers precious energy that organisms capture using specialised molecular \u2018solar panels\u2019. Only two kinds of molecules can achieve this: chlorophyll-based proteins, which enable photosynthesis, and rhodopsins. Besides capturing solar energy, rhodopsins are also present in the retina and enable us to see.<\/p>\n\n\n\n

In contrast to green chlorophyll-based proteins, which dominate on land, rhodopsins are mostly purple and found in aquatic microorganisms, especially ocean-living bacteria, archaea, algae, and even some giant viruses. <\/p>\n\n\n\n

Kirill Kovalev, an EIPOD<\/a> postdoc in the Schneider Group<\/a> at EMBL Hamburg and the Bateman Group<\/a> at EMBL-EBI, is fascinated by microbial rhodopsins. Trained as a physicist, he uses cutting-edge structural biology techniques to create molecular stop-motion visualisations showing how rhodopsins change their molecular structure to capture solar energy. With this knowledge, he designs new, more powerful rhodopsins that neuroscientists could apply as tools to control neuronal activity.<\/p>\n\n\n\n

The many colours of molecular solar panels<\/strong><\/h2>\n\n\n\n
\"Shoreline
The purple-pink colour of rhodopsins can be seen in some salty lakes with high numbers of rhodopsin-carrying microorganisms. An example is Lake Hillier in Australia, also known as the Pink Lake.
Credit: Adobe Stock.<\/figcaption><\/figure>\n\n\n\n

Why are rhodopsins and chlorophylls so colourful? The colour that we see is the light that these molecules reflect while absorbing all other wavelengths. For example, rhodopsins capture green and blue light and reflect purple wavelengths. Different types of rhodopsins reflect slightly different ranges of wavelengths, which gives them different hues of purple, violet, pink, and orange. Which wavelengths are absorbed or reflected is determined by the molecule\u2019s structure. Rhodopsins have a simpler structure than chlorophylls and are believed to be evolutionarily older.<\/p>\n\n\n\n

Switching cells on and off with light<\/strong><\/h2>\n\n\n\n

Rhodopsins\u2019 ability to absorb specific light wavelengths not only gives them their pretty colours but also makes them scientifically interesting. In particular, one group of rhodopsins found in algae, called channelrhodopsins, is studied for its unique ability to trigger electrical activity in cells when exposed to blue light. <\/p>\n\n\n\n

Scientists have adapted channelrhodopsins for human and animal cells, such that they can be used like an on- and off-switch for cellular activity. This technique, called \u2018optogenetics\u2019, was a game-changer for neuroscientists because it enables them to precisely and quickly stimulate selected neurons in the brain with just a flash of light. <\/p>\n\n\n\n

Expanding the rhodopsin colour palette<\/strong><\/h2>\n\n\n\n
\"Over
Kirill Kovalev is holding two syringes containing rhodopsin crystals. Credit: Kinga Lubowiecka\/EMBL. <\/figcaption><\/figure>\n\n\n\n

Currently, scientists have only a few channelrhodopsins to pick from, which makes certain experiments difficult or even impossible. To address this, Kovalev is on the search for new, more powerful rhodopsins that could also be activated with other colours of light.<\/p>\n\n\n\n

Using X-rays, he compares different rhodopsins found in bacteria, often in exotic places, such as salty lakes or glaciers. This lets him understand how tiny differences in the molecular structure determine protein properties and function, for instance, which colours a particular rhodopsin is sensitive to. <\/p>\n\n\n\n

\u201cOften, we are comparing almost identical rhodopsin variants,\u201d said Kovalev. \u201cA difference of just one atom is enough to change the molecule\u2019s properties. That\u2019s why we need to analyse them at atomic resolution.\u201d<\/p>\n\n\n\n

One advantage of these comparisons is that they let Kovalev predict which modifications would make rhodopsins responsive to new colours. Then, he and his collaborators can create these rhodopsins in the laboratory and test them. <\/p>\n\n\n\n

