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1. Student Attitudes Contribute to the Effectiveness of a Genomics CURE

Author

David Lopatto, Anne G. Rosenwald, Rebecca C. Burgess, Catherine Silver Key, Melanie Van Stry, Matthew Wawersik, Justin R. DiAngelo, Amy T. Hark, Matthew Skerritt, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, James E. J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Carina E. Howell, Jennifer Jemc, Christopher J. Jones, Lisa Kadlec, Jacob D. Kagey, Kimberly L. Keller, Jennifer Kennell, Adam J. Kleinschmit, Melissa Kleinschmit, Nighat P. Kokan, Olga Ruiz Kopp, Meg M. Laakso, Judith Leatherman, Lindsey J. Long, Mollie Manier, Juan C. Martinez-Cruzado, Luis F. Matos, Amie Jo McClellan, Gerard McNeil, Evan Merkhofer, Vida Mingo, Hemlata Mistry, Elizabeth Mitchell, Nathan T. Mortimer, Jennifer Leigh Myka, Alexis Nagengast, Paul Overvoorde, Don Paetkau, Leocadia Paliulis, Susan Parrish, Stephanie Toering Peters, Mary Lai Preuss, James V. Price, Nicholas A. Pullen, Catherine Reinke, Dennis Revie, Srebrenka Robic, Jennifer A. Roecklein-Canfield, Michael R. Rubin, Takrima Sadikot, Jamie Siders Sanford, Maria Santisteban, Kenneth Saville, Stephanie Schroeder, Christopher D. Shaffer, Karim A. Sharif, Diane E. Sklensky, Chiyedza Small, Sheryl Smith, Rebecca Spokony, Aparna Sreenivasan, Joyce Stamm, Rachel Sterne-Marr, Katherine C. Teeter, Justin Thackeray, Jeffrey S. Thompson, Norma Velazquez-Ulloa, Cindy Wolfe, James Youngblom, Brian Yowler, Leming Zhou, Janie Brennan, Jeremy Buhler, Wilson Leung, Sarah C. R. Elgin, and Laura K. Reed

Subjects
active learning, bioinformatics, CUREs, genomics, undergraduate education, Special aspects of education, LC8-6691, Biology (General), QH301-705.5
Abstract

ABSTRACT The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student’s epistemic beliefs to achieving positive learning outcomes.

Published
2022
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4. The impact of genetic background and cell lineage on the level and pattern of gene expression in position effect variegation

Author

Sidney H. Wang and Sarah C. R. Elgin

Subjects
PEV, Heterochromatin, Modifiers of PEV, Transcription regulation, Genetics, QH426-470
Abstract

Abstract Background Chromatin-based transcriptional silencing is often described as a stochastic process, largely because of the mosaic expression observed in position effect variegation (PEV), where a euchromatic reporter gene is silenced in some cells as a consequence of juxtaposition with heterochromatin. High levels of variation in PEV phenotypes are commonly observed in reporter stocks. To ascertain whether background mutations are the major contributors to this variation, we asked how much of the variation is determined by genetic variants segregating in the population, examining both the level and pattern of expression using the fruit fly, Drosophila melanogaster, as the model. Results Using selective breeding of a fourth chromosome PEV reporter line, 39C-12, we isolated two inbred lines exhibiting contrasting degrees of variegation (A1: low expression, D1: high expression). Within each inbred population, remarkable similarity is observed in the degree of variegation: 90% of the variation between the two inbred lines in the degree of silencing can be explained by genotype. Further analyses suggest that this result reflects the combined effect of multiple independent trans-acting loci. While the initial observations are based on a PEV phenotype scored in the fly eye (hsp70-white reporter), similar degrees of silencing were observed using a beta-gal reporter scored across the whole fly. Further, the pattern of variegation becomes almost identical within each inbred line; significant pigment enrichment in the same quadrant of the eye was found for both A1 and D1 lines despite different degrees of expression. Conclusions The results indicate that background genetic variants play the major role in determining the variable degrees of PEV commonly observed in laboratory stocks. Interestingly, not only does the degree of variegation become consistent in inbred lines, the patterns of variegation also appear similar. Combining these observations with the spreading model for local heterochromatin formation, we propose an augmented stochastic model to describe PEV in which the genetic background drives the overall level of silencing, working with the cell lineage-specific regulatory environment to determine the on/off probability at the reporter locus in each cell. This model acknowledges cell type-specific events in the context of broader genetic impacts on heterochromatin formation.

Published
2019
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8. Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

Author

David Lopatto, Anne G. Rosenwald, Justin R. DiAngelo, Amy T. Hark, Matthew Skerritt, Matthew Wawersik, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, Christopher Bazinet, James E. J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Rebecca C. Burgess, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Emily Furbee, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Carina E. Howell, Jennifer Jemc, M. Logan Johnson, Christopher J. Jones, Lisa Kadlec, Jacob D. Kagey, Kimberly L. Keller, Jennifer Kennell, S. Catherine Silver Key, Adam J. Kleinschmit, Melissa Kleinschmit, Nighat P. Kokan, Olga Ruiz Kopp, Meg M. Laakso, Judith Leatherman, Lindsey J. Long, Mollie Manier, Juan C. Martinez-Cruzado, Luis F. Matos, Amie Jo McClellan, Gerard McNeil, Evan Merkhofer, Vida Mingo, Hemlata Mistry, Elizabeth Mitchell, Nathan T. Mortimer, Debaditya Mukhopadhyay, Jennifer Leigh Myka, Alexis Nagengast, Paul Overvoorde, Don Paetkau, Leocadia Paliulis, Susan Parrish, Mary Lai Preuss, James V. Price, Nicholas A. Pullen, Catherine Reinke, Dennis Revie, Srebrenka Robic, Jennifer A. Roecklein-Canfield, Michael R. Rubin, Takrima Sadikot, Jamie Siders Sanford, Maria Santisteban, Kenneth Saville, Stephanie Schroeder, Christopher D. Shaffer, Karim A. Sharif, Diane E. Sklensky, Chiyedza Small, Mary Smith, Sheryl Smith, Rebecca Spokony, Aparna Sreenivasan, Joyce Stamm, Rachel Sterne-Marr, Katherine C. Teeter, Justin Thackeray, Jeffrey S. Thompson, Stephanie Toering Peters, Melanie Van Stry, Norma Velazquez-Ulloa, Cindy Wolfe, James Youngblom, Brian Yowler, Leming Zhou, Janie Brennan, Jeremy Buhler, Wilson Leung, Laura K. Reed, and Sarah C. R. Elgin

Subjects
Special aspects of education, LC8-6691, Biology (General), QH301-705.5
Abstract

A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students’ learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our “formative frustration” hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of “formative frustration” is an important aspect for a successful CURE.

Published
2020
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12. Bioinformatics core competencies for undergraduate life sciences education.

Author

Melissa A Wilson Sayres, Charles Hauser, Michael Sierk, Srebrenka Robic, Anne G Rosenwald, Todd M Smith, Eric W Triplett, Jason J Williams, Elizabeth Dinsdale, William R Morgan, James M Burnette, Samuel S Donovan, Jennifer C Drew, Sarah C R Elgin, Edison R Fowlks, Sebastian Galindo-Gonzalez, Anya L Goodman, Nealy F Grandgenett, Carlos C Goller, John R Jungck, Jeffrey D Newman, William Pearson, Elizabeth F Ryder, Rafael Tosado-Acevedo, William Tapprich, Tammy C Tobin, Arlín Toro-Martínez, Lonnie R Welch, Robin Wright, Lindsay Barone, David Ebenbach, Mindy McWilliams, Kimberly C Olney, and Mark A Pauley

Subjects
Medicine, Science
Abstract

Although bioinformatics is becoming increasingly central to research in the life sciences, bioinformatics skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of biology faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondent's degree of training, time since degree earned, and/or the Carnegie Classification of the respondent's institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of the syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate biology students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.

Published
2018
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14. Comparative analysis of metazoan chromatin organization Open.

Author

Joshua Wing Kei Ho, Youngsook L. Jung, Tao Liu 0022, Burak Han Alver, Soohyun Lee, Kohta Ikegami, Kyung-Ah Sohn, Aki Minoda, Michael Y. Tolstorukov, Alex Appert, Stephen C. J. Parker, Tingting Gu, Anshul Kundaje, Nicole C. Riddle, Eric Bishop, Thea A. Egelhofer, Sheng'en Shawn Hu, Artyom A. Alekseyenko, Andreas Rechtsteiner, Dalal Asker, Jason A. Belsky, Sarah K. Bowman, Q. Brent Chen, Ron A.-J. Chen, Daniel S. Day, Yan Dong, Andrea C. Dose, Xikun Duan, Charles B. Epstein, Sevinc Ercan, Elise A. Feingold, Francesco Ferrari, Jacob M. Garrigues, Nils Gehlenborg, Peter J. Good, Psalm Haseley, Daniel He, Moritz Herrmann, Michael M. Hoffman, Tess E. Jeffers, Peter V. Kharchenko, Paulina Kolasinska-Zwierz, Chitra V. Kotwaliwale, Nischay Kumar, Sasha A. Langley, Erica Larschan, Isabel Latorre, Maxwell W. Libbrecht, Xueqiu Lin, Richard Park, Michael J. Pazin, Hoang N. Pham, Annette Plachetka, Bo Qin, Yuri B. Schwartz, Noam Shoresh, Przemyslaw Stempor, Anne Vielle, Chengyang Wang, Christina M. Whittle, Huiling Xue, Robert E. Kingston, Ju Han Kim, Bradley E. Bernstein, Abby F. Dernburg, Vincenzo Pirrotta, Mitzi I. Kuroda, William S. Noble, Thomas D. Tullius, Manolis Kellis, David M. MacAlpine, Susan Strome, Sarah C. R. Elgin, Xiaole Shirley Liu, Jason D. Lieb, Julie Ahringer, Gary H. Karpen, and Peter J. Park

Published
2014
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15. Feature Selection and Instance Selection from Clinical Datasets Using Co-operative Co-evolution and Classification Using Random Forest

Author

J. Brighty, V. R. Elgin Christo, H. Khanna Nehemiah, and Arputharaj Kannan

Subjects
Co operative, business.industry, Computer science, 020208 electrical & electronic engineering, 020206 networking & telecommunications, Feature selection, 02 engineering and technology, Machine learning, computer.software_genre, Clinical decision support system, Computer Science Applications, Theoretical Computer Science, Random forest, Genetic algorithm, 0202 electrical engineering, electronic engineering, information engineering, Artificial intelligence, Instance selection, Electrical and Electronic Engineering, business, computer, Coevolution
Abstract

Co-operative co-evolution approach solves problems by breaking them into subproblems. The proposed framework for Clinical Decision Support System (CDSS) uses a co-operative coevolution approach whi...

Published
2020

17. Student Attitudes Contribute to the Effectiveness of a Genomics CURE

Author

David Lopatto, Anne G. Rosenwald, Rebecca C. Burgess, Catherine Silver Key, Melanie Van Stry, Matthew Wawersik, Justin R. DiAngelo, Amy T. Hark, Matthew Skerritt, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, James E. J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Carina E. Howell, Jennifer Jemc, Christopher J. Jones, Lisa Kadlec, Jacob D. Kagey, Kimberly L. Keller, Jennifer Kennell, Adam J. Kleinschmit, Melissa Kleinschmit, Nighat P. Kokan, Olga Ruiz Kopp, Meg M. Laakso, Judith Leatherman, Lindsey J. Long, Mollie Manier, Juan C. Martinez-Cruzado, Luis F. Matos, Amie Jo McClellan, Gerard McNeil, Evan Merkhofer, Vida Mingo, Hemlata Mistry, Elizabeth Mitchell, Nathan T. Mortimer, Jennifer Leigh Myka, Alexis Nagengast, Paul Overvoorde, Don Paetkau, Leocadia Paliulis, Susan Parrish, Stephanie Toering Peters, Mary Lai Preuss, James V. Price, Nicholas A. Pullen, Catherine Reinke, Dennis Revie, Srebrenka Robic, Jennifer A. Roecklein-Canfield, Michael R. Rubin, Takrima Sadikot, Jamie Siders Sanford, Maria Santisteban, Kenneth Saville, Stephanie Schroeder, Christopher D. Shaffer, Karim A. Sharif, Diane E. Sklensky, Chiyedza Small, Sheryl Smith, Rebecca Spokony, Aparna Sreenivasan, Joyce Stamm, Rachel Sterne-Marr, Katherine C. Teeter, Justin Thackeray, Jeffrey S. Thompson, Norma Velazquez-Ulloa, Cindy Wolfe, James Youngblom, Brian Yowler, Leming Zhou, Janie Brennan, Jeremy Buhler, Wilson Leung, Sarah C. R. Elgin, and Laura K. Reed

Subjects
General Immunology and Microbiology, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, Education
Abstract

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student's epistemic beliefs to achieving positive learning outcomes.

