Anne Baranger - Academia.edu (original) (raw)

Papers by Anne Baranger

Chemistry Education Research and Practice, Dec 31, 2023

Journal of Medicinal Chemistry, May 1, 2012

Stem-loop 3 RNA (SL3) in ψ-RNA is a highly conserved motif in different strains of HIV-1 and serv... more Stem-loop 3 RNA (SL3) in ψ-RNA is a highly conserved motif in different strains of HIV-1 and serves as a principle determinant for viral packaging. Viral encapsulation is critical for viral replication, and disruption of the nucleocapsid-ψ-RNA complex interferes with viral replication. We have used SL3 RNA as a target for identification of small molecule inhibitors of the interactions of nucleocapsid protein (NCp7) and ψ-RNA. We report the use of computational and high-throughput screening approaches to identify 16 compounds that bind SL3 RNA with micromolar affinities. Among the identified ligands, two molecules, compounds 7 and 17, bind with higher affinity to SL3 RNA than to double- and single-stranded RNAs. Four of the 16 SL3 RNA ligands inhibit interactions between SL3 RNA and NCp7 with micromolar inhibition constants. In general, the identified SL3 ligands have simple molecular structures and low molecular weights and are, therefore, possible lead compounds for the development of ligands that target the elements of ψ-RNA of HIV-1 with high affinity and specificity.

Springer eBooks, Oct 4, 2006

We review herein the relevant literature on molecular dynamics simulations of protein-nucleic aci... more We review herein the relevant literature on molecular dynamics simulations of protein-nucleic acid complexes and discuss how the procedure can be employed to gain insight into aspects of the molecular recognition mechanism such as induced fit and the role of solvent, which are not easily forthcoming in experimental studies. We present an overview of the free energy component analysis procedure

Journal of Chemical Education, Jun 2, 2022

A student-led mathematics bootcamp has been designed and implemented to help foster community bui... more A student-led mathematics bootcamp has been designed and implemented to help foster community building, improve confidence in mathematical skills, and provide mathematical resources for incoming physical chemistry doctoral students. The bootcamp is held immediately before the start of the first semester of graduate school and uses an active learning approach to review and practice undergraduate-level mathematics problems over five days in small student groups. This work includes the development and presentation of a new, publicly available mathematics curriculum for the bootcamp on select mathematics topics, including calculus, linear algebra, functions, differential equations, statistics and coding in Python, aiming at improving students' confidence and learning experiences in graduate quantum mechanics and statistical physics courses. Surveys before and after the bootcamp showed an increase in students' confidence in problem-solving in key mathematical areas and in social ...

Journal of Chemical Education

Participation in research experiences and internships may improve graduation rates and persistenc... more Participation in research experiences and internships may improve graduation rates and persistence in science, technology, engineering, and mathematics (STEM) among undergraduates, yet very little is known about the benefits of these activities for community college students. To fill this gap, we collected survey and interview data from 43 individuals who completed the Community College Internship (CCI) at Lawrence Berkeley National Laboratory (LBNL). These “CCI alumni” reported gains, including: connections with members of the LBNL community (95%); higher expectations of academic or career success (91%); development of critical skills (88%); and increased self-efficacy and/or confidence (84%), STEM identity (70%), and knowledge about STEM careers (65%). Of this group, 12% are graduate students, 84% have entered the STEM workforce, and 5% have entered the health workforce. We hope this work will encourage other scholars to contribute to what is known about the impact of internships ...

Chemistry Education Research and Practice

A central practice in the discipline of organic chemistry is the ability to solve certain fundame... more A central practice in the discipline of organic chemistry is the ability to solve certain fundamental problems, including predicting reactivity, proposing mechanisms, and designing syntheses. These problems are encountered frequently by both students and practitioners, who need to utilize vast amounts of content knowledge in specific ways to generate reasonable solutions. To gain insight into how one of these major problem types can be solved, we have investigated student approaches to complex predict-the-product problems through the detailed analysis of think-aloud interviews. This work led to the creation of a general workflow model that describes the reasoning pathways of students with varying levels of expertise when attempting to predict organic reactivity. The problems used in this study were designed to be non-trivial and potentially ambiguous to elicit “true” problem solving and discourage a purely memorization-based approach, even from more experienced organic chemists. Ric...

