Michael W Klymkowsky

Michael W Klymkowsky
University of Colorado Boulder | CUB · Department of Molecular, Cellular, and Developmental Biology (MCDB)

Ph.D.

About

175
Publications
17,697
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
8,129
Citations
Additional affiliations
February 2013 - July 2013
ETH Zurich
Position
  • Professor
January 1983 - present
University of Colorado at Boulder
January 1982 - August 1983
The Rockefeller University
Position
  • PostDoc Position
Education
September 1974 - January 1980
California Institute of Technology
Field of study
  • Biophysics / Structural Biology
September 1971 - June 1974
Pennsylvania State University
Field of study
  • Biophysics

Publications

Publications (175)
Article
Evaluating learning outcomes depends upon objective and actionable measures of what students know – that is, what can they do with what they have learned. In the context of a developmental biology course, a capstone of many molecular biology degree programs, I asked students to predict the behaviors of temporal and spatial signaling gradients. Thei...
Chapter
The idea of a concept inventory or concept test, as opposed to a conventional test, emerged during a period when education researchers and educators began to focus on identifying students’ prior conceptions that can act as barriers to learning science. The typical concept test is multiple choice in format and focused on widely applicable concepts r...
Article
Full-text available
Cytoplasmic intermediate filaments (IFs) surround the nucleus and are often anchored at membrane sites to form effectively transcellular networks. Mutations in IF proteins (IFps) have revealed mechanical roles in epidermis, muscle, liver, and neurons. At the same time, there have been phenotypic surprises, illustrated by the ability to generate via...
Article
The fundamental structure of a typical mainstream two-semester organic chemistry course, populated mostly by life science majors and taught at universities throughout the United States, has changed little since the 1970s. However, much of the research on learning in organic chemistry has been devoted to characterizing student difficulties of variou...
Preprint
For ensuring students’ continuous achievement of academic excellence, higher education institutions commonly engage in periodic and critical revision of its academic programs. Depending on the goals and the resources of the institution, these revisions can focus only on an analysis of retention-graduation rates of different entry cohorts over the y...
Preprint
Full-text available
Human trisomy 21 (Down syndrome) is the most common genetic cause of intellectual disability, and is associated with complex perturbations in protein expression during development. Brain region-specific alterations in neuronal density and composition originate prenatally in trisomy 21 individuals, and are presumed to underlie the intellectual disab...
Article
To visualize the effects of experimental perturbations on normal cellular behavior, morphology, and intracellular organization, we use a simple whole-mount immunocytochemical method with Xenopus oocytes, explants, or embryos. This method is applicable to a wide range of systems, including human-induced pluripotent stem cell-derived organoids, and c...
Article
Full-text available
Accessory proteins in Frizzled (FZD) receptor com- plexes are thought to determine ligand selectivity and signaling amplitude. Genetic evidence indicates that specific combinations of accessory proteins and ligands mediate vascular b-catenin signaling in different CNS structures. In the retina, the tetraspa- nin TSPAN12 and the ligand norrin (NDP)...
Article
Full-text available
Cilia appear to be derived, evolutionarily, from structures present in the ancestral (pre-ciliary) eukaryote, such as microtubule-based vesicle trafficking and chromosome segregation systems. Experimental observations suggest that the ciliary gate, the molecular complex that mediates the selective molecular movement between cytoplasmic and ciliary...
Article
Full-text available
Concept inventories, constructed based on an analysis of students’ thinking and their explanations of scientific situations, serve as diagnostics for identifying misconceptions and logical inconsistencies and provide data that can help direct curricular reforms. In the current project, we distributed the Biological Concepts Instrument (BCI) to 17-1...
Data
Supplemental methods and results. Description of the Biological Concepts Instrument (BCI). German version of the BCI. EVAMAR. Students’ performance comparisons. Fig A.: Percent of correct answers. Results on all BCI questions. (PDF)
Data
The dataset contains all data of the present study. (PDF)
Article
Full-text available
Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students’ ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the e...
Article
Unless directly addressed, misconceptions can persist even in particularly capable students attending elite programs. To explore the presumptions that undergraduates of two distinguished Swiss universities have common biological misconceptions, we have used the Biological Concepts Instrument (BCI) in a pre-post-test approach [1]. We find that, afte...
Preprint
Full-text available
A number of research studies indicate that students often have difficulties in understanding the presence and/or the implications of stochastic processes within biological systems. While critical to a wide range of phenomena, the presence and implications of stochastic processes are rarely explicitly considered in the course of formal instruction....
