890 research outputs found
mSphere of Influence: the Complexity of Interferon Gamma-Mediated Pathogen Control
No full textBryan D. Bryson works in the field of biological engineering with a specific interest in host-mycobacterium interactions. In this mSphere of Influence article, he reflects on how “IRG1 and inducible nitric oxide synthase act redundantly with other interferon-gamma-induced factors to restrict intracellular replication of Legionella pneumophila” by Price and colleagues (J. V. Price, D. Russo, D. X. Ji, R. A. Chavez, et al., mBio 10:e02629-19, 2019, https://doi.org/10.1128/mBio.02629-19) made an impact on him by reinforcing the complexity of intracellular pathogen control
Signaling for death: tyrosine phosphorylation in the response to glucose deprivation
No full textThe shift from oxidative phosphorylation to aerobic glycolysis in cancer has focused attention on the altered metabolism of cancer cells as a means of therapeutic intervention. Metabolic dysregulation in cancer was first proposed by Warburg in the 1930s, and this topic remains an active area of research. While previous studies have explored the connection between cellular signaling and metabolism, many have focused on a small subset of components within a complex network of proteins, enzymes, and biochemical signals. In a recent article published in Molecular Systems Biology, Graham et al (2012) endeavor to better understand the relationship between metabolism and signaling at the network level. Although the question of how cancer cells respond to glucose starvation posited by the authors is relatively simple, the answer ends up being unexpectedly complex. To answer this question, the authors use mass spectrometry and other biochemical profiling techniques to demonstrate a connection between glucose levels, reactive oxygen species (ROS), and alterations in phosphotyrosine-mediated signaling in glioblastoma cell lines
Quantitative Profiling of Lysine Acetylation Reveals Dynamic Crosstalk between Receptor Tyrosine Kinases and Lysine Acetylation
No full textLysine acetylation has been primarily investigated in the context of transcriptional regulation, but a role for acetylation in mediating other cellular responses has emerged. Multiple studies have described global lysine acetylation profiles for particular biological states, but none to date have investigated the temporal dynamics regulating cellular response to perturbation. Reasoning that lysine acetylation may be altered in response to growth factors, we implemented quantitative mass spectrometry-based proteomics to investigate the temporal dynamics of lysine acetylation in response to growth factor stimulation in cultured carcinoma cell lines. We found that lysine acetylation changed rapidly in response to activation of several different receptor tyrosine kinases by their respective ligands. To uncover the effects of lysine acetylation dynamics on tyrosine phosphorylation signaling networks, cells were treated with an HDAC inhibitor. This short-term pharmacological inhibition of histone deacetylase activity modulated signaling networks involving phosphorylated tyrosine and thereby altered the response to receptor tyrosine kinase activation. This result highlights the interconnectivity of lysine acetylation and tyrosine phosphorylation signaling networks and suggests that HDAC inhibition may influence cellular responses by affecting both types of post-translational modifications.National Institutes of Health (U.S.) (Grant R24DK090963)National Institutes of Health (U.S.) (Grant R01CA118705)National Institutes of Health (U.S.) (Grant U54CA112967)National Institutes of Health (U.S.) (Grant U24CA159988)National Institutes of Health (U.S.) (Grant P30CA14051
Ethical Awakenings: Stories of White Male Educators’ Commitment to Social Justice and the Interruption of Privilege
No full textThis study is an anti-racist counter-story of white male educators’ commitments to social justice and their attempts at interrupting privilege. The author uses a qualitative methodological approach to unite personal narrative essay and phenomenological interviewing to collate narratives around the exploration of whiteness and power. At the heart of the project is a deep interest in seeking an ethic that fosters a social justice praxis for educators by exposing the underlying structures of whiteness through “witness” testimony. Using Butler's (2005) theory of subject formation, the author advances a theory of social justice that focuses on relation.