Published
2021

18. A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

Author

Tuajuanda C. Jordan, Sandra H. Burnett, Susan Carson, Steven M. Caruso, Kari Clase, Randall J. DeJong, John J. Dennehy, Dee R. Denver, David Dunbar, Sarah C. R. Elgin, Ann M. Findley, Chris R. Gissendanner, Urszula P. Golebiewska, Nancy Guild, Grant A. Hartzog, Wendy H. Grillo, Gail P. Hollowell, Lee E. Hughes, Allison Johnson, Rodney A. King, Lynn O. Lewis, Wei Li, Frank Rosenzweig, Michael R. Rubin, Margaret S. Saha, James Sandoz, Christopher D. Shaffer, Barbara Taylor, Louise Temple, Edwin Vazquez, Vassie C. Ware, Lucia P. Barker, Kevin W. Bradley, Deborah Jacobs-Sera, Welkin H. Pope, Daniel A. Russell, Steven G. Cresawn, David Lopatto, Cheryl P. Bailey, and Graham F. Hatfull

Subjects
Microbiology, QR1-502
Abstract

ABSTRACT Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students’ interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training. IMPORTANCE Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

Published
2014
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19. A distinct type of heterochromatin at the telomeric region of the Drosophila melanogaster Y chromosome.

Author

Sidney H Wang, Ruth Nan, Maria C Accardo, Monica Sentmanat, Patrizio Dimitri, and Sarah C R Elgin

Subjects
Medicine, Science
Abstract

Heterochromatin assembly and its associated phenotype, position effect variegation (PEV), provide an informative system to study chromatin structure and genome packaging. In the fruit fly Drosophila melanogaster, the Y chromosome is entirely heterochromatic in all cell types except the male germline; as such, Y chromosome dosage is a potent modifier of PEV. However, neither Y heterochromatin composition, nor its assembly, has been carefully studied. Here, we report the mapping and characterization of eight reporter lines that show male-specific PEV. In all eight cases, the reporter insertion sites lie in the telomeric transposon array (HeT-A and TART-B2 homologous repeats) of the Y chromosome short arm (Ys). Investigations of the impact on the PEV phenotype of mutations in known heterochromatin proteins (i.e., modifiers of PEV) show that this Ys telomeric region is a unique heterochromatin domain: it displays sensitivity to mutations in HP1a, EGG and SU(VAR)3-9, but no sensitivity to Su(z)2 mutations. It appears that the endo-siRNA pathway plays a major targeting role for this domain. Interestingly, an ectopic copy of 1360 is sufficient to induce a piRNA targeting mechanism to further enhance silencing of a reporter cytologically localized to the Ys telomere. These results demonstrate the diversity of heterochromatin domains, and the corresponding variation in potential targeting mechanisms.

Published
2014
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20. Correction: Sequence-Specific Targeting of Dosage Compensation in Favors an Active Chromatin Context.

Author

Artyom A. Alekseyenko, Joshua W. K. Ho, Shouyong Peng, Marnie Gelbart, Michael Y. Tolstorukov, Annette Plachetka, Peter V. Kharchenko, Youngsook L. Jung, Andrey A. Gorchakov, Erica Larschan, Tingting Gu, Aki Minoda, Nicole C. Riddle, Yuri B. Schwartz, Sarah C. R. Elgin, Gary H. Karpen, Vincenzo Pirrotta, Mitzi I. Kuroda, and Peter J. Park

Subjects
Genetics, QH426-470
Published
2014
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21. Feature selection using competitive coevolution of bio-inspired algorithms for the diagnosis of pulmonary emphysema

Author

H. Khanna Nehemiah, Anisha Isaac, V. R. Elgin Christo, Arputharaj Kannan, and Snofy D. Dunston

Subjects
Fitness function, Pixel, Computer science, business.industry, Biomedical Engineering, Health Informatics, Feature selection, Pattern recognition, Cross-validation, Support vector machine, Signal Processing, Classifier (linguistics), Segmentation, Artificial intelligence, business, Cluster analysis
Abstract

A Computer-Aided Diagnosis (CAD) system to assist a radiologist for diagnosing pulmonary emphysema from chest Computed Tomography (CT) slices has been developed. The lung tissues are segmented from the chest CT slices using Spatial Fuzzy C-Means (SFCM) clustering algorithm and the Regions of Interest (ROIs) are extracted using pixel-based segmentation. The ROIs considered for this work are pulmonary emphysematous lesions namely, centrilobular emphysema, paraseptal emphysema and sub-pleural bullae. The extracted ROIs are then validated and labelled by an expert radiologist. From each ROI, features with respect to shape, texture and run-length are extracted. A competitive coevolution model is proposed for Feature Selection (FS). The model makes use of two bio-inspired algorithms namely, Spider Monkey Optimization (SMO) algorithm and Paddy Field Algorithm (PFA) as its building blocks. FS is performed as a wrapper approach, using the bio-inspired algorithms namely, SMO and PFA with the accuracy of the Support Vector Machine (SVM) classifier as the fitness function. Ten-fold cross validation technique is used in training the SVM classifier using the selected features. The model is tested using two datasets: Real-time emphysema dataset and CT emphysema database (CTED) dataset. The accuracy, precision, recall and specificity obtained for both the datasets are (81.95%, 93.74%), (72.92%, 90.61%), (72.92%, 90.61%), (86.46%, 95.3%), which are better compared to the performance of SMO and PFA algorithms applied individually for FS and the CAD system without performing FS.

Published
2022

22. Maternal depletion of Piwi, a component of the RNAi system, impacts heterochromatin formation in Drosophila.

Author

Tingting Gu and Sarah C R Elgin

Subjects
Genetics, QH426-470
Abstract

A persistent question in epigenetics is how heterochromatin is targeted for assembly at specific domains, and how that chromatin state is faithfully transmitted. Stable heterochromatin is necessary to silence transposable elements (TEs) and maintain genome integrity. Both the RNAi system and heterochromatin components HP1 (Swi6) and H3K9me2/3 are required for initial establishment of heterochromatin structures in S. pombe. Here we utilize both loss of function alleles and the newly developed Drosophila melanogaster transgenic shRNA lines to deplete proteins of interest at specific development stages to dissect their roles in heterochromatin assembly in early zygotes and in maintenance of the silencing chromatin state during development. Using reporters subject to Position Effect Variegation (PEV), we find that depletion of key proteins in the early embryo can lead to loss of silencing assayed at adult stages. The piRNA component Piwi is required in the early embryo for reporter silencing in non-gonadal somatic cells, but knock-down during larval stages has no impact. This implies that Piwi is involved in targeting HP1a when heterochromatin is established at the late blastoderm stage and possibly also during embryogenesis, but that the silent chromatin state created is transmitted through cell division independent of the piRNA system. In contrast, heterochromatin structural protein HP1a is required for both initial heterochromatin assembly and the following mitotic inheritance. HP1a profiles in piwi mutant animals confirm that Piwi depletion leads to decreased HP1a levels in pericentric heterochromatin, particularly in TEs. The results suggest that the major role of the piRNA system in assembly of heterochromatin in non-gonadal somatic cells occurs in the early embryo during heterochromatin formation, and further demonstrate that failure of heterochromatin formation in the early embryo impacts the phenotype of the adult.

Published
2013
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23. Feature Selection and Instance Selection from Clinical Datasets Using Co-operative Co-evolution and Classification Using Random Forest.

Author

Christo, V. R. Elgin, Nehemiah, H. Khanna, Brighty, J., and Kannan, Arputharaj

Subjects
*CLINICAL decision support systems, *FEATURE selection, *RANDOM forest algorithms, *COEVOLUTION, *SPINE
Abstract

Co-operative co-evolution approach solves problems by breaking them into subproblems. The proposed framework for Clinical Decision Support System (CDSS) uses a co-operative coevolution approach which treats Feature Selection (FS) and Instance Selection (IS) as independent subproblems. FS and IS remove less relevant features and instances, respectively, thereby improving the overall performance of the system. In this work, both Feature and Instance selection are done using the wrapper approach, which uses co-operative co-evolution and random forest classifier. The reduced dataset is used to train a random forest classifier and this trained model helped in making clinical decisions. These decisions assist physicians as the second opinion for diagnosis and treatment. Wisconsin Diagnostic Breast Cancer (WDBC), Hepatitis, Pima Indian Diabetes (PID), Cleveland Heart Disease (CHD), Statlog Heart Disease (SHD), Vertebral Column, and Hepatocellular Carcinoma (HCC) datasets from the University of California Irvine (UCI) Machine Learning repository are used for experimentation. The proposed framework achieved an accuracy of 97.1%, 82.3%, 81.01%, 93.4%, 96.8%, 91.4%, and 72.2% for datasets WDBC, Hepatitis, PID, CHD, SHD, vertebral column, and HCC, respectively. The results prove that the CDSS-developed using co-operative coevolution can efficiently assist the physicians in decision-making. [ABSTRACT FROM AUTHOR]

Published
2022
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24. Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

Author

John M. Braverman, Kenneth Saville, Mollie K. Manier, Katherine C. Teeter, Sarah C. R. Elgin, Rachel Sterne-Marr, Debaditya Mukhopadhyay, Adam Haberman, M. Logan Johnson, Jacob D. Kagey, Emily Furbee, Matthew A. Escobar, Vida Mingo, Stephanie Schroeder, Srebrenka Robic, Anya Goodman, Catherine Reinke, Yuying Gosser, Meg M. Laakso, Mary A. Smith, Daron C. Barnard, Christopher Bazinet, Nathan T. Mortimer, Mary L. Preuss, Cindy Arrigo, Paul J. Overvoorde, Elizabeth Mitchell, Rebecca C. Burgess, Wilson Leung, Diane Sklensky, Laura K. Reed, Lindsey J. Long, Don W. Paetkau, Melissa Kleinschmit, Judith Leatherman, Olga R. Kopp, Janie Brennan, Joyce Stamm, Chunguang Du, Norma A. Velázquez-Ulloa, Thomas C. Giarla, Gerard P. McNeil, Justin Thackeray, Andrew M. Arsham, Jeremy Buhler, Jennifer A. Kennell, Sara J. Anderson, Leming Zhou, Takrima Sadikot, Alexis Nagengast, Susan Parrish, Heather L. Eisler, Dennis Revie, Leocadia V. Paliulis, Chiyedza Small, Anna K. Allen, Amy T. Hark, James E. J. Bedard, Lisa Kadlec, Jeffery S. Thompson, Paula Croonquist, James V. Price, Stephanie Toering Peters, Evan C. Merkhofer, Melanie Van Stry, Matthew Skerritt, Anne G. Rosenwald, Cindy Wolfe, Nicholas Pullen, Nighat P. Kokan, Sondra Dubowsky, Jamie Siders Sanford, Rebecca Spokony, Luis F. Matos, Christopher D. Shaffer, Consuelo J. Alvarez, Justin R. DiAngelo, Jennifer Roecklein-Canfield, Maria Soledad Santisteban, Sheryl T. Smith, Juan Carlos Martínez-Cruzado, Indrani Bose, Christopher J. Jones, Adam Kleinschmit, Brian Yowler, Karim A. Sharif, S. Catherine Silver Key, Amie J. McClellan, Matthew Wawersik, Jennifer C. Jemc, Carina E. Howell, Hemlata Mistry, Rivka L. Glaser, Shan Hays, Kimberly L. Keller, Michael R. Rubin, Martin G. Burg, David Lopatto, Charles R. Hauser, James J. Youngblom, Jennifer Leigh Myka, Michael S. Foulk, and Aparna Sreenivasan

Subjects
QH301-705.5, Process (engineering), media_common.quotation_subject, Frustration, General Biochemistry, Genetics and Molecular Biology, Education, Formative assessment, 03 medical and health sciences, Mathematics education, Biology (General), Set (psychology), lcsh:QH301-705.5, 030304 developmental biology, media_common, lcsh:LC8-6691, 0303 health sciences, LC8-6691, lcsh:Special aspects of education, General Immunology and Microbiology, Research, 4. Education, 05 social sciences, 050301 education, Special aspects of education, Focus group, lcsh:Biology (General), Undergraduate research, General partnership, Working through, General Agricultural and Biological Sciences, Psychology, 0503 education
Abstract

A hallmark of the research experience is encountering experimental difficulty and working through that challenge to reach success. The ability to overcome scientific challenges is essential to being a successful scientist, but replicating these challenges can be difficult in a teaching setting. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students’ learning experience in this research is continuous and recursive, frequently beginning with frustration but eventually leading to success. In order to explore our “formative frustration” hypothesis, we gathered data about this research experience from faculty via a survey, and from students both via a general survey and a small set of focus groups administered at the end of the GEP CURE. All three datasets contained comments mentioning frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of what we have deemed “formative frustration” is an important aspect for a successful CURE.

