SEMC Re-opening Plan2020-07-17T16:13:06+00:00

SEMC COVID-19 Operations
Re-opening plan 2020

PDF of email notice sent to users March 20, 2020
PDF of email notice sent to users March 11, 2020

Re-opening plan starting June 2020.

SEMC will be re-opening under remote operations. Please note NO affiliates are permitted at NYSBC except by appointment.

Dear SEMC Users,

The NYC region started Phase II re-opening June 22, 2020. In response to this, SEMC will start to phase in remote non-COVID-19 research with 25% staffing capacity in June. We will take in grids for data collection on a limited basis beginning late-June. Operationally, we will ramp-up capacity taking guidance from the New York Forward NY State re-opening plan and NYSBC policies.

Main operations will be remote and users may drop off samples at the lobby by appointment only. We do not plan standard on-site access to resume until the NYC region opens for Phase IV industries or later. All on-site meetings, classes or workshops will be shifted to a remote format. We will update users if there are changes and work with you to minimize the impact on your research.

You may email emg [at] nysbc.org for further details.

SEMC | June 23, 2020

General Information for SEMC COVID-19 Re-opening Operations

Instrumentation Access

The major change will be that SEMC operational staff members will assist with experiments instead of the experiment being user-driven. SEMC will have limited access and operations in the following ways:

  • Until further notice users will not be permitted to use instrumentation without an appointment.
  • We will have reduced staffing and hours of operations to maintain social distancing practices.
  • Sample and grid intake will occur by appointment in a designated location (SEMC entrance).
    • Starting late-June Krios grid drop off will resume.
    • Starting in July on a limited basis we will take in user samples and staff members will assist with vitrification and screening under remote direction from the user.
    • Please note that the number of samples that we will be able to take in and the number of hours spent screening will be limited by staff availability, but we are committed to doing our best to lessen the impact of these policy changes on your research.
    • Users that have a critical need to be onsite should email emg [at] nysbc.org a proposal entitled “SEMC on-site work request – Proposal of work” including the work that needs to be done, resources required, and clearly state how the experiment may be completed in a defined period of time with minimal or no staff-assistance to maintain social distancing best practices.
  • Krios usage will resume except that users will not be on-site during their session. Users can log on and view images on the Appion and Leginon Tools webpage and provide feedback to the staff member operating the Krios.
  • During remote screening sessions, users can log on and view images on the Appion and Leginon Tools webpage (emgweb.nysbc.org) and provide feedback to the staff member operating the screening microscopes.
  • Scheduled user meetings will continue in a remote format by video conference.

Sample drop off

Users MUST schedule a confirmed appointment before the delivery of samples at the center. The user should be in communication with your appointed center staff member, and fill out following the sample drop off forms:

The completed forms should be emailed to emg [at] nysbc.org and confirmed by SEMC operations before going to the center.

We are limiting personnel on-site to maintain social distancing and there is only intake of samples when scheduled. When a staff member processes the sample, they will confirm receipt of the sample by email.

Any sample left by a user should be accompanied by a Krios drop off form (if appropriate) and shipping manifest. The NYSBC cryoEM facility is a BSL-1 (Biosafety Level 1) laboratory. All samples shipped to or worked on at SEMC and NYSBC premises should be classified as BSL-1.

Sample transfer may be done using a shipping container, transfer dewar or container. Samples should either be dropped off at the designated sample receiving area or near the security guard station (see the designated SEMC EM sample drop off table to the right), or shipped to NYSBC by dry shipper with carrier tracking info sent ahead of time. If left on the table, the outside surfaces of containers should be sterilized with wipes on the table. Otherwise, center staff will sanitize the outsize of dry shippers/containers ahead of processing when shipped using a carrier. Again forms should be filled out electronically and submitted ahead of shipping.

Note, each sample should be clearly labeled, and the outside container includes the date and time, username, institution and project ID. If grids and cryo grid boxes are submitted, then NYSBC uses a particular numbering system. Please note and order your boxes accordingly.

