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  • 1
    Online Resource
    Online Resource
    Biochemical adaptation: unity in principles, diversity in solutions
    The Company of Biologists ; 2015
    In:  Journal of Experimental Biology Vol. 218, No. 12 ( 2015-06-01), p. 1797-1798
    Details
    In: Journal of Experimental Biology, The Company of Biologists, Vol. 218, No. 12 ( 2015-06-01), p. 1797-1798
    Type of Medium: Online Resource
    ISSN: 1477-9145 , 0022-0949
    URL: Article
    DOI: 10.1242/jeb.124479
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2015
    detail.hit.zdb_id: 1482461-9
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Biochemical adaptation to ocean acidification
    The Company of Biologists ; 2015
    In:  Journal of Experimental Biology Vol. 218, No. 12 ( 2015-06-01), p. 1946-1955
    Details
    In: Journal of Experimental Biology, The Company of Biologists, Vol. 218, No. 12 ( 2015-06-01), p. 1946-1955
    Abstract: The change in oceanic carbonate chemistry due to increased atmospheric PCO2 has caused pH to decline in marine surface waters, a phenomenon known as ocean acidification (OA). The effects of OA on organisms have been shown to be widespread among diverse taxa from a wide range of habitats. The majority of studies of organismal response to OA are in short-term exposures to future levels of PCO2. From such studies, much information has been gathered on plastic responses organisms may make in the future that are beneficial or harmful to fitness. Relatively few studies have examined whether organisms can adapt to negative-fitness consequences of plastic responses to OA. We outline major approaches that have been used to study the adaptive potential for organisms to OA, which include comparative studies and experimental evolution. Organisms that inhabit a range of pH environments (e.g. pH gradients at volcanic CO2 seeps or in upwelling zones) have great potential for studies that identify adaptive shifts that have occurred through evolution. Comparative studies have advanced our understanding of adaptation to OA by linking whole-organism responses with cellular mechanisms. Such optimization of function provides a link between genetic variation and adaptive evolution in tuning optimal function of rate-limiting cellular processes in different pH conditions. For example, in experimental evolution studies of organisms with short generation times (e.g. phytoplankton), hundreds of generations of growth under future conditions has resulted in fixed differences in gene expression related to acid–base regulation. However, biochemical mechanisms for adaptive responses to OA have yet to be fully characterized, and are likely to be more complex than simply changes in gene expression or protein modification. Finally, we present a hypothesis regarding an unexplored area for biochemical adaptation to ocean acidification. In this hypothesis, proteins and membranes exposed to the external environment, such as epithelial tissues, may be susceptible to changes in external pH. Such biochemical systems could be adapted to a reduced pH environment by adjustment of weak bonds in an analogous fashion to biochemical adaptation to temperature. Whether such biochemical adaptation to OA exists remains to be discovered.
    Type of Medium: Online Resource
    ISSN: 1477-9145 , 0022-0949
    URL: Article
    DOI: 10.1242/jeb.115584
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2015
    detail.hit.zdb_id: 1482461-9
    SSG: 12
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  • 3
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    Online Resource
    Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms
    The Company of Biologists ; 2015
    In:  Journal of Experimental Biology Vol. 218, No. 12 ( 2015-06-01), p. 1880-1896
    Details
    In: Journal of Experimental Biology, The Company of Biologists, Vol. 218, No. 12 ( 2015-06-01), p. 1880-1896
    Abstract: Organisms experience a wide range of environmental factors such as temperature, salinity and hydrostatic pressure, which pose challenges to biochemical processes. Studies on adaptations to such factors have largely focused on macromolecules, especially intrinsic adaptations in protein structure and function. However, micromolecular cosolutes can act as cytoprotectants in the cellular milieu to affect biochemical function and they are now recognized as important extrinsic adaptations. These solutes, both inorganic and organic, have been best characterized as osmolytes, which accumulate to reduce osmotic water loss. Singly, and in combination, many cosolutes have properties beyond simple osmotic effects, e.g. altering the stability and function of proteins in the face of numerous stressors. A key example is the marine osmolyte trimethylamine oxide (TMAO), which appears to enhance water structure and is excluded from peptide backbones, favoring protein folding and stability and counteracting destabilizers like urea and temperature. Co-evolution of intrinsic and extrinsic adaptations is illustrated with high hydrostatic pressure in deep-living organisms. Cytosolic and membrane proteins and G-protein-coupled signal transduction in fishes under pressure show inhibited function and stability, while revealing a number of intrinsic adaptations in deep species. Yet, intrinsic adaptations are often incomplete, and those fishes accumulate TMAO linearly with depth, suggesting a role for TMAO as an extrinsic ‘piezolyte’ or pressure cosolute. Indeed, TMAO is able to counteract the inhibitory effects of pressure on the stability and function of many proteins. Other cosolutes are cytoprotective in other ways, such as via antioxidation. Such observations highlight the importance of considering the cellular milieu in biochemical and cellular adaptation.