Published
2020

25. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.

Author

Nicole C Riddle, Youngsook L Jung, Tingting Gu, Artyom A Alekseyenko, Dalal Asker, Hongxing Gui, Peter V Kharchenko, Aki Minoda, Annette Plachetka, Yuri B Schwartz, Michael Y Tolstorukov, Mitzi I Kuroda, Vincenzo Pirrotta, Gary H Karpen, Peter J Park, and Sarah C R Elgin

Subjects
Genetics, QH426-470
Abstract

Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP-chip) analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in euchromatin or pericentric heterochromatin: while there is a depletion of silencing marks at the transcription start sites (TSSs), HP1a and H3K9me3, but not H3K9me2, are enriched strongly over gene bodies. Intriguingly, genes on chromosome 4 are less frequently associated with paused polymerase. However, when the chromatin is altered by depleting HP1a or POF, the RNA pol II enrichment patterns of many chromosome 4 genes shift, showing a significant decrease over gene bodies but not at TSSs, accompanied by lower expression of those genes. Chromosome 4 genes have a low incidence of TRL/GAGA factor binding sites and a low T(m) downstream of the TSS, characteristics that could contribute to a low incidence of RNA polymerase pausing. Our data also indicate that EGG and POF jointly regulate H3K9 methylation and promote HP1a binding over gene bodies, while HP1a targeting and H3K9 methylation are maintained at the repeats by an independent mechanism. The HP1a-enriched, POF-associated chromatin structure over the gene bodies may represent one type of adaptation for genes embedded in repetitive DNA.

Published
2012
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26. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.

Author

Artyom A Alekseyenko, Joshua W K Ho, Shouyong Peng, Marnie Gelbart, Michael Y Tolstorukov, Annette Plachetka, Peter V Kharchenko, Youngsook L Jung, Andrey A Gorchakov, Erica Larschan, Tingting Gu, Aki Minoda, Nicole C Riddle, Yuri B Schwartz, Sarah C R Elgin, Gary H Karpen, Vincenzo Pirrotta, Mitzi I Kuroda, and Peter J Park

Subjects
Genetics, QH426-470
Abstract

The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at "entry sites" that contain a consensus sequence motif ("MSL recognition element" or MRE). However, this motif is only ∼2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells (which contain MSL complex) and female Kc cells (which lack the complex), we find that the presence of active chromatin modifications, together with an elevated local GC content in the surrounding sequences, has strong predictive value for functional MSL entry sites, independent of MSL binding. We tested these sites for function in Kc cells by RNAi knockdown of Sxl, resulting in induction of MSL complex. We show that ectopic MSL expression in Kc cells leads to H4K16 acetylation around these sites and a relative increase in X chromosome transcription. Collectively, our results support a model in which a pre-existing active chromatin environment, coincident with H3K36me3, contributes to MSL entry site selection. The consequences of MSL targeting of the male X chromosome include increase in nucleosome lability, enrichment for H4K16 acetylation and JIL-1 kinase, and depletion of linker histone H1 on active X-linked genes. Our analysis can serve as a model for identifying chromatin and local sequence features that may contribute to selection of functional protein binding sites in the genome.

Published
2012
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27. The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats

Author

Sarah C. R. Elgin and Nicole C. Riddle

Subjects
0301 basic medicine, Genetics, Transposable element, Autosome, Euchromatin, Heterochromatin, Chromosome, Karyotype, Biology, biology.organism_classification, 03 medical and health sciences, 030104 developmental biology, Drosophila melanogaster, Gene
Abstract

The F element of the Drosophila karyotype (the fourth chromosome in Drosophila melanogaster) is often referred to as the “dot chromosome” because of its appearance in a metaphase chromosome spread. This chromosome is distinct from other Drosophila autosomes in possessing both a high level of repetitious sequences (in particular, remnants of transposable elements) and a gene density similar to that found in the other chromosome arms, ∼80 genes distributed throughout its 1.3-Mb “long arm.” The dot chromosome is notorious for its lack of recombination and is often neglected as a consequence. This and other features suggest that the F element is packaged as heterochromatin throughout. F element genes have distinct characteristics (e.g., low codon bias, and larger size due both to larger introns and an increased number of exons), but exhibit expression levels comparable to genes found in euchromatin. Mapping experiments show the presence of appropriate chromatin modifications for the formation of DNaseI hypersensitive sites and transcript initiation at the 5′ ends of active genes, but, in most cases, high levels of heterochromatin proteins are observed over the body of these genes. These various features raise many interesting questions about the relationships of chromatin structures with gene and chromosome function. The apparent evolution of the F element as an autosome from an ancestral sex chromosome also raises intriguing questions. The findings argue that the F element is a unique chromosome that occupies its own space in the nucleus. Further study of the F element should provide new insights into chromosome structure and function.

Published
2018

28. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Author

Welkin H Pope, Deborah Jacobs-Sera, Daniel A Russell, Craig L Peebles, Zein Al-Atrache, Turi A Alcoser, Lisa M Alexander, Matthew B Alfano, Samantha T Alford, Nichols E Amy, Marie D Anderson, Alexander G Anderson, Andrew A S Ang, Manuel Ares, Amanda J Barber, Lucia P Barker, Jonathan M Barrett, William D Barshop, Cynthia M Bauerle, Ian M Bayles, Katherine L Belfield, Aaron A Best, Agustin Borjon, Charles A Bowman, Christine A Boyer, Kevin W Bradley, Victoria A Bradley, Lauren N Broadway, Keshav Budwal, Kayla N Busby, Ian W Campbell, Anne M Campbell, Alyssa Carey, Steven M Caruso, Rebekah D Chew, Chelsea L Cockburn, Lianne B Cohen, Jeffrey M Corajod, Steven G Cresawn, Kimberly R Davis, Lisa Deng, Dee R Denver, Breyon R Dixon, Sahrish Ekram, Sarah C R Elgin, Angela E Engelsen, Belle E V English, Marcella L Erb, Crystal Estrada, Laura Z Filliger, Ann M Findley, Lauren Forbes, Mark H Forsyth, Tyler M Fox, Melissa J Fritz, Roberto Garcia, Zindzi D George, Anne E Georges, Christopher R Gissendanner, Shannon Goff, Rebecca Goldstein, Kobie C Gordon, Russell D Green, Stephanie L Guerra, Krysta R Guiney-Olsen, Bridget G Guiza, Leila Haghighat, Garrett V Hagopian, Catherine J Harmon, Jeremy S Harmson, Grant A Hartzog, Samuel E Harvey, Siping He, Kevin J He, Kaitlin E Healy, Ellen R Higinbotham, Erin N Hildebrandt, Jason H Ho, Gina M Hogan, Victoria G Hohenstein, Nathan A Holz, Vincent J Huang, Ericka L Hufford, Peter M Hynes, Arrykka S Jackson, Erica C Jansen, Jonathan Jarvik, Paul G Jasinto, Tuajuanda C Jordan, Tomas Kasza, Murray A Katelyn, Jessica S Kelsey, Larisa A Kerrigan, Daryl Khaw, Junghee Kim, Justin Z Knutter, Ching-Chung Ko, Gail V Larkin, Jennifer R Laroche, Asma Latif, Kohana D Leuba, Sequoia I Leuba, Lynn O Lewis, Kathryn E Loesser-Casey, Courtney A Long, A Javier Lopez, Nicholas Lowery, Tina Q Lu, Victor Mac, Isaac R Masters, Jazmyn J McCloud, Molly J McDonough, Andrew J Medenbach, Anjali Menon, Rachel Miller, Brandon K Morgan, Patrick C Ng, Elvis Nguyen, Katrina T Nguyen, Emilie T Nguyen, Kaylee M Nicholson, Lindsay A Parnell, Caitlin E Peirce, Allison M Perz, Luke J Peterson, Rachel E Pferdehirt, Seegren V Philip, Kit Pogliano, Joe Pogliano, Tamsen Polley, Erica J Puopolo, Hannah S Rabinowitz, Michael J Resiss, Corwin N Rhyan, Yetta M Robinson, Lauren L Rodriguez, Andrew C Rose, Jeffrey D Rubin, Jessica A Ruby, Margaret S Saha, James W Sandoz, Judith Savitskaya, Dale J Schipper, Christine E Schnitzler, Amanda R Schott, J Bradley Segal, Christopher D Shaffer, Kathryn E Sheldon, Erica M Shepard, Jonathan W Shepardson, Madav K Shroff, Jessica M Simmons, Erika F Simms, Brandy M Simpson, Kathryn M Sinclair, Robert L Sjoholm, Ingrid J Slette, Blaire C Spaulding, Clark L Straub, Joseph Stukey, Trevor Sughrue, Tin-Yun Tang, Lyons M Tatyana, Stephen B Taylor, Barbara J Taylor, Louise M Temple, Jasper V Thompson, Michael P Tokarz, Stephanie E Trapani, Alexander P Troum, Jonathan Tsay, Anthony T Tubbs, Jillian M Walton, Danielle H Wang, Hannah Wang, John R Warner, Emilie G Weisser, Samantha C Wendler, Kathleen A Weston-Hafer, Hilary M Whelan, Kurt E Williamson, Angelica N Willis, Hannah S Wirtshafter, Theresa W Wong, Phillip Wu, Yun jeong Yang, Brandon C Yee, David A Zaidins, Bo Zhang, Melina Y Zúniga, Roger W Hendrix, and Graham F Hatfull

Subjects
Medicine, Science
Abstract

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.

Published
2011
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29. Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4.

Author

Welkin H Pope, Christina M Ferreira, Deborah Jacobs-Sera, Robert C Benjamin, Ariangela J Davis, Randall J DeJong, Sarah C R Elgin, Forrest R Guilfoile, Mark H Forsyth, Alexander D Harris, Samuel E Harvey, Lee E Hughes, Peter M Hynes, Arrykka S Jackson, Marilyn D Jalal, Elizabeth A MacMurray, Coreen M Manley, Molly J McDonough, Jordan L Mosier, Larissa J Osterbann, Hannah S Rabinowitz, Corwin N Rhyan, Daniel A Russell, Margaret S Saha, Christopher D Shaffer, Stephanie E Simon, Erika F Sims, Isabel G Tovar, Emilie G Weisser, John T Wertz, Kathleen A Weston-Hafer, Kurt E Williamson, Bo Zhang, Steven G Cresawn, Paras Jain, Mariana Piuri, William R Jacobs, Roger W Hendrix, and Graham F Hatfull

Subjects
Medicine, Science
Abstract

Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them--with the exception of TM4--form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species.

Published
2011
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30. Drosophila RISC component VIG and its homolog Vig2 impact heterochromatin formation.

