View source for Nsf-ari-grant

'''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 
- Have been used in the past by Biology - Chemistry people �collaboration during Keck grant?


: 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
- New faculty with new interests.  Need for new equipment that can not be supported by old facilities


: 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,......)
- A lot of faculty members do summer research with undergraduate students
- Students from BioChem major are required to do research to graduate


'''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.
:--[[User:Seuka|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.


Research description (Wendy P. Tori)
Understanding what determines female mate choice and male reproductive success is central to sexual selection theory. Differences in male mating success result from interactions among males to get access to females, and from choices females make among the males they have access to.  Mate choice is a complex issue as it is often the result of an interplay of direct (e.g. courtship feeding, paternal care, territory quality) and indirect benefits (e.g. good genes) to females. Lek-mating systems provide a unique opportunity to study these �processes�, because female benefits consist mainly of the gametes that male provide and because there are fewer confounding variables than in species that defend resources.   Using White-crowned Manakins (Pipra pipra), as a �model system�, Dr. Tori has been studying the factors underlying female mate choice and male mating success.  Some key questions for her research are: How do ecological factors (such as territory size and territory quality), behavioral factors (such as song quality, male-male interactions and display behaviors) and genetic factors (such as heterozygosity and relatedness) affect female mate choice and male reproductive success? And even more importantly, how do these factors interact to influence the outcomes of mate choice and reproductive success observed in wild populations? To do this, Dr. Tori combines information about behavioral, morphological, spatial (i.e. resource availability and territoriality), and genetic characteristics, to test hypotheses about the forces that shape sexual selection in lekking birds.  Dr. Tori�s research involves national and international collaborations, and her field research has been conducted mostly in the rainforest of eastern Ecuador and Peru.  Dr. Tori is a new faculty member at Earlham College, and is planning to extend her research agenda to study the reproductive biology of Eastern Bluebirds (Sialia sialis) in the Whitewater Valley (Indiana).  She is looking forward to start new collaborations with undergraduate students and faculty from the Biology and Chemistry departments.

Question from Wendy: Should I add previous funding sources for my research?


Research description (Lori Watson)    Synthesis and Reactivity Studies of Bisimido and Phosphinoimido Transition Metal Complexes 

My research broadly seeks to answer the question of how electronic structure and steric constraints of ligands affect the structure and reactivity of their mid to late metal complexes.  I have particular interest in synthesizing novel unsaturated bisimido and phosphinoimido metal complexes, particularly metal carbene and hydrido complexes, and investigating their reactivity toward alkene metathesis, C-X bond activation, and hydrogenation reactions Imido and phosphinoimido ligands can be variable electron donors, depending on their geometry, and thus tune the electron density available at the metal center, stabilizing unsaturation while allowing incoming substrate attack. This ability to react without the often rate-limiting step of ligand disassociation makes these unsaturated complexes useful in many catalytic applications and many such complexes, most particularly those of rhenium and osmium, have found use in several important reactions (aminohydroxylation and diaminations, for example).  My most current project, supported by a Dreyfus Foundation Start-up Grant and internal Earlham College research funds, focuses on the synthesis of imido and bisimido complexes of Re, Mo, and W, sometimes including additional variable electron donating ligands (Figure X).
In the past 5 years, 16 undergraduates have participated in this research project, many of whom have gone on to further graduate study and work in the chemical sciences.  The requested renovations, most particularly of the synthetic and analysis space, will provide an appropriate configuration and quality of space for this research.  With our two inert atmosphere gloveboxes (where much of our chemistry is carried out) in the synthesis space, along with other common equipment (i.e. rotovaps) and increased hood and bench space, closer collaboration with other synthetic groups will be fostered.  The presence of improved building utilities (house nitrogen and vacuum, in particular) will reduce the time spent in local maintenance of gas cylinders and some vacuum pumps thus increasing the time available for research and research training.


Research Description (Mark G. Stocksdale)

Though largely responsible for the Green Revolution, the application of agrochemicals has a detrimental impact on the environment.  One way to diminish this impact is to reduce the application rates of these chemicals through targeted delivery.  Grasses, which represent the economically most important group of plants, secrete molecules called phytosiderophores that bind and transport iron to the plant through the roots via a membrane bound transporter that takes up both the Fe+3 and the phytosiderophore.  Dr. Stocksdale and his collaborator Dr. George T. Davis (molecular biologist/Bloomsburg University), are utilizing this iron acquisition strategy to design, synthesize and evaluate the active uptake of synthetic phytosiderophore analogs by specific grass species as well as a yeast strain transformed with the gene that expresses the requisite transporter.  Because there is some species specificity with regard to plant-phytosiderophore interactions, this technology may have significant agronomic applications in delivering biologically active molecules while reducing the impact on non-target species and the environment.  Using funding from a current USDA SEED grant (�Uptake Specificity of Synthetic Phytosiderophore Analogs by Graminaceous Plants� CSREES#2007-03529: Stocksdale, PI; Davis Co-PI), Stocksdale has completed the synthesis of two synthetic analogs of avenic acid (the phytosiderophore from oats), and Davis has assembled a full-length cDNA for a putative Fe+3/avenic acid transporter. AvsYS1, (Genbank Accession# FJ477297) shows>85% similarity at both the nucleotide and amino acid level to HvYS1, the only known phytosiderophore transporter cDNA.