Rhodopsins in stop-motion<\/strong><\/h2>\n\n\n\n
\"Closeup
Two syringes containing crystals of sodium (pink) and proton (purple) transporting rhodopsins. Grown in syringes, the crystals will be loaded into a special injector, which is then mounted at the P14 beamline for time-resolved X-ray studies. Credit: Kinga Lubowiecka\/EMBL. <\/figcaption><\/figure>\n\n\n\n

What happens when a rhodopsin absorbs light? First, it gives rise to a complicated series of changes in the structure of the rhodopsin molecule. To visualise this process in detail, Kovalev uses a technique called time-resolved X-ray crystallography at EMBL Hamburg\u2019s beamline P14. This experimental facility is adapted for particularly demanding crystallography experiments. X-ray crystallography enables Kovalev to take snapshots of a rhodopsin at specific timepoints after absorbing light and combine them into a stop-motion movie. <\/p>\n\n\n\n

\u201cStudying a molecule that undergoes so many changes within just milliseconds is extremely challenging. Besides, rhodopsins are membrane proteins. Such proteins are notoriously difficult to crystallise, which makes them even trickier to work with,\u201d said Kovalev. \u201cBut I can do this at EMBL Hamburg\u2019s beamline P14 at PETRA III, which is one of the best in the world for this type of experiments.\u201d <\/p>\n\n\n\n

Kovalev was one of the first at EMBL Hamburg to attempt a time-resolved crystallography experiment on a membrane protein. Before he could start experiments, the Schneider Group worked together, each member contributing different expertise, to make the beamline setup suitable for Kovalev\u2019s project. Besides adjustments for membrane proteins, they installed a system to emit a flash of light to activate the rhodopsins, coordinated with the X-ray beam that would take a snapshot precisely at a selected timepoint milliseconds later. <\/p>\n\n\n\n

\"Photo
The setup for time-resolved X-ray crystallography at the EMBL Hamburg beamline P14 allows taking snapshots of molecules precisely at selected timepoints. It enables scientists to create molecular stop-motion movies of molecules that change their structure over time. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

In addition to the EMBL beamline P14, Kirill also performs experiments at the European XFEL<\/a>, which allows for time resolution in the range of femtoseconds (one quadrillionth of a second). <\/p>\n\n\n\n

\u201cThis combination of having a synchrotron and XFEL in one place is very helpful. Besides Hamburg, only Japan and Switzerland have a combo like this,\u201d said Kovalev.<\/p>\n\n\n\n

In the coming years, time-resolved experiments at EMBL Hamburg, such as this, will be further improved upon to observe how proteins work with even better time resolution. This will be possible with the planned upgrade of the synchrotron PETRA III to PETRA IV<\/a>. <\/p>\n\n\n\n

Using light to hear better<\/strong><\/h2>\n\n\n\n
\"Photo
Tubes containing bacterial rhodopsin found in a glacier. In each tube, the colour is different because of different pH values. Credit: Kirill Kovalev\/EMBL.<\/figcaption><\/figure>\n\n\n\n

Kovalev, a physicist by training, first started to work on rhodopsins during his bachelor\u2019s studies. <\/p>\n\n\n\n

\u201cWhat got me interested in biology was the opportunity to apply physics methods to solve unsolved problems. I like the thrill of being the first one to see how the molecule moves and understand how it works. I also like that my work can potentially help others in research and medicine,\u201d he said.<\/p>\n\n\n\n

One of the collaborative projects he\u2019s involved in focuses on developing optogenetic tools to treat hearing loss. Kovalev, together with the Institute of Auditory Neuroscience<\/a> at G\u00f6ttingen University, aims to develop new rhodopsins that would help improve hearing quality in patients with cochlear implants.<\/p>\n\n\n\n

In the new approach, rhodopsins will be placed into the cochlear auditory nerve using gene therapy. The nerve transmits information from the ear towards the brain, where it\u2019s interpreted as sound. Neurons at different parts of the nerve respond to different sound properties, such as pitch or intensity. A new generation of cochlear implants produces patterns of light stimuli that activate these different parts. By encoding sound information with light, these newer implants could stimulate the cochlear nerve with increased precision, allowing patients to better hear fine differences between sounds.<\/p>\n\n\n\n