Author

Elena Gracheva, Monica Dus, and Sarah C R Elgin

Subjects
Medicine, Science
Abstract

Heterochromatin formation plays an important role in gene regulation and the maintenance of genome integrity. Here we present results from a study of the D. melanogaster gene vig, encoding an RNAi complex component and its homolog vig2 (CG11844) that support their involvement in heterochromatin formation and/or maintenance. Protein null mutations vig(EP812) and vig2(PL470) act as modifiers of Position Effect Variegation (PEV). VIG and Vig2 are present in polytene chromosomes and partially overlap with HP1. Quantitative immunoblots show depletion of HP1 and HP2 (large isoform) in isolated nuclei from the vig(EP812) mutant. The vig2(PL470) mutant strain demonstrates a decreased level of H3K9me2. Pull-down experiments using antibodies specific to HP1 recovered both VIG and Vig2. The association between HP1 and both VIG and Vig2 proteins depends on an RNA component. The above data and the developmental profiles of the two genes suggest that Vig2 may be involved in heterochromatin targeting and establishment early in development, while VIG may have a role in stabilizing HP1/HP2 chromatin binding during later stages.

Published
2009
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32. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element

Author

Rachael K Bridgman, Rachel A Greenstein, Maxine E Wykle, Insun Chong, Harrison Friedman, Casey Hanson, Kelly Drumm, Tingting Gu, Marium Feliciano-Camacho, Juliana Broussard, Jackie Alexander, Patrick A Schneider, Joyce Stamm, Kevin M. Levine, Jennifer Bland, Zenyth A Sheppard, Marlee B Nelson, Adam S Rinaldi, John M. Braverman, Elizabeth Zavala-Arellano, Nicholas C. Spies, Kara Tsukashima, Monika C Lemke, Ellen N Niemiec, Dale L. Beach, Krystal L Holtcamp, Mitchell J McDonald, Nadia Safa, Karim A. Sharif, Martin G. Burg, Diana L. E. Johnson, Danielle R Perry, Amy S Li, Victoria R Zellmer, Jack Y. Yu, Joan Q Lawrence, Nighat P. Kokan, Raquel Montañez-Gonzalez, Kaitlin E Homa, Perouza Parsamian, Kaitlyn E Takach, Shane M. Patao, Matthew Simon, Adam C Wernette, Chun L Ng, S Mariel Ramey, Gabrielle L. Hussey, Charles R. Hauser, Karolyn Barker, Danielle M Kramer, Alexis M Ceasrine, Mariela Taboas-Arroyo, Rebekah Lee, Alexandra L Hertz, Charlotte M Brown, Gabriel Stancu, Dorianmarie Vargas-Franco, Lindsey J Suriano, Kyle L. Jung, Sami Mamari, Gary R. Skuse, Thomas J Quisenberry, Laura K. Reed, Don W. Paetkau, Victoria Chevee, Kerry Campbell, Adam Haberman, Ghazal Stity, Antoinette E. Fafara-Thompson, Breanna Haiker, Maddison F McEvilly, Isaac C Veysey-White, Robert J Allen, Susana S Apiz-Saab, Madeline M Martin, Edward Himelblau, Laura T Vives, Arielle M Vasquez, Nathan T. Mortimer, Catherine O'Keeffe, Elizabeth J Villafuerte, Shannon R. McCartha, Kirsten Bickford, Max Kollmer, Henry Z Gong, Grzegorz L. Polak, Joanna J Smith, Terrance Embry, Katelynn E Deibel, Matt Van Camp, Devon E Schultz, Sarah Wai-Chee Kong, Leah E Waldman, Suzette M. Arias-Mejias, Yakov Shevin, Richard McGuire, Danny Mammo, Sarah K Hilton, Max Mian Liu, Jaclyn D Campbell, Robert W. Fernandez, Baljit Bedi, Jordan A Black, Christopher Scheiber, Chengyu Liu, Lindsay M Prescod, Lindsay M Corbeill, Patricia N Claudio-Vazquez, Jeremy Buhler, Michael J Pavia, Holly Lyn Robbins, Luis A. Jimenez, Tanveer Sandhu, James J. Youngblom, Jordan E. Matthews, Katherine Gavinski, Rahul Nadendla, Olivia A Pahl, Hien P Nguyen, Sasha Jia, Stephanie M Grieb, Joseph E Marcus, Michael B. Schultz, Amber M. Gygi, Emily A Morlock, Karina M Gonzalez-Bonilla, Paola Villegas, Jeffrey W Wei, Christopher J. Jones, Guadalupe Quintana, Kaidi Wang, Hiu Man Vivian Tsang, Ruchik Patel, Heaven L Cerritos, Thomas C. Giarla, Gerard P. McNeil, Michael R. Rubin, Mary E Franks, Jordan R Ramirez, Maiye Her, Matt Segal, Mark Scheuerman, Emmy E. Ogawa, Darryl Lopez, Robert M. Gingras, Simon Hsu, Amy T. Hark, Zuzana Kocsisova, Dennis Revie, Christopher Bazinet, Kevin Ko, Jeremy S Davis, Deana Gabbard, Amanda Boozalis, Suchita Rastogi, Jeffery Bettincourt, Laura Schiraldi, Edward A Horansky, Amanda H Cox, Susan Parrish, Kristine Ostby, Sarah M. Jacobs, Jesse J Ensign, Kevin Kumimoto, Paul F Lee, Nicholas U. Schwartz, David D. Xiong, Susan E Herman, Allison E. McClish, Averill D Guo, Cody M Mittig, Heran Gebreyesus, Allison R Wagner, Katherine J Olson, Lucy Huo, William D. Barshop, Victoria R Sochor, Francisco J Rivera-Rosario, Samatha K Begley, James E. B. Docherty, Brandon Lee, Eric P. Spana, Abubakarr Bangura, Sarah A Einsteen, Luke Schmidt, Arianne E. Rodriguez, Samantha Parsons, Ryan Duggal, Karen Zhou, George Odisho, Tam Vuong, Erin Duso, Adam P Lousararian, Stephanie L Christ, Christopher D. Shaffer, Myrielis Rivera-Burgos, Sam Asinof, Dennis Y. Wu, Torie L Richardson, Heather L. Eisler, Allyson P Mallya, Brittney Stanton, Elizabeth J. Chen, Laurie Cannon, Briana D McRae, Peter B Lowery, Alicia R Carroll, Judith Leatherman, Guillermo Perez-Aragon, Joshua M Lorenz-Guertin, Delia Shen, Erica Enoch, Peter Wendland, Wilson Leung, Elaine R. Mardis, Adam Schefkind, Thomas Q. Xu, Wint Yan Aung, Darrin T. Schultz, Misha A Host, Hani Yosif, Ashleigh P O'Reilly, Eric Spencer, Melissa D. Patao, Jonathan M Sarezky, Matthew R Kroll, Casey L Personius, Alice Turski, Julie Beth Gillespie, S. Catherine Silver Key, Hashini Precht, Harriette Carrington, Stella Rosen, Yi Huang, Joseph Perez-Otero, Jeanette Hauke, Elizabeth A S Rettie, Petros Svoronos, Nicholaus Monsma, Kelsey F. Sugrue, Latia Britt, Tracy Wang, Patrick Gomez Menzies, Alycia Zoellner, Francesca M Gifford, Carlos F Carrion-Ortiz, Lyndsay D Kirkland, Ryan Moran, Vinayak S. Nikam, Spencer M Batten, Vanessa P Chu, Justin R. DiAngelo, Sheryl T. Smith, Ximena Velez, Tara Skorupa, Alen Ramic, Ricky Prasad, Richard Forka, Ken Saville, Ben Chlebina, Robert Franklin, Drew Miller-Foreman, Judith A Ingles, Rohit Venkat, Jennifer J Palomino, Debbie M Espada-Green, Cassie M Modahl, William A Hilton, Tracy Selfridge, Mona O Rodriguez, Samantha House, Srebrenka Robic, Sarah C. R. Elgin, Patrick Ng, Masud Karimi, and Zachariah Wichman

Subjects
0301 basic medicine, Genetics, Euchromatin, biology, Drosophila ananassae, heterochromatin, Retrotransposon, Investigations, QH426-470, biology.organism_classification, Genome, retrotransposons, 03 medical and health sciences, 030104 developmental biology, Codon usage bias, genome size, Drosophila, Drosophila melanogaster, Molecular Biology, Genome size, Gene, Genetics (clinical), Wolbachia
Abstract

The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae. Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5′ ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.

Published
2017

33. The Impact of Genetic Background and Cell Lineage on the Level and Pattern of Position Effect Variegation

Author

Sarah C. R. Elgin and Sidney H. Wang

Subjects
Genetics, Reporter gene, education.field_of_study, Euchromatin, Heterochromatin, Population, fungi, Locus (genetics), Position-effect variegation, Biology, biology.organism_classification, Inbred strain, Drosophila melanogaster, education
Abstract

BackgroundChromatin-based transcriptional silencing is often described as a stochastic process, largely because of the mosaic expression observed in position effect variegation (PEV), where a euchromatic reporter gene is juxtaposed with heterochromatin. Here we closely examine the impact of genetic background on PEV phenotypes in the fruit fly,Drosophila melanogaster.ResultsUsing consecutive generations of selective breeding, we isolated, from a single laboratory population, two inbred lines exhibiting contrasting degrees of variegation (A1: low expression, D1: high expression). Within each inbred population, remarkable similarity is observed in both the degree and the pattern of variegation. 89.63% of the differences between the two inbred lines in the degree of silencing can be explained by genotype, while a modest but significant sex effect is also observed. Further analyses of the PEV phenotype in the progeny of crosses between A1 and D1 suggest that the genotypic effect is the result of the combined effect of multiple independenttrans-acting loci. While the initial observations are based on a PEV phenotype scored in the fly eye (hsp70-whitereporter), similar degrees of silencing were observed using abeta-galreporter that can be scored across the whole fly. The pattern of variegatinghsp70-whiteexpression among individual flies becomes almost identical after five generations of inbreeding. Using a reporter inserted into the heterochromatic fourth chromosome, image analysis found significant enrichment of pigmentation in the ventral-posterior quadrant in both the A1 and D1 lines, and in the F1 and F2 progeny produced from a cross between A1 and D1, despite different degrees of expression.ConclusionsCombining these results with the spreading model for local heterochromatin formation, we propose an augmented stochastic model to describe PEV. In this model, the genetic background, which determines the overall level of silencing, works with the cell lineage specific regulatory environment to determine the on/ off probability at the reporter locus in each cell. This model acknowledges cell-type specific events, as well as the general impact of heterochromatin formation.

Published
2019
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34. Correlation-Based Ensemble Feature Selection Using Bioinspired Algorithms and Classification Using Backpropagation Neural Network

Author

Arputharaj Kannan, B. Minu, H. Khanna Nehemiah, and V. R. Elgin Christo

Subjects
Support Vector Machine, Article Subject, Computer science, Glowworm swarm optimization, Feature selection, Breast Neoplasms, 02 engineering and technology, lcsh:Computer applications to medicine. Medical informatics, Sensitivity and Specificity, General Biochemistry, Genetics and Molecular Biology, Hepatitis, Pattern Recognition, Automated, Machine Learning, 03 medical and health sciences, 0302 clinical medicine, 0202 electrical engineering, electronic engineering, information engineering, Humans, Computer Simulation, Diagnosis, Computer-Assisted, Fitness function, General Immunology and Microbiology, Artificial neural network, Applied Mathematics, Computational Biology, Reproducibility of Results, General Medicine, Missing data, Backpropagation, Support vector machine, ComputingMethodologies_PATTERNRECOGNITION, Modeling and Simulation, lcsh:R858-859.7, 020201 artificial intelligence & image processing, Data pre-processing, Neural Networks, Computer, Algorithm, 030217 neurology & neurosurgery, Algorithms, Software, Research Article
Abstract

A framework for clinical diagnosis which uses bioinspired algorithms for feature selection and gradient descendant backpropagation neural network for classification has been designed and implemented. The clinical data are subjected to data preprocessing, feature selection, and classification. Hot deck imputation has been used for handling missing values and min-max normalization is used for data transformation. Wrapper approach that employs bioinspired algorithms, namely, Differential Evolution, Lion Optimization, and Glowworm Swarm Optimization with accuracy of AdaBoostSVM classifier as fitness function has been used for feature selection. Each bioinspired algorithm selects a subset of features yielding three feature subsets. Correlation-based ensemble feature selection is performed to select the optimal features from the three feature subsets. The optimal features selected through correlation-based ensemble feature selection are used to train a gradient descendant backpropagation neural network. Ten-fold cross-validation technique has been used to train and test the performance of the classifier. Hepatitis dataset and Wisconsin Diagnostic Breast Cancer (WDBC) dataset from University of California Irvine (UCI) Machine Learning repository have been used to evaluate the classification accuracy. An accuracy of 98.47% is obtained for Wisconsin Diagnostic Breast Cancer dataset, and 95.51% is obtained for Hepatitis dataset. The proposed framework can be tailored to develop clinical decision-making systems for any health disorders to assist physicians in clinical diagnosis.

