Publications by authors named "Srebrenka Robic"

14 Publications

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

J Microbiol Biol Educ 2020 28;21(1). Epub 2020 Feb 28.

Biology, University of San Diego, San Diego, CA 92110, USA.

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.
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http://dx.doi.org/10.1128/jmbe.v21i1.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048401PMC
February 2020

Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction.

PLoS One 2019 18;14(11):e0224288. Epub 2019 Nov 18.

School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, United States of America.

Bioinformatics, a discipline that combines aspects of biology, statistics, mathematics, and computer science, is becoming increasingly important for biological research. However, bioinformatics instruction is not yet generally integrated into undergraduate life sciences curricula. To understand why we studied how bioinformatics is being included in biology education in the US by conducting a nationwide survey of faculty at two- and four-year institutions. The survey asked several open-ended questions that probed barriers to integration, the answers to which were analyzed using a mixed-methods approach. The barrier most frequently reported by the 1,260 respondents was lack of faculty expertise/training, but other deterrents-lack of student interest, overly-full curricula, and lack of student preparation-were also common. Interestingly, the barriers faculty face depended strongly on whether they are members of an underrepresented group and on the Carnegie Classification of their home institution. We were surprised to discover that the cohort of faculty who were awarded their terminal degree most recently reported the most preparation in bioinformatics but teach it at the lowest rate.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224288PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6860448PMC
April 2020

Bioinformatics core competencies for undergraduate life sciences education.

PLoS One 2018 5;13(6):e0196878. Epub 2018 Jun 5.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196878PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988330PMC
November 2018

Retrotransposons Are the Major Contributors to the Expansion of the Muller F Element.

G3 (Bethesda) 2017 08 7;7(8):2439-2460. Epub 2017 Aug 7.

Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405.

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 , but it is substantially larger (>18.7 Mb) in 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 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 sequences integrated into the genome are minor contributors (0.02%). Both and F-element genes exhibit distinct characteristics compared to D-element genes (, larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in Compared to , the codon bias observed in 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, 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.
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http://dx.doi.org/10.1534/g3.117.040907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555453PMC
August 2017

Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.

G3 (Bethesda) 2015 Mar 4;5(5):719-40. Epub 2015 Mar 4.

Department of Biology, Albion College, Albion, MI 49224.

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.
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http://dx.doi.org/10.1534/g3.114.015966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426361PMC
March 2015

A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics.

CBE Life Sci Educ 2014 ;13(4):711-23

Department of Biological Sciences, George Washington University, Washington, DC 20052.

In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates.
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http://dx.doi.org/10.1187/cbe.13-10-0200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255357PMC
August 2015

Transformable facultative thermophile Geobacillus stearothermophilus NUB3621 as a host strain for metabolic engineering.

Appl Microbiol Biotechnol 2014 Aug 2;98(15):6715-23. Epub 2014 May 2.

Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, room 4119, Atlanta, GA, 30322, USA.

Metabolic engineers develop inexpensive enantioselective syntheses of high-value compounds, but their designs are sometimes confounded by the misfolding of heterologously expressed proteins. Geobacillus stearothermophilus NUB3621 is a readily transformable facultative thermophile. It could be used to express and properly fold proteins derived from its many mesophilic or thermophilic Bacillaceae relatives or to direct the evolution of thermophilic variants of mesophilic proteins. Moreover, its capacity for high-temperature growth should accelerate chemical transformation rates in accordance with the Arrhenius equation and reduce the risks of microbial contamination. Its tendency to sporulate in response to nutrient depletion lowers the costs of storage and transportation. Here, we present a draft genome sequence of G. stearothermophilus NUB3621 and describe inducible and constitutive expression plasmids that function in this organism. These tools will help us and others to exploit the natural advantages of this system for metabolic engineering applications.
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http://dx.doi.org/10.1007/s00253-014-5746-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4251812PMC
August 2014

A course-based research experience: how benefits change with increased investment in instructional time.