This wouldn\u2019t be possible without new powerful and fast-acting rhodopsins that could manage the complexity of quickly changing sounds around patients.<\/p>\n\n\n\n

This project is just one example of how clinics could use designer rhodopsins. New rhodopsins might offer new applications in other areas as well. <\/p>\n\n\n\n

\u201cI believe the unique structural data we decipher will serve not only to help us understand fundamental principles of light energy use and reveal new cellular processes on Earth,\u201d Kovalev said. \u201cIt will also contribute to developing rhodopsin-based biotechnology and medicine.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"

Kirill Kovalev, an EMBL Hamburg researcher, is studying the structure of an ancient bacterial molecule to help scientists control brain cell activity<\/p>\n","protected":false},"author":96,"featured_media":54020,"parent":0,"menu_order":0,"template":"","tags":[726,53,363,409,35,489,13664,1714],"class_list":["post-53298","embletc","type-embletc","status-publish","has-post-thumbnail","hentry","tag-beamline","tag-hamburg","tag-optogenetics","tag-schneider","tag-structural-biology","tag-synchrotron","tag-time-resolved-crystallography","tag-x-ray-crystallography"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"embl","field_article_language":{"value":"english","label":"English"},"article_intro":"

Kirill Kovalev, an EMBL Hamburg researcher, is studying the structure of an ancient bacterial molecule to help scientists control brain cell activity<\/p>\n","related_links":[{"link_description":"Time-resolved crystallography (T-REXX) at EMBL beamline P14 in Hamburg","link_url":"https:\/\/www.embl.org\/groups\/macromolecular-crystallography\/p14-eh2\/"},{"link_description":"Schneider Group","link_url":"https:\/\/www.embl.org\/groups\/schneider\/"}],"source_article":false,"in_this_article":false,"press_contact":"None","article_translations":false,"languages":"","embletc_issue":[{"ID":53290,"post_author":"124","post_date":"2022-11-16 12:00:00","post_date_gmt":"2022-11-16 11:00:00","post_content":"","post_title":"Issue 99","post_excerpt":"","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"issue-99","to_ping":"","pinged":"","post_modified":"2022-11-17 11:34:48","post_modified_gmt":"2022-11-17 10:34:48","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc-issue&p=53290","menu_order":0,"post_type":"embletc-issue","post_mime_type":"","comment_count":"0","filter":"raw"}],"embletc_in_this_issue":[{"ID":53296,"post_author":"100","post_date":"2022-11-16 12:00:00","post_date_gmt":"2022-11-16 11:00:00","post_content":"\n

\"\"
Lautaro Gandara, a postdoc in EMBL\u2019s Crocker and Alexandrov groups, spends a good deal of time in Room 611, working with fruit flies to methodically discern the impacts of different pesticide ingredients upon them. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

It\u2019s a long day in room 611 with only fruit fly larvae for company \u2013 some no longer even alive. A young postdoc quickly transfers fruit fly larvae from small vials to Petri dishes with a fine-tipped paint brush. He has decided it\u2019s the gentlest process to nudge them onto the Petri dishes where he can capture their behaviour after they\u2019ve been growing in a nutrient-rich and possibly also chemical-infused medium. <\/p>\n\n\n\n

A video camera records the larvae\u2019s behaviour upon entering the Petri dish. Placed in this \u2018new world\u2019, some immediately scatter this way and that. To the untrained eye, it would seem quite random. But to Lautaro Gandara, a postdoc in EMBL\u2019s Crocker and Alexandrov groups funded by the EMBL EIPOD postdoc programme<\/a>, it has proven to be much more. He spends the next 10 days quantifying the recorded observations, measuring the stops and starts, distance gained, and other variables to yield behavioural and developmental data about the larvae.<\/p>\n\n\n\n