With a proven synthesis in hand (the two avenic acid analogs described above were completed in July 2009), Dr. Stocksdale�s primary research activities will be the continued synthesis of a variety of avenic acid analogs.  All synthesis, isolation and purification of the analogs will be performed at Earlham College.  Davis has already begun the yeast assays for the first two avenic acid analogs, and initial/preliminary results of uptake will be known shortly.  Stocksdale and Davis plan to bring the yeast assaying to Earlham College as well.  Facilitating biological yeast assaying at Earlham will allow a quicker turn-around time for this important first-level biological evaluation of all synthesized analogs.  Davis will continue to run the assay at Bloomsburg along with his plant uptake studies.


:* 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.  --[[User:Seuka|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.--[[User:Seuka|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.  



Potential collaborative research from Wendy

1) Study how hormones affect male dominance and reproductive success of Manakins / Bluebirds (Biology- Chemistry)
2) Using isotopes to infer the diet of males with different territory qualities and see if there is any relationship with their reproductive success. (Biology- Chemistry)
3) Using isotopes, examine how Manakin diets change across seasons (breeding/non breeding) and between ages (sub adult / adult) and sexes (Biology- Chemistry)
4) Study how endoparasites and/ or ectoparasites affect sexual selection signals (e.g., feather coloration / UV reflectance) and examine if this has an effect on reproductive success (Biology � Biology)


''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 
::- built in 1972 for Chemistry, Biology, Psychology
:: - space gained and converted in minimal way to research in 2002
:: - additional space gained and converted in minimal way in 2004 (EAL)


::- need details of past renovations of each area to do this
::: - renovations under Lilly grant in this area 
:::: - old hoods moved, 1 hood replaced (Bio), controls updated on all hoods


::: - 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.''


The component of the research facility located on the first floor of Stanley Hall (built in 1972) has served collaborative student-faculty research projects of biologists and chemists involving DNA, RNA, protein, and tissue both during the summer and academic year (CITE). In addition, because of its central functionality, the space is key for the preparation of undergraduates for progressively independent research work in course associate labs (CITE). Student-faculty collaborative research constitutes approximately 85% of the use of the space; the remaining 15% is for course-associated research endeavors.

The most recent reconfiguration of this space occurred in 19XX, when the offices for psychology faculty were moved to a new building and relocation of a wall expanded the facility space by 680 ft2. With a total of 1580 ft2, small areas for individual working groups of faculty and students, and shared bench spaces for routine activities (solution preparation, electrophoresis, bacterial culture, spectroscopy, microscopy, etc.), the floor plan facilitates interactions among faculty and students. Additional electrical outlets, a water purification system, a chemical hood, internet connectivity, and one updated sink were added during the past ten years to meet the most basic demands of research. The space has also been rearranged to better house the additional equipment and activities of our new faculty (see below). These modifications are superficial and make-shift; they have not improved the out-dated infrastructure, nor do they meet the needs for the quality and quantity of our research activities (including research funded by NIH, NSF and KECK), especially as we recently hired four new faculty that will use the space. Our aged research space currently houses state of the art, commonly shared equipment for cloning, PCR, DNA sequencing and fragment analysis, gel imaging, gene expression, and single-cell electrophysiology under woefully inadequate circumstances.

The constraints of the space are substantial. The benches and shelving units date from the original construction. There is minimal lighting directed at the work spaces and storage is inadequate. The facility has limited natural gas access, inadequate electrical and cyber connectivity, and no in-house vacuum or air. The single water purification system is at least 20 years old. HVAC considerations? In addition, many pieces of shared equipment, including the LI-COR 4300L DNA Analyzer and Thermo MultiSkan MCC plate reader, require more space than can currently be provided.
	
The limitations of this out-dated facility have become even more severe during the last several years due to the demands on it by new biology faculty using molecular approaches to answer ecological, behavioral and physiological questions. The needs of the new projects (research on bird mating systems, ant social biology, and neuron biochemistry) more than doubles the demands on the space in terms of the personnel and significantly strains the make-do accommodations put in place over these many years. For example, Bob Rosenberg�s electrophysiological experiments require vacuum to aspirate superfused bathing solutions carrying various agonists, antagonists, modulators, and chemical modifying reagents. The use of vacuum pumps at each set-up is less than ideal. We need a facility that can house our existing sophisticated equipment and that serves the diverse investigative projects of at least five [Bob, Chris, Kalani, Peter, Wendy] faculty and their research students (15-20) as they engage in discovering new knowledge. 

