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  1. Article: Rethinking (again) Hardy-Weinberg and genetic drift in undergraduate biology.

    Klymkowsky, Michael W

    Frontiers in genetics

    2023  Volume 14, Page(s) 1199739

    Abstract: Designing effective curricula is challenging. Content decisions can impact both learning outcomes and student engagement. As an example consider the place of Hardy-Weinberg equilibria (HWE) and genetic drift calculations in introductory biology courses, ... ...

    Abstract Designing effective curricula is challenging. Content decisions can impact both learning outcomes and student engagement. As an example consider the place of Hardy-Weinberg equilibria (HWE) and genetic drift calculations in introductory biology courses, as discussed by Masel (2012). Given that population genetics, "a fairly arcane speciality", can be difficult to grasp, there is little justification for introducing introductory students to HWE calculations. It is more useful to introduce them to the behavior of alleles in terms of basic features of biological systems, and that in the absence of selection recessive alleles are no "weaker" or preferentially lost from a population than are dominant alleles. On the other hand, stochastic behaviors, such as genetic drift, are ubiquitous in biological systems and often play functionally significant roles; they can be introduced to introductory students in mechanistic and probabilistic terms. Specifically, genetic drift emerges from the stochastic processes involved in meiotic chromosome segregation and recombination. A focus on stochastic processes may help counteract naive bio-deterministic thinking and can reinforce, for students, the value of thinking quantitatively about biological processes.
    Language English
    Publishing date 2023-06-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1199739
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  2. Book ; Online: Making sense of noise

    Klymkowsky, Michael W.

    introducing students to stochastic processes in order to better understand biological behaviors

    2023  

    Abstract: Biological systems are characterized by the ubiquitous roles of weak, that is, non-covalent molecular interactions, small, often very small, numbers of specific molecules per cell, and Brownian motion. These combine to produce stochastic behaviors at all ...

    Abstract Biological systems are characterized by the ubiquitous roles of weak, that is, non-covalent molecular interactions, small, often very small, numbers of specific molecules per cell, and Brownian motion. These combine to produce stochastic behaviors at all levels from the molecular and cellular to the behavioral. That said, students are rarely introduced to the ubiquitous role of stochastic processes in biological systems, and how they produce unpredictable behaviors. Here I present the case that they need to be and provide some suggestions as to how it might be approached.

    Comment: 10 pages, 7 embedded figures, 3 text boxes
    Keywords Quantitative Biology - Cell Behavior ; Quantitative Biology - Molecular Networks
    Publishing date 2023-01-11
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Making mechanistic sense: are we teaching students what they need to know?

    Klymkowsky, Michael W

    Developmental biology

    2021  Volume 476, Page(s) 308–313

    Abstract: 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 ... ...

    Abstract 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. Their responses led me to consider an alternative to conventional assessments, namely a process in which students are asked to build and apply plausible explanatory mechanistic models ("PEMMs"). A salient point is not whether students' models are correct, but whether they "work" in a manner consistent with underlying scientific principles. Analyzing such models can reveal the extent to which students recognize and accurately apply relevant ideas. An emphasis on model building, analysis and revision, an authentic scientific practice, can be expected to have transformative effects on course and curricular design as well as on student engagement and learning outcomes.
    MeSH term(s) Academic Success ; Education/methods ; Education/trends ; Humans ; Learning ; Models, Theoretical ; Students/psychology
    Language English
    Publishing date 2021-04-27
    Publishing country United States
    Document type Letter ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1114-9
    ISSN 1095-564X ; 0012-1606
    ISSN (online) 1095-564X
    ISSN 0012-1606
    DOI 10.1016/j.ydbio.2021.04.004
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  4. Article ; Online: Rethinking (again) Hardy-Weinberg and genetic drift in undergraduate biology

    Michael W. Klymkowsky

    Frontiers in Genetics, Vol

    2023  Volume 14

    Abstract: Designing effective curricula is challenging. Content decisions can impact both learning outcomes and student engagement. As an example consider the place of Hardy-Weinberg equilibria (HWE) and genetic drift calculations in introductory biology courses, ... ...

    Abstract Designing effective curricula is challenging. Content decisions can impact both learning outcomes and student engagement. As an example consider the place of Hardy-Weinberg equilibria (HWE) and genetic drift calculations in introductory biology courses, as discussed by Masel (2012). Given that population genetics, “a fairly arcane speciality”, can be difficult to grasp, there is little justification for introducing introductory students to HWE calculations. It is more useful to introduce them to the behavior of alleles in terms of basic features of biological systems, and that in the absence of selection recessive alleles are no “weaker” or preferentially lost from a population than are dominant alleles. On the other hand, stochastic behaviors, such as genetic drift, are ubiquitous in biological systems and often play functionally significant roles; they can be introduced to introductory students in mechanistic and probabilistic terms. Specifically, genetic drift emerges from the stochastic processes involved in meiotic chromosome segregation and recombination. A focus on stochastic processes may help counteract naive bio-deterministic thinking and can reinforce, for students, the value of thinking quantitatively about biological processes.
    Keywords genetic drift ; stochasticity ; Hardy-Weinberg equilibria ; course design ; biology education ; Genetics ; QH426-470
    Subject code 612
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Filaments and phenotypes: cellular roles and orphan effects associated with mutations in cytoplasmic intermediate filament proteins.

    Klymkowsky, Michael W

    F1000Research

    2019  Volume 8

    Abstract: 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 ...

