FISHing for RNAs: classical to single molecule approaches

Time (Europe/Berlin)	Programme
Milestones of the day	Milestones of the day: -How to use eCampus -Explain milestones -How to follow the workflow -How to use the protocol -How to use the resources -VMs -Watch pre-recorded lectures by Sunday 22nd October 2023 – the start of the course (eCampus, lectures 1, 2, 3 )
13:00 – 13:20	Welcome – virtual onboarding
13:20 – 13:40	Practical parts – Online Protocols
13:40 – 14:40	Ice breaker
14:40 – 15:00	Wrap up

Time (Europe/Berlin)	Onsite Programme	Virtual Programme
Milestones of the day		Milestones of the day: None
13:45 – 14:00	Bus from ISG hotel to EMBL	Log on and check connection
14:00 – 14:30	Welcome and house notes and course overview	Welcome and house notes and course overview
14:30 – 16:30	Ice breaking activity – Flash talks and activity in groups with concurrent coffee break	Ice breaking activity – Flash talks and activity in groups
16:30 – 17:15	Keynote Lecture 1: Applying RNA imaging methodologies to tackle ncRNAs in brain  Marie-Laure Baudet – University of Trento, Italy	Keynote Lecture 1: Applying RNA imaging methodologies to tackle ncRNAs in brain  Marie-Laure Baudet – University of Trento, Italy
17:15 – 18:00	Keynote Lecture 2: Transcriptional profiling of spermatogenesis in human and issues in infertility. Sara Di Persio – Münster University Hospital, Germany	Keynote Lecture 2: Transcriptional profiling of spermatogenesis in human and issues in infertility. Sara Di Persio – Münster University Hospital, Germany
18: 00 – 18:45	Comfort break	Comfort break
18:00 – 21:00	Moderated discussion rounds with concurrent dinner in the canteen	Moderated discussion rounds – The onsite participants will also eat during the time, please feel free to do this too.
18:45 – 19:30	Discussion to Prerecorded LECTURE 1 – Topic: Histology overview and applications Moderated by: Emerald Perlas – EMBL Rome, Italy	Discussion to Prerecorded LECTURE 1 – Topic: Histology overview and applications Moderated by: Emerald Perlas – EMBL Rome, Italy
19:30 – 20:15	Discussion to Prerecorded LECTURE 2 – Topic: RNA detection methods Moderated by: Imre Gaspar – Turbine.ai, Hungary	Discussion to Prerecorded LECTURE 2 – Topic: RNA detection methods Moderated by: Imre Gaspar – Turbine.ai, Hungary
20:15 – 21:00	Discussion to Prerecorded LECTURE 3 – Topic:ncRNA Charme in cardiac and skeletal muscle Moderated by: Monica Ballarino, University of Rome, La Sapienza, Italy	Discussion to Prerecorded LECTURE 3 – Topic:ncRNA Charme in cardiac and skeletal muscle Moderated by: Monica Ballarino, University of Rome, La Sapienza, Italy
21:00 – 21:15	Wrap up	Wrap up
21:15	Departure to Hotel