Such is the life of a molecular biologist investigating the effect of agricultural chemicals on a quick-developing organism \u2013 one that is potentially representative of the long-term impacts of pesticide use on living ecosystems.<\/p>\n\n\n\n

Gandara is but one of several researchers at EMBL whose work has intertwined in myriad ways to bring molecular biology insights into understanding the impacts of pesticides, their degradation, and ways to accelerate that degradation. <\/p>\n\n\n\n

EMBL\u2019s new programme, \u2018Molecules to Ecosystems<\/a>, applies some of EMBL\u2019s established approaches for studying molecular and cellular biology to better understand the environment. It is multidisciplinary. And it\u2019s so collaborative it\u2019s hard to see the organisational lines that divide EMBL\u2019s groups and units;  scientists converge to work toward multi-pronged, overlapping research goals within a new transversal theme of planetary biology<\/a>. <\/p>\n\n\n\n

This kind of fundamental research can inform approaches to pollution clean-up and potentially guide a new generation of agro-chemicals \u2013 chemicals that would still be potent enough for their intended objectives, but able to quickly degrade and disappear.<\/p>\n\n\n\n

A library that will keep on giving<\/strong><\/h2>\n\n\n\n

If you ask Michael Zimmermann how his research group began its work with pesticides, he talks about building a library \u2013 a library of chemicals contained in pesticides new and old that can still be found in our environment. <\/p>\n\n\n\n

\"\"
This year, Richard Jacoby (left) and Michael Zimmermann (right) worked with the Swiss water research institute, Eawag to coordinate several field campaigns to look at how biopollutants affect river ecosystems downstream.<\/figcaption><\/figure>\n\n\n\n

A group leader in EMBL\u2019s Structural and Computational Biology unit<\/a>, Zimmermann has been known for his work on the human gut microbiome. As he describes this foray into pesticides, he compares this newest challenge to deciphering how gut bacteria interact with foods and drugs and what that means to a wider collection of systems. Scientists can pinpoint genes within gut bacteria that can chemically modify drugs into metabolites. The same is true for chemicals eliminating weeds, crop pests, mould, and fungi. Once again, microbes can help degrade the chemicals.<\/p>\n\n\n\n

\u201cWe\u2019ve known for decades that bacteria absorb and convert xenobiotics \u2013 chemical substances that are foreign to animal life,\u201d Zimmermann said. \u201cI\u2019m pretty convinced we can apply the same molecular approaches we\u2019ve been using on human-associated bacteria to environmental bacteria. And again, we want to know not just which bacteria do this, but also which gene is responsible for the work.\u201d<\/p>\n\n\n\n

He began this quest by looking for a library of chemicals that his group could pair up with microbes reputed to be chemical killers. The library didn\u2019t exist. So, he and his group talked to various chemical manufacturers. As a result, he approached EMBL's Environmental Research Initiative (ERI)<\/a> for funding that comes from private citizens and Friends of EMBL<\/a>. By 2021 -- thanks to this ERI support -- EMBL had its own library of more than 1,000 chemicals found in pesticides plus the means to recruit a fellow to assist with a bigger project. EMBL\u2019s Chemical Biology Core Facility<\/a>, which already had a drug library of several thousand drug compounds, now stores the chemicals in a multi-well format readily usable for screens at large scale.<\/p>\n\n\n\n

The other half of this equation was, in fact, identifying microbes that could degrade or chemically modify pesticides. Richard Jacoby, became the ARISE research fellow<\/a> to work between the Zimmermann group and EMBL\u2019s Chemical Core Facility, scrutinising scientific literature, identifying approximately 100 environmental microbe candidates that he narrowed down to 30 to represent microbes found in nature.\u00a0<\/p>\n\n\n\n

\u201cWith the pollutants in the environment, we know they degrade and at different rates,\u201d Jacoby said. \u201cThe knowledge gap we want to fill comes from asking \u2018what controls that rate of degradation?\u2019 A lot of the time it\u2019s microbial metabolism. Microbes may break down one chemical while others are more recalcitrant. If we can find which microbe strains break down which chemicals, we can better predict how long a chemical will persist in the environment.\u201d<\/p>\n\n\n\n