The author makes active the context for tensions between his white male subjectivity and social justice praxis and then interweaves the narratives from participant interviews to elucidate how white subjectivity works with and against social justice in complex ways, especially within educational contexts. A close look is given to white educators’ experiences in communities of color and the connections between the participant narratives and the author’s own. The author highlights the significance of personal rupture, in which the self is exposed to new ontological, epistemological, and ethical possibilities at critical junctures on the life journey. A case is made for the curricular value of utilizing self-study – examples of which include personal narrative essays, autoethnography, and autobiographical approaches – in shaping students’ ethical commitments to responsibility towards others as well as potentially exposing fissures at the ontological horizon that might lead authentic personal and social changes. The author draws meaningful interpretations by discussing relevant themes shared among the personal narratives and identifies key experiences that led participants to new ways of understanding and relating to others, exemplifying ethical responsibility. By drawing connections between white subjectivity and ethical commitments to social justice, the author makes a case for the curricular value in considering new and creative ways of fostering student interaction with difference and how those interactions might draw students towards responsible action. Conclusions from the interpretations suggest the importance of relation as a key component of ethical responsibility, highlighting the significance of recognizing the self’s opacity as a form of social justice activism
Processing Beyond Drawing: A Case Study Exploring Ideation for Teaching Design
No full textCitation: Orthel, B. D., & Day, J. K. (2016). Processing Beyond Drawing: A Case Study Exploring Ideation for Teaching Design. SAGE Open, 6(3). doi:10.1177/2158244016663285Designers’ internal thought processes can be externally expressed and represented through sketching and other forms of communication. Novice designers often struggle to communicate their ideas. This article reports an analysis of student design processes during conceptual and schematic design development with the intention to inform teaching and learning activities. Interior design student teams provided sketches, written journal entries, digital drawings and models, and graphic images to illustrate their collective design processes. The work was analyzed to understand the students’ representation and development of ideas. Analysis revealed that sketching, digital media, and non-graphic process work were all valuable in the students’ design process. Significantly, the strength of the design outcomes aligned more with the overall quality of conceptual process work, rather than the way in which students represented their ideas. Ultimately, student understanding of the design process varied. Teaching and learning activities should develop direct connections with design thinking processes to improve design education. © 2016, © The Author(s) 2016
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Leveraging PhagoID to Define How Cytokines Reprogram the Phagosomal Proteome
No full textThe ability of phagocytosing diverse cargoes and maintaining tissue homeostasis under different immune contexts and challenges is what lends tissue resident macrophages their identity as immune sentinels. Previous studies that were aimed towards isolating and studying the macrophage phagosome suffered from certain limitations due to the highly dynamic and interactive nature of this organelle, making its proteomic analysis an especially arduous task. In a recent study, we reported the development of a novel tool called PhagoID which uses a proximity labeling-based strategy for resolving phagosomal lumen proteins with high specificity and efficiency, facilitating their identification using mass spectrometry and downstream proteomic analyses. Here, we validate the use of epigallocatechin gallate (EGCG) as a ROS scavenger capable of minimizing extracellular labeling in the case of PhagoID. Next, we adapted PhagoID to quantify the phagosome lumen proteome of fetal-derived alveolar-like macrophages (FLAMs) under the effect of type I interferon signaling.
The phagocytic activity of alveolar macrophages (AMs) is important both at baseline for routine cleaning of cellular debris, as well as to initiate a strong inflammatory responses to respiratory pathogens. We profiled the phagosomal proteome of FLAMs as a model for primary AMs and found proteins involved in the class I MHC pathway to be the only ER subset enriched in the phagosome on IFN-β activated FLAMs. Additionally, we identified the presence of proteins belonging to 3 families of interferon induced GTPases (IIGPs), including multiple GBPs and all IRGM proteins which have been well recognized for their role in cell autonomous immunity against bacterial infections like Mycobacterium tuberculosis and Chlamydia trachomatis. We also detected the enrichment of the enzyme aconitate decarboxylase (ACOD1/IRG1) involved in the production of the anti-microbial metabolite, itaconate. Going ahead, we propose the design of an itaconate biosensor targeted to the endosomal and lysosomal compartments to understand which host factors govern itaconate trafficking to phagosomes. Thus, using PhagoID enabled us to gain important insights into how IFN-β, a cytokine known for its highly context-dependent role in case of bacterial infections, can alter the phagosome proteome of AMs.Medical Scienc
Quantitative approaches to probe the acetylproteome