Time (Europe/Berlin)	Onsite Programme	Onsite location	Virtual Programme
Milestones of the day			Milestones of the day: Practical 1: Introduction and Preparation for practical e.g. buffer prep Practical 1: Protocol steps 1-5 Practical 2: Protocol and Video: Dye conjugation of amino-11-ddUTP (12 min)
08:30 – 09:00	Arrival and coffee
09:00 – 09:10	Overview of the day	Flex labs	Overview of the day
09:10 – 09:30	Lab safety instructions	Flex labs	Lab safety instructions
9:30 – 10:45	Interactive lecture/demo: Specimen section preparation Emerald Perlas – EMBL Rome, Italy	Training Lab A & B	LIVESTREAM PRACTICAL: Interactive lecture/demo: Specimen section preparation Emerald Perlas – EMBL Rome, Italy
10:45 – 11:00	Coffee break	Flex labs	Emerald continues and gives intro to conventional ISH for virtual participants, Imre gives an overview too
11:00 – 11:45	Keynote Lecture 7: Neuronal sorting of RNA. Marina Chekulaeva – Max Delbrück Center for Molecular Medicine, Germany	Flex labs	Keynote Lecture 7: Neuronal sorting of RNA. Marina Chekulaeva – Max Delbrück Center for Molecular Medicine, Germany
11:45 – 12:30	Keynote Lecture 4: Interplay between genetic and environmental factors in shaping body plans. Aissam Ikmi – EMBL Heidelberg, Germany	Flex labs	Keynote Lecture 4: Interplay between genetic and environmental factors in shaping body plans. Aissam Ikmi – EMBL Heidelberg, Germany
12:30 – 13:30	Lunch break	EMBL Canteen
13:30 – 14:15	Practical session 1: Introduction and theory of conventional ISH. Protocol Overview. Emerald Perlas assisted by Chiara Capponi, Sara Di Persio, and Tiziana Santini	Training Lab A & B
14:15 – 14:45	Practical session 2: Probe preparation (ddUTP + dye conjugation) Imre Gaspar assisted by 3 helpers	Training Lab A & B
14:45 – 16:45	Practical session 1: Conventional ISH; (section pre-treatment, Proteinase K digest, acetylation, hybridization set-up). Emerald Perlas assisted by Chiara Capponi, Sara Di Persio, and Tiziana Santini	Training Lab A & B
16:45 – 17:00	Coffee break	Flex labs
17:00 – 17:45	Keynote Lecture 5: Phase separation in RNA localization. Mainak Bose – EMBL Heidelberg, Germany	Flex labs	Keynote Lecture 5: Phase separation in RNA localization. Mainak Bose – EMBL Heidelberg, Germany
17:45 – 18:00	Comfort break
18:00 – 19:30	Dinner	EMBL Canteen
19:30 – 21:30	Student presentations: 10 student presentations (each: 5 min presentation plus 6 min discussion)	Flex labs	Student presentations: 10 student presentations (each: 5 min presentation plus 6 min discussion)
21:40	Departure to Hotel	ATC Entrance

Time (Europe/Berlin)	Onsite Programme	Virtual Programme
Milestones of the day		Milestones of the day: Practical 3a and 3b: -Video: smFISH probe design (part1, part 2, part3) (36 min) -Video: HCR design (part1,part2) (43 min) -OPTIONAL: Preparation of buffers for lab -Protocol steps ‘probe labelling for smFISH’ -Video: probe labelling smFsFISH (part 1, part 2, part 3) (22 min) -Video: sm FISH and HCR-ISH specimen pre-work and hybridisation set-up (8 min) Practical 1: Protocol steps 6-end
08:30 – 09:00	Arrival and coffee
09:00 – 09:10	Overview of the day
09:10 – 10:15	Practical session 1: (conventional ISH) post-hybridisation washes Emerald Perlas assisted by Chiara Capponi, Sara Di Persio, and Tiziana Santini
10:15 – 11:00	Keynote Lecture 3: RNP granule dynamics Florence Besse – University of Nice, Institut de Biologie Valrose (iBV), France	Keynote Lecture 3: RNP granule dynamics Florence Besse – University of Nice, Institut de Biologie Valrose (iBV), France
11:00 – 11:15	Coffee break
11:15 – 12:00	Practical session 1: Conventional ISH: staining set-up Emerald Perlas assisted by Chiara Capponi, Sara Di Persio, and Tiziana Santini
12:00 – 13:00	Lunch at EMBL canteen
13:00 – 13:30	Practical session 2: Theory and demo of probe design Imre Gaspar assisted by 3 helpers	LIVESTREAM PRACTICAL – Practical session 2: Theory and demo of probe design Imre Gaspar assisted by 3 helpers
13:30 – 14:30	Practical 3a and 3b: Introduction and theory smFISH and HCR Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini	LIVESTREAM PRACTICAL – Practical 3a and 3b: Introduction and theory smFISH and HCR Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini
14:30 – 15:00	Coffee break
15:00 – 16:00	Practical session 1: Conventional ISH: washing and mounting of specimen Emerald Perlas assisted by Chiara Capponi, Sara Di Persio, and Tiziana Santini
16:00 – 16:30	Practical 3a and 3b: sm FISH and HCR-ISH specimen pre-work and hybridisation set-up Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini
16:30 – 17:00	Practical 3a: sm FISH: Probe labeling set-up Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini	ON incubation sm labeling!
17:00 – 18:00	Practical 3a and 3b: continued: HCR-ISH specimen pre-work and hybridisation set-up Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini
18:00 – 19:00	Dinner at EMBL
19:00 – 21:10	11 student presentation (each: 5 min presentation plus 6 min discussion)	11 student presentation (each: 5 min presentation plus 6 min discussion)
21:15	Departure to Hotel

