Suzanne Fleiszig, Professor

Closed (1) Inhibition of programmed cell death by Pseudomonas aeruginosa

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

Pseudomonas aeruginosa is the most common cause of contact lens-mediated microbial keratitis. Our lab uses several models, including live time-lapse fluorescence microscopy of cultured corneal epithelial cells, to study P. aeruginosa interactions with host cells over time. We have discovered that the bacterial type three secreted exotoxins interfere with a cell death process initiated by exposure to otherwise avirulent P. aeruginosa mutants. Our goal is to categorize what cell death processes are initiated by bacterial exposure (e.g., pyroptosis, necroptosis, or aspects of both) and specifically what is inhibited by P. aeruginosa exotoxin S that delays cell lysis. This project may use both conventional cell death assays (i.e., LDH release) and our internally developed time-lapse microscopy assays to measure cell death rates over time, as well as simultaneously evaluate the replication of intracellular bacteria. Both manual and software-based image analysis will be conducted on large imaging data sets.

The student will begin by learning basic handling of pathogenic bacteria and how to culture of several lines of epithelial cells. Then, infections will be performed. Microscopy training will be provided and use of the microscope will be supervised until proficiency and responsibility are demonstrated. The project may also include testing primary cells from mouse models depending on progress. Students are expected to present findings in lab meeting and keep an updated electronic lab notebook.

Day-to-day supervisor for this project: Naren G Kumar, Post-Doc

Qualifications: Basic knowledge of biology is required, as well proficiency with scientific notation, calculating molarity and concentrations, dilution of concentrated solutions, and basic use of Microsoft Excel--completion or concurrent enrollment in general chemistry and biology classes should suffice. Previous lab experience such as the use of pipettes and sterile technique is useful, but not required. Ideally we would like to recruit students who are interested in a multi-year commitment and able to apply for summer fellowships in 2020 (examples include SURF: surf.berkeley.edu.) It will be necessary to schedule the hours between 9a-5p for proper attention to training and supervision.

Weekly Hours: 9-11 hrs

Related website: http://fleiszig.vision.berkeley.edu

Closed (2) Studying the mechanism of intracellular bacterial diversification by time-lapse imaging

Applications for fall 2021 are now closed for this project.

Pseudomonas aeruginosa is found to be the main causative agent of infection of human corneal and bronchial epithelial cells in bacterial keratitis and bacterial pneumonia respectively. To understand the etiology of chronic bacterial infection we look to determine the steps associated with intracellular biofilm formation by Pseudomonas aeruginosa.

We aim to answer this question by using fluorescent bacterial gene expression reporters and determine the key components used by bacteria to initiate biofilm formation and chronic colonization of corneal and bronchial epithelial cells. We look to leverage novel tools developed to track intracellular populations by time-lapse imaging to quantify the abundance of chronic type bacteria and the impact of this population on host cell death.


The student will work 1:1 with a postdoctoral fellow on a research projects starting September 2021. The research project will involve critical thinking and constant communication with the supervisor. The student will be trained to perform analysis of time lapse data on image processing softwares such as imageJ and Imaris. Data management, timely processing and reporting of data will be a key components of this training. Data acquired will be presented in a weekly lab meeting and will be considered for publication in peer-reviewed journals.

Day-to-day supervisor for this project: Naren G Kumar, Post-Doc

Qualifications: I am seeking a student with an interest in microbiology and eagerness to work on analysis of time-lapse data. Preference will be given to a student that can join our lab for multiple semesters and is self motivated to manage their time and provide timely analysis of results(6- 8 hours per week). A basic understanding of microbiology and cell biology is preferred. Should have demonstrated ability to maintain and manage datasets, work in excel and plot results for data presentation.

Weekly Hours: 6-8 hrs

Related website: http://fleiszig.vision.berkeley.edu

Closed (3) Analysis of corneal nerves and immune responses during contact lens wear

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

Contact lens wearers suffer a multitude of complications due to extended contact lens wear, including parainflammation and bacterial infection. Contact lens wear alters the normal biology of the corneal cells and also it alters the morphology of the corneal nerve. Our lab uses several models, including the proximity and interdependence of corneal nerves and immune cells recruitment in the cornea. Our lab has developed the technique to stain the corneal nerve and the immune cells using immunohistochemistry method in mice cornea. Now, our goal is to characterize the whole corneal nerve architecture of the mouse cornea and directional innervation of corneal nerves in different corneal layer (from epithelium to endothelium) and also to localize the immune cells in particular dendritic cells and neutrophils. Using the imaging software, we have developed the way to quantify the corneal nerve tortuosity and directional innervation. Therefore, both manual and software-based image analysis will be conducted on large imaging data sets.

The student will begin training in basic microscopy techniques under supervision of Dr. Ananya Datta. The project also involves the student learning software operated image analysis. The student is expected to present findings in lab meeting and keep an updated electronic lab notebook.

Day-to-day supervisor for this project: Ananya Datta, Post-Doc

Qualifications: Basic knowledge of biology and microscope is required, and basic use of Microsoft Excel, introductory biology courses should suffice. Previous lab experience such as the use of pipettes and sterile technique is useful, but not required. Previous experience with coding is useful, but not required. Ideally we would like to recruit students who are interested in a multi-year commitment and able to apply for summer fellowships in 2020 (examples include SURF: surf.berkeley.edu.). It will be necessary to schedule the hours between 9a-5p for proper attention to training and supervision.

Weekly Hours: 6-8 hrs

Related website: http://fleiszig.vision.berkeley.edu/

Closed (4) Ly6G+ Cells Dependent Corneal Immune Response in Contact Lens wear Mice Cornea

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

Contact lens wearers suffer a multitude of complications due to extended contact lens wear, including para-inflammation and bacterial infection. Contact lens wear alters the resident immune cells in the cornea specifically neutrophils after 6 days of continuous contact lens wear and this phenomenon has been observed in mice cornea. Fleiszig lab has developed several methods, including the assessment of corneal immune cells and to explore the relationships between the ocular surface microbes and immune cells during contact lens cornea in mice cornea. Also, our lab has established the technique to stain the neutrophils (Ly6G+ antibody staining) using immunohistochemistry antibody labeling method in mice cornea. Preliminary data showed the absence of transient receptor potential (TRP) channels specifically TRPA1 and TRPV1 nociceptors of corneas (TRPV1/A1 receptors in mice cornea) were unable to recruit Ly6G+ cells during contact lens wear. Now, our goal is to investigate the involvement of neutrophil cells in preventing bacterial adhesion in the presence and absence of TRPA1 and TRPV1 nociceptors in the mice cornea. Using the confocal imaging and image analysis will be conducted on large imaging data sets.

The student will begin by learning cryo-sectioning of the mice cornea, Ly6G+ cells staining in the mice cornea using immunohistochemistry method and learning basic microscopy. The use of the microscope will be supervised until proficiency and responsibility are demonstrated. The project may also include software operated image analysis. Students are expected to present findings in lab meeting and keep an updated electronic lab notebook.
, Post-Doc

Qualifications: : Basic knowledge of biology and microscope is required, and basic use of Microsoft Excel--completion or concurrent enrollment in general chemistry and biology classes should suffice. Previous lab experience such as the use of pipettes and sterile technique is useful, but not required. Ideally, we would like to recruit students who are interested in a multi-year commitment and able to apply for summer fellowships in 2020 (examples include SURF: surf.berkeley.edu.) It will be necessary to schedule the hours between 9am-5pm for proper attention to training and supervision.

Weekly Hours: 9-11 hrs

Related website: http://fleiszig.vision.berkeley.edu/