Conference Paper
Full-text available
General Chemistry is a gateway course for many students intending on careers in scientific, engineering and health care related disciplines. While there have been many attempts to improve the outcomes for these students, little has changed over the past 60 years. Recent transformation efforts have focused primarily on incorporating student engageme...
Conference Paper
Full-text available
Key questions in the context of science education are i) what do students know at the start of a course or curriculum and ii) what have they learned and what can they do with that knowledge by the end. To understand what and how students are thinking, the classic Socratic model is to ask students questions and to consider and respond to their answe...
Article
EFHC1 encodes a ciliary protein that has been linked to Juvenile Myoclonic Epilepsy. In ectodermal explants, derived from Xenopus laevis embryos, the morpholino-mediated down-regulation of EFHC1b inhibited multiciliated cell formation. In those ciliated cells that did form, axoneme but not basal body formation was inhibited. EFHC1b morphant embryos...
Article
Full-text available
Lamprey is one of only two living jawless vertebrates, a group that includes the first vertebrates. Comparisons between lamprey and jawed vertebrates have yielded important insights into the origin and evolution of vertebrate physiology, morphology, and development. Despite its key phylogenetic position, studies of lamprey have been limited by thei...
Article
Intermolecular forces (IMFs), or more broadly, noncovalent interactions either within or between molecules, are central to an understanding of a wide range of chemical and biological phenomena. In this study, we present a multiyear, multi-institutional, longitudinal comparison of how students enrolled in traditional general chemistry courses and th...
Chapter
This paper describes how BeSocratic can be used to improve learning and class interaction. BeSocratic is a novel intelligent tutoring system that aims to fill the gap between simple multiple-choice systems and free-response systems. The system includes a set of interactive modules that provide instructors with powerful tools to assess student perfo...
Article
Full-text available
Centrins (Cetns) are highly conserved, widely expressed, and multifunctional Ca(2+)-binding eukaryotic signature proteins best known for their roles in ciliogenesis and as critical components of the global genome nucleotide excision repair system. Two distinct Cetn subtypes, Cetn2-like and Cetn3-like, have been recognized and implicated in a range...
Article
Wnt signaling and ciliogenesis are core features of embryonic development in a range of metazoans. Chibby (Cby), a basal-body associated protein, regulates β-catenin-mediated Wnt signaling in the mouse but not Drosophila. Here we present an analysis of Cby's embryonic expression and morphant phenotypes in Xenopus laevis. Cby RNA is supplied materna...
Chapter
The use of technology for teaching, learning and research has become almost ubiquitous in the chemistry classroom from student response systems, simulations and virtual environments, to online courses complete with assessments. The data generated by such activities can provide insight into how students learn and how we might provide environments th...
Chapter
“Energy” is a complex scientific concept central to all scientific disciplines. Here we describe three perspectives often used to address energy in the context of introductory college level courses: the macroscopic, which involves thermodynamic and mathematical treatments of energy and energy changes, the atomic-molecular, which relates to energy c...
Article
Full-text available
Concept Inventories are multiple choice instruments that map students' conceptual understanding in a given subject area. They underpin some of the most effective teaching methods in science education, but they are labour intensive and expensive to construct, which limits their wide use in instruction. We describe how we use Latent Semantic Analysis...
Conference Paper
The development of analytical skills is a central goal of the Next Generation Science Standards and foundational to subject mastery in STEM fields. Yet, significant barriers exist to students gaining such skills. Here we describe a new “gentle-slope” cyberlearning strategy that gradually introduces students to the authoring of scientific simulation...
Article
Full-text available
In response to increasing calls for the reform of the curriculum for life science majors and pre-medical students (Bio2010, Scientific Foundations for Future Physicians, Vision & Change), an interdisciplinary team has created NEXUS/Physics: a reinvention of an introductory physics curriculum for the life sciences. The curriculum interacts strongly...
Article
The history of general chemistry is one of almost constant calls for reform, yet over the past 60 years little of substance has changed. Those reforms that have been implemented are almost entirely concerned with how the course is taught, rather than what is to be learned. Here we briefly discuss the history of the general chemistry curriculum and...
Conference Paper
This paper describes a novel intelligent tutoring system called beSocratic, which targets question types that allow students to respond with free-form input but are able to be automatically evaluated and analyzed. Using beSocratic's GraphPad module, students are able to draw data structures using a mouse, touch, or a stylus. Once a student has comp...