    Abstract 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 viable and fertile mice null for a number of IFp-encoding genes, including vimentin. Yet in humans, the vimentin (
    MeSH term(s) Animals ; Humans ; Intermediate Filament Proteins/genetics ; Intermediate Filaments/genetics ; Mice ; Mutation ; Phenotype
    Chemical Substances Intermediate Filament Proteins
    Language English
    Publishing date 2019-09-30
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.19950.1
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  6. Article ; Online: Whole-Mount Immunocytochemistry in

    Klymkowsky, Michael W

    Cold Spring Harbor protocols

    2018  Volume 2018, Issue 1

    Abstract: To visualize the effects of experimental perturbations on normal cellular behavior, morphology, and intracellular organization, we use a simple whole-mount immunocytochemical method ... ...

    Abstract To visualize the effects of experimental perturbations on normal cellular behavior, morphology, and intracellular organization, we use a simple whole-mount immunocytochemical method with
    MeSH term(s) Animals ; Immunohistochemistry/methods ; Models, Animal ; Optical Imaging/methods ; Xenopus
    Language English
    Publishing date 2018-01-02
    Publishing country United States
    Document type Journal Article
    ISSN 1559-6095
    ISSN (online) 1559-6095
    DOI 10.1101/pdb.prot097295
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  7. Article ; Online: Filaments and phenotypes

    Michael W. Klymkowsky

    F1000Research, Vol

    cellular roles and orphan effects associated with mutations in cytoplasmic intermediate filament proteins [version 1; peer review: 2 approved]

    2019  Volume 8

    Abstract: 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 ...

    Abstract 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 viable and fertile mice null for a number of IFp-encoding genes, including vimentin. Yet in humans, the vimentin (VIM) gene displays a high probability of intolerance to loss-of-function mutations, indicating an essential role. A number of subtle and not so subtle IF-associated phenotypes have been identified, often linked to mechanical or metabolic stresses, some of which have been found to be ameliorated by the over-expression of molecular chaperones, suggesting that such phenotypes arise from what might be termed “orphan” effects as opposed to the absence of the IF network per se, an idea originally suggested by Toivola et al. and Pekny and Lane.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2019-09-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: How Do Instructors Explain The Mechanism by which ATP Drives Unfavorable Processes?

    Franovic, Clare G-C / Williams, Nicholas R / Noyes, Keenan / Klymkowsky, Michael W / Cooper, Melanie M

    CBE life sciences education

    2023  Volume 22, Issue 4, Page(s) ar50

    Abstract: Concerns regarding students' difficulties with the concept of energy date back to the 1970s. They become particularly apparent for systems involving adenosine triphosphate (ATP), which plays a central role in maintaining the nonequilibrium state of ... ...

    Abstract Concerns regarding students' difficulties with the concept of energy date back to the 1970s. They become particularly apparent for systems involving adenosine triphosphate (ATP), which plays a central role in maintaining the nonequilibrium state of biological systems and in driving energetically unfavorable processes. One of the most well-documented misconceptions related to ATP is the idea that breaking bonds releases energy, when the opposite is true. This misconception is often attributed to language used in biology referring to the "high-energy bonds" in ATP. We interviewed chemistry, biology, and biochemistry instructors to learn how they think about and teach the mechanism(s) by which ATP is used as an energy source in biological systems. Across 15 interviews, we found that instructors relied primarily on two mechanisms to explain the role of ATP: 1) energy release, focused on ATP hydrolysis and bond energies; and/or 2) energy transfer, focused on phosphorylation and common intermediates. Many instructors shared negative and uncomfortable experiences related to teaching ATP and energy release. Based on these findings, we suggest instructional strategies that: 1) aim to ease the concerns expressed by introductory biology instructors, and 2) emphasize the role of ATP so as to support students' understanding of molecular mechanisms.
    MeSH term(s) Humans ; Students ; Adenosine Triphosphate/chemistry ; Learning ; Biochemistry
    Chemical Substances Adenosine Triphosphate (8L70Q75FXE)
    Language English
    Publishing date 2023-10-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2465176-X
    ISSN 1931-7913 ; 1931-7913
    ISSN (online) 1931-7913
    ISSN 1931-7913
    DOI 10.1187/cbe.23-05-0071
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  9. Book: Cytoskeletal membrane interactions and signal transduction

    Cowin, Pamela / Klymkowsky, Michael W.

    (Molecular biology intelligence unit)

    1997  

    Title variant Cytoskeletal-membrane
    Author's details Pamela Cowin ; Michael W. Klymkowsky
    Series title Molecular biology intelligence unit
    Keywords Cell Communication / physiology ; Cell Membrane / physiology ; Cytoskeletal Proteins / physiology ; Signal Transduction / physiology ; Zellkontakt
    Subject Zell-Zell-Kontakt ; Junctions ; Cell-junction ; Zell-Zell-Verbindung
    Language English
    Size 237 S. : Ill., graph. Darst.
    Publisher Springer u.a.
    Publishing place New York u.a.
    Publishing country United States
    Document type Book
    Note Literaturangaben
    HBZ-ID HT007920542
    ISBN 3-540-63079-1 ; 1-57059-455-4 ; 978-3-540-63079-1 ; 978-1-57059-455-7
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    1997 A 8211 order for loan Magazin

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  10. Article ; Online: Make room for computing.

    Klymkowsky, Michael W

    Science (New York, N.Y.)

    2009  Volume 326, Issue 5950, Page(s) 227

    MeSH term(s) Biology/education ; Computational Biology/education ; Curriculum ; Mathematical Computing
    Language English
    Publishing date 2009-10-09
    Publishing country United States
    Document type Comment ; Letter
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.326_227b
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    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 77: Show issues

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