The Development of a Test for Understanding of Scientific Attitude

This study tests the hypothesis that a valid evaluation instrument can be constructed which reliably measures the ability of junior high pupils to identify behaviors representing scientific attitude

Four small puzzles that Rosetta doesn't solve

A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on deceptively small protein and RNA puzzles, some as small as four residues. To illustrate these problems, this manuscript presents extensive Rosetta results for four well-defined test cases: the 20-residue mini-protein Trp cage, an even smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies, several lines of evidence indicate that conformational sampling is not the major bottleneck in modeling these small systems. Instead, approximations and omissions in the Rosetta all-atom energy function currently preclude discriminating experimentally observed conformations from de novo models at atomic resolution. These molecular "puzzles" should serve as useful model systems for developers wishing to make foundational improvements to this powerful modeling suite.Comment: Published in PLoS One as a manuscript for the RosettaCon 2010 Special Collectio

Knots in rings - The circular knotted protein momordica cochinchinensis trypsin inhibitor-II folds via a stable two-disulfide intermediate

The aim of this work was to elucidate the oxidative folding mechanism of the macrocyclic cystine knot protein MCoTI-II. We aimed to investigate how the six-cysteine residues distributed on the circular backbone of the reduced unfolded peptide recognize their correct partner and join up to form a complex cystine-knotted topology. To answer this question, we studied the oxidative folding of the naturally occurring peptide using a range of spectroscopic methods. For both oxidative folding and reductive unfolding, the same disulfide intermediate species was prevalent and was characterized to be a native-like two-disulfide intermediate in which the Cys(1)-Cys(18) disulfide bond was absent. Overall, the folding pathway of this head-to-tail cyclized protein was found to be similar to that of linear cystine knot proteins from the squash family of trypsin inhibitors. However, the pathway differs in an important way from that of the cyclotide kalata B1, in that the equivalent two-disulfide intermediate in that case is not a direct precursor of the native protein. The size of the embedded ring within the cystine knot motif appears to play a crucial role in the folding pathway. Larger rings contribute to the independence of disulfides and favor an on-pathway native-like intermediate that has a smaller energy barrier to cross to form the native fold. The fact that macrocyclic proteins are readily able to fold to a complex knotted structure in vitro in the absence of chaperones makes them suitable as protein engineering scaffolds that have remarkable stability

Atomic-accuracy prediction of protein loop structures through an RNA-inspired ansatz

Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased. This article introduces a modeling strategy based on a 'stepwise ansatz', recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. When harnessed to a dynamic-programming-like recursion in the Rosetta framework, the resulting stepwise assembly (SWA) protocol enables enumerative sampling of a 12 residue loop at a significant but achievable cost of thousands of CPU-hours. In a previously established benchmark, SWA recovers crystallographic conformations with sub-Angstrom accuracy for 19 of 20 loops, compared to 14 of 20 by KIC modeling with a comparable expenditure of computational power. Furthermore, SWA gives high accuracy results on an additional set of 15 loops highlighted in the biological literature for their irregularity or unusual length. Successes include cis-Pro touch turns, loops that pass through tunnels of other side-chains, and loops of lengths up to 24 residues. Remaining problem cases are traced to inaccuracies in the Rosetta all-atom energy function. In five additional blind tests, SWA achieves sub-Angstrom accuracy models, including the first such success in a protein/RNA binding interface, the YbxF/kink-turn interaction in the fourth RNA-puzzle competition. These results establish all-atom enumeration as a systematic approach to protein structure that can leverage high performance computing and physically realistic energy functions to more consistently achieve atomic resolution.Comment: Identity of four-loop blind test protein and parts of figures 5 have been omitted in this preprint to ensure confidentiality of the protein structure prior to its public releas

Interrogating and Predicting Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein

Cystine-knot miniproteins (knottins) are promising molecular scaffolds for protein engineering applications. Members of the knottin family have multiple loops capable of displaying conformationally constrained polypeptides for molecular recognition. While previous studies have illustrated the potential of engineering knottins with modified loop sequences, a thorough exploration into the tolerated loop lengths and sequence space of a knottin scaffold has not been performed. In this work, we used the Ecballium elaterium trypsin inhibitor II (EETI) as a model member of the knottin family and constructed libraries of EETI loop-substituted variants with diversity in both amino acid sequence and loop length. Using yeast surface display, we isolated properly folded EETI loop-substituted clones and applied sequence analysis tools to assess the tolerated diversity of both amino acid sequence and loop length. In addition, we used covariance analysis to study the relationships between individual positions in the substituted loops, based on the expectation that correlated amino acid substitutions will occur between interacting residue pairs. We then used the results of our sequence and covariance analyses to successfully predict loop sequences that facilitated proper folding of the knottin when substituted into EETI loop 3. The sequence trends we observed in properly folded EETI loop-substituted clones will be useful for guiding future protein engineering efforts with this knottin scaffold. Furthermore, our findings demonstrate that the combination of directed evolution with sequence and covariance analyses can be a powerful tool for rational protein engineering

The development of a master's in student affairs administration program via distance education

There is no abstract available for this creative project.Department of Educational StudiesThesis (M.A.