CBE Life Sci Educ 2014 ;13(1):111-30

Department of Biology, Washington University in St. Louis, St. Louis, MO 63130 Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130 Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909 Chemistry Department, Lindenwood University, St. Charles, MO 63301 Science Department, Cabrini College, Radnor, PA 19087 Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93405 Department of Biology, Linfield College, McMinnville, OR 97128 Department of Biology, Georgetown University, Washington, DC 20057 Biology Department, Hampden-Sydney College, Hampden-Sydney, VA 23943 Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588 Biology Department, Worcester State University, Worcester, MA 01602 Department of Biological Sciences, St. John's University, Queens, NY 11439 Department of Biology, Adams State University, Alamosa, CO 81101 Department of Computer Science & Engineering, Johnson C. Smith University, Charlotte, NC 28216 Department of Biology, Saint Joseph's University, Philadelphia, PA 19131 Departments of Biomedical Sciences & Cell and Molecular Biology, Grand Valley State, Allendale, MI 49401 Department of Biology, Saint Mary's College of California, Moraga, CA 94556 Department of Biology, University of West Florida, Pensacola, FL 32514 Technology Leadership & Innovation Department, Purdue University, West Lafayette, IN 47907 Department of Biology, Calvin College, Grand Rapids, MI 49546 Department of Biology, Hofstra University, Hempstead, NY 11549 Department of Biology & Molecular Biology, Montclair State University, Montclair, NJ 07043 Department of Biology, Missouri Western State University, St. Joseph, MO 64507 Department of Biology, University of the Cumberlands, Williamsburg, KY 40769 Department of Biology, Amherst College, Amherst, MA 01002 Department of Biological Sciences, Mount Holyoke, South Hadley, MA

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.
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http://dx.doi.org/10.1187/cbe-13-08-0152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940452PMC
October 2014

Bile acids as modulators of enzyme activity and stability.

Protein J 2011 Dec;30(8):539-45

Agnes Scott College, Decatur, GA, USA.

Bile acids deactivate certain enzymes, such as prolyl endopeptidases (PEPs), which are investigated as candidates for protease-based therapy for celiac sprue. Deactivation by bile acids presents a problem for therapeutic enzymes targetted to function in the upper intestine. However, enzyme deactivation by bile acids is not a general phenomenon. Trypsin and chymotrypsin are not deactivated by bile acids. In fact, these pancreatic enzymes are more efficient at cleaving large dietary substrates in the presence of bile acids. We targeted the origin of the apparently different effect of bile acids on prolyl endopeptidases and pancreatic enzymes by examining the effect of bile acids on the kinetics of cleavage of small substrates, and by determining the effect of bile acids on the thermodynamic stabilities of these enzymes. Physiological amounts (5 mM) of cholic acid decrease the thermodynamic stability of Flavobacterium meningosepticum PEP from 18.5 ± 2 kcal/mol to 10.5 ± 1 kcal/mol, while thermostability of trypsin and chymotrypsin is unchanged. Trypsin and chymotrypsin activation by bile and PEP deactivation can both be explained in terms of a common mechanism: bile acid-mediated protein destabilization. Bile acids, usually considered non-denaturing surfactants, in this case act as a destabilizing agent on PEP thus deactivating the enzyme. However, this level of global thermodynamic destabilization does not account for a more than 50% decrease in enzyme activity, suggesting that bile acids most likely modulate enzyme activity through specific local interactions.
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http://dx.doi.org/10.1007/s10930-011-9360-yDOI Listing
December 2011

Mathematics, thermodynamics, and modeling to address ten common misconceptions about protein structure, folding, and stability.

Authors:
Srebrenka Robic

CBE Life Sci Educ 2010 ;9(3):189-95

Agnes Scott College, Decatur, GA 30030, USA.

To fully understand the roles proteins play in cellular processes, students need to grasp complex ideas about protein structure, folding, and stability. Our current understanding of these topics is based on mathematical models and experimental data. However, protein structure, folding, and stability are often introduced as descriptive, qualitative phenomena in undergraduate classes. In the process of learning about these topics, students often form incorrect ideas. For example, by learning about protein folding in the context of protein synthesis, students may come to an incorrect conclusion that once synthesized on the ribosome, a protein spends its entire cellular life time in its fully folded native confirmation. This is clearly not true; proteins are dynamic structures that undergo both local fluctuations and global unfolding events. To prevent and address such misconceptions, basic concepts of protein science can be introduced in the context of simple mathematical models and hands-on explorations of publicly available data sets. Ten common misconceptions about proteins are presented, along with suggestions for using equations, models, sequence, structure, and thermodynamic data to help students gain a deeper understanding of basic concepts relating to protein structure, folding, and stability.
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http://dx.doi.org/10.1187/cbe.10-03-0018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2931665PMC
December 2010

Laboratory exploration of survival of probiotic cultures inside the human digestive tract using in vitro models.

Authors:
Srebrenka Robic

J Microbiol Biol Educ 2010 20;11(1):50-5. Epub 2010 May 20.

Department of Biology, Agnes Scott College, Decatur, GA 30030.