To this end, an important part of Jacoby\u2019s work involves a mass spectrometer, which is able to identify the individual components of a given substance by their molecular mass or weight.<\/p>\n\n\n\n

\u201cI culture microbes. I inoculate them with pesticides. And then I use a mass spectrometer to detect whether the microbe has degraded that pesticide,\u201d Jacoby said. \u201cIf it has, I look for what new \u2018transformation products\u2019 have been produced and the effect they could have on ecosystems.\u201d <\/p>\n\n\n\n

From this point on, Zimmermann\u2019s team looks more closely at the bacteria most effective at aiding this degradation. They chop up its genome into small pieces of DNA and clone it into the laboratory bacterium E. coli<\/em>, and look for clones which now take on the same metabolic function of degrading pesticides as the original bacteria.  When they do this with 50 thousand clones and screen them with mass spectrometry, they can identify which particular piece of DNA holds the genes that can degrade pesticides. <\/p>\n\n\n\n

\"\"
In August 2022, EMBL scientists visited Iceland for a final pilot expedition before the launch of EMBL\u2019s \u2018Traversing European Coastlines\u2019 (TREC) project in 2023. Richard Jacoby worked with Joanna Zukowska and Kiley Seitz to collect soil samples from an Icelandic coastline \u2013 samples that will also be reviewed with mass spectrometry. Credit: Joanna Zukowska\/EMBL<\/figcaption><\/figure>\n\n\n\n

But this research only represents a part of a fundamental research picture. The Zimmermann group is beginning and planning other projects that go out into the environment to literally \u2018ground truth\u2019 their work, looking for the same microbial signatures and patterns in soil sediments and waterways to verify their lab findings. <\/p>\n\n\n\n

The intersection of fruit flies and pesticides<\/strong><\/h2>\n\n\n\n

It\u2019s been a few years and \u2018several cups of coffee\u2019 since Zimmermann and Justin Crocker, another group leader but in EMBL\u2019s Developmental Biology unit<\/a>, first chatted during a conference break about the usefulness of having a pesticide library. This seemingly modest encounter ignited the spark that has built such a library and given it increasing purpose.<\/p>\n\n\n\n

It is brightly lit in Crocker\u2019s lab on a sunny summer day in Germany, and there is an air of purpose and energy, radiating from Crocker himself. Zimmermann \u2013 as well as everyone interviewed for this story \u2013 convey this same positive vibe. Their myriad approaches complement one another, and despite tedious parts in the process \u2013 babysitting a mass spectrometer or systematically observing day-to-day changes in fruit fly larvae \u2013 it\u2019s clear the involved researchers are excited about what their work will tell them and how it fits into understanding pesticides better.<\/p>\n\n\n\n

The researchers in Crocker\u2019s lab work with a model organism \u2013 fruit flies. <\/p>\n\n\n\n

\"\"
Lautaro Gandara and Justin Crocker stand in the room where fruit flies are cared for during their involvement in research at EMBL Heidelberg. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

EMBL has a history with fruit flies. Christiane N\u00fcsslein-Volhard and Erich Wieschaus were EMBL\u2019s first researchers to be awarded a Nobel Prize in Medicine. In 1995, they were recognised for conducting the first systematic genetic analysis of fruit fly embryonic development, having identified genes responsible for the body plan of the insect embryos.<\/p>\n\n\n\n

\u201cUsing fruit flies, they looked at what you can learn when you break down a system into its barest parts,\u201d Crocker explained. \u201cWe have this beautiful groundwork done here at EMBL. We\u2019re now building on that to look at the whole system \u2013 essentially, putting it back together.\u201d<\/p>\n\n\n\n

With their simple body plan and quick growth, fruit flies can quickly add to the body of knowledge that EMBL\u2019s pesticide library affords. Crocker brought with him high-throughput approaches for doing this kind of work from his own postdoc experience at Howard Hughes Medical Institutes\u2019 Janelia Research Campus in the US. <\/p>\n\n\n\n