Published
2019
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36. G-OnRamp: A Galaxy-based platform for creating genome browsers for collaborative genome annotation

Author

Wilson Leung, Jeremy Goecks, Y. Liu, Luke Sargent, and Sarah C. R. Elgin

Subjects
0303 health sciences, Source code, Computer science, media_common.quotation_subject, 0206 medical engineering, Genomics, 02 engineering and technology, Genome project, Genome, World Wide Web, 03 medical and health sciences, ComputingMethodologies_PATTERNRECOGNITION, Gene, 020602 bioinformatics, 030304 developmental biology, media_common
Abstract

Summary: G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders. Researchers can use the G-OnRamp output to visualize large genomics datasets, and can utilize the output to drive collaborative genome annotation projects in both research and educational settings. Availability and Implementation: The G-OnRamp virtual machine images and tutorials are freely available on the G-OnRamp web site (http://g-onramp.org/deployments). The G-OnRamp source code is freely available under an Academic Free License version 3.0 through the goeckslab GitHub repository (https://github.com/goeckslab). Contact: goecksj@ohsu.edu

Published
2018
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37. The

Author

Nicole C, Riddle and Sarah C R, Elgin

Subjects
Recombination, Genetic, heterochromatin, FLYBOOK, chromosome evolution, Genes, Insect, F element, Chromosomes, Insect, Evolution, Molecular, HP1a, Animals, Drosophila, Genome Organization, fourth chromosome, Repetitive Sequences, Nucleic Acid
Abstract

The F element of the Drosophila karyotype (the fourth chromosome in Drosophila melanogaster) is often referred to as the “dot chromosome” because of its appearance in a metaphase chromosome spread. This chromosome is distinct from other Drosophila autosomes in possessing both a high level of repetitious sequences (in particular, remnants of transposable elements) and a gene density similar to that found in the other chromosome arms, ∼80 genes distributed throughout its 1.3-Mb “long arm.” The dot chromosome is notorious for its lack of recombination and is often neglected as a consequence. This and other features suggest that the F element is packaged as heterochromatin throughout. F element genes have distinct characteristics (e.g., low codon bias, and larger size due both to larger introns and an increased number of exons), but exhibit expression levels comparable to genes found in euchromatin. Mapping experiments show the presence of appropriate chromatin modifications for the formation of DNaseI hypersensitive sites and transcript initiation at the 5′ ends of active genes, but, in most cases, high levels of heterochromatin proteins are observed over the body of these genes. These various features raise many interesting questions about the relationships of chromatin structures with gene and chromosome function. The apparent evolution of the F element as an autosome from an ancestral sex chromosome also raises intriguing questions. The findings argue that the F element is a unique chromosome that occupies its own space in the nucleus. Further study of the F element should provide new insights into chromosome structure and function.