Time (Europe/Berlin)	Onsite Programme	Virtual Programme
Milestones		Milestones of the day: Practical 3a and 3b: -Protocol parts: ‘smFISH in myotubes and ‘HCR’ -Video: smFISH and HCR generics (part 1, part2) (23 min) -Video: Mounting?
08:30 – 09:00	Arrival and coffee
09:00 – 09:10	Overview of the day
09:10 – 11:30	Practical 3a and 3b: smFISH: Probe purifications and measurements HCR-ISH: washes smFISH pre-hybridisation set-up for incubation HCR-ISH: Amplification set-up for reaction smFISH hybridisation Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini With concurrent coffee break
11:30 – 12:15	Keynote Lecture 8: Adaptable P body physical states differentially regulate bicoid mRNA storage during early Drosophila development Tim Weil – University of Cambridge, UK	Keynote Lecture 8: Adaptable P body physical states differentially regulate bicoid mRNA storage during early Drosophila development Tim Weil – University of Cambridge, UK
12:15 – 13:15	Lunch break at EMBL canteen
13:15 – 15:45	Practical session 1: Conventional ISH imaging Emerald Perlas assisted by Chiara Capponi, Sara Di Persio, and Tiziana Santini With concurrent coffee break	LIVESTREAM Practical with Emerald and Trainers
15:45 – 16:30	Keynote Lecture 9: Membrane associated RNA transport Michael Feldbruegge – Institute of Microbiology Heinrich Heine University, Germany	Keynote Lecture 9: Membrane associated RNA transport Michael Feldbruegge – Institute of Microbiology Heinrich Heine University, Germany
16:30 – 18:00	Practical 3a and 3b: smFISH & HCR-ISH: washes and specimen mounting Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini With concurrent coffee break
18:00 – 19:00	Dinner at EMBL
19:00 – 20:30	DISCUSSION ROUND (responsible conduct of research) Experimental design Standards and controls in the ISH field	DISCUSSION ROUND (responsible conduct of research) Experimental design Standards and controls in the ISH field
20:40	Departure to Hotel

Time (Europe/Berlin)	Onsite Programme	Virtual Programme
Milestones of the day		Milestones of the day: Prepare for discussion rounds with Emerald, Monica and co.
08:30 – 09:00	Arrival and coffee
09:00 – 09:10	Overview of the day
09:10 – 10:30	Practical 4: Imaging in groups ( smFISH and HCR-ISH) Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini
10:30 – 10:45	Coffee break and group photo	Group photo – Please take a screen shot of yourselves on Zoom, we will add this to the group photo.
10:45 – 12:15	Practical 4: Imaging in groups ( smFISH and HCR-ISH) Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini	Meet the speaker for the virtual participants
12:15 – 13:15	Lunch at EMBL canteen, table set-up based on next career steps
13:15 – 14:00	Keynote Lecture 10: RNP assembly for transport and translational control Elizabeth Gavis – Princeton University, USA	Keynote Lecture 10: RNP assembly for transport and translational control Elizabeth Gavis – Princeton University, USA
14:00 – 14:45	Keynote Lecture 6: Dynamics of localized translation of mRNA Jeffrey Chao – Friedrich Miescher Institute for Biomedical Research, Switzerland	Keynote Lecture 6: Dynamics of localized translation of mRNA Jeffrey Chao – Friedrich Miescher Institute for Biomedical Research, Switzerland
14:45 – 16:15	Meet the speakers for the on-site participants	LIVESTREAM – Practical 4: Imaging ( smFISH and HCR-ISH) with Imre Gaspar
16:15 – 16:30	Coffee break	Coffee break
16:30 – 17:15	Keynote Lecture 11: PAINT superresolution imaging of nucleic acids Ralf Jungmann – Max Planck Institute of Biochemistry, Germany	Keynote Lecture 11: PAINT superresolution imaging of nucleic acids Ralf Jungmann – Max Planck Institute of Biochemistry, Germany
17:30 – 18:00	Bus to Heidelberg
18:00 – 19:30	Heidelberg Guided City tour
19:30 -22:30	Dinner at Kulturbrauerei in downtown Heidelberg

