From Earlham Cluster Department

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Major Questions to address

1. Why are the spaces we are renovating one facility?
- one building (in fact only one end of the building)
- all spaces are for shared use (not dedicated to a single faculty user) and are organized by function
- research facility helps serve the research training needs of our shared major

2. What collaborations do we envision in our facility? How will these future collaborations improve the research at Earlham?
- past collaborations - Keck, HHMI, Merck-AAS

3. Why do we need to renovate? What do we envision doing in the new space that we cannot do now?
- building limitations (water, house air, vacuum, electrical,...)
- spaces inadequate for shared use of modern instruments and significant increase in # of instruments
- need spaces intentionally designed to facilitate collaborations (open design)
- spaces inadequate for multi-faculty, multi-project use
- increased # of faculty, students doing research needs all of the above

4. What distinguishes us from other institutions?
- history of multidisciplinary work (perhaps highlight Keck work)
- emphasis on ensuring research exposure for large number of students
- the numbers (grad school, % of majors in college,......)

Research statements Identify the senior personnel using the research facility for research/research training. Describe their research activities--identifying the specific questions being addressed, projects conducted in the facility, and sources of support, if any. In narrative or tabular form, list by number and type (e.g., senior personnel, postdoctoral fellows, graduate students, undergraduate students) the personnel using the facility on a regular basis.

  • Individual research descriptions go here

Research (K. J. Seu)

The structure and dynamics of membrane proteins is one of the most important and challenging problems in biophysical chemistry today. Dr. Kalani Seu is interested in protein-lipid interactions and the changes that occur in both the lipid bilayer and the protein as the two interact. In Seu’s research, isotope-edited FTIR is used to obtain residue specific structural and hydration information of peptides as they interact with synthetic lipid vesicles and supported lipid bilayers(1,2). Complementary techniques including ATR-FTIR, fluorescence spectroscopy, circular dichroism, and fluorescence microscopy are also used. Use of these techniques provides detailed insight into the mechanism of protein folding, insertion, hydration, and function in the presence of a lipid membrane. This information will improve our understanding of how proteins interact with and act on biological membranes, providing insights for the design and development of tools for disease treatment and drug development.

Some key questions of Seu’s research include: How are the lipids near the protein oriented to accommodate the presence of the protein and what kind of environment surrounds each of the protein residues? Are the residues hydrated, non-hydrated, or partially hydrated? Do the structural and hydration states change as the lipid composition is altered? Can isotope-edited FTIR be used to identify bilayer spanning regions of larger proteins?

Recent work by Seu has been focused on a 21-residue peptide, KL4, which has been successfully used in clinical trials to replace lung surfactant protein B. Using isotope-edited FTIR, residue specific differences were observed in the secondary structure of KL4 at different positions in the peptide backbone when incorporated into lipid vesicles of varying saturation(3). These results are in agreement with those obtained by SS-NMR4(5). Unlike SS-NMR, isotope-edited FTIR is a faster and more efficient technique that can provide the medium-resolution information necessary to map out peptide structure and hydration.

From mid-June to mid-July 2009, Seu and two students used the biochemistry research area to identify changes in the structure and solvation state of model helical peptides incorporated into lipid bilayers. These model peptides are similar in sequence to that of KL4 and have been thoroughly studied in solution. Changes in the FTIR amide I? band of these peptides in buffer, lipids, and fluorinated solvents were monitored for changes in secondary structure and shifts due to solvation state. Slight differences in peak position, peak shape, and melting curves were observed, suggesting changes in solvation state and structural stability.

(1) Decatur, S. M. Accounts of Chemical Research 2006, 39, 169. (2) Tamm, L. K.; Tatulian, S. A. Quarterly Reviews of Biophysics 1997, 30, 365. (3) Seu, K. J.; Long, J. R.; Decatur, S. M. Biophysical Journal 2009, 96, 336a. (4) Antharam, V. C.; Elliott, D. W.; Mills, F. D.; Farver, R. S.; Sternin, E.; Long, J. R. Biophysical Journal 2009, 96, 4085. (5) Mills, F. D.; Antharam, V. C.; Ganesh, O. K.; Elliott, D. W.; McNeill, S. A.; Long, J. R. Biochemistry 2008, 47, 8292.

--Seuka 19:53, 23 July 2009 (UTC)

(Bob Rosenberg)

Ion channels are important for synaptic potentials, action potentials, and other physiological signals. They control the flow of information in the nervous system, trigger the release of neurotransmitters and hormones, set the rate and strength of the heart beat, and control fluid and electrolyte transport in epithelia. Dr. Robert Rosenberg’s research focuses on the molecular mechanisms of activation and modulation of neuronal nicotinic receptors. These receptors are prototypical ligand-activated ion channels that regulate excitatory and inhibitory neurotransmission. Abnormalities in neuronal nicotinic receptors have been implicated in nicotine and alcohol addiction, Alzheimer’s disease, epilepsy, schizophrenia, and other neuropsychiatric disorders.

Dr. Rosenberg’s research combines molecular modeling of nicotinic receptors, site-directed mutagenesis (to introduce cysteine substitutions at key residues identified in the models), heterologous expression of mutant receptors in Xenopus oocytes, and voltage-clamp electrophysiological techniques to characterize the mutant receptors. We measure the effects of cysteine-modifying reagents on the mutant receptors and then test agonist- or modulator-dependent changes in the rate of chemical modification. This reports the accessibility and electrostatic microenvironment of the introduced cysteine thiol. Changes in the modification rate report conformational changes of the introduced cysteine or its local environment. The data provide information about the molecular machinery involved in receptor activation and modulation.