Published
2018

39. Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

Author

Raechel Harnoto, Morgan C. Anderson, Amy Z. Xu, Heather Hedeen, Arnaldo J. Santiago-Sanabria, Brandy L. Hammond, Kenneth Saville, Ross D. Kooienga, Christopher Chesley, Robert W. Morris, Aubree T. Gillis, Brittney Offenbacker, Katherine C. Palozola, Trisha Tomkins, Nicole Yu, Matthew Kwong, Megan E. Aldrup, Jordan E. Kus, Chelsey Friedrichs, Kenneth Stapleton, Carly E. Pelchen, Norma Chamma, Joshua F. Machone, Danielle Kulich, Andre Kennedy, Matt J. Crowley, Daniel Broomfield, Adeola Adebayo, Nicolas Ragland, Shady Messiah, Jonathan Misch, Meghan B. Rooney, Eva N. Rubio-Marrero, Will Sherrill, Joyce Stamm, Rachel R. Leads, Lindsey Shantzer, Alexis J. Scott, Andrew W. Waggoner, Kristen M. Cooper, Adam Haberman, Carmen A. Watchinski, Marcos A. Perez, Lisa Kadlec, Kiara N. Medina-Ortega, Kayla Chapman, Cheryl Bailey, Nicholas Fazzio, Insun Chong, Lasse Schmidt, Darla M. Balthaser, Megan DeShetler, Jien Shim, Anna Rogers, Chris Uitvlugt, Bryan Yarrington, Ruth A. Howe, Andrea Ochoa, Gregory J. Mullen, Young Lu Kim, Olivia L Knowles, Kevin M. Levine, Matthew M. Villerot, Thomas J. Rose, Jonathan E. Smith, Sukhjit Kaur, Roshni Patel, Olivia Plante, Tenzin Choeying, Jennifer R. Ramthun, Tiffany Y. Y. Choi, Michael Rahimi, Guzal Khayrullina, Lauren R. Boudreaux, James E. J. Bedard, Brian A. Dow, Christopher A. Louie, Kenneth S. Smith, Joannee Zumkehr, Marcus Gostelow, Melissa A. Tache, Tiffany Dai, Joan D. Zambrana-Burgos, Lauren R. Meyer, Carter Brown, Adam Brown, Travis Lamb, Carissa Belella, Hannah Gilman, David DuPuis, Ramón E. Rivera-Vicéns, Priyanka Naik, Anna L. Shipman, Jad El-Adaimi, Eric Spencer, Jonathan D. Marra, Melissa D. Patao, Sharon Ibarra, Jiayu Zhang, Ashley Vetor, Bobbi Botsford, Jenifer Winters, Nelson A. Valentín-Feliciano, Lauren M. Robinson, Christopher R. Macchi, Jennifer Hernández-Muñiz, E. Gloria C. Regisford, Jaelyn L. Johnson, Cory M. Dauphin, Tezin A. Walji, Matthew A. Zaborowicz, Stacey Winkler, Shannon M. Lowell, Marly R. McCracken, Andrew Adams, Lindsay A. Spaeder, Matthew W. Wolski, Adrese Kandahari, Fabiola Robles-Juarbe, Bryce A. Turner, Ángel L. Laboy-Corales, David T. Watson, Elaine J. Durchholz, Vanessa Rodriguez, Emily J. Teepe, Alaina C. Conturso, Eric Nyabeta Onsarigo, Tijana Martinov, Rohit Venkat, Charles R. Hauser, Priya Srikanth, Marwan Ibrahem, Karl E. Smith, Jessica M. Tucci, Ethan J. Brock, Aparna Sreenivasan, Jasmine Hales, Brianna K. Barnard, Andrew P. Stein, Jessica G. Thomas, Mallory Perella, Lorraine Rodriguez-Bonilla, Shekerah Primus, Zachary D. Moore, Caitlin M. Ament, Amber N. Hare, Brad Pamnani, Eugenia A. Soliterman, Christina Paluskievicz, Yashira M. Valentín-Feliciano, Alexandra K. Eckardt, Anya Goodman, Joseph W. Noynaert, Ashlee G. Johnson, Tyneshia C. P. Henry, Camille D. Ratliff, Ian O. Chase, Michel A. Conn, Jessica Koehler, Daniela Martiniuc, Allison J. Schepers, Megan B. Vylonis, Chrystel Dol, William Dirkes, Michelle S. Rivera-Llovet, Susana Rodríguez-Santiago, Heather L. Eisler, Mary L. Preuss, Daymon Peterson, Martin G. Burg, Aaditya Khatri, John R. Woytanowski, Holly Schiedermayer, Dara Cohn, Leah E Waldman, William M. Morris, Sharon C. Ehret, Marianna Defendini-Ávila, Jessica Fese, Suzette M. Arias-Mejias, Anna Kammrath, William D. Barshop, Edwin G. Ramírez-Aponte, Luis A. Jimenez, Carolina Marques dos Santos Vieira, Cody D. Kern, Francheska M. Delgado-Peraza, Tiffany Wan, Janice L. Krumm, Osagie Ighile, Eric D. Sassu, Jess M. Darusz, Laura Rodela, Daniel S. Nicolas, Shubha Govind, Mary Miller, Joseph E Marcus, Jason Pollack, Rostislav Castillo, Daniel Coomes, Matthew J. Borr, Diana Pérez-Afanador, Lucas A. Watson, Hannah C. Koaches, Amber Quintana, Faith H. Kung, Cameron B. Harris, Bridget M. Janssen, Cristina Zambrana-Echevarría, Jennifer K. Jones, Ian Dobbe, Benjamin M. Lewis, Lena N. Lupey, Julia A. Hilbrands, Cristina Montero Diez, Jorge L. Santiago-Ortiz, Dustin S. Woyski, Sandy D. Mach, Joseph Perez-Otero, Karim A. Sharif, Carlos Mendoza, John D. Fitzgibbons, Nelson H. Knudsen, Christy MacKinnon, Hayley M. Faber, Kwabea Agbley, Michelle Heslop, Olivia Cyrankowski, Priscilla Rodriguez, Melissa Jones, Jean M. Strelitz, Ryan A. Grove, Rachel A Greenstein, Michael Murillo, Elizabeth Greiner-Sosanko, Ciani Jean Sparks, Darryl McFarland, Franca G. Rossi, Heran Gebreyesus, Chris Kay, Danielle Ladzekpo, Chris Harward, Jordan S. Christie, Consuelo J. Alvarez, Elaine V. Morlock, Geoff Scott, Kelsey Hockenberger, Sepo Musokotwane, Adam Fearnow, Lauren J. Keny, Alaina J. Grantham, Evangelina Reza, Mike Colgan, Melanie K. Regan, Stephanie J. Potocny, Sasha L. Dorsett, Tara Skorupa, Valerie M. Gónzalez-Pérez, Vinayak S. Nikam, Anne C. Meier, Varun Sundaram, Helen B. Rankin, Andrew B. Nylander, Mariela Gines-Rosario, Laurell MacMillian, Jeannette M. Osterloh, Robert H. Allen, Melanie A. Smith, Sarah J. Spencer, Cheri M. Ackerman, Jeffrey L. Poet, Amanda J. Hay, Isaac O. Armistead, Laura K. Reed, Don W. Paetkau, Bib Yang, Enid M. Quintana-Torres, Kathryn L. Golden, Lauren A. DiLorenzo, Alen Ramic, Mark T. LeBlanc, Carl J. Minniti, Robert J. Bailey, Kristen M. Thomsen, Ashley L. Adams, Chad A. Koplinsky, Eliezer O. Perez-Colomba, Nicole A. Howey, Katie A. TerMeer, Stephanie Intriago, Christina N. Kufel, Mary Waters, Bo Liu, Thomas J. Bahr, Ashley R. Miller, Claire Pattison, Morgan R. Light, Amy T. Hark, Jennifer S. Doty, Catherine M. Mageeney, Adam J. Ronk, Nadezhda Fefelova, Andrew R. Armstrong, Maida Chen, Elizabeth Macias, Kim M. Chau, Paul Bilinski, Trevor G. Floyd, Cassidy T. Lee, Jenna C. Tenney, Bob Gardner, Patricia Ortiz-Ortiz, Elizabeth S. Jewell, Gabi Lucas, Brandon Lee, Jenifer N. Jarrell, Jimmy Hsiang-Chun Chang, Lorraine Malkowitz, Ulises Marrero-Llerena, Gabriel Stancu, Matthew R. Unzicker, Andrea P. Burgos-Bula, Michelle L. Miller, Elisandra Rivera, Kate Bagaeva, Jessica W. Polk, Jordan E. Carney, Maureen Corrielus, Jana Nietmann, Jeff Howenstein, Elizabeth Kiernan, Sabya A. Rauf, Brandon M. Katz, Elizabeth C. Nordman, Devon Shallman, Eric M. Clark, Lenin Lopez, Karen J. Kraftmann, Leslie Guadron, Julia Kuhn, Allison R. Schneiter, Satish C. Bhalla, Emily J. Howell, Blair Undem, Jeffrey S. Thompson, Arelys Flores-Vazquez, John Kiley, Cody M. Morrow, Joseline Serrano-González, John Mark Knepper, Christopher Beck, Calise Debow, Anna L. Smith, Angelica Garcia, Shelbi Christgen, Shadie Emiah, Tammy Mazur, Rachel E. VanDyken, Frank R. Soto delValle, Zachary Nichols, William R. Kennedy, Ameer Zidan, Douglas A. Herrick, Thomas Q. Xu, Elizabeth Shoop, Jessica A. Kampmeier, John M. Kerber, Caitlin Pozmanter, Emily L. Hong, Frederic J. Deuschle, Allyson B. Rivard, William Neutzling, Joseph V. Moran, Benjamin K. Johnson, Jacob Jipp, Shannon R. McCartha, Abby Vrable, Z. Goodwin, Suchita Rastogi, Alyssa M. Newman, Lionel Ortiz-Fuentes, Arjun A. Anilkumar, Bryan M. Hennessy, Hui-Min Chung, Katie L. Goeller, Carlos E. Santos-Ramos, Adam Dillman, Christine D. Wilson, Sarah J. Peacock, Andrew J. Kim, Carol I. Morales-Caraballo, Briana Brinkley, Justin Alldredge, Rebecca Krock, Kristen C. Davis, David Dunbar, Joshua L. Manghelli, Erica K. Earl, Katherine Gavinski, Sheryl T. Smith, Portia Mason, Lindsay J. Hoogenboom, Jessen T. Havill, Sonya G. Méndez-Castellanos, Darrin T. Schultz, Katherine J. Faber, Allison O’Rouke, Emily G. Miller, Yara Ashrawi, Curtiss E. Lane, Saryleine Ortiz-DeChoudens, Michael W. Sandusky, Andrew Montgomery, Rita Kabaso, Todd Aronhalt, Jonathan D. Foust, Jorge Ruiz, Eric Helmreich, Todd T. Eckdahl, Charlotte Lea, Kevin Coulson, Kristin M. French, Kate A. Woodard, Brandon J. Burkhart, Kylie McNeil, Curtis R. Edwards, Jimmy Ma, Darcie D. Elder, Tia DiTommaso, Nicholaus Monsma, Sarah A. Jelgerhuis, Stephanie J. Adams, Nichole Rigby, Heather L. Holderness, Charlotte Williams, Megan Donegan, Taylor S. Harding, Javier O. Martinez-Rodriguez, Sandeep Venkataram, Tiffany Wong, Anika Toorie, Jenny L. Rose, Ashley S. Brown, Sarah A. Popelka, Matthew Williams, Julie Bryant, Sarah C. R. Elgin, Sonali Kumar, Joshua Burkhardt, William J. Puetz, Erica L. Alvendia, Richard A. Tumminello, Kesley Parry, Joshua R. Smith, Ashley F. Custer, Carlos E. Ortiz, Yedda Li, April E. Bednarski, Simon Ng, Max Mandelbaum, Arlene J. Hoogewerf, Chelsea A. Walker, Ryan S. Lee, Jeannette Wong, Isabella Theresa Felzer-Kim, Harrison Friedman, Megan Bourland, Luis R. Colón-Cruz, Lucy Liu, Nicole C. Olson, Yi Ren, Adam P Lousararian, José M. Cruz-García, Charlie Manchee, Kyle Zoll, Kristina M. Stemler, Juliana Belén-Rodríguez, Ashley S. Timko, Jane Lopilato, England Raimey, Amy D. Melton, Joshua D. Forsyth, Christopher D. Savell, Himabindu Reddy, Alica B. Allen, Amanda Maffa, Daniel W. Cassidy, Luciann Bracero-Quiñones, Eric Lemmon, Justina R. Bartling, Bradley J. Ogden, Petros Svoronos, Mary Spratt, Lisa Sudmeier, Héctor A. Martell-Martínez, James F. Geary, Bridget J. Sessions, Christopher Campana, Kaitlyn A. Downey, Seth G. Dawson, Daniella Menillo, Casey Hanson, James M. Bellush, Justin A. Gonzales, Roy Song, Karvyn Torchon, Betsy Hoover, Michael Closser, Lacey Neufeld, Micah Shelton, Benjamin R. Does, Juan Carlos Martínez-Cruzado, Jordan S. Baumgardner, Nicole Chichearo, Mary T. Reilly, Colleen V. Kelley, Monica Yalamanchili, Dawn Lau, Abbie Morgan, Alyssa Cifelli, Milton R. Herrold, Ambreen Khan, James Messler, Kyle Westphal, James L. Kehoe, Juliana A. Wurzler, Garrett Salzman, Tracy Wang, Charlene Emerson, Lyndsey A. Reynolds, Alysha Moretti, Marita K. Abrams, Mara G. Cole, Michael B. Schultz, Samantha Cruz, Natalie Ngai, Nadia Safa, Vicente Velasquez, Ashley Townsend, Jonathan L. Crooke-Rosado, Amber M. Gygi, Ishwar S. Gill, Christopher McLaughlin, Dorianmarie Vargas-Franco, Alissa Beckett, Samantha Vue, Nadine L. Rossi, Justina Chinwong, Ryan Michael Rempe, Trip Freeburg, Amy J. Johnson, Omolara Glenn, Jade Lea Rekai, Hashini Gunasinghe, Vivienne Echendu, Marshall Strother, Morgan Baker, Christopher D. Smith, Paolo A. DaSilva, Noelle Delacruz, Tiara Tirasawasdichai, Yakov Shevin, Wilfried Guiblet, Shane M. Patao, Peterson R. Cullimore, Giancarlo F. Garbagnati, Adam E. Musick, Sarah C. Butzler, Jonathan D. Presley, Ana I. Correa-Muller, Christopher D. Shaffer, Chunguang Du, Ryan D. Mitchell, Jonathan P. Rennhack, Barbara L. Hopkins, Mary E. Shaw, Jessica E. Hill, Jeremy N. Wong, Anna Kim, Christopher B. Khoury, Julia Chapman, Amanda T. Mercer, Jessica A. Shuen, Joyce H. Lau, I.N. Falk, Sunil Rathore, Christopher J. Jones, Laura Simone Bisogno, Nighat P. Kokan, Paul Yenerall, Amber L. Price, Kelsey T. Bushhouse, Stephen L. McDaniel, Andrew P. Drake, Johnathan D. English, Sampson K. Boham, Robert A. Herbstsomer, Daniel S. Fosselman, Kevin Babilonia-Figueroa, Matthew Simon, Anne G. Rosenwald, Bryan J. Rupley, Heather Cohen, Victoria Scala, Avery B. Cromwell, Christopher E. Blunden, Yelena P. Davis, William B. Armstrong, Kristine Ostby, Joanna Haye, Lauren M. Wysocki, Lena Christiansen, Allison A. Throm, Sarah Flohr, Matthew Wawersik, Rebecca J. Cotteleer, Kristen R Ramirez, Dontae A. Jacobs, Sarah Woehlke, Gregory S. Messenger, Soham Aso, Nicole Clarke-Medley, Bryant R. Swanson, Lindsay K. Brouwer, S. Catherine Silver Key, Stephanie Zarrasola, Michael S. Salgado, Dong K. Rhee, Mai Abdelnabi, Eve VanEck, Jeremy Buhler, Sarah Kong, Turner Conrad, Jennifer Roecklein-Canfield, Marykathryn Tynon, Brian J. Maniaci, Alexa M. McDonough, Ivan G. Llavona-Cartagena, J. Devin Spencer, Todd D. Johnson, Azita Bashiri, Kimberley Ramsey, Mike Polen, Hien P Nguyen, Seantay D. Patterson, Lucia Wande, Nicholas U. Schwartz, Han Yuan, Albeliz Santiago-Colón, Joseph Medina, Samuel Thomas Crowley, Emma Shoemaker, Alex J. Feliciano-Cancela, Alexander J. Kujawski, Lillyann Asencio-Zayas, Gentry L. Pickett, Matt J. Randazzo, Erica Stagaard, Kristin M. LaForge, Gabriela A. Llaurador-Caraballo, Anastasia K. Yemelyanova, Alan Tseng, Erika E. Menyes, Julie Azarewicz, Christa Burke, Samuel I. Smith, Nazanin Ghavam, Carolina Gomez, Cameron Fick, Anthony Pinto, Lindsay Rios, Gary A Kuleck, Ashley Rich, Kayla A. Florian, Martin N. Cheramie, Yuki Kwan Wa Shum, Atlee Baker, LaJerald Augustine, Alyson Greenwell, Rasleen K. Saluja, Jason S. Macias, Wesley W. Winn, Samantha M. Schmuecker, Michelle E. M. Eisen, Pedro Benitez, Jeanette Hauke, Nora C. Goscinski, Justin R. DiAngelo, Carter T. Docking, David D. Xiong, Brittany D. Pasierb, Matt Van Camp, Yin Zheng, Nikie L. McCabe, Emily Reed, Katie Homa, Kimberly S. Kolibas, Elizabeth A. Karaska, Grace A. Dougherty, John P. Fanning, Michael Fasano, Joseph E. Sable, Robert W. Schulz, San Francisco Nguyen, Michael L. Rojas-Vargas, Kierstin L. Naylor, Emily Peoples, Jessica Neely, Lejla Cesko, Brionna D. Davis-Reyes, Roxanne Banker, Amanda K. Tilot, Jordan P. Brand, William H. Newhart, Lauriaun Johnson, Michelle M. Giddens, Nicole B. Clark, Anant Agarwalla, Thomas F. Minton, Dana W. Brooks, Amanda D. Garrett, Bethany M. Klett, Kristin M. Starkey, Antoinette E. Fafara-Thompson, Michael R. Rubin, Jonathon M. Benson, Erica Enoch, Amanda M. Damsteegt, Zackary W. Scott, Elisabeth A. Kelly, Jason M. Barnett, Wilson Leung, Luke J. Rodriguez-Giron, Krishna C. Mudumbi, Francis J. May, Nadyan M. Vargas-Barreto, Geeta Statton, José L. Torres-Castillo, Sarah Hirsch, Rachel M. Reem, Linghui Li, Deirdre Robinett, Jason Caronna, Abneris E. Rodríguez-Laboy, Samantha Lawrence, Katherine R. Reynolds, Corinne Weeks, Allison M. Sterling, Chun Leung Ng, Roman E. Ramirez, Daron C. Barnard, Leming Zhou, Eric P. Spana, John A. Toth, Alvin Lu, Krizia C. Menéndez-Serrano, Jonathan M. Heckman, Ben Chlebina, Matthew C. Fadus, Helmet T. Karim, Shailly Gaur, Timothy R. Jelsema, Nicholas Keysock, Thomas J. Carr, Zach Fusco, Evan M. Verbofsky, Monal Naik, Amanda H. Flores, Kristin A. Knouse, Olga R. Kopp, Elizabeth Feenstra, Edward P. Sweeney, Christen Johnson, Justin Crawford, Damian Urick, Victor W. Mullen, Carrie A. Dunham, Gabriella A. DeMichele, Mengyang Sun, William Harrington, Jessica M. Bodenberg, Xavier A. Collado-Méndez, T. Aaron Wiles, Michelle K. Powers, Phillip J. Minnick, Lourdes N. Irizarry-González, Valeria Silva, Steven Ovu, Nik Kolba, Peter Lindbeck, Jerome M. Molleston, Ifeanyi Obiorah, David Carranza, Lauren R. Beck, Alina M. Tamayo-Figueroa, Elaine R. Mardis, Rachel N. Lippert, Ingrid T. Rivera-Pagán, Mahdi Soos, Trung T. Nguyen, Megan Martinez, Van Kim, Benjamin L. Danner, Randall J. DeJong, Melissa M. Trieu, Andrea M. Senquiz-Gonzalez, Mary Grace Schueler, Emily E. Magnuson, Lesley E. Jackson, Hendrick Pagán-Torres, Fareed Sanusi, Dana Koenig, Vidya Chandrasekaran, Chinmoy I. Bhatiya, Dongyeon Kim, Paul J. Overvoorde, Reece Watson, Jennifer Schottler, Devry Lin, Jim Youngblom, Taylor Schauder, Nigel Madden, Isabel Valdez, Thomas John Reynolds, Kelly M. Deranek, Anne A. Welker, Jackie X. White, Nicole C. Riddle, Jacob Pfeil, Aldo Heredia-Negrón, Christine Langner, Tao Jian He, Jonathan P. Mecoli, Lissett Mayorga, Scott Chiang, Rishi Singhal, Julia C. Peairs, Michael Quach, Anne M. Eime, GiNell Elliott, Meleah J. Gross, Melissa Drewry, Julia A. Emerson, Anthony K. Lambright, Isaac Appiah, Gregory M. Robertson, Nathaniel Regenold, Philip Pham, George Odisho, Alexi Archambault, Matthew Dothager, Shana M. Baldassari, Paul J. Lee, Callie R. Merry, Jesse R. Farek, Archana Tare, Srebrenka Robic, William Vernon, Tam Vuong, Bethany Grace Bonifield, Katrina Thistle, Rose M. Dowd, Noor Tazudeen, Jennifer Weaver, Manpreet Kaur, Nicole M. Caesar, Yi Zhang, Michael C. Cristostomo, Albert Tzeng, Kayla Vondy, Emily Perling, Ramiro A. Chavez, Lanor S. Horton, Matt Kroll, Levent H. Beken, Justin R. Starcher, Sam Asinof, Nathalia M. Cruz, Eunice George, Adam T. Morrow, Heather Milnthorp, Cheryl Mazzeo, Kristen R. Hatfield, Anna L. Boudoures, Ashley A. Tewilliager, Edna P. Tascón-Peñaranda, Vilma F. Huerta, Sarah Tuberty, Mallory A. Williams, Rachel E. Weber, Sarah Spencer, Emily C. Leatherman, Yuying Gosser, Steve DeFazio, Patrick Ng, Jeri Sparks, Pavan Bhat, Mindy E. Bower, Jordan E. Matthews, Cyrus E. Kuschner, Anne Bertolet, Matt Kusner, Thomas C. Giarla, Jessica Penn, Gerard P. McNeil, Mariam Meghdari, Michael J. Wolyniak, Matthew Juergens, Karla I. Velázquez-Soto, Maria Kaisler, Jeanine Schibler, Alexis Nagengast, Susan Parrish, Frances Marín-Maldonado, Shiv Mohini, Jessica King, Danny Mammo, Katherine S. Harker, Allyson P. Hawkins, Kelly Drumm, Jennifer A. Lammers, Allyson P Mallya, Ashley Bryant, Katie Weihbrecht, Pete Wendland, Gabriela V. Bernal-Vega, Nestor A. Gutierrez, Armando G. Bermudez-Capo, Luke R. Salbert, Kirk Haltaufderhyde, Michelle L. Kappes, Mary A. Smith, York Chen, Miguel Vélez-Vázquez, Brittany E. Plescher, Francis D. Beauchamp-Pérez, Alyssa Ward, Andrea N. Clary, Don Foret, Mitchell J McDonald, Mariela Colon-Vazquez, Amanda L. Blaker, Hao Yang, James Z. Liu, Austin B. Limle, Henry Huang, Luis Vilanova-Velez, Edgar Garibay, Philip J. Freda, Laura L. Mays Hoopes, Maureen S. Hammond, Marian M. Kaehler, Rebecca Shuford, Ray Sunjed, Cynthia K. Hanson, Marielle VanderVennen, Idaliz M. Martínez-Traverso, Jack Y. Yu, Spencer L. Franchi, Michael Snavely, John E. Anderson, Lainey S. Rubin, Kelly K. Jones, Stephanie F. Mel, Stacey Lytle, Danny L. Tran, Chelsea R. Barberi, Max Mian Liu, Eric A. Nollet, Sarah E. Muller, Diana Norton, John M. Braverman, Thu A. Phan, Nelson Membreno, Colin Khoshabian, John Gooch, Cassandra Kubricky, Priscila M. Rodríguez-García, Anna Wylie, Diana L. E. Johnson, Anna K. Unruh, Deborah Hammett, Jon Sarezky, Marie Brown, Carolina Riascos-Cuero, Emily J. Diekema, Emmy E. Ogawa, Miranda Chavez, Zuzana Kocsisova, Dennis Revie, Anniken M. Lydon, Peter A. Cognetti, Ashley A. Collins, Tariq Abusheikh, Erin K. Luippold, Kevin Myirski, Brian O. Rodríguez-Echevarría, Haley J. Plasman, Lara Baatenburg, Jesse Hendriksma, Christopher R. Knob, Max Semon, Cassandra Farrar, Xiao Zhu, Ali Dobbe, Marie-Isabelle B. Seydoux, Griffin Sadovsky, Shreya Prasad, Victoria Newcomb, Chad Gier, Dmitri Serjanov, Jules Wellinghoff, Maxwell T. Smith-Gee, and Alexandra H. Scoma