    Type of Medium: Online Resource
    ISSN: 1477-9145 , 0022-0949
    URL: Article
    DOI: 10.1242/jeb.114355
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2015
    detail.hit.zdb_id: 1482461-9
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Classroom sound can be used to classify teaching practices in college science courses
    Proceedings of the National Academy of Sciences ; 2017
    In:  Proceedings of the National Academy of Sciences Vol. 114, No. 12 ( 2017-03-21), p. 3085-3090
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 114, No. 12 ( 2017-03-21), p. 3085-3090
    Abstract: Active-learning pedagogies have been repeatedly demonstrated to produce superior learning gains with large effect sizes compared with lecture-based pedagogies. Shifting large numbers of college science, technology, engineering, and mathematics (STEM) faculty to include any active learning in their teaching may retain and more effectively educate far more students than having a few faculty completely transform their teaching, but the extent to which STEM faculty are changing their teaching methods is unclear. Here, we describe the development and application of the machine-learning–derived algorithm Decibel Analysis for Research in Teaching (DART), which can analyze thousands of hours of STEM course audio recordings quickly, with minimal costs, and without need for human observers. DART analyzes the volume and variance of classroom recordings to predict the quantity of time spent on single voice (e.g., lecture), multiple voice (e.g., pair discussion), and no voice (e.g., clicker question thinking) activities. Applying DART to 1,486 recordings of class sessions from 67 courses, a total of 1,720 h of audio, revealed varied patterns of lecture (single voice) and nonlecture activity (multiple and no voice) use. We also found that there was significantly more use of multiple and no voice strategies in courses for STEM majors compared with courses for non-STEM majors, indicating that DART can be used to compare teaching strategies in different types of courses. Therefore, DART has the potential to systematically inventory the presence of active learning with ∼90% accuracy across thousands of courses in diverse settings with minimal effort.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1618693114
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2017
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 5
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    Online Resource
    Collectively Improving Our Teaching: Attempting Biology Department–wide Professional Development in Scientific Teaching
    American Society for Cell Biology (ASCB) ; 2018
    In:  CBE—Life Sciences Education Vol. 17, No. 1 ( 2018-03), p. ar2-
    Details
    In: CBE—Life Sciences Education, American Society for Cell Biology (ASCB), Vol. 17, No. 1 ( 2018-03), p. ar2-
    Abstract: Many efforts to improve science teaching in higher education focus on a few faculty members at an institution at a time, with limited published evidence on attempts to engage faculty across entire departments. We created a long-term, department-wide collaborative professional development program, Biology Faculty Explorations in Scientific Teaching (Biology FEST). Across 3 years of Biology FEST, 89% of the department’s faculty completed a weeklong scientific teaching institute, and 83% of eligible instructors participated in additional semester-long follow-up programs. A semester after institute completion, the majority of Biology FEST alumni reported adding active learning to their courses. These instructor self-reports were corroborated by audio analysis of classroom noise and surveys of students in biology courses on the frequency of active-learning techniques used in classes taught by Biology FEST alumni and nonalumni. Three years after Biology FEST launched, faculty participants overwhelmingly reported that their teaching was positively affected. Unexpectedly, most respondents also believed that they had improved relationships with departmental colleagues and felt a greater sense of belonging to the department. Overall, our results indicate that biology department–wide collaborative efforts to develop scientific teaching skills can indeed attract large numbers of faculty, spark widespread change in teaching practices, and improve departmental relations.
