A visit to the present: potential benefits of inclusion of mindfulness in study abroad programs

In this Thursday Forum, we explore benefits of inclusion of mindfulness in the study abroad setting. We describe some of the theory behind contemplative pedagogy, and offer examples of how mindfulness strategies were employed successfully in two of CSBSJU\u27s recent study abroad programs

Use of Interactive Simulations in Fundamentals of Biochemistry, a LibreText Online Educational Resource, to Promote Understanding of Dynamic Reactions

Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent properties such as memory, consciousness, and recognition of self and non-self. To understand how these interconnected reactions lead to cellular life characterized by activation, inhibition, regulation, homeostasis, and adaptation, computational analyses and simulations are essential, a fact recognized by the biological communities. At the same time, students struggle to understand and apply binding and kinetic analyses for the simplest reactions such as the irreversible first-order conversion of a single reactant to a product. This likely results from cognitive difficulties in combining structural, chemical, mathematical, and textual descriptions of binding and catalytic reactions. To help students better understand dynamic reactions and their analyses, we have introduced two kinds of interactive graphs and simulations into the online educational resource, Fundamentals of Biochemistry, a multivolume biochemistry textbook that is part of the LibreText collection. One type is available for simple binding and kinetic reactions. The other displays progress curves (concentrations vs time) for both simple reactions and more complex metabolic and signal transduction pathways, including those available through databases using systems biology markup language (SBML) files. Users can move sliders to change dissociation and kinetic constants as well as initial concentrations and see instantaneous changes in the graphs. They can also export data into a spreadsheet for further processing, such as producing derivative Lineweaver-Burk and traditional Michaelis-Menten graphs of initial velocity (v0) vs substrate concentration.Comment: 17 pages, 2 tables, 8 figures. Submitted to Biochemistry and Molecular Biology Education. Funding: MiniSidewinder: NIH/NIGMS (Grant R01-GM123032-04) LibreText: Department of Education Open Textbook Pilot Project, the UC Davis Office of the Provost, the UC Davis Library, the California State University Affordable Learning Solutions Program, and Merlo

BioSimulators: a central registry of simulation engines and services for recommending specific tools

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations

Climate for change

The science is essentially settled. The actions we need to take are clear. Our climate is changing in ways that will impact all our lives. Human activity is causing this planetary crisis. Why can’t we act if we know what we should do? The barriers to change seem largely political and religious. This forum is a prelude to a seminar (October 16) on climate change and religion by Dr. Daniel DiLeo, Director of Justice and Peace Studies, Creighton University. His talk is sponsored by the Jay Phillips Center for Interfaith Learning. This talk, “Climate for Change”, is interactive and focuses on four topics: Climate Science (for lay people) - How did we get here and where we will end up if we stay the course? Climate Action - Why is it so hard? Tipping points - What might amplify our climate crisis? Addressing Climate Change: What can we do to minimize our climate crisis

Understanding Biochemical Dissociation Constants: A Temporal Perspective

Reversible, noncovalent binding is the first obligatory step in the expression of the function of most biological macromolecules. Both binding and release of ligand should be understood for a full view of the total binding process. Binding interactions can be studied at the structural, equilibrium–thermodynamic, or kinetic level. Most biochemists use dissociation constants, KD, to characterize the strength of the dynamic binding equilibrium. Unfortunately, the multiple-term unit for KD (mol/L) does not convey an intuitive understanding of the strength of the binding interaction, other than the notion that a small KD reflects tight binding. This manuscript describes the need for (from survey data) and use of another parameter, the half-life (t1/2) of the bound complex, as an alternative measure of binding strength. This changes the interpretation of the binding parameter to a more direct and simple interpretation of how long the complex stays intact (t1/2, with units of time) from the more indirect interpretation of the magnitude of KD (with units of mol/L). Deviations from this model arising from restricted accessibility of binding surfaces, facilitated diffusion from electrostatic interactions, and conformational changes are also discussed

Differentiating biochemistry course laboratories based on student experience

Content and emphases in undergraduate biochemistry courses can be readily tailored to accommodate the standards of the department in which they are housed, as well as the backgrounds of the students in the courses. A more challenging issue is how to construct laboratory experiences for a class with both chemistry majors, who usually have little or no experience with biochemical techniques and biology and biochemistry majors who do. This manuscript describes a strategy for differentiating biochemistry labs to meet the needs of students with differing backgrounds

A project-based biochemistry laboratory promoting the understanding and uses of fluorescence spectroscopy in the study of biomolecular structures and interactions

A laboratory project for a first semester biochemistry course is described, which integrates the traditional classroom study of the structure and function of biomolecules with the laboratory study of these molecules using fluorescence spectroscopy. Students are assigned a specific question addressing the stability/function of lipids, proteins, or nucleic acids, and asked to design an experiment to answer the question using fluorescence methodologies. Students study phase equilibria and determine the critical micelle concentration of single chain amphiphiles, the melting point of multilamellar vesicles, and the melting points and thermodynamic constants (K(eq), ΔG(0) , ΔH(0) and ΔS(0)) for denaturation of ds-DNA and proteins. In addition, they examine binding properties of proteins. These laboratory experiments are designed to support student learning of the major themes of structure and function in the course

The pre-health collection within MedEdPORTAL\u27s iCollaborative: helping faculty prepare students for the competencies in the new MCAT(2015) exam

To help faculty prepare and revise courses in all the disciplines represented in the MCAT(2015) , the American Association of Medical Colleges, through its MedEdPORTAL\u27s iCollaborative, has established the Pre-health Collection, a repository of reviewed web resources that are openly and freely available to faculty, and indirectly through them to students. The Pre-health Collection initiative makes use of the Internet to centralize teaching resources and to help faculty at institutions with fewer available resources to incorporate high quality teaching material specifically reviewed to assist students in obtaining the required pre-health competencies. As biochemistry competencies are increasingly represented in the new exam, it is important to grow the number of quality teaching resources for biochemistry within the portal and to develop a community of users and contributors. A description of the Pre-Health Collection and mechanisms for contributions are presented

The Teaching of Biochemistry: An Innovative Course Sequence Based on the Logic of Chemistry

An innovative course sequence for the teaching of biochemistry is offered, which more truly reflects the common philosophy found in biochemistry texts: that the foundation of biological phenomena can best be understood through the logic of chemistry. Topic order is chosen to develop an emerging understanding that is based on chemical principles. Preeminent biological questions serve as a framework for the course. Lipid and lipid-aggregate structures are introduced first, since it is more logical to discuss the intermolecular association of simple amphiphiles to form micelle and bilayer formations than to discuss the complexities of protein structure/folding. Protein, nucleic acid, and carbohydrate structures are studied next. Binding, a noncovalent process and the simplest expression of macromolecular function, follows. The physical (noncovalent) transport of solute molecules across a biological membrane is studied next, followed by the chemical transformation of substrates by enzymes. These are logical extensions of the expression of molecular function, first involving a simpler (physical transport) and second, a more complex (covalent transformation) process. The final sequence involves energy and signal transduction. This unique course sequence emerges naturally when chemical logic is used as an organizing paradigm for structuring a biochemistry course. Traditional order, which seems to reflect historic trends in research, or even an order derived from the central dogma of biology cannot provide this logical framework

The Study of Lipid Aggregates in Aqueous Solution: Formation and Properties of Liposomes with an Encapsulated Metallochromic Dye

An inexpensive microscale lab that can be used to study the formation, structure, and properties of liposomes