The development of a master's in student affairs administration program via distance education

There is no abstract available for this creative project.Thesis (M.A.)Department of Educational Studie

A teacher behavior instrument for a multidimensional teaching model

The purpose of this study was to establish and describe the validity and reliability of an instrument based on a model of teaching behaviors conceived as magnetic lines of force.Content validity was established by reviewing the literature and identifying possible teaching behaviors which researchers felt contributed to increased pupil learning. These behaviors were presented to a panel of judges from faculty in the Teachers College, Ball State University, to ascertain behaviors which they felt increase the likelihood pupils would increase comprehension in reading. After the panel had made their suggestions, the list of behaviors was revised and used with two middle school classes at the Burris Laboratory School. Pupils were asked to identify the behaviors which they felt were associated with their increased learning. A final list of twenty items became the revised instrument for use in the study.A group of practicing teachers critiqued the list of twenty behaviors. This group was directed to identify how strongly they agreed with the placement of each of the behaviors under one of the four scales postulated.Construct validity was established by discussing the research supporting each of the scales, subscales and behaviors listed in the instrument.Each of the twenty items was judged as valid by a minimum of 70 percent of the selected panel members and the twenty items included was recognized as a valid example of the constructs identified with the exception of those items assumed to reflect firmness.It was possible to relate each of the twenty items in the instrument to research studies accepted by editors and authors in the field despite inherent weaknesses in definitions, experimental designs, and theoretical orientation. In this sense, the instrument has acceptable construct validity.The instrument was then used to gather data on a group of teacher trainees assigned to a laboratory school at Ball State University. After each teacher trainee had taught a short unit, the pupils taught filled out the instrument which had been devised.Reliability measures consisted of computing coefficient alpha for various major scales and subscales of the instrument. Computations were run by the Ball State University Center using the reliability program from the SPSS Statistical Package for the Social Sciences DEC system –10.The coefficient alpha reliability indexes of .90 for the total scale, .86 for the cognitive scale, and .78 for the affective scale were judged acceptable for use in additional research studies in the field. The coefficient alpha reliability index of .82 for the clarity subscale, .81 for the flexibility subscale, and .78 for the warmth subscale were also judged acceptable for use in additional reliability index of .68 for the firmness subscale suggest questionable reliability for all but the most general research purposes.Recommendations were formulated to encourage further development of the model and refinement of the instrument (particularly the "firmness" subscale).Thesis (D. Ed.

A teacher behavior instrument for a multidimensional teaching model

The purpose of this study was to establish and describe the validity and reliability of an instrument based on a model of teaching behaviors conceived as magnetic lines of force.Content validity was established by reviewing the literature and identifying possible teaching behaviors which researchers felt contributed to increased pupil learning. These behaviors were presented to a panel of judges from faculty in the Teachers College, Ball State University, to ascertain behaviors which they felt increase the likelihood pupils would increase comprehension in reading. After the panel had made their suggestions, the list of behaviors was revised and used with two middle school classes at the Burris Laboratory School. Pupils were asked to identify the behaviors which they felt were associated with their increased learning. A final list of twenty items became the revised instrument for use in the study.A group of practicing teachers critiqued the list of twenty behaviors. This group was directed to identify how strongly they agreed with the placement of each of the behaviors under one of the four scales postulated.Construct validity was established by discussing the research supporting each of the scales, subscales and behaviors listed in the instrument.Each of the twenty items was judged as valid by a minimum of 70 percent of the selected panel members and the twenty items included was recognized as a valid example of the constructs identified with the exception of those items assumed to reflect firmness.It was possible to relate each of the twenty items in the instrument to research studies accepted by editors and authors in the field despite inherent weaknesses in definitions, experimental designs, and theoretical orientation. In this sense, the instrument has acceptable construct validity.The instrument was then used to gather data on a group of teacher trainees assigned to a laboratory school at Ball State University. After each teacher trainee had taught a short unit, the pupils taught filled out the instrument which had been devised.Reliability measures consisted of computing coefficient alpha for various major scales and subscales of the instrument. Computations were run by the Ball State University Center using the reliability program from the SPSS Statistical Package for the Social Sciences DEC system –10.The coefficient alpha reliability indexes of .90 for the total scale, .86 for the cognitive scale, and .78 for the affective scale were judged acceptable for use in additional research studies in the field. The coefficient alpha reliability index of .82 for the clarity subscale, .81 for the flexibility subscale, and .78 for the warmth subscale were also judged acceptable for use in additional reliability index of .68 for the firmness subscale suggest questionable reliability for all but the most general research purposes.Recommendations were formulated to encourage further development of the model and refinement of the instrument (particularly the "firmness" subscale).Thesis (D. Ed.