Scientists often model complex biological phenomena in vitro, mimicking conditions found in living organisms. Understanding the power and limitations of biological models is an important topic in undergraduate science. In this activity, students develop their own in vitro model for testing the survival of bacteria from commercial probiotic supplements. Students work in groups to decide which factors are important for survival of bacteria in a chosen portion of the human digestive tract. Groups of students create their own in vitro models of organs such as stomach and/or intestines. Students expose a probiotic supplement to conditions mimicking the chosen portion of the human digestive tract, and measure the effect of those conditions on the survival of bacteria found in the supplement. Students choose to focus on conditions such as low pH found in stomach or pancreatic enzymes found in the upper intestine. Through this activity, students gain experience with serial dilutions and calculations of colony forming units (CFUs). This project also provides the students with the valuable experience of designing experiments in small groups. Students present their findings in a poster session, which provides a venue for discussing the validity and limitation of various models.
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http://dx.doi.org/10.1128/jmbe.v11.i1.139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577240PMC
May 2013

Role of residual structure in the unfolded state of a thermophilic protein.

Proc Natl Acad Sci U S A 2003 Sep 22;100(20):11345-9. Epub 2003 Sep 22.

Department of Molecular and Cell Biology, QB3 Institute, 215 Hildebrand Hall mc 3206, University of California, Berkeley, CA 94720-3206, USA.

Ribonucleases H from the thermophilic bacterium Thermus thermophilus and the mesophile Escherichia coli demonstrate a dramatic and surprising difference in their change in heat capacity upon unfolding (DeltaCp degrees ). The lower DeltaCp degrees of the thermophilic protein directly contributes to its higher thermal denaturation temperature (Tm). We propose that this DeltaCp degrees difference originates from residual structure in the unfolded state of the thermophilic protein; we verify this hypothesis by using a mutagenic approach. Residual structure in the unfolded state may provide a mechanism for balancing a high Tm with the optimal thermodynamic stability for a protein's function. Structure in the unfolded state is shown to differentially affect the thermodynamic profiles of thermophilic and mesophilic proteins.
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http://dx.doi.org/10.1073/pnas.1635051100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC208759PMC
September 2003

Energetic evidence for formation of a pH-dependent hydrophobic cluster in the denatured state of Thermus thermophilus ribonuclease H.

J Mol Biol 2003 Jun;329(4):731-43

Facultad de Ciencias, Departamento de Quimica Fisica, Universidad de Granada, 18071, Granada, Spain.

NMR studies on the denatured states of proteins indicate that residual structure often resides predominantly in hydrophobic clusters. Such hydrophobic cluster formation implies burial of apolar surface and, consequently, is expected to cause a decrease in heat capacity. We report here that, in the case of ribonuclease H from the thermophile Thermus thermophilus, a sharp decrease in denatured-state heat capacity occurs at about pH 3.8; this result points to the formation of hydrophobic clusters triggered by the protonation of several (about four) carboxylic acid groups, and indicates that the burial of apolar surface is favored by the less hydrophilic character of the uncharged forms of Asp and Glu side-chains. The process is not accompanied by large changes in optically active structure, but appears to be highly cooperative, as indicated by the sharpness of the pH-induced transition in the heat capacity. This acid-induced hydrophobic burial in denatured T.thermophilus ribonuclease H is clearly reflected in the pH dependence of the denaturation temperature (i.e. an abrupt change of slope at about pH 3.8 is seen in the plot of denaturation temperature versus pH), supporting a role for such denatured-state hydrophobic clusters in protein stability. The finding of cooperative protonation of several groups coupled to surface burial in denatured T.thermophilus ribonuclease H emphasizes the potential complexity of denatured-state electrostatics and advises caution when attempting to predict denatured-state properties on the basis of simple electrostatic models. Finally, our results suggest a higher propensity for hydrophobic cluster formation in the denatured state of T.thermophilus ribonuclease H as compared with that of its mesophilic counterpart from Escherichia coli.
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http://dx.doi.org/10.1016/s0022-2836(03)00513-8DOI Listing
June 2003

Contributions of folding cores to the thermostabilities of two ribonucleases H.

Protein Sci 2002 Feb;11(2):381-9

Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

To investigate the contribution of the folding cores to the thermodynamic stability of RNases H, we used rational design to create two chimeras composed of parts of a thermophilic and a mesophilic RNase H. Each chimera combines the folding core from one parent protein and the remaining parts of the other. Both chimeras form active, well-folded RNases H. Stability curves, based on CD-monitored chemical denaturations, show that the chimera with the thermophilic core is more stable, has a higher midpoint of thermal denaturation, and a lower change in heat capacity (DeltaCp) upon unfolding than the chimera with the mesophilic core. A possible explanation for the low DeltaCp of both the parent thermophilic RNase H and the chimera with the thermophilic core is the residual structure in the denatured state. On the basis of the studied parameters, the chimera with the thermophilic core resembles a true thermophilic protein. Our results suggest that the folding core plays an essential role in conferring thermodynamic parameters to RNases H.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373436PMC
http://dx.doi.org/10.1110/ps.38602DOI Listing
February 2002
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