From Earlham CS 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.

Research description (Mike Deibel) - not in final form, but I thought I would add this draft anyway

Dr. Michael Deibel is engaged two broad areas of research. The first area is in the analysis of trace metals in a variety of matrices. This work has focused both on the determination of heavy metals in environmental samples (water, sediment, biological) from a local lake (add ref) and on the use of a portable XRF to determine trace metal patterns in ancient pottery in collaboration with Dr. Emily Stovel, Ripon College (add ref). The environmental work has been supported by a 3 year grant from the W.M. Keck foundation. The instrumental techniques used are ICP-AES, GFAAS and XRF. In addition, we have adopted a bacterial assay that has been used to determining metal toxicity (metplate ref). The specific research questions of interests in the Keck grant are: how widespread is the heavy metal contamination at Springwood Lake, has this metal contamination spread into the biosphere, are the metals still mobile in the aquatic eco-system, what is the heavy metal binding capacity of this lake? For the pottery work we are trying to determine if portable XRF data can contribute to archaeological provenance studies?

A second area of focus has been the isolation and analysis of antioxidants and antioxidant classes from natural products, which have not previously been characterized for this ability. Antioxidant compounds (particularly phenolics) from natural products can serve as protective agents against reactive oxygen species, which have been shown to be important in aging, cancer, Alzheimer’s disease, and Parkinson’s disease. Specifically, the extracts of blue violet leaf (Viola odorata) and red root (Ceanothus americanus ) were shown to have very high antioxidant capacities. Antioxidant activities were measured by the scavenging of a stable radical (ABTS). We have also performed column chromatography (sephadex LH-20) on each extract and determined that the extract of BVL is primarily due to smaller phenolics, while RR is due more to polymeric phenolics (add ref). Continuing research involves looking at their antioxidant effectiveness in other antioxidant tests and further isolation and characterization of the compounds in each extract (both known and possibly unknown compounds).

Research Description for Chris R. Smith: Division of labor occurs when individuals within a group (also organelles within a cell, cells or tissues within an organism, etc.) perform different functions; achieving an effective division of labor is essential to both the evolution of complexity (from prokaryote to eukaryote, uni- to multi-cellularity, individuals to societies, etc.) as well as the spectacular ecological and evolutionary success of the social insects. Dr. Smith’s research focuses on developing an understanding of division of labor in societies, using ants as a model system. Dr. Smith uses tools from genomics to behavioral ecology in order to understand the essential component of insect sociality, the reproductive division of labor. Key questions addressed are: What genes and gene modifications are involved in the development of alternative phenotypes, the worker and queen? How do colonies regulate what castes are produced? And how do elaborate systems of morphological division of labor (when many distinct castes are produced) evolve, in terms of both development and selection? To address these questions Dr. Smith uses standard approaches such as morphometrics, physiological measures, and behavioral observations, coupled with modern approaches such as stable isotope analysis to infer diets, genetic markers to quantify relatedness and genetic variation, and as part of a recently funded NSF grant (DEB-IOS 0920732) genomics. This grant has funded the entire genome sequencing of the red harvester ant, Pogonomyrmex barbatus, in order to find and validate the genes responsible for reproductive caste determination, the fundamental trait of advanced sociality. While “caste genes” are the main goal in this sponsored research, we have recruited a community of researchers and students to help assemble and annotate this first ant genome, a resource certain to stimulate the budding field of socio-genomics. Dr. Smith’s research involves domestic and international collaborations and field work. He has also been involved in organizing the ant genomics community in order to facilitate the sequencing, annotation, and sharing of >10 ant genomes in the next 5 years. His research has involved collaborations with other faculty, post-docs, graduate students and undergraduates. Dr. Smith has recently moved to Earlham College after a post-doc at Arizona State University and will initiate collaborative research with undergraduates as part of a NSF sponsored project as well as new collaborative research in the Biology and Chemistry Departments.

  • ideas for collaborative research go here
- Interaction of the protein component of ant venom with lipid vesicles.(?) Particularly changes in secondary structure and solvation. Some ant venoms are of pharmacological interest, and may also function as fungi- and bacteriacides. --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)

- Mike and Kalani will work on a novel lipid vesicle model to determine the ability of natural product extracts or isolated fractions to protect lipids and membrane integrity.

- Collaborations on molecular analyses using HPLC (hormones) or GC/MS (smaller molecules or isotopic work)?

-HPLC has also been used for epigenetic assays (methylation of cysteine residues), which is something that I've been working on. Also, I have a project that uses stable isotopes (N and C) for inferring diets, and how this relates to both developmental differences as well as the evolution of sociality. Further, GC/MS could be used for studies of social interactions in insects (ants); contact pheromones in particular (hydrocarbons) are the glue that holds insect societies together.

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.