    Type of Medium: Online Resource
    ISSN: 1931-7913
    URL: Article
    DOI: 10.1187/cbe.17-06-0106
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2018
    detail.hit.zdb_id: 2465176-X
    SSG: 5,3
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  • 6
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    The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution
    Oxford University Press (OUP) ; 2019
    In:  Genome Biology and Evolution Vol. 11, No. 5 ( 2019-05-01), p. 1440-1450
    Details
    In: Genome Biology and Evolution, Oxford University Press (OUP), Vol. 11, No. 5 ( 2019-05-01), p. 1440-1450
    Type of Medium: Online Resource
    ISSN: 1759-6653
    URL: Article
    DOI: 10.1093/gbe/evz067
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2495328-3
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  • 7
    Online Resource
    Online Resource
    Antarctic notothenioid fish: what are the future consequences of ‘losses’ and ‘gains’ acquired during long-term evolution at cold and stable temperatures?
    The Company of Biologists ; 2015
    In:  Journal of Experimental Biology Vol. 218, No. 12 ( 2015-06-01), p. 1834-1845
    Details
    In: Journal of Experimental Biology, The Company of Biologists, Vol. 218, No. 12 ( 2015-06-01), p. 1834-1845
    Abstract: Antarctic notothenioids dominate the fish fauna of the Southern Ocean. Evolution for millions of years at cold and stable temperatures has led to the acquisition of numerous biochemical traits that allow these fishes to thrive in sub-zero waters. The gain of antifreeze glycoproteins has afforded notothenioids the ability to avert freezing and survive at temperatures often hovering near the freezing point of seawater. Additionally, possession of cold-adapted proteins and membranes permits them to sustain appropriate metabolic rates at exceptionally low body temperatures. The notothenioid genome is also distinguished by the disappearance of traits in some species, losses that might prove costly in a warmer environment. Perhaps the best-illustrated example is the lack of expression of hemoglobin in white-blooded icefishes from the family Channichthyidae. Loss of key elements of the cellular stress response, notably the heat shock response, has also been observed. Along with their attainment of cold tolerance, notothenioids have developed an extreme stenothermy and many species perish at temperatures only a few degrees above their habitat temperatures. Thus, in light of today's rapidly changing climate, it is critical to evaluate how these extreme stenotherms will respond to rising ocean temperatures. It is conceivable that the remarkable cold specialization of notothenioids may ultimately leave them vulnerable to future thermal increases and threaten their fitness and survival. Within this context, our review provides a current summary of the biochemical losses and gains that are known for notothenioids and examines these cold-adapted traits with a focus on processes underlying thermal tolerance and acclimation capacity.
    Type of Medium: Online Resource
    ISSN: 1477-9145 , 0022-0949
    URL: Article
    DOI: 10.1242/jeb.116129
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2015
    detail.hit.zdb_id: 1482461-9
    SSG: 12
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  • 8
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    Online Resource
    The environmentally tuned transcriptomes of Mytilus mussels
    The Company of Biologists ; 2015
    In:  Journal of Experimental Biology Vol. 218, No. 12 ( 2015-06-01), p. 1822-1833
    Details
    In: Journal of Experimental Biology, The Company of Biologists, Vol. 218, No. 12 ( 2015-06-01), p. 1822-1833
    Abstract: Transcriptomics is a powerful tool for elucidating the molecular mechanisms that underlie the ability of organisms to survive and thrive in dynamic and changing environments. Here, we review the major contributions in this field, and we focus on studies of mussels in the genus Mytilus, which are well-established models for the study of ecological physiology in fluctuating environments. Our review is organized into four main sections. First, we illustrate how the abiotic forces of the intertidal environment drive the rhythmic coupling of gene expression to diel and tidal cycles in Mytilus californianus. Second, we discuss the challenges and pitfalls of conducting transcriptomic studies in field-acclimatized animals. Third, we examine the link between transcriptomic responses to environmental stress and biogeographic distributions in blue mussels, Mytilus trossulus and Mytilus galloprovincialis. Fourth, we present a comparison of transcriptomic datasets and identify 175 genes that share common responses to heat stress across Mytilus species. Taken together, these studies demonstrate that transcriptomics can provide an informative snapshot of the physiological state of an organism within an environmental context. In a comparative framework, transcriptomics can reveal how natural selection has shaped patterns of transcriptional regulation that may ultimately influence biogeography.