Current research is examining the following questions: What residues at the junction between the extracellular ligand-binding domain and the trans-membrane ion channel domain are required for receptor activation? Do accessibility and electrostatic changes of multiple locations indicate that receptor subunits undergo rotation during activation and modulation? Do modification rate data support specific structural molecular models of nicotinic receptors?

Recent research in the Rosenberg lab, previously located at the University of North Carolina - Chapel Hill, was conducted by one graduate student, four summer undergraduate students, one postdoc, and one senior scientist. The research is supported by an NIH R01 grant from May, 2004 to December, 2009. Dr. Rosenberg moved to Earlham College in August, 2009 and will continue his research with undergraduate students.

Research description (Peter Blair)

A new era of genomic biology was initiated with the landmark publication of the first apicomplexan genomes, Plasmodium falciparum and P. yoelii. This event marked a major milestone and evolution in modern malaria research and initiated the onset and application of several post-genomic technologies including genome-wide microarray analyses and mass spectroscopy-based proteomic studies. Furthermore, this was the first organism to be sequenced possessing a markedly biased A/T-rich (80%) genome. Given the vast and imminent wealth of information provided by such large-scale sequencing projects it is essential and a necessity that current annotations and predicted gene structures be accurate when presented to the to the research community at large. An exceptional amount of time and valuable resources may perhaps be lost due to research misguided from using incorrect gene predictions. Resolving, correcting, and gaining clarity in the annotated gene structures of the rodent malaria (P. yoelii) genome is the focus of Dr. Blair’s laboratory. As large universities and sequencing centers hesitate to meticulously validate and correct published genomes, the Blair lab, solely devoted to undergraduate research and training, is a proper setting for such research. Specifically, Dr. Blair’s research aims are to: 1) revisit the P. yoelii genome by utilizing pre-existing large-scale expressed sequence tag (EST) sequencing projects and previously published sequencing efforts to resolve currently predicted exon/intron boundaries and also for identifying and validating genes not found in the current annotation, 2) utilize comparative genomics between P. yoelii and P. falciparum to improve gene annotations and to better train current gene prediction software used on other A/T-rich genomes, 3) clone and sequence selected P. yoelii ORFs to experimentally determine validated gene structures, and 4) report findings directly to the free access malaria genomics resource, PlasmoDB, for immediate data release to the genomics and malaria research communities. To date, the Blair laboratory has proofread 20.8% of the entire published genome and 15.6% of the predicted total genes characterized on PlasmoDB correcting nearly 69% (200/290) of their prioritized genes. Overall, 18.7% of all genes surveyed (n=1,225) were incorrectly called as originally published. The laboratory will continue its successes in refining the complete P. yoelii genome while initiating a similar plan with related apicomplexan eukaryotes including Toxoplasma.

  • ideas for collaborative research go here
- Interaction of the protein component of ant venom with lipid vesicles.(?) Particularly changes in secondary structure and solvation. --Seuka 20:11, 23 July 2009 (UTC)
- Previous research in Bob's lab used planar lipid bilayers to reconstitute ion channels into artificial membranes. We used electrophysiology to characterize the reconstituted channels in various lipid environments. Although we haven't done thihs type of experiment in several years, I'm bringing the equipment and I hope to set up a bilayer rig at Earlham. Is there a possible collaboration with Kalani in this area? Do any of Kalani's proteins show ion channel activity?
- The proteins I am currently working on do not show any ion channel activity. My graduate work focused on the chemical and physical properties of supported lipid bilayers, where I did a lot of vesicle fusion work (forming supported lipid bilayers) and FRAP measurements. I would eventually like to build an ATR-FTIR setup to probe proteins/peptides incorporated in planar supported lipid bilayers. I am excited to see the equipment you are bringing and definitely see the possibility for a collaboration.--Seuka 19:39, 27 July 2009 (UTC)

Identify as a single research structure with 5 shared research areas, each with a specific function (rather than dedicated for a single researcher). Describe each area (current and proposed).

1. Identify and describe the research facility including its nature, location, size, configuration, purpose, age, condition, and date of major repair, refurbishment and/or last renovation, if any.

- use description of SH as whole
- need details of past renovations of each area to do this
- renovations under Lilly grant in this area (move in hoods only?)
- other renovations - minor changes to adapt space when psychology went to LBC

2. Discuss the adequacy, limitations, and constraints of the facility and the relevant impact of these conditions on research/research training activities in that facility.

- limitations of the building (water, air, nitrogen, electric, benches,…)

- limitations that are in common
- small spaces – limit use by multiple users
- inadequate configuration (benches, hoods)
- inadequate infrastructure (benches, hoods, sinks, storage)

- special limitations – describe any that are specific to discipline
- molecular
- biochem
- analysis
- synthesis

3. Indicate what research and research training that is not now feasible in the facility would be enabled by the proposed infrastructure project.

- examples for whole building work

- examples for each area

4. Identify the specific space to be upgraded, the square footage of the facility, and indicate the percentage of time that the facility is used for research and research training and the fraction of space used for these purposes. Include the rationale for percentage determination if either is less than 100%.

- describe whole facility or describe each area

5. The description of needs should be comprehensive enough to allow reviewers to evaluate the extent to which the facility improvement is essential and appropriate.

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