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2.
mBio ; 5(1): e01051-13, 2014 Feb 04.
Artigo em Inglês | MEDLINE | ID: mdl-24496795

RESUMO

UNLABELLED: 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.


Assuntos
Bactérias/virologia , Bacteriófagos/genética , Genômica/educação , Microbiologia/educação , Adulto , Feminino , Humanos , Masculino , Estudantes , Adulto Jovem
3.
Biochem Mol Biol Educ ; 39(2): 102-9, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21445901

RESUMO

Biochemistry is a challenging subject because student learning depends on the application of previously learned concepts from general chemistry and biology to new, biological contexts. This article describes the development of a multiple-choice instrument intended to measure five concepts from general chemistry and three from biology that are considered prerequisite for biochemistry learning. This instrument is specifically designed with a factor structure that includes three multiple-choice items for each of the eight concepts and the most common incorrect ideas that students could have as distractors. It can be used as a pretest to identify students' incorrect ideas about those concepts and to determine if instruction helps students overcome those incorrect ideas when used as a posttest. Results from a confirmatory factor analysis support a very good fit for an eight-factor solution. This manuscript represents a report on the current state of instrument development. We seek to share our methods and instrument design principles with the broader community.


Assuntos
Bioquímica/educação , Biologia/educação , Química/educação , Avaliação Educacional/métodos , Humanos , Estudantes
4.
Methods Mol Biol ; 674: 161-77, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-20827591

RESUMO

Localizing the binding sites of regulatory proteins is becoming increasingly feasible and accurate. This is due to dramatic progress not only in chromatin immunoprecipitation combined by next-generation sequencing (ChIP-seq) but also in advanced statistical analyses. A fundamental issue, however, is the alarming number of false positive predictions. This problem can be remedied by improved peak calling methods of twin peaks, one at each strand of the DNA, kernel density estimators, and false discovery rate estimations based on control libraries. Predictions are filtered by de novo motif discovery in the peak environments. These methods have been implemented in, among others, Valouev et al.'s Quantitative Enrichment of Sequence Tags (QuEST) software tool. We demonstrate the prediction of the human growth-associated binding protein (GABPalpha) based on ChIP-seq observations.


Assuntos
Imunoprecipitação da Cromatina , Análise de Sequência de DNA , Fatores de Transcrição/metabolismo , Sítios de Ligação , Reações Falso-Positivas , Fator de Transcrição de Proteínas de Ligação GA/metabolismo , Humanos , Internet , Células Jurkat , Probabilidade , Sequências Reguladoras de Ácido Nucleico/genética , Reprodutibilidade dos Testes , Software
5.
Biochem Mol Biol Educ ; 37(1): 44-8, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21567687

RESUMO

This new biochemistry laboratory course moves through a progression of experiments that generates a platform for guided inquiry-based experiments. RNase One gene is isolated from prokaryotic genomic DNA, expressed as a tagged protein, affinity purified, and tested for activity and substrate specificity. Student pairs present detailed explanations of materials and methods and the semester culminates in a poster session. Experimental plans take into account the expense and time required to move from gene isolation to enzyme assays. This combination of instructor-guided and student-designed experiments is a manageable foray into guided inquiry-based learning in a biochemistry laboratory course, while providing a cohesive story and context for individual experiments.

6.
Genetics ; 179(1): 177-92, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-18493050

RESUMO

The availability of the complete DNA sequence of the Chlamydomonas reinhardtii genome and advanced computational biology tools has allowed elucidation and study of the small ubiquitin-like modifier (SUMO) system in this unicellular photosynthetic alga and model eukaryotic cell system. SUMO is a member of a ubiquitin-like protein superfamily that is covalently attached to target proteins as a post-translational modification to alter the localization, stability, and/or function of the target protein in response to changes in the cellular environment. Three SUMO homologs (CrSUMO96, CrSUMO97, and CrSUMO148) and three novel SUMO-related proteins (CrSUMO-like89A, CrSUMO-like89B, and CrSUMO-like90) were found by diverse gene predictions, hidden Markov models, and database search tools inferring from Homo sapiens, Saccharomyces cerevisiae, and Arabidopsis thaliana SUMOs. Among them, CrSUMO96, which can be recognized by the A. thaliana anti-SUMO1 antibody, was studied in detail. Free CrSUMO96 was purified by immunoprecipitation and identified by mass spectrometry analysis. A SUMO-conjugating enzyme (SCE) (E2, Ubc9) in C. reinhardtii was shown to be functional in an Escherichia coli-based in vivo chimeric SUMOylation system. Antibodies to CrSUMO96 recognized free and conjugated forms of CrSUMO96 in Western blot analysis of whole-cell extracts and nuclear localized SUMOylated proteins with in situ immunofluorescence. Western blot analysis showed a marked increase in SUMO conjugated proteins when the cells were subjected to environmental stresses, such as heat shock and osmotic stress. Related analyses revealed multiple potential ubiquitin genes along with two Rub1 genes and one Ufm1 gene in the C. reinhardtii genome.


Assuntos
Chlamydomonas reinhardtii/genética , Biologia Computacional/métodos , Proteínas Modificadoras Pequenas Relacionadas à Ubiquitina/genética , Sequência de Aminoácidos , Animais , Western Blotting , Primers do DNA/genética , Bases de Dados Genéticas , Imunofluorescência , Imunoprecipitação , Cadeias de Markov , Espectrometria de Massas , Modelos Genéticos , Dados de Sequência Molecular , Reação em Cadeia da Polimerase Via Transcriptase Reversa
7.
Biochem Mol Biol Educ ; 36(1): 61-4, 2008 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21591161

RESUMO

To promote understanding of the authority of the primary literature in students taking our biochemistry laboratory courses, a biochemistry laboratory exercise on the determination of an acceptable molar absorptivity value of 2-nitrophenol (2-NP) was developed. This made the laboratory course much more relevant by linking to a thematic thread, ß-galactosidase, that scaffolds concepts in one exercise with those in later exercises. The substrate for the continuous assay of ß-galactosidase is the chromogenic 2-nitrophenyl-ß-D-galactopyranoside that produces 2-NP. In an early laboratory exercise, students determine the wavelength of maximum absorption for the protonated and deprotonated form of 2-NP at various pH values and then determine the molar absorptivity of 2-NP. Students were encouraged to discuss apparent discrepancies not only in their own determinations of molar absorptivity values for 2-NP, but also in the published molar absorptivity values for 2-NP (2,150-21,300 M(-1) cm(-1) ) at almost the same pH and at 420 nm. Finally, the students were led to a publication that serves as an authentic source for molar absorptivity of 2-NP.

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