The Aroian Group is actively recruiting graduate students to: 1. use microbiology and genetics to develop new methods for delivery of protein therapies (anthelmintics) to the GI tract 2. discovery and mechanism of action studies of new anthelmintics to control soil-transmitted helminths 3. study how vertebrate hosts and their immune system interact with intestinal nematodes, with the particular goal of controlling autoimmune disease 4. study innate immune mechanisms that protect animals against pore-forming toxin attack
Dr. Eileen L. Berman and Stanley I. Berman Foundation Chair in Biomedical Research
Dept of Biochem & Mol Biol And Dept of Chem
Elisabeth Chair for the Dean of Medicine
The project aims to develop computational algorithms and software programs for analyzing high-throughput sequence data such as ChIP-Seq RNA-Seq small RNA sequencing data. PhD required. A strong background in computational biology especially experience with analyzing high-throughput sequencing data is highly desirable. Excellent communication and writing skills and the ability to work with experimental and computational collaborators are essential. To apply please forward CV cover letter and three references to: Zhiping.Weng@umassmed.edu
Please contact Dr. Weng for information on rotations that are available in her lab.
Worcester Foundation for Biomedical Research Chair II
Focus: Mucosal inflammation, host: pathogen interactions, and cancer biology
Rotation projects We apply X-ray crystallography and biochemical methods to understand the mechanisms employed by the ribosome. Potential rotation projects are 1) to understand various aspects of translation via mutagenesis/biochemical assays, 2) to crystallize and work on determining the structures of translation factors and functional ribosome complexes, and 3) to improve computational methods used to determine crystal structures of macromolecules. Feel free to contact the lab for a more detailed discussion.
Rotation Projects Study the interaction of the ssDNA annealing protein Bet and its cognate exonuclease with dsDNA ends. Compare wild type Bet with one or mutant Bet proteins. Use both genetic and biochemical studies to answer the question of how this annealase binds to ssDNA and promotes recombination. Develop recombineering technologies for M. tuberculosis involving the electroporation of oligos containing clinically relevant single nucleotide polymorphisms (SNPs). Generate a recombineering system for Pseudomonas aeruginosa via the electroporation of PCR substrates into electrocompetent cells containing PA phage Red-like recombination systems.
Focus: DNA Mismatch repair mechanisms in M. smegmatis; recombineering technology for gene replacement in bacterial pathogens, M. tuberculosis drug discovery.
Project 1 Investigate the lethal expression of P35 in dam lysogens. Plus inducer No inducer Lysogenic cultures of p35/dam (top) and p35/wildtype (bottom) were diluted and aliquots spotted on media with and without inducer.
If you are interesting in applying computational methods to biological problems please contact me. Potential projects in my lab are Modeling of transcription factor gene expression control in innate immune cells Evolutionary analysis of gene transcription factor networks in mammals Epigenetics inheritance in mice: From male sperm to phenotypic effect in grandchildren Application of genome and exome sequencing to newborn screening Development of computational methods for analysis of RNA-protein interactions
Neil and Margery Blacklow Chair in Infectious Diseases and Immunology
Rotation projects are available related to microbiota-gut brain axis and antibiotic usage and the sequelae of antibiotic use in hospitalized patients which include Clostridium difficile and multi-drug resistant organism infection and colonization.
Background for Student Rotation Projects <p >See Politz, Hogan and Pederson (2009) and Politz et al. (2005) in the above list. The novel microRNA work may be the most suitable for student rotations. Potential Rotation Projects <p >Are the nucleolar microRNAs pri-, pre- or mature? <p >Are they complexed with other nucleolar RNAs? <p >Do the cell cycle related proteins in the nucleolus exist as heterotypic complexes? <p >Does the nucleolus of human embryonic stem cells also share these features (which we have so far looked for, and found, only in transformed human cell lines)? <p >Can vanadium tagging be used to detect specific proteins by electron microscopy, perhaps exceeding the limitations of immuno-EM?
A postdoctoral position is available to study in this laboratory. Contact Dr. Rogaev for additional details.
Gretchen Stone Cook Chair in Biomedical Sciences
A postdoctoral position is available to study in this laboratory. Contact Dr. Zamore for additional details
Potential Rotation Projects Our laboratory uses a combination of biochemistry, cell biology, and genetics to dissect the RNAi pathway. A rotation project is available to explore the mechanisms that underlie the RNAi phenomenon or the biological pathways in which RNAi enzymes participate in flies, mice and humans.