When Gandara isn\u2019t gathering data in room 611 or in the \u2018Fly Room\u2019 studying adult fruit flies, he is in Crocker\u2019s lab. He follows each generation of fruit flies from larva to adulthood to track various chemicals\u2019 effects on growth and development.<\/p>\n\n\n\n

The fruit flies he observed on the Petri dishes \u2013 bending, rolling, stopping, starting \u2013 are moved to bigger vials to observe daily until they reach adulthood \u2013 approximately 10 days. Two incubation rooms have been set up \u2013 each with different temperatures to control the speed of the fruit fly life cycle. Vials reside within both, each filled with a cornmeal-based medium cushioning and nourishing the flies until maturity. So far, Gandara has collected data on acute toxicity, impact of chemicals on fruit fly activity levels, and survival rates. <\/p>\n\n\n\n

Additionally, the Crocker group has \u2018germ-free\u2019 fruit flies they use in a \u2018gnotobiotic\u2019 environment \u2013 essentially a completely sterile environment where the only microbes present are the ones the researchers introduce. By isolating microbes and fruitflies in this way, they gain control of microbiome variables and can see the impact they have on the presence of pesticides in the fruit flies\u2019 microbiomes.<\/p>\n\n\n\n

\u201cUltimately, we\u2019ll have three complete datasets for the chemicals,\u201d Gandara said. \u201cThese datasets will inform us about the effects of these chemicals on normal fruit flies, germ-free flies, and bacterial microbes isolated directly from the flies\u2019 guts.\u201d<\/p>\n\n\n\n

\u201cBy looking at how pesticides affect the insect microbiome, we are filling a major knowledge gap,\u201d Jacoby said. \u201cMost work on insect pesticide toxicology has ignored the microbiome. This could provide a wealth of new information about how pesticides affect this host-microbe system.\u201d<\/p>\n\n\n\n

But Gandara\u2019s work doesn\u2019t end there. His position at EMBL crosses unit lines, and his next role in this research involves mass spectrometry and metabolomics, through EMBL\u2019s Alexandrov group.<\/p>\n\n\n\n

Nature vs. nurture and the role of metabolomics<\/strong><\/h2>\n\n\n\n

Metabolomics studies small molecules commonly known as metabolites, products of metabolism that fill and fuel all cells, biofluids, tissues, and organs. Because metabolites are influenced by both genetic and environmental factors, they are able to indicate individual cells\u2019 underlying biochemical activity and their current state or status. Researchers use mass spectrometry to suss out this information.<\/p>\n\n\n\n

\n
\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n
Lautaro Gandara and Mans Olof Ekelof conduct metabolomics studies to produce a deeper phenotypic analysis for understanding pesticide impacts. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

In the case of fruit flies\u2019 response to myriad chemicals, Theodore Alexandrov, an EMBL team leader in EMBL\u2019s Structural and Computational Biology unit, had already been working with the Crocker Group prior to the pesticide library.<\/p>\n\n\n\n

\u201cWe considered what would be a good way to profile molecular changes caused by environmental stimuli,\u201d Alexandrov said. \u201cPesticides are just one such stimuli. It could just as easily have been temperature or any other environmental factor.\u201d<\/p>\n\n\n\n

Gandara works with Mans Olof Ekelof, an Imaging Mass Spectrometrist in the Alexandrov group, to produce a deeper phenotypic analysis that metabolomics affords. By placing larvae onto glass slides, scanning them with a laser that desorbs or releases amino acids, carbohydrates, and lipids, they can identify and measure spatial distributions of metabolites within the larvae. In this way, Ekelof\u2019s mass spectrometry data is able to confirm Gandara\u2019s biological observations.<\/p>\n\n\n\n

In the coming months, Gandara and Ekelof will leverage this cutting-edge technology to study metabolic changes triggered by different agrochemicals. By doing so, they hope to provide a comprehensive view \u2013 encompassing development, behaviour, and metabolism \u2013 of how organisms deal with stressful environmental conditions. <\/p>\n\n\n\n