Article
Full-text available
Helping students understand "chemical energy" is notoriously difficult. Many hold inconsistent ideas about what energy is, how and why it changes during the course of a chemical reaction, and how these changes are related to bond energies and reaction dynamics. There are (at least) three major sources for this problem: 1) the way biologists talk ab...
Conference Paper
Data structures are one of the fundamental concepts that all computer scientist students must learn if they are to succeed in their careers. Therefore, it is important to develop and assess questions targeted at improving the teaching of data structures. Unfortunately, research suggests that multiple choice or matching questions cannot be used to p...
Poster
Biology education has been moving away from learning large numbers of facts to the understanding of underlying concepts. Various reports describe important misconceptions of basic ideas in biology held by many students. Effective learning requires the identification and subsequent change of these misconceptions. To identify frequent misconceptions,...
Article
Despite deep evolutionary roots in the metazoa, the gene regulatory network driving germ layer specification is surprisingly labile both between and within phyla. In Xenopus laevis, SoxB1- and SoxF-type transcription factors are intimately involved in germ-layer specification, in part through their regulation of Nodal signaling. However, it is uncl...
Article
Previously, we found that: (i) many students were unable to construct representations of simple molecular structures; (ii) a majority of students fail to make the important connection between these representations and macroscopic properties of the material; and (iii) they were unable to decode the information contained in such representations. Assu...
Article
Full-text available
While evolutionary theory follows from observable facts and logical inferences (Mayr, 1985), historically, the origin of novel inheritable variations was a major obstacle to acceptance of natural selection (Bowler, 1992; Bowler, 2005). While molecular mechanisms address this issue (Jablonka and Lamb, 2005), analysis of responses to the Biological C...
Article
Today, most higher education institutions use broad learning management systems such as Blackboard, Moodle, or Instructure Canvas to aid in assessment. Additionally, specialized systems (such as Mastering software series, OWL, etc.) exist for individual disciples and courses. While these systems have shown improvements in student learning, the majo...
Article
Full-text available
Studies on the role of the E-box binding transcription factor Snail2 (Slug) in the induction of neural crest by mesoderm (Shi et al., 2011) revealed an unexpected increase in the level of sizzled RNA in the dorsolateral mesodermal zone (DMLZ) of morphant Xenopus embryos. sizzled encodes a secreted protein with both Wnt and BMP inhibitor activities....
Article
Biological systems, from the molecular to the ecological, involve dynamic interaction networks. To examine student thinking about networks we used graphical responses, since they are easier to evaluate for implied, but unarticulated assumptions. Senior college level molecular biology students were presented with simple molecular level scenarios; su...
Article
In many educational institutions today, online assessment systems are being used to evaluate student knowledge and understanding. Unfortunately, these systems often only allow teachers to ask questions in the form of multiple choice or free text responses. While these question types have value, they are either too limited to gain insight into stude...
Article
Full-text available
The neural crest is an induced tissue that is unique to vertebrates. In the clawed frog Xenopus laevis, neural crest induction depends on signals secreted from the prospective dorsolateral mesodermal zone during gastrulation. The transcription factors Snail2 (Slug), Snail1 and Twist1 are expressed in this region. It is known that Snail2 and Twist1...
Article
Full-text available
A key to effective teaching is an awareness and accurate understanding of the thinking and implicit assumptions that students bring to the subject to be learned. In the absence of extensive Socratic interactions with students, one strategy to assess student thinking involves the use of concept inventories (CIs). CIs are typically multiple-choice as...
Article
Full-text available
Not until the core concepts of biology are clearly defined and become the focus of instruction and assessment can we expect meaningful improvements in biological literacy and the removal of unnecessary barriers to student engagement.
Article
While it is clear that mitochondria play integral roles in cellular homeostasis, adaptation, cellular and survival, recent studies suggest possible roles for mitochondria as modulators of what were previously considered cytoplasmic/nuclear signaling systems. Embryonic patterning has been linked to asymmetries in mitochondria-based respiratory activ...
Article
Full-text available
Well-designed "controls" distinguish experimental from non-experimental studies. Surprisingly, we found that a high percentage of students had difficulty identifying control experiments even after completing three university-level laboratory courses. To address this issue, we designed and ran a revised cell biology lab course in which students part...
Article
A commonly accepted model of Wnt/β-catenin signaling involves target gene activation by a complex of β-catenin with a T-cell factor (TCF) family member. TCF3 is a transcriptional repressor that has been implicated in Wnt signaling and plays key roles in embryonic axis specification and stem cell differentiation. Here we demonstrate that Wnt protein...