Arthur F. and Helen P. Koskinas Professor in Biochemistry and Molecular Biotechnology
Postdoctoral Fellow Applications are being accepted for one position. A position is available to develop Cys2His2 zinc finger proteins (ZFPs) for the treatment of monogenic disorders. This project will focus on the creation of ZFPs with novel DNA-binding specificity to recognize sequence elements within genomic loci of therapeutic interest. In collaboration with other laboratories, we will evaluate the activity of these ZFP-based gene therapy reagents in vitro and in vivo in relevant disease models. Applicants will also have the opportunity to learn to apply Cas9 and Cas12a editing systems in vivo.
Potential Rotation Projects Improving the Precision of CRISPR/Cas9 nucleases for gene therapy applications: We are working to improve the precision of the CRISPR/Cas9 system to generate nucleases that will cleave at only a single site in the genome. These engineering efforts focus on increasing the DNA-editing precision of Cas9 and using protein engineering to introduce new properties into the nuclease. Much of this work is now transitioning to the use of Cas9 (and Cas12a) protein-RNA complexes. These modified nucleases will then be applied to patient derived cell-culture systems for the targeted repair or inactivation of disease-causing alleles. With the eventual goal of creating therapeutics for Sickle Cell Disease, beta-Thalassemia, HIV, Limb Girdle Muscular Dystrophy, Hermansky Pudlak Syndrome and other monogenic disorders. ex vivo genome editing in CD34+ HSPCs: We are developing improved Cas9 proteins for delivery ex vivo into CD34+ HSPCs for therapeutic application to sickle cell disease and beta-thalassemia. The goal is to modify the hematopoietic stem cells of a patient to complement the loss of function of the beta-globin gene and then return these cells to the patient through an autologous transplant. Development of Cys2His2 Zinc fingers proteins (ZFPs) as targeted therapeutics: We are developing artificial ZFPs for the regulation of target genes to change their gene expression profiles for therapeutic applications.
Maroun Semaan Chair in Biomedical Research
A postdoctoral position is available to study in this laboratory. Please contact Dr. Walhout for additional details.
Rotation Projects <p >We have identified a number of bacterial pathways that are required for bacterial viability or virulence. We are particularly interested in: Phosphosignaling systems that regulate cell wall synthesis Metabolic regulatory mechanisms that trigger the “dormancy” response observed during infection. <p >A variety of genetic, biochemical, and informatic methods will be used to define the functions of these genes and the role played by each during infection. <p >
Potential Rotation Projects <p >Our laboratory combines genetic and biochemical approaches to investigate the molecular underpinnings of adaptation. Potential rotation projects are available in two general (and partially overlapping) areas: exploring fitness landscapes through systematic approaches and investigating the molecular mechanism of the Hsp90 chaperone in signal transduction. Please contact the lab to discuss specific rotation projects in more detail.
We are looking for rotation students to visit our lab and participate in one of our ongoing research projects. Different aspects of the projects require different toolsets ranging from experimental biology to quantitative biology and mathematical modeling. Rotation students will have a chance to acquire new skill-sets and develop expertise required for implementing a quantitative approach for understanding cell regulation, signaling and evolution. Interested students should email Amir directly and briefly describe their academic background, future plans and interest in the lab. Current rotation projects: Investigating bacterial response to host-targeted drugs: As part of our research into the tumor-microbiome (tumor assosiated bacteria), we are testing how bacterial growth is inhibited by cytotoxic drugs that target cancer cells. Rotation students will run genetic screens in bacteria to identify bacterial toxicity and resistance mechanisms. In addition the students will test if bacteria can rapidly become drug resistance by evolutionary adaptation. Monitoring recovery dynamcis of melanoma cells in response to targeted therapy: The project involves examining and quantifying different aspects of cell behavior, population dynamics and adaptive resistance to targeted therapy. Rotation students will examine cellular behavior of established cell-lines and will clone and engineer new live-cell reporters for microscopy based assays.
Focus: Host-microbiome interaction, computational biology, synthetic biology
Biochemistry and Molecular Biotechnology
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Healthcare Delivery and Population Sciences at UMass Chan - Baystate
Joseph D. Early Chair in Biomedical Research