The future<\/strong><\/h2>\n\n\n\n
\"\"
Quince fruit in EMBL Heidelberg. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

Right now, these research groups are still compiling data. That doesn\u2019t stop them from thinking about follow-on projects. The Crocker group looks to a time when they can collect fruit flies from around the world to further understand the natural biomes they inhabit. <\/p>\n\n\n\n

The Zimmermann group has just recently become involved with Eawag, a leading water research institute in Zurich. With funding from the Swiss National Science Foundation and the German Research Foundation, they coordinated several field campaigns this year to look at how biopollutants affect the river ecosystem downstream. Targeting six wastewater treatment facilities in Switzerland, they are just beginning to look at the microbiomes upstream and downstream from these facilities to observe microbes in action in the real world. <\/p>\n\n\n\n

Additionally, other EMBL researchers are engaged in pesticide research projects unrelated to the library at this point. <\/p>\n\n\n\n

Recently, <\/a>ERI announced that their latest grant would support the Pepperkok team as it explores how microbial mats in the ocean break down chemical pollutants using spatial-omics. Once again, <\/a>Friends of EMBL and other citizens provided this new funding.<\/p>\n\n\n\n

Members of the Bork group are also hoping to establish interaction maps between chemical compounds and microbes, individually and in communities using advanced multi-omics approaches, with application for human (e.g., individualised diet) or planetary health (e.g., pesticide response biomarkers).<\/p>\n\n\n\n

And this latest work by Jacoby follows on a previous project he pursued \u2013 also thanks to ERI funding \u2013 that measured toxic pollutants in specific plankton species to better understand their mechanisms of bioaccumulation with the intent that his findings might also inform the design of green chemicals.<\/p>\n\n\n\n

\u201cI\u2019m quite positive about being at EMBL during this new five-year programme where I\u2019m encouraged to think about and pursue molecular approaches to planetary biology issues,\u201d Jacoby said. \u201cOur modern life has come to depend on the chemical industry for necessary pharmaceutical drugs and agricultural production. If we discontinued their use, what would happen to global health? To agricultural production? Hopefully, we can help others have information they need to build degradable replacements to these chemicals.\u201d<\/p>\n","post_title":"The power of a pesticide library","post_excerpt":"EMBL research groups apply molecular biology and its research tools to better understand agricultural pesticides\n","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"the-power-of-a-pesticide-library","to_ping":"","pinged":"","post_modified":"2023-03-31 14:36:15","post_modified_gmt":"2023-03-31 12:36:15","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=53296","menu_order":0,"post_type":"embletc","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":53300,"post_author":"47","post_date":"2022-11-16 12:00:00","post_date_gmt":"2022-11-16 11:00:00","post_content":"\n

Having one bioinformatician on a research team used to be enough, but as biology becomes more data-driven, bioinformaticians are in high demand. <\/p>\n\n\n\n

This is certainly the case in Latin America, where the data revolution is well underway in the life sciences. But one thing that is still missing is a critical mass of bioinformaticians to manage, analyse, and share the data more widely. <\/p>\n\n\n\n

\"Aerial
Aerial shot taken during a CABANA visit to Bel\u00e9m in Brazil. Credit: Jeff Dowling\/EMBL-EBI<\/figcaption><\/figure>\n\n\n\n

Bioinformatics - getting insights from big data<\/strong><\/h2>\n\n\n\n

Bioinformatics is the science of analysing, managing, storing and sharing biological data, usually on a large scale. Discovery and innovation rely on scientists sharing the data generated by their experiments; this way, the data can be reused by others to explore different scientific questions and gain new insights. <\/p>\n\n\n\n

But as the number and scale of experiments increase \u2013 and more data are generated \u2013 the need for specialist databases, analysis tools, and data experts becomes urgent.<\/p>\n\n\n\n

Bioinformatics enables scientists to exploit the large datasets available in public data resources such as the ones managed by EMBL\u2019s European Bioinformatics Institute (EMBL-EBI), to answer diverse research questions, for example:<\/p>\n\n\n\n