In addition to the student-faculty collaborative projects described above, the facility space will continue to support the investigative projects associated with courses. Our biology curriculum engages students in scientific inquiry from their first course and builds independence and sophistication progressively. For instance, the introductory level genetics laboratory has students test hypotheses relating to the presence/absence of soil bacteria using PCR and electrophoresis. Other courses involve students performing SDS-PAGE, Western analysis, fluorescent microscopy, and chromatography as part of course-associated experiments. More than 150 students per year have access to equipment and bench space in the facility for these course-related purposes. This number will likely grow in the coming years as more molecular techniques (e.g. ELISA assays, others?) are used by students in physiology and neurobiology projects.

The vision for the proposed renovation is to provide the infrastructure necessary for a state of the art shared research laboratory that not only accommodates the faculty, students and instrumentation we have in place, but also has the flexibility to support future research directions as staffing and research interests evolve. Upgrades will bring the space out of the 1970�s  and into the 21st century. The space will then be able to accommodate research projects in subdisciplines including cell/molecular biology, electrophysiology, biochemistry, and behavior/evolution/ecology. The faculty of the Biology and Chemistry departments envision a collaborative workspace for all faculty engaged in research utilizing molecular-level approaches. For instance, at least three faculty are or will be utilizing using nucleic acid analysis for proofing genome annotation, assigning paternity, estimating relatedness, transcriptomics, and gene expression. There is also overlapping research on membrane function between faculty in Biology and Chemistry. The recent directions of the Biology and Chemistry departments towards multi-disciplinary approaches (CITE KECK) places even greater demands on the space.  A guiding principle of the renovation is to create an even more open structure in order to promote interaction among faculty/student research groups working on topics ranging from single genes/proteins to biological communities. This renovation will increase the ability of the Earlham science faculty to adequately train students for careers at the front lines of the life sciences. 

Our proposed renovation of this space specifically includes the following (refer to Figures x and y): 

1) Removal of a wall remaining from the previous modifications in 19XX. Installation of new benches and shelving units along three exterior walls. Installation of  XX double-sided benches and shelve units projecting into the room.  Total bench space will increase from XXX ft to XXX ft. New benches will have work-top lighting. Improved storage facilities for supplies will provide a safer, less cluttered environment.

2) Installation of gas, air, vacuum, electrical, and internet connections on all benches. Installation of X purified water systems. 

3) Installation of a second fume hood. 

4) what else???? Sinks? New ceiling? New lighting (in addition to the bench-top)? To be worked on in early August when all parties are on campus and can see the spaces.


We know from our prior conceptualization of this space as a facility shared by multiple faculty, that aggregation of our resources allows a synergism among faculty and students working on diverse systems/questions that broadens the research addressed.



The component of our shared research facility that is located in the basement of Stanley Hall has provided support for research in the molecular research laboratory on the first floor, namely animal rearing and experimentation.  Currently this space is occupied by five small rooms.  While designed for animal rearing, these rooms have very little climate control capacity.  Our new faculty will continue to have needs to rear/maintain vertebrate and invertebrate animals for research.  We propose to renovate two of these rooms, converting one into an environmental chamber and the other into a cold-room (Fig. XX).  The environmental chamber will have precise temperature and humidity control for the rearing of invertebrates.  Ant colonies stored in this space will be used in an NSF sponsored research project (DEB-IOS 0920732) designed to unravel the molecular basis of reproductive division of labor in ant societies. The cold room will serve a dual purpose, serving for storage of temperature sensitive reagents as well as to house equipment.  Our BioRad LPLC (and newly funded preparatory HPLC?) column chromatography systems will be housed in the cold room.  This will provide optimal conditions for maintaining the activity and function of both natural and synthetic proteins and peptides purified with these instruments.  Proteins purified in the cold room will be used in isotope-edited FTIR studies to investigate secondary structure and hydration changes associated with lipid membrane interactions.  The cold room will also provide a preparatory area for any heat-sensitive biological or biochemical samples.

The basement lab will also be used for a component of Bob Rosenberg�s electrophysiological experiments. He performs single-channel experiments on ligand- and voltage-gated ion channels reconstituted into planar lipid bilayers. These experiments are extremely vibration-sensitive, so the basement lab is ideal. However, the experiments also require lab facilities that are currently lacking (benches, sinks, internet, shelves, air/water/gas/vacuum).  We propose to update the basement lab with these facilities in order to make it functional for these (and other) experiments.  
Bob Rosenberg�s research combines site-directed mutagenesis, heterologous expression, and single-cell electrophysiology to characterize the conformational changes of neuronal nicotinic receptors during activation, modulation, and desensitization.