Subjects
Transposable element, Codon Adaptation Index, Euchromatin, Heterochromatin, transposons, evolution of heterochromatin, Investigations, Genome, Evolution, Molecular, 03 medical and health sciences, gene size, 0302 clinical medicine, melting characteristics, Species Specificity, codon bias, Genetics, Animals, Drosophila Proteins, Selection, Genetic, Codon, Molecular Biology, Genetics (clinical), 030304 developmental biology, Polytene Chromosomes, Repetitive Sequences, Nucleic Acid, Gene Rearrangement, 0303 health sciences, biology, Computational Biology, Molecular Sequence Annotation, Gene rearrangement, Exons, Genomics, biology.organism_classification, Introns, Drosophila melanogaster, Codon usage bias, DNA Transposable Elements, Drosophila, 030217 neurology & neurosurgery
Abstract

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

Published
2015

40. Intelligent UAV-Assisted Localisation to Conserve Battery Energy in Military Sensor Networks

Author

V. Rhymend Uthariaraj, P. Shunmuga Perumal, and V. R. Elgin Christo

Subjects
Engineering, Event (computing), business.industry, Mechanical Engineering, General Chemical Engineering, Node (networking), Computation, Real-time computing, Biomedical Engineering, General Physics and Astronomy, Computer Science Applications, Key distribution in wireless sensor networks, Sensor node, Embedded system, Mobile wireless sensor network, Electrical and Electronic Engineering, business, Wireless sensor network, Energy (signal processing)
Abstract

Wireless sensor networks (WSNs) are extensively used in military applications for border area monitoring, battle-field surveillance, tracking enemy troops, where the sensor nodes run on battery power. Localisation of sensor nodes is extremely important to identify the location of event in military applications for further actions. Existing localisation algorithms consume more energy by heavy computation and communication overheads. The objective of the proposed research is to increase the lifetime of the military sensor networks by reducing the power consumption in each sensor node during localisation. For the state-of-the-art, we propose a novel intelligent unmanned aerial vehicle anchor node (IUAN) with an intelligent arc selection (IAS)-based centralised localisation algorithm, which removes computation cost and reduces communication cost at every sensor node. The IUAN collects the signal strength, distance data from sensor nodes and the central control station (CCS) computes the position of sensor nodes using IAS algorithm. Our approach significantly removes computation cost and reduces communication cost at each sensor node during localisation, thereby radically extends the lifetime and localisation coverage of the military sensor networks. Science Journal, Vol. 64, No. 6, November 2014, pp.557-563, DOI:http://dx.doi.org/10.14429/dsj.64.5295

Published
2014

41. Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education

Author

David Ebenbach, Jeffrey D. Newman, Anne G. Rosenwald, Lonnie R. Welch, Melissa A. Wilson Sayres, Srebrenka Robic, Sarah C. R. Elgin, James M. Burnette, William Tapprich, Arlín Toro-Martínez, Neal Grandgenett, William Morgan, John R. Jungck, Rafael Tosado-Acevedo, Tammy C. Tobin, William R. Pearson, Mindy McWilliams, Edison Fowlks, Sam S Donovan, Mark A. Pauley, Charles R. Hauser, Elizabeth F. Ryder, Jennifer C. Drew, Anya Goodman, Michael Sierk, Jason Williams, Eric W. Triplett, Sebastian Galindo-Gonzalez, Elizabeth A. Dinsdale, Todd M. Smith, Carlos C. Goller, and Robin Wright

Subjects
Computer science, 4. Education, Underrepresented Minority, 0206 medical engineering, 05 social sciences, ComputingMilieux_COMPUTERSANDEDUCATION, 050301 education, 02 engineering and technology, Bioinformatics, 0503 education, Curriculum, 020602 bioinformatics
Abstract

Bioinformatics, a discipline that combines aspects of biology, statistics, and computer science, is increasingly important for biological research. However, bioinformatics instruction is rarely integrated into life sciences curricula at the undergraduate level. To understand why, the Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE, “nibbles”) recently undertook an extensive survey of life sciences faculty in the United States. The survey responses to open-ended questions about barriers to integration were subjected to keyword analysis. The barrier most frequently reported by the ~1,260 respondents was lack of faculty training. Faculty at associate’s-granting institutions report the least training in bioinformatics and the least integration of bioinformatics into their teaching. Faculty from underrepresented minority groups (URMs) in STEM reported training barriers at a higher rate than others, although the number of URM respondents was small. Interestingly, the cohort of faculty with the most recently awarded PhD degrees reported the most training but were teaching bioinformatics at a lower rate than faculty who earned their degrees in previous decades. Other barriers reported included lack of student interest in bioinformatics; lack of student preparation in mathematics, statistics, and computer science; already overly full curricula; and limited access to resources, including hardware, software, and vetted teaching materials. The results of the survey, the largest to date on bioinformatics education, will guide efforts to further integrate bioinformatics instruction into undergraduate life sciences education.

Published
2017
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42. An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

Author

Sarah C. R. Elgin, Charles R. Hauser, Jacob D. Kagey, Jennifer A. Kennell, Brianna Derr, S. Catherine Silver Key, Chiyedza Small, Marisol Santisteban, Srebrenka Robic, Hemlata Mistry, Leocadia V. Paliulis, Paula Croonquist, Melanie Van Stry, Christopher J. Jones, Joyce Stamm, Elena O. Gracheva, Jamie Siders Sanford, Wilson Leung, Rebecca Spokony, Carina Howell, and Meg M. Laakso

Subjects
Structure (mathematical logic), Computer science, Eukaryotic gene, General Medicine, Bioinformatics, Curriculum
Published
2017

43. A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

Author

Juan Carlos Martínez-Cruzado, Gary A Kuleck, Shubha Govind, Christopher D. Smith, Judith Leatherman, Jeffrey S. Thompson, Daron C. Barnard, Christopher J. Jones, Paul J. Overvoorde, Matthew Wawersik, Amy Frary, Randall J. DeJong, Dale L. Beach, Todd T. Eckdahl, Laura L. Mays Hoopes, Marian M. Kaehler, David Lopatto, Justin R. DiAngelo, Michael R. Rubin, Mary A. Smith, Carina E. Howell, Donald R. Frohlich, Chunguang Du, Leming Zhou, Eric P. Spana, Stephanie F. Mel, John M. Braverman, Karim A. Sharif, Consuelo J. Alvarez, Gary R. Skuse, Cheryl Bailey, Anya Goodman, Kari Clase, Laura K. Reed, Anne G. Rosenwald, Don W. Paetkau, James E. J. Bedard, Mary L. Preuss, Gerard P. McNeil, Michael J. Wolyniak, Martin G. Burg, Lisa Kadlec, Alexis Nagengast, Susan Parrish, Hemlata Mistry, Hui-Min Chung, Joyce Stamm, April E. Bednarski, Sheryl T. Smith, Aparna Sreenivasan, Paul Szauter, Celeste Peterson, Stephanie Schroeder, Nighat P. Kokan, Satish C. Bhalla, Arlene J. Hoogewerf, Heather L. Eisler, Christy MacKinnon, Mary Spratt, Christopher Bazinet, Amy T. Hark, Wilson Leung, Olga R. Kopp, Diana S Johnson, Elaine R. Mardis, Mary E. Shaw, Catherine Reinke, David Dunbar, Yuying Gosser, Jane Lopilato, Vidya Chandrasekaran, Srebrenka Robic, Sarah C. R. Elgin, Kenneth Saville, Adam Haberman, Dennis Revie, Christopher D. Shaffer, Jennifer Roecklein-Canfield, Julia A. Emerson, Adam Kleinschmit, Jeremy Buhler, Charles R. Hauser, James J. Youngblom, S. Catherine Silver Key, and O'Dowd, Diane K