Time (Europe/Berlin)	Onsite Programme	Virtual Programme
Milestones of the day		Milestones of the day: None
08:30 – 09:00
09:00 – 10:00	Discussion on Practical 4: Summary of Image taking, including best practices and standards Monica Ballarino, Imre Gaspar, Eleonora D’Ambra, Tiziana Santini
10:00 – 10:30	Coffee break
10:30 – 11:50	Practical session 5: Basics ISH image analysis Imre Gaspar assisted by 3 helpers	LIVESTREAM – Practical 5: Basics ISH image analysis with Imre Gaspar
11:50 – 13:20	Practical session 5: ISH image analysis (incl. standards in the field) Imre Gaspar assisted by 3 helpers	LIVESTREAM – Practical 5: ISH image analysis with Imre Gaspar
13:20 – 14:20	Lunch at EMBL canteen
14:20 – 15:20	Group work: Participants preparing group presentations supported by trainers with concurrent coffee break	Virtual participants welcome to join, but no virtual presentation possible
15:20 – 16:20	Discussion: Group Data Presentations incl. Discussions with concurrent coffee break	Discussion: Group Data Presentations incl. Discussions
16:20 – 17:20	Wrap up	Wrap up
17:45	Bus to Heidelberg train station and city center

Time (Europe/Berlin)	Onsite Programme	Virtual Programme
13:00-15:00	Postcourse day: Virtual session – Open discussion round on questions to practicals (first questions will be collected via EMBL eCampus) All main-trainers	Postcourse day: Virtual session – Open discussion round on questions to practicals (first questions will be collected via EMBL eCampus) All main-trainers

The course is limited to 16 onsite participants and 5 virtual. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

On-site registration fees include admission, course materials, meals and coffee breaks. This EMBO course includes accommodation and transportation to and from the ISG Hotel to the venue.

Virtual registration fees include access to live-streamed course content (lectures, Q&A sessions with speakers and trainers, discussion rounds) as well as virtual learning activities in the learning platform.

On-site Academia	€500
On-site PhD Student	€500
On-site Industry	€1200
Virtual Academia	€190
Virtual PhD Student	€190
Virtual Industry	€250

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively, you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

• The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
• If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
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For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset childcare costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.

Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course

– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Hotel

Accommodation has been pre-booked for you at the ISG Hotel for the default dates of Sunday 22 October to Friday 27 October 2023 (5 nights).

Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfasts, for your stay at the ISG. In case you would like to have a single room, please let us know and please note that you will be required to pay an additional cost of 24€ per night. This should be paid by you directly to the ISG during your stay. Any additional nights need to be booked and paid for by you.

We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a wide variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

No food or drinks are allowed in the laboratories.

Electricity and charging station

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EMBL Merchandise

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Health and safety notes

Please read EMBL’s COVID-19 safety policy for on-site events.
Do not smoke in any EMBL building.
Eating and drinking is prohibited in all laboratories.
Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required …

• The first aid room is located next to the ATC Registration Desk (room 10- 205).
• Dial the Emergency number 222 from any EMBL internal phone only.
• Where is the accident? What happened? How many injured?
• Emergency number 06221-387 7821 from mobile phones.
• Please report all accidents to the conference officer at the registration desk.

In case of fire …

• Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
• A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
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Beyond first aid…

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg. In any case, the EMBL Course and Conference Office will assist you to get to the pharmacy and a doctor of your choice if necessary.

Internet

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Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the conference.

Luggage

There are lockers available on-site to store your luggage, which require a 2 EURO coin to operate. There is another luggage room on level E0, which is free to use but remains unlocked during the conference.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.

Photography

During the conference, an EMBL Photographer may be taking photos. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.

Printing

We can help to print your boarding pass/train ticket. Please send it to events@embl.de and collect your print-outs at the registration desk.

Room for prayer, yoga, and meditation

There is a room for prayer, meditation, and yoga located on level E0 behind the Auditorium. Please be respectful of others using the room.

Sightseeing

A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

Travel to and from the venue

During the event, we provide conference shuttle buses to and from EMBL. In addition, there is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time. Information on the shuttle buses can be found on the individual event website and more detailed information on travelling to EMBL can be found on our Travel Information page.

• Map to walk from ISG Hotel to EMBL

Additional information

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

• ATC orientation map

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.