    Type of Medium: Online Resource
    ISSN: 1477-9145 , 0022-0949
    URL: Article
    DOI: 10.1242/jeb.118190
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2015
    detail.hit.zdb_id: 1482461-9
    SSG: 12
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  • 9
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    Online Resource
    The emerging role of RNA editing in plasticity
    The Company of Biologists ; 2015
    In:  Journal of Experimental Biology Vol. 218, No. 12 ( 2015-06-01), p. 1812-1821
    Details
    In: Journal of Experimental Biology, The Company of Biologists, Vol. 218, No. 12 ( 2015-06-01), p. 1812-1821
    Abstract: All true metazoans modify their RNAs by converting specific adenosine residues to inosine. Because inosine binds to cytosine, it is a biological mimic for guanosine. This subtle change, termed RNA editing, can have diverse effects on various RNA-mediated cellular pathways, including RNA interference, innate immunity, retrotransposon defense and messenger RNA recoding. Because RNA editing can be regulated, it is an ideal tool for increasing genetic diversity, adaptation and environmental acclimation. This review will cover the following themes related to RNA editing: (1) how it is used to modify different cellular RNAs, (2) how frequently it is used by different organisms to recode mRNA, (3) how specific recoding events regulate protein function, (4) how it is used in adaptation and (5) emerging evidence that it can be used for acclimation. Organismal biologists with an interest in adaptation and acclimation, but with little knowledge of RNA editing, are the intended audience.
    Type of Medium: Online Resource
    ISSN: 1477-9145 , 0022-0949
    URL: Article
    DOI: 10.1242/jeb.119065
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2015
    detail.hit.zdb_id: 1482461-9
    SSG: 12
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  • 10
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    Online Resource
    Adaptations of protein structure and function to temperature: there is more than one way to ‘skin a cat’
    The Company of Biologists ; 2015
    In:  Journal of Experimental Biology Vol. 218, No. 12 ( 2015-06-01), p. 1801-1811
    Details
    In: Journal of Experimental Biology, The Company of Biologists, Vol. 218, No. 12 ( 2015-06-01), p. 1801-1811
    Abstract: Sensitivity to temperature helps determine the success of organisms in all habitats, and is caused by the susceptibility of biochemical processes, including enzyme function, to temperature change. A series of studies using two structurally and catalytically related enzymes, A4-lactate dehydrogenase (A4-LDH) and cytosolic malate dehydrogenase (cMDH) have been especially valuable in determining the functional attributes of enzymes most sensitive to temperature, and identifying amino acid substitutions that lead to changes in those attributes. The results of these efforts indicate that ligand binding affinity and catalytic rate are key targets during temperature adaptation: ligand affinity decreases during cold adaptation to allow more rapid catalysis. Structural changes causing these functional shifts often comprise only a single amino acid substitution in an enzyme subunit containing approximately 330 residues; they occur on the surface of the protein in or near regions of the enzyme that move during catalysis, but not in the active site; and they decrease stability in cold-adapted orthologs by altering intra-molecular hydrogen bonding patterns or interactions with the solvent. Despite these structure–function insights, we currently are unable to predict a priori how a particular substitution alters enzyme function in relation to temperature. A predictive ability of this nature might allow a proteome-wide survey of adaptation to temperature and reveal what fraction of the proteome may need to adapt to temperature changes of the order predicted by global warming models. Approaches employing algorithms that calculate changes in protein stability in response to a mutation have the potential to help predict temperature adaptation in enzymes; however, using examples of temperature-adaptive mutations in A4-LDH and cMDH, we find that the algorithms we tested currently lack the sensitivity to detect the small changes in flexibility that are central to enzyme adaptation to temperature.
    Type of Medium: Online Resource
    ISSN: 1477-9145 , 0022-0949
    URL: Article
    DOI: 10.1242/jeb.114298
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2015
    detail.hit.zdb_id: 1482461-9
    SSG: 12
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