An Initiative to Broaden Diversity in Undergraduate Biomathematics Training

At North Carolina A&T State University (NCATSU), there was a critical need to better coordinate genuine research and classroom experiences for undergraduates early in their academic career. We describe the development and implementation of a faculty alliance across academic departments to increase biomathematics research opportunities for underrepresented minorities. Our faculty alliance is called the Integrative Biomathematical Learning and Empowerment Network for Diversity (iBLEND). The fundamental purpose of the iBLEND alliance was to inspire underrepresented minorities to pursue research careers by increasing the visibility of research conducted at the interface of mathematics and biology at NCATSU. Because of the many positive impacts, iBLEND gained significant buy-in from administration, faculty, and students by 1) working from the ground up with administration to promote campus-wide biomathematics research and training, 2) fostering associations between research and regular undergraduate academic courses, 3) creating and disseminating biomathematics teaching and learning modules, and 4) enhancing learning community support at the interface of mathematics and biology. Currently, iBLEND is viewed as a productive site for graduate schools to recruit underrepresented minority students having specific competencies related to mathematical biology

Online Interactive Teaching Modules Enhance Quantitative Proficiency of Introductory Biology Students

There is widespread agreement within the scientific and education communities that undergraduate biology curricula fall short in providing students with the quantitative and interdisciplinary problem-solving skills they need to obtain a deep understanding of biological phenomena and be prepared fully to contribute to future scientific inquiry. MathBench Biology Modules were designed to address these needs through a series of interactive, Web-based modules that can be used to supplement existing course content across the biological sciences curriculum. The effect of the modules was assessed in an introductory biology course at the University of Maryland. Over the course of the semester, students showed significant increases in quantitative skills that were independent of previous math course work. Students also showed increased comfort with solving quantitative problems, whether or not they ultimately arrived at the correct answer. A survey of spring 2009 graduates indicated that those who had experienced MathBench in their course work had a greater appreciation for the role of mathematics in modern biology than those who had not used MathBench. MathBench modules allow students from diverse educational backgrounds to hone their quantitative skills, preparing them for more complex mathematical approaches in upper-division courses

Mathematical Manipulative Models: In Defense of Beanbag Biology

Mathematical manipulative models have had a long history of influence in biological research and in secondary school education, but they are frequently neglected in undergraduate biology education. By linking mathematical manipulative models in a four-step process-1) use of physical manipulatives, 2) interactive exploration of computer simulations, 3) derivation of mathematical relationships from core principles, and 4) analysis of real data sets-we demonstrate a process that we have shared in biological faculty development workshops led by staff from the BioQUEST Curriculum Consortium over the past 24 yr. We built this approach based upon a broad survey of literature in mathematical educational research that has convincingly demonstrated the utility of multiple models that involve physical, kinesthetic learning to actual data and interactive simulations. Two projects that use this approach are introduced: The Biological Excel Simulations and Tools in Exploratory, Experiential Mathematics (ESTEEM) Project (http://bioquest.org/esteem) and Numerical Undergraduate Mathematical Biology Education (NUMB3R5 COUNT; http://bioquest.org/numberscount). Examples here emphasize genetics, ecology, population biology, photosynthesis, cancer, and epidemiology. Mathematical manipulative models help learners break through prior fears to develop an appreciation for how mathematical reasoning informs problem solving, inference, and precise communication in biology and enhance the diversity of quantitative biology education

Effects of common haplotypes of the ileal sodium dependent bile acid transporter gene on the development of sporadic and familial colorectal cancer: A case control study

<p>Abstract</p> <p>Background</p> <p>The genetics of sporadic and non-syndromic familial colorectal cancer (CRC) is not well defined. However, genetic factors that promote the development of precursor lesions, i.e. adenomas, might also predispose to CRC. Recently, an association of colorectal adenoma with two variants (c.507C>T;p.L169L and c.511G>T;p.A171S) of the ileal sodium dependent bile acid transporter gene (<it>SLC10A2</it>) has been reported. Here, we reconstructed haplotypes of the <it>SLC10A2 </it>gene locus and tested for association with non-syndromic familial and sporadic CRC compared to 'hyper-normal' controls who displayed no colorectal polyps on screening colonoscopy.</p> <p>Methods</p> <p>We included 150 patients with sporadic CRC, 93 patients with familial CRC but exclusion of familial adenomatous polyposis and Lynch's syndrome, and 204 'hyper-normal' controls. Haplotype-tagging <it>SLC10A2 </it>gene variants were identified in the Hapmap database and genotyped using PCR-based 5' exonuclease assays with fluorescent dye-labelled probes. Haplotypes were reconstructed using the PHASE algorithm. Association testing was performed with both SNPs and reconstructed haplotypes.</p> <p>Results</p> <p>Minor allele frequencies of all <it>SLC10A2 </it>polymorphisms are within previously reported ranges, and no deviations from Hardy-Weinberg equilibrium are observed. However, we found no association with any of the <it>SLC10A2 </it>haplotypes with sporadic or familial CRC in our samples (all P values > 0.05).</p> <p>Conclusion</p> <p>Common variants of the <it>SLC10A2 </it>gene are not associated with sporadic or familial CRC. Hence, albeit this gene might be associated with early stages of colorectal neoplasia, it appears not to represent a major risk factor for progression to CRC.</p

A model-independent approach to infer hierarchical codon substitution dynamics

<p>Abstract</p> <p>Background</p> <p>Codon substitution constitutes a fundamental process in molecular biology that has been studied extensively. However, prior studies rely on various assumptions, e.g. regarding the relevance of specific biochemical properties, or on conservation criteria for defining substitution groups. Ideally, one would instead like to analyze the substitution process in terms of raw dynamics, independently of underlying system specifics. In this paper we propose a method for doing this by identifying groups of codons and amino acids such that these groups imply closed dynamics. The approach relies on recently developed spectral and agglomerative techniques for identifying hierarchical organization in dynamical systems.</p> <p>Results</p> <p>We have applied the techniques on an empirically derived Markov model of the codon substitution process that is provided in the literature. Without system specific knowledge of the substitution process, the techniques manage to "blindly" identify multiple levels of dynamics; from amino acid substitutions (via the standard genetic code) to higher order dynamics on the level of amino acid groups. We hypothesize that the acquired groups reflect earlier versions of the genetic code.</p> <p>Conclusions</p> <p>The results demonstrate the applicability of the techniques. Due to their generality, we believe that they can be used to coarse grain and identify hierarchical organization in a broad range of other biological systems and processes, such as protein interaction networks, genetic regulatory networks and food webs.</p

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

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