A group-based undergraduate research program (GURP) have been developed by the Alivisatos researc... more A group-based undergraduate research program (GURP) have been developed by the Alivisatos research group at the University of California, Berkeley. To assist other groups who may be interested in developing their own undergraduate research program, we have deposited some materials from our courses here, including raw datasets, lessons, and assignments.

Journal of Chemical Education, 2021

Increasing access to undergraduate research is critical in efforts to retain students pursuing ca... more Increasing access to undergraduate research is critical in efforts to retain students pursuing careers in STEM. Alternatives to traditional research positions, such as course based undergraduate research experiences (CUREs), have played important roles in engaging more undergraduates in research. However, these opportunities are only a subset of possible nontraditional research experiences which can enrich the undergraduate experience. In this study, we critically examined and improved the research-group-led undergraduate research program (GURP) to better meet the needs of undergraduates seeking research. Specifically, we investigated if the program was successful with a greater diversity of data sets, if assessments of learning were consistent across different data sets and teaching environments, and if the program promoted student engagement in research. We have found that this model is scalable, robust, and adaptable to different implementations while producing consistent and positive learning outcomes for students. Especially remarkable are students’ increased self-identification as scientists and statistically significant gains in self-perceived competency across multiple domains of knowledge. This program model has shown promising results as a partially and fully online research experience for undergraduates and has benefited program alumni in their research careers. To assist research groups starting similar programs, we have created public data sets and instructional resources. We believe that GURP programs can work in a variety of situations and hope that they can become a tool to increase interest and build communities for young researchers.

Chemistry Education Research and Practice, 2021

Understanding the impact of undergraduate research experiences (UREs) and course-based undergradu... more Understanding the impact of undergraduate research experiences (UREs) and course-based undergraduate research experiences (CUREs) is crucial as universities debate the value of allocating scarce resources to these activities. We report on the Berkeley Undergraduate Research Evaluation Tools (BURET), designed to assess the learning outcomes of UREs and CUREs in chemistry and other sciences. To validate the tools, we administered BURET to 70 undergraduate students in the College of Chemistry and 19 students from other STEM fields, comparing the performance of students who had less than one year of undergraduate research to those with more than one year of research experience. Students wrote reflections and responded to interviews during poster presentations of their research project. BURET asks students to communicate the significance of their project, analyze their experimental design, interpret their data, and propose future research. Scoring rubrics reward students for integrating ...

ACS Central Science, 2021

Historically, efforts to improve academic climate have been siloedmany efforts involve the colle... more Historically, efforts to improve academic climate have been siloedmany efforts involve the collection of data to understand issues affecting diversity at an institutional level, while others prioritize recruitment and retention of historically marginalized groups. Few initiatives, however, effectively combine the two in order to create concrete action plans to eliminate structural barriers that hinder the retention of minorities in STEM. In this Editorial, we present the history and details of a collaborative effort to improve the academic climate of the

ChemInform, Aug 12, 2010

Transfer of Oxygen and Sulfur from Organic Molecules to a Zr-Ir Bond. Evidence for an Unusually R... more Transfer of Oxygen and Sulfur from Organic Molecules to a Zr-Ir Bond. Evidence for an Unusually Rapid Atom Abstraction Reaction.-The heterobimetallic complex (I) undergoes oxygen and sulfur abstraction reactions with Me3P=S, S8, H2S and various thiiranes to form bridging sulfido complexes and with pyridine N-oxide, NO2 and styrene oxide to form bridging oxo compplexes.