Signing up or assignment of an instrument session

Krios access will be assigned in consultation with your Institutional Representative (IR).

  • Krios sessions will be queued access where we plan on loading multiple users in a cassette. Krios users will be allotted up to 2 grids per Krios weekday. If you have a 2-day session, then that would be up to 4 grids. You may submit up to 2 buttons or grid boxes with up to 8 grids per drop off. If there is additional space in the autoloader we may be able to load more grids, but not guaranteed. Grids will be loaded in this order: b1g1, b1g2, b1g3, b1g4 and if room b2g1, b2g2, b2g3, b2g4. Please arrange your grids appropriately as staff will not be able to re-order your grids.
  • Your samples will only be placed in the queue for a Krios session when your grids are clipped, you have an active Leginon account, and data collection parameters that have been confirmed.
  • Rapid access will still be available, but limited due to available capacity. You may submit samples after emailing emg [at] nysbc.org and your IR a rapid access request. We will then be in contact to arrange logistics.

Screening microscope or sample prep instrumentation will be by request.

  • Please note that the number of samples that we will be able to take in and the number of hours spent screening will be limited by staff availability, but we are committed to doing our best to lessen the impact of these policy changes on your research.
  • Users that have a critical need to be onsite should email emg [at] nysbc.org a proposal entitled “SEMC sample prep request – Proposal of work” including the work that needs to be done, resources required, and clearly state how the experiment may be completed in a defined period of time.
    • We will then schedule a project meeting with you to work out the details.

SEMC staff assistance with sample preparation and screening

General reminders:

  • Please note that the number of samples that we will be able to take in and the number of hours spent screening will be limited by staff availability, but we are committed to doing our best to lessen the impact of these policy changes on your research.
  • Screening microscope or sample prep instrumentation will be by request. If you would like SEMC to assist you with your sample preparation then there will be a multiple-step process.

A. Project meeting:
Email emg [at] nysbc.org to schedule a project meeting. Typically Tuesday or Thursdays at 3pm.

During the meeting please prepare 3-5 slide deck with the following information:

  1. Include the registered Leginon project.
  2. Brief background and proposed experiment.
  3. Quality assessment of the sample (including purification, sample MW, concentration, sample buffer).
  4. EM work including negative stain or cryo screening with representative micrograph, 2D classes and 3D if available.

B. Freezing session:

A SEMC operational staff member will coordinate with you for sample drop off after the project meeting.

  1. We will aim to plunge freeze 1 box of 4 grids for a sample (limit for up to 2 samples).
  2. We will then arrange for a grid retrieval time with you.

C. Screening session:

If you require screening, then after the grids are made we will enter 1 box (up to 4 grids) into the sample screening queue. These details will be worked out on a case by case basis with the staff.

  1. A SEMC operational staff member will coordinate with you about when your session will be scheduled.
  2. If you have additional grids to be screened outside the sample preparation process, then they may be entered into the queue. But only 1 sample will be screened at a time.
  3. Note we have limited capacity for screening and there may be a significant turnaround time between samples due to social distancing policies and limited staffing.

General hygiene practices upon arrival at SEMC

There is restricted onsite access to staff, vendors and affiliates. Anyone on site must adhere to these policies:

NYSBC COVID-19 policies:

  • All people going to the center must be pre-registered with the center and the security guard
  • Stay home if ill or if members of your household are ill or showing symptoms
    •  Cough
    • Repeated shaking with chills
    • Fever
    • Chills
    • New loss of taste or smell
    • Shortness of breath or difficulty breathing
    • Muscle pain
    • Headache
    • Sore throat
  • Inform us when you are onsite and when you leave as we need to practice social distancing and keep the numbers of staff/vendors on-site to a minimum
  • Practice social distancing (6 feet minimum)
  • Temperature Checks
    • You must check your temperature within two hours of entering the Center.
    • The guard will ask you to confirm that your temperature is less than 100.4 degrees Fahrenheit (38.0 degrees Celsius).
  • Wear a face covering that protects your nose and mouth
    • Surgical masks are to be worn in the Center by staff unless they are alone in your lab.
    • If near other people, N95 masks are to be worn.
  • Wash your hands often with soap and water for at least 20 seconds, especially:
    •    each time you enter NYSBC
    •    after going to the bathroom, before eating, and after blowing your nose, coughing, or sneezing
  • Use hand sanitizers and wipes after touching common surfaces; throw out wipes right after using
  • Do not touch your eyes, nose, or mouth
  • Cough or sneeze into elbow or tissue (to be disposed of immediately)
  • No handshaking
  • Use gloves when handling common reagents (e.g. buffers, enzymes, etc.) and immediately dispose of used gloves
  • Keep interior doors open to the extent practicable
  • Try to avoid touching door handles and other surfaces
  • Clean benches and common areas frequently with 70% isopropyl alcohol
  • In your work area, before anything else, use disinfectant to wipe down any surfaces you will be touching, computer keyboard, bench top, etc.
  • Kitchen and NCCAT kitchen area are closed and may be accessed only to use the refrigerator (bring your own thermos for coffee, tea, etc.)
    •    Use sanitizing wipes to wipe down refrigerator before and after use
  • Use sanitizing wipes to wipe down water coolers before and after use
  • Use only designated bathrooms
    •    One lobby bathroom has been designated for use by security staff
    •    One NCCAT bathroom has been designated for use by outside contractors
    •    Use sanitizing wipes to wipe down bathroom before and after use
  • Upon leaving, wipe down those same surfaces

If you have been exposed to/diagnosed with COVID-19

If you have been exposed to COVID-19 and visted the center, please notify health officials and emg [at] nysbc.org as soon as possible.

FAQ: Frequently Asked Questions

Re-opening FAQ

  • Is the facility open to users?
    • Currently SEMC is running under remote operations, focusing on autoloader systems such as the Krios and Glacios with no outside users allowed on site.
  • What are the hours the facility is open?
    • Business hours continue to be 9am to 5pm Monday to Friday.
  • Can I use the plunge freezers? 
    • If you cannot prepare samples at your home institution, there is an option to have your samples frozen by an EMG staff member for an upcoming screening session. You will need to schedule a project meeting with EMG staff first, typically scheduled Tuesdays and Thursdays at 3pm. Please note that we are running with limited staff capacity and we appreciate your patience while we find availability. Email emg [at] nysbc.org to schedule a project meeting.
  • What about the F20, T12?
    • If you have grids premade and ready to go, you may drop off grids at our drop off table. Please set up an appointment to drop off grids in order to practice proper social distancing practices by emailing emg [at] nysbc.org. Since we are focusing on remote operations, the Glacios will be the primary screening microscope.
  • Can I use the plunge freezer or screening microscope if I am an independent user and do not need assistance? 
    • Right now, NYSBC is not allowing affiliate users on site. As New York City enters Phase IV of reopening, we will allow independent users to schedule time on instrumentation. 
  • How many grids can I drop off for a screening session?
    • You may drop off up to 4 grids per screening session. If you have more than 4, they will be added to the end of the queue. 
  • When can I drop off grids?
    • In order to adhere to safe social distancing practices, EMG will schedule you a 30 minute window to drop off grids. Please do come within your time slot as to not overlap with staff or another user.
  • Do I have to provide any materials? 
    • Users must provide their sample and all consumables including grids and grid boxes.
  • Can I set up time if the sample is new and has not been screened before? 
    • Yes, this can be discussed during your pre-sample prep project meeting.
  •  Can I choose which screening microscope I want my samples to be screened on?
    • The screening microscope chosen for your screening session will be dependent on staff availability. The Glacios is favorable due to its high turnover rate.
  • Can I make an appointment to make negative stain grids?
    • Yes, we can add you to the queue of sample prep grids. This is also dependent on staff availability so there may be a long wait to do so.