Subjects
Value (ethics), Program evaluation, Time Factors, General Biochemistry, Genetics and Molecular Biology, Information science, Education, Surveys and Questionnaires, Mathematics education, ComputingMilieux_COMPUTERSANDEDUCATION, Humans, Learning, Cooperative Behavior, Curriculum, Biology, Mathematics, Data collection, Genome, Data Collection, Research, Molecular Sequence Annotation, Articles, Genomics, Investment (macroeconomics), Faculty, Research Personnel, Variety (cybernetics), Knowledge, Undergraduate research, Attitude, Self Report, Curriculum and Pedagogy, Program Evaluation
Abstract

While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students., There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Published
2014

44. Improving societies' harassment policies

Author

Muhammad H. Zaman, Joseph M. Jez, Ariel D. Anbar, Diane K. O'Dowd, Sarah C. R. Elgin, and Beth Shapiro

Subjects
Multidisciplinary, 010504 meteorology & atmospheric sciences, Political science, Harassment, Library science, 01 natural sciences, 0105 earth and related environmental sciences
Abstract

As Howard Hughes Medical Institute (HHMI) professors, teachers, and mentors, we are acutely aware of the harm that can be done by sexual harassment and other discriminatory behaviors, which negatively affect the careers of young scientists and hamper our efforts to diversify the scientific workforce and professoriate. We applaud the recent report on sexual harassment of women, climate, and culture from the National Academies of Sciences, Engineering, and Medicine and the recommendations therein ([ 1 ][1]). Scientific societies can play an important role in changing discriminatory culture. A number of societies have recently implemented or improved codes of conduct. The American Geophysical Union includes harassment as a form of scientific misconduct under its new ethics policy ([ 2 ][2], [ 3 ][3]). The Society of HHMI Professors has recently changed its policies so that membership, either initial or continuing, requires that the person be in good standing at their university or other employer in terms of relevant codes of conduct ([ 4 ][4]). AAAS (the publisher of Science ) is in the process of writing a new policy ([ 5 ][5]), and there is a petition urging the U.S. National Academy of Sciences to enact such policies as well ([ 5 ][5]). We encourage all professional societies to do likewise. These steps, if taken by all, will help the scientific community to maintain respect for all members, foster an environment of inclusion, and support a diverse workforce. Full List of Signatories [www.sciencemag.org/content/361/6406/984.2/suppl/DC1][6] 1. [↵][7]National Academies of Sciences, Engineering, and Medicine, “Sexual harassment of women: Climate, culture, and consequences in academic sciences, engineering, and medicine” (The National Academies Press, Washington, DC, 2018). 2. [↵][8]1. M. J. McPhaden, 2. L. Gundersen, 3. B. M. Williams , Eos 98, 10.1029/2017EO082469 (2017), 3. [↵][9]1. E. Davidson , “AGU's revised ethics policy: Where we are 6 months later,” From the Prow (2018); [https://fromtheprow.agu.org/agus-revised-ethics-policy-where-we-are-6-months-later/][10]. 4. [↵][11]The Society of HHMI Professors, Mission Statement and Rules of Order (2018); [www.hhmi.org/sites/default/files/society\_of\_hhmi\_professors\_mission\_and\_rules\_of\_order.approved_2018.i2.pdf][12]. 5. [↵][13]1. M. Wadman , Science 360, 949 (2018). [OpenUrl][14][Abstract/FREE Full Text][15] 6. The full list of signatories is available as supplementary material. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: #ref-4 [5]: #ref-5 [6]: http://www.sciencemag.org/content/361/6406/984.2/suppl/DC1 [7]: #xref-ref-1-1 "View reference 1 in text" [8]: #xref-ref-2-1 "View reference 2 in text" [9]: #xref-ref-3-1 "View reference 3 in text" [10]: http://fromtheprow.agu.org/agus-revised-ethics-policy-where-we-are-6-months-later/ [11]: #xref-ref-4-1 "View reference 4 in text" [12]: http://www.hhmi.org/sites/default/files/society_of_hhmi_professors_mission_and_rules_of_order.approved_2018.i2.pdf [13]: #xref-ref-5-1 "View reference 5 in text" [14]: {openurl}?query=rft.jtitle%253DScience%26rft.stitle%253DScience%26rft.aulast%253DWadman%26rft.auinit1%253DM.%26rft.volume%253D360%26rft.issue%253D6392%26rft.spage%253D949%26rft.epage%253D950%26rft.atitle%253DWill%2BU.S.%2Bacademies%2Bexpel%2Bsexual%2Bharassers%253F%26rft_id%253Dinfo%253Adoi%252F10.1126%252Fscience.360.6392.949%26rft_id%253Dinfo%253Apmid%252F29853665%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [15]: /lookup/ijlink/YTozOntzOjQ6InBhdGgiO3M6MTQ6Ii9sb29rdXAvaWpsaW5rIjtzOjU6InF1ZXJ5IjthOjQ6e3M6ODoibGlua1R5cGUiO3M6NDoiQUJTVCI7czoxMToiam91cm5hbENvZGUiO3M6Mzoic2NpIjtzOjU6InJlc2lkIjtzOjEyOiIzNjAvNjM5Mi85NDkiO3M6NDoiYXRvbSI7czoyNDoiL3NjaS8zNjEvNjQwNi85ODQuMi5hdG9tIjt9czo4OiJmcmFnbWVudCI7czowOiIiO30=

Published
2018

45. Heterochromatin Protein 1a (HP1a) Partner Specificity Is Determined by Critical Amino Acids in the Chromo Shadow Domain and C-terminal Extension

Author

Sarah C. R. Elgin, Rebecca E. K. Mandt, and Deanna L. Mendez

Subjects
Models, Molecular, endocrine system, Chromosomal Proteins, Non-Histone, Heterochromatin, Molecular Sequence Data, Peptide binding, Plasma protein binding, Biology, Biochemistry, Animals, Drosophila Proteins, Amino Acid Sequence, Amino Acids, Heterochromatin assembly, Molecular Biology, Chromo shadow domain, Peptide sequence, Sequence Homology, Amino Acid, urogenital system, Binding protein, Cell Biology, Cell biology, Drosophila melanogaster, Heterochromatin protein 1, Dimerization, Molecular Biophysics, Protein Binding
Abstract

Drosophila melanogaster Heterochromatin Protein 1a (HP1a) is an essential protein critical for heterochromatin assembly and regulation. Its chromo shadow domain (CSD) homodimerizes, a requirement for binding protein partners that contain a PXVXL motif. How does HP1a select among its many different PXVXL-containing partners? HP1a binds tightly to Heterochromatin Protein 2 (HP2), but weakly to PIWI. We investigated differences in homodimerization and the impact of the C-terminal extension (CTE) by contrasting HP1a to its paralogue, HP1b. HP1a and HP1b differ in the dimerization interface, with HP1a having an Arg at position 188 rather than Glu. We find that while this substitution reduces the dimerization constant, it does not impact the binding surface as demonstrated by unchanged partner binding affinities. However, the CTE (only 4 residues in HP1a as compared with 87 residues in HP1b) is critical; the charged residues in HP1a are necessary for tight peptide binding. Examining a panel of amino acid substitutions in the HP1a CSD, we find that Leu-165 in HP1a interacts with HP2 but not PIWI, supporting the conclusion that different sites in the binding surface provide discrimination for partner selection. Partner sequence is also critical for affinity, as the remaining difference in binding between HP2 and PIWI polypeptides is eliminated by swapping the PXVXL motifs between the two. Taken together, these studies indicate that the binding surface of the HP1a CSD plus its short CTE provide the needed discrimination among HP1a's partners, and that the CTE is important for differentiating the interactions of the Drosophila HP1 paralogs.

Published
2013

46. Targeting heterochromatin formation to transposable elements in Drosophila: Potential roles of the piRNA system

Author

Sarah C. R. Elgin, Sidney H. Wang, and Monica F. Sentmanat

Subjects
Genetics, Transposable element, Heterochromatin, fungi, Piwi-interacting RNA, General Medicine, Biology, biology.organism_classification, Biochemistry, Genome, Genomic Instability, Chromatin, Cell biology, DNA Transposable Elements, Animals, Drosophila, RNA Interference, Heterochromatin protein 1, RNA, Small Interfering, Heterochromatin assembly, Drosophila melanogaster
Abstract

Successful heterochromatin formation is critical for genome stability in eukaryotes, both to maintain structures needed for mitosis and meiosis and to silence potentially harmful transposable elements. Conversely, inappropriate heterochromatin assembly can lead to inappropriate silencing and other deleterious effects. Hence targeting heterochromatin assembly to appropriate regions of the genome is of utmost importance. Here we focus on heterochromatin assembly in Drosophila melanogaster, the model organism in which variegation, or cell-to-cell variable gene expression resulting from heterochromatin formation, was first described. In particular, we review the potential role of transposable elements as genetic determinants of the chromatin state and examine how small RNA pathways may participate in the process of targeted heterochromatin formation.

Published
2013

47. The GEP: Crowd-Sourcing Big Data Analysis with Undergraduates

Author

Adam Kleinschmit, Charles R. Hauser, Teresa M. Holzen, Sarah C. R. Elgin, Judith Leatherman, and Christopher J. Jones

Subjects
0301 basic medicine, business.industry, Science, 05 social sciences, Big data, Statistics as Topic, 050301 education, Computational Biology, Biology, Science education, Data science, 03 medical and health sciences, 030104 developmental biology, Undergraduate research, Crowd sourcing, General partnership, ComputingMilieux_COMPUTERSANDEDUCATION, Genetics, Crowdsourcing, Humans, business, 0503 education, Education, Medical, Undergraduate
Abstract

The era of ‘big data' is also the era of abundant data, creating new opportunities for student–scientist research partnerships. By coordinating undergraduate efforts, the Genomics Education Partnership produces high-quality annotated data sets and analyses that could not be generated otherwise, leading to scientific publications while providing many students with research experience.

Published
2016

49. Insights from a Convocation: Integrating Discovery-Based Research into the Undergraduate Curriculum

Author

Jay B. Labov, Mary A. Smith, Sean M. Decatur, Sarah C. R. Elgin, Elvyra F. San Juan, Erin L. Dolan, Kerry Brenner, Susan R. Wessler, Gabriela C. Weaver, Wendy C. Newstetter, Laura Guertin, and Gita Bangera

Subjects
Feature, 0301 basic medicine, Universities, Integrated curriculum, General Biochemistry, Genetics and Molecular Biology, Education, 03 medical and health sciences, Undergraduate curriculum, Pedagogy, ComputingMilieux_COMPUTERSANDEDUCATION, Humans, Sociology, Discovery learning, Student research, Students, Curriculum, Research, 05 social sciences, 050301 education, From the National Academies, Quality Education, 030104 developmental biology, Undergraduate research, Engineering ethics, 0503 education, Research education, Curriculum and Pedagogy
Abstract

The National Academies of Sciences, Engineering, and Medicine organized a convocation in 2015 to explore and elucidate opportunities, barriers, and realities of course-based undergraduate research experiences, known as CUREs, as a potentially integral component of undergraduate science, technology, engineering, and mathematics education. This paper summarizes the convocation and resulting report.

Published
2016

50. A Hands-on Introduction to Hidden Markov Models

Author

Wilson Leung, Zongtai Qi, Sarah C. R. Elgin, Christopher D. Shaffer, Elena O. Gracheva, Anton E. Weisstein, and Z. Goodwin

Subjects
business.industry, Computer science, General Medicine, Artificial intelligence, business, Hidden Markov model
Published
2016

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