No full textThesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2013.Cataloged from PDF version of thesis.Includes bibliographical references (p. 173-175).Lysine acetylation is a prevalent post-translational modification whose multi-varied biological roles have recently emerged. While having all the necessary components of a signaling network, lysine acetylation studies have been limited to a small subset of proteins and pathways. Using a quantitative unbiased mass spectrometry approach, we explored the role of growth factor stimulation on lysine acetylation. Although the growth factors bind receptor tyrosine kinases, growth factor stimulation resulted in rapid and dynamic changes in lysine acetylation. Furthermore, we demonstrated that short-term HDAC inhibition alters phosphotyrosine-signaling networks. To better understand this behavior, a suite of biochemical and computational methods were developed. Bromodomains were engineered to explore binding preferences using degenerate peptide arrays as well as develop acetyllysine affinity reagents as an alternative to anti-acetyllysine antibodies. Additionally, bioorthogonal proteomics were employed to identify acetyltransferase substrates. Taken together, the knowledge generated and the methods developed provide a toolkit for the analysis of lysine acetylation networks in the context of many biological processes as well as diseases.by Bryan David Bryson.Ph.D
Changes over time in union relative wage effects in the UK and the US revisited
No full textThis paper examines the impact of trade unions in the US and the UK and elsewhere. In both the US and the UK, despite declining membership numbers, unions are able to raise wages substantially over the equivalent non-union wage. Unions in other countries, such as Australia, Austria, Brazil, Canada, Chile, Cyprus, Denmark, Japan, New Zealand, Norway, Portugal and Spain, are also able to raise wages by significant amounts. In countries where union wage settlements frequently spill over into the non-union sector (e.g. France, Germany, Italy, the Netherlands and Sweden) there is no significant union wage differential. The estimates from the seventeen countries we examined averages out at 12 per cent. Time series evidence from both the US and the UK suggests three interesting findings. First, the union differential in the US is higher on average than that found in the UK (18 per cent compared with 10 per cent). Second, the union wage premium in both countries was untrended in the years up to the mid-1990s. Third, in both countries the wage premium has fallen in the boom years since 1994/95. It is too early to tell whether the onset of a downturn in 2002 will cause the differential to rise again or whether there is a trend change in the impact of unions. It is our view that most likely what has happened is that the tightening of the labor market has resulted in a temporary decline in the size of the union wage premium. Time will tell whether the current loosening of the labor market, that is occurring in both countries, will return the union wage premium to its long run values of 10 per cent in the case of the UK and 18 per cent in the case of the US. On the basis of past experience it seems likely that they will.
Computer aided manual validation of mass spectrometry-based proteomic data
No full textAdvances in mass spectrometry-based proteomic technologies have increased the speed of analysis and the depth provided by a single analysis. Computational tools to evaluate the accuracy of peptide identifications from these high-throughput analyses have not kept pace with technological advances; currently the most common quality evaluation methods are based on statistical analysis of the likelihood of false positive identifications in large-scale data sets. While helpful, these calculations do not consider the accuracy of each identification, thus creating a precarious situation for biologists relying on the data to inform experimental design. Manual validation is the gold standard approach to confirm accuracy of database identifications, but is extremely time-intensive. To palliate the increasing time required to manually validate large proteomic datasets, we provide computer aided manual validation software (CAMV) to expedite the process. Relevant spectra are collected, catalogued, and pre-labeled, allowing users to efficiently judge the quality of each identification and summarize applicable quantitative information. CAMV significantly reduces the burden associated with manual validation and will hopefully encourage broader adoption of manual validation in mass spectrometry-based proteomics.National Institutes of Health (U.S.) (Grant R24DK090963)National Institutes of Health (U.S.) (Grant U54CA112967)National Cancer Institute (U.S.). Integrative Cancer Biology Program (Fellowship)Charles S. Krakauer FellowshipHugh Hampton Young Fellowshi
Engineered bromodomains to explore the acetylproteome
No full textMass spectrometry-based analysis of the acetylproteome has highlighted a role for acetylation in a wide array of biological processes including gene regulation, metabolism, and cellular signaling. To date, anti-acetyllysine antibodies have been used as the predominant affinity reagent for
enrichment of acetyllysine-containing peptides and proteins; however, these reagents suffer from high non-specific binding and lot-to-lot variability. Bromodomains represent potential affinity reagents for acetylated proteins and peptides, given their natural role in recognition of acetylated
sequence motifs in vivo. To evaluate their efficacy, we generated recombinant proteins representing all known yeast bromodomains. Bromodomain specificity for acetylated peptides was determined using degenerate peptide arrays, leading to the observation that different
bromodomains display a wide array of binding specificities. Despite their relatively weak affinity, we demonstrate the ability of selected bromodomains to enrich acetylated peptides from a complex biological mixture prior to mass spectrometric analysis. Finally, we demonstrate a method for improving the utility of bromodomain enrichment for mass spectrometry through engineering novel affinity reagents using combinatorial tandem bromodomain pairs.National Institutes of Health (U.S.) (Grants R24DK090963, R01CA118705, U54CA112967, R01ES015339, R01 GM104047, U24CA159988 and P30CA14051)Charles S. Krakauer FellowshipHugh Hampton Young Fellowshi
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