Article
Full-text available
The neural crest is an evolutionary adaptation, with roots in the formation of mesoderm. Modification of neural crest behavior has been is critical for the evolutionary diversification of the vertebrates and defects in neural crest underlie a range of human birth defects. There has been a tremendous increase in our knowledge of the molecular, cellu...
Conference Paper
Much as been made of the approaching challenges and solutions to science, technology, engineering and mathematical (STEM) literacy for the next generation. To meet these challenges, we have to explicitly recognize and tackle a range of challenges that can obstruct the recruitment, training, support, and success (i.e. student learning) of STEM teach...
Article
Full-text available
Although P. Pevzner and R. Shamir, as well as the Bio2010 project, are right about the importance of computational, mathematical, and modeling skills for the next generation of biologists (“Computing has changed biology—biology education must catch up,” Education Forum, 31 July, p. [541][1]),
Article
A NF-kappaB-Twist-Snail network controls axis and mesoderm formation in Drosophila. Using translation-blocking morpholinos and hormone-regulated proteins, we demonstrate the presence of an analogous network in the early Xenopus embryo. Loss of twist (twist1) function leads to a reduction of mesoderm and neural crest markers, an increase in apoptosi...
Article
Epithelial-mesenchymal transition (EMT) describes a series of rapid changes in cellular phenotype. During EMT, epithelial cells down-modulate cell-cell adhesion structures, alter their polarity, reorganize their cytoskeleton, and become isolated, motile, and resistant to anoikis. The term EMT is often applied to distinct biological events as if it...
Article
While researching the Biology Concept Inventory (BCI) we found that a wide class of student difficulties in genetics and molecular biology can be traced to deep-seated misconceptions about random processes and molecular interactions. Students believe that random processes are inefficient, while biological systems are very efficient, and are therefo...
Article
Full-text available
While researching student assumptions for the development of the Biology Concept Inventory (BCI; http://bioliteracy.net), we found that a wide class of student difficulties in molecular and evolutionary biology appears to be based on deep-seated, and often unaddressed, misconceptions about random processes. Data were based on more than 500 open-end...
Article
Genes of the Eya family and of the Six1/2 subfamily are expressed throughout development of vertebrate cranial placodes and are required for their differentiation into ganglia and sense organs. How they regulate placodal neurogenesis, however, remains unclear. Through loss of function studies in Xenopus we show that Eya1 and Six1 are required for n...
Article
Rohon-Beard mechanosensory neurons (RBs), neural crest cells, and neurogenic placodes arise at the border of the neural- and non-neural ectoderm during anamniote vertebrate development. Neural crest cells require BMP expressing non-neural ectoderm for their induction. To determine if epidermal ectoderm-derived BMP signaling is also involved in the...
Article
Full-text available
Recognizing student misconceptions is critical for effective teaching. Tools that reveal student thinking indicate that misunderstanding randomness interferes with learning of molecular dynamics and evolutionary processes.
Article
Asymmetries in the egg, established during oogenesis, set the stage for a cascade of intercellular signaling events leading to differential gene expression and subsequent tissue and organ formation. Maternally supplied Sox-type transcription factors have recently emerged as key components in the patterning of the early embryo and the regulation of...
Chapter
Wnt signaling lies at the heart of metazoan development. The Wnt pathway bifurcates a number of times and regulates cell polarity, migration, adhesion and gene expression. I review the complexity of this network with a focus on the role of SOX proteins in its regulation.
Article
Full-text available
The meeting "Conceptual Assessment in the Biological Sciences" was held March 3-4, 2007, in Boulder, Colorado. Sponsored by the National Science Foundation and hosted by University of Colorado, Boulder's Biology Concept Inventory Team, the meeting drew together 21 participants from 13 institutions, all of whom had received National Science Foundati...
Article
Note from the Editor Textbooks are ubiquitous. They are available for almost every conceivable subdiscipline of biology, and few of us would consider teaching a course without using a textbook. Over the years, they have become more colorful, more encyclopedic, and accompanied by more ancillary materials such as CD-ROMs, study guides, and websites....
Article
Full-text available
There is widespread concern about the level of scientific literacy in the U. S. An important, although often overlooked, point, is that student learning is generally only a good as the assessments used to measure it. Unfortunately, most assessments measure recall and recognition rather than conceptual understanding, and as a result over-estimate le...