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Research Faculty Laboratory Equipment and Support Needs

Equipment Needs

Proposed for Common Space and/or shared use

Andrew Jones, Sidi Bencherif and Sara Hashmi

CELLINK Bioprinter – a high end model is $42,000 a low end model is $23,000 both with  installation, startup supplies, and training. A 3D bioprinter would add the capability to test biofilm growth, development, and antibiotic susceptibility in complex structured tissues like urethras and skin. While all of my lab is equipped to study biofilms in vitro, these tissue structures make the results more applicable to real world scenarios without the need to do more costly animal studies. These types of studies are being requested more by NIH study sections and journal reviewers.

Andrew Jones and Sidi Bencherif

Parker-Porter Instruments CM-400 and $1800 and three Mass Flow Controllers ($1000) each

Benjamin Woolston

GC-MS, which would allow us to measure headspace gases in bacterial cultures, and compounds that don’t ionize well in LCMS systems. I think these run ~80K

Carolyn Lee-Parsons

2 cell culture incubators to replace the broken ones from my start up – $15,000 each

Laminar flow hood to replace the used one from my start up – $15,000

Rebecca Carrier

We very much need a fluorescence plate reader for assays for multiple projects noted above, and a pH stat instrument for conducting in vitro lipid digestion experiments!  $30,000

Ryan Koppes

We desire to expand our ability to do this material characterization. We currently have low max, high resolution load cells for softer materials like biological samples, but could use additional higher max load cells to broaden our testable range. Along those lines, TA instruments makes a number of environmental testing chambers that we can easily add onto our system. This includes an oven to look at material properties at higher temperatures as well as bath chambers to replicate hydrated testing environments. The oven is in the $50k range and the bath chamber is $15k last time I got a quote.

Richard West (Moved ahead of Ebong, so it is not lost after her lengthy request)

Computers with high performance GPUs for training machine learning models. As AI becomes increasingly popular the shared resources of the university are heavily subscribed. My research group owns one dedicated multi-GPU node ($24k) but additional one(s) would be a great help. Now that we have our algorithms in place, GPU processing time is our current bottle-neck.

Eno Essien Ebong

RF/FS Resources Needed: Blood vessels are lined with a coat, called glycocalyx, consisting of mostly of sugar molecules and proteins. This glycocalyx is the primary focus of my work. My students and I are learning about how the glycocalyx functions in order to protect the blood vessels. As function is determined by structure, we use microscopy heavily in our lab to study the glycocalyx structure. Primarily we are using confocal microscopy which is available on campus. Confocal microscopy resolution is limited to several tenths of a micrometer, giving a limited view of the glycocalyx. Rapid freezing and freeze substitution (RF/FS) transmission electron microscopy (TEM) will make visible the nanoscale features of the glycocalyx [Ebong et al. Arterioscler Thromb Vasc Biol. 2011;31:1908-1915], including void fraction and the length and density of fibrous elements. RF/FS sample preparation for TEM does not cause any damage or collapse of the glycocalyx, and stabilizes the structure in its hydrated and protein-rich configuration. Once glycocalyx coated endothelial cells are optimally preserved by TEM, the glycocalyx can be viewed with nanometer spatial resolution. Therefore, RF/FS TEM can provide added insights for glycocalyx research. I should note that I last performed RF/FS studies as a postdoctoral fellow. The published results of my previous work is in my highest cited paper. I have tried to continue this work at Northeastern University, but the resources are not available. I’ve going to Harvard and MIT work core facilities and collaborations, but their resources are over-subscribed. It would be ideal if I can have RF/FS resources at my home institution. (I know that at least Rebecca Carrier will also benefit from this equipment, as well as faculty in other departments and colleges.)

Other Resources Needed: These include a new biosafety cabinet because our lab is growing and we do not have enough cabinet space for everyone to work in. We need COMSOL for modeling flow in the cell culture incubation chambers that we make. New pumps are needed to perfuse flow through our cell culture incubation chambers. Transepithelial/transendothelial electrical resistance (TEER) equipment is needed to quantify the leakiness of the blood vessel wall. A new pipet, new Western blot incubation trays, a new cell counting machine, and a new plate reader will be helpful for our cell culture, molecular biology, nanoparticle characterization, and other work.

Equipment/Software Cost
Leica EM ICE High Pressure Freezer $237,461
Vitrobot Plunge Freezer $57,553
Leica EM AFS2 Freeze Substitution System $35,942
RF/FS Consumables $8,354
TEM Usage ($35/hr; 100 hours) $3,500
4 foot biosafety cabinet for cell culture $10,000.00
COMSOL Multiphysics Modeling Software $8,000
Pump Head $346
Pump $2,345
Epithelial Volt/Ohm Meter (TEER) $2,122
Cell Culture Cup Chambers for TEER Measurements $1,153
0.5-5mL Pipet $282
Western Blot Incubation Tray; 6x9cm $43
Western Blot Incubation Tray; 5x7cm $43
Cell Counting Machine $3,000
SpectraMax iD3 – Multi Mode (Fluo, Lum, Abs); Easy interface; upgradable $25,000

To clarify, RF/FS = Rapid freezing and freeze substitution. It is a specialized method used for hydrated material preparation for electron microscopy visualization. In this method, hydrated material is quickly frozen at liquid nitrogen temperature, to preserve it in vitrified water form (non-crystalline glassy ice), and the vitrified water is subsequently dehydrated through a process called freeze substitution. After freeze substitution, the material remains as if in its hydrated form. Typical material preparation protocol calls for dehydration that collapses structures and obstructs material characterization.

Other faculty inside and outside of the department should be able to use this equipment. In the few institutions where I’ve seen this specialized equipment, it usually lies in a core facility although I know of one case where it is in an individual faculty member’s lab.

RF/FS = Rapid freezing and freeze substitution is enabled by using a High Pressure Freezer or a Plunge Freezer (depending on the sample) + Leica EM AFS2 Freeze Substitution System + RF/FS Consumables. For subsequent EM, we can use the core facility:

Support Needs

Sidi Bencherif

Since most senior faculty members are too busy to review grant applications and some do not have the expertise needed, having an external consultant to review our grant applications would benefit the department by increasing our success rate, especially for junior faculty members.

Lucas Landherr

As to additional funding opportunities that directly relate to my personal research – there is nothing equipment specific that would be able to help my work.  However, a donation of $10,000 would effectively allow for me to hire a professional artist and produce between 50-75 pages of educational comics that I could produce and implement in our classrooms.  The comics that have been utilized in our courses so far have shown improvements in student interest and confidence in the subject matter, and have the potential for improvement in student understanding.  I would primarily focus on developing a series of comics for our conservation principles, transport, and thermodynamics courses.

Sara Hashmi

Another possibility for funding, seconding Lucas’s suggestion, is a free-lance graphics designer to help develop graphics for web design and also cover art and graphical abstracts in publications.  Web design graphics could be utilized by individual labs and/or to market the department as a whole.  Ideally, this person could be available for anyone in the department: students, faculty, and staff.