Journal of the American Chemical Society, Feb 7, 2003

The RNA recognition motif (RRM), one of the most common RNA binding domains, contains three highl... more The RNA recognition motif (RRM), one of the most common RNA binding domains, contains three highly conserved aromatic amino acids that participate in stacking interactions with RNA bases. We have investigated the contribution of these highly conserved aromatic amino acids to the affinity of the complex formed between the N-terminal RRM of the U1A protein and stem loop 2 of U1 snRNA. Previously, we found that substitution of one of these conserved aromatic amino acids, Phe56, with Ala resulted in a large destabilization of the complex. Here, we have modified A6, the base in stem loop 2 RNA that stacks with Phe56, to compensate for a portion of the destabilization caused by the Phe56Ala mutation. We have designed two modified adenosines, A-3CPh and A-4CPh, in which a phenyl group is linked to the adenosine such that it may replace the phenyl group that is eliminated by the Phe56Ala mutation in the complex. We have found that incorporation of A-3CPh into stem loop 2 RNA stabilizes the complex formed with Phe56Ala by 0.6 kcal/mol, while incorporation of A-4CPh into stem loop 2 RNA stabilizes this complex by 1.8 kcal/mol. Either base modification destabilizes the wild-type complex by 0.8-0.9 kcal/mol. Experiments with other U1A mutant proteins suggest that the stabilization of the complex between the Phe56Ala U1A protein and stem loop 2 RNA is due to a specific interaction between the Phe56Ala U1A protein and A6-4CPh stem loop 2 RNA.

ChemInform, Aug 31, 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was e... more ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform, Aug 21, 2010

ChemInform Abstract The clusters (I) react with methyl fumarate (IIa) and methyl maleate (IIb) to... more ChemInform Abstract The clusters (I) react with methyl fumarate (IIa) and methyl maleate (IIb) to form the same products (III). These result from the diastereospecific insertion of the C=C double bond into the metal-hydrogen function with subsequent CO elimination and formation of metallacyclic five-membered ring as shown by crystal structure determinations of the RuCoW and OsCoW compounds (IIIb) (for both space group P21/c, Z=4). Deuteration experiments point to a rapid exchange between the cluster olefin insertion product and its free components. CO or PPh3 liberate methyl maleate from the adducts, hydrogenation with H2 cannot be achieved. Catalytic amounts of the RuCoMo or RuCoW cluster affect the conversion of various fumaric esters to the corresponding maleic esters with high turnover numbers. The course of the catalytic reaction can be completely derived from the stoichiometric reactions and their products.

Journal of Chemical Education, Jun 9, 2016

In this undergraduate analytical chemistry experiment, students quantitatively assess the antibac... more In this undergraduate analytical chemistry experiment, students quantitatively assess the antibacterial activity of essential oils found in thyme leaves (Thymus vulgaris) in an authentic, research-like environment. This multiweek experiment aims to instill green chemistry principles as intrinsic to chemical problem solving. Students progress through various techniques including extraction, chromatography (TLC and HPLC), culturing bacteria, and disk diffusion via a process of guided exploration that emphasizes green experimental design. Approximately 600 undergraduate students carried out the experiment and self-reported substantial learning gains.

Journal of Chemical Education, 2019

Over the past several decades, green chemistry has gained prominence in chemistry education. Howe... more Over the past several decades, green chemistry has gained prominence in chemistry education. However, the development of green chemistry curricula has not reached all levels of education equally, focusing mainly on elective and upper division courses. We deliberately focused our green chemistry curriculum redesign on a high enrollment introductory general chemistry laboratory course at the University of California, Berkeley. We developed over 30 new experiments that introduced students to green chemistry concepts and applications, while maintaining canonical general chemistry learning goals. The context of the curriculum and required course assignments encouraged students to use green chemistry principles to explore and solve real-world problems. After completing this redesigned course, we hypothesized that students would value green chemistry and feel more confident in their green chemistry knowledge. We developed new methods to measure students' attitudes toward and understanding of green chemistry as a system instead of isolated reactions or processes. These assessments allowed us to better understand both the progression and limitations in student green chemistry and systems-thinking. Since over 2000 students complete the laboratory course each year, we used a combination of fixed response items and free response items from online surveys and in-class assignments and exams. This approach allowed efficient assessment of thousands of students, while still gaining valuable and nuanced views of student understanding and attitudes. These assessments indicated that the new general chemistry laboratory curriculum succeeded in providing an environment in which students learned green chemistry concepts and realized that chemistry has connections to their future courses and professions.